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Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage

Luca Pesce
Luca Pesce
Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
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http://orcid.org/0000-0001-6364-9577

Claudio Perego
Claudio Perego
Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
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http://orcid.org/0000-0001-8885-3080

Angela B. Grommet
Angela B. Grommet
Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Rafal Klajn
Rafal Klajn
Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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http://orcid.org/0000-0002-6320-8875

, and

Giovanni M. Pavan*
Giovanni M. Pavan
Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland
Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy
*[email protected]
More by Giovanni M. Pavan
http://orcid.org/0000-0002-3473-8471

Cite this: J. Am. Chem. Soc. 2020, 142, 21, 9792–9802

Publication Date (Web):April 30, 2020

https://doi.org/10.1021/jacs.0c03444

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Abstract

Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions.

Introduction

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Photochromic molecular switches such as azobenzene,(1) spiropyran,(2,3) or arylazopyrazole(4,5) are responsive molecules that isomerize upon irradiation with light. Achieving fine control of these compounds’ isomerization kinetics is important since they represent crucial components for the development of functional photoresponsive materials,(3,6−9) light-powered molecular machines,(10−15) and in photopharmacology,(16,17) where spatiotemporal control of molecular transitions/reactions is needed. In nature, a widely employed strategy for controlling chemical reactions involves accommodating the reactants in a confined space, where encapsulation may influence and control reaction mechanism and kinetics. Enzymes, for example, can catalyze and control reactions with exquisite efficiency and fidelity by exploiting principles of molecular confinement and selective molecular/supramolecular host–guest interactions.(18−21)

In the attempt to mimic natural catalytic systems, chemists have designed synthetic cavities that exploit specific and nonspecific interactions to accommodate reactants with high selectivity in a confined space.(22) Notable examples of synthetic confined spaces are nanopores within metal–organic frameworks,(23−25) surfaces of nanoparticles(26−28) and nanopores within their aggregates,(29) microemulsion droplets,(30,31) and cavities within molecular capsules.(32) Alternatively, cavities can be found within self-assembled cages(33−38) that can encapsulate reactants in solution.(39,40) Confinement inside such cavities has been shown to be crucial in accelerating chemical reactions(29,41−43) or stabilizing otherwise unstable species.(44−48) Notable studies have reported that the photoisomerization of molecular switches can be accelerated,(49) slowed down,(50) or even completely inhibited within crowded molecular environments.(51,52) In some cases, the isomerization of photoresponsive guests may also result in expulsion of the guest(53,54) and even in disassembly of the cage.(55) A key role is attributed to the structural rigidity of synthetic host cavities, which are not capable of accommodating the large conformational changes associated with the photoisomerization of the guest.(1,3,56,57) For this reason, much interest has recently been directed toward the design of flexible molecular cages.(58−61)

In this sense, an interesting example is self-assembled metal–organic cage shown in Figure 1A.(61) This cage has been observed to encapsulate and allow for water solubilization of several different molecular switches, including azobenzene (AZB), methoxylated azobenzene (M-AZB), fluorinated azobenzene (F-AZB), various spiropyrans, as well as arylazopyrazole (AZP) (Figure 1B).(62−64) NMR and UV/vis absorption studies provided useful information about the guest encapsulation and the host−guest stoichiometry in these systems.(62−64) X-ray crystallography provided additional experimental insight on the conformations of the crystallized complexes.(62,64) Qualitatively, these efforts indicated that encapsulation and switching of the guests are enabled by large distortions within the cage structure, while confinement alters the isomerization behavior of the guests.(63)

Figure 1. Model host–guest systems. (A, top) Structure of the supramolecular cage studied herein, formed via the self-assembly of triimidazole-based donors and *cis*-blocked Pd acceptors. (A, bottom) Atomistic model of the supramolecular host cage, along with a schematic representation of its octahedral structure, which can be described by the axial and equatorial distances, D1 (red) and D2 (green). (B) Structural formulas and atomistic models of the guests studied herein: azobenzene (AZB), methoxylated azobenzene (M-AZB), fluorinated azobenzene (F-AZB), and arylazopyrazole (AZP) (here shown as *trans* isomers).

These findings suggest that the flexibility of the cage enables adaptation of its cavity in response to the isomerization of encapsulated guests. However, a clear understanding of the flexibility exhibited by such cages in solution is difficult to obtain experimentally. In particular, correlating such effects with isomerization events that occur on very fast time scales(52) (the trans → cis isomerization of excited azobenzene occurs on the order of picoseconds in the absence of confinement) and studying the mechanisms that control photoswitching under confinement are prohibitive tasks. In these cases, however, molecular simulations are extremely useful. Quantum mechanics/molecular mechanics (QM/MM), all-atom (AA), and coarse-grained (CG) simulations have been used to investigate azobenzenes and their isomerization within dense monolayers, nanocavities, supramolecular tubules, nanoparticles, and vesicles,(6,8,29,49,50,52,65−68) to name a few. Molecular models can provide detailed insight on the isomerization process(49,52) as well as on the effect of these molecular transitions on the stability(8,66,69) and out-of-equilibrium behavior of the system.(50)

Here we used AA molecular simulations to obtain an exhaustive characterization of the host–guest systems involving azo compounds AZB, M-AZB, F-AZB, and AZP (Figure 1B) as the guests and cage shown in Figure 1A as the host. Combining molecular dynamics (MD) and metadynamics (MetaD) simulations, our approach allows a thorough exploration of the flexibility of the cage in solution and of the mechanisms of guest encapsulation and release under realistic conditions. Coupled with a kinetic study of the isomerization of the excited guests within the cage, these simulations allow us to reconstruct the role of confinement on guest switching and to study the molecular factors that may allow control over this process. We found structure–reactivity relationships having a general character, which may have a profound impact on the rational design of molecular systems with programmable photoswitching properties.

Results and Discussion

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Characterization of Cage Flexibility in Solution

The first step to understanding the behavior of the system is to determine the most favorable conformation(s) assumed by the cage, and how flexible this is in solution under realistic conditions (solvent, temperature, etc.). We started by considering the native cage, without incorporated guests. We developed an atomistic model of the cage (Figure 1A, bottom), starting from the crystal structure for the same cage containing two trans-F-AZB guests (which have been manually deleted).(62) Starting from this extended conformation of the cage, we ran a classical MD simulation in explicit water molecules at 297 K and 1 atm (see SI Methods section for details). During this MD run, we analyzed the structural rearrangements of the cage by monitoring two variables describing the geometry of the cage: D1, the axial distance between the “top” and “bottom” Pd atoms (Figure 1A, bottom; points A and B), and D2, the distance between the midpoints of the two opposite equatorial edges of the octahedral cage (points C and D). In agreement with previous studies,(63) this preliminary MD simulation showed a significant flexibility within the cage. As seen in Figure S1, D1 and D2 have been found to undergo large structural fluctuations, which, however, are observed rarely during 1 μs of a MD simulation.

To better characterize the conformational landscape and the slow structural dynamics of the cage, we turned to MetaD,(70) which allows a more exhaustive exploration of the conformational space of the cage in solution. Using the same operative conditions, we ran a MetaD simulation exploring the possible structural conformations that the cage can dynamically assume in the solvent. In the MetaD run, we used D1 and D2 as the collective variables, descriptors of the cage conformations (see SI Methods for details). From this simulation, we could reconstruct the free-energy surface (FES) for the system as a function of D1 and D2. Shown in Figure 2, the FES shows the conformational landscape of the cage (i.e., all the possible conformations that the cage can assume) associated with its relative free-energy. Dark regions in the FES identify the minimum energy (most favorable) configurations for the cage, while red, orange, yellow regions identify conformations that are increasingly higher in free-energy. We can observe a single free-energy minimum (the black region in figure) in which the cage is mildly elongated along the D1 axis (top left snapshot in Figure 2), and is generally less extended than the initial crystal structure for the cage, which is found ∼4–5 kcal/mol higher in free-energy (Figure 2, top right snapshot). Exploiting the rotation of the 12 imidazole-rings with respect to the central benzene ring,(62) the MetaD allows the system to explore a wide range of conformations (including very elongated shapes), a selection of which are shown in Figure 2. In most cases, these configurations are considerably higher in free-energy and are thus unlikely to be observed in solution. Furthermore, we calculated the probability associated with the different colored regions of the FES (see SI Methods). The result of this analysis (Figure 2B) shows that, from a statistical point of view, only the cage configurations lying within 1.5 kcal/mol of the global minimum are really accessible by the cage (dark regions on the FES and first three bins of Figure 2B). This means that the cage will most likely assume configurations within D1 ∼ 1.4–1.9 nm and D2 ∼ 0.9–1.3 nm (dark FES region). Under these conditions, these conformations will constitute ∼90% of the global population of cages in the system. It is worth adding that the shape of the FES minimum also provides important information about the flexibility of the cage in solution. In this case, the FES minimum is quite broad, which is in agreement with the experimentally observed(63) high flexibility of the cage. Altogether, this analysis provides interesting information not only on the level of flexibility of the cage under experimentally relevant conditions, but also on what we could reasonably/statistically expect to find in terms of the structural diversity of the cage in a realistic solution.

Figure 2. Conformational free-energy landscape of the empty cage. (A) Free-energy surface (FES) as a function of D1 (distance between the axial/red Pd atoms) and D2 (distance between the midpoints of opposite edges of the cage identified by the equatorial/green Pd atoms). The color scale in the FES indicates the free-energy associated with cage conformations on the D1–D2 plane (scale and legend shown in B). Four representative snapshots are shown: the starting, extended configuration (top right) corresponding to the crystal structure of the cage,(62) the energetic minimum of the FES (top left), a D1-elongated structure (bottom right), and a D2-elongated structure (bottom left). Axial and equatorial Pd atoms are colored in red and green, respectively, while the connectivity scheme is colored in orange to facilitate interpretation of the structures. (B) Probability associated with all cage conformations as a function of the relative free-energy (bin width, 0.5 kcal/mol).

Effects of Guest Encapsulation on Cage Flexibility

The flexibility of the cage influences its ability to encapsulate guest molecules. Conversely, guest encapsulation itself may have an effect on the flexibility of the cage. For our next step, we thus studied the effect of guest encapsulation on the cage. Starting again from the crystal structure of the cage containing two trans-F-AZB guests,(62) we deleted one guest and replaced the remaining one, where necessary, in order to obtain starting models for the cage encapsulating one F-AZB, M-AZB, AZP, or AZB guest (Figure 1B). These starting host–guest complex models were then equilibrated via 1 μs of MD simulation (see SI Methods for details). In particular, we compared the effect of incorporating either trans or cis conformers of all guests, analogous to the states of the cage before and after the isomerization. In all cases, we monitored the equilibrium conformations of the cage in terms of D1 and D2. We could observe that all guests remained steadily bound within the cage during the whole MD simulation time. Figure 3 shows the equilibrium configuration for the cage in terms of D1 and D2 in all cases (colored points) on the FES of the empty cage. The colored isolines in Figure 3 identify the associated free-energy regions within 0.5 kcal/mol of the global minima for each case (the same isoline for the empty cage is shown in white).

Figure 3. Free-energy cost of guest encapsulation. Representative equilibrium conformations (in the D1–D2 plane) of the cage encapsulating different *trans* (left) or *cis* (right) guests. For each host–guest system, we report the position of the minimum-energy conformation (colored points) and the associated isolines (same colors) enclosing all conformations within 0.5 kcal/mol from the minimum of each system. The data are projected onto the FES of the empty cage (same as Figure 2), for which we also indicate the global minimum and associated 0.5 kcal/mol isoline (in white).

On the basis of the data in Figure 3, we can draw the following conclusions. In order to incorporate a guest, the cage must undergo structural rearrangements, specifically to open up, which is accompanied by a free-energy cost. The FES data in Figure 3 allows us to assess the free-energy penalty associated with encapsulation of each guest. This value can be calculated as the difference in free-energy between the white point (empty cage) and the colored points (a higher free-energy configuration that the cage has to reach to encapsulate the guest). We have found values for ΔG in the range ∼3–5 kcal/mol, depending on the guest. Such a free-energy penalty can be seen as an entropic cost (i.e., unfavorable) for the encapsulation, as the cage elongates both axially and equatorially upon encapsulating the guest. From the data in Figure 3 we can also observe how guest encapsulation affects the flexibility of the cage. In general, the colored isolines encompass a smaller area than the white isoline associated with the empty cage. This observation suggests that the cage loses flexibility upon encapsulating a guest, the effect being more pronounced for trans (left panel) than for cis guests (right panel). Moreover, by comparing the regions occupied by the cage when hosting trans or cis guests, we note that they enclose similar free-energy values. This result suggests that isomerization of the encapsulated guest would not require a consistent free-energy cost in terms of host deformation, thus demonstrating the energetic accessibility of the process. These results are consistent with the evidence that the trans → cis isomerization of the guests occurs inside the cage, and the resulting cis complexes remain stable also after isomerization.(62−64)

Experiments have shown that our cage can often accommodate two trans guest molecules at the same time.(62,64) On the basis of these observations, we have modeled two additional systems wherein the cage encapsulates two trans-AZBs or two trans-F-AZBs, and have obtained equilibrated configurations for these complexes via 1 μs of MD simulation. In these cases, we observed that the cage undergoes considerable deformations compared to when only one encapsulated trans guest is present in the cavity of the model cage (see Figure S2). However, the stability observed for two-guest complexes suggests that the affinity between the encapsulated guests and the cage is significant. We anticipate that this competition between the free-energy penalty associated with the crowding inside the cage cavity and the host–guest affinity represents a crucial factor that can regulate the reactivity of these host–guest complexes.

Trans–Cis Isomerization of Azobenzenes Inside the Cage

An interesting question is how, and to what extent, the switching of excited azobenzenes is affected by encapsulation inside the cage. The trans → cis isomerization of azobenzenes occurs mainly via a rotational mechanism involving the torsion of the central N–N bond, which produces the out-of-plane rotation of one end of the molecule(71,72) (see snapshots in Figure 4A). To simulate the trans → cis transition of the guests within the cage, we use a model for excited trans-azobenzenes (S*) that has been recently employed to study azobenzene switching inside self-assembled tubules via atomistic and coarse-grained simulations.(50) In this atomistic model, the central CNNC dihedral potential term for the azobenzene unit is modified from the black curve (unperturbed trans-azobenzene) into the blue curve in the inset of Figure 4. In this model, the trans-azobenzene guest, which is assumed to reach the excited state (S*), undergoes spontaneous trans → cis switching according to the correct transition pathway and kinetics during classical MD runs.(50) Starting from the equilibrated models for the cage encapsulating single molecules of each trans guest (Figure 3, left), we studied the kinetics of their switching inside and outside the cage by means of MD simulations.

Figure 4. *Trans* → *cis* transitions of azo-switches inside and outside the cage. (A) Kinetics of *trans* → *cis* isomerization of the excited M-AZB (top) and F-AZB (bottom) outside the cage (in solution) reported as examples. The measured transition times, reported below the isomerization arrows, are obtained from MD simulations using an atomistic model where the CNNC dihedral potential term for the *trans*-azobenzene derivatives (E_dih, reported in the plot as a function of the dihedral angle), is changed from the black curve (native/unperturbed state) to the blue curve (excited *trans*-azobenzene, S*).(50) (B) Kinetics of *trans* → *cis* isomerization of excited M-AZB (top) and F-AZB (bottom) switches confined inside the cage. Transition times for all the guests in the cage are reported in Table 1.

As shown in Figure 4A, the isomerization of all excited unbound trans-azobenzenes studied here occurs on the time scale of picoseconds, consistent with the kinetics of isomerization for free azobenzenes (unconstrained conditions).(52) However, the process can become significantly slower as a result of encapsulation within the cage (see Figure 4B) (i.e., molecular crowding).(50) The trans → cis isomerization times for the guests studied herein are reported in Table 1. Interestingly, the slowing of the transition can be negligible or different by of orders of magnitude, depending on the encapsulated guest. For example, in the case of AZB and AZP, the transition kinetics is not significantly affected by the confinement in the cage. On the other hand, the switching is ∼3 or even up to ∼100 times slower for confined F-AZB and M-AZB, respectively (Figure 4B). Moreover, it is worth noting that such a considerable switching deceleration is obtained using a model where the excited trans guests cannot de-excite back.(50) Considering that the lifetime of the excited state S* of trans-azobenzene is on the order of picoseconds,(52) however, de-excitation of S* to the ground state is a non-negligible event in real systems. This suggests that the considerable deceleration in transition rates associated with encapsulated F-AZB and M-AZB could actually be, at worst, underestimated by our model. Such a difference is interesting, especially considering that cases have been reported in which azobenzene isomerization may become rare (as in highly ordered self-assembled tubules(50)) or impossible (such as within dense azobiphenyl monolayers(52)).

Table 1. Thermodynamic and Kinetic Data for trans Guest Binding and Isomerization Inside the Cage

guest	ΔG [kcal/mol]	τ_off [s]	K_b [M^–1]	k_off [s^–1]	k_ona [M^–1 s^–1]	τ_trans–cis [s]
AZB	–5.3 ± 0.3	(3.9 ± 0.2) × 10^–4	7.87 × 10³	2.65 × 10³	2.1 × 10⁷	(1.05 ± 0.05) × 10^–12
M-AZB	–7.9 ± 1.3	(1.2 ± 0.1) × 10^–2	6.41 × 10⁵	8.3 × 10¹	5.32 × 10⁷	(1.00 ± 0.05) × 10^–10
F-AZB	–5.3 ± 0.9	(3.8 ± 0.1) × 10^–3	7.87 × 10³	2.63 × 10²	2.1 × 10⁶	(3.0 ± 0.1) × 10^–12
AZP	–5.7 ± 0.8	(4.2 ± 0.1) × 10^–4	1.55 × 10⁴	2.38 × 10³	3.7 × 10⁷	(1.25 ± 0.05) × 10^–12

^{^a}

Guest concentration in the model systems is ∼11.4 mM; to obtain the effective k_on values in [s^–1], the values in the table should be multiplied by 11.4 mM.

In our specific systems, guest isomerization may even result in an unstable complex. This is the case when the cage incorporates two trans-F-AZB guests at the same time. Right after isomerization is triggered in this system, one of the two encapsulated guests is expelled from the cage.(62) Interestingly, we found the same behavior in our simulations (Figure S3). Co-encapsulation of one trans- and one cis-F-AZB guest inside the cage leads to a highly unstable species, leading to the release of one of the two guests within short time scales (∼10–100 ns). The molecular factors that may affect the switching process inside the cage cavity will be discussed more in detail in the last section. Nonetheless, these results indicate that in order to fully understand and characterize the transitions in these systems, it is first necessary to study the intrinsic dynamics of the host–guest complexes and the kinetics of guest encapsulation and release.

Mechanisms of Guest Encapsulation/Release and Switching

The results discussed in the previous section provide information about the kinetics of trans → cis switching of excited guests inside the cage. However, this information is not sufficient to draw conclusions about whether the isomerization occurs inside or outside the cage, or about the stability of the guest encapsulation inside the host before and after the transition. To obtain a complete picture of the transition mechanism, we have studied the thermodynamics and kinetics of the guest encapsulation and expulsion in/out the cage. In fact, the ΔG for guest encapsulation (and the related k_on vs k_off) determines the effective probability of finding the guests inside/outside the cage and their residence time inside the cage.

Since guest encapsulation and release are, in general, rare events in these systems, it is difficult to study them via classical MD simulations. Consequently, we used MetaD simulations to investigate the thermodynamics and kinetics of guest binding/release. Starting from the equilibrated trans complexes, we conducted MetaD simulations during which the guests exchange multiple times in and out of the cage, allowing for a thorough exploration of the bound and unbound states and of the transition between them. These simulations allowed us to retrieve the free-energy difference, ΔG, between the encapsulated and free states and to calculate the corresponding K_b values (see Figure 5 and Table 1 for the data for all trans guests; the complete series including cis guests is listed in Tables S1 and S2). These data offer an exhaustive picture of the thermodynamics governing guest encapsulation, which is crucial to uncovering the probability of guest binding/release. We found that formation of the host–guest complex is energetically favored in all the tested cases, with a free-energy gain ranging from ∼3.6 kcal/mol for cis-F-AZB up to ∼8 kcal/mol for trans-M-AZB.

Figure 5. Thermodynamics and kinetics of *trans* guest binding/release. (A) Representative MetaD snapshots of the reversible binding and release of *trans*-M-AZB inside the cage; k_off and k_on denote the kinetic constants for the expulsion and encapsulation processes (the k_on value inside the brackets is explicitly calculated, accounting for the guest concentration used in the model ∼11.4 mM, providing the actual rate). (B) Thermodynamic and kinetic scheme representing the expulsion and encapsulation mechanisms for *trans*-AZB in/out the cage as a function of the distance between the guests’ and the cage’s centers of mass (identifying IN and OUT states). (C) Thermodynamic schemes representing the expulsion/encapsulation of the *trans* isomers of M-AZB (green), F-AZB (cyan), and AZP (violet) guests. All ΔG differences between IN vs OUT states were computed from converged MetaD simulations, while the transition barriers were more accurately estimated from multiple infrequent MetaD runs (see the SI Methods section for further details).

As recently done to study the kinetics of monomer exchange in supramolecular polymers,(73) we then studied the kinetics of guest binding/release by means of infrequent MetaD simulations(74) (see SI Methods for details). From multiple infrequent MetaD runs activating/biasing guest release out from the cage, we could reconstruct unbiased kinetics for the event and estimate residence times for the encapsulated guest, τ_off. The kinetic constant for guest release can be calculated as k_off = 1/τ_off. The kinetic constant for guest encapsulation (k_on) can be then derived as follows: K_b = k_on/k_off. In this way we can obtain the complete thermodynamic and dynamic characterization of these host–guest systems, as represented in the thermodynamic schemes in Figure 5 and in the data collected in Tables 1, S1, and S2. These results reveal some subtle aspects of the binding/release processes. For example, we found that the cis conformers on average exhibit shorter residence times inside the cage with respect to the corresponding trans isomers, including more weakly binding trans isomers such as trans-AZB and trans-AZP. This effect is attributed to the lower free-energy barrier that the cis guest has to overcome to leave the cage as compared to the trans guest (see Table S2), which could be correlated with the relatively high flexibility of the host cage while accommodating cis guests (see Figure 3). Most importantly, we can observe from Table 1 that the characteristic transition times for trans → cis isomerization (τ_trans–cis) are orders of magnitude shorter than the characteristic time for the release of trans guests from the cage (τ_off). This indicates that isomerization in these systems occurs most probably inside the cage.

We also conducted MetaD simulations to study the encapsulation of a second trans guest in the case where one trans guest is already encapsulated inside the cage. We know from the experimental results(62) and from the plain MD simulations (see previous sections), that the cage can often incorporate two trans guests (e.g., F-AZB or AZB). Conversely, other molecules, such as M-AZB, can only form complexes incorporating one guest molecule.(62) The FESs obtained from MetaD simulations with two M-AZB vs two F-AZB or two AZB guests are consistent with this picture (Figure S4). In particular, these results clearly demonstrate that while incorporation of a second F-AZB, or AZB, guest in the cage is an energetically favored event (Figure S4, center and right), in the case of M-AZB, this process is highly unfavorable and unlikely (Figure S4, left). This is consistent, for example, with the available crystal structures, showing that two trans-F-AZB and two trans-AZB guests can be encapsulated within one cage, while the same cage accommodates only one trans-M-AZB at a time.(62) Moreover, while quantities such as the ΔG, K_b, k_on, and k_off of guest encapsulation/expulsion can be difficult to determine experimentally, the overall binding constant governing encapsulation of two trans-AZB guests within the cage could be estimated from NMR experiments, giving a value in the range of ∼10⁹ M^–2.(62) We could also estimate such overall binding constant (K_b(tot)) from the MetaD simulations using the K_b values associated with the first and the second trans-AZB guests (i.e., as K_b(tot) = K_b(guest-1) × K_b(guest-2)). The calculated value for K_b(tot) is ∼0.3 × 10⁹ M^–2 (see Table S3), which is consistent with the value obtained experimentally. The results of our simulations are also qualitatively consistent with the experimental evidence available for the other systems, for which experimental K_b values could not be obtained. We conducted infrequent MetaD simulations to compare the residence times of two F-AZB guests inside the cage before and after trans → cis isomerization of one guest. We found that while the switching similarly occurs within the cage, one of the two guests is then expelled promptly, within very fast time scales (nanoseconds)—orders of magnitude shorter than in the two-trans case (see Figure S3). In particular, the expulsion of cis-F-AZB is ten times more likely (or faster) than that of the trans isomer (residence times inside the cage of ∼10 ns and ∼100 ns, respectively; see also Figure S5). This finding is consistent with the experimental results(62) demonstrating that the (trans+cis)-cage ternary complex is unstable and that the isomerization of trans-F-AZB produced the rapid expulsion from the cage of one out of the two guests (most likely the cis isomer). Together, these results support the reliability of our models and provide a comprehensive characterization of the system both from thermodynamic and kinetic points of view. They also show how, in order to characterize the transition kinetics inside the cage, it is also necessary to characterize the binding and release of the guests in/out the cage.

Molecular Determinants of Guest Transitions in the Cage

In the final step, we analyzed the results from our simulations to investigate the molecular determinants that control in-cavity isomerization of the guests in these systems. Table 1 lists data describing dynamic host–guest binding in the systems and the kinetics of isomerization inside the cage cavity. Interestingly, by comparing the τ_trans–cis with the τ_off data, we obtain a nontrivial relationship between the residence time of the guests inside the host and the characteristic time scale needed for guest switching. In particular, we can observe that longer residence times in the cavity correspond to slower transitions (Figure 6A), suggesting that the same molecular factors regulating the stability of host–guest binding have an impact on the switching rates of the guests.

Figure 6. Molecular determinants of isomerization under confinement. (A) Relationship between isomerization rate (τ*_trans–cis*) and residence times (τ_off) of the guests inside the cage. (B) Relationship between τ*_trans–cis* and potential energy of host–guest interactions, ΔE_HG. (C) Relationship between τ*_trans–cis* and the number of contacts between the cage and the guest. (D) Relationship between τ*_trans–cis* and the volume (V) of guest molecules (see the SI Methods section for details on guest volume estimation). (E) Switching deceleration, τ*_trans–cis*/τ₀, as a function of the increase in guest volume (%ΔV_guest), in which τ₀ denotes isomerization time measured at the original volume of each guest. In plots A–E, the points correspond to guests AZB (black), M-AZB (green), F-AZB (cyan), and AZP (violet). (F) Average τ*_trans–cis*/τ₀ as a function of the average increase in guest volume (%ΔV_guest), obtained by averaging all data from plot E between systems with similar %ΔV_guest. The error bars indicate the standard deviation of %ΔV_guest and τ*_trans–cis*/τ₀ values. Inset: cartoon showing the volume of encapsulated M-AZB (green) inside the cage (white). The dashed lines in all plots are the logarithmic fit of the data.

In general, the energy of the host–guest interaction ΔE_HG correlates with τ_off. When this interaction is stronger, guest release from the cage is slower, meaning that the guest spends more time in the cage. Molecular crowding in the cavity has a similar effect. When there is a higher number of contacts between the host and the guest, τ_off is longer, and guest release is less probable. We can clearly observe this effect for all simulated systems, both with trans and cis guests (see Figure S6A,B). This result is reasonable, as the interactions and the number of contacts between the host and the guest are intimately correlated to one another (see Figure S6C). This correlation is especially relevant when considering flexible hosts: stronger affinity between the host and guest leads to larger deformation of the host, as a flexible cage can structurally adapt to enhance contacts with the guest. At the same time, the relationship obtained in Figure 6A indicates that both host–guest affinity and molecular crowding impact the transition rate (τ_trans–cis). This relationship between τ_trans–cis and ΔE_HG, and between τ_trans–cis and the number of contacts, is demonstrated by the trends in Figure 6B and C, respectively. These results suggest that both host–guest affinity and molecular crowding can in principle be used to control the transition rates in the system.

Because extrapolating design principles from these plots is not trivial, we chose a more elegant strategy. We started from the simplistic consideration that, for a given impact of host–guest contacts on the switching process, the ratio between the volume occupied by the guest and the volume accessible in the cage (e.g., V_guest/V_cavity) constitutes a discriminant parameter governing transitions in the system. Given that the cage is the same in all systems, and assuming that the variations in V_cavity are negligible when comparing between the various systems (simplification), we plotted V_guest against τ_trans–cis (Figure 6D) and obtained a trend similar to those described above. Even considering the approximations required to make this observation, this qualitative trend reveals a molecular-level relationship between the volume of the guest and the transition rate under confinement.

Recently, we demonstrated how reliable chemically relevant molecular models can be used as “toy models” to obtain pseudomolecular, yet useful information. By “playing” with these flexible models, we can then learn about the factors that control the system.(50,73) Having observed that guest volume has a strong impact on transition rate within the cage, we developed a computational strategy to increase the number of available data points in this trend. Starting from equilibrated models of the cage encapsulating one trans guest of each type, we artificially increased the radii of guests’ atoms in the models to increase V_guest. In all cases, the atomic radii have been increased to achieve a global increase of ∼5, 10, 20, or 30% for V_guest. Repeating the isomerization simulations for all these cases then allowed us to monitor transition deceleration as a function of the increase in guest volume (%ΔV_guest). In this way, we obtained the trends shown in Figure 6E for the various guests.

These results show that transition rate generally slows down as %ΔV_guest increases. Some variability between the different guests can be expected (e.g., M-AZB in green), as other features of the guest, such as chemical structure and shape, can also impact isomerization. These results are in agreement with our observation that host–guest affinity also has an impact on the rate of isomerization (Figure 6B). We also note that for some guests (M-AZB and AZP), the series is incomplete because isomerization does not occur inside the cage over a certain %ΔV_guest (∼20% for AZP and ∼5–10% for M-AZB). In these cases, isomerization is either impeded by the cage or results in the release of the isomerizing guest. This observation is consistent with experimental results and with the simulations for two-guest systems. In fact, encapsulating two guests inside the cage can be assumed to be comparable to a %ΔV_guest of ∼100%, well over the maximum %ΔV_guest for which isomerization occurs inside the cage. As previously shown, isomerization of one guest produces rapid expulsion of one guest from two-guest systems (see Figure S3).

Finally, if we average the rate deceleration data at different values of %ΔV_guest for the various systems (Figure 6E), we obtain the plot shown in Figure 6F, which shows a clear general trend between the average increase in guest volume and the deceleration of guest transitions. This trend is clearly qualitative, as other variables may also be important in controlling guest isomerization under confinement. Nevertheless, this result demonstrates a direct correlation between guest volume, crowding within the cage, and the guest transition rates. This observation helps rationalize experimental(62,75) and computational results,(50,52,76) showing that azobenzene isomerization may be hindered in highly crowded molecular systems. The generality of the computational approach presented herein offers a context for developing the idea that molecular environments can be, in principle, rationally designed to control molecular switching processes.

Conclusions

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Learning how to control chemical reactions inside confined spaces will unlock many applications. Here we used atomistic simulations to investigate the mechanisms and molecular factors that control trans → cis isomerization of various azo compounds within a coordination cage. Classical molecular dynamics and metadynamics simulations allowed us to characterize these host–guest systems from thermodynamic and kinetic points of view. In this way, we obtained an exhaustive mechanistic understanding of guest encapsulation, reversible guest uptake/release dynamics and guest switching transitions, and results in agreement with experimental observations.

To elucidate the kinetics of molecular transitions under confinement, we show that it is necessary to understand the intrinsic dynamics of guest binding and release processes. We demonstrate how this equilibrium is influenced by the free-energy cost associated with host reconfiguration upon guest encapsulation, and by the energy gain due to host–guest interactions. This competition determines the residence time of encapsulated azobenzene guests inside the cage and the slowing rate of their isomerization. We identify molecular crowding and host–guest affinity as two key factors governing isomerization rate/probability in these systems. Our results demonstrate that, in principle, tuning the volume of the guest may have a direct impact on the transition rate inside the cage, or even dictate whether the transition will occur inside or outside the cage.

Overall, the advantages of the approach employed herein are many. Our approach enables a thorough characterization of (i) the flexibility and conformations accessible by the cage under given conditions of solvent and temperature, (ii) the isomerization rates for encapsulated guests, and (iii) the effect of guest encapsulation and isomerization on the flexibility and conformational distortion of the cage. The metadynamics simulations allow us to obtain molecular-level information on the thermodynamics and kinetics of the host–guest encapsulation, providing values for, e.g., k_on, k_off, ΔG, free-energy barriers, etc., which can be challenging to determine experimentally. From a holistic point of view, this reveals the synergies between structure, thermodynamics, and dynamics within these complex molecular systems, which concur to determine the behavior of these host−guest molecular systems. In principle, the molecular simulations approaches described herein are versatile and can be applied to investigate not only other cages but also stimuli-responsive host–guest systems in general. Our approach can provide clearer insight into the molecular factors that control structure, host–guest affinity, and dynamics, thus guiding the rational design, or customization, of systems with controllable reactivity. We envisage that this approach will find application in fields ranging from the rational design of photoresponsive host–guest systems and artificial enzymes to the control of chemical reactions in confined spaces.

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.0c03444.

Details on the creation and parametrization of the molecular systems, simulation setup, and analysis of molecular dynamics and metadynamics simulations; additional data and figures from the simulations (PDF)

ja0c03444_si_001.pdf (2.6 MB)

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Author Information

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Corresponding Author
- Giovanni M. Pavan - Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland; Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; http://orcid.org/0000-0002-3473-8471; Email: [email protected]
Authors
- Luca Pesce - Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland; http://orcid.org/0000-0001-6364-9577
- Claudio Perego - Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, CH-6928 Manno, Switzerland; http://orcid.org/0000-0001-8885-3080
- Angela B. Grommet - Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
- Rafal Klajn - Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel; http://orcid.org/0000-0002-6320-8875
Notes
The authors declare no competing financial interest.

Acknowledgments

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GMP acknowledges the funding received by the Swiss National Science Foundation (SNSF grant number 200021_175735) and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 818776 – DYNAPOL). The authors also acknowledge the computational resources provided by the Swiss National Supercomputing Center (CSCS). RK acknowledges funding from the Minerva Foundation. ABG acknowledges funding from the Zuckerman STEM Leadership Program.

References

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Stoddart, J. Fraser
Angewandte Chemie, International Edition (2017), 56 (37), 11094-11125CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
An autobiog. for J. Fraser Stoddart, born May 24, 1942 in Edinburgh, United Kingdom, is presented. Stoddart is a professor of chem. and head of the Stoddart Mechanostereochem. Group at Northwestern University in the United States.
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Dri, C.; Peters, M. V.; Schwarz, J.; Hecht, S.; Grill, L. Spatial Periodicity in Molecular Switching. Nat. Nanotechnol. 2008, 3, 649– 653, DOI: 10.1038/nnano.2008.269
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13
Spatial periodicity in molecular switching
Dri, Carlo; Peters, Maike V.; Schwarz, Jutta; Hecht, Stefan; Grill, Leonhard
Nature Nanotechnology (2008), 3 (11), 649-653CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
The ultimate miniaturization of future devices will require the use of functional mols. at the nanoscale and their integration into larger architectures. Switches represent a prototype of such functional mols. because they exhibit characteristic states of different phys./chem. properties, which can be addressed reversibly. Recently, various switching entities have been studied and switching of single mols. on surfaces has been demonstrated. However, for functional mols. to be used in a future device, it will be necessary to selectively address individual mols., preferentially in an ordered pattern. Here, we show that azobenzene derivs. in the trans form, adsorbed in a homogeneous two-dimensional layer, can be collectively switched with spatial selectivity, thus forming a periodic pattern of cis isomers. We find that the probability of a mol. switching is not equally distributed, but is strongly dependent on both the surrounding mols. and the supporting surface, which precisely det. the switching capability of each individual mol. Consequently, exactly the same lattices of cis isomers are created in repeated erasing and re-switching cycles. Our results demonstrate a conceptually new approach to spatially addressing single functional mols.
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Kassem, S.; Lee, A. T. L.; Leigh, D. A.; Marcos, V.; Palmer, L. I.; Pisano, S. Stereodivergent Synthesis with a Programmable Molecular Machine. Nature 2017, 549, 374– 378, DOI: 10.1038/nature23677
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14
Stereodivergent synthesis with a programmable molecular machine
Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Marcos, Vanesa; Palmer, Leoni I.; Pisano, Simone
Nature (London, United Kingdom) (2017), 549 (7672), 374-378CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
It has been convincingly argued that mol. machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångstrom precision are unlikely to be realized. However, biol. mol. machines routinely position rather less reactive substrates in order to direct chem. reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered mols. are passed from active site to active site in multi-enzyme complexes. Artificial mol. machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host mol. has been described that is able to mech. twist a bound mol. guest, and mol. fragments have been selectively transported in either direction between sites on a mol. platform through a ratchet mechanism. Here we detail an artificial mol. machine that moves a substrate between different activating sites to achieve different product outcomes from chem. synthesis. This mol. robot can be programmed to stereoselectively produce, in a sequential one-pot operation, an excess of any one of four possible diastereoisomers from the addn. of a thiol and an alkene to an α,β-unsatd. aldehyde in a tandem reaction process. The stereodivergent synthesis includes diastereoisomers that cannot be selectively synthesized through conventional iminium-enamine organocatalysis. We anticipate that future generations of programmable mol. machines may have significant roles in chem. synthesis and mol. manufg.
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Katsonis, N.; Lubomska, M.; Pollard, M. M.; Feringa, B. L.; Rudolf, P. Synthetic Light-Activated Molecular Switches and Motors on Surfaces. Prog. Surf. Sci. 2007, 82, 407– 434, DOI: 10.1016/j.progsurf.2007.03.011
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15
Synthetic light-activated molecular switches and motors on surfaces
Katsonis, Nathalie; Lubomska, Monika; Pollard, Michael M.; Feringa, Ben L.; Rudolf, Petra
Progress in Surface Science (2007), 82 (7-8), 407-434CODEN: PSSFBP; ISSN:0079-6816. (Elsevier B.V.)
A review. Recent advances in synthetic methods and anal. techniques provide a basis for the construction and characterization of organized arrays of mol. switches and motors on surfaces. Among them, mol. systems that can be controlled by light are particularly promising because of their ease of addressability, fast response times and the compatibility of light with a wide range of condensed phases. The aim of this contribution is to highlight selected recent advances in building functional monolayers of light-activated mols. Special focus is given to monolayers of mols. whose collective switching properties were harnessed to produce macroscopic effects. The design, structure, and function of monolayers composed of bistable photochromic switches, which can control chirality, wettability, cond. and self-assembly are described. A recent report on the successful demonstration of light-driven rotary motors functioning while grafted on gold surfaces will also be discussed, followed by a brief conclusion.
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Broichhagen, J.; Frank, J. A.; Trauner, D. A Roadmap to Success in Photopharmacology. Acc. Chem. Res. 2015, 48, 1947– 1960, DOI: 10.1021/acs.accounts.5b00129
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A Roadmap to Success in Photopharmacology
Broichhagen, Johannes; Frank, James Allen; Trauner, Dirk
Accounts of Chemical Research (2015), 48 (7), 1947-1960CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
Light is a fascinating phenomenon that ties together physics, chem., and biol. It is unmatched in its ability to confer information with temporal and spatial precision and has been used to map objects on the scale of tens of nanometers (10-8 m) to light years (1016 m). This information, gathered through super-resoln. microscopes or space-based telescopes, is ultimately funneled through the human visual system, which is a miracle in itself. It allows us to see the Andromeda galaxy at night, an object that is 2.5 million light years away and very dim, and ski the next day in bright sunlight at an intensity that is 12 orders of magnitude higher. Human vision is only one of many photoreceptive systems that have evolved on earth and are found in all kingdoms of life. These systems rely on mol. photoswitches, such as retinal or tetrapyrrols, which undergo transient bond isomerizations or bond formations upon irradn. The set of chromophores that have been employed in Nature for this purpose is surprisingly small. Nevertheless, they control a wide variety of biol. functions, which have recently been significantly increased through the rapid development of optogenetics. Optogenetics originated as an effort to control neural function with genetically encoded photoreceptors that use abundant chromophores, in particular retinal. It now covers a variety of cellular functions other than excitability and has revolutionized the control of biol. pathways in neuroscience and beyond. Chem. has provided a large repertoire of synthetic photoswitches with highly tunable properties. Like their natural counterparts, these chromophores can be attached to proteins to effectively put them under optical control. This approach has enabled a new type of synthetic photobiol. that has gone under various names to distinguish it from optogenetics. We now call it photopharmacol. Here we trace our involvement in this field, starting with the first light-sensitive potassium channel (SPARK) and concluding with our most recent work on photoswitchable fatty acids. Instead of simply providing a historical account of our efforts, we discuss the design criteria that guided our choice of mols. and receptors. As such, we hope to provide a roadmap to success in photopharmacol. and make a case as to why synthetic photoswitches, properly designed and made available through well-planned and efficient syntheses, should have a bright future in biol. and medicine.
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Weston, C. E.; Krämer, A.; Colin, F.; Yildiz, Ö.; Baud, M. G. J.; Meyer-Almes, F.-J.; Fuchter, M. J. Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors. ACS Infect. Dis. 2017, 3, 152– 161, DOI: 10.1021/acsinfecdis.6b00148
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Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors
Weston, Claire E.; Kramer, Andreas; Colin, Felix; Yildiz, Ozkan; Baud, Matthias G. J.; Meyer-Almes, Franz-Josef; Fuchter, Matthew J.
ACS Infectious Diseases (2017), 3 (2), 152-161CODEN: AIDCBC; ISSN:2373-8227. (American Chemical Society)
Photopharmacol. agents exhibit light-dependent biol. activity and may have potential in the development of new antimicrobial agents/modalities. Amidohydrolase enzymes homologous to the well-known human histone deacetylases (HDACs) are present in bacteria, including resistant organisms responsible for a significant no. of hospital-acquired infections and deaths. We report photopharmacol. inhibitors of these enzymes, using two classes of photoswitches embedded in the inhibitor pharmacophore: azobenzenes and arylazopyrazoles. Although both classes of inhibitor show excellent inhibitory activity (nM IC50 values) of the target enzymes and promising differential activity of the switchable E- and Z-isomeric forms, the arylazopyrazoles exhibit better intrinsic photoswitch performance (more complete switching, longer thermal lifetime of the Z-isomer). We also report protein-ligand crystal structures of the E-isomers of both an azobenzene and an arylazopyrazole inhibitor, bound to bacterial histone deacetylase-like amidohydrolases (HDAHs). These structures not only uncover interactions important for inhibitor binding but also reveal conformational differences between the two photoswitch inhibitor classes. As such, our data may pave the way for the design of improved photopharmacol. agents targeting the HDAC superfamily.
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Fiedler, D.; Leung, D.; Bergman, R.; Raymond, K. Selective Molecular Recognition, C-H Bond Activation, and Catalysis in Nanoscale Reaction Vessels. Acc. Chem. Res. 2005, 38, 349– 358, DOI: 10.1021/ar040152p
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Selective Molecular Recognition, C-H Bond Activation, and Catalysis in Nanoscale Reaction Vessels
Fiedler, Dorothea; Leung, Dennis H.; Bergman, Robert G.; Raymond, Kenneth N.
Accounts of Chemical Research (2005), 38 (4), 349-358CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
A review. Supramol. chem. represents a way to mimic enzyme reactivity by using specially designed container mols. We have shown that a chiral self-assembled M4L6 supramol. tetrahedron can encapsulate a variety of cationic guests with varying degrees of stereoselectivity. Reactive iridium guests can be encapsulated, and the C-H bond activation of aldehydes occurs with the host cavity controlling the ability of substrates to interact with the metal center based upon size and shape. In addn., the host container can act as a catalyst by itself. By restricting reaction space and preorganizing the substrates into reactive conformations, it accelerates the sigmatropic rearrangement of enammonium cations.
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Tripp, B. C.; Smith, K.; Ferry, J. G. Carbonic Anhydrase: New Insights for an Ancient Enzyme. J. Biol. Chem. 2001, 276, 48615– 48618, DOI: 10.1074/jbc.R100045200
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Carbonic anhydrase: new insights for an ancient enzyme
Tripp, Brian C.; Smith, Kerry; Ferry, James G.
Journal of Biological Chemistry (2001), 276 (52), 48615-48618CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
A review, discussing advances in the study of the structure and biol. chem. of carbonic anhydrases of the classes α, β, and γ. The catalytic mechanisms for both the β- and γ-class carbonic anhydrases were further elucidated, particularly in the proton transfer pathway. A possible fourth class (δ) represented by the Thalassiosira weissflogii enzyme is also described.
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Zhang, X.; Houk, K. N. Why Enzymes Are Proficient Catalysts: Beyond the Pauling Paradigm. Acc. Chem. Res. 2005, 38, 379– 385, DOI: 10.1021/ar040257s
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20
Why enzymes are proficient catalysts: beyond the Pauling paradigm
Zhang, Xiyun; Houk, K. N.
Accounts of Chemical Research (2005), 38 (5), 379-385CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
A review. Linus Pauling (1948) proposed that "enzymes are mols. that are complementary in structure to the activated complexes of the reactions that they catalyze, ..., [rather than] entering into reactions". This paradigm has dominated thinking in the field. While complementarity of the type proposed by Pauling can account for acceleration up to 11 orders of magnitude, most enzymes exceed that proficiency. Enzymes with proficiencies [(kcat/Km)/kuncat] > 1011 M-1 achieve >15 kcal/mol of "transition state binding" not merely by a concatenation of noncovalent effects but by covalent bond formation between enzyme or cofactor and transition state, involving a change in mechanism from that in aq. soln. Enzymes enter into reactions with substrates and do not merely complement the transition states of the uncatalyzed reactions.
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Whicher, J. R.; Dutta, S.; Hansen, D. A.; Hale, W. A.; Chemler, J. A.; Dosey, A. M.; Narayan, A. R. H.; Håkansson, K.; Sherman, D. H.; Smith, J. L.; Skiniotis, G. Structural Rearrangements of a Polyketide Synthase Module during Its Catalytic Cycle. Nature 2014, 510, 560– 564, DOI: 10.1038/nature13409
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21
Structural rearrangements of a polyketide synthase module during its catalytic cycle
Whicher, Jonathan R.; Dutta, Somnath; Hansen, Douglas A.; Hale, Wendi A.; Chemler, Joseph A.; Dosey, Annie M.; Narayan, Alison R. H.; Hakansson, Kristina; Sherman, David H.; Smith, Janet L.; Skiniotis, Georgios
Nature (London, United Kingdom) (2014), 510 (7506), 560-564CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
The polyketide synthase (PKS) mega-enzyme assembly line uses a modular architecture to synthesize diverse and bioactive natural products that often constitute the core structures or complete chem. entities for many clin. approved therapeutic agents. The architecture of a full-length PKS module from the pikromycin pathway of Streptomyces venezuelae creates a reaction chamber for the intramodule acyl carrier protein (ACP) domain that carries building blocks and intermediates between acyltransferase, ketosynthase and ketoreductase active sites (see accompanying paper). Here we det. electron cryo-microscopy structures of a full-length pikromycin PKS module in three key biochem. states of its catalytic cycle. Each biochem. state was confirmed by bottom-up liq. chromatog./Fourier transform ion cyclotron resonance mass spectrometry. The ACP domain is differentially and precisely positioned after polyketide chain substrate loading on the active site of the ketosynthase, after extension to the β-keto intermediate, and after β-hydroxy product generation. The structures reveal the ACP dynamics for sequential interactions with catalytic domains within the reaction chamber, and for transferring the elongated and processed polyketide substrate to the next module in the PKS pathway. During the enzymic cycle the ketoreductase domain undergoes dramatic conformational rearrangements that enable optimal positioning for reductive processing of the ACP-bound polyketide chain elongation intermediate. These findings have crucial implications for the design of functional PKS modules, and for the engineering of pathways to generate pharmacol. relevant mols.
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Grommet, A. B.; Feller, M.; Klajn, R. Chemical Reactivity under Nanoconfinement. Nat. Nanotechnol. 2020, 15, 256– 271, DOI: 10.1038/s41565-020-0652-2
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Chemical reactivity under nanoconfinement
Grommet, Angela B.; Feller, Moran; Klajn, Rafal
Nature Nanotechnology (2020), 15 (4), 256-271CODEN: NNAABX; ISSN:1748-3387. (Nature Research)
A review. Confining mols. can fundamentally change their chem. and phys. properties. Confinement effects are considered instrumental at various stages of the origins of life, and life continues to rely on layers of compartmentalization to maintain an out-of-equil. state and efficiently synthesize complex biomols. under mild conditions. As interest in synthetic confined systems grows, we are realizing that the principles governing reactivity under confinement are the same in abiol. systems as they are in nature. In this Review, we categorize the ways in which nanoconfinement effects impact chem. reactivity in synthetic systems. Under nanoconfinement, chem. properties can be modulated to increase reaction rates, enhance selectivity and stabilize reactive species. Confinement effects also lead to changes in phys. properties. The fluorescence of light emitters, the colors of dyes and electronic communication between electroactive species can all be tuned under confinement. Within each of these categories, we elucidate design principles and strategies that are widely applicable across a range of confined systems, specifically highlighting examples of different nanocompartments that influence reactivity in similar ways.
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Janiak, C.; Vieth, J. K. MOFs, MILs and More: Concepts, Properties and Applications for Porous Coordination Networks (PCNs). New J. Chem. 2010, 34, 2366– 2388, DOI: 10.1039/c0nj00275e
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MOFs, MILs and more: concepts, properties and applications for porous coordination networks (PCNs)
Janiak, Christoph; Vieth, Jana K.
New Journal of Chemistry (2010), 34 (11), 2366-2388CODEN: NJCHE5; ISSN:1144-0546. (Royal Society of Chemistry)
A review. Discussion summarizes metal-org. frameworks (MOFs), Materials Institute Lavoisier (MILs), iso-reticular metal-org. frameworks (IR-MOFs), porous coordination networks (PCNs), zeolitic metal-org. frameworks (ZMOFs) and porous coordination polymers (PCPs) with selected examples of their structures, concepts for linkers, syntheses, post-synthesis modifications, metal nanoparticle formations in MOFs, porosity and zeolitic behavior for applications in gas storage for H, CO2, methane and applications in cond., luminescence and catalysis.
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Goettmann, F.; Sanchez, C. How Does Confinement Affect the Catalytic Activity of Mesoporous Materials?. J. Mater. Chem. 2007, 17, 24– 30, DOI: 10.1039/B608748P
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How does confinement affect the catalytic activity of mesoporous materials?
Goettmann, Frederic; Sanchez, Clement
Journal of Materials Chemistry (2007), 17 (1), 24-30CODEN: JMACEP; ISSN:0959-9428. (Royal Society of Chemistry)
A review. So-called confinement effects in porous materials are known to strongly affect diffusion, phase transformations, catalytic properties, etc. In the field of catalysis, it is generally admitted that antagonistic effects at the mesoscale result in the existence of an optimal catalytic efficiency depending on pore size. Herein we highlight some recent examples of pore size effects and their proposed mechanisms. Confinement studies on periodically organized mesoporous materials must be developed because they should provide a certain clearness of arguments and understanding.
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Boyd, P. G.; Chidambaram, A.; García-Díez, E.; Ireland, C. P.; Daff, T. D.; Bounds, R.; Gładysiak, A.; Schouwink, P.; Moosavi, S. M.; Maroto-Valer, M. M.; Reimer, J. A.; Navarro, J. A. R.; Woo, T. K.; Garcia, S.; Stylianou, K. C.; Smit, B. Data-Driven Design of Metal–Organic Frameworks for Wet Flue Gas CO₂ Capture. Nature 2019, 576, 253– 256, DOI: 10.1038/s41586-019-1798-7
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Data-driven design of metal-organic frameworks for wet flue gas CO2 capture
Boyd, Peter G.; Chidambaram, Arunraj; Garcia-Diez, Enrique; Ireland, Christopher P.; Daff, Thomas D.; Bounds, Richard; Gladysiak, Andrzej; Schouwink, Pascal; Moosavi, Seyed Mohamad; Maroto-Valer, M. Mercedes; Reimer, Jeffrey A.; Navarro, Jorge A. R.; Woo, Tom K.; Garcia, Susana; Stylianou, Kyriakos C.; Smit, Berend
Nature (London, United Kingdom) (2019), 576 (7786), 253-256CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
Limiting the increase of CO2 in the atm. is one of the largest challenges of our generation1. Because carbon capture and storage is one of the few viable technologies that can mitigate current CO2 emissions2, much effort is focused on developing solid adsorbents that can efficiently capture CO2 from flue gases emitted from anthropogenic sources3. One class of materials that has attracted considerable interest in this context is metal-org. frameworks (MOFs), in which the careful combination of org. ligands with metal-ion nodes can, in principle, give rise to innumerable structurally and chem. distinct nanoporous MOFs. However, many MOFs that are optimized for the sepn. of CO2 from nitrogen4-7 do not perform well when using realistic flue gas that contains water, because water competes with CO2 for the same adsorption sites and thereby causes the materials to lose their selectivity. Although flue gases can be dried, this renders the capture process prohibitively expensive8,9. Here we show that data mining of a computational screening library of over 300,000 MOFs can identify different classes of strong CO2-binding sites-which we term 'adsorbaphores'-that endow MOFs with CO2/N2 selectivity that persists in wet flue gases. We subsequently synthesized two water-stable MOFs contg. the most hydrophobic adsorbaphore, and found that their carbon-capture performance is not affected by water and outperforms that of some com. materials. Testing the performance of these MOFs in an industrial setting and consideration of the full capture process-including the targeted CO2 sink, such as geol. storage or serving as a carbon source for the chem. industry-will be necessary to identify the optimal sepn. material.
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Chu, Z.; Han, Y.; Bian, T.; De, S.; Král, P.; Klajn, R. Supramolecular Control of Azobenzene Switching on Nanoparticles. J. Am. Chem. Soc. 2019, 141, 1949– 1960, DOI: 10.1021/jacs.8b09638
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Supramolecular Control of Azobenzene Switching on Nanoparticles
Chu, Zonglin; Han, Yanxiao; Bian, Tong; De, Soumen; Kral, Petr; Klajn, Rafal
Journal of the American Chemical Society (2019), 141 (5), 1949-1960CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene's hydrophobic nature, most of these examples have been realized only in org. solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-sol. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amt. of azobenzene on the functionalized nanoparticles. Mol. dynamics simulations helped us to identify two distinct supramol. architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aq. solubilities. Azobenzenes adsorbed on these water-sol. nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aq. media and, in the long run, in biol. environments.
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Ahrens, J.; Bian, T.; Vexler, T.; Klajn, R. Irreversible Bleaching of Donor–Acceptor Stenhouse Adducts on the Surfaces of Magnetite Nanoparticles. ChemPhotoChem. 2017, 1, 230– 236, DOI: 10.1002/cptc.201700009
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Irreversible Bleaching of Donor-Acceptor Stenhouse Adducts on the Surfaces of Magnetite Nanoparticles
Ahrens, Johannes; Bian, Tong; Vexler, Tom; Klajn, Rafal
ChemPhotoChem (2017), 1 (5), 230-236CODEN: CHEMYH ISSN:. (Wiley-VCH Verlag GmbH & Co. KGaA)
Two novel donor-acceptor Stenhouse adducts (DASAs) featuring the catechol moiety were synthesized and characterized. Both compds. bind strongly to the surfaces of magnetite nanoparticles. An adrenaline-derived DASA renders the particles insol. in all common solvents, likely because of poor solvation of the zwitterionic isomer generated on the nanoparticle surfaces. Well-sol. nanoparticles were successfully obtained using dopamine-derived DASA equipped with a long alkyl chain. Upon its attachment to nanoparticles, this DASA undergoes an irreversible decoloration reaction owing to the formation of the zwitterionic form. The reaction follows first-order kinetics and proceeds more rapidly on large nanoparticles. Interestingly, decoloration can be suppressed in the presence of free DASA mols. in soln. or at high nanoparticle concns.
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Zdobinsky, T.; Sankar Maiti, P.; Klajn, R. Support Curvature and Conformational Freedom Control Chemical Reactivity of Immobilized Species. J. Am. Chem. Soc. 2014, 136, 2711– 2714, DOI: 10.1021/ja411573a
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28
Support curvature and conformational freedom control chemical reactivity of immobilized species
Zdobinsky Tino; Maiti Pradipta Sankar; Klajn Rafal
Journal of the American Chemical Society (2014), 136 (7), 2711-4 ISSN:.
We show that bimolecular reactions between species confined to the surfaces of nanoparticles can be manipulated by the nature of the linker, as well as by the curvature of the underlying particles.
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Zhao, H.; Sen, S.; Udayabhaskararao, T.; Sawczyk, M.; Kučanda, K.; Manna, D.; Kundu, P. K.; Lee, J.-W.; Král, P.; Klajn, R. Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks. Nat. Nanotechnol. 2016, 11, 82– 88, DOI: 10.1038/nnano.2015.256
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Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks
Zhao, Hui; Sen, Soumyo; Udayabhaskararao, T.; Sawczyk, Michal; Kucanda, Kristina; Manna, Debasish; Kundu, Pintu K.; Lee, Ji-Woong; Kral, Petr; Klajn, Rafal
Nature Nanotechnology (2016), 11 (1), 82-88CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
The chem. behavior of mols. can be significantly modified by confinement to vols. comparable to the dimensions of the mols. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous org. frameworks and colloidal nanocrystal assemblies, the slow diffusion of mols. in and out of these materials has greatly hampered studying the effect of confinement on their physicochem. properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of UV and visible light irradn. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various mols. from the surrounding bulk soln. Once trapped, these mols. can undergo chem. reactions with increased rates and with stereoselectivities significantly different from those in bulk soln. Illumination with visible light disassembles these nanoflasks, releasing the product in soln. and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chem. reactivities in confined environments and for synthesizing mols. that are otherwise hard to achieve in bulk soln.
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Fallah-Araghi, A.; Meguellati, K.; Baret, J.-C.; Harrak, A. E.; Mangeat, T.; Karplus, M.; Ladame, S.; Marques, C. M.; Griffiths, A. D. Enhanced Chemical Synthesis at Soft Interfaces: A Universal Reaction-Adsorption Mechanism in Microcompartments. Phys. Rev. Lett. 2014, 112, 028301 DOI: 10.1103/PhysRevLett.112.028301
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Enhanced chemical synthesis at soft interfaces: a universal reaction-adsorption mechanism in microcompartments
Fallah-Araghi, Ali; Meguellati, Kamel; Baret, Jean-Christophe; El Harrak, Abdeslam; Mangeat, Thomas; Karplus, Martin; Ladame, Sylvain; Marques, Carlos M.; Griffiths, Andrew D.
Physical Review Letters (2014), 112 (2), 028301/1-028301/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
A bimol. synthetic reaction (imine synthesis) was performed compartmentalized in micrometer-diam. emulsion droplets. The apparent equil. const. (Keq) and apparent forward rate const. (k1) were both inversely proportional to the droplet radius. The results are explained by a noncatalytic reaction-adsorption model in which reactants adsorb to the droplet interface with relatively low binding energies of a few kBT, react and diffuse back to the bulk. Reaction thermodn. is therefore modified by compartmentalization at the mesoscale-without confinement on the mol. scale-leading to a universal mechanism for improving unfavorable reactions.
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Franco, C.; Rodríguez-San-Miguel, D.; Sorrenti, A.; Sevim, S.; Pons, R.; Platero-Prats, A. E.; Pavlovic, M.; Szilágyi, I.; Ruiz Gonzalez, M. L.; González-Calbet, J. M.; Bochicchio, D.; Pesce, L.; Pavan, G. M.; Imaz, I.; Cano-Sarabia, M.; Maspoch, D.; Pané, S.; de Mello, A. J.; Zamora, F.; Puigmartí-Luis, J. Biomimetic Synthesis of Sub-20 nm Covalent Organic Frameworks in Water. J. Am. Chem. Soc. 2020, 142, 3540– 3547, DOI: 10.1021/jacs.9b12389
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Biomimetic Synthesis of Sub-20 nm Covalent Organic Frameworks in Water
Franco, Carlos; Rodriguez-San-Miguel, David; Sorrenti, Alessandro; Sevim, Semih; Pons, Ramon; Platero-Prats, Ana E.; Pavlovic, Marko; Szilagyi, Istvan; Ruiz Gonzalez, M. Luisa; Gonzalez-Calbet, Jose M.; Bochicchio, Davide; Pesce, Luca; Pavan, Giovanni M.; Imaz, Inhar; Cano-Sarabia, Mary; Maspoch, Daniel; Pane, Salvador; de Mello, Andrew J.; Zamora, Felix; Puigmarti-Luis, Josep
Journal of the American Chemical Society (2020), 142 (7), 3540-3547CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Covalent org. frameworks (COFs) are commonly synthesized under harsh conditions yielding unprocessable powders. Control in their crystn. process and growth has been limited to studies conducted in hazardous org. solvents. Herein, we report a one-pot synthetic method that yields stable aq. colloidal solns. of sub-20 nm cryst. imine-based COF particles at room temp. and ambient pressure. Addnl., through the combination of exptl. and computational studies, we investigated the mechanisms and forces underlying the formation of such imine-based COF colloids in water. Further, we show that our method can be used to process the colloidal soln. into 2D and 3D COF shapes as well as to generate a COF ink that can be directly printed onto surfaces. These findings should open new vistas in COF chem., enabling new application areas.
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Zhang, G.; Mastalerz, M. Organic Cage Compounds – from Shape-Persistency to Function. Chem. Soc. Rev. 2014, 43, 1934– 1947, DOI: 10.1039/C3CS60358J
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Organic cage compounds - from shape-persistency to function
Zhang, Gang; Mastalerz, Michael
Chemical Society Reviews (2014), 43 (6), 1934-1947CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
A review. Syntheses, properties and applications of org. cage mols. were reviewed. Covalent bonds can be made in two ways, applying irreversible reactions or reversible reactions. By introducing dynamic covalent chem. (DCC), cages have become accessible in good yields from rather simple precursors. Both methods were compared and highlighted those that give very good yields. Furthermore, the use of org. cage compds. in sorption, recognition, sensing, sepn. and stabilization of mols. was discussed.
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Kang, J.; Rebek, J. Acceleration of a Diels–Alder Reaction by a Self-Assembled Molecular Capsule. Nature 1997, 385, 50– 52, DOI: 10.1038/385050a0
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33
Acceleration of a Diels-Alder reaction by a self-assembled molecular capsule
Kang, Jongmin; Rebek, Julius, Jr.
Nature (London) (1997), 385 (6611), 50-52CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)
The interior of cage-like mols. can be considered to provide a new phase of matter, in which it becomes possible to stabilized reactive intermediates and to observe new forms of stereoisomerism. Cage-like mol. complexes that self-assemble through weak intermol. forces are dynamic species, encapsulating guest mols. reversibly. They can persist over timescales ranging from microseconds to hours, long enough for chem. processes to take place within them. Here we report the acceleration of a Diels-Alder reaction by encapsulation of the reactants in a self-assembling mol. capsule. Although product inhibition (lacking of dissocn.) prevents the system from showing true catalytic behavior, there is clear evidence for a rate increase of over two orders of magnitude owing to the effective enhancement of concn. inside the capsule.
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Yoshizawa, M.; Klosterman, J. K.; Fujita, M. Functional Molecular Flasks: New Properties and Reactions within Discrete, Self-Assembled Hosts. Angew. Chem., Int. Ed. 2009, 48, 3418– 3438, DOI: 10.1002/anie.200805340
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Functional Molecular Flasks: New Properties and Reactions within Discrete, Self-Assembled Hosts
Yoshizawa, Michito; Klosterman, Jeremy K.; Fujita, Makoto
Angewandte Chemie, International Edition (2009), 48 (19), 3418-3438CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
A review. Self-assembled hosts applied as "mol. flasks" can alter and control the reactivity and properties of mols. encapsulated within their well-defined, confined spaces. A variety of functional hosts of differing sizes, shapes, and utility have been prepd. by using the facile and modular concepts of self-assembly. The application of self-assembled hosts as "mol. flasks" has pptd. a surge of interest in the reactivity and properties of mols. within well-defined confined spaces. The facile and modular synthesis of self-assembled hosts has enabled a variety of hosts of differing sizes, shapes, and properties to be prepd. This Review briefly highlights the various mol. flasks synthesized before focusing on their use as functional mol. containers-specifically for the encapsulation of guest mols. to either engender unusual reactions or unique chem. phenomena. Such self-assembled cavities now constitute a new phase of chem., which cannot be achieved in the conventional solid, liq., and gas phases.
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35
Roy, B.; Ghosh, A. K.; Srivastava, S.; D’Silva, P.; Mukherjee, P. S. A Pd₈ Tetrafacial Molecular Barrel as Carrier for Water Insoluble Fluorophore. J. Am. Chem. Soc. 2015, 137, 11916– 11919, DOI: 10.1021/jacs.5b08008
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A Pd8 Tetrafacial Molecular Barrel as Carrier for Water Insoluble Fluorophore
Roy, Bijan; Ghosh, Aloke Kumar; Srivastava, Shubhi; D'Silva, Patrick; Mukherjee, Partha Sarathi
Journal of the American Chemical Society (2015), 137 (37), 11916-11919CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
A new carbazole-based tetraimidazole ligand 1,3,6,8-tetra(1H-imidazol-1-yl)-9-methyl-9H-carbazole (L) has been synthesized. The unsym. nature of L as well as the rotational freedom of imidazole donor moieties around C-N bond make it a special building unit, which upon treatment with cis-(tmeda)Pd(NO3)2 produced an unprecedented single linkage-isomeric Pd8 tetrafacial mol. nanobarrel (PSMBR-1) [tmeda = N,N,N',N'-tetramethylethane-1,2-diamine]. Unlike closed architectures, open barrel architecture of water-sol. PSMBR-1 makes it an ideal host for some water insol. polyarom. hydrocarbons in aq. medium; one such inclusion complex coronene⊂PSMBR-1 was characterized by X-ray diffraction study. Moreover, the potential application of PSMBR-1 as carrier in aq. medium for the transportation of water insol. fluorophore (perylene) for live cell imaging is explored.
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Wang, K.; Cai, X.; Yao, W.; Tang, D.; Kataria, R.; Ashbaugh, H. S.; Byers, L. D.; Gibb, B. C. Electrostatic Control of Macrocyclization Reactions within Nanospaces. J. Am. Chem. Soc. 2019, 141, 6740– 6747, DOI: 10.1021/jacs.9b02287
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Electrostatic Control of Macrocyclization Reactions within Nanospaces
Wang, Kaiya; Cai, Xiaoyang; Yao, Wei; Tang, Du; Kataria, Rhea; Ashbaugh, Henry S.; Byers, Larry D.; Gibb, Bruce C.
Journal of the American Chemical Society (2019), 141 (16), 6740-6747CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The intrinsic structural complexity of proteins makes it hard to identify the contributions of each noncovalent interaction behind the remarkable rate accelerations of enzymes. Coulombic forces are evidently primary, but despite developments in artificial nanoreactor design, a picture of the extent to which these can contribute has not been forthcoming. Here we report on two supramol. capsules that possess structurally identical inner-spaces that differ in the electrostatic potential (EP) field that envelops them: one pos. and one neg. This architecture means that only changes in the EP field influence the chem. properties of encapsulated species. We quantify these influences via acidity and rates of cyclization measurements for encapsulated guests, and we confirm the primary role of Coulombic forces with a simple math. model approximating the capsules as Born spheres within a continuum dielec. These results reveal the reaction rate accelerations possible under Coulombic control and highlight important design criteria for nanoreactors.
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Cook, T. R.; Stang, P. J. Recent Developments in the Preparation and Chemistry of Metallacycles and Metallacages via Coordination. Chem. Rev. 2015, 115, 7001– 7045, DOI: 10.1021/cr5005666
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Recent Developments in the Preparation and Chemistry of Metallacycles and Metallacages via Coordination
Cook, Timothy R.; Stang, Peter J.
Chemical Reviews (Washington, DC, United States) (2015), 115 (15), 7001-7045CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
A review.
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Sepehrpour, H.; Fu, W.; Sun, Y.; Stang, P. J. Biomedically Relevant Self-Assembled Metallacycles and Metallacages. J. Am. Chem. Soc. 2019, 141, 14005– 14020, DOI: 10.1021/jacs.9b06222
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Biomedically relevant self-assembled metallacycles and metallacages
Sepehrpour, Hajar; Fu, Wenxin; Sun, Yan; Stang, Peter J.
Journal of the American Chemical Society (2019), 141 (36), 14005-14020CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
A review. Diverse metal-org. complexes (MOCs), shaped as rectangles, triangles, hexagons, prisms, and cages, can be formed by coordination between metal ions (Pt, Pd, Ru, Rh, Ir, Zn, Co, and Cd) and org. ligands, with potential applications as alternatives to conventional biomedical materials for therapeutic, sensing, and imaging purposes. MOCs have been investigated as anticancer drugs in the treatment of malignant tumors in lung, cervical, breast, colon, liver, prostate, ovarian, brain, stomach, bone, skin, mouth, thyroid, and other cancers. MOCs with one, two, and three cavities have also been investigated as drug carriers and prepd. for the loading and release of different drugs. In addn., MOCs can target proteins by the shape effect and recognize sugars and DNA by electrostatic interactions, as well as estradiol by host-guest interactions, etc. This Perspective mainly covers achievements in the biomedical application of MOCs. We aim to identify some key trends in the reported MOC structures in relation to their biomedical activity and potential applications.
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Liu, M.; Zhang, L.; Little, M. A.; Kapil, V.; Ceriotti, M.; Yang, S.; Ding, L.; Holden, D. L.; Balderas-Xicohténcatl, R.; He, D.; Clowes, R.; Chong, S. Y.; Schütz, G.; Chen, L.; Hirscher, M.; Cooper, A. I. Barely Porous Organic Cages for Hydrogen Isotope Separation. Science 2019, 366, 613– 620, DOI: 10.1126/science.aax7427
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Barely porous organic cages for hydrogen isotope separation
Liu, Ming; Zhang, Linda; Little, Marc A.; Kapil, Venkat; Ceriotti, Michele; Yang, Siyuan; Ding, Lifeng; Holden, Daniel L.; Balderas-Xicohtencatl, Rafael; He, Donglin; Clowes, Rob; Chong, Samantha Y.; Schutz, Gisela; Chen, Linjiang; Hirscher, Michael; Cooper, Andrew I.
Science (Washington, DC, United States) (2019), 366 (6465), 613-620CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
The sepn. of hydrogen isotopes for applications such as nuclear fusion is a major challenge. Current technologies are energy intensive and inefficient. Nanoporous materials have the potential to sep. hydrogen isotopes by kinetic quantum sieving, but high sepn. selectivity tends to correlate with low adsorption capacity, which can prohibit process scale-up. In this study, we use org. synthesis to modify the internal cavities of cage mols. to produce hybrid materials that are excellent quantum sieves. By combining small-pore and large-pore cages together in a single solid, we produce a material with optimal sepn. performance that combines an excellent deuterium/hydrogen selectivity (8.0) with a high deuterium uptake (4.7 mmol per g).
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Merget, S.; Catti, L.; Piccini, G.; Tiefenbacher, K. Requirements for Terpene Cyclizations inside the Supramolecular Resorcinarene Capsule: Bound Water and Its Protonation Determine the Catalytic Activity. J. Am. Chem. Soc. 2020, 142, 4400– 4410, DOI: 10.1021/jacs.9b13239
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Requirements for Terpene Cyclizations inside the Supramolecular Resorcinarene Capsule: Bound Water and Its Protonation Determine the Catalytic Activity
Merget, Severin; Catti, Lorenzo; Piccini, GiovanniMaria; Tiefenbacher, Konrad
Journal of the American Chemical Society (2020), 142 (9), 4400-4410CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The elucidation of the requirements for efficient catalysis within supramol. host systems is an important prerequisite for developing novel supramol. catalysts. The resorcinarene hexamer has recently been shown to be the first supramol. catalyst to promote the tail-to-head terpene cyclization in a biomimetic fashion. We herein present the synthesis of a no. of resorcinarene-based macrocycles composed of different ratios of resorcinol and pyrogallol units capable of self-assembly and compare the corresponding assemblies regarding their catalytic activity in the cyclization of monoterpenes. The assemblies were investigated in detail with respect to a no. of properties including the encapsulation of substrate and ion pairs, the structural incorporation of water, and the response to externally added acid (HCl). The results obtained strongly indicate that water incorporated into the hydrogen-bond network of the self-assembled structure plays an integral role for catalysis, effectively acting as a proton shuttle to activate the encapsulated substrate. These findings are also supported by mol. dynamics simulations, providing further insight into the protonation pathway and the relative energies of the intermediates involved.
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Yoshizawa, M.; Tamura, M.; Fujita, M. Diels-Alder in Aqueous Molecular Hosts: Unusual Regioselectivity and Efficient Catalysis. Science 2006, 312, 251– 254, DOI: 10.1126/science.1124985
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Diels-Alder in Aqueous Molecular Hosts: Unusual Regioselectivity and Efficient Catalysis
Yoshizawa, Michito; Tamura, Masazumi; Fujita, Makoto
Science (Washington, DC, United States) (2006), 312 (5771), 251-254CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Self-assembled, hollow mol. structures are appealing as synthetic hosts for mediating chem. reactions. However, product binding has inhibited catalytic turnover in such systems, and selectivity has rarely approached the levels obsd. in more structurally elaborate natural enzymes. We found that an aq. organopalladium cage induces highly unusual regioselectivity in the Diels-Alder coupling of anthracene and phthalimide guests, promoting reaction at a terminal rather than central anthracene ring. Moreover, a similar bowl-shaped host attains efficient catalytic turnover in coupling the same substrates (although with the conventional regiochem.), most likely because the product geometry inhibits the arom. stacking interactions that attract the planar reagents to the host.
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Ueda, Y.; Ito, H.; Fujita, D.; Fujita, M. Permeable Self-Assembled Molecular Containers for Catalyst Isolation Enabling Two-Step Cascade Reactions. J. Am. Chem. Soc. 2017, 139, 6090– 6093, DOI: 10.1021/jacs.7b02745
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Permeable Self-Assembled Molecular Containers for Catalyst Isolation Enabling Two-Step Cascade Reactions
Ueda, Yoshihiro; Ito, Hiroaki; Fujita, Daishi; Fujita, Makoto
Journal of the American Chemical Society (2017), 139 (17), 6090-6093CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Establishment of a general one-pot cascade reaction protocol would dramatically reduce the effort of multistep org. synthesis. We demonstrate that the unique structure of M12L24 self-assembled complexes gives them the potential to serve as catalyst carriers for enabling continuous chem. transformations. A stereoselective cascade reaction (allylic oxidn. followed by Diels-Alder cyclization) with two intrinsically incompatible catalysts was demonstrated. Our system is advantageous in terms of availability, scalability, and predictability.
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Maestri, M.; Iglesia, E. First-Principles Theoretical Assessment of Catalysis by Confinement: NO–O₂ Reactions within Voids of Molecular Dimensions in Siliceous Crystalline Frameworks. Phys. Chem. Chem. Phys. 2018, 20, 15725– 15735, DOI: 10.1039/C8CP01615A
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First-principles theoretical assessment of catalysis by confinement: NO-O2 reactions within voids of molecular dimensions in siliceous crystalline frameworks
Maestri, Matteo; Iglesia, Enrique
Physical Chemistry Chemical Physics (2018), 20 (23), 15725-15735CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
D. functional theory methods that include dispersive forces are used to show how voids of mol. dimensions enhance reaction rates by the mere confinement of transition states analogous to those involved in homogeneous routes and without requiring specific binding sites or structural defects within confining voids. These van der Waals interactions account for the obsd. large rate enhancements for NO oxidn. in the presence of purely siliceous cryst. frameworks. The min. free energy paths for NO oxidn. within chabazite (CHA) and silicalite (SIL) frameworks involve intermediates similar in stoichiometry, geometry, and kinetic relevance to those involved in the homogeneous route. The termol. transition state for the kinetically-relevant cis-NOO2NO isomerization to trans-NOO2NO is strongly stabilized by confinement within CHA (by 36.3 kJ mol-1 in enthalpy) and SIL (by 39.2 kJ mol-1); such enthalpic stabilization is compensated, in part, by concomitant entropy losses brought forth by confinement (CHA: 44.9; SIL: 45.3, J mol-1 K-1 at 298 K). These enthalpy and entropy changes upon confinement agree well with those measured and combine to significantly decrease activation free energies and are consistent with the rate enhancements that become larger as temp. decreases because of the more neg. apparent activation energies in confined systems compared with homogeneous routes. Calcd. free energies of confinement are in quant. agreement with measured rate enhancements and with their temp. sensitivity. Such quant. agreements reflect preeminent effects of geometry in detg. the van der Waals contributions from contacts between the transition states (TS) and the confining walls and the weak effects of the level of theory on TS geometries. NO oxidn. reactions are chosen here to illustrate these remarkable effects of confinement because detailed kinetic anal. of rate data are available, but also because of their crit. role in the treatment of combustion effluents and in the synthesis of nitric acid and nitrates. Similar effects are evident from rate enhancements by confinement obsd. for Diels-Alder and alkyne oligomerization reactions. These reactions also occur in gaseous media at near ambient temps., for which enthalpic stabilization upon confinement of their homogeneous transition states becomes the preeminent component of activation free energies.
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Mal, P.; Breiner, B.; Rissanen, K.; Nitschke, J. R. White Phosphorus Is Air-Stable Within a Self-Assembled Tetrahedral Capsule. Science 2009, 324, 1697, DOI: 10.1126/science.1175313
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White Phosphorus Is Air-Stable Within a Self-Assembled Tetrahedral Capsule
Mal, Prasenjit; Breiner, Boris; Rissanen, Kari; Nitschke, Jonathan R.
Science (Washington, DC, United States) (2009), 324 (5935), 1697-1699CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
The air-sensitive nature of white phosphorus underlies its destructive effect as a munition; tetrahedral P4 mols. readily react with atm. dioxygen, leading this form of the element to spontaneously combust upon exposure to air. Here, hydrophobic P4 mols. are rendered air-stable and water-sol. within the hydrophobic hollows of self-assembled tetrahedral container mols., [Fe4L6]4- (L = 4,4'-bis(2-pyridylmethyleneamino)-1,1'-biphenyl-2,2'-disulfonate), which form in water from simple org. subcomponents and iron(II) ions. The host-guest complex with P4 was characterized by x-ray crystallog. This stabilization is not achieved through hermetic exclusion of O2 but rather by constriction of individual P4 mols.; the addn. of oxygen atoms to P4 would gave oxidized species too large for their containers. The phosphorus can be released in controlled fashion without disrupting the cage by adding the competing guest benzene.
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Yamashina, M.; Sei, Y.; Akita, M.; Yoshizawa, M. Safe Storage of Radical Initiators within a Polyaromatic Nanocapsule. Nat. Commun. 2014, 5, 4662, DOI: 10.1038/ncomms5662
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Safe storage of radical initiators within a polyaromatic nanocapsule
Yamashina, Masahiro; Sei, Yoshihisa; Akita, Munetaka; Yoshizawa, Michito
Nature Communications (2014), 5 (), 4662CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
2,2'-Azobisisobutyronitrile and its derivs. are std. reagents for polymer and org. synthesis that generate radical species on stimuli by light or heat. Radical initiators like the azo compds. are unstable so that they should be kept in the dark at low temp. to avoid photochem. and thermal decompn. as well as accidental explosion. Here we report the spontaneous and quant. encapsulation of the radical initiators by a supramol. nanocapsule in aq. soln. We demonstrate the remarkable stability of the initiators toward light and heat in the well-defined cavity shielded by the polyarom. capsule shell. The incarcerated and stabilized initiators can be directly utilized for the radical polymn. of olefins on spontaneous release of the initiators from the capsule under the reaction conditions.
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Galan, A.; Ballester, P. Stabilization of Reactive Species by Supramolecular Encapsulation. Chem. Soc. Rev. 2016, 45, 1720– 1737, DOI: 10.1039/C5CS00861A
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46
Stabilization of reactive species by supramolecular encapsulation
Galan, Albano; Ballester, Pablo
Chemical Society Reviews (2016), 45 (6), 1720-1737CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
A review. Mol. containers have attracted the interest of supramol. chemists since the early beginnings of the field. Cavitands' inner cavities were quickly exploited by Cram and Warmuth to construct covalent containers able to stabilize and assist the characterization of short-lived reactive species such as cyclobutadiene or o-benzyne. Since then, more complex mol. architectures have been prepd. able to store and isolate a myriad of fleeting species (i.e. organometallic compds., cationic species, radical initiators...). In this review we cover selected examples of the stabilization of reactive species by encapsulation in mol. containers from the first reports of covalent containers described by Cram et al. to the most recent examples of containers with self-assembled structure (metal coordination cages and hydrogen bonded capsules). Finally, we briefly review examples reported by Rebek et al. in which elusive reaction intermediates could be detected in the inner cavities of self-folding resorcin[4]arene cavitands by the formation of covalent host-guest complexes. The utilization of encapsulated reactive species in catalysis or synthesis is not covered.
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Qiu, Y.; Antony, L. W.; Torkelson, J. M.; de Pablo, J. J.; Ediger, M. D. Tenfold Increase in the Photostability of an Azobenzene Guest in Vapor-Deposited Glass Mixtures. J. Chem. Phys. 2018, 149, 204503, DOI: 10.1063/1.5052003
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47
Tenfold increase in the photostability of an azobenzene guest in vapor-deposited glass mixtures
Qiu, Yue; Antony, Lucas W.; Torkelson, John M.; de Pablo, Juan J.; Ediger, M. D.
Journal of Chemical Physics (2018), 149 (20), 204503/1-204503/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Improvements to the photostability of org. glasses for use in electronic applications have generally relied on the modification of the chem. structure. We show here that the photostability of a guest mol. can also be significantly improved-without chem. modification-by using phys. vapor deposition to pack mols. more densely. Photoisomerization of the substituted azobenzene, 4,4'-diphenyl azobenzene, was studied in a vapor-deposited glass matrix of celecoxib. We directly measure photoisomerization of trans- to cis-states via UV-visible (UV-Vis) spectroscopy and show that the rate of photoisomerization depends upon the substrate temp. used during co-deposition of the glass. Photostability correlates reasonably with the d. of the glass, where the optimum glass is about tenfold more photostable than the liq.-cooled glass. Mol. simulations, which mimic photoisomerization, also demonstrate that photoreaction of a guest mol. can be suppressed in vapor-deposited glasses. From the simulations, we est. that the region that is disrupted by a single photoisomerization event encompasses approx. 5 mols. (c) 2018 American Institute of Physics.
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Qiu, Y.; Antony, L. W.; de Pablo, J. J.; Ediger, M. D. Photostability Can Be Significantly Modulated by Molecular Packing in Glasses. J. Am. Chem. Soc. 2016, 138, 11282– 11289, DOI: 10.1021/jacs.6b06372
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Photostability Can Be Significantly Modulated by Molecular Packing in Glasses
Qiu, Yue; Antony, Lucas W.; de Pablo, Juan J.; Ediger, M. D.
Journal of the American Chemical Society (2016), 138 (35), 11282-11289CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
While previous work has demonstrated that mol. packing in org. crystals can strongly influence photochem. stability, efforts to tune photostability in amorphous materials have shown much smaller effects. Here, it is shown that phys. vapor deposition can substantially improve the photostability of org. glasses. Disperse Orange 37 (DO37), an azobenzene deriv., is studied as a model system. Photostability is assessed through changes in the d. and mol. orientation of glassy thin films during light irradn. By optimizing the substrate temp. used for deposition, the photostability is increased by a factor of 50 relative to the liq.-cooled glass. Photostability correlates with glass d., with d. increases of up to 1.3%. Coarse-grained mol. simulations, which mimic glass prepn. and the photoisomerization reaction, also indicate that glasses with higher d. have substantially increased photostability. These results provide insights that may assist in the design of org. photovoltaics and light-emission devices with longer lifetimes.
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Fregoni, J.; Granucci, G.; Persico, M.; Corni, S. Strong Coupling with Light Enhances the Photoisomerization Quantum Yield of Azobenzene. Chem. 2020, 6, 250– 265, DOI: 10.1016/j.chempr.2019.11.001
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50
Bochicchio, D.; Kwangmettatam, S.; Kudernac, T.; Pavan, G. M. How Defects Control the Out-of-Equilibrium Dissipative Evolution of a Supramolecular Tubule. ACS Nano 2019, 13, 4322– 4334, DOI: 10.1021/acsnano.8b09523
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How Defects Control the Out-of-Equilibrium Dissipative Evolution of a Supramolecular Tubule
Bochicchio, Davide; Kwangmettatam, Supaporn; Kudernac, Tibor; Pavan, Giovanni M.
ACS Nano (2019), 13 (4), 4322-4334CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
Supramol. architectures that work out-of-equil. or that can change in specific ways when absorbing external energy are ubiquitous in nature. Gaining the ability to create via self-assembly artificial materials possessing such fascinating behaviors would have a major impact in many fields. However, the rational design of similar dynamic structures requires to understand and, even more challenging, to learn how to master the mol. mechanisms governing how the assembled systems evolve far from the equil. Typically, this represents a daunting challenge due to the limited mol. insight that can be obtained by the expts. or by classical modeling approaches. Here we combine coarse-grained mol. models and advanced simulation approaches to study at submol. (<5 Å) resoln. a supramol. tubule, which breaks and disassembles upon absorption of light energy triggering isomerization of its azobenzene-contg. monomers. Our approach allows us to investigate the mol. mechanism of monomer transition in the assembly and to elucidate the kinetic process for the accumulation of the transitions in the system. Despite the stochastic nature of the excitation process, we demonstrate how these tubules preferentially dissipate the absorbed energy locally via the amplification of defects in their supramol. structure. We find that this constitutes the best kinetic pathway for accumulating monomer transitions in the system, which dets. the dynamic evolution out-of-equil. and the brittle behavior of the assembly under perturbed conditions. Thanks to the flexibility of our models, we finally come out with a general principle, where defects explain and control the brittle/soft behavior of such light-responsive assemblies.
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Kusukawa, T.; Fujita, M. Ship-in-a-Bottle” Formation of Stable Hydrophobic Dimers of Cis-Azobenzene and -Stilbene Derivatives in a Self-Assembled Coordination Nanocage. J. Am. Chem. Soc. 1999, 121, 1397– 1398, DOI: 10.1021/ja9837295
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"Ship-in-a-Bottle" Formation of Stable Hydrophobic Dimers of cis-Azobenzene and -Stilbene Derivatives in a Self-Assembled Coordination Nanocage
Kusukawa, Takahiro; Fujita, Makoto
Journal of the American Chemical Society (1999), 121 (6), 1397-1398CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The cage compd. [Pd6(en)6L4](NO3)12 (I) (L = 2,4,6-tris(4-pyridyl)-1,3,5-triazine) is capable of selective enclathration of C-shaped mols. as hydrophobic dimers, such as cis-azobenzenes and cis-stilbenes to give I.2Q (Q = cis-p-methylazobenzene, cis-p-methylstilbene, cis-p-methoxystilbene, cis-azobenzene and cis-bis(4-methoxyphenyl)ethane). The ship-in-a-bottle assembly of the hydrophobic dimer in the cage is suggested by NMR data.
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Cantatore, V.; Granucci, G.; Rousseau, G.; Padula, G.; Persico, M. Photoisomerization of Self-Assembled Monolayers of Azobiphenyls: Simulations Highlight the Role of Packing and Defects. J. Phys. Chem. Lett. 2016, 7, 4027– 4031, DOI: 10.1021/acs.jpclett.6b02018
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52
Photoisomerization of Self-Assembled Monolayers of Azobiphenyls: Simulations Highlight the Role of Packing and Defects
Cantatore, Valentina; Granucci, Giovanni; Rousseau, Guillaume; Padula, Giancarlo; Persico, Maurizio
Journal of Physical Chemistry Letters (2016), 7 (19), 4027-4031CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
We present surface hopping simulations of the photodynamics of self-assembled monolayers (SAMs) of 4'-(biphenyl-4-ylazo)-biphenyl-4-thiol (ABPT) on Au(111). We show that trans → cis photoisomerization is suppressed because of steric hindrance in a well-ordered SAM. Photoisomerization is instead viable in the presence of defects. Two particularly important defects are the boundaries between domains of trans-ABPT mols. leaning in different directions (a line defect) and single cis mols. embedded in a SAM of trans (a point defect). Our findings explain the cooperative behavior obsd. during the photoisomerization of a trans-ABPT SAM, leading to large domains of pure cis and trans isomers. The line and point defects are predicted to produce different patterns of cis-ABPT mols. during the early stages of the photoconversion.
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Clever, G. H.; Tashiro, S.; Shionoya, M. Light-Triggered Crystallization of a Molecular Host-Guest Complex. J. Am. Chem. Soc. 2010, 132, 9973– 9975, DOI: 10.1021/ja103620z
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53
Light-Triggered Crystallization of a Molecular Host-Guest Complex
Clever, Guido H.; Tashiro, Shohei; Shionoya, Mitsuhiko
Journal of the American Chemical Society (2010), 132 (29), 9973-9975CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The control of structural changes in supramol. assemblies is a key point in the development of mol. machines. The reversible photoisomerization of org. compds. such as azobenzene using light as an external input is esp. suited because no waste products are generated. Based on the authors previous studies on the quant. encapsulation of suitably sized bis-sulfonate guests by a self-assembled, metal-org. cage consisting of four rigid, bent bis-monodentate pyridyl ligands and two Pd(II) ions, the authors show here how the light-switchable guest cis-4,4'-azobenzene bis-sulfonate can be expelled from its 1:1 host-guest complex triggered by its photoisomerization to the trans-isomer. Using a highly sol., PEGylated cage deriv., the full reversibility of this light-driven encapsulation/release process is demonstrated. In contrast, a sample of the less sol., unsubstituted cages including 1 equiv of the cis-guest was shown to result in immediate crystn. upon photoisomerization of the guest. X-ray structure anal. confirmed the guest mols. having left the cavity of the host and on the contrary joining the cages into a polymeric material by binding to their Pd(II) centers from outside.
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Dube, H.; Ajami, D.; Rebek, J. Photochemical Control of Reversible Encapsulation. Angew. Chem., Int. Ed. 2010, 49, 3192– 3195, DOI: 10.1002/anie.201000876
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54
Photochemical Control of Reversible Encapsulation
Dube, Henry; Ajami, Dariush; Rebek, Julius, Jr.
Angewandte Chemie, International Edition (2010), 49 (18), 3192-3195, S3192/1-S3192/16CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
Photoisomerization can be indirectly used as a method to control encapsulation phenomena. This remote control is a consequence of the snug fit of trans-4,4'-dimethylazobenzene (trans-I) in a cylindrical mol. capsule. Photoisomerization causes trans-I to "break out" of the capsule, thus allowing the entry of other guest species.
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Mohan Raj, A.; Raymo, F. M.; Ramamurthy, V. Reversible Disassembly–Assembly of Octa Acid–Guest Capsule in Water Triggered by a Photochromic Process. Org. Lett. 2016, 18, 1566– 1569, DOI: 10.1021/acs.orglett.6b00405
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55
Reversible Disassembly-Assembly of Octa Acid-Guest Capsule in Water Triggered by a Photochromic Process
Mohan Raj, A.; Raymo, Francisco M.; Ramamurthy, V.
Organic Letters (2016), 18 (7), 1566-1569CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
Octa acid (OA), a calixarene-based cavitand, forms a 1:2 capsular assembly with neutral 1,3,3-trimethyl-6'-nitrospiro[2H-1]benzopyran-2,2'-indoline and 1:1 cavitandplex with its open zwitterionic merocyanine form. Photochromic interconversion between the spiropyran and merocyanine leads to unprecedented reversible capsular disassembly and assembly. OA provides stability to the merocyanine in both the ground and excited states. The photochem. controlled disassembly and assembly process established here points toward the opportunity of using the OA capsule in delivering small mols. at the desired locations.
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Yang, Y.; Hughes, R. P.; Aprahamian, I. Visible Light Switching of a BF₂-Coordinated Azo Compound. J. Am. Chem. Soc. 2012, 134, 15221– 15224, DOI: 10.1021/ja306030d
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56
Visible Light Switching of a BF2-Coordinated Azo Compound
Yang, Yin; Hughes, Russell P.; Aprahamian, Ivan
Journal of the American Chemical Society (2012), 134 (37), 15221-15224CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Here the synthesis and characterization of a BF2-azo complex that can be induced to isomerize without the need of deleterious UV light is reported. The complexation of the azo group with BF2, coupled with the extended conjugation of the N=N π-electrons, increases the energy of the n-π* transitions and introduces new π-nonbonding (πnb) to π* transitions that dominate the visible region. The well sepd. πnb-π* transitions of the trans and cis isomers enable the efficient switching of the system by using only visible light. The complexation also leads to a slow cis → trans thermal relaxation rate (t1/2 = 12.5 h). Theor. calcns. indicate that the absorption bands in the visible range can be tuned using different Lewis acids, opening the way to a conceptually new strategy for the manipulation of azo compds. using only visible light.
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Helmy, S.; Leibfarth, F. A.; Oh, S.; Poelma, J. E.; Hawker, C. J.; Read de Alaniz, J. Photoswitching Using Visible Light: A New Class of Organic Photochromic Molecules. J. Am. Chem. Soc. 2014, 136, 8169– 8172, DOI: 10.1021/ja503016b
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57
Photoswitching Using Visible Light: A New Class of Organic Photochromic Molecules
Helmy, Sameh; Leibfarth, Frank A.; Oh, Saemi; Poelma, Justin E.; Hawker, Craig J.; Read de Alaniz, Javier
Journal of the American Chemical Society (2014), 136 (23), 8169-8172CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
A versatile new class of org. photochromic mols. that offers an unprecedented combination of phys. properties including tunable photoswitching using visible light, excellent fatigue resistance, and large polarity changes is described. These unique features offer significant opportunities in diverse fields ranging from biosensors to targeted delivery systems while also allowing non-experts ready synthetic access to these materials.
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Zhang, D.; Ronson, T. K.; Mosquera, J.; Martinez, A.; Guy, L.; Nitschke, J. R. Anion Binding in Water Drives Structural Adaptation in an Azaphosphatrane-Functionalized Fe^II₄L₄ Tetrahedron. J. Am. Chem. Soc. 2017, 139, 6574– 6577, DOI: 10.1021/jacs.7b02950
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Anion Binding in Water Drives Structural Adaptation in an Azaphosphatrane-Functionalized FeII4L4 Tetrahedron
Zhang, Dawei; Ronson, Tanya K.; Mosquera, Jesus; Martinez, Alexandre; Guy, Laure; Nitschke, Jonathan R.
Journal of the American Chemical Society (2017), 139 (19), 6574-6577CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Anion-templated aq. self-assembly resulted in the formation of an endohedrally functionalized FeII4L4 tetrahedron from azaphosphatrane-based subcomponents. This new water-sol. cage is flexible and able to encapsulate anions with vols. ranging from 35 to 219 Å3 via hydrogen bonding and electrostatic interactions. It structurally adapts in response to the size and shape of the template anions, dynamically adopting a conformation either where all four azaphosphatrane +P-H vectors point inward, or else where one points outward and the other three inward. The two cage isomers can coexist in soln. and interconvert. A shape memory phenomenon was obsd. during guest displacement because guest exchange occurs more rapidly than structural reconfiguration.
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Rizzuto, F. J.; Nitschke, J. R. Stereochemical Plasticity Modulates Cooperative Binding in a Co^II₁₂L₆ Cuboctahedron. Nat. Chem. 2017, 9, 903– 908, DOI: 10.1038/nchem.2758
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59
Stereochemical plasticity modulates cooperative binding in a CoII12L6 cuboctahedron
Rizzuto, Felix J.; Nitschke, Jonathan R.
Nature Chemistry (2017), 9 (9), 903-908CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)
Biomol. receptors are able to process information by responding differentially to combinations of chem. signals. Synthetic receptors that are likewise capable of multi-stimuli response can form the basis of programmable mol. systems, wherein specific input sequences create distinct outputs. Here the authors report a pseudo-cuboctahedral assembly capable of cooperatively binding anionic and neutral guest species. The binding of pairs of fullerene guests was obsd. to effect the all-or-nothing cooperative templation of an S6-sym. host stereoisomer. This bis-fullerene adduct exhibits different cooperativity in binding pairs of anions from the fullerene-free parent: in one case, pos. cooperativity is obsd., while in another all binding affinities are enhanced by an order of magnitude, and in a third the binding events are only minimally perturbed. This intricate modulation of binding affinity, and thus cooperativity, renders the authors' new cuboctahedral receptor attractive for incorporation into systems with complex, programmable responses to different sets of stimuli.
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Mondal, P.; Sarkar, S.; Rath, S. P. Cyclic Bis-Porphyrin-Based Flexible Molecular Containers: Controlling Guest Arrangements and Supramolecular Catalysis by Tuning Cavity Size. Chem. - Eur. J. 2017, 23, 7093– 7103, DOI: 10.1002/chem.201700577
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Cyclic Bis-porphyrin-Based Flexible Molecular Containers: Controlling Guest Arrangements and Supramolecular Catalysis by Tuning Cavity Size
Mondal, Pritam; Sarkar, Sabyasachi; Rath, Sankar Prasad
Chemistry - A European Journal (2017), 23 (29), 7093-7103CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
Three cyclic zinc(II) bis-porphyrins (CB) with highly flexible linkers were employed as artificial mol. containers that efficiently encapsulate/coordinate various arom. aldehydes within their cavities. The arrangements of guests and their reactivity inside the mol. clefts are significantly influenced by the cavity size of the cyclic containers. In the presence of polycyclic arom. aldehydes, such as 3-formylperylene, as a guest, the cyclic bis-porphyrin host with a smaller cavity (CB1) forms a 1:1 sandwich complex. Upon slightly increasing the spacer length and thereby the cavity size, the cyclic host (CB2) encapsulates two mols. of 3-formylperylene that are also stacked together due to strong π-π interactions between them and CH-π interactions with the porphyrin rings. However, in the cyclic host (CB3) with an even larger cavity, two metal centers of the bis-porphyrin axially coordinate two mols. of 3-formylperylene within its cavity. Different arrangements of guest inside the cyclic bis-porphyrin hosts were studied by using UV/visible, ESI-MS, and 1H NMR spectroscopy, along with x-ray structure detn. of the host-guest complexes. Moreover, strong binding of guests within the cyclic bis-porphyrin hosts support the robust nature of the host-guest assemblies in soln. Such preferential binding of the bis-porphyrinic cavity towards arom. aldehydes through encapsulation/coordination was employed successfully to catalyze the Knoevenagel condensation of a series of polycyclic aldehydes with active methylene compds. (such as Meldrum's acid and 1,3-dimethylbarbituric acid) under ambient conditions. The yields of the condensed products significantly increase upon increasing spacer lengths of the cyclic bis-porphyrins because more substrates can then be encapsulated within the cavity. Such controllable cavity size of the cyclic containers has profound implications for constructing highly functional and modular enzyme mimics.
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Samanta, D.; Mukherjee, S.; Patil, Y. P.; Mukherjee, P. S. Self-Assembled Pd₆ Open Cage with Triimidazole Walls and the Use of Its Confined Nanospace for Catalytic Knoevenagel- and Diels–Alder Reactions in Aqueous Medium. Chem. - Eur. J. 2012, 18, 12322– 12329, DOI: 10.1002/chem.201201679
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Self-Assembled Pd6 Open Cage with Triimidazole Walls and the Use of Its Confined Nanospace for Catalytic Knoevenagel- and Diels-Alder Reactions in Aqueous Medium
Samanta, Dipak; Mukherjee, Sandip; Patil, Yogesh P.; Mukherjee, Partha Sarathi
Chemistry - A European Journal (2012), 18 (39), 12322-12329, S12322/1-S12322/13CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
The two-component self-assembly of a 90° PdII acceptor and a triimidazole donor gave a water-sol. semi-cylindrical cage with a hydrophobic cavity, which was sep. crystd. with hydrophilic- and hydrophobic guests. The parent cage was found to catalyze the Knoevenagel condensation reaction of arom. mono-aldehydes with active methylene compds., such as Meldrum's acid or 1,3-dimethylbarbituric acid. The confined hydrophobic nanospace within this cage was also used in the catalytic Diels-Alder reactions of 9-(hydroxymethyl)anthracene with N-phenylmaleimide or N-cyclohexylmaleimide.
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Samanta, D.; Gemen, J.; Chu, Z.; Diskin-Posner, Y.; Shimon, L. J. W.; Klajn, R. Reversible Photoswitching of Encapsulated Azobenzenes in Water. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 9379– 9384, DOI: 10.1073/pnas.1712787115
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62
Reversible photoswitching of encapsulated azobenzenes in water
Samanta, Dipak; Gemen, Julius; Chu, Zonglin; Diskin-Posner, Yael; Shimon, Linda J. W.; Klajn, Rafal
Proceedings of the National Academy of Sciences of the United States of America (2018), 115 (38), 9379-9384CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Efficient mol. switching in confined spaces is crit. for the successful development of artificial mol. machines. However, mol. switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene-the key building block of light-controlled mol. machines-in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-sol. coordination cage, and investigated their light-responsive behavior. Using UV/visible absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host-guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its pptn. from the soln. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light.
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Samanta, D.; Galaktionova, D.; Gemen, J.; Shimon, L. J. W.; Diskin-Posner, Y.; Avram, L.; Král, P.; Klajn, R. Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage. Nat. Commun. 2018, 9, 641, DOI: 10.1038/s41467-017-02715-6
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Reversible chromism of spiropyran in the cavity of a flexible coordination cage
Samanta Dipak; Gemen Julius; Klajn Rafal; Galaktionova Daria; Kral Petr; Shimon Linda J W; Diskin-Posner Yael; Avram Liat; Kral Petr; Kral Petr
Nature communications (2018), 9 (1), 641 ISSN:.
Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches-entities that can be toggled between two or more forms upon exposure to an external stimulus-often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating-and solubilizing in water-several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments.
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Hanopolskyi, A. I.; De, S.; Białek, M. J.; Diskin-Posner, Y.; Avram, L.; Feller, M.; Klajn, R. Reversible Switching of Arylazopyrazole within a Metal–Organic Cage. Beilstein J. Org. Chem. 2019, 15, 2398– 2407, DOI: 10.3762/bjoc.15.232
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Reversible switching of arylazopyrazole within a metal-organic cage
Hanopolskyi, Anton I.; De, Soumen; Bialek, Michal J.; Diskin-Posner, Yael; Avram, Liat; Feller, Moran; Klajn, Rafal
Beilstein Journal of Organic Chemistry (2019), 15 (), 2398-2407CODEN: BJOCBH; ISSN:1860-5397. (Beilstein-Institut zur Foerderung der Chemischen Wissenschaften)
Arylazopyrazoles represent a new family of mol. photoswitches characterized by a near-quant. conversion between two states and long thermal half-lives of the metastable state. Here, we investigated the behavior of a model arylazopyrazole in the presence of a self-assembled cage based on Pd-imidazole coordination. Owing to its high water soly., the cage can solubilize the E isomer of arylazopyrazole, which, by itself, is not sol. in water. NMR spectroscopy and X-ray crystallog. have independently demonstrated that each cage can encapsulate two mols. of E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calcns. suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with green light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization reaction also proceeded in the dark, with a rate significantly higher than in the absence of the cage.
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Böckmann, M.; Peter, C.; Site, L. D.; Doltsinis, N. L.; Kremer, K.; Marx, D. Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals. J. Chem. Theory Comput. 2007, 3, 1789– 1802, DOI: 10.1021/ct7000733
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Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals
Bockmann Marcus; Peter Christine; Site Luigi Delle; Doltsinis Nikos L; Kremer Kurt; Marx Dominik
Journal of chemical theory and computation (2007), 3 (5), 1789-802 ISSN:1549-9618.
An atomistic force field has been adapted for use in molecular dynamics simulations of molecular materials that contain azobenzene (AB) functional groups. Force field parameters for bonded interactions and partial charges in the AB unit have been derived from ab initio molecular dynamics reference calculations. First applications of the new force field to liquid trans- and cis-AB are presented, both using a purely classical approach (MM) and a hybrid quantum-classical (QM/MM) simulation scheme. Detailed structural analysis confirms that QM/MM and purely MM simulations yield results that are in good agreement with each other. The force field of the AB core has been extended to include aliphatic chains that are attached via ether bridges to the two AB benzene rings. This allows for studying temperature induced phase transitions in the liquid-crystalline 8AB8 system. Using replica exchange techniques the new force field has successfully reproduced the smectic to isotropic-phase transition.
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Peter, C.; Site, L. D.; Kremer, K. Classical Simulations from the Atomistic to the Mesoscale and Back: Coarse Graining an Azobenzene Liquid Crystal. Soft Matter 2008, 4, 859– 869, DOI: 10.1039/b717324e
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66
Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal
Peter, Christine; Delle Site, Luigi; Kremer, Kurt
Soft Matter (2008), 4 (4), 859-869CODEN: SMOABF; ISSN:1744-683X. (Royal Society of Chemistry)
The authors describe the development of a coarse grained model for mol. dynamics (MD) simulations of a liq.-cryst. (LC) compd. with an azobenzene mesogen. It is studied how coarse graining methods originally developed to simulate amorphous polymeric systems can be extended to liq. crystals. The coarse grained (CG) model is constructed in a way that it allows carrying over of chem. details (i.e., the form of specific/attractive interactions) from the atomistic to the CG level, devising a new route to construct mesoscale models for liq. crystals with a close link to chem. more realistic atomistic ones. In addn. it is possible to switch between the atomistic and the CG levels of resoln. on demand through an inverse mapping procedure. By this the authors obtain representative large-scale atomistic coordinates based on CG structures and long-time atomistic trajectories generated from CG mesoscale simulations.
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Ilnytskyi, J. M.; Slyusarchuk, A.; Saphiannikova, M. Photocontrollable Self-Assembly of Azobenzene-Decorated Nanoparticles in Bulk: Computer Simulation Study. Macromolecules 2016, 49, 9272– 9282, DOI: 10.1021/acs.macromol.6b01871
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Photocontrollable Self-Assembly of Azobenzene-Decorated Nanoparticles in Bulk: Computer Simulation Study
Ilnytskyi, Jaroslav M.; Slyusarchuk, Arsen; Saphiannikova, Marina
Macromolecules (Washington, DC, United States) (2016), 49 (23), 9272-9282CODEN: MAMOBX; ISSN:0024-9297. (American Chemical Society)
Decoration of nanoparticles by specific functional groups provides means of controlling their aggregation and self-assembly into ordered morphologies. We study the photocontrollable self-assembly of the azobenzene-functionalized nanoparticles using coarse-grained mol. dynamics simulations. With no illumination applied, a monodomain smectic morphol. is formed only via cooling the isotropic system at sufficiently slow rate. Quenching the system below the smectic-isotropic transition results in formation of a polydomain glass-like state with restricted dynamics of nanoparticles. Upon irradn. with appropriate wavelength and intensity, the azobenzenes undergo trans-cis-trans photoisomerization cycles which unlock the interdomain links and induce uniaxial orientation of domains with their local director perpendicular to the polarization axis of irradn. As demonstrated by the simulations, this transition can spead-up essentially the self-assembly of decorated nanoparticles from the isotropic to the monodomain smectic phase, both via gradual cooling down and via quenching in a broad temp. interval below the smectic-isotropic transition.
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Osella, S.; Minoia, A.; Beljonne, D. Combined Molecular Dynamics and Density Functional Theory Study of Azobenzene–Graphene Interfaces. J. Phys. Chem. C 2016, 120, 6651– 6658, DOI: 10.1021/acs.jpcc.6b00393
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68
Combined Molecular Dynamics and Density Functional Theory Study of Azobenzene-Graphene Interfaces
Osella, Silvio; Minoia, Andrea; Beljonne, David
Journal of Physical Chemistry C (2016), 120 (12), 6651-6658CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
Here, the authors first investigate the formation of 4-(decyloxy)azobenzene mol. monolayers on a single graphene layer through mol. dynamics (MD) simulations and assess the assocd. change in work function (WF) at the d. functional theory (DFT) level. The authors show that the major contribution to the WF shift arises from electrostatic effects induced by the azobenzene elec. dipole component normal to graphene and that the conformational distribution of the mol. switches in either their trans or cis forms can be convoluted into WF distributions for the hybrid systems. The authors next use this strategy to build a statistical ensemble for the work functions of graphene decorated with fluorinated azobenzene deriv. designed to maximize the change in WF upon photoswitching.
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Döbbelin, M.; Ciesielski, A.; Haar, S.; Osella, S.; Bruna, M.; Minoia, A.; Grisanti, L.; Mosciatti, T.; Richard, F.; Prasetyanto, E. A.; De Cola, L.; Palermo, V.; Mazzaro, R.; Morandi, V.; Lazzaroni, R.; Ferrari, A. C.; Beljonne, D.; Samorì, P. Light-Enhanced Liquid-Phase Exfoliation and Current Photoswitching in Graphene–Azobenzene Composites. Nat. Commun. 2016, 7, 11090, DOI: 10.1038/ncomms11090
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69
Light-enhanced liquid-phase exfoliation and current photoswitching in graphene-azobenzene composites
Dobbelin, Markus; Ciesielski, Artur; Haar, Sebastien; Osella, Silvio; Bruna, Matteo; Minoia, Andrea; Grisanti, Luca; Mosciatti, Thomas; Richard, Fanny; Prasetyanto, Eko Adi; De Cola, Luisa; Palermo, Vincenzo; Mazzaro, Raffaello; Morandi, Vittorio; Lazzaroni, Roberto; Ferrari, Andrea C.; Beljonne, David; Samori, Paolo
Nature Communications (2016), 7 (), 11090CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
Multifunctional materials can be engineered by combining multiple chem. components, each conferring a well-defined function to the ensemble. Graphene is at the center of an ever-growing research effort due to its combination of unique properties. Here, we show that the large conformational change assocd. with the trans-cis photochem. isomerization of alkyl-substituted azobenzenes can be used to improve the efficiency of liq.-phase exfoliation of graphite, with the photochromic mols. acting as dispersion-stabilizing agents. We also demonstrate reversible photo-modulated current in two-terminal devices based on graphene-azobenzene composites. We assign this tuneable elec. characteristics to the intercalation of the azobenzene between adjacent graphene layers and the resulting increase in the interlayer distance on (photo)switching from the linear trans-form to the bulky cis-form of the photochromes. These findings pave the way to the development of new optically controlled memories for light-assisted programming and high-sensitive photosensors.
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Laio, A.; Parrinello, M. Escaping Free-Energy Minima. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 12562– 12566, DOI: 10.1073/pnas.202427399
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70
Escaping free-energy minima
Laio, Alessandro; Parrinello, Michele
Proceedings of the National Academy of Sciences of the United States of America (2002), 99 (20), 12562-12566CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the min. in the FES, allowing the efficient exploration and accurate detn. of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissocn. of a NaCl mol. in water and in the study of the conformational changes of a dialanine in soln.
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Pederzoli, M.; Pittner, J.; Barbatti, M.; Lischka, H. Nonadiabatic Molecular Dynamics Study of the Cis–Trans Photoisomerization of Azobenzene Excited to the S1 State. J. Phys. Chem. A 2011, 115, 11136– 11143, DOI: 10.1021/jp2013094
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71
Nonadiabatic Molecular Dynamics Study of the cis-trans Photoisomerization of Azobenzene Excited to the S1 State
Pederzoli, Marek; Pittner, Jiri; Barbatti, Mario; Lischka, Hans
Journal of Physical Chemistry A (2011), 115 (41), 11136-11143CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
Ab initio nonadiabatic dynamics simulations of cis-to-trans isomerization of azobenzene upon S1 (n-π*) excitation are carried out employing the fewest-switches surface hopping method. Azobenzene photoisomerization occurs purely as a rotational motion of the central CNNC moiety. Two nonequivalent rotational pathways corresponding to clockwise or counterclockwise rotation are available. The course of the rotational motion is strongly dependent on the initial conditions. The internal conversion occurs via an S0/S1 crossing seam located near the midpoint of both of these rotational pathways. Based on statistical anal., it is shown that the occurrence of one or other pathway can be completely controlled by selecting adequate initial conditions.
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Tiago, M. L.; Ismail-Beigi, S.; Louie, S. G. Photoisomerization of Azobenzene from First-Principles Constrained Density-Functional Calculations. J. Chem. Phys. 2005, 122, 094311 DOI: 10.1063/1.1861873
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72
Photoisomerization of azobenzene from first-principles constrained density-functional calculations
Tiago, Murilo L.; Ismail-Beigi, Sohrab; Louie, Steven G.
Journal of Chemical Physics (2005), 122 (9), 094311/1-094311/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Despite considerable work in the field, the precise mechanism for the photoisomerization of azobenzene, C12H10N2, is still an open issue. Early theor. studies of the problem indicated that isomerization occurs through an in-plane inversion path, and this has been used to explain recent time-resolved UV-visible spectroscopy measurements. On the other hand, a no. of recent theor. studies have concluded that a torsion of the N-N bond ("rotation path") is probably the most favorable mechanism for photoisomerization involving the first excited state. We have performed first-principles calcns. using constrained d.-functional theory (DFT) and time-dependent DFT in the local-d. approxn., with results that also favor the rotation path mechanism. Our results are compared with other analyses, primarily based on CI.
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Bochicchio, D.; Salvalaglio, M.; Pavan, G. M. Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution. Nat. Commun. 2017, 8, 147, DOI: 10.1038/s41467-017-00189-0
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73
Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution
Bochicchio Davide; Pavan Giovanni M; Salvalaglio Matteo
Nature communications (2017), 8 (1), 147 ISSN:.
To rationally design supramolecular polymers capable of self-healing or reconfiguring their structure in a dynamically controlled way, it is imperative to gain access into the intrinsic dynamics of the supramolecular polymer (dynamic exchange of monomers) while maintaining a high-resolution description of the monomer structure. But this is prohibitively difficult at experimental level. Here we show atomistic, coarse-grained modelling combined with advanced simulation approaches to characterize the molecular mechanisms and relative kinetics of monomer exchange in structural variants of a synthetic supramolecular polymer in different conditions. We can capture differences in supramolecular dynamics consistent with the experimental observations, revealing that monomer exchange in and out the fibres originates from the defects present in their supramolecular structure. At the same time, the submolecular resolution of this approach offers a molecular-level insight into the dynamics of these bioinspired materials, and a flexible tool to obtain structure-dynamics relationships for a variety of polymeric assemblies.Accessing the dynamics of soft self-assembled materials at high resolution is very difficult. Here the authors show atomistic and coarse-grained modelling combined with enhanced sampling to characterize the molecular mechanisms and kinetics of monomer exchange in synthetic supramolecular polymers.
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Tiwary, P.; Parrinello, M. From Metadynamics to Dynamics. Phys. Rev. Lett. 2013, 111, 230602, DOI: 10.1103/PhysRevLett.111.230602
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74
From metadynamics to dynamics
Tiwary, Pratyush; Parrinello, Michele
Physical Review Letters (2013), 111 (23), 230602/1-230602/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted no. of collective variables it can explore complex free energy surfaces characterized by several metastable states sepd. by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calcg. the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable min. in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased mol. dynamics runs.
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Pace, G.; Ferri, V.; Grave, C.; Elbing, M.; von Hänisch, C.; Zharnikov, M.; Mayor, M.; Rampi, M. A.; Samorì, P. Cooperative Light-Induced Molecular Movements of Highly Ordered Azobenzene Self-Assembled Monolayers. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 9937, DOI: 10.1073/pnas.0703748104
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75
Cooperative light-induced molecular movements of highly ordered azobenzene self-assembled monolayers
Pace, Giuseppina; Ferri, Violetta; Grave, Christian; Elbing, Mark; von Haenisch, Carsten; Zharnikov, Michael; Mayor, Marcel; Rampi, Maria Anita; Samori, Paolo
Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (24), 9937-9942CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Photochromic systems can convert light energy into mech. energy, thus they can be used as building blocks for the fabrication of prototypes of mol. devices that are based on the photomech. effect. Hitherto a controlled photochromic switch on surfaces has been achieved either on isolated chromophores or within assemblies of randomly arranged mols. The authors show by scanning tunneling microscopy imaging the photochem. switching of a new terminally thiolated azobiphenyl rigid rod mol. Interestingly, the switching of entire mol. 2D cryst. domains is obsd., which is ruled by the interactions between nearest neighbors. This observation of azobenzene-based systems displaying collective switching might be of interest for applications in high-d. data storage.
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Titov, E.; Granucci, G.; Götze, J. P.; Persico, M.; Saalfrank, P. Dynamics of Azobenzene Dimer Photoisomerization: Electronic and Steric Effects. J. Phys. Chem. Lett. 2016, 7, 3591– 3596, DOI: 10.1021/acs.jpclett.6b01401
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Dynamics of Azobenzene Dimer Photoisomerization: Electronic and Steric Effects
Titov, Evgenii; Granucci, Giovanni; Goetze, Jan Philipp; Persico, Maurizio; Saalfrank, Peter
Journal of Physical Chemistry Letters (2016), 7 (18), 3591-3596CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
While azobenzenes readily photoswitch in soln., their photoisomerization in densely packed self-assembled monolayers (SAMs) can be suppressed. Reasons for this can be steric hindrance and/or electronic quenching, e.g., by exciton coupling. The authors address these possibilities by means of nonadiabatic mol. dynamics with trajectory surface hopping calcns., investigating the trans → cis isomerization of azobenzene after excitation into the ππ* absorption band. The authors consider a free monomer, an isolated dimer and a dimer embedded in a SAM-like environment of addnl. azobenzene mols., imitating in this way the gradual transition from an unconstrained over an electronically coupled to an electronically coupled and sterically hindered, mol. switch. Simulations reveal that in comparison to the single mol. the quantum yield of the trans → cis photoisomerization is similar for the isolated dimer, but greatly reduced in the sterically constrained situation. Other implications of dimerization and steric constraints are also discussed.
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Abstract
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Figure 1
Figure 1. Model host–guest systems. (A, top) Structure of the supramolecular cage studied herein, formed via the self-assembly of triimidazole-based donors and cis-blocked Pd acceptors. (A, bottom) Atomistic model of the supramolecular host cage, along with a schematic representation of its octahedral structure, which can be described by the axial and equatorial distances, D1 (red) and D2 (green). (B) Structural formulas and atomistic models of the guests studied herein: azobenzene (AZB), methoxylated azobenzene (M-AZB), fluorinated azobenzene (F-AZB), and arylazopyrazole (AZP) (here shown as trans isomers).
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Figure 2
Figure 2. Conformational free-energy landscape of the empty cage. (A) Free-energy surface (FES) as a function of D1 (distance between the axial/red Pd atoms) and D2 (distance between the midpoints of opposite edges of the cage identified by the equatorial/green Pd atoms). The color scale in the FES indicates the free-energy associated with cage conformations on the D1–D2 plane (scale and legend shown in B). Four representative snapshots are shown: the starting, extended configuration (top right) corresponding to the crystal structure of the cage,(62) the energetic minimum of the FES (top left), a D1-elongated structure (bottom right), and a D2-elongated structure (bottom left). Axial and equatorial Pd atoms are colored in red and green, respectively, while the connectivity scheme is colored in orange to facilitate interpretation of the structures. (B) Probability associated with all cage conformations as a function of the relative free-energy (bin width, 0.5 kcal/mol).
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Figure 3
Figure 3. Free-energy cost of guest encapsulation. Representative equilibrium conformations (in the D1–D2 plane) of the cage encapsulating different trans (left) or cis (right) guests. For each host–guest system, we report the position of the minimum-energy conformation (colored points) and the associated isolines (same colors) enclosing all conformations within 0.5 kcal/mol from the minimum of each system. The data are projected onto the FES of the empty cage (same as Figure 2), for which we also indicate the global minimum and associated 0.5 kcal/mol isoline (in white).
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Figure 4
Figure 4. Trans → cis transitions of azo-switches inside and outside the cage. (A) Kinetics of trans → cis isomerization of the excited M-AZB (top) and F-AZB (bottom) outside the cage (in solution) reported as examples. The measured transition times, reported below the isomerization arrows, are obtained from MD simulations using an atomistic model where the CNNC dihedral potential term for the trans-azobenzene derivatives (E_dih, reported in the plot as a function of the dihedral angle), is changed from the black curve (native/unperturbed state) to the blue curve (excited trans-azobenzene, S*).(50) (B) Kinetics of trans → cis isomerization of excited M-AZB (top) and F-AZB (bottom) switches confined inside the cage. Transition times for all the guests in the cage are reported in Table 1.
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Figure 5
Figure 5. Thermodynamics and kinetics of trans guest binding/release. (A) Representative MetaD snapshots of the reversible binding and release of trans-M-AZB inside the cage; k_off and k_on denote the kinetic constants for the expulsion and encapsulation processes (the k_on value inside the brackets is explicitly calculated, accounting for the guest concentration used in the model ∼11.4 mM, providing the actual rate). (B) Thermodynamic and kinetic scheme representing the expulsion and encapsulation mechanisms for trans-AZB in/out the cage as a function of the distance between the guests’ and the cage’s centers of mass (identifying IN and OUT states). (C) Thermodynamic schemes representing the expulsion/encapsulation of the trans isomers of M-AZB (green), F-AZB (cyan), and AZP (violet) guests. All ΔG differences between IN vs OUT states were computed from converged MetaD simulations, while the transition barriers were more accurately estimated from multiple infrequent MetaD runs (see the SI Methods section for further details).
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Figure 6
Figure 6. Molecular determinants of isomerization under confinement. (A) Relationship between isomerization rate (τ_trans–cis) and residence times (τ_off) of the guests inside the cage. (B) Relationship between τ_trans–cis and potential energy of host–guest interactions, ΔE_HG. (C) Relationship between τ_trans–cis and the number of contacts between the cage and the guest. (D) Relationship between τ_trans–cis and the volume (V) of guest molecules (see the SI Methods section for details on guest volume estimation). (E) Switching deceleration, τ_trans–cis/τ₀, as a function of the increase in guest volume (%ΔV_guest), in which τ₀ denotes isomerization time measured at the original volume of each guest. In plots A–E, the points correspond to guests AZB (black), M-AZB (green), F-AZB (cyan), and AZP (violet). (F) Average τ_trans–cis/τ₀ as a function of the average increase in guest volume (%ΔV_guest), obtained by averaging all data from plot E between systems with similar %ΔV_guest. The error bars indicate the standard deviation of %ΔV_guest and τ_trans–cis/τ₀ values. Inset: cartoon showing the volume of encapsulated M-AZB (green) inside the cage (white). The dashed lines in all plots are the logarithmic fit of the data.
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13. 13
  Dri, C.; Peters, M. V.; Schwarz, J.; Hecht, S.; Grill, L. Spatial Periodicity in Molecular Switching. Nat. Nanotechnol. 2008, 3, 649– 653, DOI: 10.1038/nnano.2008.269
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  13
  Spatial periodicity in molecular switching
  Dri, Carlo; Peters, Maike V.; Schwarz, Jutta; Hecht, Stefan; Grill, Leonhard
  Nature Nanotechnology (2008), 3 (11), 649-653CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
  The ultimate miniaturization of future devices will require the use of functional mols. at the nanoscale and their integration into larger architectures. Switches represent a prototype of such functional mols. because they exhibit characteristic states of different phys./chem. properties, which can be addressed reversibly. Recently, various switching entities have been studied and switching of single mols. on surfaces has been demonstrated. However, for functional mols. to be used in a future device, it will be necessary to selectively address individual mols., preferentially in an ordered pattern. Here, we show that azobenzene derivs. in the trans form, adsorbed in a homogeneous two-dimensional layer, can be collectively switched with spatial selectivity, thus forming a periodic pattern of cis isomers. We find that the probability of a mol. switching is not equally distributed, but is strongly dependent on both the surrounding mols. and the supporting surface, which precisely det. the switching capability of each individual mol. Consequently, exactly the same lattices of cis isomers are created in repeated erasing and re-switching cycles. Our results demonstrate a conceptually new approach to spatially addressing single functional mols.
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14. 14
  Kassem, S.; Lee, A. T. L.; Leigh, D. A.; Marcos, V.; Palmer, L. I.; Pisano, S. Stereodivergent Synthesis with a Programmable Molecular Machine. Nature 2017, 549, 374– 378, DOI: 10.1038/nature23677
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  14
  Stereodivergent synthesis with a programmable molecular machine
  Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Marcos, Vanesa; Palmer, Leoni I.; Pisano, Simone
  Nature (London, United Kingdom) (2017), 549 (7672), 374-378CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
  It has been convincingly argued that mol. machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångstrom precision are unlikely to be realized. However, biol. mol. machines routinely position rather less reactive substrates in order to direct chem. reaction sequences, from sequence-specific synthesis by the ribosome to polyketide synthases, where tethered mols. are passed from active site to active site in multi-enzyme complexes. Artificial mol. machines have been developed for tasks that include sequence-specific oligomer synthesis and the switching of product chirality, a photo-responsive host mol. has been described that is able to mech. twist a bound mol. guest, and mol. fragments have been selectively transported in either direction between sites on a mol. platform through a ratchet mechanism. Here we detail an artificial mol. machine that moves a substrate between different activating sites to achieve different product outcomes from chem. synthesis. This mol. robot can be programmed to stereoselectively produce, in a sequential one-pot operation, an excess of any one of four possible diastereoisomers from the addn. of a thiol and an alkene to an α,β-unsatd. aldehyde in a tandem reaction process. The stereodivergent synthesis includes diastereoisomers that cannot be selectively synthesized through conventional iminium-enamine organocatalysis. We anticipate that future generations of programmable mol. machines may have significant roles in chem. synthesis and mol. manufg.
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15. 15
  Katsonis, N.; Lubomska, M.; Pollard, M. M.; Feringa, B. L.; Rudolf, P. Synthetic Light-Activated Molecular Switches and Motors on Surfaces. Prog. Surf. Sci. 2007, 82, 407– 434, DOI: 10.1016/j.progsurf.2007.03.011
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  15
  Synthetic light-activated molecular switches and motors on surfaces
  Katsonis, Nathalie; Lubomska, Monika; Pollard, Michael M.; Feringa, Ben L.; Rudolf, Petra
  Progress in Surface Science (2007), 82 (7-8), 407-434CODEN: PSSFBP; ISSN:0079-6816. (Elsevier B.V.)
  A review. Recent advances in synthetic methods and anal. techniques provide a basis for the construction and characterization of organized arrays of mol. switches and motors on surfaces. Among them, mol. systems that can be controlled by light are particularly promising because of their ease of addressability, fast response times and the compatibility of light with a wide range of condensed phases. The aim of this contribution is to highlight selected recent advances in building functional monolayers of light-activated mols. Special focus is given to monolayers of mols. whose collective switching properties were harnessed to produce macroscopic effects. The design, structure, and function of monolayers composed of bistable photochromic switches, which can control chirality, wettability, cond. and self-assembly are described. A recent report on the successful demonstration of light-driven rotary motors functioning while grafted on gold surfaces will also be discussed, followed by a brief conclusion.
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16. 16
  Broichhagen, J.; Frank, J. A.; Trauner, D. A Roadmap to Success in Photopharmacology. Acc. Chem. Res. 2015, 48, 1947– 1960, DOI: 10.1021/acs.accounts.5b00129
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  16
  A Roadmap to Success in Photopharmacology
  Broichhagen, Johannes; Frank, James Allen; Trauner, Dirk
  Accounts of Chemical Research (2015), 48 (7), 1947-1960CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
  Light is a fascinating phenomenon that ties together physics, chem., and biol. It is unmatched in its ability to confer information with temporal and spatial precision and has been used to map objects on the scale of tens of nanometers (10-8 m) to light years (1016 m). This information, gathered through super-resoln. microscopes or space-based telescopes, is ultimately funneled through the human visual system, which is a miracle in itself. It allows us to see the Andromeda galaxy at night, an object that is 2.5 million light years away and very dim, and ski the next day in bright sunlight at an intensity that is 12 orders of magnitude higher. Human vision is only one of many photoreceptive systems that have evolved on earth and are found in all kingdoms of life. These systems rely on mol. photoswitches, such as retinal or tetrapyrrols, which undergo transient bond isomerizations or bond formations upon irradn. The set of chromophores that have been employed in Nature for this purpose is surprisingly small. Nevertheless, they control a wide variety of biol. functions, which have recently been significantly increased through the rapid development of optogenetics. Optogenetics originated as an effort to control neural function with genetically encoded photoreceptors that use abundant chromophores, in particular retinal. It now covers a variety of cellular functions other than excitability and has revolutionized the control of biol. pathways in neuroscience and beyond. Chem. has provided a large repertoire of synthetic photoswitches with highly tunable properties. Like their natural counterparts, these chromophores can be attached to proteins to effectively put them under optical control. This approach has enabled a new type of synthetic photobiol. that has gone under various names to distinguish it from optogenetics. We now call it photopharmacol. Here we trace our involvement in this field, starting with the first light-sensitive potassium channel (SPARK) and concluding with our most recent work on photoswitchable fatty acids. Instead of simply providing a historical account of our efforts, we discuss the design criteria that guided our choice of mols. and receptors. As such, we hope to provide a roadmap to success in photopharmacol. and make a case as to why synthetic photoswitches, properly designed and made available through well-planned and efficient syntheses, should have a bright future in biol. and medicine.
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17. 17
  Weston, C. E.; Krämer, A.; Colin, F.; Yildiz, Ö.; Baud, M. G. J.; Meyer-Almes, F.-J.; Fuchter, M. J. Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors. ACS Infect. Dis. 2017, 3, 152– 161, DOI: 10.1021/acsinfecdis.6b00148
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  17
  Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors
  Weston, Claire E.; Kramer, Andreas; Colin, Felix; Yildiz, Ozkan; Baud, Matthias G. J.; Meyer-Almes, Franz-Josef; Fuchter, Matthew J.
  ACS Infectious Diseases (2017), 3 (2), 152-161CODEN: AIDCBC; ISSN:2373-8227. (American Chemical Society)
  Photopharmacol. agents exhibit light-dependent biol. activity and may have potential in the development of new antimicrobial agents/modalities. Amidohydrolase enzymes homologous to the well-known human histone deacetylases (HDACs) are present in bacteria, including resistant organisms responsible for a significant no. of hospital-acquired infections and deaths. We report photopharmacol. inhibitors of these enzymes, using two classes of photoswitches embedded in the inhibitor pharmacophore: azobenzenes and arylazopyrazoles. Although both classes of inhibitor show excellent inhibitory activity (nM IC50 values) of the target enzymes and promising differential activity of the switchable E- and Z-isomeric forms, the arylazopyrazoles exhibit better intrinsic photoswitch performance (more complete switching, longer thermal lifetime of the Z-isomer). We also report protein-ligand crystal structures of the E-isomers of both an azobenzene and an arylazopyrazole inhibitor, bound to bacterial histone deacetylase-like amidohydrolases (HDAHs). These structures not only uncover interactions important for inhibitor binding but also reveal conformational differences between the two photoswitch inhibitor classes. As such, our data may pave the way for the design of improved photopharmacol. agents targeting the HDAC superfamily.
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18. 18
  Fiedler, D.; Leung, D.; Bergman, R.; Raymond, K. Selective Molecular Recognition, C-H Bond Activation, and Catalysis in Nanoscale Reaction Vessels. Acc. Chem. Res. 2005, 38, 349– 358, DOI: 10.1021/ar040152p
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  18
  Selective Molecular Recognition, C-H Bond Activation, and Catalysis in Nanoscale Reaction Vessels
  Fiedler, Dorothea; Leung, Dennis H.; Bergman, Robert G.; Raymond, Kenneth N.
  Accounts of Chemical Research (2005), 38 (4), 349-358CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
  A review. Supramol. chem. represents a way to mimic enzyme reactivity by using specially designed container mols. We have shown that a chiral self-assembled M4L6 supramol. tetrahedron can encapsulate a variety of cationic guests with varying degrees of stereoselectivity. Reactive iridium guests can be encapsulated, and the C-H bond activation of aldehydes occurs with the host cavity controlling the ability of substrates to interact with the metal center based upon size and shape. In addn., the host container can act as a catalyst by itself. By restricting reaction space and preorganizing the substrates into reactive conformations, it accelerates the sigmatropic rearrangement of enammonium cations.
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19. 19
  Tripp, B. C.; Smith, K.; Ferry, J. G. Carbonic Anhydrase: New Insights for an Ancient Enzyme. J. Biol. Chem. 2001, 276, 48615– 48618, DOI: 10.1074/jbc.R100045200
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  19
  Carbonic anhydrase: new insights for an ancient enzyme
  Tripp, Brian C.; Smith, Kerry; Ferry, James G.
  Journal of Biological Chemistry (2001), 276 (52), 48615-48618CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
  A review, discussing advances in the study of the structure and biol. chem. of carbonic anhydrases of the classes α, β, and γ. The catalytic mechanisms for both the β- and γ-class carbonic anhydrases were further elucidated, particularly in the proton transfer pathway. A possible fourth class (δ) represented by the Thalassiosira weissflogii enzyme is also described.
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20. 20
  Zhang, X.; Houk, K. N. Why Enzymes Are Proficient Catalysts: Beyond the Pauling Paradigm. Acc. Chem. Res. 2005, 38, 379– 385, DOI: 10.1021/ar040257s
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  20
  Why enzymes are proficient catalysts: beyond the Pauling paradigm
  Zhang, Xiyun; Houk, K. N.
  Accounts of Chemical Research (2005), 38 (5), 379-385CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)
  A review. Linus Pauling (1948) proposed that "enzymes are mols. that are complementary in structure to the activated complexes of the reactions that they catalyze, ..., [rather than] entering into reactions". This paradigm has dominated thinking in the field. While complementarity of the type proposed by Pauling can account for acceleration up to 11 orders of magnitude, most enzymes exceed that proficiency. Enzymes with proficiencies [(kcat/Km)/kuncat] > 1011 M-1 achieve >15 kcal/mol of "transition state binding" not merely by a concatenation of noncovalent effects but by covalent bond formation between enzyme or cofactor and transition state, involving a change in mechanism from that in aq. soln. Enzymes enter into reactions with substrates and do not merely complement the transition states of the uncatalyzed reactions.
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21. 21
  Whicher, J. R.; Dutta, S.; Hansen, D. A.; Hale, W. A.; Chemler, J. A.; Dosey, A. M.; Narayan, A. R. H.; Håkansson, K.; Sherman, D. H.; Smith, J. L.; Skiniotis, G. Structural Rearrangements of a Polyketide Synthase Module during Its Catalytic Cycle. Nature 2014, 510, 560– 564, DOI: 10.1038/nature13409
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  21
  Structural rearrangements of a polyketide synthase module during its catalytic cycle
  Whicher, Jonathan R.; Dutta, Somnath; Hansen, Douglas A.; Hale, Wendi A.; Chemler, Joseph A.; Dosey, Annie M.; Narayan, Alison R. H.; Hakansson, Kristina; Sherman, David H.; Smith, Janet L.; Skiniotis, Georgios
  Nature (London, United Kingdom) (2014), 510 (7506), 560-564CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
  The polyketide synthase (PKS) mega-enzyme assembly line uses a modular architecture to synthesize diverse and bioactive natural products that often constitute the core structures or complete chem. entities for many clin. approved therapeutic agents. The architecture of a full-length PKS module from the pikromycin pathway of Streptomyces venezuelae creates a reaction chamber for the intramodule acyl carrier protein (ACP) domain that carries building blocks and intermediates between acyltransferase, ketosynthase and ketoreductase active sites (see accompanying paper). Here we det. electron cryo-microscopy structures of a full-length pikromycin PKS module in three key biochem. states of its catalytic cycle. Each biochem. state was confirmed by bottom-up liq. chromatog./Fourier transform ion cyclotron resonance mass spectrometry. The ACP domain is differentially and precisely positioned after polyketide chain substrate loading on the active site of the ketosynthase, after extension to the β-keto intermediate, and after β-hydroxy product generation. The structures reveal the ACP dynamics for sequential interactions with catalytic domains within the reaction chamber, and for transferring the elongated and processed polyketide substrate to the next module in the PKS pathway. During the enzymic cycle the ketoreductase domain undergoes dramatic conformational rearrangements that enable optimal positioning for reductive processing of the ACP-bound polyketide chain elongation intermediate. These findings have crucial implications for the design of functional PKS modules, and for the engineering of pathways to generate pharmacol. relevant mols.
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22. 22
  Grommet, A. B.; Feller, M.; Klajn, R. Chemical Reactivity under Nanoconfinement. Nat. Nanotechnol. 2020, 15, 256– 271, DOI: 10.1038/s41565-020-0652-2
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  22
  Chemical reactivity under nanoconfinement
  Grommet, Angela B.; Feller, Moran; Klajn, Rafal
  Nature Nanotechnology (2020), 15 (4), 256-271CODEN: NNAABX; ISSN:1748-3387. (Nature Research)
  A review. Confining mols. can fundamentally change their chem. and phys. properties. Confinement effects are considered instrumental at various stages of the origins of life, and life continues to rely on layers of compartmentalization to maintain an out-of-equil. state and efficiently synthesize complex biomols. under mild conditions. As interest in synthetic confined systems grows, we are realizing that the principles governing reactivity under confinement are the same in abiol. systems as they are in nature. In this Review, we categorize the ways in which nanoconfinement effects impact chem. reactivity in synthetic systems. Under nanoconfinement, chem. properties can be modulated to increase reaction rates, enhance selectivity and stabilize reactive species. Confinement effects also lead to changes in phys. properties. The fluorescence of light emitters, the colors of dyes and electronic communication between electroactive species can all be tuned under confinement. Within each of these categories, we elucidate design principles and strategies that are widely applicable across a range of confined systems, specifically highlighting examples of different nanocompartments that influence reactivity in similar ways.
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23. 23
  Janiak, C.; Vieth, J. K. MOFs, MILs and More: Concepts, Properties and Applications for Porous Coordination Networks (PCNs). New J. Chem. 2010, 34, 2366– 2388, DOI: 10.1039/c0nj00275e
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  23
  MOFs, MILs and more: concepts, properties and applications for porous coordination networks (PCNs)
  Janiak, Christoph; Vieth, Jana K.
  New Journal of Chemistry (2010), 34 (11), 2366-2388CODEN: NJCHE5; ISSN:1144-0546. (Royal Society of Chemistry)
  A review. Discussion summarizes metal-org. frameworks (MOFs), Materials Institute Lavoisier (MILs), iso-reticular metal-org. frameworks (IR-MOFs), porous coordination networks (PCNs), zeolitic metal-org. frameworks (ZMOFs) and porous coordination polymers (PCPs) with selected examples of their structures, concepts for linkers, syntheses, post-synthesis modifications, metal nanoparticle formations in MOFs, porosity and zeolitic behavior for applications in gas storage for H, CO2, methane and applications in cond., luminescence and catalysis.
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24. 24
  Goettmann, F.; Sanchez, C. How Does Confinement Affect the Catalytic Activity of Mesoporous Materials?. J. Mater. Chem. 2007, 17, 24– 30, DOI: 10.1039/B608748P
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  24
  How does confinement affect the catalytic activity of mesoporous materials?
  Goettmann, Frederic; Sanchez, Clement
  Journal of Materials Chemistry (2007), 17 (1), 24-30CODEN: JMACEP; ISSN:0959-9428. (Royal Society of Chemistry)
  A review. So-called confinement effects in porous materials are known to strongly affect diffusion, phase transformations, catalytic properties, etc. In the field of catalysis, it is generally admitted that antagonistic effects at the mesoscale result in the existence of an optimal catalytic efficiency depending on pore size. Herein we highlight some recent examples of pore size effects and their proposed mechanisms. Confinement studies on periodically organized mesoporous materials must be developed because they should provide a certain clearness of arguments and understanding.
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25. 25
  Boyd, P. G.; Chidambaram, A.; García-Díez, E.; Ireland, C. P.; Daff, T. D.; Bounds, R.; Gładysiak, A.; Schouwink, P.; Moosavi, S. M.; Maroto-Valer, M. M.; Reimer, J. A.; Navarro, J. A. R.; Woo, T. K.; Garcia, S.; Stylianou, K. C.; Smit, B. Data-Driven Design of Metal–Organic Frameworks for Wet Flue Gas CO₂ Capture. Nature 2019, 576, 253– 256, DOI: 10.1038/s41586-019-1798-7
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  25
  Data-driven design of metal-organic frameworks for wet flue gas CO2 capture
  Boyd, Peter G.; Chidambaram, Arunraj; Garcia-Diez, Enrique; Ireland, Christopher P.; Daff, Thomas D.; Bounds, Richard; Gladysiak, Andrzej; Schouwink, Pascal; Moosavi, Seyed Mohamad; Maroto-Valer, M. Mercedes; Reimer, Jeffrey A.; Navarro, Jorge A. R.; Woo, Tom K.; Garcia, Susana; Stylianou, Kyriakos C.; Smit, Berend
  Nature (London, United Kingdom) (2019), 576 (7786), 253-256CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
  Limiting the increase of CO2 in the atm. is one of the largest challenges of our generation1. Because carbon capture and storage is one of the few viable technologies that can mitigate current CO2 emissions2, much effort is focused on developing solid adsorbents that can efficiently capture CO2 from flue gases emitted from anthropogenic sources3. One class of materials that has attracted considerable interest in this context is metal-org. frameworks (MOFs), in which the careful combination of org. ligands with metal-ion nodes can, in principle, give rise to innumerable structurally and chem. distinct nanoporous MOFs. However, many MOFs that are optimized for the sepn. of CO2 from nitrogen4-7 do not perform well when using realistic flue gas that contains water, because water competes with CO2 for the same adsorption sites and thereby causes the materials to lose their selectivity. Although flue gases can be dried, this renders the capture process prohibitively expensive8,9. Here we show that data mining of a computational screening library of over 300,000 MOFs can identify different classes of strong CO2-binding sites-which we term 'adsorbaphores'-that endow MOFs with CO2/N2 selectivity that persists in wet flue gases. We subsequently synthesized two water-stable MOFs contg. the most hydrophobic adsorbaphore, and found that their carbon-capture performance is not affected by water and outperforms that of some com. materials. Testing the performance of these MOFs in an industrial setting and consideration of the full capture process-including the targeted CO2 sink, such as geol. storage or serving as a carbon source for the chem. industry-will be necessary to identify the optimal sepn. material.
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26. 26
  Chu, Z.; Han, Y.; Bian, T.; De, S.; Král, P.; Klajn, R. Supramolecular Control of Azobenzene Switching on Nanoparticles. J. Am. Chem. Soc. 2019, 141, 1949– 1960, DOI: 10.1021/jacs.8b09638
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  26
  Supramolecular Control of Azobenzene Switching on Nanoparticles
  Chu, Zonglin; Han, Yanxiao; Bian, Tong; De, Soumen; Kral, Petr; Klajn, Rafal
  Journal of the American Chemical Society (2019), 141 (5), 1949-1960CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene's hydrophobic nature, most of these examples have been realized only in org. solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-sol. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amt. of azobenzene on the functionalized nanoparticles. Mol. dynamics simulations helped us to identify two distinct supramol. architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aq. solubilities. Azobenzenes adsorbed on these water-sol. nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aq. media and, in the long run, in biol. environments.
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27. 27
  Ahrens, J.; Bian, T.; Vexler, T.; Klajn, R. Irreversible Bleaching of Donor–Acceptor Stenhouse Adducts on the Surfaces of Magnetite Nanoparticles. ChemPhotoChem. 2017, 1, 230– 236, DOI: 10.1002/cptc.201700009
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  27
  Irreversible Bleaching of Donor-Acceptor Stenhouse Adducts on the Surfaces of Magnetite Nanoparticles
  Ahrens, Johannes; Bian, Tong; Vexler, Tom; Klajn, Rafal
  ChemPhotoChem (2017), 1 (5), 230-236CODEN: CHEMYH ISSN:. (Wiley-VCH Verlag GmbH & Co. KGaA)
  Two novel donor-acceptor Stenhouse adducts (DASAs) featuring the catechol moiety were synthesized and characterized. Both compds. bind strongly to the surfaces of magnetite nanoparticles. An adrenaline-derived DASA renders the particles insol. in all common solvents, likely because of poor solvation of the zwitterionic isomer generated on the nanoparticle surfaces. Well-sol. nanoparticles were successfully obtained using dopamine-derived DASA equipped with a long alkyl chain. Upon its attachment to nanoparticles, this DASA undergoes an irreversible decoloration reaction owing to the formation of the zwitterionic form. The reaction follows first-order kinetics and proceeds more rapidly on large nanoparticles. Interestingly, decoloration can be suppressed in the presence of free DASA mols. in soln. or at high nanoparticle concns.
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28. 28
  Zdobinsky, T.; Sankar Maiti, P.; Klajn, R. Support Curvature and Conformational Freedom Control Chemical Reactivity of Immobilized Species. J. Am. Chem. Soc. 2014, 136, 2711– 2714, DOI: 10.1021/ja411573a
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  28
  Support curvature and conformational freedom control chemical reactivity of immobilized species
  Zdobinsky Tino; Maiti Pradipta Sankar; Klajn Rafal
  Journal of the American Chemical Society (2014), 136 (7), 2711-4 ISSN:.
  We show that bimolecular reactions between species confined to the surfaces of nanoparticles can be manipulated by the nature of the linker, as well as by the curvature of the underlying particles.
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29. 29
  Zhao, H.; Sen, S.; Udayabhaskararao, T.; Sawczyk, M.; Kučanda, K.; Manna, D.; Kundu, P. K.; Lee, J.-W.; Král, P.; Klajn, R. Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks. Nat. Nanotechnol. 2016, 11, 82– 88, DOI: 10.1038/nnano.2015.256
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  29
  Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks
  Zhao, Hui; Sen, Soumyo; Udayabhaskararao, T.; Sawczyk, Michal; Kucanda, Kristina; Manna, Debasish; Kundu, Pintu K.; Lee, Ji-Woong; Kral, Petr; Klajn, Rafal
  Nature Nanotechnology (2016), 11 (1), 82-88CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
  The chem. behavior of mols. can be significantly modified by confinement to vols. comparable to the dimensions of the mols. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous org. frameworks and colloidal nanocrystal assemblies, the slow diffusion of mols. in and out of these materials has greatly hampered studying the effect of confinement on their physicochem. properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of UV and visible light irradn. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various mols. from the surrounding bulk soln. Once trapped, these mols. can undergo chem. reactions with increased rates and with stereoselectivities significantly different from those in bulk soln. Illumination with visible light disassembles these nanoflasks, releasing the product in soln. and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chem. reactivities in confined environments and for synthesizing mols. that are otherwise hard to achieve in bulk soln.
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30. 30
  Fallah-Araghi, A.; Meguellati, K.; Baret, J.-C.; Harrak, A. E.; Mangeat, T.; Karplus, M.; Ladame, S.; Marques, C. M.; Griffiths, A. D. Enhanced Chemical Synthesis at Soft Interfaces: A Universal Reaction-Adsorption Mechanism in Microcompartments. Phys. Rev. Lett. 2014, 112, 028301 DOI: 10.1103/PhysRevLett.112.028301
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  30
  Enhanced chemical synthesis at soft interfaces: a universal reaction-adsorption mechanism in microcompartments
  Fallah-Araghi, Ali; Meguellati, Kamel; Baret, Jean-Christophe; El Harrak, Abdeslam; Mangeat, Thomas; Karplus, Martin; Ladame, Sylvain; Marques, Carlos M.; Griffiths, Andrew D.
  Physical Review Letters (2014), 112 (2), 028301/1-028301/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
  A bimol. synthetic reaction (imine synthesis) was performed compartmentalized in micrometer-diam. emulsion droplets. The apparent equil. const. (Keq) and apparent forward rate const. (k1) were both inversely proportional to the droplet radius. The results are explained by a noncatalytic reaction-adsorption model in which reactants adsorb to the droplet interface with relatively low binding energies of a few kBT, react and diffuse back to the bulk. Reaction thermodn. is therefore modified by compartmentalization at the mesoscale-without confinement on the mol. scale-leading to a universal mechanism for improving unfavorable reactions.
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31. 31
  Franco, C.; Rodríguez-San-Miguel, D.; Sorrenti, A.; Sevim, S.; Pons, R.; Platero-Prats, A. E.; Pavlovic, M.; Szilágyi, I.; Ruiz Gonzalez, M. L.; González-Calbet, J. M.; Bochicchio, D.; Pesce, L.; Pavan, G. M.; Imaz, I.; Cano-Sarabia, M.; Maspoch, D.; Pané, S.; de Mello, A. J.; Zamora, F.; Puigmartí-Luis, J. Biomimetic Synthesis of Sub-20 nm Covalent Organic Frameworks in Water. J. Am. Chem. Soc. 2020, 142, 3540– 3547, DOI: 10.1021/jacs.9b12389
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  31
  Biomimetic Synthesis of Sub-20 nm Covalent Organic Frameworks in Water
  Franco, Carlos; Rodriguez-San-Miguel, David; Sorrenti, Alessandro; Sevim, Semih; Pons, Ramon; Platero-Prats, Ana E.; Pavlovic, Marko; Szilagyi, Istvan; Ruiz Gonzalez, M. Luisa; Gonzalez-Calbet, Jose M.; Bochicchio, Davide; Pesce, Luca; Pavan, Giovanni M.; Imaz, Inhar; Cano-Sarabia, Mary; Maspoch, Daniel; Pane, Salvador; de Mello, Andrew J.; Zamora, Felix; Puigmarti-Luis, Josep
  Journal of the American Chemical Society (2020), 142 (7), 3540-3547CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  Covalent org. frameworks (COFs) are commonly synthesized under harsh conditions yielding unprocessable powders. Control in their crystn. process and growth has been limited to studies conducted in hazardous org. solvents. Herein, we report a one-pot synthetic method that yields stable aq. colloidal solns. of sub-20 nm cryst. imine-based COF particles at room temp. and ambient pressure. Addnl., through the combination of exptl. and computational studies, we investigated the mechanisms and forces underlying the formation of such imine-based COF colloids in water. Further, we show that our method can be used to process the colloidal soln. into 2D and 3D COF shapes as well as to generate a COF ink that can be directly printed onto surfaces. These findings should open new vistas in COF chem., enabling new application areas.
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32. 32
  Zhang, G.; Mastalerz, M. Organic Cage Compounds – from Shape-Persistency to Function. Chem. Soc. Rev. 2014, 43, 1934– 1947, DOI: 10.1039/C3CS60358J
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  Organic cage compounds - from shape-persistency to function
  Zhang, Gang; Mastalerz, Michael
  Chemical Society Reviews (2014), 43 (6), 1934-1947CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
  A review. Syntheses, properties and applications of org. cage mols. were reviewed. Covalent bonds can be made in two ways, applying irreversible reactions or reversible reactions. By introducing dynamic covalent chem. (DCC), cages have become accessible in good yields from rather simple precursors. Both methods were compared and highlighted those that give very good yields. Furthermore, the use of org. cage compds. in sorption, recognition, sensing, sepn. and stabilization of mols. was discussed.
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33. 33
  Kang, J.; Rebek, J. Acceleration of a Diels–Alder Reaction by a Self-Assembled Molecular Capsule. Nature 1997, 385, 50– 52, DOI: 10.1038/385050a0
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  Acceleration of a Diels-Alder reaction by a self-assembled molecular capsule
  Kang, Jongmin; Rebek, Julius, Jr.
  Nature (London) (1997), 385 (6611), 50-52CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)
  The interior of cage-like mols. can be considered to provide a new phase of matter, in which it becomes possible to stabilized reactive intermediates and to observe new forms of stereoisomerism. Cage-like mol. complexes that self-assemble through weak intermol. forces are dynamic species, encapsulating guest mols. reversibly. They can persist over timescales ranging from microseconds to hours, long enough for chem. processes to take place within them. Here we report the acceleration of a Diels-Alder reaction by encapsulation of the reactants in a self-assembling mol. capsule. Although product inhibition (lacking of dissocn.) prevents the system from showing true catalytic behavior, there is clear evidence for a rate increase of over two orders of magnitude owing to the effective enhancement of concn. inside the capsule.
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34. 34
  Yoshizawa, M.; Klosterman, J. K.; Fujita, M. Functional Molecular Flasks: New Properties and Reactions within Discrete, Self-Assembled Hosts. Angew. Chem., Int. Ed. 2009, 48, 3418– 3438, DOI: 10.1002/anie.200805340
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  34
  Functional Molecular Flasks: New Properties and Reactions within Discrete, Self-Assembled Hosts
  Yoshizawa, Michito; Klosterman, Jeremy K.; Fujita, Makoto
  Angewandte Chemie, International Edition (2009), 48 (19), 3418-3438CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
  A review. Self-assembled hosts applied as "mol. flasks" can alter and control the reactivity and properties of mols. encapsulated within their well-defined, confined spaces. A variety of functional hosts of differing sizes, shapes, and utility have been prepd. by using the facile and modular concepts of self-assembly. The application of self-assembled hosts as "mol. flasks" has pptd. a surge of interest in the reactivity and properties of mols. within well-defined confined spaces. The facile and modular synthesis of self-assembled hosts has enabled a variety of hosts of differing sizes, shapes, and properties to be prepd. This Review briefly highlights the various mol. flasks synthesized before focusing on their use as functional mol. containers-specifically for the encapsulation of guest mols. to either engender unusual reactions or unique chem. phenomena. Such self-assembled cavities now constitute a new phase of chem., which cannot be achieved in the conventional solid, liq., and gas phases.
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35. 35
  Roy, B.; Ghosh, A. K.; Srivastava, S.; D’Silva, P.; Mukherjee, P. S. A Pd₈ Tetrafacial Molecular Barrel as Carrier for Water Insoluble Fluorophore. J. Am. Chem. Soc. 2015, 137, 11916– 11919, DOI: 10.1021/jacs.5b08008
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  35
  A Pd8 Tetrafacial Molecular Barrel as Carrier for Water Insoluble Fluorophore
  Roy, Bijan; Ghosh, Aloke Kumar; Srivastava, Shubhi; D'Silva, Patrick; Mukherjee, Partha Sarathi
  Journal of the American Chemical Society (2015), 137 (37), 11916-11919CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  A new carbazole-based tetraimidazole ligand 1,3,6,8-tetra(1H-imidazol-1-yl)-9-methyl-9H-carbazole (L) has been synthesized. The unsym. nature of L as well as the rotational freedom of imidazole donor moieties around C-N bond make it a special building unit, which upon treatment with cis-(tmeda)Pd(NO3)2 produced an unprecedented single linkage-isomeric Pd8 tetrafacial mol. nanobarrel (PSMBR-1) [tmeda = N,N,N',N'-tetramethylethane-1,2-diamine]. Unlike closed architectures, open barrel architecture of water-sol. PSMBR-1 makes it an ideal host for some water insol. polyarom. hydrocarbons in aq. medium; one such inclusion complex coronene⊂PSMBR-1 was characterized by X-ray diffraction study. Moreover, the potential application of PSMBR-1 as carrier in aq. medium for the transportation of water insol. fluorophore (perylene) for live cell imaging is explored.
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36. 36
  Wang, K.; Cai, X.; Yao, W.; Tang, D.; Kataria, R.; Ashbaugh, H. S.; Byers, L. D.; Gibb, B. C. Electrostatic Control of Macrocyclization Reactions within Nanospaces. J. Am. Chem. Soc. 2019, 141, 6740– 6747, DOI: 10.1021/jacs.9b02287
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  36
  Electrostatic Control of Macrocyclization Reactions within Nanospaces
  Wang, Kaiya; Cai, Xiaoyang; Yao, Wei; Tang, Du; Kataria, Rhea; Ashbaugh, Henry S.; Byers, Larry D.; Gibb, Bruce C.
  Journal of the American Chemical Society (2019), 141 (16), 6740-6747CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  The intrinsic structural complexity of proteins makes it hard to identify the contributions of each noncovalent interaction behind the remarkable rate accelerations of enzymes. Coulombic forces are evidently primary, but despite developments in artificial nanoreactor design, a picture of the extent to which these can contribute has not been forthcoming. Here we report on two supramol. capsules that possess structurally identical inner-spaces that differ in the electrostatic potential (EP) field that envelops them: one pos. and one neg. This architecture means that only changes in the EP field influence the chem. properties of encapsulated species. We quantify these influences via acidity and rates of cyclization measurements for encapsulated guests, and we confirm the primary role of Coulombic forces with a simple math. model approximating the capsules as Born spheres within a continuum dielec. These results reveal the reaction rate accelerations possible under Coulombic control and highlight important design criteria for nanoreactors.
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37. 37
  Cook, T. R.; Stang, P. J. Recent Developments in the Preparation and Chemistry of Metallacycles and Metallacages via Coordination. Chem. Rev. 2015, 115, 7001– 7045, DOI: 10.1021/cr5005666
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  37
  Recent Developments in the Preparation and Chemistry of Metallacycles and Metallacages via Coordination
  Cook, Timothy R.; Stang, Peter J.
  Chemical Reviews (Washington, DC, United States) (2015), 115 (15), 7001-7045CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
  A review.
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38. 38
  Sepehrpour, H.; Fu, W.; Sun, Y.; Stang, P. J. Biomedically Relevant Self-Assembled Metallacycles and Metallacages. J. Am. Chem. Soc. 2019, 141, 14005– 14020, DOI: 10.1021/jacs.9b06222
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  38
  Biomedically relevant self-assembled metallacycles and metallacages
  Sepehrpour, Hajar; Fu, Wenxin; Sun, Yan; Stang, Peter J.
  Journal of the American Chemical Society (2019), 141 (36), 14005-14020CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  A review. Diverse metal-org. complexes (MOCs), shaped as rectangles, triangles, hexagons, prisms, and cages, can be formed by coordination between metal ions (Pt, Pd, Ru, Rh, Ir, Zn, Co, and Cd) and org. ligands, with potential applications as alternatives to conventional biomedical materials for therapeutic, sensing, and imaging purposes. MOCs have been investigated as anticancer drugs in the treatment of malignant tumors in lung, cervical, breast, colon, liver, prostate, ovarian, brain, stomach, bone, skin, mouth, thyroid, and other cancers. MOCs with one, two, and three cavities have also been investigated as drug carriers and prepd. for the loading and release of different drugs. In addn., MOCs can target proteins by the shape effect and recognize sugars and DNA by electrostatic interactions, as well as estradiol by host-guest interactions, etc. This Perspective mainly covers achievements in the biomedical application of MOCs. We aim to identify some key trends in the reported MOC structures in relation to their biomedical activity and potential applications.
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39. 39
  Liu, M.; Zhang, L.; Little, M. A.; Kapil, V.; Ceriotti, M.; Yang, S.; Ding, L.; Holden, D. L.; Balderas-Xicohténcatl, R.; He, D.; Clowes, R.; Chong, S. Y.; Schütz, G.; Chen, L.; Hirscher, M.; Cooper, A. I. Barely Porous Organic Cages for Hydrogen Isotope Separation. Science 2019, 366, 613– 620, DOI: 10.1126/science.aax7427
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  39
  Barely porous organic cages for hydrogen isotope separation
  Liu, Ming; Zhang, Linda; Little, Marc A.; Kapil, Venkat; Ceriotti, Michele; Yang, Siyuan; Ding, Lifeng; Holden, Daniel L.; Balderas-Xicohtencatl, Rafael; He, Donglin; Clowes, Rob; Chong, Samantha Y.; Schutz, Gisela; Chen, Linjiang; Hirscher, Michael; Cooper, Andrew I.
  Science (Washington, DC, United States) (2019), 366 (6465), 613-620CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)
  The sepn. of hydrogen isotopes for applications such as nuclear fusion is a major challenge. Current technologies are energy intensive and inefficient. Nanoporous materials have the potential to sep. hydrogen isotopes by kinetic quantum sieving, but high sepn. selectivity tends to correlate with low adsorption capacity, which can prohibit process scale-up. In this study, we use org. synthesis to modify the internal cavities of cage mols. to produce hybrid materials that are excellent quantum sieves. By combining small-pore and large-pore cages together in a single solid, we produce a material with optimal sepn. performance that combines an excellent deuterium/hydrogen selectivity (8.0) with a high deuterium uptake (4.7 mmol per g).
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40. 40
  Merget, S.; Catti, L.; Piccini, G.; Tiefenbacher, K. Requirements for Terpene Cyclizations inside the Supramolecular Resorcinarene Capsule: Bound Water and Its Protonation Determine the Catalytic Activity. J. Am. Chem. Soc. 2020, 142, 4400– 4410, DOI: 10.1021/jacs.9b13239
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  40
  Requirements for Terpene Cyclizations inside the Supramolecular Resorcinarene Capsule: Bound Water and Its Protonation Determine the Catalytic Activity
  Merget, Severin; Catti, Lorenzo; Piccini, GiovanniMaria; Tiefenbacher, Konrad
  Journal of the American Chemical Society (2020), 142 (9), 4400-4410CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  The elucidation of the requirements for efficient catalysis within supramol. host systems is an important prerequisite for developing novel supramol. catalysts. The resorcinarene hexamer has recently been shown to be the first supramol. catalyst to promote the tail-to-head terpene cyclization in a biomimetic fashion. We herein present the synthesis of a no. of resorcinarene-based macrocycles composed of different ratios of resorcinol and pyrogallol units capable of self-assembly and compare the corresponding assemblies regarding their catalytic activity in the cyclization of monoterpenes. The assemblies were investigated in detail with respect to a no. of properties including the encapsulation of substrate and ion pairs, the structural incorporation of water, and the response to externally added acid (HCl). The results obtained strongly indicate that water incorporated into the hydrogen-bond network of the self-assembled structure plays an integral role for catalysis, effectively acting as a proton shuttle to activate the encapsulated substrate. These findings are also supported by mol. dynamics simulations, providing further insight into the protonation pathway and the relative energies of the intermediates involved.
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41. 41
  Yoshizawa, M.; Tamura, M.; Fujita, M. Diels-Alder in Aqueous Molecular Hosts: Unusual Regioselectivity and Efficient Catalysis. Science 2006, 312, 251– 254, DOI: 10.1126/science.1124985
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  Diels-Alder in Aqueous Molecular Hosts: Unusual Regioselectivity and Efficient Catalysis
  Yoshizawa, Michito; Tamura, Masazumi; Fujita, Makoto
  Science (Washington, DC, United States) (2006), 312 (5771), 251-254CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
  Self-assembled, hollow mol. structures are appealing as synthetic hosts for mediating chem. reactions. However, product binding has inhibited catalytic turnover in such systems, and selectivity has rarely approached the levels obsd. in more structurally elaborate natural enzymes. We found that an aq. organopalladium cage induces highly unusual regioselectivity in the Diels-Alder coupling of anthracene and phthalimide guests, promoting reaction at a terminal rather than central anthracene ring. Moreover, a similar bowl-shaped host attains efficient catalytic turnover in coupling the same substrates (although with the conventional regiochem.), most likely because the product geometry inhibits the arom. stacking interactions that attract the planar reagents to the host.
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42. 42
  Ueda, Y.; Ito, H.; Fujita, D.; Fujita, M. Permeable Self-Assembled Molecular Containers for Catalyst Isolation Enabling Two-Step Cascade Reactions. J. Am. Chem. Soc. 2017, 139, 6090– 6093, DOI: 10.1021/jacs.7b02745
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  42
  Permeable Self-Assembled Molecular Containers for Catalyst Isolation Enabling Two-Step Cascade Reactions
  Ueda, Yoshihiro; Ito, Hiroaki; Fujita, Daishi; Fujita, Makoto
  Journal of the American Chemical Society (2017), 139 (17), 6090-6093CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  Establishment of a general one-pot cascade reaction protocol would dramatically reduce the effort of multistep org. synthesis. We demonstrate that the unique structure of M12L24 self-assembled complexes gives them the potential to serve as catalyst carriers for enabling continuous chem. transformations. A stereoselective cascade reaction (allylic oxidn. followed by Diels-Alder cyclization) with two intrinsically incompatible catalysts was demonstrated. Our system is advantageous in terms of availability, scalability, and predictability.
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43. 43
  Maestri, M.; Iglesia, E. First-Principles Theoretical Assessment of Catalysis by Confinement: NO–O₂ Reactions within Voids of Molecular Dimensions in Siliceous Crystalline Frameworks. Phys. Chem. Chem. Phys. 2018, 20, 15725– 15735, DOI: 10.1039/C8CP01615A
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  43
  First-principles theoretical assessment of catalysis by confinement: NO-O2 reactions within voids of molecular dimensions in siliceous crystalline frameworks
  Maestri, Matteo; Iglesia, Enrique
  Physical Chemistry Chemical Physics (2018), 20 (23), 15725-15735CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
  D. functional theory methods that include dispersive forces are used to show how voids of mol. dimensions enhance reaction rates by the mere confinement of transition states analogous to those involved in homogeneous routes and without requiring specific binding sites or structural defects within confining voids. These van der Waals interactions account for the obsd. large rate enhancements for NO oxidn. in the presence of purely siliceous cryst. frameworks. The min. free energy paths for NO oxidn. within chabazite (CHA) and silicalite (SIL) frameworks involve intermediates similar in stoichiometry, geometry, and kinetic relevance to those involved in the homogeneous route. The termol. transition state for the kinetically-relevant cis-NOO2NO isomerization to trans-NOO2NO is strongly stabilized by confinement within CHA (by 36.3 kJ mol-1 in enthalpy) and SIL (by 39.2 kJ mol-1); such enthalpic stabilization is compensated, in part, by concomitant entropy losses brought forth by confinement (CHA: 44.9; SIL: 45.3, J mol-1 K-1 at 298 K). These enthalpy and entropy changes upon confinement agree well with those measured and combine to significantly decrease activation free energies and are consistent with the rate enhancements that become larger as temp. decreases because of the more neg. apparent activation energies in confined systems compared with homogeneous routes. Calcd. free energies of confinement are in quant. agreement with measured rate enhancements and with their temp. sensitivity. Such quant. agreements reflect preeminent effects of geometry in detg. the van der Waals contributions from contacts between the transition states (TS) and the confining walls and the weak effects of the level of theory on TS geometries. NO oxidn. reactions are chosen here to illustrate these remarkable effects of confinement because detailed kinetic anal. of rate data are available, but also because of their crit. role in the treatment of combustion effluents and in the synthesis of nitric acid and nitrates. Similar effects are evident from rate enhancements by confinement obsd. for Diels-Alder and alkyne oligomerization reactions. These reactions also occur in gaseous media at near ambient temps., for which enthalpic stabilization upon confinement of their homogeneous transition states becomes the preeminent component of activation free energies.
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44. 44
  Mal, P.; Breiner, B.; Rissanen, K.; Nitschke, J. R. White Phosphorus Is Air-Stable Within a Self-Assembled Tetrahedral Capsule. Science 2009, 324, 1697, DOI: 10.1126/science.1175313
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  44
  White Phosphorus Is Air-Stable Within a Self-Assembled Tetrahedral Capsule
  Mal, Prasenjit; Breiner, Boris; Rissanen, Kari; Nitschke, Jonathan R.
  Science (Washington, DC, United States) (2009), 324 (5935), 1697-1699CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
  The air-sensitive nature of white phosphorus underlies its destructive effect as a munition; tetrahedral P4 mols. readily react with atm. dioxygen, leading this form of the element to spontaneously combust upon exposure to air. Here, hydrophobic P4 mols. are rendered air-stable and water-sol. within the hydrophobic hollows of self-assembled tetrahedral container mols., [Fe4L6]4- (L = 4,4'-bis(2-pyridylmethyleneamino)-1,1'-biphenyl-2,2'-disulfonate), which form in water from simple org. subcomponents and iron(II) ions. The host-guest complex with P4 was characterized by x-ray crystallog. This stabilization is not achieved through hermetic exclusion of O2 but rather by constriction of individual P4 mols.; the addn. of oxygen atoms to P4 would gave oxidized species too large for their containers. The phosphorus can be released in controlled fashion without disrupting the cage by adding the competing guest benzene.
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45. 45
  Yamashina, M.; Sei, Y.; Akita, M.; Yoshizawa, M. Safe Storage of Radical Initiators within a Polyaromatic Nanocapsule. Nat. Commun. 2014, 5, 4662, DOI: 10.1038/ncomms5662
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  Safe storage of radical initiators within a polyaromatic nanocapsule
  Yamashina, Masahiro; Sei, Yoshihisa; Akita, Munetaka; Yoshizawa, Michito
  Nature Communications (2014), 5 (), 4662CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
  2,2'-Azobisisobutyronitrile and its derivs. are std. reagents for polymer and org. synthesis that generate radical species on stimuli by light or heat. Radical initiators like the azo compds. are unstable so that they should be kept in the dark at low temp. to avoid photochem. and thermal decompn. as well as accidental explosion. Here we report the spontaneous and quant. encapsulation of the radical initiators by a supramol. nanocapsule in aq. soln. We demonstrate the remarkable stability of the initiators toward light and heat in the well-defined cavity shielded by the polyarom. capsule shell. The incarcerated and stabilized initiators can be directly utilized for the radical polymn. of olefins on spontaneous release of the initiators from the capsule under the reaction conditions.
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46. 46
  Galan, A.; Ballester, P. Stabilization of Reactive Species by Supramolecular Encapsulation. Chem. Soc. Rev. 2016, 45, 1720– 1737, DOI: 10.1039/C5CS00861A
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  Stabilization of reactive species by supramolecular encapsulation
  Galan, Albano; Ballester, Pablo
  Chemical Society Reviews (2016), 45 (6), 1720-1737CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
  A review. Mol. containers have attracted the interest of supramol. chemists since the early beginnings of the field. Cavitands' inner cavities were quickly exploited by Cram and Warmuth to construct covalent containers able to stabilize and assist the characterization of short-lived reactive species such as cyclobutadiene or o-benzyne. Since then, more complex mol. architectures have been prepd. able to store and isolate a myriad of fleeting species (i.e. organometallic compds., cationic species, radical initiators...). In this review we cover selected examples of the stabilization of reactive species by encapsulation in mol. containers from the first reports of covalent containers described by Cram et al. to the most recent examples of containers with self-assembled structure (metal coordination cages and hydrogen bonded capsules). Finally, we briefly review examples reported by Rebek et al. in which elusive reaction intermediates could be detected in the inner cavities of self-folding resorcin[4]arene cavitands by the formation of covalent host-guest complexes. The utilization of encapsulated reactive species in catalysis or synthesis is not covered.
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47. 47
  Qiu, Y.; Antony, L. W.; Torkelson, J. M.; de Pablo, J. J.; Ediger, M. D. Tenfold Increase in the Photostability of an Azobenzene Guest in Vapor-Deposited Glass Mixtures. J. Chem. Phys. 2018, 149, 204503, DOI: 10.1063/1.5052003
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  47
  Tenfold increase in the photostability of an azobenzene guest in vapor-deposited glass mixtures
  Qiu, Yue; Antony, Lucas W.; Torkelson, John M.; de Pablo, Juan J.; Ediger, M. D.
  Journal of Chemical Physics (2018), 149 (20), 204503/1-204503/10CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
  Improvements to the photostability of org. glasses for use in electronic applications have generally relied on the modification of the chem. structure. We show here that the photostability of a guest mol. can also be significantly improved-without chem. modification-by using phys. vapor deposition to pack mols. more densely. Photoisomerization of the substituted azobenzene, 4,4'-diphenyl azobenzene, was studied in a vapor-deposited glass matrix of celecoxib. We directly measure photoisomerization of trans- to cis-states via UV-visible (UV-Vis) spectroscopy and show that the rate of photoisomerization depends upon the substrate temp. used during co-deposition of the glass. Photostability correlates reasonably with the d. of the glass, where the optimum glass is about tenfold more photostable than the liq.-cooled glass. Mol. simulations, which mimic photoisomerization, also demonstrate that photoreaction of a guest mol. can be suppressed in vapor-deposited glasses. From the simulations, we est. that the region that is disrupted by a single photoisomerization event encompasses approx. 5 mols. (c) 2018 American Institute of Physics.
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48. 48
  Qiu, Y.; Antony, L. W.; de Pablo, J. J.; Ediger, M. D. Photostability Can Be Significantly Modulated by Molecular Packing in Glasses. J. Am. Chem. Soc. 2016, 138, 11282– 11289, DOI: 10.1021/jacs.6b06372
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  48
  Photostability Can Be Significantly Modulated by Molecular Packing in Glasses
  Qiu, Yue; Antony, Lucas W.; de Pablo, Juan J.; Ediger, M. D.
  Journal of the American Chemical Society (2016), 138 (35), 11282-11289CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  While previous work has demonstrated that mol. packing in org. crystals can strongly influence photochem. stability, efforts to tune photostability in amorphous materials have shown much smaller effects. Here, it is shown that phys. vapor deposition can substantially improve the photostability of org. glasses. Disperse Orange 37 (DO37), an azobenzene deriv., is studied as a model system. Photostability is assessed through changes in the d. and mol. orientation of glassy thin films during light irradn. By optimizing the substrate temp. used for deposition, the photostability is increased by a factor of 50 relative to the liq.-cooled glass. Photostability correlates with glass d., with d. increases of up to 1.3%. Coarse-grained mol. simulations, which mimic glass prepn. and the photoisomerization reaction, also indicate that glasses with higher d. have substantially increased photostability. These results provide insights that may assist in the design of org. photovoltaics and light-emission devices with longer lifetimes.
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49. 49
  Fregoni, J.; Granucci, G.; Persico, M.; Corni, S. Strong Coupling with Light Enhances the Photoisomerization Quantum Yield of Azobenzene. Chem. 2020, 6, 250– 265, DOI: 10.1016/j.chempr.2019.11.001
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50. 50
  Bochicchio, D.; Kwangmettatam, S.; Kudernac, T.; Pavan, G. M. How Defects Control the Out-of-Equilibrium Dissipative Evolution of a Supramolecular Tubule. ACS Nano 2019, 13, 4322– 4334, DOI: 10.1021/acsnano.8b09523
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  50
  How Defects Control the Out-of-Equilibrium Dissipative Evolution of a Supramolecular Tubule
  Bochicchio, Davide; Kwangmettatam, Supaporn; Kudernac, Tibor; Pavan, Giovanni M.
  ACS Nano (2019), 13 (4), 4322-4334CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
  Supramol. architectures that work out-of-equil. or that can change in specific ways when absorbing external energy are ubiquitous in nature. Gaining the ability to create via self-assembly artificial materials possessing such fascinating behaviors would have a major impact in many fields. However, the rational design of similar dynamic structures requires to understand and, even more challenging, to learn how to master the mol. mechanisms governing how the assembled systems evolve far from the equil. Typically, this represents a daunting challenge due to the limited mol. insight that can be obtained by the expts. or by classical modeling approaches. Here we combine coarse-grained mol. models and advanced simulation approaches to study at submol. (<5 Å) resoln. a supramol. tubule, which breaks and disassembles upon absorption of light energy triggering isomerization of its azobenzene-contg. monomers. Our approach allows us to investigate the mol. mechanism of monomer transition in the assembly and to elucidate the kinetic process for the accumulation of the transitions in the system. Despite the stochastic nature of the excitation process, we demonstrate how these tubules preferentially dissipate the absorbed energy locally via the amplification of defects in their supramol. structure. We find that this constitutes the best kinetic pathway for accumulating monomer transitions in the system, which dets. the dynamic evolution out-of-equil. and the brittle behavior of the assembly under perturbed conditions. Thanks to the flexibility of our models, we finally come out with a general principle, where defects explain and control the brittle/soft behavior of such light-responsive assemblies.
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51. 51
  Kusukawa, T.; Fujita, M. Ship-in-a-Bottle” Formation of Stable Hydrophobic Dimers of Cis-Azobenzene and -Stilbene Derivatives in a Self-Assembled Coordination Nanocage. J. Am. Chem. Soc. 1999, 121, 1397– 1398, DOI: 10.1021/ja9837295
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  51
  "Ship-in-a-Bottle" Formation of Stable Hydrophobic Dimers of cis-Azobenzene and -Stilbene Derivatives in a Self-Assembled Coordination Nanocage
  Kusukawa, Takahiro; Fujita, Makoto
  Journal of the American Chemical Society (1999), 121 (6), 1397-1398CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  The cage compd. [Pd6(en)6L4](NO3)12 (I) (L = 2,4,6-tris(4-pyridyl)-1,3,5-triazine) is capable of selective enclathration of C-shaped mols. as hydrophobic dimers, such as cis-azobenzenes and cis-stilbenes to give I.2Q (Q = cis-p-methylazobenzene, cis-p-methylstilbene, cis-p-methoxystilbene, cis-azobenzene and cis-bis(4-methoxyphenyl)ethane). The ship-in-a-bottle assembly of the hydrophobic dimer in the cage is suggested by NMR data.
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52. 52
  Cantatore, V.; Granucci, G.; Rousseau, G.; Padula, G.; Persico, M. Photoisomerization of Self-Assembled Monolayers of Azobiphenyls: Simulations Highlight the Role of Packing and Defects. J. Phys. Chem. Lett. 2016, 7, 4027– 4031, DOI: 10.1021/acs.jpclett.6b02018
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  52
  Photoisomerization of Self-Assembled Monolayers of Azobiphenyls: Simulations Highlight the Role of Packing and Defects
  Cantatore, Valentina; Granucci, Giovanni; Rousseau, Guillaume; Padula, Giancarlo; Persico, Maurizio
  Journal of Physical Chemistry Letters (2016), 7 (19), 4027-4031CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
  We present surface hopping simulations of the photodynamics of self-assembled monolayers (SAMs) of 4'-(biphenyl-4-ylazo)-biphenyl-4-thiol (ABPT) on Au(111). We show that trans → cis photoisomerization is suppressed because of steric hindrance in a well-ordered SAM. Photoisomerization is instead viable in the presence of defects. Two particularly important defects are the boundaries between domains of trans-ABPT mols. leaning in different directions (a line defect) and single cis mols. embedded in a SAM of trans (a point defect). Our findings explain the cooperative behavior obsd. during the photoisomerization of a trans-ABPT SAM, leading to large domains of pure cis and trans isomers. The line and point defects are predicted to produce different patterns of cis-ABPT mols. during the early stages of the photoconversion.
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53. 53
  Clever, G. H.; Tashiro, S.; Shionoya, M. Light-Triggered Crystallization of a Molecular Host-Guest Complex. J. Am. Chem. Soc. 2010, 132, 9973– 9975, DOI: 10.1021/ja103620z
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  53
  Light-Triggered Crystallization of a Molecular Host-Guest Complex
  Clever, Guido H.; Tashiro, Shohei; Shionoya, Mitsuhiko
  Journal of the American Chemical Society (2010), 132 (29), 9973-9975CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  The control of structural changes in supramol. assemblies is a key point in the development of mol. machines. The reversible photoisomerization of org. compds. such as azobenzene using light as an external input is esp. suited because no waste products are generated. Based on the authors previous studies on the quant. encapsulation of suitably sized bis-sulfonate guests by a self-assembled, metal-org. cage consisting of four rigid, bent bis-monodentate pyridyl ligands and two Pd(II) ions, the authors show here how the light-switchable guest cis-4,4'-azobenzene bis-sulfonate can be expelled from its 1:1 host-guest complex triggered by its photoisomerization to the trans-isomer. Using a highly sol., PEGylated cage deriv., the full reversibility of this light-driven encapsulation/release process is demonstrated. In contrast, a sample of the less sol., unsubstituted cages including 1 equiv of the cis-guest was shown to result in immediate crystn. upon photoisomerization of the guest. X-ray structure anal. confirmed the guest mols. having left the cavity of the host and on the contrary joining the cages into a polymeric material by binding to their Pd(II) centers from outside.
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54. 54
  Dube, H.; Ajami, D.; Rebek, J. Photochemical Control of Reversible Encapsulation. Angew. Chem., Int. Ed. 2010, 49, 3192– 3195, DOI: 10.1002/anie.201000876
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  Photochemical Control of Reversible Encapsulation
  Dube, Henry; Ajami, Dariush; Rebek, Julius, Jr.
  Angewandte Chemie, International Edition (2010), 49 (18), 3192-3195, S3192/1-S3192/16CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
  Photoisomerization can be indirectly used as a method to control encapsulation phenomena. This remote control is a consequence of the snug fit of trans-4,4'-dimethylazobenzene (trans-I) in a cylindrical mol. capsule. Photoisomerization causes trans-I to "break out" of the capsule, thus allowing the entry of other guest species.
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55. 55
  Mohan Raj, A.; Raymo, F. M.; Ramamurthy, V. Reversible Disassembly–Assembly of Octa Acid–Guest Capsule in Water Triggered by a Photochromic Process. Org. Lett. 2016, 18, 1566– 1569, DOI: 10.1021/acs.orglett.6b00405
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  55
  Reversible Disassembly-Assembly of Octa Acid-Guest Capsule in Water Triggered by a Photochromic Process
  Mohan Raj, A.; Raymo, Francisco M.; Ramamurthy, V.
  Organic Letters (2016), 18 (7), 1566-1569CODEN: ORLEF7; ISSN:1523-7052. (American Chemical Society)
  Octa acid (OA), a calixarene-based cavitand, forms a 1:2 capsular assembly with neutral 1,3,3-trimethyl-6'-nitrospiro[2H-1]benzopyran-2,2'-indoline and 1:1 cavitandplex with its open zwitterionic merocyanine form. Photochromic interconversion between the spiropyran and merocyanine leads to unprecedented reversible capsular disassembly and assembly. OA provides stability to the merocyanine in both the ground and excited states. The photochem. controlled disassembly and assembly process established here points toward the opportunity of using the OA capsule in delivering small mols. at the desired locations.
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56. 56
  Yang, Y.; Hughes, R. P.; Aprahamian, I. Visible Light Switching of a BF₂-Coordinated Azo Compound. J. Am. Chem. Soc. 2012, 134, 15221– 15224, DOI: 10.1021/ja306030d
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  Visible Light Switching of a BF2-Coordinated Azo Compound
  Yang, Yin; Hughes, Russell P.; Aprahamian, Ivan
  Journal of the American Chemical Society (2012), 134 (37), 15221-15224CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  Here the synthesis and characterization of a BF2-azo complex that can be induced to isomerize without the need of deleterious UV light is reported. The complexation of the azo group with BF2, coupled with the extended conjugation of the N=N π-electrons, increases the energy of the n-π* transitions and introduces new π-nonbonding (πnb) to π* transitions that dominate the visible region. The well sepd. πnb-π* transitions of the trans and cis isomers enable the efficient switching of the system by using only visible light. The complexation also leads to a slow cis → trans thermal relaxation rate (t1/2 = 12.5 h). Theor. calcns. indicate that the absorption bands in the visible range can be tuned using different Lewis acids, opening the way to a conceptually new strategy for the manipulation of azo compds. using only visible light.
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57. 57
  Helmy, S.; Leibfarth, F. A.; Oh, S.; Poelma, J. E.; Hawker, C. J.; Read de Alaniz, J. Photoswitching Using Visible Light: A New Class of Organic Photochromic Molecules. J. Am. Chem. Soc. 2014, 136, 8169– 8172, DOI: 10.1021/ja503016b
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  Photoswitching Using Visible Light: A New Class of Organic Photochromic Molecules
  Helmy, Sameh; Leibfarth, Frank A.; Oh, Saemi; Poelma, Justin E.; Hawker, Craig J.; Read de Alaniz, Javier
  Journal of the American Chemical Society (2014), 136 (23), 8169-8172CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  A versatile new class of org. photochromic mols. that offers an unprecedented combination of phys. properties including tunable photoswitching using visible light, excellent fatigue resistance, and large polarity changes is described. These unique features offer significant opportunities in diverse fields ranging from biosensors to targeted delivery systems while also allowing non-experts ready synthetic access to these materials.
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58. 58
  Zhang, D.; Ronson, T. K.; Mosquera, J.; Martinez, A.; Guy, L.; Nitschke, J. R. Anion Binding in Water Drives Structural Adaptation in an Azaphosphatrane-Functionalized Fe^II₄L₄ Tetrahedron. J. Am. Chem. Soc. 2017, 139, 6574– 6577, DOI: 10.1021/jacs.7b02950
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  58
  Anion Binding in Water Drives Structural Adaptation in an Azaphosphatrane-Functionalized FeII4L4 Tetrahedron
  Zhang, Dawei; Ronson, Tanya K.; Mosquera, Jesus; Martinez, Alexandre; Guy, Laure; Nitschke, Jonathan R.
  Journal of the American Chemical Society (2017), 139 (19), 6574-6577CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
  Anion-templated aq. self-assembly resulted in the formation of an endohedrally functionalized FeII4L4 tetrahedron from azaphosphatrane-based subcomponents. This new water-sol. cage is flexible and able to encapsulate anions with vols. ranging from 35 to 219 Å3 via hydrogen bonding and electrostatic interactions. It structurally adapts in response to the size and shape of the template anions, dynamically adopting a conformation either where all four azaphosphatrane +P-H vectors point inward, or else where one points outward and the other three inward. The two cage isomers can coexist in soln. and interconvert. A shape memory phenomenon was obsd. during guest displacement because guest exchange occurs more rapidly than structural reconfiguration.
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59. 59
  Rizzuto, F. J.; Nitschke, J. R. Stereochemical Plasticity Modulates Cooperative Binding in a Co^II₁₂L₆ Cuboctahedron. Nat. Chem. 2017, 9, 903– 908, DOI: 10.1038/nchem.2758
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  Stereochemical plasticity modulates cooperative binding in a CoII12L6 cuboctahedron
  Rizzuto, Felix J.; Nitschke, Jonathan R.
  Nature Chemistry (2017), 9 (9), 903-908CODEN: NCAHBB; ISSN:1755-4330. (Nature Publishing Group)
  Biomol. receptors are able to process information by responding differentially to combinations of chem. signals. Synthetic receptors that are likewise capable of multi-stimuli response can form the basis of programmable mol. systems, wherein specific input sequences create distinct outputs. Here the authors report a pseudo-cuboctahedral assembly capable of cooperatively binding anionic and neutral guest species. The binding of pairs of fullerene guests was obsd. to effect the all-or-nothing cooperative templation of an S6-sym. host stereoisomer. This bis-fullerene adduct exhibits different cooperativity in binding pairs of anions from the fullerene-free parent: in one case, pos. cooperativity is obsd., while in another all binding affinities are enhanced by an order of magnitude, and in a third the binding events are only minimally perturbed. This intricate modulation of binding affinity, and thus cooperativity, renders the authors' new cuboctahedral receptor attractive for incorporation into systems with complex, programmable responses to different sets of stimuli.
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60. 60
  Mondal, P.; Sarkar, S.; Rath, S. P. Cyclic Bis-Porphyrin-Based Flexible Molecular Containers: Controlling Guest Arrangements and Supramolecular Catalysis by Tuning Cavity Size. Chem. - Eur. J. 2017, 23, 7093– 7103, DOI: 10.1002/chem.201700577
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  Cyclic Bis-porphyrin-Based Flexible Molecular Containers: Controlling Guest Arrangements and Supramolecular Catalysis by Tuning Cavity Size
  Mondal, Pritam; Sarkar, Sabyasachi; Rath, Sankar Prasad
  Chemistry - A European Journal (2017), 23 (29), 7093-7103CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
  Three cyclic zinc(II) bis-porphyrins (CB) with highly flexible linkers were employed as artificial mol. containers that efficiently encapsulate/coordinate various arom. aldehydes within their cavities. The arrangements of guests and their reactivity inside the mol. clefts are significantly influenced by the cavity size of the cyclic containers. In the presence of polycyclic arom. aldehydes, such as 3-formylperylene, as a guest, the cyclic bis-porphyrin host with a smaller cavity (CB1) forms a 1:1 sandwich complex. Upon slightly increasing the spacer length and thereby the cavity size, the cyclic host (CB2) encapsulates two mols. of 3-formylperylene that are also stacked together due to strong π-π interactions between them and CH-π interactions with the porphyrin rings. However, in the cyclic host (CB3) with an even larger cavity, two metal centers of the bis-porphyrin axially coordinate two mols. of 3-formylperylene within its cavity. Different arrangements of guest inside the cyclic bis-porphyrin hosts were studied by using UV/visible, ESI-MS, and 1H NMR spectroscopy, along with x-ray structure detn. of the host-guest complexes. Moreover, strong binding of guests within the cyclic bis-porphyrin hosts support the robust nature of the host-guest assemblies in soln. Such preferential binding of the bis-porphyrinic cavity towards arom. aldehydes through encapsulation/coordination was employed successfully to catalyze the Knoevenagel condensation of a series of polycyclic aldehydes with active methylene compds. (such as Meldrum's acid and 1,3-dimethylbarbituric acid) under ambient conditions. The yields of the condensed products significantly increase upon increasing spacer lengths of the cyclic bis-porphyrins because more substrates can then be encapsulated within the cavity. Such controllable cavity size of the cyclic containers has profound implications for constructing highly functional and modular enzyme mimics.
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61. 61
  Samanta, D.; Mukherjee, S.; Patil, Y. P.; Mukherjee, P. S. Self-Assembled Pd₆ Open Cage with Triimidazole Walls and the Use of Its Confined Nanospace for Catalytic Knoevenagel- and Diels–Alder Reactions in Aqueous Medium. Chem. - Eur. J. 2012, 18, 12322– 12329, DOI: 10.1002/chem.201201679
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  61
  Self-Assembled Pd6 Open Cage with Triimidazole Walls and the Use of Its Confined Nanospace for Catalytic Knoevenagel- and Diels-Alder Reactions in Aqueous Medium
  Samanta, Dipak; Mukherjee, Sandip; Patil, Yogesh P.; Mukherjee, Partha Sarathi
  Chemistry - A European Journal (2012), 18 (39), 12322-12329, S12322/1-S12322/13CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
  The two-component self-assembly of a 90° PdII acceptor and a triimidazole donor gave a water-sol. semi-cylindrical cage with a hydrophobic cavity, which was sep. crystd. with hydrophilic- and hydrophobic guests. The parent cage was found to catalyze the Knoevenagel condensation reaction of arom. mono-aldehydes with active methylene compds., such as Meldrum's acid or 1,3-dimethylbarbituric acid. The confined hydrophobic nanospace within this cage was also used in the catalytic Diels-Alder reactions of 9-(hydroxymethyl)anthracene with N-phenylmaleimide or N-cyclohexylmaleimide.
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62. 62
  Samanta, D.; Gemen, J.; Chu, Z.; Diskin-Posner, Y.; Shimon, L. J. W.; Klajn, R. Reversible Photoswitching of Encapsulated Azobenzenes in Water. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, 9379– 9384, DOI: 10.1073/pnas.1712787115
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  Reversible photoswitching of encapsulated azobenzenes in water
  Samanta, Dipak; Gemen, Julius; Chu, Zonglin; Diskin-Posner, Yael; Shimon, Linda J. W.; Klajn, Rafal
  Proceedings of the National Academy of Sciences of the United States of America (2018), 115 (38), 9379-9384CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
  Efficient mol. switching in confined spaces is crit. for the successful development of artificial mol. machines. However, mol. switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene-the key building block of light-controlled mol. machines-in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-sol. coordination cage, and investigated their light-responsive behavior. Using UV/visible absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host-guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its pptn. from the soln. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light.
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63. 63
  Samanta, D.; Galaktionova, D.; Gemen, J.; Shimon, L. J. W.; Diskin-Posner, Y.; Avram, L.; Král, P.; Klajn, R. Reversible Chromism of Spiropyran in the Cavity of a Flexible Coordination Cage. Nat. Commun. 2018, 9, 641, DOI: 10.1038/s41467-017-02715-6
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  Reversible chromism of spiropyran in the cavity of a flexible coordination cage
  Samanta Dipak; Gemen Julius; Klajn Rafal; Galaktionova Daria; Kral Petr; Shimon Linda J W; Diskin-Posner Yael; Avram Liat; Kral Petr; Kral Petr
  Nature communications (2018), 9 (1), 641 ISSN:.
  Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches-entities that can be toggled between two or more forms upon exposure to an external stimulus-often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating-and solubilizing in water-several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments.
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64. 64
  Hanopolskyi, A. I.; De, S.; Białek, M. J.; Diskin-Posner, Y.; Avram, L.; Feller, M.; Klajn, R. Reversible Switching of Arylazopyrazole within a Metal–Organic Cage. Beilstein J. Org. Chem. 2019, 15, 2398– 2407, DOI: 10.3762/bjoc.15.232
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  Reversible switching of arylazopyrazole within a metal-organic cage
  Hanopolskyi, Anton I.; De, Soumen; Bialek, Michal J.; Diskin-Posner, Yael; Avram, Liat; Feller, Moran; Klajn, Rafal
  Beilstein Journal of Organic Chemistry (2019), 15 (), 2398-2407CODEN: BJOCBH; ISSN:1860-5397. (Beilstein-Institut zur Foerderung der Chemischen Wissenschaften)
  Arylazopyrazoles represent a new family of mol. photoswitches characterized by a near-quant. conversion between two states and long thermal half-lives of the metastable state. Here, we investigated the behavior of a model arylazopyrazole in the presence of a self-assembled cage based on Pd-imidazole coordination. Owing to its high water soly., the cage can solubilize the E isomer of arylazopyrazole, which, by itself, is not sol. in water. NMR spectroscopy and X-ray crystallog. have independently demonstrated that each cage can encapsulate two mols. of E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calcns. suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with green light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization reaction also proceeded in the dark, with a rate significantly higher than in the absence of the cage.
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65. 65
  Böckmann, M.; Peter, C.; Site, L. D.; Doltsinis, N. L.; Kremer, K.; Marx, D. Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals. J. Chem. Theory Comput. 2007, 3, 1789– 1802, DOI: 10.1021/ct7000733
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  65
  Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals
  Bockmann Marcus; Peter Christine; Site Luigi Delle; Doltsinis Nikos L; Kremer Kurt; Marx Dominik
  Journal of chemical theory and computation (2007), 3 (5), 1789-802 ISSN:1549-9618.
  An atomistic force field has been adapted for use in molecular dynamics simulations of molecular materials that contain azobenzene (AB) functional groups. Force field parameters for bonded interactions and partial charges in the AB unit have been derived from ab initio molecular dynamics reference calculations. First applications of the new force field to liquid trans- and cis-AB are presented, both using a purely classical approach (MM) and a hybrid quantum-classical (QM/MM) simulation scheme. Detailed structural analysis confirms that QM/MM and purely MM simulations yield results that are in good agreement with each other. The force field of the AB core has been extended to include aliphatic chains that are attached via ether bridges to the two AB benzene rings. This allows for studying temperature induced phase transitions in the liquid-crystalline 8AB8 system. Using replica exchange techniques the new force field has successfully reproduced the smectic to isotropic-phase transition.
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66. 66
  Peter, C.; Site, L. D.; Kremer, K. Classical Simulations from the Atomistic to the Mesoscale and Back: Coarse Graining an Azobenzene Liquid Crystal. Soft Matter 2008, 4, 859– 869, DOI: 10.1039/b717324e
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  Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal
  Peter, Christine; Delle Site, Luigi; Kremer, Kurt
  Soft Matter (2008), 4 (4), 859-869CODEN: SMOABF; ISSN:1744-683X. (Royal Society of Chemistry)
  The authors describe the development of a coarse grained model for mol. dynamics (MD) simulations of a liq.-cryst. (LC) compd. with an azobenzene mesogen. It is studied how coarse graining methods originally developed to simulate amorphous polymeric systems can be extended to liq. crystals. The coarse grained (CG) model is constructed in a way that it allows carrying over of chem. details (i.e., the form of specific/attractive interactions) from the atomistic to the CG level, devising a new route to construct mesoscale models for liq. crystals with a close link to chem. more realistic atomistic ones. In addn. it is possible to switch between the atomistic and the CG levels of resoln. on demand through an inverse mapping procedure. By this the authors obtain representative large-scale atomistic coordinates based on CG structures and long-time atomistic trajectories generated from CG mesoscale simulations.
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67. 67
  Ilnytskyi, J. M.; Slyusarchuk, A.; Saphiannikova, M. Photocontrollable Self-Assembly of Azobenzene-Decorated Nanoparticles in Bulk: Computer Simulation Study. Macromolecules 2016, 49, 9272– 9282, DOI: 10.1021/acs.macromol.6b01871
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  Photocontrollable Self-Assembly of Azobenzene-Decorated Nanoparticles in Bulk: Computer Simulation Study
  Ilnytskyi, Jaroslav M.; Slyusarchuk, Arsen; Saphiannikova, Marina
  Macromolecules (Washington, DC, United States) (2016), 49 (23), 9272-9282CODEN: MAMOBX; ISSN:0024-9297. (American Chemical Society)
  Decoration of nanoparticles by specific functional groups provides means of controlling their aggregation and self-assembly into ordered morphologies. We study the photocontrollable self-assembly of the azobenzene-functionalized nanoparticles using coarse-grained mol. dynamics simulations. With no illumination applied, a monodomain smectic morphol. is formed only via cooling the isotropic system at sufficiently slow rate. Quenching the system below the smectic-isotropic transition results in formation of a polydomain glass-like state with restricted dynamics of nanoparticles. Upon irradn. with appropriate wavelength and intensity, the azobenzenes undergo trans-cis-trans photoisomerization cycles which unlock the interdomain links and induce uniaxial orientation of domains with their local director perpendicular to the polarization axis of irradn. As demonstrated by the simulations, this transition can spead-up essentially the self-assembly of decorated nanoparticles from the isotropic to the monodomain smectic phase, both via gradual cooling down and via quenching in a broad temp. interval below the smectic-isotropic transition.
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68. 68
  Osella, S.; Minoia, A.; Beljonne, D. Combined Molecular Dynamics and Density Functional Theory Study of Azobenzene–Graphene Interfaces. J. Phys. Chem. C 2016, 120, 6651– 6658, DOI: 10.1021/acs.jpcc.6b00393
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  68
  Combined Molecular Dynamics and Density Functional Theory Study of Azobenzene-Graphene Interfaces
  Osella, Silvio; Minoia, Andrea; Beljonne, David
  Journal of Physical Chemistry C (2016), 120 (12), 6651-6658CODEN: JPCCCK; ISSN:1932-7447. (American Chemical Society)
  Here, the authors first investigate the formation of 4-(decyloxy)azobenzene mol. monolayers on a single graphene layer through mol. dynamics (MD) simulations and assess the assocd. change in work function (WF) at the d. functional theory (DFT) level. The authors show that the major contribution to the WF shift arises from electrostatic effects induced by the azobenzene elec. dipole component normal to graphene and that the conformational distribution of the mol. switches in either their trans or cis forms can be convoluted into WF distributions for the hybrid systems. The authors next use this strategy to build a statistical ensemble for the work functions of graphene decorated with fluorinated azobenzene deriv. designed to maximize the change in WF upon photoswitching.
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69. 69
  Döbbelin, M.; Ciesielski, A.; Haar, S.; Osella, S.; Bruna, M.; Minoia, A.; Grisanti, L.; Mosciatti, T.; Richard, F.; Prasetyanto, E. A.; De Cola, L.; Palermo, V.; Mazzaro, R.; Morandi, V.; Lazzaroni, R.; Ferrari, A. C.; Beljonne, D.; Samorì, P. Light-Enhanced Liquid-Phase Exfoliation and Current Photoswitching in Graphene–Azobenzene Composites. Nat. Commun. 2016, 7, 11090, DOI: 10.1038/ncomms11090
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  Light-enhanced liquid-phase exfoliation and current photoswitching in graphene-azobenzene composites
  Dobbelin, Markus; Ciesielski, Artur; Haar, Sebastien; Osella, Silvio; Bruna, Matteo; Minoia, Andrea; Grisanti, Luca; Mosciatti, Thomas; Richard, Fanny; Prasetyanto, Eko Adi; De Cola, Luisa; Palermo, Vincenzo; Mazzaro, Raffaello; Morandi, Vittorio; Lazzaroni, Roberto; Ferrari, Andrea C.; Beljonne, David; Samori, Paolo
  Nature Communications (2016), 7 (), 11090CODEN: NCAOBW; ISSN:2041-1723. (Nature Publishing Group)
  Multifunctional materials can be engineered by combining multiple chem. components, each conferring a well-defined function to the ensemble. Graphene is at the center of an ever-growing research effort due to its combination of unique properties. Here, we show that the large conformational change assocd. with the trans-cis photochem. isomerization of alkyl-substituted azobenzenes can be used to improve the efficiency of liq.-phase exfoliation of graphite, with the photochromic mols. acting as dispersion-stabilizing agents. We also demonstrate reversible photo-modulated current in two-terminal devices based on graphene-azobenzene composites. We assign this tuneable elec. characteristics to the intercalation of the azobenzene between adjacent graphene layers and the resulting increase in the interlayer distance on (photo)switching from the linear trans-form to the bulky cis-form of the photochromes. These findings pave the way to the development of new optically controlled memories for light-assisted programming and high-sensitive photosensors.
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70. 70
  Laio, A.; Parrinello, M. Escaping Free-Energy Minima. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 12562– 12566, DOI: 10.1073/pnas.202427399
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  Escaping free-energy minima
  Laio, Alessandro; Parrinello, Michele
  Proceedings of the National Academy of Sciences of the United States of America (2002), 99 (20), 12562-12566CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
  We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the min. in the FES, allowing the efficient exploration and accurate detn. of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissocn. of a NaCl mol. in water and in the study of the conformational changes of a dialanine in soln.
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71. 71
  Pederzoli, M.; Pittner, J.; Barbatti, M.; Lischka, H. Nonadiabatic Molecular Dynamics Study of the Cis–Trans Photoisomerization of Azobenzene Excited to the S1 State. J. Phys. Chem. A 2011, 115, 11136– 11143, DOI: 10.1021/jp2013094
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  Nonadiabatic Molecular Dynamics Study of the cis-trans Photoisomerization of Azobenzene Excited to the S1 State
  Pederzoli, Marek; Pittner, Jiri; Barbatti, Mario; Lischka, Hans
  Journal of Physical Chemistry A (2011), 115 (41), 11136-11143CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)
  Ab initio nonadiabatic dynamics simulations of cis-to-trans isomerization of azobenzene upon S1 (n-π*) excitation are carried out employing the fewest-switches surface hopping method. Azobenzene photoisomerization occurs purely as a rotational motion of the central CNNC moiety. Two nonequivalent rotational pathways corresponding to clockwise or counterclockwise rotation are available. The course of the rotational motion is strongly dependent on the initial conditions. The internal conversion occurs via an S0/S1 crossing seam located near the midpoint of both of these rotational pathways. Based on statistical anal., it is shown that the occurrence of one or other pathway can be completely controlled by selecting adequate initial conditions.
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72. 72
  Tiago, M. L.; Ismail-Beigi, S.; Louie, S. G. Photoisomerization of Azobenzene from First-Principles Constrained Density-Functional Calculations. J. Chem. Phys. 2005, 122, 094311 DOI: 10.1063/1.1861873
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  Photoisomerization of azobenzene from first-principles constrained density-functional calculations
  Tiago, Murilo L.; Ismail-Beigi, Sohrab; Louie, Steven G.
  Journal of Chemical Physics (2005), 122 (9), 094311/1-094311/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
  Despite considerable work in the field, the precise mechanism for the photoisomerization of azobenzene, C12H10N2, is still an open issue. Early theor. studies of the problem indicated that isomerization occurs through an in-plane inversion path, and this has been used to explain recent time-resolved UV-visible spectroscopy measurements. On the other hand, a no. of recent theor. studies have concluded that a torsion of the N-N bond ("rotation path") is probably the most favorable mechanism for photoisomerization involving the first excited state. We have performed first-principles calcns. using constrained d.-functional theory (DFT) and time-dependent DFT in the local-d. approxn., with results that also favor the rotation path mechanism. Our results are compared with other analyses, primarily based on CI.
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73. 73
  Bochicchio, D.; Salvalaglio, M.; Pavan, G. M. Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution. Nat. Commun. 2017, 8, 147, DOI: 10.1038/s41467-017-00189-0
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  Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution
  Bochicchio Davide; Pavan Giovanni M; Salvalaglio Matteo
  Nature communications (2017), 8 (1), 147 ISSN:.
  To rationally design supramolecular polymers capable of self-healing or reconfiguring their structure in a dynamically controlled way, it is imperative to gain access into the intrinsic dynamics of the supramolecular polymer (dynamic exchange of monomers) while maintaining a high-resolution description of the monomer structure. But this is prohibitively difficult at experimental level. Here we show atomistic, coarse-grained modelling combined with advanced simulation approaches to characterize the molecular mechanisms and relative kinetics of monomer exchange in structural variants of a synthetic supramolecular polymer in different conditions. We can capture differences in supramolecular dynamics consistent with the experimental observations, revealing that monomer exchange in and out the fibres originates from the defects present in their supramolecular structure. At the same time, the submolecular resolution of this approach offers a molecular-level insight into the dynamics of these bioinspired materials, and a flexible tool to obtain structure-dynamics relationships for a variety of polymeric assemblies.Accessing the dynamics of soft self-assembled materials at high resolution is very difficult. Here the authors show atomistic and coarse-grained modelling combined with enhanced sampling to characterize the molecular mechanisms and kinetics of monomer exchange in synthetic supramolecular polymers.
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74. 74
  Tiwary, P.; Parrinello, M. From Metadynamics to Dynamics. Phys. Rev. Lett. 2013, 111, 230602, DOI: 10.1103/PhysRevLett.111.230602
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  From metadynamics to dynamics
  Tiwary, Pratyush; Parrinello, Michele
  Physical Review Letters (2013), 111 (23), 230602/1-230602/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
  Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted no. of collective variables it can explore complex free energy surfaces characterized by several metastable states sepd. by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calcg. the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable min. in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased mol. dynamics runs.
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75. 75
  Pace, G.; Ferri, V.; Grave, C.; Elbing, M.; von Hänisch, C.; Zharnikov, M.; Mayor, M.; Rampi, M. A.; Samorì, P. Cooperative Light-Induced Molecular Movements of Highly Ordered Azobenzene Self-Assembled Monolayers. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 9937, DOI: 10.1073/pnas.0703748104
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  Cooperative light-induced molecular movements of highly ordered azobenzene self-assembled monolayers
  Pace, Giuseppina; Ferri, Violetta; Grave, Christian; Elbing, Mark; von Haenisch, Carsten; Zharnikov, Michael; Mayor, Marcel; Rampi, Maria Anita; Samori, Paolo
  Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (24), 9937-9942CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
  Photochromic systems can convert light energy into mech. energy, thus they can be used as building blocks for the fabrication of prototypes of mol. devices that are based on the photomech. effect. Hitherto a controlled photochromic switch on surfaces has been achieved either on isolated chromophores or within assemblies of randomly arranged mols. The authors show by scanning tunneling microscopy imaging the photochem. switching of a new terminally thiolated azobiphenyl rigid rod mol. Interestingly, the switching of entire mol. 2D cryst. domains is obsd., which is ruled by the interactions between nearest neighbors. This observation of azobenzene-based systems displaying collective switching might be of interest for applications in high-d. data storage.
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  Titov, E.; Granucci, G.; Götze, J. P.; Persico, M.; Saalfrank, P. Dynamics of Azobenzene Dimer Photoisomerization: Electronic and Steric Effects. J. Phys. Chem. Lett. 2016, 7, 3591– 3596, DOI: 10.1021/acs.jpclett.6b01401
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  Dynamics of Azobenzene Dimer Photoisomerization: Electronic and Steric Effects
  Titov, Evgenii; Granucci, Giovanni; Goetze, Jan Philipp; Persico, Maurizio; Saalfrank, Peter
  Journal of Physical Chemistry Letters (2016), 7 (18), 3591-3596CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
  While azobenzenes readily photoswitch in soln., their photoisomerization in densely packed self-assembled monolayers (SAMs) can be suppressed. Reasons for this can be steric hindrance and/or electronic quenching, e.g., by exciton coupling. The authors address these possibilities by means of nonadiabatic mol. dynamics with trajectory surface hopping calcns., investigating the trans → cis isomerization of azobenzene after excitation into the ππ* absorption band. The authors consider a free monomer, an isolated dimer and a dimer embedded in a SAM-like environment of addnl. azobenzene mols., imitating in this way the gradual transition from an unconstrained over an electronically coupled to an electronically coupled and sterically hindered, mol. switch. Simulations reveal that in comparison to the single mol. the quantum yield of the trans → cis photoisomerization is similar for the isolated dimer, but greatly reduced in the sterically constrained situation. Other implications of dimerization and steric constraints are also discussed.
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Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage

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Abstract

Introduction

Figure 1

Results and Discussion

Characterization of Cage Flexibility in Solution

Figure 2

Effects of Guest Encapsulation on Cage Flexibility

Figure 3

Trans–Cis Isomerization of Azobenzenes Inside the Cage

Figure 4

Mechanisms of Guest Encapsulation/Release and Switching

Figure 5

Molecular Determinants of Guest Transitions in the Cage

Figure 6

Conclusions

Supporting Information

Terms & Conditions

Author Information

Acknowledgments

References

Cited By

Abstract

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

References

Supporting Information

Supporting Information

Terms & Conditions

STEP 1:

STEP 2:

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