Water-Controlled Switching in Rotaxanes

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C: Physical Processes in Nanomaterials and Nanostructures

Water-Controlled Switching in Rotaxanes Shuangli Du, Haohao Fu, Xueguang Shao, Christophe Chipot, and Wensheng Cai J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b01993 • Publication Date (Web): 06 Apr 2018 Downloaded from http://pubs.acs.org on April 7, 2018

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The Journal of Physical Chemistry

Water-Controlled Switching in Rotaxanes Shuangli Du,† Haohao Fu,† Xueguang Shao,†,‡,$,# Christophe Chipot,§,¶,┴ and Wensheng Cai*,†,‡,# †

Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin

300071, China ‡

Tianjin Key Laboratory of Biosensing and Molecular Recognition, Tianjin 300071, China

$

State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China

#

Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300071, China

§

Laboratoire International Associé Centre National de la Recherche Scientifique et University of

Illinois at Urbana−Champaign, Unité Mixte de Recherche No. 7565, Université de Lorraine, B.P. 70239, 54506 Vandoeuvre−lès−Nancy cedex, France ¶

Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science

and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States ┴

Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,

United States

ACS Paragon Plus Environment

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ABSTRACT: In biological and abiological molecular machines, water is generally considered to act as a lubricant. But, does water only act as a lubricant? Here, a [2]rotaxane composed of a dibenzo[24]-crown-8 and an H-shaped axle was investigated at the atomic level using molecular dynamics. At low pH, the rotaxane behaves as a molecular shuttle, but becomes a molecular rotor at high pH. The free-energy profiles describing the shuttling and rotary motions in pure acetonitrile and in an acetonitrile-water mixture reveal that water plays different roles in these two movements. In the electrostatically-controlled shuttling, water in small amount acts as a lubricant, decreasing the free-energy barrier. Conversely, in the rotary movement controlled by hydrophobic interactions, water causes an increase of the free-energy barrier, and, thus, plays a damping role. The effect of water on rotaxane motion, therefore, differs as a function of not only the nature of the driving force at play, but also the aqueous content of the environment. The microscopic mechanism of water lubrication and damping revealed in the present work paves the way for strategies designed to control motion in molecular machines and opens the way to novel, multifunctional, smart materials by regulating the aqueous fraction of the solvent.


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INTRODUCTION The special properties of water, such as minimal steric hindrance, high polarity and strong hydrogen-bond donor and acceptor ability, make it the most important solvent in molecular machines.1-3 In particular, due to its crucial role in lubricating the motion in biological motors,4-7 water is considered to be the “lubricant of life”, as phrased by Barron et al. in 1997.8 Many efforts have been invested to study the role of water in biological phenomena, like driving protein folding9 and promoting conformational interconversion of polypeptides.10 Further evidence of this concept has been provided by Hunt et al.,11 who used Kerr-effect spectroscopy to observe the fast motion of water around a homopolypeptide, and demonstrated that the structural changes from helix to coil could be ascribed to variations in solvent-peptide hydrogen bonding. In addition, Leigh12 and coworkers have demonstrated that, compared with other solvents, water could significantly accelerate the rate of shuttling of the macrocycle in a hydrogen-bonded rotaxane. The detailed, molecular-level mechanism has been addressed by Fu et al.,13 who showed that water can markedly weaken the hydrogen bonds between the ring and the molecular thread, thereby facilitating shuttling. Recently, in a theoretical investigation of ATP hydrolysis, Singharoy et al.7,14 revealed that water can lubricate the stalk rotation of V1ATPase by reducing the energetic barriers underlying side-chain dissociation and association. In recent years, both experiment and theory have brought to light the lubrication function of water.15-18 Does water only accelerate the molecular movements? And does acceleration just apply to hydrogen-bonded molecular machines? To examine the role played by water in a systematic fashion, a newly developed [2]rotaxane19 formed by a dibenzo[24]-crown-8 and an H-shaped axle containing two T-shaped benzimidazole groups and a 1,2-bis(pyridinium)ethane dicationic


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moiety, was investigated in the present contribution. According to Zhu et al., the [2]rotaxane represents an acid-base switchable molecular shuttle and can potentially be applied to the development of functional molecular machines. The nature of the movements in the rotaxane and the corresponding driving forces can be tuned up as a function of the environment. At low pH, the macrocycle shuttles between two benzimidazolium groups, whereas at high pH, stays in the middle of the axle, without shuttling. A preliminary molecular dynamics (MD) simulation indicates that for the latter, although no shuttling occurs, the ring rotates about the axle. To explore the effect of water on translational versus rotational movements, we have determined the free-energy landscapes characterizing the shuttling and rotary motions both in acetonitrile and in an acetonitrile-water mixture. Surprisingly, water is found to accelerate electrostaticallycontrolled shuttling at low pH, and to slow down rotation controlled by hydrophobic interactions at high pH. Deciphering the molecular mechanisms that underlie shuttling and rotation unveils the physical origin of the different roles played by the aqueous environment. SIMULATION DETAILS Movements and Transition Coordinate. The structure of the rotaxane investigated herein is depicted in Scheme 1. At low pH, the two benzimidazole groups can be protonated. In our preliminary simulations of the protonated rotaxane, four movements were observed, namely, (i) that of the macrocyclic wheel shuttled between the two benzimidazolium groups, (ii) a conformational change of the ring between a C and an S-shaped motif (see Figure 1), (iii) rotation of the ring around the axle, and (iv) spin of the T-shaped bulky stopper. Moreover, shuttling was found to be highly coupled with the conformational change, which constitute the primary movements in the rotaxane. Two coarse variables, ξ and C1, describing translocation and isomerization (defined in Figure 1A) were, therefore, chosen to form the transition coordinate. At


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high pH, the two benzimidazole groups were neutralized, leading to the disappearance of shuttling. The macrocyclic ring was found to reside in the middle of the 1,2bis(pyridinium)ethane moiety, rotating about the axle, accompanied by its conformational transition between a C and an S-shaped motif. The coarse variables θ and C2 were selected to characterize the rotary movement and the conformational change (see Figure 1B).

Scheme 1. Structure of the rotaxane investigated in this work (the two benzimidazole groups can be protonated at low pH). The free-energy landscapes characterizing the dynamic behavior of the rotaxane were generated using the recently developed extended adaptive biasing force (eABF)20, 21 method. The least free-energy pathways connecting the local minima of the two-dimensional free-energy landscapes were determined using the LFEP algorithm.22 Detail of the methodology is available in the Methods Section in Supporting Information. In addition, two different solvents were used


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to investigate the effect of the water on rotaxane motion, i.e., acetonitrile (anhydrous solvent), and acetonitrile mixed with 5% (vwater/vacetonitrile) water (hydrous solvent). The observation that the [2]rotaxane represents an acid-base switchable molecular shuttle was reported in acetonitrile.19 Furthermore, acetonitrile can ensure the solubility of the rotaxane and increase the association constant of the crown ether and the axle.23

Figure 1. Deﬁnition of the coarse variables. (A) For shuttling, two primary coarse variables (ξ, C1) are utilized to explore the putative transition pathways. ξ, extending from -12 to +12 Å, denotes the projection along the z direction of Cartesian space of the vector connecting the


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barycenter of the crown ether and that of the axle. V1 and V2 are defined as the projection onto the z-axle of the orientation of the benzo groups of the crown ether. C1 = ±2.4 Å indicate two Cshaped conformations. C1 = 0 Å indicates an S-shaped conformation. (B) For the rotary movement, θ and C2 are used to characterize the rotational angle of the macrocyclic ring and its conformational change, respectively. θ is the rotational angle of the macrocyclic ring about the H-shaped axle. C2 = ±2.4 Å indicate two S-shaped conformations. C2 = 0 Å indicates a C-shaped conformation. (C) Isomerization of the macrocyclic ring, S-shaped and C-shaped. RESULTS AND DISCUSSION Low pH environment Free-energy landscapes underlying the shuttling movement. Figure 2 depicts the twodimensional free-energy landscapes delineating shuttling of the crown ether in the protonated rotaxane in an anhydrous and a hydrous environment. In each case, two pronounced and symmetric low-energy areas appear around ξ = ±9.8 Å, namely the benzimidazolium sites, wherein two minima can be found at ξ = -9.8 Å, C1 = -2 Å (S1 or S1’), and ξ = +9.8 Å, C1 = +2 Å (S3 or S3’). In the corresponding structures shown in Figure 3, the macrocycle adopts a Cshaped conformation. The least free-energy pathways connecting these two minima represent the most reasonable transition path for the shuttling of the macrocycle between these two binding sites. Figure 2C shows the one-dimensional free-energy profiles for shuttling as a function of the position (s) along the least free-energy pathways, where s is an order parameter that varies between 0 and 1. From the result in the anhydrous solvent, the energy barrier to be overcome for shuttling is inferred to be equal to 21.4 kcal/mol, in very good agreement with the experimental measurement of 20.9 kcal/mol. The corresponding free-energy barrier in the hydrous solvent is


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estimated to be only 16.2 kcal/mol, much lower than that in the anhydrous solvent, thereby indicating that the rate of shuttling will be effectively increased. It can be concluded that water has a lubricating effect on the rotaxane motion.

Figure 2. Free-energy landscapes characterizing the shuttling and conformational change of the protonated rotaxane in acetonitrile (A) and in an acetonitrile-water mixture (B). (C) The black lines highlight the least free-energy pathways for shuttling. Free-energy changes for the shuttling movements in two different solvents as a function of the position (s) along the least free-energy pathways. s = 0.0 and s = 1.0 represent the locations ξ = -9.8 Å, C1 = -2.0 Å and ξ = +9.8 Å, C1 = +2.0 Å on the pathways, respectively. To provide an unambiguous explanation of the effect of water on the shuttling movement, variation of the electrostatic and van der Waals interactions of the axle-ring along the transition coordinate for the protonated rotaxane in acetonitrile are shown in Figure S1 in Supporting Information. Our results demonstrate that disruption of the electrostatic interactions constitutes the main factor for the emergence of free-energy barriers. Analysis of the MD trajectories indicates that the electrostatic interactions are composed of strong N－H…O hydrogen bonds formed by N－H moieties of the thread and oxygen atoms of the crown ether, together with iondipole interactions. Representative structures are shown in Figure 3. In hydrous solution, water


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molecule can form hydrogen bonds with the N－H group of the benzimidazolium moiety and with the oxygen atoms of the crown ether, thus weakening the axle-ring hydrogen-bonding interactions. The average number of hydrogen bonds formed between the macrocycle and the Tshaped benzimidazolium groups of the axle is provided in Figure S2 in Supporting Information. Moreover, water around the binding sites can also weaken the axle-ring ion–dipole interactions due to its high polarity. Variations of the electrostatic interactions of the rotaxane and the solvents along the transition coordinate are shown in Figure 3. These interactions are found to become energetically more favorable upon addition of a small amount of water, which is manifested around the two ridges (ξ = ±7.5 Å) of the free-energy surface of Figure 2. This result can be rationalized by the formation of hydrogen bonds between water, on the one hand, and both the N－H moieties of the thread and the oxygen atoms of the crown ether, on the other hand. These favorable interactions compensate for the energy dissipated in the disruption of the hydrogen bonds between the axle and the ring. As a result, the free-energy barrier against shuttling between the two benzimidazolium stations is sharply reduced. It can, therefore, be concluded that water plays a lubrication role, in line with previous observations in biological and abiological machines consisting of hydrogen-bonded components.7,13


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Figure 3. Representative structures during shuttling in acetonitrile (A) and in an acetonitrilewater mixture (B). Upper right panel: Hydrogen bonds formed among the benzimidazolium groups, the crown ether and the water molecules. Only the closest water molecules are shown. Lower right panel: Variation of the electrostatic interactions of the rotaxane and the solvents along the transition coordinate formed by ξ and C1, for the protonated rotaxane in acetonitrile and in an acetonitrile-water mixture.

High pH environment


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At high pH, the two benzimidazole moieties are neutralized. To investigate whether these moieties are still the binding sites for the macrocycle, the same free-energy landscapes for the shuttling were determined under these premises, as shown in Figure 4. In sharp contrast with the free-energy landscapes obtained at low pH (see Figure 2), the two benzimidazole groups (ξ = ±9.8 Å) are no longer energetically favorable sites. Instead, the S-shaped macrocycle binding with the 1,2-bis(pyridinium)ethane group, corresponding to the structure at the global minimum (ξ = 0 Å, C1= 0 Å), is found to be much more stable. This result implies that shuttling between the two benzimidazole groups is very unlikely to occur. Moreover, Figure 4A and B appear to be almost identical, suggesting that water does not alter the propensity towards shuttling at high pH. In addition, the basin spanning -2.3 ≤ C1 ≤ +2.3 Å indicates that when located in the middle of the 1,2-bis(pyridinium)ethane axle, the crown ether could isomerize between the S-shaped (C1 = 0 Å) and C-shaped (C1 = ±2.3 Å) motifs. This conformational transition may accompany the rotation of the macrocycle about the axle.

Figure 4. Free-energy landscapes characterizing the shuttling movement and the conformational change of the rotaxane in acetonitrile (A) and in an acetonitrile-water mixture (B). Free-energy landscapes for the rotary movement. Similar to the rotaxane designed by Leigh and coworkers,12 the rotary movement of the crown ether was found to be coupled with a


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conformational change. Just like in the theoretical framework put forth by Liu,24 we selected two coarse variables, θ and C2, defined in Figure 1, to describe these two movements, respectively. To examine the effect of water on the latter, two-dimensional free-energy maps were generated along the transition coordinate formed by θ and C2, in anhydrous and hydrous solvents, as depicted in Figure 5. Both free-energy maps are found to feature two basins at the position near C2 = ±2.3 Å, namely the 1,2-bis(pyridinium)ethane site, wherein two minima are located at C2 = -2.3 Å, θ = -92.5 º (S1 or S1’), and C2 = +2.3 Å, θ = +92.5 º (S4 or S4’). In addition, the macrocycle adopting a C-shaped conformation is found at two metastable states (appear around C2 = 0 Å). The least free-energy pathways connecting the minima are determined along which the representative structures along these pathways are shown in Figure S4 in Supporting Information, illuminating that the conformation of the macrocycle undergoes a transition from an S-shaped to C-shaped motif, and then returns to the former. Figure 5C depicts the one-dimensional free-energy profiles for the rotary motion as a function of the position (s) along the least free-energy pathways. Interestingly, the variation of the energy barrier in the anhydrous and hydrous solvents amounts to 4.3 and 5.6 kcal/mol, respectively. The energy barrier becomes higher upon addition of a small amount of water, demonstrating that latter plays a damping role.


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Figure 5. Free-energy landscapes characterizing the rotary movement and conformational change of the rotaxane in acetonitrile (A) and in an acetonitrile-water mixture (B). The black lines highlight the least free-energy pathways for rotation. (C) Free-energy changes for the rotary movements in two different solvents as a function of the position (s) along the least free-energy pathways. s = 0.0 and s = 1.0 represent the locations C2 = -2.3 Å, θ = -92.5 º and C2 = +2.3 Å, θ = +92.5 º on the pathways, respectively. To shed new light into the nature of this phenomenon, the axle-macrocycle interactions were decomposed into van der Waals and electrostatic contributions, as shown in Figure S5 in Supporting Information. It can be seen that van der Waals interactions constitute the dominating force for the rotary movement, notwithstanding the strength of the electrostatic interactions. Further analysis indicates that the interactions of the wheel with the 1,2-bis(pyridinium)ethane moiety consist of (i) C－H…O hydrogen bonds, much weaker than N－H…O, (ii) N+…O ion－ dipole interactions, and (iii) π-stacking interactions of the aromatic rings of the crown ether and the electron-poor pyridinium rings. The contribution of the π-stacking interactions is mirrored in the van der Waals term of Figure S5B in Supporting Information. It is well known that π-π stacking interactions are strengthened by the addition of a small amount of water,25 which can be ascribed to the solvophobic effect of π-π stacking interactions.26 The noteworthy damping role of water, therefore, be intuitively explained by the stronger π-π stacking interactions at play. It is not unreasonable to extend this conclusion to hydrophobic interactions. CONCLUSION The solvent properties, such as the polarity, the hydrogen-bond donor and acceptor ability, and the size of the solvent molecule may have an influence on the molecular movement of the


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rotaxane.13 From this perspective, water is particularly unique. In the present contribution, the effect of water on the motion of rotaxanes has been explored in distinct environments. For shuttling at low pH primarily controlled by electrostatic interactions, the energy barrier to be overcome is decreased upon addition of a small amount of water, cogently demonstrating the lubricating role of water. While for the rotary movement of the macrocycle at high pH chiefly controlled by hydrophobic π-π interaction, the addition of water results in a higher energy barrier, thereby proves the damping role of water. We also extend our investigation to shuttling in the presence of a large fraction of water. As expected, increasing the aqueous content to 50% further reduced the free-energy barrier against shuttling. Interestingly enough, in doing so, the 1,2-bis(pyridinium)ethane moiety became to be the most stable station, instead of the two benzimidazolium groups. This result implies that water can act not only as a “lubricant”, but also as an external stimulus to switch off shuttling (detailed information is provided in Figure S6 in Supporting Information). Utilizing the unique properties of water, shuttling and rotation of the macrocycle can be finetuned as a function of the dominating force in the rotaxane. They may also be adjusted through the fraction of water in the solvent. A large amount of water may cause the movement to be switched off. The present results offer a broadened view of the subtle effects of water on supramolecular assemblies, while providing the theoretical basis for the design of tailored, watercontrolled molecular engines. In addition, our investigation provides a proof of concept for smart, versatile molecular machines, capable of performing complex tasks. ASSOCIATED CONTENT Supporting Information


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Methods, simulation details, variation of the electrostatic and van der Waals interactions of the axle-ring in the shuttling process for the protonated and nonprotonated rotaxanes in acetonitrile, distribution of hydrogen bonds formed between the macrocycle and the T-shaped benzimidazolium groups of the axle in acetonitrile and in an acetonitrile-water mixture, variation of the electrostatic and van der Waals interactions for the rotary movement in the rotating process for the nonprotonated rotaxane in acetonitrile, representative structures of the rotary movement in acetonitrile and acetonitrile-water, detailed information about the shuttling movement in a large amount of water. This material is available free of charge via the Internet at http://pubs.acs.org.

AUTHOR INFORMATION Corresponding Authors *

E-mail: [email protected]. (W.C.)

Notes The authors declare no competing financial interest.

ACKNOWLEDGMENTS This study is supported by National Natural Science Foundation of China (Nos. 21373117 and 21773125). The Special Program for Applied Research on Super Computation of the NSFCGuangdong Joint Fund (the second phase) under Grant No. U1501501 and the CINES, Montpellier, France, are gratefully acknowledged for provision of generous amounts of CPU


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time. The authors acknowledge support from the Centre National de la Recherche Scientifique through an integrated program of scientific cooperation (PICS) with China. REFERENCES (1) Fecko, C. J.; Eaves, J. D.; Loparo, J. J.; Tokmakoff, A.; Geissler, P. L. Ultrafast HydrogenBond Dynamics in the Infrared Spectroscopy of Water. Science 2003, 301, 1698-1702. (2) Cowan, M. L.; Bruner, B. D.; Huse, N.; Dwyer, J. R.; Chugh, B.; Nibbering, E. T. J.; Elsaesser, T.; Miller, R. J. D. Ultrafast Memory Loss and Energy Redistribution in the Hydrogen Bond Network of Liquid H2O. Nature 2005, 434, 199-202. (3) Chi, X.; Yu, G.; Shao, L.; Chen, J.; Huang, F. A Dual-Thermoresponsive Gemini-Type Supra-amphiphilic Macromolecular [3]Pseudorotaxane Based on Pillar[10]arene/Paraquat Cooperative Complexation. J. Am. Chem. Soc. 2016, 138, 3168-3174. (4) Raschke, T. M. Water Structure and Interactions with Protein Surfaces. Curr. Opin. Struct. Biol. 2006, 16, 152-159. (5) Dirama, T. E.; Carri, G. A.; Sokolov, A. P. Coupling between Lysozyme and Glycerol Dynamics: Microscopic Insights from Molecular-Dynamics Simulations. J. Chem. Phys. 2005, 122, 244910. (6) Bizzarri, A. R.; Cannistraro, S. Molecular Dynamics of Water at the Protein−Solvent Interface. J. Phys. Chem. B 2002, 106, 6617-6633. (7) Singharoy, A.; Chipot, C.; Moradi, M.; Schulten, K. Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V-Type ATPases. J. Am. Chem. Soc. 2017, 139, 293-310.


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Water-Controlled Switching in Rotaxanes

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