Theoretical Study on Conformation Dynamics of Three-Station

Article pubs.acs.org/JPCA

Theoretical Study on Conformation Dynamics of Three-Station Molecular Shuttle in Different Environments and its Influence on NMR Chemical Shifts and Binding Interactions Pingying Liu,†,‡ Wei Li,† Li Liu,† Leyong Wang,† and Jing Ma*,† †

School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing 210093, People’s Republic of China ‡ School of Materials Science and Engineering, Jingdezhen Ceramic Institute, Jingdezhen 333403, China S Supporting Information *

ABSTRACT: Microscopic information on conformational flexibility and macrocycle−thread binding interactions is helpful in rational design of novel multistation molecular shuttles with interesting topology and functions. Molecular dynamics (MD) was applied to simulate conformational changes of thread and macrocycle of a three-station molecular shuttle in different chemical environments (vacuum, CD3CN-CDCl3 solution, and crystal). In contrast with the highly distorted thread conformation in the gas phase and nonpolar CDCl3 solution, the solvated thread in CD3CN-CDCl3 (1:1) mix solvents exhibited a relatively rigid structure. Experimental observations of preferential binding at the protonated dibenzylammonium group (station I) were rationalized by quantum chemical calculations of macrocycle−thread binding energies at three different stations. The orthogonality of site-specific binding interactions at three different stations was also revealed by the nearly constant binding energy obtained at each specific recognition center with the replacement of different neighboring groups and terminal stoppers on the thread. Conformational flexibility has little effect on NMR signals of binding sites, but for some protons that are close to the solvent molecules in the first solvent shell, their chemical shifts are sensitive to the local electrostatic environment caused by nearby solvents. In crystal, π stacking induced evident upfield shifts of NMR signals in comparison with the isolated monomer.

1. INTRODUCTION The stimuli-responsive molecular shuttles have received considerable attention due to their potential applications in the creation of artificial molecular machines and electronic devices for information storage and processing, energy harvesting, targeted delivery, and transport, etc.1−5 As shown in Figure 1, a molecular shuttle, also called a rotaxane, usually consists of a dumbbell-shaped thread and the interlocking macrocyclic component(s). Various external stimuli (radiation, temperature, pH-variation, etc.) have been used to control the relative motion of the macrocycle along a rod. In order to prevent the escape of the macrocycle, two bulky stopper units are used to cap the two ends of thread. The last decade witnessed rapid expansion of various interesting interlocked molecular architectures with controllable binding sites (stations), reversible shuttling behavior, and even rate-tunable properties.6−20 Control of the sophisticated ringthread interactions under different chemical environments lies at the heart of rational design of those novel molecular shuttles with desired functions and activities. Some general relationship of the site-specific interactions has been recognized on the basis of numerous experimental and theoretical calculations.21−24 Relative displacements and binding positions of the macrocycle © 2014 American Chemical Society

on thread can be detected by a variety of techniques, such as NMR, absorption and emission, and electrochemical spectroscopy. For the complicated rotaxane systems in solution, however, it is hard to unambiguously assign those spectra due to the conformational flexibility of rotaxane and subtle perturbations from the surrounding solvent molecules. In this aspect, theoretical computations are hence useful to assign the main spectroscopic features and to understand the role of various noncovalent (hydrogen-bonding, cation-π, and π−π) interactions played in the stabilization of the encircled coconformations of molecular shuttles. Computational modeling of NMR chemical shifts with quantum chemical models has seen a marked increase in both accuracy and affordability.25−36 Density functional theory (DFT) has been widely applied to predict proton chemical shifts in various chemical systems. MP2 (second-order Møller− Plesset) perturbation theory was also used to understand the Special Issue: International Conference on Theoretical and High Performance Computational Chemistry Symposium Received: February 27, 2014 Revised: June 4, 2014 Published: July 21, 2014 9032

dx.doi.org/10.1021/jp5020516 | J. Phys. Chem. A 2014, 118, 9032−9044

The Journal of Physical Chemistry A

Article

Figure 1. Schematic illustration of the three-station molecular shuttle, [2]rotaxane, with three recognition sites, protonated dibenzylammonium (DBA+, station I), urea (station II), and phosphine oxide (station III), respectively.

systematic investigation is highly desired to understand the selective recognition and variations in NMR spectra with the changes in coconformations and binding interactions in different solutions. In the present work, we will study a newly developed threestation molecular shuttle,45 shown in Figure 1, by using both quantum chemical calculations and MD simulations. There are three functional moieties (stations) on the thread at which the macrocycle can contact through hydrogen-bonding interactions. In the experiment, the macrocycle can be shifted from the protonated dibenzylammonium (DBA+) unit (called station I) to the urea site (station II) by means of base addition. By addition of acetate anions (Ac−) to the neutral rotaxane, the wheel can be further shifted from station II to the phosphine oxide group (station III). The purpose of this work is 3-fold: (1) to study the conformational flexibility of rotaxane in different environments (vacuum, solution, crystal); (2) to elucidate differences in binding strength of macrocycle at three different stations on thread; and (3) to explore the environmental effect on 1H NMR signals of the molecular shuttle. The general picture drawn at the atomistic level for site-specific interactions and conformational flexibility is a basis for the future construction of switchable molecular machines.

nature of noncovalent interactions. With the addition of explicit solvent molecules, modeling of conformational changes and the shuttling process of solvated rotaxane needs the employment of molecular dynamics (MD) simulations. Car−Parrinello MD simulations were carried out to generate the conformation ensemble for NMR chemical shift calculations for liquid water and solvated amino acids in water clusters, achieving good agreement with the experimental spectra.29,30,36 However, ab initio MD simulations are too computationally expensive to be affordable for a real solvated rotaxane system with thousands of atoms. In this context, the combination of force field based MD conformational sampling and DFT calculations of NMR chemical shift is a compromise for reproducing experimental NMR spectra of molecular shuttles. To rationalize the experimentally detected upfield shift for methylene protons from the free to interlocked station, Zazza et al. simulated the 1 H NMR chemical shifts for a molecular shuttle under experimental conditions by using MD simulations with the Gromos96 force field and DFT-based computations.35 With an emphasis on the solvent-dependent conformational flexibility, Naresh K. Jena et al. performed a MD study on the diketopyrrolopyrrole-based [2]rotaxane in the TIP3P water environment or in chloroform and DMSO solvents (which were treated by an amber force field).37 MD simulations were also successfully adopted in visualizing the behavior and configuration of the absorbed fumaramide [2]rotaxane film on Ag(111) and Au(111) substrates.38 Until now, most theoretical simulations were focused on dual station [2]rotaxanes with two switchable binding sites (stations) on thread, although several tristable molecular shuttles were recently created with three different stations.39−45 The existence of three binding units on the long thread adds the complexity of the subtle noncovalent interactions between the macrocycle and the different stations, especially when the explicit solvent molecules are involved. To build the sitespecific interaction relationship for three-station [2]rotaxanes, a

2. COMPUTATIONAL DETAILS DFT calculations of binding interactions and NMR signals were performed using the Gaussian 0946 with a 6-31G (d, p) basis set. Six different kinds of functionals, B3LYP, CAM-B3LYP, PBEPBE, mPW1PW91, M06-2X, and WB97X-D, respectively, were applied in the calculations. Some related references for those functionals were presented in the Supporting Information. The DFT-based 1H NMR chemical shifts, δ, were computed by using gauge invariant/including atomic orbital (GIAO) method.47−51 To test the applicability of various DFT functionals in describing the nonbonded interactions in the interlocked system, MP2 binding energies were also computed 9033



Article

Figure 2. (a) Electrostatic potential maps (isovalue: 0.0004 au) of macrocycle and thread models with three different binding sites, stations I, II, and III(III′), respectively. (b) The BSSE-corrected GEBF-MP2 binding energies, Eb‑MP2, and the difference of DFT binding energies using different functionals, Eb‑DFT, with respect to the GEBF-MP2 results.

nonbonded van der Waals and Coulomb interaction were treated using the atom-based and Ewald truncation methods, respectively, and the cutoff distances for both nonbonded interactions were set to be 15.5 Å. The equations of the motion were integrated by the velocity Verlet algorithm78 with a time step of 1 fs. All MD simulations were carried out by using the Discover module of Materials Studio.79

by using the generalized energy-based fragmentation (GEBF) method.52−55 The strength of hydrogen bonding, cation−π, and π−π interactions were estimated by using natural bond orbital (NBO)56−62 analysis. To simulate the conformational changes of [2]rotaxane in solution, MD simulations of a single solute molecule solvated in CD3CN and CDCl3 solvent molecules were carried out in the canonical (NVT) ensemble with a periodic boundary condition (PBC). The cubic PBC box, whose length is about 69.3 Å, included 1777 CD3CN and 1223 CDCl3 solvent molecules, respectively, leading to a density of 1.13 g/cm3. Table S1 of the Supporting Information gave more details for simulation models. The selection of a suitable force field is a key to the application of classical MD simulation. In our previous work, three kinds of force fields (i.e., CVFF, PCFF, and COMPASS) were tested on a similar encircled system with a proton encapsulated inside the macrocycle with and without the external electric field.63 Replacement of the default charges in PCFF64−67 by DFT-based NBO charges gave similar results to that from a MP2 approach.63 We also applied PCFF to study the packing structures of the π-conjugated molecules in amorphous phases, solutions, and interfaces.68−76 PCFF is also employed in the present MD simulations of the molecular shuttle binding at different stations. The temperature was controlled at 298.15K by using an Andersen thermostat.77 The

3. RESULTS AND DISCUSSION 3.1. Binding Interactions at Different Stations. The control of macrocycle motion along the thread depends on the site-specific interactions at different stations. To reveal the main driving forces responsible for the site-specific recognition, molecular electrostatic potential maps were drawn in Figure 2a to display the electron-deficient (proton donor, D) and electron-rich (proton acceptor, A) groups in macrocycle and threads. The electrostatic potential of the isolated macrocycle (thread) was computed with the geometry taken from the optimized structures of the interlocked rotaxane at the M062X/6-31G (d, p) level. It can be seen from Figure S1 of the Supporting Information that the electrostatic picture of electron-rich or -deficient groups is not changed much when the conformation changes along MD trajectory. We are interested in several different thread models, representing the contact of macrocycle with three different 9034



Article

Figure 3. Calculated binding energies, Eb, of the DBA+-, urea-based, and phosphine oxide-based pseudorotaxanes and [2]rotanxanes.

much loss of accuracy, the linear-scaling generalized energybased fragmentation (GEBF) method52−55 was employed to make MP2 calculations feasible for the large-sized system. The central idea of the GEBF method is to decompose the largesized system into small fragments and to obtain energy and properties of the whole molecule from a combination of those of subsystems. The BSSE-corrected binding energies for the macrocycle binding at different stations were computed by using the GEBF-MP2 method with the lower scaling quantum chemistry (LSQC) package.83 In the GEBF calculations, to build the subsystem, the distance threshold for fragmentation is set as 3.5 Å. For macrocycle attaching at station I, the central unit (NH2+) of the protonated DBA group and the counterion, PF6−, were taken as two fragments in the GEBF-MP2 calculations, respectively. Figure 2b listed the calculated GEBF-MP2 binding energies, Eb‑MP2, with a 6-31G (d, p) basis set. Among the three binding sites on the thread, the macrocycle−thread binding interaction at station I is the strongest, which is in good agreement with the experimental observations of the preferential binding at the DBA+ group.45 It should be mentioned that the preference of binding at station II over station III (without acetate anion) cannot be directly seen from the calculated binding energies. This implies that the selective binding at station II may be not only a thermodynamically controlled but also a kinetically controlled process. DFT calculations using B3LYP, CAM-B3LYP, PBEPBE, mPW1PW91, M06-2X, and wB97X-D functionals gave quite different results from each other. The optimized geometries with six different functionals for the interlocked shuttle at three stations demonstrate some differences (Figure S2 of the Supporting Information). As shown in Figure S2 of the Supporting Information, the optimized geometries with M062X and WB97X-D functionals take a more folded conformation (with smaller bending angle, θ) than the other four functionals. Computations of the binding energies for nonbonded subsystems, which are held mainly by the hydrogen bonding, cation−π, and π−π interactions, require the specific functionals designed for the weak noncovalent interactions. Taking the GEBF-MP2 binding energy as a reference, Figure 2b also shows derivations of DFT values, Eb‑DFT, calculated with six different functionals. Most of the selected DFT functionals gave

binding sites, stations I, II, and III (III′), respectively. Among the studied thread models, the protonated amino −NH2+- unit (station I) in the DBA+ group has the strongest proton donating ability, making it easy to be paired with the electronrich polyether chain (proton acceptor) in the macrocycle. Figure 2a also indicates that the proton-donating ability of the neutral amino −NH-group of urea (station II) is significantly reduced in comparison to that of station I (bearing with the −NH2+ center). Fortunately, the carbonyl (CO) unit in the same urea group works as a weak proton acceptor with some electron-rich character, which interacted with the weak donating amino units in the head of the macrocycle. Ongoing to the other end of the thread, the phosphine oxide group (station III) can act as a proton acceptor (A) with evident negative electrostatic potential. The energetically favorable binding of station III with the upper amino units (D) in the ring is hence expected to stabilize the molecular shuttle when the macrocycle resides over this station. One may also find that the proton accepting ability of the terminal phosphine oxide group was not affected much with (III′) and without (III) protonation. 3.1.1. Binding Energies. To evaluate the relative binding strength of macrocycle with respect to different recognition regions on the thread, the binding energy, Eb, is calculated by using the following expression, E b = Ethread + macrocycle − Ethread − Emacrocycle

(1)

where Ethread+macrocycle is the total energy of the interlocked molecular shuttle, and the individual energies of macrocycle and thread are described by Ethread and Emacrocycle, respectively. A more negative value of Eb means a stronger binding interaction between the ring and rod in a molecular shuttle. The basis set superposition error (BSSE)80 was computed by the counterpoise method81,82 at different theoretical levels. The MP2 method was often used to gain reasonable predictions on the noncovalent interactions. However, for the investigated molecular shuttle system [with basis functions of 1688, 1574, 1649, and 1729, respectively, for binding at stations I, II, III, and III′ at the level of 6-31G (d, p)], the computational demanding of the conventional MP2 method is quite formidable. To reduce the computational cost without 9035



Article

ring)]. The total stabilization energy of these two kinds of hydrogen-bonding interactions at station II is about 17.4 kcal/ mol. The N−H···OP hydrogen-bonding interactions between the phosphine oxide group of thread and the upper amino unit of the macrocycle holds the macrocycle residing at station III (III′), with the stabilization energy of about 9.9 kcal/mol (10.2 kcal/mol for III′). In addition, the NBO analysis based on the extracted snapshots from 1 ns MD simulations of three stations shows there is a strong N+H···π interaction (∼16.9 kcal/mol) between macrocycle and thread for station I. And for stations II and III, π−π interactions (∼2.8 kcal/mol) also contributed to the macrocycle−thread interactions. 3.2. Conformational Flexibility: MD Simulations. Conformational changes of the interlocked [2]rotaxane, with or without solvent molecules moving around it, were investigated by MD simulations. To illustrate the conformational changes of thread and macrocycle in different media, several structural parameters are defined in Table 1. In fact, the

significant underestimations of binding strength (by 20−60%), except for M06-2X and WB97X-D. M06-2X binding energy is quite close to the GEBF-MP2 result, but WB97X-D overestimates the binding energy by 20−30%. Thus, M06-2X was used to study variations in binding energies of the interlocked [2]rotaxane (binding at station I) in solution along the MD trajectory (Figure S1 of the Supporting Information). Ten energetically low-lying conformations were selected from the 1 ns MD simulation. As shown in Figure S1 of the Supporting Information, the macrocycle−thread binding interaction is rather strong in solution with slight fluctuations of Eb values among these conformations. The binding strength in the solvated molecular shuttle is also comparable to that calculated with the crystal structure. To further test the generality and orthogonality of sitespecific binding interaction in those [2]rotaxanes with the same macrocycle, three pseudorotaxanes without ending stoppers, bearing with the similar recognition centers, were also studied with the optimized structures shown in Figure S3 of the Supporting Information. Figure 3 compares the BSSE corrected binding energies at the GEBF-MP2/6-31G(d, p) level of these three pseudorotaxanes with the similar binding sites as stations I, II, and III in [2]rotaxane. Identical to the above-mentioned results for the molecular shuttle, the binding strength of the DBA+-based pseudorotaxane is stronger than those of the urea and phosphine oxide based pesudorotaxanes. The calculated binding energies of pesudorotaxanes correlated well with the experimentally determined association constant, Ka.12,14,45 The calculated binding energies of pseudorotaxane are close to that of [2]rotaxane when it is interlocked at the same binding site (station I: −50.9 vs −54.5 kcal/mol; station II: −34.7 vs −37.5 kcal/mol; and station III: −31.4 vs −46.8 kcal/mol). It means that the binding interactions between the macrocycle and different recognition sites (DBA+, urea, and phosphine oxide groups) are orthogonal to each other, and the calculated binding strength is insensitive to the neighboring groups and terminal stoppers. Such general binding selectivity can be applied to design some new multistation shuttles by elegantly aligning the orthogonal recognizing groups in a thread. 3.1.2. NBO Analysis of Intermolecular Orbital Interactions. The formation of hydrogen-bonding interactions at station I, in virtue of the favorable donor−acceptor pairing, can be further demonstrated by the natural bond orbital (NBO) second-order perturbation analysis56−62 at M06-2X/6-31G(d, p) level. The strength of the interaction between unperturbed donor φ(0) i (e.g., a valence lone pair) with acceptor φ0j* (e.g., a valence antibonded) can be obtained by the following equation: (0) (0) 2 (0) (0) ΔE i(2) → j * = − 2⟨φi |F|φj * ⟩ /(εj * − εi )

Table 1. Structural Parameters for Molecular Shuttle Binding at Station I, with the Geometries Taken from M062X/6-31G (d, p) Optimization in Gas Phase, MD EnsembleAveraged in CD3CN-CDCl3 Mix Solvents, and Crystal Structure, Respectively

thread L (Å) L1 (Å) θ (deg) macrocycle W1 (Å) W2 (Å)

(2)

Table S2 of the Supporting Information illustrates energies for orbital interactions between donor and acceptor in the molecular shuttle. The binding of the macrocycle at station I is stabilized by hydrogen bonds between the protonated amino unit of thread and the polyether chain in the ring, with the stabilization energy, E(2), of about 17.5 kcal/mol. There is evident electron delocalization from the donating orbital, oxygen lone pair orbital, nO, to the electron-accepting antibonding σN−H* orbitals or σC−H*. Station II binds with the ring through two kinds of hydrogen bonds [i.e., N−H···O binding (between the −NH-group and the lower polyether chain of macrocycle) and the N−H···OC interaction (between the carbonyl group and upper amino group in the

gas phase

mix solvents

crystal

13.9 8.0 87.4

18.7 10.2 111.8

15.5 8.5 94.7

10.9 7.0

12.1 7.4

11.0 7.3

dumbbell-shaped thread takes a bent (folded) conformation. To illustrate the bent degree of thread, the bent angle, θ, is defined as an angle between P−N and N−C bonds. The endto-end length, L, is estimated from the distance between the P atom of phosphine oxide group (station III) and the C atom of the terminal 3,5-dimethylphenyl group (stopper) on the thread. The parameter, L1, is used to denote the length of thread “arm”, which is measured as a distance from the P atom to the central atom of DBA group (station I). For the macrocycle, parameters, W1 and W2, were adopted to illustrate the cavity size of the ring. The value of W1 is the distance between the C atom (of 2,6-pyridinediamide) and the O atom (of polyether 9036



Article

Figure 4. Schematic illustration of conformation dynamics and MD trajectories of noncovalent bonding distances and bent angle, starting from different initial geometries when the macrocycle was laid on the position (a) between stations III and I and (b) between stations I and II.

chain), and W2 is the separation between two centriods of aromatic rings in the macrocycle. As shown in Table 1, the optimized geometry of the isolated molecular shuttle in gas phase shows a rather bent thread with an end-to-end length, L = 13.9 Å, shorter than that (24 Å) of the fully extended rod. When the macrocycle is interlocked with thread at station I, in fact, there are two nearly energetically degenerate configurations, which are different from each other in the orientation of the 2,6-pyridinediamide group (called “head”) of macrocycle, as illustrated in Table 1. The small energy difference (0.37 kcal/mol) between these two conformations shows the possibility of free swinging of the macrocycle head. In spite of two different orientations of ring head, little impact on the calculated 1H NMR signals was found for the molecular shuttle (as shown in Figure S4 of the Supporting Information).

In order to study the solvent influence on the conformational flexibility of molecular shuttle, MD simulation was then carried out on a solvated molecular shuttle in CD3CN and CDCl3 mix solvents. The MD-averaged structural parameters in CD3CNCDCl3 mix solvents were listed in the third column of Table 1. In comparison with the highly folded geometry of isolated molecule in gas phase (with θ = 87.4°), the skeleton of the molecular shuttle interlocked at station I is surprisingly less bent (with θ = 111.8°). A closer look at the superimposed conformations (extracted at every 20 ps from 50 snapshots) in Table 1 further displayed the evident solvent-triggered swing motions of macrocycle “head” and roll of benzene rings of thread stoppers. As shown in Figure S5 of the Supporting Information, MD simulations for the molecular shuttle, with and without nonpolar CDCl3 solvent molecules, were carried out for comparison to the situation of using the CD3CN− CDCl3 (1:1) mix solvents. It is interesting to find that 9037



Article

Figure 5. Schematic illustration of conformation dynamics and MD trajectories of noncovalent bonding distances and bent angle, starting from different initial geometries when the macrocycle was laid on the position (a) around station II and (b) between station II and the end of the thread.

fluctuations of geometrical parameters in the CD3CN−CDCl3 mix solvents are all smaller than those with and without CDCl3 solvents. Further analysis on the selected snapshots (which were sampled at 313, 544, 748, and 983 ps, respectively) in different solvent environments shows that the alkyl chain of thread has distinct conformational changes in the CDCl3 solvents relative to that in the CD3CN−CDCl3 mix solvents. Especially, the end-to-end distance, L, undergoes dramatic changes in the CDCl3 solvents within a broad range of 18−24 Å. This indicates that the CD3CN−CDCl3 mix solvent environment plays an important role in stabilizing the interlocked molecular shuttle by depressing the conformation variations of the thread. In the last column of Table 1, structural parameters of a monomer in crystal were also given for comparison. The skeleton of thread demonstrates a deeper folding in crystal than that in solution (with θ = 94.7° vs 111.8°). Different from the flexible thread, the macrocycle is rather rigid with nearly constant size, no matter in what environment.

In addition, a series of MD simulations were performed with the macrocycle residing over different initial positions on the thread. When the macrocycle is slightly moved away from the binding position (e.g., station I) toward the two ends, in left and right directions, respectively, the resultant interlocked states at intermediate positions (denoted by III/I and I/II) are energetically less stable. MD trajectories displayed that starting from those intermediate positions (III/I and I/II), the macrocycle can move back quickly (within 3 ps) to station I (Figure 4). The facial formation of N+−H···O hydrogen bonds between protonated amino hydrogen of DBA+ group in thread and oxygen of diethylene glycol group in macrocycle is evidently shown from the immediate appearance of short hydrogen-bonding distances of N+−H···O of about 2 Å in both III/I → I (Figure 4a) and I/II → I (Figure 4b) MD processes. During the III/I → I evolution (Figure 4a), the macrocycle is not solely held by the N+−H···O hydrogen bonds at all time. Since there are two aromatic rings in the investigated macrocycle, it is also possible to form a N+−H···π interaction, 9038



Article

Figure 6. Schematic illustration of conformation dynamics and MD trajectories of noncovalent bonding distances and bent angle, starting from an initial geometry when the macrocycle was laid on station III.

Table 2. Calculated [at the M06-2X/6-31G (d, p) Level] and Experimental 1H NMR Chemical Shifts, δ, of the Free Thread and Macrocycle and their Variations, ΔδStationI Locked , upon Interlocking of Macrocycle and Thread at Station I

δ (ppm) proton (moiety) threadopen‑end 8(Ar−H) 9(−CH2) 10(−NH) 11(Ar−H) threaddumbbell 8(Ar−H) 9(−CH2) 10(−NH2+) 11(Ar−H) macrocycle 24 (−OCH2) 25 (−OCH2) 26 (−OCH2) a

gas

MD

Solu.

I Δδstation locked (ppm) a

(exp )

8.44 3.78 0.62 8.23

8.52 4.00 0.12 8.17

(7.27) (3.68) (4.13) (7.10)

9.00 4.55 5.52 7.74

8.48 4.84 4.38 8.55

(7.24) (4.08) (7.54) (7.29)

4.46 3.68 3.63

5.46 (4.41) 4.01 (3.53) 4.19 (3.53)

crystal

gas

Solu.MD (expa)

crystal

−0.82 +1.55 −6.64 +0.32

+0.08 +1.05 −5.12 +0.07

(+0.32) (+1.18) (−3.07) (+0.15)

6.31 1.32 −0.74 5.49

−0.26 +2.32 −1.74 −0.17

+0.04 +1.89 −0.86 +0.45

(+0.29) (+1.58) (+0.34) (+0.34)

−0.39 +2.25 −1.12 +0.38

0.82 0.01 −0.30

−0.14 −0.48 +0.24

+0.84 (+0.20) −0.03 (−0.05) +0.17 (+0.23)

−0.27 +0.02 +0.90

The experimental data taken for ref 45.

whose bonding distance is estimated from the separation between the protonated amino hydrogen of the DBA+ group in the thread and the centroid of the aromatic ring in the macrocycle. Although the strength of the N+−H···π interaction (2 kcal/mol predicted by NBO analysis in vacuum, 11 kcal/mol

in average for solvated conformations) is much weaker than that (32.7 kcal/mol in vacuum, ∼20 kcal/mol in solution) of N+−H···O hydrogen bonding, such a cation−π interaction competes with the hydrogen bond interactions, rendering the macrocycle ceaselessly moving up and down over the station I. 9039



Article

Figure 7. Calculated 1H NMR chemical shifts and electrostatic potential maps (isovalue: 0.0004 a.u.) for molecular shuttle binding at station I at the M06-2X/6-31G (d, p) level, with (a) PCM, and cluster models, (b) including two CH3CN and two CHCl3 solvent molecules with background point charges, (c) two CH3CN solvents with background point charges, and (d) two CH3CN solvents without background point charges.

When the macrocycle is slightly pulled away from station II, the interlocked macrocycle shows some tendency to move to the more favorable binding site, station I, but finally, the N− H···OC hydrogen bonding interaction with the urea group is strong enough to draw the macrocycle back to station II (i.e., II → I/II → II process in Figure 5a). The translation of macrocycle nearby station II permits the coexistence of the competing N−H···OC hydrogen-bonding interaction and the π−π interaction (which is measured as a separation between the center of the aromatic ring on the thread between DBA and the urea group and the center of the aromatic ring of the macrocycle). In comparison with the above-mentioned hydrogen-bonding interactions and cation−π interaction, the π−π interaction (of about 2.8 kcal/mol in solution) is the weakest, making such an “intermediate” state only last a very short time period during MD simulations. The macrocycle is also hard to escape far away from station II, even when the initial ring position is set close to the end stopper (labeled as II/end, Figure 5b). When the macrocycle resides over station III, MD simulation gave a similar picture of competing hydrogen-bonding interaction and π−π interaction, as shown in Figure 6. It is also interesting to note from Figures 4−6 that the perpendicular movement of the interlocked macrocycle induced the significant conformational changes with bent angle θ changing from 30° (Λ- or U-shaped) to 180° (linear rod). In accompanying the horizontal shifting of the macrocycle along

the thread, the ring also rotated around the thread for achieving favorable hydrogen-bonding interactions. 3.3. NMR Chemical Shifts: Solvent Models and Crystal Stacking Effect. To test the influence of the choice of DFT functionals on the calculated chemical shifts, six different functionals, B3LYP, CAM-B3LYP, PBEPBE, mPW1PW91, M06-2X, and WB97X-D, respectively, were applied in calculations with the X-ray crystallographic structure. Acetonitrile was used as a reference (is 30.05 ppm) in calculations of NMR spectra. The calculated 1H NMR chemical shift differences with respect to the M06-2X results were shown in Figure S6a of the Supporting Information. Six functionals gave similar results of δ except for the proton 26 in the macrocycle. The M06-2X functional was then selected in the calculations of 1 H NMR shifts of molecular shuttle in various solvent models. Before being interlocked by the macrocycle, the open-ended and the dumbbell-shaped threads differ from each in their optimized geometries (Table 2). The free open-ended thread with only one stopper group capping at one end is nearly linear, but the addition of another stopper at the other end in the dumbbell-shaped thread makes the rod significantly bent. A comparison of the chemical shift, δ, between the open-ended and dumbbell-shaped threads shows the little difference for the protons around the binding station I, except for proton 10. In fact, these two different threads, with and without the second stopper, bear different contact centers for recognition with the 9040



Article

electrostatic interactions between the charged centers without adding much computational cost. 8 5 In Figure 7b (2CH3CN&2CHCl3 with background charges) and Figure 7c (2CH3CN with background charges), some distant solvent molecules have been treated as background point charges. In Figure 7d, a cluster model without background point charges (2CH3CN without background charges) has also been built for comparison. A comparison between panels a and b of Figure 7 demonstrates that the PCM-based chemical shifts are close to those obtained from explicit solvent model, except for the protons close to the CH3CN solvent molecules. The evident difference in local electrostatic environment between different solvent models is also clearly shown by the electrostatic potential map. For −NH (of macrocycle) and −CH (of thread) that adjacent to solvents, obvious differences in chemical shifts were also found with and without the involvement of background point charges in calculations, as shown in Figure 7 (panels c and d). It indicates that chemical shifts are sensitive to the electrostatic environment caused by solvents. It is also interesting to investigate the shift of calculated NMR data associated with crystal stacking. The crystal stacking structures are shown in Figure 8. There are evident

macrocycle. In the free open-ended thread, the binding center of station I is the −NH- (called proton 10) but in the dumbbell one is the −NH2+-group. For all the other adjacent protons, 8 (representing Ar−H), 9 (Me-H of the protonated DBA+ group), and 11 (Ar−H close to urea group), the geometrical difference and the adding of another stopper brought about little changes in NMR chemical shifts. In order to show the proton shielding variations driven by the thread-macrocycle interlocking at station I, the change in NMR chemical shifts, is defined as follows stationI Δδ locked = δthread(or macrocycle) − δthread + macrocyle

(3)

where δthread(or macrocycle) is the chemical shift of a proton in the free macrocycle (or thread) before interlocking of the ring and rod, and δthread+macrocyle is the chemical shift for the same proton I in the shuttle. The Δδstation locked value is useful to demonstrate the extent of conformational change of the macrocycle (or thread) after interlocking. For the macrocycle, the ethylene glycol protons (labeled as 24, 25, and 26) prefer to contact the −NH2+-recognition center (station I) of the thread by means of N+−H···O hydrogen bonds. This picture has been revealed by the experimental 1H NMR spectra, which were measured in the mixed CD3CN− CDCl3 (1:1, v/v, δ = 1.94 ppm) solvent media at 400 MHz and 298 K.45 The significant upfield shifts (of about 0.04−1.89 ppm) of methylene protons (9) and aromatic protons (8 and 11) of the DBA+ group encircled in the macrocycle, relative to those of free thread, indicate the aromatic shielding effect of the macrocycle and the binding of the macrocycle on station I. In Table 2, the simulated (called Solu.MD) chemical shifts change, between the free and interlocked thread (macrocycle) and also show such upfield shifts upon encapsulation. The Solu.MD values are averaged from DFT calculations on random 100 MD snapshots (sampled at every 10 ps). Table S3 of the Supporting Information lists the time-averaged 1H NMR chemical shifts for all the protons in the studied molecular shuttle. The NMR convergence along the MD trajectory is also tested along the MD trajectories (Figure S6b of the Supporting Information). The average chemical shifts during the 200, 400, 600, 800, and 1000 ps time durations were plotted, respectively, from which the gradually converged curves were founded. Especially the 1H NMR chemical shifts of the proton 10 of the −NH2+- binding center (on the thread) and the protons 25 and 26 of the ethylene glycol chain (in macrocycle) are nearly constant from the beginning to the end of 1 ns. The little effect of the conformational flexibility and solvent dynamics on the NMR chemical shifts of the strongly bounded site may suggest a shortcut for the assignment of experimental spectra through DFT calculations on the basis of the implicit polarizable continuum model (PCM).84 To further clarify differences in the calculated 1H NMR data with different solvent models, both implicit PCM (Figure 7a) and explicit solvent cluster models (Figure 7, panels b, c, and d) were employed. It is impossible to include hundreds of solvent molecules in DFT-based NMR calculations, so we built the solvent cluster models from the first solvent shell (which was determined from the radial distribution function in Figure S7 of the Supporting Information, same as what was done previously72). Two different cluster models have been used, including four solvents (two CH3CN and two CHCl3) and two solvents (two CH3CN), respectively. It is a simple way to use the background point charges to consider the long-range

Figure 8. Difference in M06-2X NMR chemical shifts between monomer and trimer, Δδstack = δtrimer − δmonomer, and difference in Mullikan charges, Δqstack = qtrimer − qmonomer caused by crystal stacking. Negative variations are labeled in blue color.

intermolecular π−π stacking interactions between the nearest neighboring molecular shuttles with the face-to-face stacking distance of 3.80 Å (between a thread and its adjacent macrocycle) and 3.53 Å (between two neighboring macrocycles), respectively. At the crystal structure, the calculated 1H NMR chemical shifts for most protons exhibit evident upfield shifts (0.48−2.60 ppm) in comparison to those obtained in an isolated monomer. It can also be found from Figure 8 that the crystal stacking brings about redistributions of charges to some degree. Ongoing from monomer to the stacked trimer, almost all the Mullikan charges are decreased by 0.02−0.04e (shown in blue in Figure 8), with only one exception for the proton of amide (−NH) group in macrocycle. The increased charge population in the amide unit by 0.02e (shown in black) may be responsible for the downfield shift of 0.83 ppm. 9041



Article

4. CONCLUSIONS The macrocycle−thread binding interaction at station I was predicted to be the strongest, which was interlocked through N+−H···O hydrogen bonding (between protonated amino hydrogen of the DBA+ group in the thread and the oxygen of the diethylene glycol group in macrocycle). The interlocked conformation of macrocycle residing over the urea group of station II was stabilized by the formation of N−H···OC hydrogen bonding. Similarly, the N−H···OP hydrogenbonding interactions between the phosphine oxide group of the thread and the upper amino unit of the macrocycle held the ring residing over station III. The specific binding interactions between the macrocycle and different sites, DBA+, urea, and phosphine oxide groups, along the thread were orthogonal to each other, and the binding strength was not sensitive to the neighboring groups and terminal stoppers. The selectivity for the shuttling between three different stations depended on the relative binding strength of the macrocycle with the specific stations. In comparison with GEBF-based MP2 results, M06-2X gave more reasonable binding energies of noncovalently interlocked molecular shuttle than the other DFT functionals. The conformational flexibility of the three-station molecular shuttle, for both the interlocked macrocycle and thread, in different chemical environments has been demonstrated by using molecular dynamics simulations. Different from the rigid macrocycle, the thread is rather flexible. The thread in the CD3CN-CDCl3 (1:1) mix solvents appeared less bent than what was found in the vacuum and nonpolar CDCl3 solvents. Furthermore, MD simulations of the conformational changes upon the shift of macrocycle away from these three stations demonstrated both perpendicular and rotating motions of macrocycle around the thread. At the same time, the thread was bending up (U-shaped) and down (Λ-like) to keep the hydrogen-bonding interactions between the macrocycle and thread. The competitive cation−π and π−π interactions, weaker than the hydrogen-bonding interactions, also existed in some “intermediate” conformations during the translation of macrocycle from one station to another. DFT calculations discovered the little influence of the conformational flexibility and solvent dynamics on 1H NMR chemical shifts of the strongly bounded sites. The calculated chemical shifts are sensitive to the local electrostatic environment caused by the nearby solvents, which can be described by background point charges and explicit solvent clusters. In addition, the significant bulk effect was revealed by remarkable differences in the calculated chemical shifts due to the crystal stacking. Our calculation results may provide some clue to design new multistation molecular shuttles with interesting topology and functions.

■

chemical shifts for two degenerate molecular shuttle conformations binding at station I (Figure S4). The MD trajectories of molecular shuttle binding at station I in different solvents (Figure S5). Comparison of the differences of computed 1H NMR chemical shifts using different DFT functionals with respect to the M06-2X functional results and convergence test along the MD trajectory (Figure S6). Calculated 1H NMR chemical shifts with PCM model and explicit solvent model (MD ensemble-average) for molecular shuttle binding at station I at M06-2X/6-31G (d, p) level (Table S3). The radial distribution function of 1 ns snapshot of MD simulation of station I (Figure S7). This material is available free of charge via the Internet at http://pubs.acs.org.

■

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Tel: (86)25-83597408. Notes

The authors declare no competing financial interest.

■

ACKNOWLEDGMENTS This work was supported by the National Basic Research Program (Grant 2011CB808604) and the National Natural Science Foundation of China (Grants 21290192, 21273102, 21103086, and 21333004). We are grateful to the High Performance Computing Center of Nanjing University for doing the quantum chemical calculations in this paper on its IBM Blade cluster system.

■

REFERENCES

(1) Amabilino, D. B.; Stoddart, J. F. Interlocked and Intertwined Structures and Superstructures. Chem. Rev. 1995, 95, 2725−2828. (2) Balzani, V.; Credi, A.; Raymo, F. M.; Stoddart, J. F. Artificial Molecular Machines. Angew. Chem., Int. Ed. 2000, 39, 3349−3391. (3) Kay, E. R.; Leigh, D. A.; Zerbetto, F. Synthetic Molecular Motors and Mechanical Machines. Angew. Chem., Int. Ed. 2007, 46, 72−191. (4) Ma, X.; Tian, H. Bright Functional Rotaxanes. Chem. Soc. Rev. 2010, 39, 70−80. (5) Coskun, A.; Banaszak, M.; Astumian, R. D.; Stoddart, J. F.; Grzybowski, B. A. Great Expectations: Can Artificial Molecular Machines Deliver on Their Promise? Chem. Soc. Rev. 2012, 41, 19−30. (6) Ashton, P. R.; Ballardini, R.; Balzani, V.; Baxter, I.; Credi, A.; Fyfe, M. C. T.; Gandolfi, M. T.; Gomez-Lopez, M.; Martinez-Diaz, M. V.; Piersanti, A.; et al. Acid-Base Controllable Molecular Shuttles. J. Am. Chem. Soc. 1998, 120, 11932−11942. (7) Gatti, F. G.; Leon, S.; Wong, J. K.; Bottari, G.; Altieri, A.; Morales, M. A.; Teat, S. J.; Frochot, C.; Leigh, D. A.; Brouwer, A. M.; et al. Photoisomerization of a Rotaxane Hydrogen Bonding Template: Light-Induced Acceleration of a Large Amplitude Rotational Motion. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 10−14. (8) Altieri, A.; Gatti, F. G.; Kay, E. R.; Leigh, D. A.; Martel, D.; Paolucci, F.; Slawin, A. M. Z.; Wong, J. K. Y. Electrochemically Switchable Hydrogen-Bonded Molecular Shuttles. J. Am. Chem. Soc. 2003, 125, 8644−8654. (9) Badjic, J. D.; Balzani, V.; Credi, A.; Silvi, S.; Stoddart, J. F. A Molecular Elevator. Science 2004, 303, 1845−1849. (10) Leigh, D. A.; Thomson, A. R. Switchable Dual Binding Mode Molecular Shuttle. Org. Lett. 2006, 8, 5377−5379. (11) Vella, S. J.; Tiburcio, J.; Loeb, S. J. Optically Sensed, Molecular Shuttles Driven by Acid-Base Chemistry. Chem. Commun. 2007, 45, 4752−4754. (12) Huang, Y.-L.; Hung, W.-C.; Lai, C.-C.; Liu, Y.-H.; Peng, S.-M.; Chiu, S.-H. Using Acetate Anions to Induce Translational Isomerization in a Neutral Urea-Based Molecular Switch. Angew. Chem. 2007, 119, 6749−6753.

ASSOCIATED CONTENT

S Supporting Information *

The reference list for six DFT functionals, B3LYP, CAMB3LYP, PBEPBE, mPW1PW91, M06-2X, and WB97X-D, which were used in geometry optimization and 1H NMR chemical shifts calculations. MD simulation details (Table S1). Relative energy, binding energies, and electrostatic potential maps of MD conformation ensemble (Figure S1). Optimized geometries for three stations with six different functionals (Figure S2). Optimized geometries for pseudorotaxanes at the B3LYP/6-31G (d, p) level (Figure S3). NBO analysis of the orbital interaction energies (Table S2). Calculated 1H NMR 9042



Article

(13) Hirose, K.; Shiba, Y.; Ishibashi, K.; Doi, Y.; Tobe, Y. A Shuttling Molecular Machine with Reversible Brake Function. Chem.Eur. J. 2008, 14, 3427−3433. (14) Hung, W.-C.; Wang, L.-Y.; Lai, C.-C.; Liu, Y.-H.; Peng, S.-M.; Chiu, S.-H. Two [2]Pseudorotaxane-Like Complexes and Their Corresponding [2]Rotaxanes Stabilized via Interactions on Opposite Ends of the Same Macrocycle. Tetrahedron Lett. 2009, 50, 267−270. (15) Coutrot, F.; Busseron, E. Controlling the Chair Conformation of a Mannopyranose in a Large-Amplitude [2]Rotaxane Molecular Machine. Chem.Eur. J. 2009, 15, 5186−5190. (16) Zheng, H.; Zhou, W.; Lv, J.; Yin, X.; Li, Y.; Liu, H.; Li, Y. A Dual-Response [2]Rotaxane Based on a 1,2,3-Triazole Ring as a Novel Recognition Station. Chem.Eur. J. 2009, 15, 13253−13262. (17) Jiang, Q.; Zhang, H. Y.; Han, M.; Ding, Z. J.; Liu, Y. PHControlled Intramolecular Charge-Transfer Behavior in Bistable [3]Rotaxane. Org. Lett. 2010, 12, 1728−1731. (18) Jiang, Y.; Guo, J. B.; Chen, C. F. A New [3]Rotaxane Molecular Machine Based on a Dibenzylammonium Ion and a Triazolium Station. Org. Lett. 2010, 12, 4248−4251. (19) Suzuki, S.; Nakazono, K.; Takata, T. Selective Transformation of a Crown Ether/sec-Ammonium Salt-Type Rotaxane to N-Alkylated Rotaxanes. Org. Lett. 2010, 12, 712−715. (20) Gan, Q.; Ferrand, Y.; Bao, C.; Kauffmann, B.; Grelard, A.; Jiang, H.; Huc, I. Helix-Rod Host-Guest Complexes with Shuttling Rates Much Faster than Disassembly. Science 2011, 331, 1172−1175. (21) Cheng, P. N.; Huang, P. Y.; Li, W. S.; Ueng, S. H.; Hung, W. C.; Liu, Y. H.; Lai, C. C.; Wang, Y.; Peng, S. M.; Chao, I.; et al. Is [N+− H···O] Hydrogen Bonding the Most Important Noncovalent Interaction in Macrocycle-Dibenzylammonium Ion Complexes? J. Org. Chem. 2006, 71, 2373−2383. (22) Foster, M. E.; Sohlberg, K. Theoretical Study of Binding Site Preference in [2]Rotaxanes. J. Chem. Theory Comput. 2007, 3, 2221− 2233. (23) Rijs, A. M.; Compagnon, I.; Oomens, J.; Hannam, J. S.; Leigh, D. A.; Buma, W. J. Stiff, and Sticky in the Right Places: Binding Interactions in Isolated Mechanically Interlocked Molecules Probed by Mid-Infrared Spectroscopy. J. Am. Chem. Soc. 2009, 131, 2428−2429. (24) Rijs, A. M.; Kay, E. R.; Leigh, D. A.; Buma, W. J. IR Spectroscopy on Jet-Cooled Isolated Two-Station Rotaxanes. J. Phys. Chem. A 2011, 115, 9669−9675. (25) Wolinski, K.; Hinton, J. F.; Pulay, P. Efficient Implementation of the Gauge-Independent Atomic Orbital Method for NMR ChemicalShift Calculations. J. Am. Chem. Soc. 1990, 112, 8251−8260. (26) Schatz, J.; Backes, A. C.; Siehl, H.-U. Geometry and GIAO-DFT Chemical Shift Calculations of Calixarene Complexes: The Inclusion of Carbon Disulfide in p-tert-Butylcalix[4]Arene. J. Chem. Soc., Perkin Trans. 2 2000, 609−610. (27) Backes, A. C.; Schatz, J.; Siehl, H.-U. GIAO-DFT Calculated and Experimentally Derived Complexation-Induced Chemical Shifts of Calix[4]Arene−Solvent Inclusion Complexeselectronic Supporting Information (ESI) Available: Calculated and Observed NMR Data and Geometrical Details for Complexes 1−3, 1−4 and 1−5. J. Chem. Soc., Perkin Trans. 2 2002, 484−488. (28) Klarner, F. G.; Kahlert, B.; Nellesen, A.; Zienau, J.; Ochsenfeld, C.; Schrader, T. Molecular Tweezer and Clip in Aqueous Solution: Unexpected Self-Assembly, Powerful Host-Guest Complex Formation, Quantum Chemical 1H NMR Shift Calculation. J. Am. Chem. Soc. 2006, 128, 4831−4841. (29) Dracinsky, M.; Kaminsky, J.; Bour, P. Structure of the Alanine Hydration Shell as Probed by NMR Chemical Shifts and Indirect SpinSpin Coupling. J. Phys. Chem. B 2009, 113, 14698−14707. (30) Banyai, D. R.; Murakhtina, T.; Sebastiani, D. NMR Chemical Shifts as a Tool to Analyze First Principles Molecular Dynamics Simulations in Condensed Phases: the Case of Liquid Water. Magn. Reson. Chem. 2010, 48, S56−60. (31) Dracinsky, M.; Bour, P. Computational Analysis of Solvent Effects in NMR Spectroscopy. J. Chem. Theory Comput. 2010, 6, 288− 299.

(32) Klarner, F. G.; Kahlert, B.; Nellesen, A.; Zienau, J.; Ochsenfeld, C.; Schrader, T. Molecular Tweezer and Clip in Aqueous Solution: Unexpected Self-Assembly, Powerful Host-Guest Complex Formation, Quantum Chemical 1H NMR Shift Calculation. J. Am. Chem. Soc. 2006, 128, 4831−4841; J. Am. Chem. Soc. 2010, 132, 4029. (33) Mugridge, J. S.; Bergman, R. G.; Raymond, K. N. 1H NMR Chemical Shift Calculations as a Probe of Supramolecular Host-Guest Geometry. J. Am. Chem. Soc. 2011, 133, 11205−11212. (34) Lodewyk, M. W.; Siebert, M. R.; Tantillo, D. J. Computational Prediction of 1H And 13C Chemical Shifts: A Useful Tool for Natural Product, Mechanistic, and Synthetic Organic Chemistry. Chem. Rev. 2012, 112, 1839−1862. (35) Zazza, C.; Mancini, G.; Brancato, G.; Sanna, N.; Barone, V. Neutral Molecular Shuttle in Acetonitrile Dilute Solution Investigated by Molecular Dynamics and Density Functional Theory. Comput. Theor. Chem. 2012, 985, 53−61. (36) Dračínský, M.; Möller, H. M.; Exner, T. E. Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions. J. Chem. Theory Comput. 2013, 9, 3806−3815. (37) Jena, N. K.; Murugan, N. A. Solvent-Dependent Conformational States of a [2]Rotaxane-Based Molecular Machine: A Molecular Dynamics Perspective. J. Phys. Chem. C 2013, 117, 25059−25068. (38) Mendoza, S. M.; Whelan, C. M.; Jalkanen, J. P.; Zerbetto, F.; Gatti, F. G.; Kay, E. R.; Leigh, D. A.; Lubomska, M.; Rudolf, P. Experimental and Theoretical Study of the Adsorption of Fumaramide [2]Rotaxane on Au(111) and Ag(111) Surfaces. J. Chem. Phys. 2005, 123, 244708. (39) Bottari, G.; Dehez, F.; Leigh, D. A.; Nash, P. J.; Perez, E. M.; Wong, J. K.; Zerbetto, F. Entropy-Driven Translational Isomerism: A Tristable Molecular Shuttle. Angew. Chem., Int. Ed. 2003, 42, 5886− 5889. (40) Leigh, D. A.; Wong, J. K. Y.; Dehez, F.; Zerbetto, F. Unidirectional Rotation in a Mechanically Interlocked Molecular Rotor. Nature 2003, 424, 174−179. (41) Collin, J. P.; Durola, F.; Lux, J.; Sauvage, J. P. A Rapidly Shuttling Copper-Complexed [2]Rotaxane with Three Different Chelating Groups in its Axis. Angew. Chem., Int. Ed. 2009, 48, 8532−8535. (42) Busseron, E.; Romuald, C.; Coutrot, F. Bistable or Oscillating State Depending on Station and Temperature in Three-Station Glycorotaxane Molecular Machines. Chem.−Eur. J. 2010, 16, 10062− 10073. (43) Zhao, Y.; Li, Y.; Lai, S. W.; Yang, J.; Liu, C.; Liu, H.; Che, C. M.; Li, Y. Construction of a Functional [2]Rotaxane with Multilevel Fluorescence Responses. Org. Biomol. Chem. 2011, 9, 7500−7503. (44) You, Y. C.; Tzeng, M. C.; Lai, C. C.; Chiu, S. H. Using Oppositely Charged Ions To Operate a Three-Station [2]Rotaxane in Two Different Switching Modes. Org. Lett. 2012, 14, 1046−1049. (45) Liu, L.; Liu, Y.; Liu, P.; Wu, J.; Guan, Y.; Hu, X.; Lin, C.; Yang, Y.; Sun, X.; Ma, J.; Wang, L. Phosphine Oxide Functional Group Based Three-Station Molecular Shuttle. Chem. Sci. 2013, 4, 1701− 1706. (46) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; et al. Gaussian 09, revision B.01; Gaussian, Inc.: Wallingford, CT, 2010. (47) London, F. The Quantic Theory of Inter-Atomic Currents in Aromatic Combinations. J. Phys. Radium 1937, 8, 397−409. (48) McWeeny, R. Perturbation Theory for the Fock-Dirac Density Matrix. Phys. Rev. 1962, 126, 1028−1034. (49) Ditchfield, R. Self-Consistent Perturbation Theory of Diamagnetism. 1. Gauge-Invariant LCAO Method for N.M.R. Chemical Shifts. Mol. Phys. 1974, 27, 789−807. (50) Wolinski, K.; Hinton, J. F.; Pulay, P. Efficient Implementation of the Gauge-Independent Atomic Orbital Method for NMR ChemicalShift Calculations. J. Am. Chem. Soc. 1990, 112, 8251−8260. 9043



Article

Chemical and Molecular Dynamics Simulations. J. Phys. Chem. B 2008, 112, 4313−4322. (73) Wen, J.; Ma, J. The Role of Substrate in Packing Structures of Sexithiophenes on Ag (111) Surface: Molecular Dynamics Simulations and Quantum Chemical Calculations. J. Chem. Theory Comput. 2009, 8, 677−690. (74) Wen, J.; Ma, J. Oligothiophene Template Effects on Packings and Orientations of C60Molecules on Ag(111) Surface. Langmuir 2010, 26, 5595−5602. (75) Liu, Z.; Ma, J. Effects of External Electric Field and SelfAggregations on Conformational Transition and Optical Properties of Azobenzene-Based D-π-A Type Chromophore in THF Solution. J. Phys. Chem. A 2011, 115, 10136−10145. (76) Wang, X.; Chen, S.; Wen, J.; Ma, J. Exploring the Possibility of Noncovalently Surface Bound Molecular Quantum-Dot Cellular Automata: Theoretical Simulations of Deposition of Double-Cage Fluorinated Fullerenes on Ag(100) Surface. J. Phys. Chem. C 2013, 117, 1308−1314. (77) Andersen, H. C. Molecular Dynamics Simulations at Constant Pressure and/or Temperature. J. Chem. Phys. 1980, 72, 2384. (78) Allen; M. P.; Tildesley, D. J. Computational Simulation of Liquids; Oxford University Press: Oxford, 1987. (79) Materials Studio, version 4.0; Accelrys, Inc.: San Diego, 2006. (80) Ransil, B. J. Studies in Molecular Structure. IV. Potential Curve for the Interaction of Two Helium Atoms in Single Configuration LCAO MO SCF Approximation. J. Chem. Phys. 1961, 34, 2109−2211. (81) Boys, S. F.; Bernardi, F. The Calculation of Small Molecular Interactions by the Differences of Separate Total Energies. Some Procedures with Reduced Errors. Mol. Phys. 1970, 19, 553−566. (82) Simon, S.; Duran, M.; Dannenberg, J. J. How does Basis Set Superposition Error Change the Potential Surfaces for Hydrogen Bonded Dimers? J. Chem. Phys. 1996, 105, 11024−11031. (83) Li, S.; Li, W.; Fang, T.; Ma, J.; Hua, W.; Hua, S.; Jiang, Y. LSQC Program; version 2.2; Nanjing University; Nanjing, 2012; see http:// itcc.nju.edu.cn/lsqc. (84) Tomasi, J.; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models. Chem. Rev. 2005, 105, 2999−3094. (85) Jiang, N.; Ma, J.; Jiang, Y. Electrostatic Field-Adapted Molecular Fractionation with Conjugated Caps for Energy Calculations of Charged Biomolecules. J. Chem. Phys. 2006, 124, 11411.

(51) Cheeseman, J. R.; Trucks, G. W.; Keith, T. A.; Frisch, M. J. A Comparison of Models for Calculating Nuclear Magnetic Resonance Shielding Tensors. J. Chem. Phys. 1996, 104, 5497−5509. (52) Li, S. H.; Li, W.; Fang, T. An Efficient Fragment-Based Approach for Predicting the Ground-State Energies and Structures of Large Molecules. J. Am. Chem. Soc. 2005, 127, 7215−7226. (53) Li, W.; Li, S. H.; Jiang, Y. S. Generalized Energy-Based Fragmentation Approach for Computing the Ground-State Energies and Properties of Large Molecules. J. Phys. Chem. A 2007, 111, 2193− 2199. (54) Hua, W. J.; Fang, T.; Li, W.; Yu, J. G.; Li, S. H. Geometry Optimizations and Vibrational Spectra of Large Molecules from a Generalized Energy-Based Fragmentation Approach. J. Phys. Chem. A 2008, 112, 10864−10872. (55) Li, S.; Li, W.; Ma, J. Generalized Energy-Based Fragmentation Approach and Its Applications to Macromolecules and Molecular Aggregates. Acc. Chem. Res. 2014, DOI: 10.1021/ar500038z. (56) Foster, J. P.; Weinhold, F. Natural Hybrid Orbitals. J. Am. Chem. Soc. 1980, 102, 7211−7218. (57) Reed, A. E.; Weinhold, F. Natural Bond Orbital Analysis Of near-Hartree-Fock Water Dimer. J. Chem. Phys. 1983, 78, 4066−4073. (58) Reed, A. E.; Weinstock, R. B.; Weinhold, F. Natural-Population Analysis. J. Chem. Phys. 1985, 83, 735−746. (59) Reed, A. E.; Weinhold, F. Natural Localized Molecular-Orbitals. J. Chem. Phys. 1985, 83, 1736−1740. (60) Carpenter, J. E.; Weinhold, F. Analysis of the Geometry of the Hydroxymethyl Radical by the Different Hybrids for Different Spins Natural Bond Orbital Procedure. J. Mol. Struct.: THEOCHEM 1988, 46, 41−62. (61) Reed, A. E.; Curtiss, L. A.; Weinhold, F. Intermolecular Interactions from a Natural Bond Orbital, Donor-Acceptor Viewpoint. Chem. Rev. 1988, 88, 899−926. (62) Weinhold, F. and Carpenter, J. E. In The Structure of Small Molecules and Ions; Naaman, R. Vager, Z., Eds.; Plenum: New York, 1988; pp 227−236. (63) Jiang, N.; Ma, J. Can a Proton be Encapsulated in Tetraamido/ Diamino Quaternized Macrocycles in Aqueous Solution and Electric Field? ChemPhysChem 2011, 12, 2453−2460. (64) Marder, S. R.; Perry, J. W.; Tiemann, B. G.; Gorman, C. B.; Gilmour, S.; Biddle, S.; Bourhill, G. Direct Observation of Reduced Bond Length Alternation in Donor/Acceptor Polyenes. J. Am. Chem. Soc. 1993, 115, 2524−2526. (65) Hwang, M. J.; Stockfiscb, T. P.; Hagler, A. T. Derivation of Class I1 Force Fields. 2. Derivation and Characterization of a Class I1 Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules. J. Am. Chem. Soc. 1994, 116, 2515−2525. (66) Sun, H. Ab Initio Calculations and Force Field Development for Computer Simulation of Polysilanes. Macromolecules 1995, 28, 701− 712. (67) Sun, H.; Mumby, S. J.; Maple, J. R.; Hagler, A. T. Ab Initio Calculations on Small Molecule Analogues of Polycarbonates. J. Phys. Chem. 1995, 99, 5873−5882. (68) Zhang, G. L.; Pei, Y.; Ma, J.; Yin, K. L.; Chen, C. L. Packing Structures and Packing Effects on Excitation Energies of Amorphous Phase Oligothiophenes. J. Phys. Chem. B 2004, 108, 6988−6995. (69) Pei, Y.; Ma, J. Comparative Study on Reactions and SelfDirected Growth Mechanisms of Styrene Molecules on H-Terminated Si(111) and Si(100): Combining Quantum Chemistry and Molecular Mechanics Simulations. Langmuir 2006, 22, 3040−3048. (70) Meng, S. C.; Ma, J.; Jiang, Y. S. Solvent Effects on Electronic Structures and Chain Conformations of Alpha-Oligothiophenes in Polar and Apolar Solutions. J. Phys. Chem. B 2007, 111, 4128−4136. (71) Zhang, G. L.; Ma, J.; Wen, J. Interchain Impacts on Electronic Structures of Heterocyclic Oligomers and Polymers Containing Group 14, 15, and 16 Heteroatoms: Quantum Chemical Calculations in Combination with Molecular Dynamics Simulations. J. Phys. Chem. B 2007, 111, 11670−11679. (72) Meng, S.; Ma, J. Solvatochromic Shift of Donor-Acceptor Substituted Bithiophene in Solvents of Different Polarity: Quantum 9044


Theoretical Study on Conformation Dynamics of Three-Station

Recommend Documents