Molecular Dynamics Study of Î²-CyclodextrinâPhenylalanine (1:1

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Molecular Dynamics Study of #-CyclodextrinPhenylalanine (1:1) Inclusion Complex in Aqueous Medium Madhurima Jana, and Sanjoy Bandyopadhyay J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/jp404348u • Publication Date (Web): 12 Jul 2013 Downloaded from http://pubs.acs.org on July 23, 2013

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The Journal of Physical Chemistry

Molecular Dynamics Study of β-Cyclodextrin-Phenylalanine (1:1) Inclusion Complex in Aqueous Medium Madhurima Jana‡ and Sanjoy Bandyopadhyay† ‡

Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela - 769008, India †

Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India

Abstract

Atomistic molecular dynamics (MD) simulations of host-guest inclusion complexes of β-cyclodextrin (BCD) and zwitterionic phenylalanine (zPHE) following two possible orientations of zPHE in aqueous solutions have been carried out. The guest induced structural changes of BCD and the microscopic properties of surrounding water have been explored. The results obtained for the complex molecules were compared with those obtained for free BCD and free zPHE molecules. It is found that irrespective of the orientation, the complexation of BCD and zPHE (1:1) is associated with loss of configurational entropy. Besides, the net configurational entropy is found to differ depending upon its orientation inside BCD cavity. Interestingly, within the simulation length scale it is found that the relatively hydrophobic aromatic moiety of zPHE prefers to stay within the hydrophobic cavity of BCD, irrespective of its orientation. Further, nonuniform distribution and altered tetrahedral ordering of hydration water molecules around the complex molecules as compared to that around the free forms are correlated well with their conformational flexibilities. To whom correspondence [email protected]

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Introduction

Cyclodextrins (CD) are one of the most popular and widely used organic host molecules in the area of host-guest chemistry. The macromolecules are torus shaped cyclic oligosaccharides containing several D-glucopyranose units linked by α(1-4) glycosidic bonds.1 The hydroxyl groups of the glucopyranose residues are arranged in way that the exterior of CDs is hydrophilic whereas the cavity of the molecule is hydrophobic. The wider sections of these toroidal shaped molecules are formed by the secondary hydroxyl groups, and the narrower sections contain the primary hydroxyl groups. Due to such structural diversity the molecules can efficiently accommodate a wide variety of guest molecules in the cavities to form inclusion complexes2, 3 in solution or in crystalline state and water is a typical choice. CDs modify the physicochemical properties of encapsulated guests and are most popularly used for the enhancement of solubility, modification of taste, controlled release of drugs, chromatographic separation etc. As a result, CDs are extensively used in pharmaceutical, food, cosmetics, textile industries as well as in environmental science.4 Considering various applications of CD-guest complexes a microscopic understanding of CD-guest interactions are of fundamental importance. Further, in biology and therapeutics study molecular recognition is of vivid importance. However the recognition phenomena is still not clearly understood. CD-guest systems can be considered as a mimic system of large biomolecular complexes such as protein-ligand. Considering the importance of CD-guest complexes several aspects of the systems have been studied by using different experimental, analytical and simulation methods. In an early review Szejtli stated that the main driving force of CD-guest inclusion complex formation is the substitution of high-enthalpy water molecules by suitable guest molecules.2 In an another review Liu and Guo5 mentioned that in aqueous medium the inclusion complexation of CDs is governed by hydrophobic as well as polar interactions.

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Bhattacharyya and co-workers6 have done significant work to study solvation dynamics inside CD nanocavities by using a wide number of fluorescent probe molecules as guests. Their study demonstrated that there exists strong coupling between the guest molecule and the water molecules inside cavity.7 Fluorescence spectroscopy has been used to study the binding constants and stability constants of CD-guest complexes.8, 9 The results showed that CDs have high molecular selectivity based on the size/shapefit concept. Using fluorescence correlation spectroscopy Granadero and co-workers10 have determined the stoichiometry and the association equilibrium constant of CDguest complexes. Yamaguchi et al.11 used ultrasonic method to study the amino acid recognition by BCD in aqueous medium from the kinetic view-point. By using calorimetric technique Castronuovo and Niccoli12 showed that the association of BCDs with guest molecules is governed by van der Waals interactions and hydrogen bonding. Bouchemal and Mazzaferro13 used isothermal titration calorimetry (ITC) technique to study various thermodynamics properties of CD-guest complex molecules. Auletta and co-workers14 measured rupture forces of CD-guest complexes in aqueous medium by single molecule force spectroscopic technique using an atomic force microscope. Mele and co-workers15 used single-crystal X-ray along with NMR experiment and inferred that the intermolecular interactions between guest molecule and host CD play important role to stabilize the host-guest complex. several theoretical and simulation studies are also attempted to explore different properties of the CD-guest complex molecules. In an early study Nandi and Bagchi16 showed how the long time component of the solvation of coumarin is affected within the cavity of a CD molecule by using the principles of molecular hydrodynamics theory (MHT) and multi-shell continuum model (MSCM). Yamazaki and Kovalenko17 proposed a decompositional analysis method to study the thermodynamic properties associated with solvation and complex formation ability of CD molecules. Gilson et al18 used second generation mining minima method to calculate configurational entropy

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of CD-guest complexes. ab-initio theoretical calculations and temperature dependent crystallographic study of CD amino-acid complexes showed the presence of bridging water molecule which favours the complex formation.19 From quantum chemical calculations and MD simulation study of inclusion complexes formed between CDs and small guest molecules Nagaraju and Sastry20 inferred that the stability of inclusion compounds depends on the type of CD and the physicochemical properties of the involved guest. K¨ ohler and Grczelschak-Mick21 investigated the BCD-benzene complex at different temperature by using molecular dynamics, quantum mechanics and COSMO-RS techniques. Cai et al.22 studied inclusion mechanism of steroid drugs into BCD by employing adaptive biasing force and free energy perturbation methods. From molecular docking simulation along with NMR spectroscopic study Sompornpisut and co-workers23 found that the cavity of CD can be occupied by phenylalanine with two possible arrangements. They found that the change in entropy is linear with the changes in mean potential and solvation energy. Rosa et al.24 carried out computer simulation studies of α- and β-CD-phenylalanine complex in vacuo as well as in aqueous solutions. They inferred that phenylalanine forms stable complex with βCD as compared to the α-CD. Raffaini and Ganazzoli25 carried out MD simulation to study the formation and stiochiometry of the CD-C60 fullerene complexes in explicit water. Pi˜ neiro and co-workers26 performed MD simulation at several temperature to characterize the supramolecular complexes formed between CDs and sodium dodecyl sulfate (SDS) of different stoichiometries in aqueous medium. Tan and co-workers27 performed MD simulation and studied structural deformations of CD in presence of guest in alcohol-water mixture. Pricl et al.28 performed combined molecular mechanics and molecular dynamics of BCD-guest complex in continuum solvent model and inferred that along with van der Waals interaction, dipole moments and H-bonds between host and guest play important role in stabilizing these inclusion complexes. Although a large number of studies have been carried out to investigate various

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properties of CD and guest molecules, however proper knowledge of CD-guest interactions and the role of solvent in forming such complexes are still unclear. Therefore, in this article, we have investigated microscopic properties of the 1:1 inclusion complex formed between BCD and the zwitterionic form of phenylalanine (zPHE) in aqueous medium. Among various CD-guest complexes, the complex formation between CD and aromatic-amino acid are of great interest since they can be treated as models for enzyme-substrate bindings. There exists experimental and theoretical evidences in support of the existence of BCD-zPHE (1:1) inclusion complex.23, 29 Two different complex forms have been considered depending upon the orientation of zPHE inside BCD cavity. Firstly, the aromatic ring of zPHE was placed towards the wider rim of the BCD molecule. For convenience we will refer this complex as ‘up’ complex. In an another complex the aromatic ring of zPHE was placed towards the narrower rim of the BCD molecule, henceforth will be referred as ‘down’ complex. Conformational flexibilities of these complexed forms as well as the microscopic structure and ordering of water molecules around them have been studied. The effects of formation of the host-guest complex on different properties were explored and the results obtained for the complexed forms were compared with that obtained for the free forms of BCD and zPHE. The rest of the article is organized as follows. In Section 2, we provide a brief description of the setup of the systems and the simulation methods employed. The results obtained from our investigations are presented and discussed in the next section (Section 3). The important findings from our study and the conclusions reached therefrom are highlighted in Section 4.

2

System Setup and Simulation Methods

Four separate simulations involving ‘up’ and ‘down’ complexes, free BCD and free zPHE in aqueous medium were carried out. The initial coordinates of the two molecules were taken from the literature.30, 31 The initial configuration of the ‘up’ complex was 5



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prepared by placing the center of the zPHE molecule at the center of the BCD in such a way so that the aromatic ring of zPHE remains toward the wider rim of BCD. Similarly, opposite orientation was considered for zPHE to obtain the ‘down’ complex. The molecules were then immersed in a cubic cell of 45 ˚ A dimension containing 2920 well-equilibrated water molecules by carefully avoiding unfavorable contacts. At first, a short MD run of 100 ps was carried out by keeping the zPHE molecule flexible and the BCD and water molecules frozen at their starting positions. Next, both BCD and zPHE were allowed to move for another 400 ps MD run. Initially, the temperature of the system was kept low, which then gradually increased to the room temperature of 300 K. Lastly, the water molecules were allowed to move and the system was equilibrated at constant temperature (T = 300 K) and pressure (Pext = 0) (NPT) for about 500 ps. During this period the volumes of the simulation cells were allowed to fluctuate isotropically. At the end of this equilibration run, the volumes of the systems attained steady values with box edge lengths of 44.63 ˚ A and 44.62 ˚ A for the ‘up’ and ‘down’ complexes, respectively. At this point we fixed the cell dimensions and the simulation conditions were changed to constant temperature (300 K) and volume (NVT). The NVT equilibration run was continued further for another 1 ns duration. This was followed by a NVT production run of approximately 28 ns duration. Hence the total simulation length becomes 30 ns. The MD trajectories were stored during the NVT runs with a time resolution of 400 fs for subsequent analysis. Similar protocols were employed for simulating the BCD and zPHE molecules in their free forms. The BCD and zPHE molecules were immersed in two separate cubic cells of equilibrated water molecules with edge lengths of 45 ˚ A containing 2903 water molecules and 30 ˚ A containing 905 water molecules, respectively. These two systems were then simulated for about 30 ns duration following the procedure as described before. The final edge lengths of the simulation cells for the free BCD and zPHE systems were 44.5 ˚ A and 30.18 ˚ A, respectively.

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The temperatures of the systems were controlled by employing Nos´e-Hoover chain thermostat extended system method32 as implemented in the PINY-MD code.33 The reversible multiple time step algorithm, RESPA32 was used that allowed us to integrate the equations of motions with a time step of 4 fs. This was achieved using a threestage force decomposition into intramolecular forces (torsion/bend-bond), short-range intermolecular forces, and long-range intermolecular forces. In these calculations, the intramolecular forces were computed every 1 fs, while the short- and long-range intermolecular forces were computed every 2 fs. Electrostatic interactions were calculated by using the particle-mesh Ewald (PME) method.34 The minimum image convention35 was employed to calculate the Lennard-Jones interactions and the real-space part of the Ewald sum, using a spherical truncation of 7 and 10 ˚ A, respectively, for the short- and the long-range parts of the force decomposition. The potential parameters for the BCD and the zPHE molecules were taken from the GROMOS36, 37 force field, while the rigid three-site extended simple point charge (SPC/E) model38 was employed for water.

3 3.1

Results and Discussion Structural Features

The snapshots of the complexes, that represent their best average conformations as obtained from the simulations are displayed in Figure 1. The initial configurations of the two complexes are also shown for comparison. It is apparent from the figure that the aromatic ring of the zPHE molecule preferentially occupies the hydrophobic cavity of the host BCD while its zwitterionic tail part tends to stick out of the cavity openings by orienting itself toward the polar solvent. This is found to be true for both the ‘up’ and ‘down’ forms of the complex. To visualize structural deviations of the complexes as well as the free molecules from their starting configuration, we have superimposed several of their configurations taken from the equilibrated trajectories at a regular time interval of 6 ns, which are shown in Figure 2. This is done by removing 7



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the translational and rotational degrees of freedom of the selected configurations with respect to their initial configurations. For comparison the initial structures are also included in the figure. We found that the simulated configurations are structurally alike to their starting configurations, however, flexibilities of these molecules are evident from the figure. Interestingly, fluctuation of zPHE inside BCD cavities as compared to their starting structures are evident from the figure. It is clearly visible from the figure that the aromatic moiety of zPHE molecule which is hydrophobic in nature always lie inside the hydrophobic region of the BCD molecules i.e inside cavity. Whereas, the terminal hydrophilic NH3 + and COO− groups preferred to stay outside the hydrophobic zone of the BCD molecule. This indicates that the terminals of zPHE are more water exposure. One of the reasons of such exposureness may be due to the ability of these groups to form hydrogen bonds with the surrounding water molecules as well as with the hydroxyl groups of the BCD molecule. In Figure 3 we have shown a typical snapshot of a complexed zPHE that forms hydrogen bonds with water and hydroxyl group of BCD. To quantify the differences between the simulated and initial structures of the BCD and zPHE, we have calculated root mean square deviations (RMSD) between them. The RMSDs of these molecules in their free forms are also calculated for comparison. The calculations are carried out over the entire simulated trajectories for all the nonhydrogen heavy atoms of BCD and zPHE. Time evolutions of the RMSDs are displayed in Figure 4. Reduction in flexibility of these molecules on complex formation is apparent from the figure. The effect is particularly prominent in the ‘up’ complexed form. The average RMSD values for the two molecules in their complexed and free forms as calculated over the equilibrated trajectories of the simulations (28 ns each) are listed in Table 1. It can be seen that the average RMSDs of BCD with respect to its free form are reduced by 47% in the ‘up’ complex and by 25% in the ‘down’ complex. On the other hand, though the RMSDs of zPHE are relatively less influenced, but once again

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the effect seems to be more in the ‘up’ (∼25% reduction) as compared to the ‘down’ complex (∼11% reduction). Thus, it is clear that the formation of the ‘up’ complex is associated with larger reductions in flexibilities of the two components.

3.2

Configurational Entropy

In a host-guest complexation process the binding is expected to be governed by the changes in configurational entropies of the participant molecules. Therefore, by estimating the entropy change it is possible to understand its effect on the stability of the complex formed with respect to the free forms. In this section, we calculate the configurational entropy by using the method as proposed by Schlitter.39 In this method, the absolute entropy (Sabs ) can be calculated directly from the cartesian coordinates by adapting one-dimensional quantum mechanical harmonic oscillator approximation as 1 kB T e2 1/2 Sabs < S = kB ln det[1 + M σM1/2 ] 2 ~2

(1)

where, kB is Boltzmann’s constant, T is the temperature, e is Euler’s number, M is the 3N dimensional diagonal matrix containing N atomic masses of the solute, σ is the covariance matrix of atom positional fluctuations, and ~ is Planck’s constant divided by 2π. The elements of the covariance matrix, σij , are given by σij = h(xi − hxi i)(xj − hxj i)i

(2)

where, xi are the cartesian coordinates of the atoms after removal of the center of mass translation and rotation around the center of mass of the particular molecule with respect to its reference structure. This ensures that the calculated entropy (S) is the conformational entropy of the tagged molecule. Here, the initial configurations of the analyzed trajectories are considered as the reference structures. Further details of the method and its application can be found elsewhere.39–43 Since the matrix 1+

kB T e2 M1/2 σM1/2 ~2

is a symmetric positive-definite one, the determinant has been 9



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evaluated by using a more efficient triangularization procedure, known as the Cholesky decomposition method.40 The elements of the covariance matrix are calculated by taking the time averages over the whole trajectory. In Figure 5 we show the calculated cumulative configurational entropies of the ‘up’ UB DB (SUC ) and the ‘down’ (SD C ) complexes, as well as that of the BCD (SC and SC ) and the

zPHE (SUC P and SDP C ) molecules in the two complexed forms. For comparison, the corP responding data for the two molecules in their free forms (SB F and SF ) are also included

in the figure. It may be noted that the calculations are carried out by including the non-hydrogen atoms of the two molecules. In general, all the curves exhibit rapid entropy build-ups before converging to almost steady values. This signifies near complete conformational samplings of the molecules. Small but noticeable decrease in entropies of the components on complexation is evident from the figure. The calculated cumulative configurational entropy values are listed in Table 2. The formation of a host-guest complex like that between BCD and zPHE is expected to occur first by structural adaptations of the two components followed by binding between the adapted forms.44 The calculated entropy changes due to structural adaptations of BCD, ∆SXB = SXB a C XP SB = SXP - SPF (X corresponds to ‘up’ (U) or ‘down’ (D) complexed F and zPHE, ∆Sa C

forms), along with the entropy changes due to binding of the structurally adapted forms X XB (∆SX - SXP C ), and the ‘net’ entropy changes due to complex formations b = SC - SC XB from the free forms of BCD and zPHE (∆SX + ∆SXP + ∆SX net = ∆Sa a b ) are also listed

in the table. The calculations reveal that both structural adaptations and subsequent binding between the adapted forms of BCD and zPHE contribute significantly to the net entropy loss (∆SX net ) associated with the complex formation. In particular, the structural adaptations of the host BCD molecule in both the complexes lead to large reductions in entropy values. The effect is more for the ‘up’ complex as compared to the ‘down’ complex. This is consistent with increasingly reduced flexibility of the ‘up’ complex as described earlier.

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Further, we have calculated average interaction energy between BCD and zPHE in the two complexes. Interestingly, the energy is found to be around -38.3 (± 3.88) kcal mol−1 for the ‘up’ and -27.7 (± 3.72) kcal mol−1 for the ‘down’ complexes respectively. The relatively lower interaction energy between BCD and zPHE in ‘up’ complex can compensate the entropy cost for its formation, and hence it can be stated that the stability of ‘up’ complex is relatively higher than the ‘down’ complex. To further analyze the binding mode of such inclusion complexes, we have estimated the free energy changes of the ligand zPHE upon binding with the host BCD. This is done by calculating the changes in translational and rotational entropies (∆SPtr and ∆SProt ) of zPHE due to complexation. The translational and rotational entropies are calculated from the principal rms fluctuation of center of mass and Euler angles.45 The calculations reveal that for the ‘up’ and the ‘down’ complexes the changes in translational entropies of zPHE are -4.96 and -2.14 cal K−1 mol−1 , whereas that in rotational entropies are -7.56 and -3.02 cal K−1 mol−1 , respectively. The values once again suggest restricted motions of the guest species upon binding. Then, we have estimated the total entropy changes of zPHE (∆SPtot ) due to binding by summing up ∆SXP (see a Table 2), ∆SPtr , and ∆SProt values for the two complexes. By considering the interaction energies between BCD and zPHE in the two complexes as the enthalpy changes due to binding, the corresponding free energy changes ∆GP of zPHE due to binding can be estimated. The calculated ∆GP values are found to be -21.39 and -18.54 kcal mol−1 for the ‘up’ and ‘down’ complexes, respectively. The results indicate favorable binding of zPHE inside BCD cavity. It may be noted at this stage that, to estimate the overall free energy changes due to complexation, one has to additionally compute free energies of the host BCD as well as that of the surrounding water molecules.

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3.3

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Effects of Complexation on Water Structure and Local Ordering

We showed recently how the microheterogeneous environment in and around cyclodextrins affects the properties of the surrounding water molecules.46 It would be interesting to probe how the presence of a guest molecule like zPHE influences water behavior around BCD. This in turn may provide valuable information on the role played by water in forming such inclusion complexes and controlling their properties. In this section, we study the microscopic arrangement and ordering of water molecules in and around the two forms of the BCD-zPHE complex and compare the results with that obtained from the free BCD molecule. The arrangements of water molecules in and around the complexed and free BCD molecules are analysed by calculating the pair distribution function or the radial distribution function, g(r), of the water molecules with respect to the centers of the BCD molecules. The results are shown in Figure 6. This will provide a clear picture of the relative arrangement of water molecules that are present inside the cavity and those surrounding the BCD molecules. The differential intensities at the first peak position (the peak heights) for the three systems as evident from the figure indicate strong influence of the guest species on the structural arrangement of the water molecules present inside the cavity of the host BCD. For free BCD, there is a clear internal and external distributions of water upto 4 ˚ A and beyond 5 ˚ A respectively. In between two distributions there lies the rim of BCD molecule. Interestingly, we found that the structuring of cavity water diminishes with complexation, particularly for the ‘up’ complex. This is quite relevant with our previous findings. It is apparent that the relative lower flexibility of the host BCD and guest zPHE in the ‘up’ complex, and preference of the guest to remain near the center of the BCD cavity prevents the entry of water molecules into the cavity. On the other hand, relatively higher flexibility of the ‘down’ complex and the movement of zPHE towards the exterior of BCD allows water 12


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molecules to enter into the cavity leading to their higher structuring. As expected, the probability of finding water at the exterior of the BCD is almost same in all cases since the influence of the guest is restricted within the cavity. Further, to get a more quantitative idea about the effect of complex formation on local ordering of water molecules, we have measured the tetrahedral order parameter (qtet ), for water hydrating the complex and free molecules. The tetrahedral order parameter (qtet ), is defined as47–52 qtet

3 4 3X X 1 =1− (cosψjk + )2 8 j=1 k=j+1 3

(3)

Here, ψjk is the angle between the bond vectors rij and rik , where j and k are the four nearest neighbor atoms of the i-th water molecule. Here, it is assumed that nonhydrogen atoms of the BCD molecules can also act as neighboring atoms for those tagged water molecules that are present close to them. The estimated average tetrahedral order parameters of the water molecules, hqtet i(r), as a function of distance from the center of BCD in the complexed forms are shown in Figure 7. The results are compared with that obtained for the free form of the molecule. Reduction of tetrahedral ordering of water inside the BCD cavities, particularly in the complexed forms are evident from the figure. It may be noted that on average 3 and 5 water molecules are found within the cavities of the BCD molecule in its ‘up’ and ‘down’ complexed forms, respectively, whereas the number of cavity water is 8 for the free BCD molecule. Note that the cavity water molecules have been identified following the same approach as described in our earlier work.53 According to this approach, the vectors connecting pairs of non-hydrogen atoms of the CDs are first constructed. These vectors are then divided into fine grids with 0.1 ˚ A resolution. After carefully avoiding any over-counting, the oxygen atoms of those water molecules that are found within spheres of radius 0.5 ˚ A around the grid points are considered as cavity waters. In Figure 8 we display representative snapshots of water molecules present inside the cavity of BCD in its free and in the two complexed forms as obtained from the corresponding simulated trajectories. 13



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Interestingly, we find that the centers of BCDs in ‘up’ and ‘down’ forms of the complexes are almost devoid of tetrahedrally ordered water upto short distances of about 1.5 ˚ A and 0.5 ˚ A, respectively. This is consistent with the water arrangements inside the cavities as discussed earlier (see Figure 6). It once again confirms the presence of zPHE near the center of BCD in ‘up’ complex. Once again, beyond the distance of 5˚ A from the center, almost identical ordering patterns of water molecules similar to that of pure bulk water (∼0.63) are observed. The distance dependent hqtet i(r) plot further confirms that the replacement of cavity water occurs due to the formation of inclusion complex, and the guest molecule like zPHE generally stays near the center of the BCD.

4

Conclusions

In this article we have presented results obtained from atomistic MD simulations of 1:1 inclusion complex formed between β-cyclodextrins (BCD) and zwitterionic form of phenylalanine (zPHE) in aqueous solutions. Depending upon the orientation of zPHE inside BCD cavity two complexes named as, ‘up’ and ‘down’ complex were considered. The results are compared between these two complexes as well as with those obtained from the separate simulations of the free forms of the two molecules in aqueous solutions. Our calculations revealed that the flexibility of BCD and zPHE reduces upon complexation irrespective of the orientation of the guest molecule inside the cavity. The reduction in flexibility is particularly noticed for the BCD molecule in the ‘up’ complex. Therefore, our simulations suggest that the complexation process is likely to be associated with the restricted conformational fluctuations of the structurally adapted forms of the molecules. Further, we have calculated the relative changes in configurational entropies associated with the ‘up’ and ‘down’ complex formations by using Schlitter’s method.39 The calculation reveals that the BCD-zPHE (1:1) inclusion complex for14


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mation is associated with loss in configurational entropy. Our study indicates that relatively lower interaction energy between BCD and zPHE in ‘up’ complex can compensate the entropy cost for its formation, and hence may increase the stability of ‘up’ complex. It is further demonstrated that the guest molecule has significant influence on the properties of surrounding water, particularly for the water present inside the cavity of the host BCD molecule. We find that the water molecules present inside the cavity of complexed BCD are poorly structured, and less tetrahedrally ordered as compared to the corresponding free form. This clearly suggests that the expulsion of cavity water occurs due to complex formation. This is particularly true for the ‘up’ complex. To the best of our knowledge this is the first report where the associated configurational entropy changes as well as the effect of presence of guest on water properties around the BCD-zPHE (1:1) inclusion complex have been studied. It would be interesting to estimate the associated free energy changes of the host-guest inclusion process in aqueous medium and to explore the effect of solvents on such process. Presently, we are investigating such aspects in our laboratory.

5

Acknowledgment

MJ thanks IIT-Kharagpur for providing high performance computing facilities.

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[15] Raffaini, G.; Ganazzoli, F.; Malpezzi, L.; Fuganti, C.; Fronza, G.; Panzeri, W.; Mele, A. J. Phys. Chem. B 2009, 113, 9110-9122. [16] Nandi, N.; Bagchi, B. J. Phys. Chem. 1996, 100, 13914-13919. [17] Yamazaki, T.; Kovalenko, A. J. Chem. Theory Comput. 2009, 5, 1723-1730. [18] Chen, W.; Chang, C-E.; Gilson, M. K. Biophys. J. 2004, 87, 3035-3049. [19] Clark, J. L.; Peinado, J.; Stezowski, J. J.; Vold, R. L.; Huang, Y.; Hoatson, G. L. J. Phys. Chem. B 2006, 110, 26375-26387. [20] Nagaraju, M.; Sastry, G. N. J. Phys. Chem. A 2009, 113, 95339542. [21] K¨ ohler, J. E. H.; Grczelschak-Mick, N. Beilstein J. Org. Chem. 2013, 9, 118-134. [22] Cai, W.; Sun, T.; Liu, P.; Chipot, C.; Shao, X. J. Phys. Chem. B 2009, 113, 7836-7843. [23] Sompornpisut, P.; Deechalao, N.; Vongsvivut, J. ScienceAsia 2002, 28, 263-270. [24] Grigera, J. R.; Caffarena, E. R.; Rosa, S. D. Carbohydrate Res. 1998, 310, 253-259. [25] Raffaini, G.; Ganazzoli, F. J. Phys. Chem. B 2010, 114, 7133-7139. [26] Brocos, P.; D´iaz-Vergara, N.; Banquy, X.; P´ erez-Casas, S.; Costas, M.; Pi˜ neiro, A. J. Phys. Chem. B 2010, 114, 12455-12467. [27] Zhang, H.; Ge, C.; van der Spoel, D.; Feng, W.; Tan, T. J. Phys. Chem. B 2012, 116, 3880-3889. [28] Fermeglia, M.; Ferrone, M.; Lodi, A.; Pricl, S. Carbohydrate Polymers 2003, 53, 15-44. ˘ Rohonczy, J. J Incl Phenom Macrocycl Chem [29] Sebesty˘ en, Z.; Buv˘ ari-Barcza, A.; 2012, 73, 199-210. 17



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[30] Sharff, A. J.; Rodseth, L. E.; Quiocho, F. A. Biochemistry 1993, 32, 10553-10559. [31] Alexander, M. J.; Clark, J. L.; Brett, T. J.; Stezowski, J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5115-5120. [32] Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Mol. Phys. 1996, 87, 1117-1157. [33] Tuckerman, M. E.; Yarne, D. A.; Samuelson, S. O.; Hughs, A. L.; Martyna, G. J. J. Comput. Phys. Commun. 2000, 128, 333-376. [34] Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092. [35] Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon: Oxford, 1987. [36] Koehler, J. E. H.; Saenger, W.; van Gunsteren, W. F. Eur. Biophys. J. 1987, 15, 197-210. [37] Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. J. Comput. Chem. 2004, 25, 1656-1676. [38] Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269-6271. [39] Schlitter, J. Chem. Phys. Lett. 1993, 215, 617-621. [40] Andricioaei, I.; Karplus, M. J. Chem. Phys. 2001, 115, 6289-6292. [41] Hsu, S. D.; Peter, C.; van Gunsteren, W. F.; Bonvin, A. M. J. J. Biophys. J. 2005, 88, 15-24. [42] Dolenc, J.; Baron, R.; Oostenbrink, C.; Koller, J.; van Gunsteren, W. F. Biophys. J. 2006, 91, 1460-1470.

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[43] Sinha, S. K.; Chakraborty, S.; Bandyopadhyay, S. Langmuir 2010, 26, 9911-9916 [44] Dixit, S. B.; Andrews, D. Q.; Beveridge, D. L. Biophys. J. 2005, 88, 3147. ˚ [45] Carlsson, J.; Aqvist, J. J. Phys. Chem. B 2005, 109, 6448-6456. [46] Jana, M.; Bandyopadhyay, S. J. Chem. Phys. 2011, 134, 025103. [47] Errington, J. R.; Debenedetti, P. G. Nature 2001, 409, 318-321. [48] Kumar, P.; Buldyrev, S. V.; Stanley, H. E. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 22130-22134. [49] Chau, P. L.; Hardwick, A. J. Mol. Phys. 1998, 93, 511-518. [50] Lee, S. L.; Debenedetti, P. G.; Errington, J. R. J. Chem. Phys. 2005, 122, 204511. [51] Agarwal, M.; Kushwaha, H. R.; Chakravarty, C. J. Phys. Chem. B 2010, 114, 651-659. [52] Sharma, R.; Chakraborty, S. N.; Chakravarty, C. J. Chem. Phys. 2006, 125, 204501. [53] Jana, M.; Bandyopadhyay, S. Langmuir 2009, 25, 13084-13091.

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Table 1: The average RMSD (in ˚ A) values of all the non-hydrogen atoms of BCD and zPHE in their complexed and free forms. The values in the parenthesis are the standard deviations. system BCD zPHE

up 0.86 (0.008) 0.91 (0.11)

down 1.23 (0.11) 1.08 (0.17)

free 1.63 (0.14) 1.21 (0.25)

Table 2: Configurational Entropies (in cal K−1 mol−1 ) of the ‘Up’ and ‘Down’ Complexes (SX C ) and the Individual BCD and zPHE Molecules in the Complexed Form B P (SXB and SXP C C ) and in the Respective Free Forms (SF and SF ). Entropy Changes Due XP to Structural Adaptations of BCD (∆SXB a ) and zPHE (∆Sa ), Due to Binding of the X Adapted Forms (∆Sb ), and the Net Entropy Changes on Complexations (∆SX net ) Are Also Listed. ‘X’ Corresponds to ‘up’ (U) or ‘down’ (D) Complexed Forms, Respectively.

system

SX C

SXB C

up

2128.66

1810.00

down

2230.97

1871.89

BCD SB F

∆SXB a (SXB - SB C F) -140.10

SXP C 373.80

-78.21

392.28

1950.10

zPHE SP F

∆SXP a (SXP - SP C F) -43.84

∆SX b

∆SX net

XB XP (SX C -SC -SC ) -55.14

(∆SXB + ∆SXP + ∆SX a a b ) -239.08

-25.36

-33.20

-136.77

417.64

20


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FIGURE CAPTIONS Figure 1: The initial and the representative simulated configuration of BCD-zPHE ‘up’ complex are shown in (a) and (b), respectively. The same for ‘down’ complex are shown in (c) and (d), respectively. Figure 2: Top (left) and side (right) views of superposition of several simulated configurations of BCD-zPHE in (a) ‘up’ complex and (b) ‘down’ complex. The superimposed configurations for the free BCD (left) and free zPHE (right) are shown in (c). All the molecules were taken at regular intervals from the equilibrated simulation trajectories. The hydrogen atoms are not shown for visual clarity. The initial configurations are shown in black. Figure 3: A snapshot of the simulated BCD-zPHE (1:1) ‘up’ complex highlighting hydrogen bonds formed between water molecules or hydroxyl groups of BCD molecule with the terminal hydrophilic NH3 + and COO− groups of encapsulated zPHE molecule. The water present inside cavity is shown in magenta whereas the water present outside of cavity is shown in orange. Figure 4: Time evolutions of the root mean square deviations (RMSD) for all the non-hydrogen atoms of (a) the BCD molecules in the complexed and in the free forms with respect to their initial structures and (b) the zPHE molecules in the complexed and in the free forms with respect to their initial structures. Figure 5: Cumulative configurational entropy of the up and ‘down’ complexes are shown in (a) and that of individual BCD and zPHE molecules in the complexed and free forms are shown in (b) and (c), respectively. The calculations are carried out by considering the non-hydrogen atoms of the respective molecules.

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Figure 6: Pair distribution function, g(r), for the center of BCDs and the water molecules. Figure 7: Average tetrahedral order parameter, hqtet i(r), of water as a function of distance from the center of complexed and free BCD molecules. Figure 8: Representative snapshots of water molecules present inside the cavity of BCD in its (a) free form, and (b) ‘up’- and (c) ‘down’-complexed forms.

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Figure 1: Jana and Bandyopadhyay 23



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Figure 3: Jana and Bandyopadhyay

25



RMSD[Å]

up-complex down-complex free

(a)

3 2 1 0

(b)

3

RMSD [Å]

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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2 1 0

0

10

20

t [ns]



30

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2 1 -1

(a) 0

-1

S (x 10 ) [cal K mol ]

2 up-complex down-complex free

1

3

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(b) 0 0.4 0.2

(c) 0

0

10

20

t [ns]



30


2 up-complex down-complex free

1.5

g (r)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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1 0.5 0

0

3

9

6

12

r [Å]


28


15

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0.6 (r)

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up-complex down-complex free

0.5 0.4 0

2

4

6

8

r [Å]


29


10


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30


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-1 -1

2 1

up-complex down-complex

3

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


S (x 10 ) [cal K mol ]

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0

0

10

20

30

t [ns]

TOC Graphic

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