Molecular dynamics simulation of aqueous solutions of glycine betaine

Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine-N-oxide, a bioprotectant closely related to glycine betaine.     

Molecular dynamics study on hydrophobic effects in aqueous urea solutions.

Hydrophobic effects in aqueous urea were analyzed by molecular dynamics simulations. The contribution of solvents to the potential of mean force between two methane molecules was calculated by using molecular dynamics simulations and was compared with the solubility data of hydrocarbons in aqueous urea. Both the simulation results and the solubility data indicated that urea stabilizes methane-methane association. The stabilization was due to increasing the solvation free energies of small hydrocarbons such as methane by addition of urea. The solvation free energies of larger hydrocarbons, on the other hand, are decreased by addition of urea. This effect of the solute size on hydrophobic free energies in aqueous urea was also analyzed by using molecular dynamics simulations by means of division of the solvation process into two parts: the cavity formation and the introduction of the solute-solvent attractive interactions. In the cavity formation, urea increased hydrophobic free energies, and in the introduction of the solute-solvent attractive interactions, urea decreased hydrophobic free energies. The influence of urea on hydrophobic free energies was determined by the balance of effects of the two parts of the solvation process.     

Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface

The adsorption of bovine serum albumin (BSA) onto a hydrophobic graphite surface is studied using molecular-dynamics simulation. In addition to the free, that is, unsteered, adsorption, we also investigate forced adsorption, in which the action of an AFM tip pushing the protein with constant force to the surface is modeled. Using an implicit inviscid water model, the adsorption dynamics and energetics are monitored for two different initial protein orientations toward the surface. In all cases, we find that the protein partially unfolds and spreads on the surface. The spreading is in agreement with the well-known high biocompatibility of graphite-based implants. The denaturation is, however, greatly enhanced in the case of forced adsorption. We follow the position of the so-called lipid-binding pocket found in subdomain IIIA (Sudlow site II) during adsorption and find that it is tilted and moved toward the graphite surface in all cases, in agreement with its hydrophobic character. The relevance of our findings for the common measurement procedure of studying protein adhesion using AFM experiments is discussed.     

Molecular dynamics simulation of water near nanostructured hydrophobic surfaces: interfacial energies.

We present results from molecular dynamics simulations of water near structured hydrophobic surfaces. The surface structures reported herein are a planar alkane crystal as a reference and crystals with a hole and a protrusion of approximately 2.5 nm diameter and 0.5 nm depth or height. All indicators show that surface structuring increases the hydrophobicity: The water density is reduced near the structure elements, and the number of residual contacts between water and the surface decreases by about 40 % with respect to the planar surface. Thermodynamic integration shows that the interfacial energy of the structured surfaces is about 7 mJ m(-2) higher for structured surfaces than for the planar surface. The hydrophobicity increases by a similar amount for the hole and the protrusion geometries compared to the planar surface.     

Molecular aggregates in aqueous solutions of bile acid salts. Molecular dynamics simulation study

The aggregation behavior of two bile acid salts (i.e., sodium cholate and sodium deoxycholate) has been studied in their aqueous solutions of three different concentrations (i.e., 30, 90,and 300 mM) by means of molecular dynamics computer simulations. To let the systems reach thermodynamic equilibrium, rather long simulations have been performed: the equilibration period, lasting for 20-50 ns, has been followed by a 20 ns long production phase, during which the average size of the bile aggregates (regarded to be the slowest varying observable) has already fluctuated around a constant value. The production phase of the runs has been about an order of magnitude longer than the average lifetime of both the monomeric bile ions and the bonds that link two neighboring bile ions together to be part of the same aggregate. This has allowed the bile ions belonging to various aggregates to be in a dynamic equilibrium with the isolated monomers. The observed aggregation behavior of the studied bile ions has been found to be in good qualitative agreement with experimental findings. The analysis of the results has revealed that, due to their molecular structure, which is markedly different from that of the ordinary aliphatic surfactants, the bile ions form rather different aggregates than the usual spherical micelles. In the lowest concentration solution studied, the bile ions only form small oligomers. In the case of deoxycholate, these oligomers, such as the ordinary micelles, are kept together by hydrophobic interactions, whereas in the sodium cholate system, small hydrogen-bonded aggregates (mostly dimers) are also present. In the highest concentration systems, the bile ions form large secondary micelles, which are kept together both by hydrophobic interactions and by hydrogen bonds. Namely, in these secondary micelles, small hydrophobic primary micelles are linked together via the formation of hydrogen bonds between their hydrophilic outer surfaces.     

Molecular dynamics simulation study on adsorption and diffusion processes of a hydrophilic chain on a hydrophobic surface

Molecular dynamics simulations are applied to investigate the adsorption and diffusion processes of a single hydrophilic poly(vinyl alcohol) (PVA) chain with different chain lengths on a hydrophobic graphite surface. It is expected that the chain and the surface "dislike" each other because one is hydrophilic and the other is hydrophobic. But surprisingly, a short PVA chain is well adsorbed on the surface, accompanied by large changes in the chain configuration. With increasing degree of polymerization (N), the chain turns gradually from two-dimensional adsorption to possessing certain height in the direction perpendicular to the surface. Moreover, the adsorption energy increases and the diffusion coefficient decreases with increasing N. In particular, for N = 20 in equilibrium, the hydroxyls of this short chain are close to the graphite surface in the stable adsorption configuration. In addition, we change the effective dielectric constant to 76.0 to mimic good solvent condition. The chain configurations and the diffusion coefficients both vary in contrast to the foregoing results.     

Molecular dynamics simulations of aqueous solutions of ethanolamines

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.     

Molecular dynamics simulation of solution structure and dynamics of aqueous sodium chloride solutions from dilute to supersaturated concentration

Constant-temperature and constant-pressure (NpT) molecular dynamics simulations were performed to study the effects of salt concentration ranging from dilute to supersaturated concentrations on solution structure and dynamical properties of aqueous sodium chloride solutions at 298 K. The rigid SPC/E model was used for water molecules, and sodium and chloride ions were modeled as charged Lennard–Jones particles. Na⁺–Cl⁻ radial distribution functions showed the presence of contact ion pairs and solvent separated ion pairs. The coordination numbers of Na⁺–Cl⁻ ion pairs increased with salt concentration up to saturated concentration, although the number of contact ion pairs was almost constant in supersaturated regions. The tracer diffusion coefficients of both ions decreased with salt concentration up to saturated concentration, while that of sodium ion was almost constant in supersaturated regions. The tracer diffusion coefficients of both ions were therefore quite close to each other. The constant number of the contact ion pairs and the almost equality of the tracer diffusion coefficients of both ions would lead to the formation of clusters in supersaturated solutions.     

Molecular dynamics simulations of hydrophobic associations in aqueous salt solutions indicate a connection between water hydrogen bonding and the Hofmeister effect

Although the often profound effects of neutral salts on protein solubility were first identified over a century ago by Hofmeister, a general molecular explanation of these effects-capable of accounting even for salts with highly anomalous behavior-has yet to be established. As one way toward developing such an explanation, we aim here to quantify how eight simple monovalent salts alter the association thermodynamics of hydrophobic solute-pairs in a series of 1 micros explicit-solvent molecular dynamics simulations. For both methane-methane and neopentane-neopentane associations, the salt-induced strengthening of the hydrophobic interaction observed in the simulations is found to be highly correlated with corresponding experimental solubility data; the computed changes in interaction free energy are also found to be quantitatively predictable using the preferential interaction formalism of Timasheff (Timasheff, S. N. Adv. Protein Chem. 1998, 51, 355-432). From additional simulations of 20 different pure salt solutions-in which no hydrophobic solutes are present-a strong correlation is also observed between the extent of water-water hydrogen bonding and experimental solubility data for hydrophobic solutes; this suggests that the Hofmeister effects of the simple salts investigated here may primarily be a manifestation of salt-induced changes in the water structure. Importantly, all of the strong correlations with experiment obtained here extend even to salts of lithium, whose unusual behavior has previously been unexplained; lithium's anomalous behavior can be rationalized in part by its formation of alternating, linear clusters (strings) with halide anions. The close agreement between simulation and experiment obtained in the present study reinforces previous work, showing that molecular simulations can be a valuable tool for understanding salt-related phenomena and indicating that this can be so even when the simulations employ the simple, nonpolarizable potential functions widely used in simulations of biological macromolecules.     

Molecular structure and dynamics of liquids: aqueous urea solutions

In this review a multi-technical approach to the analysis of the structure and dynamics of the urea/water system is described. The reorientational movement of the solute molecule is investigated by the analysis of spectral band-shapes, as well as with the use of the optical Kerr effect (OKE) and molecular dynamics simulation (MDS). The effect of solute concentration on the structure and dynamics of the aqueous solutions (aggregation, orientational distribution, solvation...) is studied by molecular dynamics simulation and neutron scattering. The results obtained by other techniques are included to provide a critical analysis. Finally, the low-frequency Raman spectra of the system are interpreted on the basis of the semi-quantitative information obtained by molecular dynamics simulation.     

Molecular dynamics and interactions of aqueous and dichloromethane solutions of polyvinylpyrrolidone

We have investigated the dynamics of polyvinylpyrrolidone solutions (PVP, M(w)=10 000) on time scales from 20 fs to 42 ps using femtosecond optically heterodyne-detected Raman-induced Kerr effect spectroscopy. To compare the dynamics of polymer solutions with those of the analogous monomer, we also characterized solutions of 1-ethyl-2-pyrrolidone (EP). Dynamics of both PVP and EP solutions have been characterized for sample concentrations of 6.4, 12.7, 24.5, 33.3, and 40.7 wt %. The longest time scale relaxations observed in the Kerr transients for these solutions occur on the picosecond time scale and are best fit to triexponential functions. The intermediate and slow relaxation time constants for PVP and EP solutions are concentration dependent. The time constants for the PVP solutions are not consistent with the predictions of hydrodynamic models, while the analogous time constants for the EP solutions do display hydrodynamic scaling. The predominant relaxation of the polymer is assigned to reorientations of the pyrrolidone side group or torsional motions of the constitutional repeat unit, with additional relaxation pathways including hydrogen bond reorganization in aqueous solution and segmental motion of multiple repeat units. The vibrational dynamics of PVP and EP solutions occur on the femtosecond time scale. These dynamics are analyzed with a focus on the additional degrees of freedom experienced by EP relative to PVP that result from the absence of the tether from the pyrrolidone group on the main chain backbone. The intermolecular Kerr spectra of PVP in H(2)O and CH(2)Cl(2) differ because H(2)O can donate a hydrogen bond to the carbonyl acceptor group on the pyrrolidone ring, while CH(2)Cl(2) cannot.     

Molecular dynamics simulation of glycine zwitterion in aqueous solution

A classical molecular dynamics method was used to study the modifications of the solution structure and the properties of glycine zwitterion in aqueous solution due to the increase of glycine zwitterion concentration and the incorporation of Na(+) and Cl(-) ions to the solution. The glycine zwitterion had fundamentally a hydrophilic behavior at infinite dilution, establishing around six hydrogen bonds with the water molecules that surrounded it, which formed a strong hydration layer. Because of the increase of glycine zwitterion concentration, the hydration structure became more compact and the quantity of water molecules bound to this molecule decreased. The Na(+) ion bound to the CO(2) group of glycine, while the Cl(-) ion bound mainly to the NH(3) group of this molecule. The integration of the ions to the hydration layer of the glycine zwitterion produced modifications in the orientational correlation between atoms of glycine zwitterion and water that surrounded them and an increase of the approaches between the glycine zwitterion molecules. The incorporation of ions to the solution also produced changes in the water-water orientational correlation. Decreases of the water-water hydrogen bonds and diffusion coefficient of all molecules were observed when the glycine zwitterion concentration increased and when the ions were incorporated to the solution.     

Molecular dynamics simulation study of interaction between model rough hydrophobic surfaces

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work, we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes: it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions, we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in the case of the charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo as the two plates are brought together.     

Colloidal dynamics near a particle-covered surface

How the diffusive dynamics of colloidal spheres changes in the vicinity of a particle-coated surface is of importance for industrial challenges such as fouling and sedimentation as well as for fundamental studies into confinement effects. We addressed this question by studying colloidal dynamics in a partially coated surface layer, using video microscopy. Particle mean squared displacement (MSD) functions were measured as a function of a (local) effective volume fraction (EVF), which was varied by making use of gravity settling. Comparison of MSDs at the bare and coated surfaces for EVF of 0.2-0.4 revealed that at the latter surface the motion amplitudes are strongly reduced, accompanied by a sharp transition from diffusive to nearly caged motion. This clearly indicates that the surface-attached particles cannot be taken into account via volume fraction and that their immobility has a distinct effect. For EVF > 0.45, the caging becomes dominated by the suspended particles, making the dynamics at the bare and coated surfaces similar.     

不同浓度下NaCl水溶液的分子动力学模拟

采用分子动力学模拟的方法在298K时对1.33mol/L,2.71mol/L,4.14mol/L和5.12mol/L的NaCl水溶液的微观结构进行了研究。模拟发现浓度对离了近程水化结构的影响不大,浓溶液中Na^+,Cl^-之间有两种缔合方式,接触缔合离子对和溶剂分隔的缔合离子对。这表明在建立可适用于高浓度条件下的电解质溶液热力学模型时应考虑离子缔合的贡献。     

Transport properties of acetone aqueous solutions: molecular dynamics simulation and NMR studies

Two quantities η_rel and are applied to study the nonideal acetone–water association mixture. An all-atom acetone model and a TIP5P water model have been adopted for molecular dynamics simulation. We study the transport properties of the system comparing the 's of strong hydrogen bond and weak contact based on transport properties, MD simulations together with NMR experimental data and find good agreement of concentration dependence, which exhibits the cooperation effect.     

Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface

We report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison with our previous results for two albumin fragments.     

Molecular dynamics simulation of the free surface of liquid formamide

Molecular dynamics simulations of liquid formamide (HCONH₂) were carried out using the GROMOS software. The formamide molecule is represented by all of its atoms with all internal degrees of freedom. In contrast to other simulations dealing with bulk properties, this study focuses on the interface liquid–vacuum for the first time. We show that the molecular plane is tilted out of the surface, exposing the HCO group to the vacuum. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63 : 1123–1131, 1997     

Molecular dynamics simulation study of the structural features and inclusion capacities of cucurbit[6]uril derivatives in aqueous solutions

Molecular dynamics (MD) simulations were performed for cucurbit[6]uril (CB6) methyl and cyclohexyl derivatives in aqueous solutions. Furthermore, MD simulations have been conducted to study the inclusion complexes between each CB6 derivative with α,ω-pentane diammonium ion (NH₃⁺(CH₂)₅NH₃⁺) to estimate the binding free energies, the complex geometries and the intermolecular forces responsible for complex formation. Results show a complete inclusion of the guest molecule in the cavity of the host for all complexes. Results also indicate that the guest dynamics inside the cavity of the substituted host is similar to that for the unsubstituted host. This demonstrates that the molecular recognition of the host is not affected by the alkyl substitution at the equator. Also, there is an insignificant conformational change of the macrocyclic structure upon inclusion of the guest. Molecular mechanics/Poisson Boltzmann surface area method was used to estimate the binding free energy of each complex. Results indicate that host–guest electrostatic interactions make the largest contribution to the complex binding free energy. Moreover, van der Waals interactions add significantly to the complex stability. The guest molecules show more or less similar binding free energies with the substituted CB6 that exhibits slightly more negative values than unsubstituted CB6 which is proved also by umbrella sampling.     

Molecular dynamics simulation of shock compression of metals: Iron and iron-sulfur solutions

The embedded atom model potential suggested earlier was improved to correctly describe iron at high pressures and temperatures. Correction was introduced using the shock compression data. The properties of body- and face-centered cubic (BCC and FCC) lattices and liquid iron at compression degrees up to 50% of the normal volume and temperatures up to 10000 K were calculated. At degrees of compression 0.7–0.6 and 0 K, the FCC lattice is thermodynamically stable. The temperature of fusion increases to ≈9700 K at compression to 50% of initial volume (pressure 585 GPa). The pressure of pure iron at 5000 K and density 12.5 g/cm³ is ≈250 GPa and is substantially lower than in the center of the Earth according to the geophysical data (360 GPa). An embedded atom model potential for a 10 at % solution of sulfur in iron which allows the properties of the melt in the center of the Earth to be described correctly is suggested; the viscosity of the melt under these conditions is not high (0.0156 Pa s); these results are close to those obtained in ab initio calculations. The possibility of partial Earth core crystallization is shown.