Free energy landscape of A-DNA to B-DNA conversion in aqueous solution

The interconversion between the well-characterized A- and B-forms of DNA is a structural transition for which the intermediate states and the free energy difference between the two endpoints are not known precisely. In the present study, the difference between the Root Mean Square Distance (RMSD) from canonical A-form and B-form DNA is used as an order parameter to characterize this free energy difference using umbrella sampling molecular dynamics (MD) simulations with explicit solvent. The constraint imposed along this order parameter allows relatively unrestricted evolution of the intermediate structures away from both canonical A- and B-forms. The free energy difference between the A- and B-forms for the hexamer DNA sequence CTCGAG in aqueous solution is conservatively estimated to be at least 2.8 kcal/mol. A continuum of intermediate structures with no well-defined local minima links the two forms. The absence of any major barriers in the free energy surface is consistent with spontaneous conversion of the A-form DNA to B-form DNA in unconstrained simulations. The extensive sampling in the MD simulations (>0.1 mus) also allowed quantitative energetic characterization of local backbone conformational variables such as sugar pseudorotation angles and BI/BII state equilibria and their dependence on base identity. The absolute minimum in the calculated free energy profile corresponds closely to the crystal structure of the hexamer sequence, indicating that the present method has the potential to identify the most stable state for an arbitrary DNA sequence in water.     

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 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.     

MD simulation of the transitions between B-DNA and A-DNA in the framework of a coarse-grained model

Transitions between the B and A forms of a short DNA double helix (12 base pairs) at different salt concentrations in an aqueous solution have been studied by the molecular dynamics method in the framework of a coarse-grained model with explicit ions but without friction. It has been shown that the A-DNA, stable at high salt concentrations, is a dynamic conglomerate of the molecule and the ions coming from the solution into the deep major groove and then leaving it. In such a short helix, in the model without friction, even at low salt concentrations, transitions from B-DNA to A-DNA and back are frequent and fast. Stable ADNA (without transitions to B-DNA) forms at salt concentrations greater than 0.45 mol/L.     

Molecular dynamics of a vanadate-dipeptide complex in aqueous solution

Static geometry optimizations and Car-Parrinello molecular dynamics simulations with the BP86 density functional, as well as NMR chemical shift calculations at the GIAO-B3LYP level, have been used to assess structure, speciation, and dynamics of aqueous solutions of the vanadate-glycylglycine complex. According to the simulations, this complex should be formulated as five-coordinate, anionic [VO2(GlyGly')]- (GlyGly' = H2N-CH2-C(O)-N-CH2-CO2). The neutral conjugate acid is unstable in water, where it is deprotonated within a few picoseconds. Six-coordinate structural alternatives, [VO(OH)2(GlyGly')]-, are disfavored energetically and/or entropically. The hydration shell around [VO2(GlyGly')]- in water is characterized in terms of suitable pair correlation functions.     

Molecular simulation of a concentrated aqueous KCl solution

A 1.0 M aqueous KCl solution was studied by molecular dynamics simulations at 293 K in order to study the influence of the ionic concentration on the hydration structure of the ions as well as the formation of ion clusters. The hydration structures of the ions are almost independent of the ionic concentration unless in respect to the perturbation that appears due to ionic clustering. Fractions equal to 31.9% of the anions and 37.8% of the cations are associated. Clusters constituted by two, three and four ions were detected. Their mean lifetimes are always affected by thermal effects, reorientational relaxation while the longest lifetimes are a consequence of ionic cloud relaxations. The pairs constituted by two anions or two cations are stabilized by water molecules belonging to the solvation shells of both ions. The neutral K⁺Cl⁻ pairs are formed under the influence of the electrostatic attraction that, however, is small due to the ionic radii of these ions. Consequently, this kind of pairs contains only 8.8% of the ions while the fraction of ions in the negative and positive pairs are equal to 29.2 and 39.3%, respectively, when the same ion can pertain to more than one pair.     

Molecular dynamics simulation of monoalkyl glycoside micelles in aqueous solution: influence of carbohydrate headgroup stereochemistry

Comparative molecular dynamics simulations of n-octyl-beta-D-galactopyranoside (beta-C8Gal) and n-octyl-beta-D-glucopyranoside (beta-C8Glc) micelles in aqueous solution have been performed to explore the influence of carbohydrate stereochemistry on glycolipid properties at the atomic level. In particular, we explore the hypothesis that differences in T(m) and T(c) for beta-C8Gal and beta-C8Glc in lyotropic systems arise from a more extensive hydrogen bonding network between beta-C8Gal headgroups relative to beta-C8Glc, due to the axial 4-OH group in beta-C8Gal. Good agreement of the 13 ns micelle-water simulations with available experimental information is found. The micelles exhibit a similar shape, size, and degree of exposed alkyl chain surface area. We find net inter- and intra-headgroup hydrogen bonding is also similar for beta-C8Gal and beta-C8Glc, although n-octyl-beta-D-galactopyranoside micelles do exhibit a slightly greater degree of inter- and intra-headgroup hydrogen bonding. However, the main distinction in the calculated microscopic behavior of beta-C8Glc and beta-C8Gal micelles lies in solvent interactions, where beta-d-glucosyl headgroups are considerably more solvated (mainly at the equatorial O4 oxygen). These results agree with preceding theoretical and experimental studies of monosaccharides in aqueous solution. A number of long water residence times are found for solvent surrounding both micelle types, the largest of which are associated with surface protrusions involving headgroup clusters. Our simulations, therefore, predict differences in hydrogen bonding for the two headgroup stereochemistries, including a small difference in inter-headgroup interactions, which may contribute to the higher T(m) and T(c) values of beta-C8Gal surfactants relative to beta-C8Glc in lyotropic systems.     

Structure of small associates of glycyrrhizic acid with cholesterol in aqueous solution: Molecular dynamics simulation

In a recent work by Zelikman et al.(J. Struct. Chem., 2015, 56(1)), the molecular dynamics simulation of dimers of glycyrrhizic acid (GA) arising from the spontaneous collision of two GA molecules in water is performed. Several relatively stable dimer structures are found, and when a cholesterol molecule is inserted, associates are observed constituting a GA dimer with a cholesterol molecule “stuck” to it. Here, we simulate the associates consisting of three and four GA molecules and a cholesterol molecule. It appears that the cholesterol molecule, as a rule, also locates at the surface of the GA associate. Therewith, the trimers do not form any clear characteristic structures, as dimers do, and the tetramers can be two stuck dimers.     

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 simulation study of glass transition in hydrated Nafion

The thermal transition of Nafion is studied using a molecular dynamics simulation through a chemically realistic model. Static and dynamic properties of polymer melts with different water contents are investigated over a wide range of temperatures to obtain viscometric and calorimetric glass transition temperatures. The effect of cooling rate of the simulation on the glass transition of the hydrated polymer is also examined within the well‐known Williams–Landel–Ferry (WLF) equation. Variation of relaxation times versus temperature shows a fragile‐to‐strong transition. The hydration level has a significant impact on the static and dynamic properties of the polymer chains and water molecules confined in nanometric spaces between polymer chains. The results of this study are useful to predict the behavior of Nafion for various applications including fuel cells, sensors, actuators, and shape memory devices at different temperatures. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 907–915     

Molecular dynamics simulation and thermodynamic modeling of the self-assembly of the triterpenoids asiatic acid and madecassic acid in aqueous solution

The self-assembly behavior of the triterpenoids asiatic acid (AA) and madecassic acid (MA), both widely studied bioactive phytochemicals that are similar in structure to bile salts, were investigated in aqueous solution through atomistic-level molecular dynamics (MD) simulation. AA and MA molecules initially distributed randomly in solution were observed to aggregate into micelles during 75 ns of MD simulation. A "hydrophobic contact criterion" was developed to identify micellar aggregates from the computer simulation results. From the computer simulation data, the aggregation number of AA and MA micelles, the monomer concentration, the principal moments of the micelle radius of gyration tensor, the one-dimensional growth exhibited by AA and MA micelles as the aggregation number increases, the level of internal ordering within AA and MA micelles (quantified using two different orientational order parameters), the local environment of atoms within AA and MA in the micellar environment, and the total, hydrophilic, and hydrophobic solvent accessible surface areas of the AA and MA micelles were each evaluated. The MD simulations conducted provide insights into the self-assembly behavior of structurally complex, nontraditional surfactants in aqueous solution. Motivated by the high computational cost required to obtain an accurate estimate of the critical micelle concentrations (CMCs) of AA and MA from evaluation of the average monomer concentration present in the AA and MA simulation cells, a modified computer simulation/molecular-thermodynamic model (referred to as the MCS-MT model) was formulated to quantify the free-energy change associated with optimal AA and MA micelle formation in order to predict the CMCs of AA and MA. The predicted CMC of AA was found to be 59 microM, compared with the experimentally measured CMC of 17 microM, and the predicted CMC of MA was found to be 96 microM, compared with the experimentally measured CMC of 62 microM. The AA and MA CMCs predicted using the MCS-MT model are much more accurate than the CMCs inferred from the monomer concentrations of AA and MA present in the simulation cells after micelle self-assembly (2390 microM and 11,300 microM, respectively). The theoretical modeling results obtained for AA and MA indicate that, by combining computer simulation inputs with molecular-thermodynamic models of surfactant self-assembly, reasonably accurate estimates of surfactant CMCs can be obtained with a fraction of the computational expense that would be required by using computer simulations alone.     

ZnCI~2-KCI系溶液的分子动力学模拟

用Busing离子间势,对ZnCI~2-KCI 系熔盐液的结构作分子动力学计算机模拟研究,模拟结果与中子衍射,X射线衍射,Raman光谱和红外光谱的若干结构相符.     

Molecular simulation studies on the interaction between different polymers in aqueous solution

A molecular dynamics simulation was performed to investigate the aggregates of mixing and the interaction between different polymers in aqueous solution. These polymers include partially hydrolyzed polyacryamide (HPAM), hydroxyethylcellulose (HEC) and polyvinylpyrrolidone (PVP). The structures of mixed aggregates were analyzed from the dihedral angle distribution of: (1) pure HPAM; (2) HPAM in aqueous solution; (3) HPAM with small segments of PVP or HEC in aqueous solution. At the same time, the simulated IR spectra and the calculated interaction parameters were used to distinguish the different interactions between HPAM and PVP or HEC. In order to confirm the validity of the simulated predictions, experimental IR spectra of polymer systems were made, and the specific viscosity of the HPAM and PVP or HEC system was measured using capillary viscometry. It can be seen from the viscosity measurements that the viscosity of the HPAM/PVP system in aqueous solution decreases linearly with an increase in concentration of PVP, whereas a maximum viscosity value appears with the increase in concentration of HEC in the HPAM/HEC system. The conclusion was drawn that the interaction between HPAM and HEC is stronger than the one between HPAM and PVP, and that molecular simulation can be considered as an adjunct to experiments and can provide otherwise inaccessible (or, not easily accessible) microscopic information that experimentalists can use.     

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 of the structure of poly(ethylene oxide) brushes on nonpolar surfaces in aqueous solution

The structure of poly(ethylene oxide) (PEO, M(w) = 526) brushes of various grafting density (sigma) on nonpolar graphite and hydrophobic (oily) surfaces in aqueous solution has been studied using atomistic molecular dynamics simulations. Additionally, the influence of PEO-surface interactions on the brush structure was investigated by systematically reducing the strength of the (dispersion) attraction between PEO and the surfaces. PEO chains were found to adsorb strongly to the graphite surface due primarily to the relative strength of dispersion interactions between PEO and the atomically dense graphite compared to those between water and graphite. For the oily surface, PEO-surface and water-surface dispersion interactions are much weaker, greatly reducing the energetic driving force for PEO adsorption. This reduction is mediated to some extent by a hydrophobic driving force for PEO adsorption on the oily surface. Reduction in the strength of PEO-surface attraction results in reduced adsorption of PEO for both surfaces, with the effect being much greater for the graphite surface where the strong PEO-surface dispersion interactions dominate. At high grafting density (sigma approximately 1/R(g)(2)), the PEO density profiles exhibited classical brush behavior and were largely independent of the strength of the PEO-surface interaction. With decreasing grafting density (sigma < 1/R(g)(2)), coverage of the surface by PEO requires an increasingly large fraction of PEO segments resulting in a strong dependence of the PEO density profile on the nature of the PEO-surface interaction.     

Clustering of glycine molecules in aqueous solution studied by molecular dynamics simulation

The nature of glycine--glycine interactions in aqueous solution has been studied using molecular dynamics simulations at four different concentrations and, in each case, four different temperatures. Although evidence is found for formation of small, transient hydrogen-bonded clusters of glycine molecules, the main type of interaction between glycine molecules is found to be single NH...OC hydrogen bonds. Double-hydrogen-bonded "dimers", which have often been cited as a significant species present in aqueous solutions of glycine, are only observed infrequently. When double-hydrogen-bonded dimers are formed, they dissociate quickly (typically within less than ca. 4 ps), although the broken hydrogen bonds have a higher than average probability of reforming. Several aspects of the clustering of glycine molecules are investigated as a function of both temperature and concentration, including the size distribution of glycine clusters, the radii of gyration of the clusters, and aspects of the lifetimes of glycine-glycine hydrogen bonding by means of hydrogen-bond correlation functions. Diffusion coefficients for the glycine clusters and water molecules are also investigated and provide results in realistic agreement with experimental results.     

Molecular dynamics simulation studies of absorption in piperazine activated MDEA solution

Development of more efficient solvent solutions for removal of CO(2) from natural gas and flue gases is a major task, which contributes to improved design of process plants and leads to decreased costs for its removal. Understanding the mechanisms of CO(2) absorption as well as analysis of undesired simultaneous processes is crucially important in this regard. In this work, we have applied Molecular Dynamics (MD) to investigate the absorption of CO(2) from a binary mixture of CO(2) and CH(4) into aqueous piperazine activated MDEA solution. The MD simulations were performed at a constant temperature of 298 K for five different systems with a loading factor of 0.07 to provide insight into molecular distribution in the amine solution and to enhance understanding of absorption mechanisms on the molecular scale. Force field parameters that were missing from the OPLS-AA force field, as well as charge distribution of piperazine (PZ), protonated piperazine (PZH(+)), piperazine carbamate (PZCOO(-)) and MDEA were obtained by QM calculations. The results of our simulations emphasize the importance of piperazine and piperazine carbamate in accelerating the absorption process. For the first time, we have shown the undesirable trapping of CH(4) by the amine solution and revealed that amine groups are mainly responsible for both absorption of CO(2) and the undesired trapping of CH(4).