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1.
A series of molecular dynamics simulations of water-formic acid mixtures containing either an ionic solute or a neutral hydrophobic solute has been performed to study the extent of nonideality in the dynamics of these solutes for varying composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to show nonideal behavior with variation of composition, and similar nonideality is also observed for the diffusion and orientational relaxation of solvent molecules in these mixtures. The diffusion coefficient of a neutral hydrophobic solute, however, decreases monotonically with increase in water concentration. We have also investigated some of the pair dynamical properties such as water-water and water-formic acid hydrogen bond relaxation and residence dynamics of water molecules in water and formic acid hydration shells. The lifetimes of water-water hydrogen bonds are found to be longer than those between formic acid carbonyl oxygen-water hydrogen bonds, whereas the lifetimes of formic acid hydroxyl hydrogen-water hydrogen bonds are longer than those of water-water hydrogen bonds. In general, the hydrogen bond lifetimes for both water-water and water-formic acid hydrogen bonds are found to decrease with increase in water concentration. Residence times of water molecules also show the same trend with increase in formic acid concentration. Interestingly, these pair dynamical properties show a monotonic dependence on composition without any maximum or minimum and behave almost ideally with respect to changes in the composition of the mixtures. The present calculations are performed with fixed-charge nonpolarizable models of the solvent and solute molecules without taking into account many-body polarization effects in an explicit manner.  相似文献   

2.
We have carried out a series of molecular-dynamics simulations of water-methanol mixtures containing either an ionic or a neutral atomic solute to investigate the effects of composition of the mixture on the diffusion of these solutes. Altogether, we have considered 17 different systems of varying composition ranging from pure water to pure methanol. The diffusion coefficients of ionic solutes are found to show nonideal behavior with variation of composition of the solvent mixture. The extent of nonideality of the solute diffusion is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and methanol molecules in these mixtures and is attributed to the enhanced stability of the hydrogen bonds and formation of interspecies complexes in the mixtures. The neutral solute shows characteristics of hydrophobic solvation and its diffusion decreases monotonically with increase of methanol concentration. The present simulation results are compared with those of experiments wherever available.  相似文献   

3.
Molecular dynamics simulations of charged and neutral solutes in dimethyl sulfoxide (DMSO)-chloroform mixtures reveal pronounced nonideality in the solute diffusion with changes of composition of the mixtures. The diffusion coefficient of the anionic solute first decreases, passes through a minimum at DMSO mole fraction of about 0.50, and then increases to reach its value for pure DMSO. The diffusion coefficients of the cationic and neutral solutes are found to decrease with increase in DMSO content of the solvent mixture. The extent of nonideality in the diffusion and orientational relaxation of solvent molecules is found to be somewhat stronger than that in diffusion of the anionic solute in these mixtures. We have also calculated the relaxation of hydrogen bonds formed between DMSO and chloroform molecules. The lifetimes of DMSO-chloroform hydrogen bonds are found to increase monotonically with increase in DMSO concentration. The average number of hydrogen bonds and their average energies are also computed. It is found that an increase in DMSO concentration causes a decrease in the number of DMSO-chloroform hydrogen bonds per DMSO or chloroform molecules but increases the strength of these hydrogen bonds.  相似文献   

4.
To understand the mechanism of protein protection by the osmolyte trimethylamine-N-oxide (TMAO) at high pressure, using molecular dynamics (MD) simulations, solvation of hydrophobic group is probed in aqueous solutions of TMAO over a wide range of pressures relevant to protein denaturation. The hydrophobic solute considered in this study is neopentane which is a considerably large molecule. The concentrations of TMAO range from 0 to 4 M and for each TMAO concentration, simulations are performed at five different pressures ranging from 1 atm to 8000 atm. Potentials of mean force are calculated and the relative stability of solvent-separated state over the associated state of hydrophobic solute are estimated. Results suggest that high pressure reduces association of hydrophobic solutes. From computations of site-site radial distribution function followed by analysis of coordination number, it is found that water molecules are tightly packed around the nonpolar particle at high pressure and the hydration number increases with increasing pressure. On the other hand, neopentane interacts preferentially with TMAO over water and although hydration of neopentane reduces in presence of this osmolyte, TMAO does not show any tendency to prevent the pressure-induced dispersion of neopentane moieties. It is also observed that TMAO molecules prefer a side-on orientation near the neopentane surface, allowing its oxygen atom to form favorable hydrogen bonds with water while maintaining some hydrophobic contacts with neopentane. Analysis of hydrogen-bond properties and solvation characteristics of TMAO reveals that TMAO can form hydrogen bonds with water and it reduces the identical nearest neighbor water molecules caused by high hydrostatic pressures. Moreover, TMAO enhances life-time of water-water hydrogen bonds and makes these hydrogen bonds more attractive. Implication of these results for counteracting effect of TMAO against protein denaturation at high pressures are discussed.  相似文献   

5.
The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li(+) ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li(+) ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li(+) ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen bonds.  相似文献   

6.
Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.  相似文献   

7.
The liquid structures of water-tetrahydrofuran (THF) and water-acetone binary mixtures were investigated by the X-ray scattering method. Comparison of the X-ray scattering data revealed that only one kind of intermolecular water-organic molecule interaction is commonly involved throughout all mole fractions of these liquid mixtures, in addition to the intermolecular water-water and organic molecule-organic molecule interactions, which are present in neat water and organic liquids, respectively. On the basis of this finding, we proposed a new analytical method for studying liquid mixtures. By this method the structural information on the intermolecular water-organic molecule interaction as well as the concentrations of the intermolecular water-water, water-organic molecules, and organic molecule-organic molecule interactions were obtained. Combining the concentrations of the intermolecular water-water interaction with the concentrations of water in the liquid mixtures, the number of water-water hydrogen bonds at various mole fractions was experimentally determined for the first time. From the dependence of the number of water-water hydrogen bonds on the composition of the liquid mixtures, the change of the size of the self-associated water-water clusters was deduced.  相似文献   

8.
We have carried out a series of molecular dynamics simulations to investigate the dynamics of X(-)-water (X = F, Cl, Br, and I) and water-water hydrogen bonds in aqueous alkali halide solutions at room temperature and also of Cl(-)-water and water-water hydrogen bonds at seven different temperatures ranging from 238 to 318 K. The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The results of the hydrogen bond dynamics are obtained for two different cutoff values for the angular criterion. In both cases, similar dynamical behavior of the hydrogen bonds is found with respect to their dependence on ion size and temperature. The fluoride ion-water hydrogen bonds are found to break at a much slower rate than water-water hydrogen bonds, while the lifetimes of chloride and bromide ion-water hydrogen bonds are found to be shorter than those of fluoride ion-water ones but still longer than water-water hydrogen bonds. The short-time dynamics of iodide ion-water hydrogen bonds is found to be slightly faster, while its long-time dynamics is found to be slightly slower than the corresponding water-water hydrogen bond dynamics. Correlations of the observed dynamics of anion(water)-water hydrogen bonds with those of rotational and translational diffusion and residence times of water molecules in ion(water) hydration shells are also discussed. With variation of temperature, the lifetimes of both Cl(-)-water and water-water hydrogen bonds are found to show Arrhenius behavior with a slightly higher activation energy for the Cl(-)-water hydrogen bonds.  相似文献   

9.
Using molecular dynamics experiments, we analyze equilibrium and dynamical characteristics related to the solvation of excess protons in water-acetone mixtures. Our approach is based on the implementation of an extended valence-bond Hamiltonian, which incorporates translocation of the excess charge between neighboring water molecules. Different mixtures have been analyzed, starting from the pure water case down to solutions with a water molar fraction x(w) = 0.25. In all cases, we have verified that the structure of the first solvation shell of the H(3)O(+) moiety remains practically unchanged, compared to the one observed in pure water. This shell is composed by three water molecules acting as hydrogen bond acceptors, with no evidence of hydrogen bond donor-like connectivity. Moreover, the increment in the acetone concentration leads to a gradual stabilization of Eigen-like [H(3)O[middle dot](H(2)O)(3)](+) configurations, in detriment of Zundel-like [H[middle dot](H(2)O)(2)](+) ones. Rates of proton transfer and proton diffusion coefficients have been recorded at various water-acetone relative concentrations. In both cases, we have found a transition region, in the vicinity of x(w) ~ 0.8, where the concentration dependences of the two magnitudes change at a quantitative level. A crude estimate shows that, at this tagged concentration, the volumes "occupied" by the two solvents become comparable. The origins of this transition separating water-rich from acetone-rich realms is rationalized in terms of modifications operated in the nearby, second solvation shell, which in the latter solutions, normally includes at least, one acetone molecule. Our results would suggest that one possible mechanism controlling the proton transfer in acetone-rich solutions is the exchange of one of these tagged acetone molecules, by nearby water ones. This exchange would give rise to Zundel-like structures, exhibiting a symmetric, first solvation shell composed exclusively by water molecules, and would facilitate the transfer between neighboring water molecules along the resonant complex.  相似文献   

10.
The formation of structured hydrogen bond networks in the solvation shells immediate to hydrophobic solutes is crucial for a large number of water mediated processes. A long lasting debate in this context regards the mutual influence of the hydrophobic solute into the bulk water and the role of the hydrogen bond network of the bulk in supporting the solvation structure around a hydrophobic molecule. In this context we present a molecular dynamics study of the solvation of various hydrophobic molecules where the effect of different regions around the solvent can be analyzed by employing an adaptive resolution method, which can systematically separate local and nonlocal factors in the structure of water around a hydrophobic molecule. A number of hydrophobic solutes of different sizes and two different model potential interactions between the water and the solute are investigated.  相似文献   

11.
The molecular mechanism of urea-induced protein denaturation is not yet fully understood. Mainly two opposing mechanisms are controversially discussed, according to which either hydrophobic, or polar interactions are the dominant driving force. To resolve this question, we have investigated the interactions between urea and all 20 amino acids by comprehensive molecular dynamics simulations of 22 tripeptides. Calculation of atomic contact frequencies between the amino acids and solvent molecules revealed a clear profile of solvation preferences by either water or urea. Almost all amino acids showed preference for contacts with urea molecules, whereas charged and polar amino acids were found to have slight preferences for contact with water molecules. Particularly strong preference for contacts to urea were seen for aromatic and apolar side-chains, as well as for the protein backbone of all amino acids. Further, protein-urea hydrogen bonds were found to be significantly weaker than protein-water or water-water hydrogen bonds. Our results suggest that hydrophobic interactions are the dominant driving force, while hydrogen bonds between urea and the protein backbone contribute markedly to the overall energetics by avoiding unfavorable unsatisfied hydrogen bond sites on the backbone. In summary, we suggest a combined mechanism that unifies the two current and seemingly opposing views.  相似文献   

12.
Monte Carlo simulations have been performed to explore the solution structure of ethyl, isopropyl, isobutyl, and tertiary butyl alcohols in pure water, pure acetonitrile, and different mixtures of the two solvents. The explicit solvent studies in NpT ensembles at T = 298 K illustrate that the solute "discriminates" the solvent's components and that the composition of the first solvation shell differs from that of the bulk solution. Since the polarizable continuum dielectric method (PCM) does not presently model the solvation of molecules with both polar and apolar sites in mixed protic solvents, we suggest a direction for further program development wherein a continuum dielectric method would accept more than one solvent and the solute sites would be solvated by user-defined solvent components. The prevailing solvation model will be determined upon the lowest free energy calculated for a particular solvation pattern of the solute having a specific conformational/tautomeric state. Characterization of equilibrium hydrogen-bond formation becomes a complicated problem that depends on the chemical properties of the solute and its conformation, as well as upon the varying nature of the first solvation shell. For example, while the number of hydrogen bonds to secondary and tertiary alcohol solutes are nearly constant in pure water and in water-acetonitrile mixtures with at least 50% water content, the number of hydrogen bonds to primary alcohols gradually decreases for most of their conformations when acetonitrile content is increased. Nonetheless, the calculations indicate that O-H...O(water) hydrogen bonds are still possible in a small fraction of the arrangements for the solution models with water content of 30% or less. The isopentene solute does not form any observable hydrogen bonds, despite having an electron-rich, double-bond site.  相似文献   

13.
Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within this layer, water molecules show marked orientations relative to a peptide surface. Using the two-particle contribution to entropy as a measure of structural ordering of water, we found that the first solvation shell contributes 95% or more to the total water ordering around the peptide molecule. In investigating the dynamic properties of water, diffusion coefficients and lifetime of the hydrogen bond, clear differences between solvation layer and the bulk water were observed. It was found that the translational diffusion coefficient, D(T), decreases by 30% or more compared to bulk water; also, the lifetime of the water-water hydrogen bond clearly increases. The rotational diffusion coefficient, however, decreases only slightly, no more than approximately 10%. These differences correspond to the slightly higher energy of the hydrogen bond, and to its slightly distorted geometry. Analyzing the translational dynamics of water in the vicinity of the peptide molecule, it was deduced that the structure of the first solvation shell becomes more rigid than the structure of the bulk water. Investigation of a "pure hydrophobic" form of the polypeptide shows that the structure and the properties of water within the solvation shell are predominantly determined by the hydrophobic effect. The specific interactions between water molecules and various charge groups of the peptide molecule modifies this effect only slightly.  相似文献   

14.
We have carried out a series of molecular dynamics simulations to investigate the hydrogen bond and residence dynamics of X(-)-water (X=F, Cl, and I) and pairs in aqueous solutions at a temperature of 673 K. The calculations are done at six different water densities ranging from 1.0 to 0.15 g cm(-3). The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The F(-)-water hydrogen bonds are found to have a longer lifetime than all other hydrogen bonds considered in the present study. The lifetime of Cl(-)-water hydrogen bonds is shorter than that of F(-)-water hydrogen bonds but longer than the lifetime of water-water hydrogen bonds. The lifetimes of I(-)-water and water-water hydrogen bonds are found to be very similar. Generally, the lifetimes of both anion-water and water-water hydrogen bonds are found to be significantly shorter than those found under ambient conditions. In addition to hydrogen bond lifetimes, we have also calculated the residence times and the orientational relaxation times of water molecules in ion(water) hydration shells and have discussed the correlations of these dynamical quantities with the observed dynamics of anion(water)-water hydrogen bonds as functions of the ion size and density of the supercritical solutions.  相似文献   

15.
The enthalpies of solution of uracil and its alkylated derivatives in water, methanol, N,N-dimethylformamide (DMF) and water+DMF mixtures were measured at 25°C. The enthalpies of solvation were determined. The enthalpies of cavity formation, corresponding to the enthalpies of solvent-solvent interactions were calculated and the enthalpies of solute-solvent interactions were obtained. The presence of the alkyl groups was found to have different effects on the enthalpy of interaction depending on the position and size of the substitution. The effect of alkylation at the nonpolar side of the uracil ring was found to arise mostly from the enhancement of the van der Waals interactions. The alkyl substitutions at the polar side resulted also in the removal of the solvent molecules interacting specifically with the polar groups of uracil. The enthalpy of those specific interactions was determined and found to be stronger in methanol and DMF than in water. Enthalpies of solvation in the binary water+DMF solvent were found to depend in a nonlinear way on the solvent composition. The nonlinearities in the water-rich region were found to arise from the decay of the hydrophobic hydration of the solutes with the increasing DMF content. The substitution of two methyl groups caused the uracil molecule to bahave as a predominantly hydrophobic solute. The nonlinearities in the DMF-rich region were found only for those solutes which can form hydrogen bonds with DMF.  相似文献   

16.
Molecular dynamics simulations of dilute and concentrated aqueous NaCl solutions are carried out to investigate the changes of the hydrogen bonded structures in the vicinity of ions for different ion concentrations. An analysis of the hydrogen bond population in the first and second solvation shells of the ions and in the bulk water is done. Although essentially no effect of ions on the hydrogen bonding is observed beyond the first solvation shell of the ions for the dilute solutions, for the concentrated solutions a noticeable change in the average number of water-water hydrogen bonds is observed in the second solvation shells of the ions and even beyond. However, the changes in the average number of hydrogen bonds are found to be relatively less when both water-water and ion-water hydrogen bonds are counted. Thus, the changes in the total number of hydrogen bonds per water are not very dramatic beyond the first solvation shell even for concentrated solutions.  相似文献   

17.
The solvation of tetramethylammonium chloride (Me4NCl) and tetra-n-butylammonium chloride (Bu4NCl) in water-acetonitrile mixtures was investigated by mass spectrometry of clusters isolated from the solution. As far as the positive ions are concerned, clusters composed of alkylammonium ions and acetonitrile molecules only were observed, even for mixtures with high water content. In contrast, for the negative ions, clusters composed of chloride with both water and/or acetonitrile molecules were observed. For the smaller system (Me4NCl) we performed quantum chemical calculations and molecular dynamics simulations. It was found that even though water is present in the solvation shell of Me4N+, only acetonitrile has a strong electrostatic interaction with the cation. Water molecules around Me4N+ form hydrogen bonds with other water molecules, and they interact with Me4N+ mainly via dispersive interactions. These results indicate that Me4N+ behaves like a hydrophobic solute. On the other hand, the interaction of Cl- with water and acetonitrile is of comparable strength and, in both cases, the electrostatic interaction dominates. Herein we demonstrate experimentally and theoretically that positive and negative ions give rise to characteristic solvation structures in mixed solvents: even a relatively small organic cation, such as Me4N+, exhibits a hydrophobic-like solvation shell.  相似文献   

18.
We study the solvation of iodide in water using density functional theory based molecular-dynamics simulations. Detailed analysis of the structural and dynamical properties of the first solvation shell is presented, showing a disruptive influence of the ion on the local water structure. Iodide-water hydrogen bonding is weak, compared to water-water hydrogen bonds. This effective repulsive ion-water interaction leads to the formation of a quite unstructured solvation shell. The dynamics of water molecules surrounding the iodide is relatively fast. The intramolecular structural and electronical properties of water molecules around the ion are not affected.  相似文献   

19.
The time dependent change in the intermolecular response of solvent molecules following photoexcitation of Coumarin 102 (C102) has been measured in acetonitrile-water binary mixtures. Experiments were performed on mixtures of composition x(CH3CN) = 0.25, 0.50, 0.75, and 1.00. At low water concentrations (x(H2O) < or = 0.25) the solvent response is consistent with previous measurements probing dipolar solvation. With increasing water concentration (x(H2O) > or = 0.50) an additional response is found subsequent to dipolar solvation, exhibited as a rapid gain in the solvent's polarizability on a approximately 250 fs time scale. Monte Carlo simulations of the C102:binary mixture system were performed to quantify the number of hydrogen-bonding interactions between C102 and water. These simulations indicate that the probability of the C102 solute being hydrogen bound with two water molecules, both as donors at the carbonyl site, increases in a correlated fashion with the amplitude of the additional response in the measurements. We conclude that excitation of C102 simultaneously weakens and strengthens hydrogen bonding in complexes with two inequivalently bound waters.  相似文献   

20.
Mean spherical approximation (MSA) for electrolyte solution has been extended to investigate the role of partial solvent polarization densities around an ion in a completely asymmetric binary dipolar mixture. The differences in solvent diameters, dipole moments, and ionic size are incorporated systematically within the MSA framework in the present theory for the first time. In addition to the contributions due to difference in dipole moments, the solvent-solvent and ion-solvent size ratios are found to significantly affect the nonideality in binary dipolar mixtures. Subsequently, the theory is used to investigate the role of ion-solvent and solvent-solvent size ratios in determining the nonideality in Born free energy of solvation of a unipositive rigid ion in alcohol-water and dimethyl sulfoxide-acetonitrile mixtures, where the solvent components are represented only by their molecular diameters and dipole moments. Nonideality in Born free energy of solvation in such simplified mixtures is found to be stronger for smaller ions. The slope of the nonideality for smaller alkali metal ions in methanol-water mixture is found to be opposite to that for larger ion, such as quaternary tertiary butyl ammonium ion. For ethanol-water mixtures, the slopes are in the same direction for all the ions studied here. These results are in qualitative agreement with experiments, which is surprising as the present MSA approach does not include the hydrogen bonding and hydrophobic interactions present in the real mixtures. The calculated partial polarization densities around a unipositive ion also show the characteristic deviation from ideality and reveal the microscopic origin of the ion and solvent size dependent preferential solvation. Also, the excess free energy of mixing (in the absence of any ion) for these binary mixtures has been calculated and a good agreement between theory and experiment has been found.  相似文献   

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