Structure-breaking effects of solvated Rb(I) in dilute aqueous solution--an ab initio QM/MM MD approach

Structural properties of the hydrated Rb(I) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at the double-zeta HF quantum mechanical level. The first shell coordination number was found to be 7.1, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and theta-angle distributions allowed the full characterization of the hydration structure of the Rb(I) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions, as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes, and rate constants were also analyzed. The mean ligand residence time for the first shell was determined as tau = 2.0 ps.     

Atomistic simulations of hydrated nafion and temperature effects on hydronium ion mobility

The effects of hydration level and temperature on the nanostructure of an atomistic model of a Nafion (DuPont) membrane and the vehicular transport of hydronium ions and water molecules were examined using classical molecular dynamics simulations. Through the determination and analysis of structural and dynamical parameters such as density, radial distribution functions, coordination numbers, mean square deviations, and diffusion coefficients, we identify that hydronium ions play an important role in modifying the hydration structure near the sulfonate groups. In the regime of low level of hydration, short hydrogen bonded linkages made of water molecules and sometimes hydronium ions alone give a more constrained structure among the sulfonate side chains. The diffusion coefficient for water was found to be in good accord with experimental data. The diffusion coefficient for the hydronium ions was determined to be much smaller (6-10 times) than that for water. Temperature was found to have a significant effect on the absolute value of the diffusion coefficients for both water and hydronium ions.     

The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation

The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.     

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. II. Two-dimensional infrared and peak shift observables within different theoretical approximations

In a previous report, we calculated the infrared absorption spectrum and both the isotropic and anisotropic pump-probe signals for the OD stretch of isotopically dilute water in dilauroylphosphatidylcholine (DLPC) multi-bilayers as a function of the lipid hydration level. These results were then compared to recent experimental measurements and are in generally good agreement. In this paper, we will further investigate the structure and dynamics of hydration water using molecular dynamics simulations and calculations of the two-dimensional infrared and vibrational echo peak shift observables for hydration water in DLPC membranes. These observables have not yet been measured experimentally, but future comparisons may provide insight into spectral diffusion processes and hydration water heterogeneity. We find that at low hydration levels the motion of water molecules inside the lipid membrane is significantly arrested, resulting in very slow spectral diffusion. At higher hydration levels, spectral diffusion is more rapid, but still slower than in bulk water. We also investigate the effects of several common approximations on the calculation of spectroscopic observables by computing these observables within multiple levels of theory. The impact of these approximations on the resulting spectra affects our interpretation of these measurements and reveals that, for example, the cumulant approximation, which may be valid for certain systems, is not a good approximation for a highly heterogeneous environment such as hydration water in lipid multi-bilayers.     

Nonideality in diffusion of ionic and hydrophobic solutes and pair dynamics in water-acetone mixtures of varying composition

We have performed a series of molecular dynamics simulations of water-acetone mixtures containing either an ionic solute or a neutral hydrophobic solute to study the extent of nonideality in the dynamics of these solutes with variation of composition of the mixtures. The diffusion coefficients of the charged solutes, both cationic and anionic, are found to change nonmonotonically with the composition of the mixtures showing strong nonideality of their dynamics. Also, the extent of nonideality in the diffusion of these charged solutes is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and acetone molecules in these mixtures which show a somewhat similar changes in the solvation characteristics of charged and dipolar solutes with changes of composition of water-acetone mixtures. The diffusion of the hydrophobic solute, however, shows a monotonic increase with increase of acetone concentration showing its different solvation characteristics as compared to the charged and dipolar solutes. The links between the nonideality in diffusion and solvation structures are further confirmed through calculations of the relevant solute-solvent and solvent-solvent radial distribution functions for both ionic and hydrophobic solutes. We have also calculated various pair dynamical properties such as the relaxation of water-water and acetone-water hydrogen bonds and residence dynamics of water molecules in water and acetone hydration shells. The lifetimes of both water-water and acetone-water hydrogen bonds and also the residence times of water molecules are found to increase steadily with increase in acetone concentration. No maximum or minimum was found in the composition dependence of these pair dynamical quantities. The lifetimes of water-water hydrogen bonds are always found to be longer than that of acetone-water hydrogen bonds in these mixtures. The residence times of water molecules are also found to follow a similar trend.     

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.     

Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: a proton conducting electrolytic component in fuel cells

Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.     

Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables

The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations.     

Structural and dynamical properties of the Hg2+ aqua ion: a molecular dynamics study

Molecular dynamics simulations of the Hg2+ ion in aqueous solution have been carried out using an effective two-body potential derived from quantum mechanical calculations. A stable heptacoordinated structure of the Hg2+ first hydration shell has been observed and confirmed by extended X-ray absorption fine structure (EXAFS) experimental data. The structural properties of the Hg2+ hydration shells have been investigated using radial and angular distribution functions, while the dynamical behavior has been discussed in terms of reorientational correlation functions, mean residence times of water molecules in the first and second hydration shells, and self-diffusion coefficients. The effect of water-water interactions on the Hg2+ hydration properties has been evaluated using the SPC/E and TIP5P water models.     

Comparison of the hydration and diffusion of protons in perfluorosulfonic acid membranes with molecular dynamics simulations. scui@utk.edu

Classical molecular dynamics (MD) simulations were performed to determine the hydrated morphology and hydronium ion diffusion coefficients in two different perfluorosulfonic acid (PFSA) membranes as functions of water content. The structural and transport properties of 1143 equivalent weight (EW) Nafion, with its relatively long perfluoroether side chains, are compared to the short-side-chain (SSC) PFSA ionomer at an EW of 977. The separation of the side chains was kept uniform in both ionomers consisting of -(CF 2) 15- units in the backbone, and the degree of hydration was varied from 5 to 20 weight % water. The MD simulations indicated that the distribution of water clusters is more dispersed in the SSC ionomer, which leads to a more connected water-channel network at the low water contents. This suggests that the SSC ionomer may be more inclined to form sample-spanning aqueous domains through which transport of water and protons may occur. The diffusion coefficients for both hydronium ions and water molecules were calculated at hydration levels of 4.4, 6.4, 9.6, and 12.8 H 2O/SO 3H for each ionomer. When compared to experimental proton diffusion coefficients, this suggests that as the water content is increased the contribution of proton hopping to the overall proton diffusion increases.     

Influence of concentration and temperature on the dynamics of water in the hydrophobic hydration shell of tetramethylurea

We study the influence of the amphipilic compound tetramethylurea (TMU) on the dynamical properties of water, using dielectric relaxation spectroscopy in the regime between 0.2 GHz and 2 THz. This technique is capable of resolving different water species, their relative fractions, and their corresponding reorientation dynamics. We find that the reorientation dynamics of water molecules in the hydration shell of the hydrophobic groups of TMU is between 3 (at low concentrations) and 10 (at higher concentrations) times slower than the dynamics of bulk water. The data indicate that the effect of hydrophobic groups on water is strong but relatively short-ranged. With increasing temperature, the fraction of water contained in the hydrophobic hydration shell decreases, which implies that the overall effect of hydrophobic groups on water becomes smaller.     

Atomistic simulation of nafion membrane. 2. Dynamics of water molecules and hydronium ions

We have performed a detailed and comprehensive analysis of the dynamics of water molecules and hydronium ions in hydrated Nafion using classical molecular dynamics simulations with the DREIDING force field. In addition to calculating diffusion coefficients as a function of hydration level, we have also determined mean residence time of H(2)O molecules and H(3)O(+) ions in the first solvation shell of SO(3)(-) groups. The diffusion coefficient of H(2)O molecules increases with increasing hydration level and is in good agreement with experiment. The mean residence time of H(2)O molecules decreases with increasing membrane hydration from 1 ns at a low hydration level to 75 ps at the highest hydration level studied. These dynamical changes are related to the changes in membrane nanostructure reported in the first part of this work. Our results provide insights into slow proton dynamics observed in neutron scattering experiments and are consistent with the Gebel model of Nafion structure.     

Dynamics of fresh and freeze-dried strawberry and red onion by quasielastic neutron scattering

The microscopic behavior of fresh and freeze-dried strawberry and red onion at different water contents (45 and 20 wt % water) has been investigated by quasielastic neutron scattering (QENS). To distinguish between the dynamics of the water and the biological material isotopic (H/D) substitution was used. The results show that all samples exhibit an onset of anharmonic motions on the experimental time scale (3-100 ps) at about 230-240 K. Above 250 K the dynamics is mainly of translational character and strongly dependent on the hydration level. The diffusion constant increases rapidly with increasing water content and at 280 K it is approximately 20% higher for the hydration water in freeze-dried strawberry than in freeze-dried red onion and around 2 orders of magnitude faster for the hydration water than for the biological material. Moreover, the diffusion constant of the biological part is about 50% faster in freeze-dried strawberry than in freeze-dried red onion. It was also found that the average relaxation time is slightly faster in fresh strawberry than in freeze-dried strawberry. From the results we can conclude that the water dynamics is not only promoting motions in the biological material, it is also affected by the structure (and possibly also the dynamics) of the biological material. Thus, the microscopic properties of the biological materials are interrelated with the properties of their hydration water.     

Single particle and pair dynamics in water-formic acid mixtures containing ionic and neutral solutes: nonideality in dynamical properties

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.     

Asymmetry of lipid bilayers induced by monovalent salt: atomistic molecular-dynamics study

Interactions between salt ions and lipid components of biological membranes are essential for the structure, stability, and functions of the membranes. The specific ionic composition of aqueous buffers inside and outside of the cell is known to differ considerably. To model such a situation we perform atomistic molecular-dynamics (MD) simulations of a single-component phosphatidylcholine lipid bilayer which separates two aqueous reservoirs with and without NaCl salt. To implement the difference in electrolyte composition near two membrane sides, a double bilayer setup (i.e., two bilayers in a simulation box) is employed. It turns out that monovalent salt, being in contact with one leaflet only, induces a pronounced asymmetry in the structural, electrostatic, and dynamical properties of bilayer leaflets after 50 ns of MD simulations. Binding of sodium ions to the carbonyl region of the leaflet which is in contact with salt results in the formation of "Na-lipids" complexes and, correspondingly, reduces mobility of lipids of this leaflet. In turn, attractive interactions of chloride ions (mainly located in the aqueous phase close to the water-lipid interface) with choline lipid groups lead to a substantial (more vertical) reorientation of postphatidylcholine headgroups of the leaflet adjoined to salt. The difference in headgroup orientation on two sides of a bilayer, being coupled with salt-induced reorientation of water dipoles, leads to a notable asymmetry in the charge-density profiles and electrostatic potentials of bilayer constitutes of the two leaflets. Although the overall charge density of the bilayer is found to be almost insensitive to the presence of salt, a slight asymmetry in the charge distribution between the two bilayer leaflets results in a nonzero potential difference of about 85 mV between the two water phases. Thus, a transmembrane potential of the order of the membrane potential in a cell can arise without ionic charge imbalance between two aqueous compartments.     

Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization

N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.     

Simulations of lipid adsorption on TiO2 surfaces in solution

Molecular dynamics simulations are carried out to study the adsorption of three lipids, namely, DOPC, DOPS, and DMTAP, on TiO2(110) rutile surfaces and the influence of the interface on their conformational properties. Three types of rutile (110) surfaces, characterized by a different degree of hydroxylation (the neutral nonhydroxylated and hydroxylated surfaces and a partially hydroxylated surface with charge density corresponding to physiological pH) are investigated using force fields derived from ab initio calculations and experimental data. It is found that the stability of the adsorbate and the strength of the attachment are strictly connected with the nature of both the lipid and the surface. Direct coordination of the phosphate or carbonyl oxygens of the lipids with available titanium sites, observed in the case of partially or nonhydroxylated layers, determines stronger adsorption and, as a consequence, reduced dynamics. For a given hydration state of the surface, the adsorption strengths are in the order DOPS > DOPC > DMTAP, in agreement with experimental data according to which the presence of DOPS units inside lipid bilayers favors stronger adsorption and lower mobility. The adsorption geometry, the hydration state of the lipid headgroups, and the dynamical processes (detachment, diffusion, etc.) occurring at the lipid/oxide interface are analyzed in detail, putting on a roughly quantitative basis time scales and energy barriers of the latter processes.     

Molecular dynamics simulation of nanoscale distribution and mobility of water and dimethylmethylphosphonate in sulfonated polystyrene

The interest in a better understanding of the specific interactions of phosphor-organic compounds and water with sulfonated polystyrene (sPS) is motivated by the use of block copolymers as protective membranes against chemical warfare agents. Using classical molecular dynamics simulations, we explored the nanoscale segregation and diffusion of water and nerve gas simulant dimethylmethylphosphonate (DMMP) in sPS neutralized with calcium counterions at different sulfonation and hydration levels. The water content was varied from 15 to 54% of dry polymer weight, and the DMMP content was varied from 0 to 100 wt %. We found that, in the 40% sulfonated polystyrene, water forms well defined aggregates, which grow in size as the hydration increases, reaching approximately 20 A at the maximum water content. In the 100% sulfonated polystyrene, the overall structure of hydrated polymer is more uniform with smaller water aggregates. Diffusion of water at the same number of water molecules per sulfonate group is faster at a lower sulfonation level. The solvation of sPS in water-DMMP binary mixtures was found to differ substantially from Nafion, where DMMP forms a layer between the hydropholic and hydrophobic subphases. In sPS with divalent Ca(2+) counterions, DMMP and water compete for the solvation of the sulfonate group. At high water and DMMP contents, the diffusion of DMMP turned out to be rather fast with a diffusion coefficient of ca. 30% of that of water. At the same time, water diffusion slows down as the DMMP concentration increases. This observation suggests that although sPS is permeable for both solvents, water and DMMP are partially segregated on the scale of 1-2 nm and have different pathways through the system. The nonuniform nanoscale distribution of water and DMMP in sPS is confirmed by analyses of different pair correlation functions. This feature may significantly affect the perm-selective properties of sPS-contained block copolymer membranes.