Dynamics Simulations Of Aqueous Solutions Research Articles

Dynamical properties of water in aqueous solutions of l-ascorbic and dehydroascorbic acids; molecular dynamics simulations

Molecular dynamics simulations of aqueous solutions of l-ascorbic acid and l-dehydroascorbic acid were performed to evaluate their influence on the dynamical properties and structure of water. The simulations show that the presence of vitamin C very strongly disturbs the hydrogen bonding pattern of the SPC/E water as well as its dynamics properties, producing a simultaneous decrease in water bonded molecules and a diminution of the diffusion coefficient, the oxidized form being responsible for the more remarkable changes. These results are in agreement with those observed by low-frequency Raman scattering, which states that the AA influences the deformations on the temporal tetrahedral water structure.

Molecular dynamics simulation in aqueous solution of N -methylazetidinone as a model of β -lactam antibiotics

In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model β-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the effect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of β-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to different hydrolysis mechanisms having similar energy barriers at the rate-limiting step of the reaction path. In the first type, the β-lactam-water interaction takes place through the oxygen carbonyl atom and there is agreement between the maxima of the RDFs obtained here and the ab initio structure of the complexes previously reported. In the second type, the interaction takes place through the nitrogen atom and we do not predict a coordination layer around the β-lactam nitrogen atom. The results suggest that in aqueous solution hydrolysis of the carbonyl group is the most probable starting point for the overall hydrolysis reaction. Some discussion on the use of cluster models to represent the solvent effect is included.

Molecular Dynamics Simulations of 1,2-Dimethoxyethane in Aqueous Solution: Influence of the Water Potential

We have performed molecular dynamics simulations of aqueous solutions of 1,2-dimethoxyethane (DME), an oligomer of poly(ethylene oxide), employing several potentials for water. Specifically, we investigated the structural, conformational, and dynamic properties of DME/water solutions as a function of composition using the TIP4P, MCY, SPC, and SPC/E potentials for water. DME/DME interactions were described using our previously derived quantum-chemistry-based potential, while the DME/water potential was parametrized for each water model to best represent the energy of a DME/water complex as determined from high-level quantum chemistry calculations. For dilute (water-rich) solutions, static and dynamic properties were found to depend only weakly on the water model employed. For more concentrated solutions, important differences between the models were observed, particularly in the structure of the solutions (e.g., the size of water clusters) and the self-diffusion coefficient of water.

Atomic Charges of the Water Molecule and the Water Dimer

Atomic charges in the water molecule and the water dimer have been calculated by two different schemes for partitioning the total charge distribution: Mulliken charges and atomic polar tensor-based charges. Large-scale calculations have been carried out where the basis set has been increased systematically toward the basis-set limit. The Mulliken charges are highly sensitive to the choice of basis, and no convergence is observed. In contrast, atomic charges obtained from the trace of the atomic polar tensor exhibit rapid basis-set convergence. We have also investigated the effects of electron correlation on the atomic charges of the water molecule. Finally, the polarization and charge-transfer effects on the atomic charges have been calculated for the water dimer. The importance of such terms in a water potential used in molecular dynamics simulations of aqueous solutions is discussed.

Computer simulation of the effect of salt on the hydrophobic effect

Molecular dynamics simulations of aqueous solutions containing methane and sodium chloride reveal the existence of a structured hydration shell around the non-polar solutes, although this hydration shell is less well defined than in the case where salt is absent. It was also observed that hydrogen bonds made from the hydration shell across to the bulk are weaker than those in the bulk, with or without salt. Although the geometry of the hydrogen bonds is preserved, there is a larger fraction of broken hydrogen bonds in the hydration shell of the non-polar solutes than in the bulk of the solution, the difference increasing with increasing temperature. The number of broken H bonds is significantly larger in the presence of salt, and should contribute to an increase in the free energy of dissolution and hence to a lowering of the solubility and an increase in the hydrophobic interaction.

Conformational Free Energy Landscape of ApApA from Molecular Dynamics Simulations

A conformational free energy landscape of the biological macromolecule adenylyl-3‘,5‘-adenylyl-3‘,5‘-adenosine is presented. The aim was to explore the stacking−unstacking process of the trimer. The free energy landscape was created from two-dimensional potential of mean force calculations based on 324 molecular dynamics simulations in aqueous solution. A large number of conformational states and substrates with various transition barriers were observed. In the free energy landscape we can follow the changes of the stacking to unstacking process for the trimer. The lowest minimum in the free energy landscape was observed for the trimer having all three bases stacked. Local minima were found for the trimer having two bases stacked and one unstacked.

Hydrogen-bonding behaviour in the hydrophobic hydration of simple hydrocarbons in water

The results of a series of molecular dynamics simulations of aqueous solutions of methane and ethane and of pure water are reported. The results imply a larger fraction of broken hydrogen bonds in the hydration shell of non-polar solutes with respect to bulk water, the difference increasing with rise of temperature. Evidence is found of stronger hydrogen bonds in the hydration shell. The results can be related to Muller's modified hydration-shell hydrogen-bond model of hydrophobic hydration, based on the notion of hydrogen bonds in the hydration shell of non-polar solutes having smaller bond-breaking Gibbs energies. This picture of hydrogen-bonding is reinterpreted in the light of recent themodynamic models of hydrophobic hydration.

Molecular simulation study of solvation structure in supercritical aqueous solutions

We report new molecular dynamics simulations of aqueous solutions that consist of various solutes (xenon, NaCl, benzene, toluene, and benzonitrile) at infinite dilution in supercritical water at two thermodynamic states: one at the critical density and at 5% above the critical temperature, the other at 50% above the critical density and along the critical isotherm. These new simulations complement our previous simulations of infinitely dilute supercritical aqueous solutions of argon, Na +, Cl −, and methanol at the same state points. The aim of this work is to determine the solvation structure around various solutes in supercritical water with the goal of developing a molecular understanding of the solubility of nonpolar noble gases, ionic fluids and organics in supercritical water. Such an understanding can provide important insight into fundamental aspects of supercritical water oxidation of organic wastes. In addition, we report thermodynamic properties and solute—solvent structural quantities for the various solutes.

Solution structure of HIV-1 protease-allophenylnorstatine derivative inhibitor complex obtained from molecular dynamics simulation.

Structures of two enzyme-inhibitor complexes of human immunodeficiency virus-1 protease with allophenylnorstatine derivatives were obtained from molecular dynamics simulation in aqueous solution. The stronger inhibitor gave considerably smaller fluctuation at P3 site, which formed hydrogen bonding with the enzyme flap region.

Conformations of triglycyl‐lysylvasopressin: 1H NMR spectroscopic and molecular dynamics study

AbstractThe conformation of N‐(Gly‐Gly‐Gly)‐Lys‐vasopressin (TGVP) in aqueous solution was determined by 1H NMR spectroscopy. The structural data were compared with those obtained in DMSO. Refinement of the structure derived from NMR data and a description of the conformational dynamics were accomplished by molecular dynamics simulations in aqueous solution.

Three-Dimensional Structure and Molecular Dynamics of cis(Z)- and trans(E)-Chlorprothixene

cis( Z)-Chlorprothixene has antidopaminergic potency, while trans(E)-chlorprothixene is virtually inactive. In order to reveal the structural features causing the difference in activity, the three- dimensional molecular and electronic structures of cis(Z)- and trans(E)- chlorprothixene were examined by computer graphics and molecular mechanical and quantum mechanical calculations. The internal molecular motions of the isomers were studied by molecular dynamics simulations in vacuo and In aqueous solution. The cis(2)-isomer had lower potential molecular energy than the trans(E)-isomer, mainly due to electrostatic interactions within the side-chain and between the dimeth- ylamino group and the chlorine atom. During molecular dynamics simulations in aqueous solution, the side-chain of the trans(E)-isomer stayed closer to the central S-C axis of the ring system than did the side-chain of the cis(Z)-isomer. The molecular electrostatic potentials were significantly lower in the vicinity of the chlorine atom in the trans(E)- than in the cis(Z)-isomer. Differences in molecular electrostatic potentials and in three-dimensional structure are suggested to be the main reasons for the difference in pharmacological activities of cis(Z)- and trans(E)- chlorprothixene.

Molecular structure and dynamics of serotonin

The electronic structure and low-energy conformations of the protonated serotonin molecule were examined by quantum mechanical and molecular mechanical calculations based on the AMBER force field. The flexibility and internal motions of the molecule, which may be important for its mode of receptor interaction, were examined by molecular dynamics simulations in vacuo and in aqueous solution. Two crystal structures and four computed serotonin structures were used as starting points in the calculations. Both gauche and anti conformers were observed during molecular dynamics simulations in aqueous solution, but only gauche conformers of serotonin were observed in vacuo. The simulations demonstrated that the side chain conformation may adjust in order to fit into a receptor binding site. Energy refined gauche conformers had lowest molecular energies both in vacuo and in aqueous solution. Ab initio molecular electrostatic potentials were calculated in 4 layers surrounding the molecule and projected into net atomic point charges. The effect of the hydroxyl group in lowering the molecular electrostatic potentials around the phenyl ring was highly dependent on the conformation of the side chain. Conformers with an extended side chain had significantly lower electrostatic potentials over the phenyl ring than those with a folded conformation.

Estimation of the OH-vibrational frequency shifts from MD simulations of aqueous electrolyte solutions

Interaction energy parameters obtained from molecular dynamics simulations of aqueous solutions of CsF, LiI and NaClO 4 have been employed to calculate OH-vibration frequency shifts by means of the formula given by Buckingham. The calculations reproduce the trends of experimentally observed spectral changes correctly; quantitative deviations are discussed as cooperativity and IR band intensity changes.

Polarization constraints in molecular dynamics simulation of aqueous solutions: The surface constraint all atom solvent (SCAAS) model

A dynamical all-atom surface-constrained model for simulation of ions in polar solvents is presented. This model, which is based on the previously proposed SCSSD model, concentrates on the key electrostatic aspect of solvent polarization. The constraints of the model ensure that the polarization and other properties of the surface molecules in systems with a small number of solvent molecules will be similar to the corresponding properties in an infinite system. The model is quite effective and is expected to be very useful in reducing the convergence problems associated with using periodic boundary conditions.