Molecular dynamics at constant pressure and temperature

Methods are discussed for generating by molecular dynamics isobaric-isoenthalpic, NPH, isochoric-isothermal, NVT, and isobaric-isothermal, NPT, ensembles. Andersen's constant-pressure method is reformulated so that the ensemble rather than the scaled system is directly calculated. Four constant-temperature schemes were considered. Two involve the addition of a stochastic collision term to the molecular trajectories. The Andersen method and a stochastic dynamics approach were examined. The latter employed a velocity damping term in addition to the random force. Two other methods employed uniform velocity scaling applied to all molecules. The NPT algorithm induces a transition to the dilute phase for a Lennard-Jones fluid in the spinodal region (p^* = 0.5, T^* = 1.28) of the phase diagram. The thermodynamic equivalence of the ensembles is demonstrated by long calculations of the chemical potential of Lennard-Jones states by the particle insertion method. The internal energy, pressure, constant volume and pressure specific heats, adiabatic compressibilities, pair radial distribution functions and self-diffusion coefficients are also evaluated. Only for second-order thermodynamic quantities is there evidence of an ensemble dependence.     

Direct dynamics study of the hydrogen-abstraction reaction of 1,1,2,2,3-fluorinated propane with the hydroxyl radical

The hydrogen abstraction reactions by a hydroxyl radical from 1,1,2,2,3-fluorinated propane (CF2HCF2CFH2) have been investigated by the dual-level direct dynamics method. Three equilibrium conformers (I, II, III) of CF2HCF2CFH2, one with Cs and two with C1 symmetries, are identified by the rotations of -CFH2 and -CF2H groups. Two transition states are located for the conformer I (Cs symmetry) + OH --> products (R1) reaction, and three distinct transition states are identified for conformers II and III (C1 symmetry) + OH --> products (R2 and R3). The optimized geometries and harmonic vibrational frequencies of all reactants, complexes, transition states, and products are calculated at the BB1K/6-31+G(d,p) level of theory. The single-point energy calculations are performed at the G3(MP2) level using the BB1K geometries. Using improved canonical variational transition-state theory (ICVT) with the small-curvature tunneling correction (SCT), the rate constants for each channel are calculated over a wide temperature range of 200-2000 K. It is found that the H-abstraction reaction from the -CFH2 group is the predominant product channel for three reactions. The total rate constant is evaluated by the Boltzmann distribution function, and the agreement between theoretical and experimental values is good.     

Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion

One nanosecond molecular dynamics (MD) simulation of a thymine glycol (TG)-lesioned part of human lymphoblast AG9387 was performed to determine structural changes in DNA molecule caused by the presence of a lesion. These changes can be significant for proper recognition of lesions by a repair enzyme. Thymine glycol is the DNA oxidative lesion formed by addition of OH radicals to C5 and C6 atoms of the thymine base. This lesion is known as causing Cockayne Syndrome-inherited genetic disorder. Distribution of water molecules in a hydration shell around the DNA molecule was analyzed for its contribution to the recognition of the TG lesion by the repair enzyme. The results of MD simulation show there is a specific DNA structural configuration formed at the lesion. After 500 ps the DNA is bent in a kink at the TG site. This change dislocates the glycosyl bond at C5' to a position closer to the DNA surface, and thus its atoms are more exposed to the surrounding water shell. The increased number of water molecules that are close to the TG site indicates that the glycosyl bond may be easily contacted by the repair enzyme. In addition, the higher number of water molecules at the TG site substantiates the importance of water-mediated hydrogen bonds created between the repair enzyme and the DNA upon formation of the complex. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1723-1731, 2001     

Molecular dynamics simulations of peptide carboxylate hydration

Aqueous solvation of carboxylate groups, as present in the glycine zwitterion and the dipeptide aspartylalanine, is studied employing a force-field that includes distributed multipole electrostatics and induction contributions (Amoebapro: P. Ren and J. W. Ponder, J. Comput. Chem., 2002, 23, 1497; P. Ren and J. W. Ponder, J. Phys. Chem. B, 2003, 107, 5933; J. W. Ponder and D. A. Case, Adv. Protein Chem., 2003, 66, 27). Radial and orientation distribution functions, as well as hydration numbers, are calculated and compared with existing simulation data derived from Car-Parrinello molecular dynamics (CPMD), and also distributed-charge force-fields. Connections are also made with experimental data for solvation of carboxylates in water. Our findings show that Amoebapro yields carboxylate solvation properties in very good agreement with CPMD results, significantly closer agreement than can be obtained from traditional force-fields. We also demonstrate that the influence of solvation on the conformation of the dipeptide is markedly different using Amoebapro compared with the other force-fields.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

Molecular simulation study of temperature effect on ionic hydration in carbon nanotubes

Molecular dynamics simulations have been performed to investigate the hydration of Li(+), Na(+), K(+), F(-), and Cl(-) inside the carbon nanotubes at temperatures ranging from 298 to 683 K. The structural characteristics of the coordination shells of ions are studied, including the ion-oxygen radial distribution functions, the coordination numbers, and the orientation distributions of the water molecules. Simulation results show that the first coordination shells of the five ions still exist in the nanoscale confinement. Nevertheless, the first coordination shell structures of cations change more significantly than those of anions because of the preferential orientation of the water molecules induced by the carbon nanotube. The first coordination shells of cations are considerably less ordered in the nanotube than in the bulk solution, whereas the change of the first coordination shell structures of the anions is minor. Furthermore, the confinement induces the anomalous behavior of the coordination shells of the ions with temperature. The first coordination shell of K(+) are found to be more ordered as the temperature increases only in the carbon nanotube with the effective diameter of 1.0 nm, implying the enhancement of the ionic hydration with temperature. This is contrary to that in the bulk solution. The coordination shells of the other four ions do not have such behavior in the carbon nanotube with the effective diameter ranging from 0.73 to 1.00 nm. The easier distortion of the coordination shell of K(+) and the match of the shell size and the nanotube size may play roles in this phenomenon. The exchange of water molecules in the first coordination shells of the ions with the solution and the ion diffusion along the axial direction of the nanotube are also investigated. The mobility of the ions and the stability of the coordination shells are greatly affected by the temperature in the nanotube as in the bulk solutions. These results help to understand the biological and chemical processes at the high temperature.     

Molecular dynamics simulation study of the dynamics of fluids at solid-liquid interfaces

The dynamics of fluids at solid-liquid interfaces is investigated. In particular, we consider a simple Lennard-Jones fluid as well as a melt of hexadecane chains. For the Lennard-Jones fluid, the numerical results are compared with analytical calculations based on the diffusion equation, which shows that the numerical results can very well by described by the solution of the diffusion equation for reflecting surfaces. The diffusion coefficient is practically independent of the position within the film, although the fluid is inhomogeneous perpendicular to the surface. In contrast, the dynamics of the centers of mass of hexadecane molecules perpendicular to repulsive surfaces is severely slowed down due to their extended and anisotropic nature and cannot be described by a single particle diffusion equation.     

Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field

The abnormal physicochemical characteristics of ethanol solvation in water are commonly attributed to the phenomenon of hydrophobic hydration. To investigate the structural organization of hydrophobic hydration in water-ethanol mixtures, we use molecular dynamics simulations based on detailed atomic models. Induced polarization is incorporated into the potential function on the basis of the classical Drude oscillator model. Water-ethanol mixtures are simulated at 11 ethanol molar fractions, from 0.05 to 0.9. Although the water and ethanol models are parametrized separately to reproduce the vaporization enthalpy, static dielectric constant, and self-diffusion constant of neat liquids at ambient conditions, they also reproduce the energetic and dynamical properties of the mixtures accurately. Furthermore, the calculated dielectric constant for the various water-alcohol mixtures is in excellent agreement with experimental data. The simulations provide a detailed structural characterization of the mixtures. A depletion of water-water hydrogen bonding in the first hydration shell of ethanol is compensated by an enhancement in the second hydration shell. The structuring effect from the second solvation shell gives rise to a net positive hydrogen-bonding excess for ethanol molar fractions up to approximately 0.5. For larger molar fractions, the second hydration shell is not sufficiently populated to overcome the net H-bond depletion from the first shell.     

Molecular dynamics study of screening at ionic surfaces

Molecular dynamics simulations of NaCl fluid are used to understand the behavior of ionic fluid to screen the field generated by charges on the ionic crystal surfaces in absence of any external electric field. The NaCl fluid in the strongly coupled regime (corresponding to the melt) in contact with the charged octopolar (111) NaCl surface shows that the spatial correlations decay in an oscillatory manner, with a screening length lambdaQ given by the envelope of the damped oscillations. By contrast to the Debye-Huckel theory, in the strongly coupled regime, lambdaQ increases with increasing coupling strength (also seen in bulk ionic simulations). The NaCl fluid confined between neutral (100) NaCl surfaces also shows weak oscillatory charge decay near the surface. Similar oscillatory exponential decay was seen when the NaCl fluid was confined between two analytically smooth neutral walls. The origin of these oscillations was due to the difference in ion sizes. NaCl fluid confined between neutral octopolar (110) and dipolar (110) surface show stronger density oscillations than (100) surface but comparatively very weak charge oscillations. This paper shows that the strength of the charges on the crystal surfaces is enough to induce a characteristic spatial distribution of charges in the contacting fluid and the extent of distribution depends on the type of surface.     

Mechanistic pathways of the hydroxyl radical reactions of quinoline. 2. Computational analysis of hydroxyl radical attack at C atoms

Density functional theory (DFT) calculations are employed to compare the mechanism of the *OH attacks at all carbon atoms in quinoline. The computational analysis of the energy surface for the reaction of *OH with quinoline reveals that the formation of OH adducts proceeds through exothermic formation of pi-complexes/H-bonded complexes. The gas-phase reactions have activation energies ranging from <1.3 kcal/mol for the attack at positions C3 through C8 to 8.6 kcal/mol for the attack at the C2 position. Solvation, as described by the CPCM cavity model, lowers these activation barriers so that the attack at all carbon atoms except C2 is effectively barrierless. The *OH attack at C2 in solution is significantly different than at all other quinoline positions because it involves the only transition structure with energy higher than that of the starting materials and with an energetic barrier of 5.1 kcal/mol. The specific solvation approach also corroborates this finding because the attack at C2 was shown to have an energy barrier of 2.3 kcal/mol compared to the barrierless attack at C5. These results are in agreement with our recent experimental studies but differ from literature reports on the degradation of quinoline using the photo-Fenton reaction.     

Molecular constants of vibrationally excited hydroxyl radical from electron paramagnetic resonance

Hydroxyl radicals in the vibrational states v = 5 to v = 9 of the ground ²π_3/2 J =3/2 state have been detected by electron paramagnetic resonance at X-band frequencies. From an analysis of the complete spectra, five molecular parameters were obtained for each v Adopting Van Vleck's hypothesis of pure precession, we have determined λ_v and the matrix element (Π{|BL_y}|Σ_υ.     

Langevin model of the temperature and hydration dependence of protein vibrational dynamics

The modification of internal vibrational modes in a protein due to intraprotein anharmonicity and solvation effects is determined by performing molecular dynamics (MD) simulations of myoglobin, analyzing them using a Langevin model of the vibrational dynamics and comparing the Langevin results to a harmonic, normal mode model of the protein in vacuum. The diagonal and off-diagonal Langevin friction matrix elements, which model the roughness of the vibrational potential energy surfaces, are determined together with the vibrational potentials of mean force from the MD trajectories at 120 K and 300 K in vacuum and in solution. The frictional properties are found to be describable using simple phenomenological functions of the mode frequency, the accessible surface area, and the intraprotein interaction (the displacement vector overlap of any given mode with the other modes in the protein). The frictional damping of a vibrational mode in vacuum is found to be directly proportional to the intraprotein interaction of the mode, whereas in solution, the friction is proportional to the accessible surface area of the mode. In vacuum, the MD frequencies are lower than those of the normal modes, indicating intramolecular anharmonic broadening of the associated potential energy surfaces. Solvation has the opposite effect, increasing the large-amplitude vibrational frequencies relative to in vacuum and thus vibrationally confining the protein atoms. Frictional damping of the low-frequency modes is highly frequency dependent. In contrast to the damping effect of the solvent, the vibrational frequency increase due to solvation is relatively temperature independent, indicating that it is primarily a structural effect. The MD-derived vibrational dynamic structure factor and density of states are well reproduced by a model in which the Langevin friction and potential of mean force parameters are applied to the harmonic normal modes.     

A molecular dynamics computer simulation study of the temperature dependence of hydration of 1,4-dioxane and 1,3-dioxane

This paper describes a study of the hydration of 1,3-dioxane and 1,4-dioxane at two different temperatures using different molecular dynamics (MD) computer simulation techniques. Three major conclusions have been drawn. Firstly, the simulations of 1,4-dioxane—water and 1,3-dioxane—water at constant pressure lead essentially to the same conclusions as earlir MD studies at constant volume. Secondly, the numerical values of dynamic properties depend critically on the density of the system. Simulations at constant pressure provide densities which are dependent on the periodicity requirement imposed on the system by the periodic boundary conditions. The smaller the periodic box, the stronger this effect is. Thirdly, in 1,4-dioxane—water an increase in temperature results in an enhanced mobility of water molecules in the solvation shell, whereas in the case of 1,3-dioxane—water these water molecules become more strongly bound by the solute. This effect is entirely due to a reduction of the mobility of water molecules in the 1,3-dioxane oxygen hydration subshells. The contrasting behavior is explained in terms of a situation where solvent—solvent interactions dominate solute—solvent interactions in 1,4-dioxane—water at both temperatures and in 1,3-dioxane—water at the lower temperature, while the opposite situation holds for 1,3-dioxane—water at the higher temperature.     

Use of the hydroxyl radical and gel electrophoresis to study DNA structure

The hydroxyl radical has been used as a chemical probe to study in solution the structure of DNA and DNA-protein complexes. The hydroxyl radical abstracts a deoxyribose hydrogen atom, cleaving one strand of the DNA. The cutting pattern, visualized by separating the cleavage products using gel electrophoresis, shows the reactivity of each backbone position toward the radical. This method has been applied to studies of DNA bending and helical twist. Phased runs of adenines (adenine tracts) cause sequence-directed DNA bending. The hydroxyl radical cleavage of a bent DNA fragment containing short adenine tracts phased with the helix screw gives rise to an unusual cutting pattern. The hydroxyl radical cleavage rate decreases in the 5' to 3' direction along each adenine tract, with a minimum at the 3' end of each adenine tract. The cleavage of the matching thymine tract is similar, but the minimum in the pattern is offset in the 3' direction. This pattern on the autoradiograph of the gel is interpreted to indicate that bending is accompanied by a narrow minor groove in the DNA molecule. Furthermore, hydroxyl radical cleavage results in different cutting patterns for two similar sequences, (CGA4T4)5 and (CGT4A4)5, which have been shown to be bent and relatively straight, respectively. The hydroxyl radical method has also been used to determine the helical repeat of the metallothionein IIA gene to be about 10.5 base pairs per turn. Methods of optimizing the hydroxyl radical reaction for DNA-protein footprinting are discussed. Because individual gel bands give information about cutting frequency at particular positions in the backbone, gel resolution and clear autoradiographs are important to this work.(ABSTRACT TRUNCATED AT 250 WORDS)     

Kinetic study of the reactions of the hydroxyl radical with ethane and propane

Absolute rate coefficients for the reactions of the hydroxyl radical with ethane (k₁, 297–300 K) and propane (k₂, 297–690 K) were measured using the flash photolysis–resonance fluorescence technique. The rate coefficient data were fit by the following temperature-dependent expressions, in units of cm³/molecule·s: k₁(T) = 1.43 × 10^?14T^1.05 exp (?911/T) and k₂(T) = 1.59 × 10^?15T^1.40 exp (-428/T). Semiquantitative separation of OH-propane reactivity into primary and secondary H-atom abstraction channels was obtained.     

A shock tube study of the reaction of the hydroxyl radical with propane

The rate coefficient for the reaction of the hydroxyl radical, OH, with propane has been measured at 1220 K in shock tube experiments, and a value of (1.58 ± 0.24) × 10¹³ cm³/mol s was obtained. This measured value is compared with previous experimental results and a transition-state theory calculation.     

Molecular dynamics simulation of planar elongational flow at constant pressure and constant temperature

Molecular dynamics simulations of liquid systems under planar elongational flow have mainly been performed in the NVT ensemble. However, in most material processing techniques and common experimental settings, at least one surface of the fluid is kept in contact with the atmosphere, thus maintaining the sample in the NpT ensemble. For this reason, an implementation of the Nose-Hoover integral-feedback mechanism for constant pressure is presented, implemented via the SLLOD algorithm for elongational flow. The authors test their procedure for an atomic liquid and compare the viscosity obtained with that in the NVT ensemble. The scheme is easy to implement, self-starting and reliable, and can be a useful tool for the simulation of more complex liquid systems, such as polymer melts and solutions.     

Molecular dynamics study of the hydration of lanthanum(III) and europium(III) including many-body effects

Lanthanides complexes are widely used as contrast agents in magnetic resonance imaging (MRI) and are involved in many fields such as organic synthesis, catalysis, and nuclear waste management. The complexation of the ion by the solvent or an organic ligand and the resulting properties (for example the relaxivity in MRI) are mainly governed by the structure and dynamics of the coordination shells. All of the MD approaches already carried out for the lanthanide(III) hydration failed due to the lack of accurate representation of many-body effects. We present the first molecular dynamics simulation including these effects that accounts for the experimental results from a structural and dynamic (water exchange rate) point of view.     

A solid-state NMR study of the fast and slow dynamics of collagen fibrils at varying hydration levels

We report solid-state NMR investigations of the effect of temperature and hydration on the molecular mobility of collagen isolated from bovine achilles tendon. (13)C cross-polarization magic angle spinning (MAS) experiments were performed on samples at natural abundance, using NMR methods that detect motionally averaged dipolar interactions and chemical shift anisotropies and also slow reorientational processes. Fast motions with correlation times much shorter than 40 micro s scale dipolar couplings and chemical shift anisotropies of the carbon sites in collagen. These motionally averaged anisotropic interactions provide a measure of the amplitudes of the segmental motions expressed by a molecular order parameter. The data reveal that increasing hydration has a much stronger effect on the amplitude of the molecular processes than increasing temperature. In particular, the Cgamma carbons of the hydroxyproline residues exhibit a strong dependence of the amplitude of motion on the hydration level. This could be correlated with the effect of hydration on the hydrogen bonding structure in collagen, for which this residue is known to play a crucial role. The applicability of 1D MAS exchange experiments to investigate motions on the millisecond time-scale is discussed and first results are presented. Slow motions with correlation times of the order of milliseconds have also been detected for hydrated collagen.