液态水几何构型的分子动力学模拟

利用ＭＣＹＬ势对液态水进行分子动力学模拟，以探求近程和远程相互作用及液体的有序结构对水分子几何构型的影响，并确定对液态中水分子几何构型起作用的主要范围。模拟给出的液态水中原子对径向分布函数和水分子键长键角的变化与实验值能较好地符合。研究结果表明，液态水分子几何构型除与氢键的形成有关外，还与液体的近程有序结构有很大关系。键长的变化对这种近程有序结构虽不敏感，但键角的变化则对此非常灵敏。液态中第二水合     

Molecular dynamics simulation of metastable ices IV and XII

The method of molecular dynamics with the use of Poltev-Malenkov potential is applied to simulate crystalline ices IV and XII, which do not have the regions of stability in the phase diagrams of H₂O and D₂O ices. Ice IV appears to undergo a partial destruction, whereas the ice XII structure is retained during the simulation. For different crystal types of water molecules in considered ices the mean square displacement of the center of mass of a water molecule with time is calculated together with the density of states of translational and librational vibrations.     

Proton magnetic shielding in H2O and (H2O)2

The proton magnetic shielding constants in the water molecule and its linear perpendicular dimer are computed from SCF-MO-LCGO wave functions by using the uncoupled Hartree-Fock variation-perturbation procedure due to Karplus and Kolker. The convergence of the calculated shielding constants as well as their gauge dependence is studied. The final results for 17-term polynomial variation function indicate that the best choice for the gauge origin corresponds to the molecular electronic centroid.The calculated proton magnetic shielding constant in the water molecule is in remarkable agreement with experimental data and favourably compares with the best coupled Hartree-Fock results. It follows from the calculations for the water dimer that the H-bond NMR-shift amounts in this case —1.0 ppm and qualitatively agrees with the experimental data for the liquid water.     

Iso-energy cutoff for the calculation of interionic potential of mean force in water

An iso-energy cutoff scheme is introduced for the calculation of the potential of mean force between two ions in water. The cutoff criterion is based on the optimal interaction of the water dipole with the ion pair, for which analytical expressions are derived. Formulas are also derived to characterize the solvent reorganization contribution to the potential of mean force. Treatment of the contributions from waters outside the cutoff is also discussed. © 1994 John Wiley & Sons, Inc.     

The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff

Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA.     

An analysis of molecular packing and chemical association in liquid water using quasichemical theory

We calculate the hydration free energy of liquid TIP3P water at 298 K and 1 bar using a quasi-chemical theory framework in which interactions between a distinguished water molecule and the surrounding water molecules are partitioned into chemical associations with proximal (inner-shell) waters and classical electrostatic-dispersion interactions with the remaining (outer-shell) waters. The calculated free energy is found to be independent of this partitioning, as expected, and in excellent agreement with values derived from the literature. An analysis of the spatial distribution of inner-shell water molecules as a function of the inner-shell volume reveals that water molecules are preferentially excluded from the interior of large volumes as the occupancy number decreases. The driving force for water exclusion is formulated in terms of a free energy for rearranging inner-shell water molecules under the influence of the field exerted by outer-shell waters in order to accommodate one water molecule at the center. The results indicate a balance between chemical association and molecular packing in liquid water that becomes increasingly important as the inner-shell volume grows in size.     

Methodological problems in pressure profile calculations for lipid bilayers

From molecular dynamics simulations of a dipalmitoyl-phosphatidyl-choline (DPPC) lipid bilayer in the liquid crystalline phase, pressure profiles through the bilayer are calculated by different methods. These profiles allow us to address two central and unresolved problems in pressure profile calculations: The first problem is that the pressure profile is not uniquely defined since the expression for the local pressure involves an arbitrary choice of an integration contour. We have investigated two different choices leading to the Irving-Kirkwood (IK) and Harasima (H) expressions for the local pressure tensor. For these choices we find that the pressure profile is almost independent of the contour used, which indicates that the local pressure is well defined for a DPPC bilayer in the liquid crystalline phase. This may not be the case for other systems and we therefore suggest that both the IK and H profiles are calculated in order to test the uniqueness of the profile. The second problem is how to include electrostatic interactions in pressure profile calculations when the simulations are conducted without truncating the electrostatic potential, i.e., using the Ewald summation technique. Based on the H expression for the local pressure, we present a method for calculating the contribution to the lateral components of the local pressure tensor from electrostatic interactions evaluated by the Ewald summation technique. Pressure profiles calculated with an electrostatic potential truncation (cutoff) from simulations conducted with Ewald summation are shown to depend on the cutoff in a subtle manner which is attributed to the existence of long-ranged charge ordering in the system. However, the pressure profiles calculated with relatively long cutoffs are qualitatively similar to the Ewald profile for the DPPC bilayer studied here.     

Extracting effective normal modes from equilibrium dynamics at finite temperature

A general method for obtaining effective normal modes of a molecular system from molecular dynamics simulations is presented. The method is based on a localization criterion for the Fourier transformed velocity time-correlation functions of the effective modes. For a given choice of the localization function used, the method becomes equivalent to the principal mode analysis (PMA) based on covariance matrix diagonalization. On the other hand, a proper choice of the localization function leads to a novel method with a strong analogy with the usual normal mode analysis of equilibrium structures, where the Hessian system at the minimum energy structure is replaced by the thermal averaged Hessian, although the Hessian itself is never actually calculated. This method does not introduce any extra numerical cost during the simulation and bears the same simplicity as PMA itself. It can thus be readily applied to ab initio molecular dynamics simulations. Three such examples are provided here. First we recover effective normal modes of an isolated formaldehyde molecule computed at 20 K in very good agreement with the results of a normal mode analysis performed at its equilibrium structure. We then illustrate the applicability of the method for liquid phase studies. The effective normal modes of a water molecule in liquid water and of a uracil molecule in aqueous solution can be extracted from ab initio molecular dynamics simulations of these two systems at 300 K.     

Calculation of the surface tension of oxygen using molecular-dynamics simulations

The surface tension of oxygen at the liquid-vapor interface is calculated for the temperature range of 60-90 K using molecular-dynamics simulations and is shown to be within 1.0% error of experimental values for most of the temperatures studied. The potential used here is the same as in our previous study on liquid oxygen alone [S. D. Bembenek and B. M. Rice, J. Chem. Phys. 113, 2354 (2000)] and was optimized with an innovative statistical-mechanical method. The potential does not use a long-range cutoff nor a tail correction, which are usually considered necessary to obtain accurate values for the surface tension. We reason that the accuracy in surface tension is directly related to our parametrization method for the potential.     

Two-particle entropy and structural ordering in liquid water

Entropies of simple point charge (SPC) water were calculated over the temperature range 278-363 K using the two-particle correlation function approximation. Then, the total two-particle contribution to the entropy of the system was divided into three parts, which we call translational, configurational, and orientational. The configurational term describes the contribution to entropy, which originates from spatial distribution of surrounding water molecules (treated as points, represented by the center of mass) around the central one. It has been shown that this term can serve as the metric of the overall orientational ordering in liquid water. Analyzing each of these three terms as a function of intermolecular distance, r, we also find a rational definition of the hydration shell around the water molecule; the estimated radii of the first and second hydration shells are 0.35 nm and 0.58 nm, respectively. We find, moreover, that the first hydration shell around the water molecule participates roughly in 70% of the total orientational entropy of water, and this rate is roughly temperature independent.     

Electronic properties of liquid water by sequential molecular dynamics/density functional theory

Electronic properties of liquid water were analysed by a sequential molecular dynamics (MD)/density functional theory approach. MD simulations are based on a polarisable model for water. Emphasis was placed on the prediction of the water dipole moment, liquid state polarisability, ionisation potential (IP), and vertical electron affinity. The dipole moment of the water molecule in liquid water is not dependent on the number of molecules included in the quantum mechanical calculations. The polarisability of the water molecule in liquid water is 4% lower than its gas phase value. The IP of liquid water (9.7 ± 0.06 eV) is in good agreement with recent experimental data.     

Multiple time scale behaviors and network dynamics in liquid methanol

Canonical ensemble molecular dynamics simulations of liquid methanol, modeled using a rigid-body, pair-additive potential, are used to compute static distributions and temporal correlations of tagged molecule potential energies as a means of characterizing the liquid state dynamics. The static distribution of tagged molecule potential energies shows a clear multimodal structure with three distinct peaks, similar to those observed previously in water and liquid silica. The multimodality is shown to originate from electrostatic effects, but not from local, hydrogen bond interactions. An interesting outcome of this study is the remarkable similarity in the tagged potential energy power spectra of methanol, water, and silica, despite the differences in the underlying interactions and the dimensionality of the network. All three liquids show a distinct multiple time scale (MTS) regime with a 1/ f (alpha) dependence with a clear positive correlation between the scaling exponent alpha and the diffusivity. The low-frequency limit of the MTS regime is determined by the frequency of crossover to white noise behavior which occurs at approximately 0.1 cm (-1) in the case of methanol under standard temperature and pressure conditions. The power spectral regime above 200 cm (-1) in all three systems is dominated by resonances due to localized vibrations, such as librations. The correlation between alpha and the diffusivity in all three liquids appears to be related to the strength of the coupling between the localized motions and the larger length/time scale network reorganizations. Thus, the time scales associated with network reorganization dynamics appear to be qualitatively similar in these systems, despite the fact that water and silica both display diffusional anomalies but methanol does not.     

Instantaneous normal mode analysis of orientational motions in liquid water: local structural effects

We have investigated the effects of local structures on the orientational motions in liquid water in terms of the instantaneous normal mode (INM) analysis. The local structures of a molecule in liquid water are characterized by two different kinds of index: the asphericity parameter of its Voronoi polyhedron and the numbers of the H bonds donated and accepted by the molecule. According to the two kinds of index, the molecules in the simulated water are classified into subensembles, for which the rotational contributions to the INM spectrum are calculated. Our results indicate that by increasing the asphericity, the rotational contribution has a shift toward the high-frequency end in the real spectrum and a decrease in the fraction of the imaginary modes. Furthermore, we find that this shift essentially relies on the number of the donated H bonds of a molecule, but has almost nothing to do with that of the accepted H bonds. The local structural effects resulting from the geometry of water molecule are also discussed.     

A simple analysis of the influence of the solvent-induced electronic polarization on the <Superscript>15</Superscript>N magnetic shielding of pyridine in water

Electronic polarization induced by the interaction of a reference molecule with a liquid environment is expected to affect the magnetic shielding constants. Understanding this effect using realistic theoretical models is important for proper use of nuclear magnetic resonance in molecular characterization. In this work, we consider the pyridine molecule in water as a model system to briefly investigate this aspect. Thus, Monte Carlo simulations and quantum mechanics calculations based on the B3LYP/6-311++G (d,p) are used to analyze different aspects of the solvent effects on the ¹⁵N magnetic shielding constant of pyridine in water. This includes in special the geometry relaxation and the electronic polarization of the solute by the solvent. The polarization effect is found to be very important, but, as expected for pyridine, the geometry relaxation contribution is essentially negligible. Using an average electrostatic model of the solvent, the magnetic shielding constant is calculated as −58.7 ppm, in good agreement with the experimental value of −56.3 ppm. The explicit inclusion of hydrogen-bonded water molecules embedded in the electrostatic field of the remaining solvent molecules gives the value of −61.8 ppm.     

Quantum-Chemical Calculation of the Mechanism of Gas-Phase Hydrolysis of Benzenesulfonyl Chloride

The potential energy surface of gas-phase hydrolysis of benzenesulfonyl chloride was calculated by PM3 quantum-chemical method. The structural and energy parameters were calculated for all the intermediates and transition states; activation parameters and the thermodynamic functions of the reaction were determined. The axial orientation of the nucleophilic attack is preferred when the reactive center is attacked by the water molecule occurring at the axis of the C-S bond from the sulfonyl group. Gas-phase hydrolysis of benzenesulfonyl chloride is an exothermic process involving formation of an unstable five-coordinate intermediate. The calculated apparent rate constants and activation parameters of the process are compared with the published data on hydrolysis of benzenesulfonyl chloride in water and aqueous-organic solvents.     

Ewald summation versus direct summation of shifted-force potentials for the calculation of electrostatic interactions in solids: A quantitative study

The calculated Madelung energies and Madelung forces of the electrostatic interaction for nine crystal structures are reported. The method of direct summation with two different shifted-force potentials is compared to the Ewald summation. There is a considerable difference in the convergence of the energy and the force for the two shifted-force potentials regarding the cutoff radius. The convergence depends not only on the potential itself, but also on the crystal structure. One of the shifted-force potentials used is implemented in the CHARMM force field. The energy calculated with this potential shows a good convergence for small cutoff radii. With the other shifted-force potential, the force shows a better convergence for small cutoff radii. The number of pair interactions for obtaining the Madelung limit using the Ewald summation and the direct summation of a shifted-force potential is also reported. For complex structures like zeolites, the number of relevant pair interactions is smaller using the direct summation of a shifted-force potential. For simple structures such as cesium chloride, the number of significant pair interactions is smaller using the Ewald summation. © 1997 by John Wiley & Sons, Inc.     

Unified theory of the dielectric properties and lattice vibrational intensities of the HCN crystal

The effective polarizability of the HCN molecule in its two crystal phases is calculated from the mean crystal dielectric constant and molecular- orbital dipole moment calculations, using lattice dipole sums for molecules treated as one, two and three points. The axial polarizability agrees with the gas-phase value, but the transverse polarizability from each calculation is roughly twice the gas-phase value. The lattice infrared absorption intensities and LO-TO splitting are calculated; the three-point treatment with the crystal-phase polarizability yields agreement with experiment. The lattice Raman intensities are also calculated; they depend markedly on the choice of polarizability. The results illustrate how several properties can be calculated within one model. Some inconsistencies for HCN may be attributable to the effects of hydrogen bonding, but could be resolved by dielectric tensor, refractive index, or lattice Raman intensity measurements.     

Molecular-dynamics evaluation of fluid-phase equilibrium properties by a novel free-energy perturbation approach: application to gas solubility and vapor pressure of liquid hexane

A novel free-energy perturbation method is developed for the computation of the free energy of transferring a molecule between fluid phases. The methodology consists in drawing a free-energy profile of the target molecule moving across a binary-phase structure built in the computer. The novelty of the method lies in the difference of the definition of the free-energy profile from the common definition. As an important element of the method, the process of making a correction to the transfer free energy with respect to the cutoff of intermolecular forces is elucidated. In order to examine the performance of the method in the application to fluid-phase equilibrium properties, molecular-dynamics computations are carried out for the evaluation of gas solubility and vapor pressure of liquid n-hexane at 298.15 K. The gas species treated are methane, ethane, propane, and n-butane, with the gas solubility expressed as Henry's constant. It is shown that the method works fine and calculated results are generally in good agreement with experiments. It is found that the cutoff correction is strikingly large, constituting a dominant part of the calculated transfer free energy at the cutoff of 8 A.