Note: Accounting for pressure effects on the calculated equilibrium structure of glassy GeSe(2)

First-principles molecular dynamics (FPMD) data on the structural properties of glassy GeSe(2) under ambient conditions are produced by carefully considering and minimizing the effect of a residual pressure on the periodic system. When compared to previous FPMD results, this strategy leads to an improved agreement between theory and neutron diffraction experiments.     

Temperature effects on the structure and dynamics of liquid dimethyl sulfoxide: A molecular dynamics study

The molecular dynamics (MD) simulation technique has been employed to investigate the thermodynamic properties and transport coefficients of the neat liquid dimethyl sulfoxide (DMSO). The fluid has been studied at temperatures in the range 298–353 K and at a pressure equal to 1 atm. The simulations employed a nine-site potential model, which is presented for the first time here, and all the available non-polarizable models. The performance of each model is tested using the same statistical mechanical ensemble and simulation method under the same conditions, revealing its weaknesses and strengths. Thermodynamic properties, microscopic structure and dynamic properties, such as transport coefficients, rotational and single-dipole correlation times have been calculated and compared with available experimental results. Estimations of transport coefficients from various theoretical and empirical models are tested against experimental and MD results. Translational and rotational dynamics suggest the existence of the cage effect and agree with the Stokes–Einstein–Debye relation. The dipole relaxation times calculated are discussed in terms of simple and useful approximations, such as the Glarum–Powles and Fatuzzo–Mason models.     

Characterization of the solvation dynamics of an ionic liquid via molecular dynamics simulation

The solvation dynamics of ionic liquids have been the subject of intense experimental study but remain poorly understood. We present the results of molecular dynamics simulations of the solvation dynamics of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate in response to photoexcitation of the fluorescent dye coumarin-153. We reproduce the time-resolved fluorescence Stokes shift using linear response theory, then use novel statistical techniques to analyze cation and anion contributions to the signal. We find that the solvation dynamics are dominated by collective ionic motion and characterize the time scale for various features of the collective response. Further, we use the Steele analysis [Mol. Phys. 61, 1031 (1987)] to characterize the contributions to the observed Stokes shift made by translational and rovibrational degrees of freedom. Our results indicate that in contrast to molecular liquids, the rovibrational response is trivial and the observed fluorescence response arises almost entirely from ionic translation. Our results resolve previously open questions in the literature about the nature of the rapid dynamics in room-temperature ionic liquids and offer insight into the physical principles governing ionic liquid behavior on longer time scales.     

Early stages in the degradation of metal-organic frameworks in liquid water from first-principles molecular dynamics

IRMOF-1 structures are known to suffer lattice break-up when exposed to water-rich environments, a limiting factor in their everyday use. To shed light on the underlying mechanism of disruption, the role of the metal in the secondary building unit (SBU) has been systematically investigated, and the global behaviour of IRMOF-1-type structures with the three metals Zn, Mg, and Be studied by Born-Oppenheimer Molecular Dynamics in liquid water. Results show that fully hydrated Be based compounds are stable up to 500 K while the equivalent structures with Mg or Zn break down already at 300 K. The reasons behind this instability are in the tendency of the metal atom to form penta- and hexa-coordination spheres and in the strength of the M-O bond. These are the key factors that generate unique breaking patterns for Mg and Zn IRMOF-1 analogues, as well as the reason for the high hydrothermal stability of the Be-IRMOF-1.     

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) method for a large number of configurations generated from MD simulations. The method includes electron correlation effects at the coupled cluster singles and doubles level and the use of a large correlation consistent basis set. A polarizable force field has been used for the molecular dynamics part in both the CC/MM method and in the MD simulation. We describe how the methodology can be optimized with respect to computational costs while maintaining the quality of the results. Using the optimized method we study the energetic properties including the heat of vaporization and electronic excitation energies as well as electric dipole and quadrupole moments, the frequency dependent electric (dipole) polarizability, and electric-field-induced second harmonic generation first and second hyperpolarizabilities. Comparisons with experiments are performed where reliable data are available. Furthermore, we discuss the important issue on how to compare the calculated microscopic nonlocal properties to the experimental macroscopic measurements.     

Investigation of the microstructure of micelles formed by hard-sphere chains interacting via size nonadditivity by discontinuous molecular dynamics simulation

Micelle formation by short nonadditive hard surfactant chains was investigated at different size ratios, reduced densities, and nonadditivity parameters using molecular dynamics simulation. It was found that spherical, cylindrical, lamellar, and reverse micelles can form in systems with different head, tail, and solvent characteristics. Hard-core surfactant chains composed of a head segment and three tail segments were simulated in a solvent of hard spheres. The formation of micelles was found to be a strong function of the packing fraction and nonadditivity parameter. Micelles were more stable at higher densities and larger nonadditivity parameters. At lower densities, micelles tended to break into small, dynamic globules.     

Impact of the exchange-correlation functional on the structure of glassy GeSe2

The structural properties of glassy GeSe₂ were studied by using first-principles molecular dynamics with the Becke, Lee, Yang and Parr (BLYP) expression for the exchange-correlation energy within density functional theory. A comparison is made with the results previously obtained for this material by using first-principles molecular dynamics with the Perdew and Wang (PW) exchange-correlation functional. Overall, the structures of the BLYP-GeSe₂ and PW-GeSe₂ networks are quite similar, the BLYP approach favoring a larger number of Ge–Ge homopolar bonds, in better agreement with the experimental results. The BLYP network does, however, feature a smaller fraction of corner-sharing motifs by comparison with the PW network but the fraction of edge-sharing motifs is the same for both structures, at least within the confines of an approach based on a single temporal trajectory. Further studies are required to determine whether agreement between the BLYP structure and experiment can be improved by taking the average over a larger number of temporal trajectories or whether additional developments are required for the exchange-correlation part of the energy functional.     

Far-infrared absorption of water clusters by first-principles molecular dynamics

Based on first-principle molecular dynamic simulations, we calculate the far-infrared spectra of small water clusters (H(2)O)(n) (n = 2, 4, 6) at frequencies below 1000 cm(-1) and at 80 K and at atmospheric temperature (T>200 K). We find that cluster size and temperature affect the spectra significantly. The effect of the cluster size is similar to the one reported for confined water. Temperature changes not only the shape of the spectra but also the total strength of the absorption, a consequence of the complete anharmonic nature of the classical dynamics at high temperature. In particular, we find that in the frequency region up to 320 cm(-1), the absorption strength per molecule of the water dimer at 220 K is significantly larger than that of bulk liquid water, while tetramer and hexamer show bulklike strengths. However, the absorption strength of the dimer throughout the far-infrared region is too small to explain the measured vapor absorption continuum, which must therefore be dominated by other mechanisms.     

Ionicity in disordered GeSe2: a comparison of first-principles and atomistic potential models

The structural properties of liquid GeSe(2), generated using two distinct computational methodologies, are compared. The results of molecular dynamics simulations, utilizing both first-principles density functional and a potential model which account for aspects of many-body interactions, are considered. The potential model favors ionic character in the bonding, resulting in a structure with very little chemical disorder and no homopolar bonds, in contrast to experimental observation. The use of a relatively simple potential model is shown to be useful in order to understand differences between the observed experimental structure and those obtained from the first-principles approach, the latter being affected by insufficient account of ionic character in the bonding. Both computational schemes are able to predict the appearance of the first sharp diffraction peak in the total neutron structure factor and in some of the partial structure factors as well as the concomitant presence of corner- and edge-sharing tetrahedral connections. For the potential model, this holds true provided the system temperatures are set to values high enough to allow for diffusion properties typical of a liquid. Structural properties obtained for the two sets of configurations are in closer agreement when the potential model is applied at very high temperatures.     

Finite system size effects in the interfacial dynamics of binary liquid films

We study the relaxation dynamics of capillary waves in the interface between two confined liquid layers by means of molecular dynamics simulations. We measure the autocorrelations of the interfacial Fourier modes and find that the finite thickness of the liquid layers leads to a marked increase of the relaxation times as compared to the case of fluid layers of infinite depth. The simulation results are in good agreement with a theoretical first-order perturbation derivation, which starts from the overdamped Stokes' equation. The theory also takes into account an interfacial friction, but the difference with no-slip interfacial conditions is small. When the walls are sheared, it is found that the relaxation times of modes perpendicular to the flow are unaffected. Modes along the flow direction are relatively unaffected as long as the equilibrium relaxation time is sufficiently short compared to the rate of deformation. We discuss the consequences for experiments on thin layers and on ultralow surface tension fluids, as well as computer simulations.     

Exploring the hydration of Pb2+: ab initio studies and first-principles molecular dynamics

Even though lead is a well-known toxicant widely scattered throughout the world since antiquity, its chemistry is poorly documented at the molecular level. Here we investigate the hydration of the Pb(2+) ion by means of first-principles molecular dynamics (Car-Parrinello molecular dynamics, CPMD). We found that the hydrated cation is heptacoordinated in a dynamically holodirected arrangement roughly corresponding to a fluxional distorted pentagonal bipyramid. The time-averaged Pb-O bond length is especially large and amounts to 2.70 A with an associated root-mean-square deviation of 0.26 A. This results from a dynamic exchange between short (<2.6 A), intermediate (2.6-3.0 A) and long (>3.0 A) Pb-O bonds. The latter very long Pb-O distance implies that the determination of the coordination number n(c) from experimental work may not necessarily yield values directly comparable to the theoretical value of n(c)=7, since not all experimental techniques would recognize such a long distance as a bond to the metal cation. Pronounced disorders are evidenced in the second shell, characteristic of a chaotropic cation, and exchanges between the first and second shells cannot be excluded on a timescale of a few tens of picoseconds.     

Local structure of liquid Ti: Ab initio molecular dynamics study

Local order of liquid Ti is studied by ab initio molecular dynamics to address the unique liquid structure factor in experiments reported recently. The present study reveals that the local order of liquid Ti is in the form of fragments of the distorted icosahedral short range order, where the distortion is induced by strong bond order effects. We show that the fragments in the short-bond rich region separated from the background liquid account for the pronounced feature in structure factor of liquid Ti.     

Electrolysis of water in the diffusion layer: first-principles molecular dynamics simulation

With Car-Parrinello molecular dynamics simulations the elementary reaction steps of the electrolysis of bulk water are investigated. To simulate the reactions occurring near the anode and near the cathode, electrons are removed or added, respectively. The study focuses on the reactions in pure water. Effects depending on a particular electrode surface or a particular electrolyte are ignored. Under anodic conditions, the reaction continues till molecular oxygen is formed, under cathodic conditions the formation of molecular hydrogen is observed. In addition the formation of hydrogen peroxide is observed as an intermediate of the anodic reaction. The simulations demonstrate that the electrochemistry of oxygen formation without direct electrode contact can be explained by radical reactions in a solvent. These reactions may involve the intermediate formation of ions. The hydrogen formation is governed by rapid proton transfers between water molecules.     

Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation

Accurate calculation of pK(a) values and free energies for acid/base reactions in the condensed phase has been a long-standing goal of theoretical chemistry. We present a novel application of the Car-Parrinello molecular dynamics method to the problem of relative pK(a) determination. As a particular example, we focus on the second stage in the dissociation of histidine, a process that holds special importance for biology. Using constrained molecular dynamics, we have analyzed the structural, electronic, and dynamical transformations taking place along a preselected, intuitive reaction coordinate. By integrating the potentials of mean force for the deprotonation of histidine and for a reference reaction, autodissociation of water, we obtain a pK(a) value of 6.8, which appears to be in good agreement with the experimental estimate of 6.1. Detailed analysis was undertaken to determine the value of the constraint, which transformed the N*-H* from a covalent to a hydrogen bond. This helped to identify a number of properties that could be successfully used in monitoring the dissociation process. Additional analysis in terms of electron localization functions provided valuable insight into the nature of the deprotonation reaction.     

System size and control parameter effects in reverse perturbation nonequilibrium molecular dynamics

The issue of system size effects in the reverse perturbation nonequilibrium molecular dynamics method for determining transport coefficients of fluids is examined for the case of the Lennard-Jones model. It is found that when adequate precautions are observed in obtaining linear temperature or momentum profiles, a 250 atom system is adequate for determining the thermal conductivity and the shear viscosity. Also, a means of determining the uncertainties in the transport coefficients is described. The conclusion is that this method is computationally competitive with other simulation methods for estimating transport coefficients.     

Investigation of structure of liquid 2,2,2 trifluoroethanol: neutron diffraction, molecular dynamics, and ab initio quantum chemical study

The molecular conformation and intermolecular H bonding in liquid 2,2,2 trifluoroethanol (TFE) have been studied by neutron diffraction with hydrogen/deuterium isotopic substitution at room temperature. For comparison, conformations of molecules and their dimers in the gas phase have also been calculated, based on the density functional theory. Energies, geometry, and vibrational frequencies of dimers were analyzed. Diffraction data analyzed by the "Monte Carlo determination of g(r)" (MCGR) method resulted in a molecular structure in agreement with the findings from gas phase electron diffraction experiments and density functional calculations. The intermolecular structure functions were compared to the same functions obtained from a molecular dynamics simulation. All of the composite radial distribution functions are in good agreement with the simulation results. According to our calculation the hydrogen-bonded aggregation size is smaller in pure liquid TFE than in pure liquid ethanol.     

Investigating hydrogen bonds in liquid ethylene glycol structure by means of molecular dynamics

Models of liquid ethylene glycol are built by means of molecular dynamics at temperatures ranging between 268 and 443 K, with 1000 molecules in rectangular parallelepiped basic cells. The dependences of structures of O-H…O hydrogen bonds on modeling time and temperature are analyzed. It is found that the hydrogen bonds emerge at different sites of a model, thus forming a hydrogen bonds network that is continuously rebuilt under the action of thermal fluctuations. The number of hydrogen bonds in the models is observed to decrease when the temperature is raised. The energy of hydrogen bond formation is found to be ?20.0 ± 2.6 kJ mol^?1, the average bond lifetime is 370 ps at 268 K and 147 ps at 323 K, and the activation energy of hydrogen bond rupture at these temperatures is ～12.1 kJ mol^?1. It is concluded that the data on the breaking of H-bonds at temperatures of 323 to 443 K can be explained by the molecules moving away from each other as a result of diffusive motion, accompanied by rearrangement of the hydrogen bonds network. The concentration of dimers in the models is shown to be rather low, while the average energy of forming a dimer from two ethylene glycol molecules is ?35.4 kJ mol^?1.     

Investigation of finite system-size effects in molecular dynamics simulations of lipid bilayers

In the absence of external stress, the surface tension of a lipid membrane vanishes at equilibrium, and the membrane exhibits long wavelength undulations that can be described as elastic (as opposed to tension-dominated) deformations. These long wavelength fluctuations are generally suppressed in molecular dynamics simulations of membranes, which have typically been carried out on membrane patches with areas <100 nm2 that are replicated by periodic boundary conditions. As a result, finite system-size effects in molecular dynamics simulations of lipid bilayers have been subject to much discussion in the membrane simulation community for several years, and it has been argued that it is necessary to simulate small membrane patches under tension to properly model the tension-free state of macroscopic membranes. Recent hardware and software advances have made it possible to simulate larger, all-atom systems allowing us to directly address the question of whether the relatively small size of current membrane simulations affects their physical characteristics compared to real macroscopic bilayer systems. In this work, system-size effects on the structure of a DOPC bilayer at 5.4 H2O/lipid are investigated by performing molecular dynamics simulations at constant temperature and isotropic pressure (i.e., vanishing surface tension) of small and large single bilayer patches (72 and 288 lipids, respectively), as well as an explicitly multilamellar system consisting of a stack of five 72-lipid bilayers, all replicated in three dimensions by using periodic boundary conditions. The simulation results are compared to X-ray and neutron diffraction data by using a model-free, reciprocal space approach developed recently in our laboratories. Our analysis demonstrates that finite-size effects are negligible in simulations of DOPC bilayers at low hydration, and suggests that refinements are needed in the simulation force fields.