Computer simulation of the properties of liquid metals: Gallium,lead, and bismuth

The embedded atom model (EAM) potentials of liquid gallium, lead, and bismuth calculated by the author using the Schommers algorithm were refined and written in a unified analytic form more convenient for applications. Pair contributions to EAM potentials are described by piecewise continuous functions. The form of EAM potentials admits the transition to a high-density state characteristic of shock compression. Series of models of these liquid metals were constructed by the molecular dynamics method at temperatures up to 1500 (Zn), 3000 (Ga, Pb), and 1800 K (Bi). For all the metals, close agreement with experiment was obtained over the whole temperature range for density, structure, bulk compression modulus, and self-diffusion coefficient. The standard deviations of model pair correlation functions (PCF) from the diffraction PCFs of gallium and lead were on the order of 0.01. As distinct from alkali metals, the calculated energy of gallium and lead models was close to actual energy over the whole temperature range, and excess electronic heat conductivity was almost unobservable. With bismuth, agreement with experiment for energy and structural characteristics was noticeably worse, which shows that the embedded atom model is less applicable to bismuth.     

Structural transitions in liquid cesium

Two series of models of liquid cesium at temperatures of 493 and 623 K and pressures lower than 18 GPa are constructed by means of molecular dynamics using the potential of the embedded atom model. The thermodynamic properties of the models, pair correlation functions, pair radial distribution functions, structure factors, coordination numbers, and distributions of the Voronoi polyhedra and Delaunay simplexes are analyzed. No indications of structural transitions in liquid cesium of the first-order phase transition type are observed near a pressure of 3.9 GPa. Divergences from the results of some X-ray diffraction studies could be due to incorrect determination of the coordination numbers via the standard method because of the strong asymmetry of the first peaks of the pair radial distribution functions.     

[Er(C_4H_4O_5)_3]·2NaClO_4·6H_2O晶体中Er~(3+)离子能级的配位场分析

采用点群链R(3)*O*D3*关系标记D3*点群的斯塔克能级。基于双层点电荷配位场(DSCPCF)和经典的简单点电荷配位场(PCF)两种模型,利用自编的计算程序对三角对称(D3)的[Er(C4H4O5)3].2NaC lO4.6H2O晶体中Er3+离子的65个配位场微扰能级进行了理论计算和归属,计算结果与实验能级进行比较,DSCPCF模型得到的均方根偏差(σ)为19.9 cm-1,而PCF模型计算的为25.5 cm-1,表明前者模型更为优越,它是基于实际的配位结构并且仅包含较少的拟合参数。     

A set of molecular models for alkali and halide ions in aqueous solution

This work presents new molecular models for alkali and halide ions in aqueous solution. The force fields were parameterized with respect to the reduced liquid solution density at 293.15 K and 1 bar, considering all possible ion combinations simultaneously. The experimental target data are reproduced with a high accuracy over a wide range of salinity. The ion models predict structural properties of electrolyte solutions well, such as pair correlation functions and hydration numbers. The force fields provide good predictions of the properties studied here in combination with different models for water.     

Potential of mean force between hydrophobic solutes in the Jagla model of water and implications for cold denaturation of proteins

Using the Jagla model potential we calculate the potential of mean force (PMF) between hard sphere solutes immersed in a liquid displaying water-like properties. Consistent estimates of the PMF are obtained by (a) umbrella sampling, (b) calculating the work done by the mean force acting on the hard spheres as a function of their separation, and (c) determining the position dependent chemical potential after calculating the void space in the liquid. We calculate the PMF for an isobar along which cold denaturation of a model protein has previously been reported. We find that the PMF at contact varies non-monotonically, which is consistent with the observed cold denaturation. The Henry constant also varies non-monotonically with temperature. We find, on the other hand, that a second (solvent separated) minimum of the PMF becomes deeper as temperature decreases. We calculate the solvent-solvent pair correlation functions for solvents near the solute and in the bulk, and show that, as temperature decreases, the two pair correlation functions become indistinguishable, suggesting that the perturbation of solvent structure by the solute diminishes as temperature decreases. The solvent-solute pair correlation function at contact grows as the temperature decreases. We calculate the cavity correlation function and show the development of a solvent-separated peak upon decrease of temperature. These observations together suggest that cold denaturation occurs when the solvent penetrates between hydrophobic solutes in configurations with favorable free energy. Our results thus suggest that cold denatured proteins are structured and that cold denaturation arises from strong solvent-solute interactions, rather than from entropic considerations as in heat denaturation.     

The solvation of Li and Na in acetonitrile from ab initio-derived many-body ion–solvent potentials

Several Li⁺- and Na⁺-acetonitrile models were derived from ab initio calculations at the counterpoise-corrected MP2/TZV++(d,p) level for distorted ion-(MeCN)_n clusters with n=1, 4 and 6. Two different many-body ion-acetonitrile models were constructed: an effective three-body potential for use with the six-site effective pair model of Böhm et al., and an effective polarizable many-body model. The polarizable acetonitrile model used in the latter model is a new empirical model which was also derived in the present paper. Mainly for comparative purposes, two ion-acetonitrile pair potentials were also constructed from the ab initio cluster calculations: one pure pair potential and one effective pair potential. Using all these potential models, MD simulations in the NPT ensemble were performed for the pure acetonitrile liquid and for Li⁺(MeCN) and Na⁺(MeCN) solutions with 1 ion in 512 solvent molecules and with a simulation time of at least 120 ps per system. Thermodynamic properties, solvation-shell structure and the self-diffusion coefficient of the ions and of the solvent molecules were calculated and compared between the different models and with experimental data, where available. The Li⁺ ion is found to be four-coordinated when the new many-body potentials are used, in contrast to the six-coordinated structure obtained for the pure pair and effective pair potentials. The coordination number of Na⁺ is close to six for all the models derived here, although the coordination number becomes slightly smaller with the many-body potentials. For both ions, the solvent molecules in the first shell point their nitrogen ends towards the cation, while in the second shell the opposite orientation is the most common.     

α-quartz型GeO2高压相变的分子动力学研究

采用在经典离子晶体作用势中附加Morse势,并进行必要的量子化修正,对α-quartz型GeO2结构随压力变化特性,进行分子动力学计算模拟,获得了在压力高于6.0 GPa, α-quartz型GeO2从晶相向非晶相相变的模拟结果,并利用其摩尔体积变化、键角、径向分布、配位数等重要信息对模拟结果作了深入的探讨;相变后的非晶相,由占体积66%的八面体结构和33%的四面体结构组成的非晶体,其中还有极少量的α-quartz型GeO2存在。     

A simple method for evaluation of the self-consistency of the radial distribution functions and the orientation of water molecules in the first coordination sphere from the results of molecular dynamics calculations

A simple method for determination of the angular orientation of water molecules in the first coordination sphere from the radial distribution functions is proposed. A comparative analysis of the ability of the model potentials of pair interaction to take into account the effects of manybody interactions (MBI) was performed. The responses of the model pair potentials to the MBI effects in the first and second coordination spheres were found to be poorly correlated with each other. It was concluded that it is necessary to derive a new analytical type of potential functions of pair interaction. Published inIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 11, pp. 1842–1846. November. 2000.     

Modeling platinum group metal complexes in aqueous solution

We construct force fields suited for the study of three platinum group metals (PGM) as chloranions in aqueous solution from quantum chemical computations and report experimental data. Density functional theory (DFT) using the local density approximation (LDA), as well as extended basis sets that incorporate relativistic corrections for the transition metal atoms, has been used to obtain equilibrium geometries, harmonic vibrational frequencies, and atomic charges for the complexes. We found that DFT calculations of [PtCl(6)](2-).3H(2)O, [PdCl(4)](2-).2H(2)O, and [RhCl(6)](3-).3H(2)O water clusters compared well with molecular mechanics (MM) calculations using the specific force field developed here. The force field performed equally well in condensed phase simulations. A 500 ps molecular dynamics (MD) simulation of [PtCl(6)](2-) in water was used to study the structure of the solvation shell around the anion. The resulting data were compared to an experimental radial distribution function derived from X-ray diffraction experiments. We found the calculated pair correlation functions (PCF) for hexachloroplatinate to be in good agreement with experiment and were able to use the simulation results to identify and resolve two water-anion peaks in the experimental spectrum.     

Double-sphere coordination point-charge field model and some relevant problems

Summary An electrostatic three-centre model for diatomic bonds and a double-sphere coordination point-charge field (DSCPCF) model are proposed and discussed. The DSCPCF model has been applied to the spectral analyses and the properties of transition metal and rare earth metal complexes with various site symmetries and electron configurations. It has also been used to investigate the energy levels and activities of biology and drug molecule-metal complexes. Special emphasis is put on the discussion of the basic assumptions, effectivity of the characteristic parameters and advantages of these two models in applications. By comparison with the classical coordination point-charge field (PCF) model, it can be proved that the DSCPCF model is more successful in spectral analyses of transition metal and rare earth metal complexes.     

A clustering algorithm based on two distance functions for MEC model

Haplotype reconstruction, based on aligned single nucleotide polymorphism (SNP) fragments, is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. This paper first presents two distance functions, which are used to measure the difference degree and similarity degree between SNP fragments. Based on the two distance functions, a clustering algorithm is proposed in order to solve MEC model. The algorithm involves two sections. One is to determine the initial haplotype pair, the other concerns with inferring true haplotype pair by re-clustering. The comparison results prove that our algorithm utilizing two distance functions is effective and feasible.     

Computational study of structural and dynamical properties of formamide-water mixtures

A molecular dynamics simulation study of structural and dynamical properties in liquid mixtures of formamide and water is presented. Site-site radial pair distribution functions, local mole fractions, pair energy distributions, and tetrahedral orientational order are the quantities analyzed to investigate the local structure in the simulated mixtures, along with a review of the intermolecular structure in terms of the distribution of hydrogen bonds. Our results indicate that there is a substitution of formamide molecules by water in the hydrogen bonds and a formation of a common hydrogen bond network. By analyzing the extent of tetrahedral order in the liquid as a function of composition, it is observed that whereas the tetrahedral network of liquid water is progressively lost by increasing the formamide concentration, the water structure within the first coordination shell is preserved and somewhat enhanced. The hydrogen-bond mean lifetimes were estimated by performing a time integration of the autocorrelation functions of bond occupation numbers. The lifetimes associated with hydrogen bonds between water, formamide, and interspecies pairs are found to increase with increasing formamide concentration. The lifetimes of the water hydrogen bonds show the largest variations, supporting the picture of an enhancement of the water structure among the nearest neighbors within the first coordination shell. We have used two different force field models for water, SPC/E [J. C. Berendsen et al., J. Phys. Chem. 91, 6269 (1987)] and TIP4P/2005 [J. L. F. Abascal and C. Vega, J. Chem. Phys. 123, 234505 (2005)]. Our results for structural and dynamical properties yield very small differences between those models, the TIP4P/2005 predicting a slightly more structured liquid and, consequently, exhibiting a slightly slower translational and librational dynamics.     

Structure of an accurate ab initio model of the aqueous Cl- ion at high temperatures

The structure of an accurate ab initio model of aqueous chloride ion was calculated at two high-temperature state points (573 K, 0.725 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure. First, the structure of an approximate model was calculated from a molecular dynamics simulation of the model. Then the difference between the structure of the ab initio model and the approximate model was calculated by non-Boltzmann weighting of a sample of configurations taken from the approximate model simulation. Radial distribution functions, average coordination numbers, the distribution of coordination numbers, an analysis of orientations of water in the first coordination shell, and the free energy of hydration of the chloride ion are reported for both state points. The most common water structure has one hydrogen close to the chloride ion and one pointing away (46% at 573 K and 57% at 723 K). Waters in the first coordination shell that are not strongly bound to the chloride ions are common. Several variations of the method were tested. Models in which the water-water interaction is calculated with ab initio methods predict only a slightly different structure than models in which water-water interactions are determined from the approximate models. Similarly, using the approximate model for solute-water interactions when the water is far from the chloride ion did not affect the results. Uncertainties due to the limited sample of configurations are estimated and found to be small. The results are in qualitative agreement with X-ray and neutron diffraction experiments and with simulations of approximate models.     

The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields

The multiscale coarse-graining (MS-CG) method is a method for constructing a coarse-grained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MS-CG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MS-CG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)], in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarse-grained models: a solvent free model of a two component solution made of identical Lennard-Jones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations.     

Computer simulation of dissociative equilibrium in aqueous NaCl electrolyte with account for polarization and ion recharging. Ionization mechanism

The Monte Carlo method in a system with periodic boundary conditions was used within the model with explicit account for many-bod interactions to calculate ion-water correlation functions and the mean force ion-ion potential for extremely dilute aqueous electrolyte. Many-body interactions result in a decrease in the first coordination number of ions by approximately one molecule. The same effect is observed in the case of hydration in water vapors. Partial displacement of molecules from the lower layer into the higher hydrate layers occurs mainly by means of interactions of dipoles induced on molecules. Many-body interactions enhance the stability of unrecombined ion pairs separated by solvent molecules (SSIP states). The depth of the minimum in the dependence of the ion-ion mean force potential with account for many-body interaction forces is several times higher than in primitive interaction models. The value of effective relative dielectric permeability of the solvent at short distances from the ions grows faster than 1/R. Due to solvent polarization, counterions are strongly repelled at distances corresponding to overlapping of their hydrate shells and are weakly attracted at large distances. Stability of ion pair SSIP states in liquid electrolyte is due to rearrangement of the molecular structure of the solvent in the interion space and is an entropy effect. This mechanism differs qualitatively from that observed under hydration in water vapor and the depth of the minimum corresponding to SSIP states is by an order of magnitude lower in liquid electrolyte as compared to that in saturated water vapor.     

Force-field parametrization based on radial and energy distribution functions

We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

The coordination of uranyl in water: a combined quantum chemical and molecular simulation study

The coordination environment of uranyl in water has been studied using a combined quantum mechanical and molecular dynamics approach. Multiconfigurational wave function calculations have been performed to generate pair potentials between uranyl and water. The quantum chemically determined energies have been used to fit parameters in a polarizable force field with an added charge transfer term. Molecular dynamics simulations have been performed for the uranyl ion and up to 400 water molecules. The results show a uranyl ion with five water molecules coordinated in the equatorial plane. The U-O(H(2)O) distance is 2.40 A, which is close to the experimental estimates. A second coordination shell starts at about 4.7 A from the uranium atom. No hydrogen bonding is found between the uranyl oxygens and water. Exchange of waters between the first and second solvation shell is found to occur through a path intermediate between association and interchange. This is the first fully ab initio determination of the solvation of the uranyl ion in water.     

A coarse-grained model for polyethylene glycol polymer

A coarse-grained (CG) model of polyethylene glycol (PEG) was developed and implemented in CG molecular dynamics (MD) simulations of PEG chains with degree of polymerization (DP) 20 and 40. In the model, two repeat units of PEG are grouped as one CG bead. Atomistic MD simulation of PEG chains with DP = 20 was first conducted to obtain the bonded structural probability distribution functions (PDFs) and nonbonded pair correlation function (PCF) of the CG beads. The bonded CG potentials are obtained by simple inversion of the corresponding PDFs. The CG nonbonded potential is parameterized to the PCF using both an inversion procedure based on the Ornstein-Zernike equation with the Percus-Yevick approximation (OZPY(-1)) and a combination of OZPY(-1) with the iterative Boltzmann inversion (IBI) method (OZPY(-1)+IBI). As a simple one step method, the OZPY(-1) method possesses an advantage in computational efficiency. Using the potential from OZPY(-1) as an initial guess, the IBI method shows fast convergence. The coarse-grained molecular dynamics (CGMD) simulations of PEG chains with DP = 20 using potentials from both methods satisfactorily reproduce the structural properties from atomistic MD simulation of the same systems. The OZPY(-1)+IBI method yields better agreement than the OZPY(-1) method alone. The new CG model and CG potentials from OZPY(-1)+IBI method was further tested through CGMD simulation of PEG with DP = 40 system. No significant changes are observed in the comparison of PCFs from CGMD simulations of PEG with DP = 20 and 40 systems indicating that the potential is independent of chain length.     

On attractive interaction of a colloid pair of like charge at infinite dilution

Numerical data on the potential of mean force W(r) at infinite dilution of a highly charged colloid pair embedded in a 1:1 electrolyte are reported. The authors obtain attractive minima (W<0) at short interparticle distance in these potential functions in hypernetted chain (HNC) approximation, as salt concentration is increased. These minima, however, disappear in all system sets studied when a self-consistent Zerah-Hansen (ZH) closure is used. The authors infer that the attractive minima obtained in a HNC closure are spurious and result from the neglect of bridge diagrams in HNC approximation. An expression of bridge function, which the ZH closure in effect incorporates in W(r) to remove attractive minima, is derived in terms of modification of correlation functions. Features of repulsive pair potentials obtained using the ZH closure, their dependence on particle charge and salt concentration, and their agreement with those of the Derajguin-Landau-Verwey-Overbeek theory are investigated.     

Influence of Mg(2+) on the guanine-cytosine tautomeric equilibrium: simulations of the induced intermolecular proton transfer

Metallic ions are essential for stabilizing the nucleic acid structure, and are also involved in the majority of RNA and DNA biological functions. However, at large concentrations metals may play an opposite role by promoting alterations in the genetic code (mutagenicity). To contribute to the understanding of this effect, theoretical tools are used to investigate the influence of the magnesium dication on the guanine-cytosine (GC) base pair structure and stability. To this end, a fully hydrated Mg(2+) cation is inserted in two models: an isolated GC base pair, and a more realistic DNA model corresponding to a hydrated double-stranded trimer. Calculations performed with a hybrid ONIOM approach reveal that the Mg(2+) cation coordination to the GC base pair alters drastically the natural tautomeric equilibria in DNA by promoting single proton transfer. Nevertheless, the generated rare tautomer will have a limited impact on the total spontaneous mutation due to the low back-reaction barrier allowing a quick return to the canonical form. Additionally, it is demonstrated that the major effects of biological environment arise from the hydration and stacking influence, whereas the impact of phosphate groups is minor.