Conformational search using a molecular dynamics–minimization procedure: Applications to clusters of coulombic charges,Lennard–Jones particles,and waters

A new conformational search method, molecular dynamics–minimization (MDM), is proposed, which combines a molecular dynamics sampling strategy with energy minimizations in the search for low-energy molecular structures. This new method is applied to the search for low energy configurations of clusters of coulombic charges on a unit sphere, Lennard–Jones clusters, and water clusters. The MDM method is shown to be efficient in finding the lowest energy configurations of these clusters. A closer comparison of MDM with alternative conformational search methods on Lennard–Jones clusters shows that, although MDM is not as efficient as the Monte Carlo–minimization method in locating the global energy minima, it is more efficient than the diffusion equation method and the method of minimization from randomly generated structures. Given the versatility of the molecular dynamics sampling strategy in comparison to Monte Carlo in treating molecular complexes or molecules in explicit solution, one anticipates that the MDM method could be profitably applied to conformational search problems where the number of degrees of freedom is much greater. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 60–70, 1998     

Mixing rules for binary Lennard–Jones chains: theory and Monte Carlo simulation

Theoretically-based van der Waals one-fluid (vdW1) mixing rules are derived for Lennard–Jones (LJ) chain mixtures. The rules provide equivalent one-fluid segment parameters for LJ size (σ) and energy () parameter as well as chain length (m) based on the parameters of the individual mixture components and the component mole fractions. The mixing rules are tested by performing Monte Carlo simulations of eight different binary mixtures and the equivalent vdW1 pure fluid, each at three densities. The simulations test the effects of changing LJ size parameter, LJ energy parameter and chain length individually and together. The effects of mole fraction and density are also examined. The mixing rules are tested for accuracy in predicting compressibility factors and radial distribution functions. It is found that the vdW1 rules provide excellent agreement when size and energy parameter are varied. Good agreement is found for mixtures with different chain lengths. The discrepancy is worst at very high densities when all component parameters are varied simultaneously.     

High-pressure vapor–liquid equilibria in the nitrogen–n-pentane system

New experimental vapor–liquid equilibrium data of the N₂–n-pentane system were measured over a wide temperature range from 344.3 to 447.9 K and pressures up to 35 MPa. A static-analytic apparatus with visual sapphire windows and pneumatic capillary samplers was used in the experimental measurements. Equilibrium phase compositions and vapor–liquid equilibrium ratios are reported. The new results were compared with those reported by other authors. The comparison showed that the pressure–composition data reported in this work are in good agreement with those determined by others but they are closer to the mixture critical point at each temperature level. The experimental data were modeled with the PR and PC-SAFT equations of state by using one-fluid mixing rules and a single temperature independent interaction parameter. Results of the modeling showed that the PC-SAFT equation fit the data satisfactorily even at the highest temperatures of study.     

Pressure and temperature dependencies of excess molar enthalpies of two-component Lennard–Jones fluid mixtures in the supercritical region

Monte Carlo (MC) simulations have been carried out for mixtures of Lennard–Jones (LJ) fluids near or in the supercritical region. Excess molar enthalpy at equimolar concentration, H_p,x=0.5^E, has been obtained for four kinds of model mixtures each having different combining rule for unlike interactions. The pressure and temperature dependencies of H_p,x=0.5^E are investigated. The unique pressure and temperature dependencies of H_p,x=0.5^E for real systems such as (ethane+ethene) in the supercritical condition have been reproduced by the present simple model systems. Excess molar internal energies at constant volumes, U_V,x=0.5^E, are also evaluated. They are compared with H_p,x=0.5^E to investigate the volumetric contributions to H_p,x=0.5^E or excess molar internal energies at constant pressure, U_V,x=0.5^E. Calculated U_V,x=0.5^E for the present model systems are quite simple compared to the excess molar internal energy at constant pressure, U_V,x=0.5^E. They are very small in magnitude and show linear dependencies on the density of mixtures.     

The intermolecular potential function of Smith–Thakkar type for C60

The intermolecular potential function of Smith–Thakkar type for C₆₀ has been proposed, and its expression is as follows

The unit of u(r) is J/mol, r is the distance between two C₆₀ molecules center and the unit is nm. Some properties of C₆₀ in the gas and crystal have been studied using the interaction potential of Smith–Thakkar type, such as stability of C₆₀ crystals, virial coefficient and lattice dynamics.     

Coordination networks constructed with supramolecular synthon RX–CCAgn (n = 4, 5; RX = halophenyl)

Eight new silver(I) double salts: AgL¹·2AgCF₃COO (1), AgL¹·3AgNO₃ (2), 2AgL²·5AgCF₃COO·2CH₃CN·H₂O (3), 4AgL³·6AgCF₃COO·5CH₃CN (4), 4AgL⁴·6AgCF₃COO·5CH₃CN (5), 2AgL⁵·4AgCF₃COO·NC(CH₂)₄CN (6), 2AgL⁵·4AgCF₃COO·2CH₃CN (7) and AgL⁶·2CF₂(CF₂COOAg)₂·2CH₃CN (8) (L¹ = 4-iodophenylethynide; L² = 3,4-dichlorophenylethynide; L³ = 3-chlorophenylethynide; L⁴ = 3-bromophenylethynide; L⁵ = 2-chlorophenylethynide; L⁶ = 2-fluorophenylethynide) have been synthesised and characterized by X-ray crystallography. All compounds contain the silver–halophenylethynide supramolecular synthon R_X−CCAg_n (n = 4, 5). In particular, the three-dimensional supramolecular structures in 1 and 2 are stabilized by strong AgI interactions, while that in 3 is consolidated by both AgCl and van der Waals type FCl interactions. In isomorphous compounds 4 and 5, the presence of respective FCl or FBr contact contributes to the stability of the network. The silver aggregates in 6, 7 and 8 are stabilized by AgCl or AgF interactions between the ortho-halo substituent and the Ag_n basket.     

The impact of surface area,volume, curvature,and Lennard–Jones potential to solvation modeling

This article explores the impact of surface area, volume, curvature, and Lennard–Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent–solute interfaces, and define a generalized Poisson–Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each other's, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the LJ potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature‐based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature, and LJ potential are less than 0.42 kcal/mol for all test sets. © 2016 Wiley Periodicals, Inc.     

The liquid–gas interface of oxygen–nitrogen solutions 2: Description in the Framework of the van der Waals gradient theory

The van der Waals gradient theory (vdW GT) is used to calculate surface tension, density profiles, adsorption, the Tolman length and to determine the position of dividing surfaces in the liquid–gas interface of an oxygen–nitrogen solution. The Helmholtz energy density (HED) is determined via an equation of state (EOS), unified for a liquid and gas, which describes stable, metastable and two-phase states of solutions. The influence parameters are calculated from data on the surface tension of pure components with the use of the mixing rule. At temperatures T > 100 K the vdW GT describes experimental data on the surface tension of oxygen–nitrogen solutions [V.G. Baidakov, A.M. Kaverin, V.N. Andbaeva, The liquid–gas interface of oxygen–nitrogen solutions: 1. Surface tension, Fluid Phase Equilib. 270 (2008) 116–120] within the experimental error. It is shown that the Tolman length, which determines the dependence of surface tension on the curvature of the dividing surface, depends considerably on the solution concentration.     

Description of the pVT behavior of ionic liquids and the solubility of gases in ionic liquids using an equation of state

A molecular thermodynamic model developed previously for fluids of chain-like molecules has been extended to correlate the pVT behavior of ionic liquids and the solubilities of gases such as CO₂, C₃H₆, C₃H₈, C₄H₁₀ in various ionic liquids. The relative deviation between the calculated molar volume and experimental data is less than 0.2%. It is shown that this equation of state can be used to correlate the solubility of CO₂ in ionic liquids with only one temperature-independent adjustable interaction parameter, and the accuracy of the correlation can be further improved using two temperature-independent adjustable parameters. The water content of ionic liquids has a large influence on the calculated results. For systems with water content lower than 0.1%, the average relative deviations of bubble point pressure are 3.14 and 4.90% using two parameters and one parameter, respectively. For systems containing C₃H₆, C₃H₈ and C₄H₁₀ two temperature dependent adjustable parameters are needed to obtain a good fit, and the corresponding deviation of the gas solubility is less than 2%, except for C₃H₈.     

An ab initio study on the vibrational and electronic spectra of the molybdenum–sulfur clusters with Mo2OnS4−n(n=0–4) core

Using the ab initio method, the vibrational and electronic spectra of binuclear molybdenum clusters which contain Mo₂O_nS_4−n(n=0–4) core were investigated. The main absorption bands in the IR spectra of these clusters are assigned and compared with each other, especially for the case of the trans isomers. The electronic spectra were studied by performing the CIS calculations. The ground state and the first excited state of the clusters were discussed by using the natural bond orbital method. It is shown that the band corresponding to the longest wavelength can be assigned to three kinds of transition types. Two transitions, σ(Mo–Mo)→π*(Mo–X_t)(X=S,O) and σ(Mo–Mo)→σ*(Mo–Mo), can be seen in most cases.     

The effect of the intermolecular potential formulation on the state‐selected energy exchange rate coefficients in N2–N2 collisions

The rate coefficients for N₂–N₂ collision‐induced vibrational energy exchange (important for the enhancement of several modern innovative technologies) have been computed over a wide range of temperature. Potential energy surfaces based on different formulations of the intramolecular and intermolecular components of the interaction have been used to compute quasiclassically and semiclassically some vibrational to vibrational energy transfer rate coefficients. Related outcomes have been rationalized in terms of state‐to‐state probabilities and cross sections for quasi‐resonant transitions and deexcitations from the first excited vibrational level (for which experimental information are available). On this ground, it has been possible to spot critical differences on the vibrational energy exchange mechanisms supported by the different surfaces (mainly by their intermolecular components) in the low collision energy regime, though still effective for temperatures as high as 10,000 K. It was found, in particular, that the most recently proposed intermolecular potential becomes the most effective in promoting vibrational energy exchange near threshold temperatures and has a behavior opposite to the previously proposed one when varying the coupling of vibration with the other degrees of freedom. © 2014 Wiley Periodicals, Inc.     

The distribution pattern of squares on the stability of F4F6-(BN)n (n = 10–22) polyhedrons

To gain an insight into the structures and stability of F₄F₆-(BN)_n polyhedrons with alternation of B and N atoms, a density functional theory study was performed on all isomers of F₄F₆-(BN)_n polyhedrons with n between 10 and 22. The calculation results demonstrate that the lowest energy isomers do not contain B₄₄ bonds (the bonds shared by two squares) and the energies of those isomers containing B₄₄ bonds increase with the number of B₄₄ bonds linearly, indicating that the energetically favored structures of F₄F₆-(BN)_n polyhedrons satisfy the isolated square rule and square adjacency penalty rule. The structural analysis reveals that the stability is determined by the pyramidalization of B and N atoms at the square–square fusion. The binding energy is fitted to the numbers of edges and a model is proposed for predicting the relative stability of these B–N polyhedral molecules.     

The infrared-driven cis–trans isomerization of nitrous acid HONO III: A mixed quantum–classical simulation

A mixed quantum–classical simulation of the IR-driven cis–trans isomerization of HONO in a Kr matrix at 30 K is presented, treating the hydrogen atom as quantum particle and the Kr matrix as well as intermolecular degrees of freedom of the ONO-body as classical. A new method is presented to time-propagate the coupled set of equations in a DVR basis in internal spherical coordinates, rather than in laboratory frame fixed cartesian coordinates. In spherical coordinates, a much more precise computation of the weak vibrational couplings is possible using a still manageable basis size. Good qualitative agreement between simulation and experiment is obtained, underestimating relaxation and isomerization rates by a modest factor ≈5. Upon matrix fluctuations, frequent curve crossings occur between the initially excited OH-stretch vibration and a closely lying combination mode of torsional and bending coordinate that lead to a transfer of population. The subsequent pathway of energy flow is deduced and discussed within a tier model, where trans-states, that belong to the second tier, are populated through a first tier of states that is composed of combinations of bending and torsional excitations. No specific energy pathway is revealed that would funnel the hydrogen atom directly towards the trans-side, hence the experimentally observed high cis → trans quantum yield of close to one probably has to be explained in a statistical scenario on a timescale much longer than that of the present simulation.     

Vapor–liquid equilibrium data and critical points for the system H2S+COS. Extension of the PSRK group contribution equation of state

Isothermal vapor–liquid equilibrium data for the binary system hydrogen sulfide+carbonyl sulfide were measured in the temperature range from 232 to 293 K using the static-synthetic technique. From the isothermal P−x data, the azeotropic conditions were derived. The critical line of this system was visually detected in a flow apparatus. Interaction parameters for this binary system were fitted simultaneously to all the experimental VLE and critical data for the Predictive Soave–Redlich–Kwong group contribution equation of state.     

New complex oxides of the A3n+3mA′nB3m+nO9m+6n family: Ba6A′Mn4O15 (A′=Mg, Ni)

Complex oxides Ba₆AMn₄O₁₅, where A=Mg (I) and Ni (II), belonging to the homologous series A_3n+3mA′_nB_3m+nO_9m+6n (n=1, m=1) were obtained by solid state reaction method from Ba carbonate and oxides MgO, NiO, MnO₂. Both new oxides are incommensurate. Their crystal structures were interpreted as composite ones with two subcells: a=10.042(3) Å, c₁=4.318(2) Å, c₂=2.565(1) Å, c₁/c₂=1.6834 for (I) and a=10.044(3) Å, c₁=4.308(2) Å, c₂=2.551(1) Å, c₁/c₂=1.6887 for (II). Magnetic susceptibility measurements in the range 2–850 K revealed antiferromagnetic correlations in Ba₆MgMn₄O₁₅ (T_N=7 K) and a pseudo-square-planar environment of some Ni²⁺ cations in Ba₆NiMn₄O₁₅.     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

Density functional theory analysis of CaRgn complexes: (Rg=He, Ne, Ar; n=1–4)

CaRg_n⁺ (Rg=He, Ne, Ar) complexes with n=1–4, are investigated by performing using the B3LYP/6-311+G (3df) density functional theory calculations. The CaHe_n⁺ (n=1–4) complexes are found to be stable. In the case of CaNe_n⁺ and CaAr_n⁺, stable structures and stationary point were found only for n=1 and 2. For n=3 in the C_3V and the D_3h point group as well as for n=4 in the T_d (tetrahedral) point group a saddle point (imaginary frequency) is observed and global minimum could be obtained along the potential energy surface.     

Structural, magnetic, and thermal characteristics of the phase transitions in Gd5GaxGe4−x magnetocaloric materials

Temperature-dependent, single crystal and powder X-ray diffraction studies as well as magnetization, and heat capacity measurements were carried out on two phases of the Gd₅Ga_xGe_4−x system: for x=0.7 and 1.0. Gd₅Ga_0.7Ge_3.3 shows three structure types as a function of temperature: (i) from 165 K to room temperature, the orthorhombic Sm₅Ge₄-type structure exists; (ii) below 150 K, it transforms to a orthorhombic Gd₅Si₄-type structure; and (iii) a monoclinic Gd₅Si₂Ge₂-type component is observed for the intermediate temperature range of 150 K≤T≤165 K. This is the first time that all these three structure types have been observed for the same composition. For Gd₅Ga_1.0Ge_3.0, the room temperature phase belongs to the orthorhombic Pu₅Rh₄-type structure with interslab contacts between main group atoms of 2.837(4) Å. Upon heating above 523 K, it transforms to a Gd₅Si₄-type structure with this distance decreasing to 2.521(7) Å before decomposing above 573 K.     

Ab initio study of spin–orbit interaction in the ground electronic states of XH (X = C, Si, Ge and Sn) molecules

Electronic structure and spectroscopic properties for the ground electronic states of CH, SiH, GeH and SnH molecules were obtained using the multiconfigurational self-consistent field followed by spin–orbit multireference multistate perturbation theory. Spin–orbit splitting calculations for ground states of the four molecules were carried out with model core potential (MCP) and all-electron (AE) methods. MCP results are compared with corresponding AE values to estimate the accuracy of the saving cost MCP calculations. The potential energy curves, calculated for the Ω states CH(X₁²Π_1/2 and X₂²Π_3/2), SiH(X₁²Π_1/2 and X₂²Π_3/2), GeH(X₁²Π_1/2 and X₂²Π_3/2) and SnH(X₁²Π_1/2 and X₂²Π_3/2) using the MCP method, were fitted to analytical potential energy function using Murrell–Sorbie potential energy function. Based on the analytical potential energy function, force constants and spectroscopic constants for the Ω states were obtained.     

Experimental measurement and modeling of the vapor–liquid equilibrium of carbon dioxide + chloroform

Isothermal bubble and dew points, saturated molar volumes, and mixture critical points for binary mixtures of carbon dioxide+chloroform (trichloromethane) (CO₂/CHCl₃) have been measured in the temperature region 303.15–333.15 K and at pressures up to 100 bar. Mixture critical points are reported at 313.15, 323.15, and 333.15 K. The data were modeled with the Peng–Robinson equation of state using both the van der Waals-1 (vdW-1) mixing rule and the Wong–Sandler (WS) mixing rule incorporating the UNIQUAC excess free energy model. The WS mixing rule provided a better representation of the data than did the vdW-1 mixing rule, though with three adjustable parameters instead of one. The extrapolating ability of both of the mixing rules was investigated. Using the parameters regressed at 323.15 K, the WS mixing rule yielded better extrapolations for the composition dependence at 303.15, 313.15, and 333.15 K than the vdW-1 mixing rule.