Spatial correlations of interatomic voids in molecular liquids studied using Delaunay simplices

Pair correlation functions are calculated for interatomic voids determined using Delaunay simplices. Various modifications of these functions are suggested in relation to the problem formulated. In the simplest case, this correlator is a conventional radial distribution function g(r), but its calculation employs the centers of voids, but not the centers of atoms. For analysis of nonuniform systems, it is suggested that a “weighted” radial distribution function be used, where pair distances are taken with weights that depend on the volume of the voids. To study structural differences between molecular liquids (e.g., alkane isomers) we use the partial radial distribution functions that take into account only relatively “wide” voids. The ion-void distance distribution functions define voids in the hydration shells of ions an aqueous salts.     

Structural properties of liquidN-methylformamide

Monte Carlo simulation of liquidN-methylformamide was carried out at 298 K. The atom-atom spatial distribution functions, concentrations of closed cycles of H-bonds, radial distribution functions of geometric centers of the cycles, and other characteristics of the system of hydrogen bonds and the network built of the lines connecting neighboring molecules were calculated. The effects of electrostatic and van der Waals interactions as well as molecular conformations on the regularities of mutual arrangement of the molecules were investigated. It was found that open chains of H-bonds dominate over closed cycles. Spatial structure of liquidN0methylformamide is determined by packing of the molecules and steric factors and is close to the structure of a random closely packed system of soft spheres. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 235–247, February, 2000.     

Structural properties of liquid formamide

Computer simulations of liquid formamide were carried out by the Monte Carlo method at 298 and 348 K. The atom-atom spatial distribution functions, the concentrations of closed H-bonded ring, the radial distributions functions of the geometric centers of the rings, and a number of other characteristics of hydrogen-bonded systems were calculated. It was found that the open chains dominate over cyclic structures, which are prone to association and formation of structural heterogeneities. Characteristic types of molecular associates were determined. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1911–1917, October, 1998.     

Prepeak in the structural factor. Inhomogeneous packings of Lennard-Jones atoms

This work reports on the effects of structural inhomogeneities within the models of spherical atomic packings on the radial distribution function (RDF) and the structural factor (SF). Models of inhomogeneous packings were constructed by removing some atoms from homogeneous packing according to a predetermined template. Thus various additional voids, leading to specific structural correlations of atoms on a middle scale (several atomic sizes), are introduced in the model. A dense noncrystalline packing of 27,000 Lennard-Jones atoms serves as the initial system. Three various templates were used, and models containing different fractions of additional voids were constructed with each of these templates. It is demonstrated that RDF is only slightly sensitive to such inhomogeneities; in contrast, the SF has additional peaks at small q, these peaks being notable even after removal of a small fraction of atoms. Some models yield a single narrow prepeak, which is akin to that observed in diffraction experiment for some glasses.     

Estimations of energy of noncovalent bonding from integrals over interatomic zero‐flux surfaces: Correlation trends and beyond

Bonding energies of 50 associates composed by neutral molecules (atoms) and bounded by various weak noncovalent interactions are calculated within the DFT framework using the PBE0/aug‐cc‐pVTZ combination. The electronic virial and electron density values at bond critical points together with their integrals over interatomic surfaces are tested to check their ability to estimate bonding energies. Two correlations schemes dealing with integrals over interatomic surface are suggested to estimate bonding energy of any noncovalent interaction. The physical meaning of explored and several known correlations is discussed. Methods to estimate interatomic surface integrals of electronic virial and electron density are proposed. © 2018 Wiley Periodicals, Inc.     

Structural properties of dilute aqueous solutions of dimethylformamide and acetone based on computer simulation

The Monte Carlo simulation of molecular configurations for aqueous solutions ofN,N-dimethylformamide and acetone was carried out. The atom-atom radial distribution functions were determined. The topological properties of the H-bond system were investigated. The concentrations of closed H-bond cycles and the radial distribution functions of their geometric centers were found. It was shown that the local arrangement of molecules and supermolecular assemblies typical of the H-bond network in neat water is retained in the solutions studied. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 592–599, April, 1998.     

Atom-atom partitioning of total (super)molecular energy: the hidden terms of classical force fields

Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom-atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange).     

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.     

Optical properties of passivated silicon nanoclusters: the role of synthesis

The effect of preparation conditions on the structural and optical properties of silicon nanoparticles is investigated. Nanoscale reconstructions, unique to curved nanosurfaces, are presented for silicon nanocrystals and shown to have lower energy and larger optical gaps than bulk-derived structures. We find that high-temperature synthesis processes can produce metastable noncrystalline nanostructures with different core structures than bulk-derived crystalline clusters. The type of core structure that forms from a given synthesis process may depend on the passivation mechanism and time scale. The effect of oxygen on the optical of different types of silicon structures is calculated. In contrast to the behavior of bulklike nanostructures, for noncrystalline and reconstructed crystalline structures surface oxygen atoms do not decrease the gap. In some cases, the presence of oxygen atoms at the nanocluster surface can significantly increase the optical absorption gap, due to decreased angular distortion of the silicon bonds. The relationship between strain and the optical gap in silicon nanoclusters is discussed.     

Online resource for theoretical study of hydration of biopolymers

An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.     

Online resource for theoretical study of hydration of biopolymers

An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.     

<Emphasis Type="Italic">Ab initio</Emphasis> calculations of chemical bond parameters and the band structure of a two-dimensional system: Graphene/MnO(001)

The results of the DFT studies of the band structure, Fermi surface, and chemical bond in ultrathin graphene/MnO(001) and MnO(001) films are presented, and the features of the interatomic interactions at the initial stage of the growth of graphene islands on the manganese oxide surface are considered. The features of spin state in the valence band and at the Fermi level in these systems are discussed. The magnetic moment on the Mn atom is estimated, and the effect of spin polarization on oxygen and carbon atoms is found. Their nature is discussedBased on the structural energy calculations of 2D graphene/MnO(001) and 2D MnO(001), the stability of the systems is established, and the chemical bond energy is determined.     

1,3-二(4-吡啶基)-丙烷与邻苯二甲酸构筑的过渡金属配合物的合成、结构和荧光性质

以1,3-二(4-吡啶基)-丙烷(bpp)和邻苯二甲酸(1,2-H2bdc)为配体,通过水热法合成了过渡金属配合物M2(1,2-bdc)2(bpp)2·2H2O[M=Co(1),Ni(2)]和Cd(1,2-bdc)(bpp)·H2O(3).配合物1和2属单斜晶系P21空间群,具有相似的三维骨架结构.配合物中存在2种配位环境相似的金属中心,每个金属中心采取六配位的畸变八面体构型,与来自2个1,2-bdc配体的3个氧原子和2个bpp配体的2个氮原子以及1个水分子配位.1,2-bdc配体采取单齿/双齿螯合的配位模式将金属离子连接成M1-(1,2-bdc)-M2右手螺旋链.bpp配体采取Trans-Gauche(TG)构型,连接相邻的金属离子形成M1-(bpp)-M1链和M2-(bpp)-M2链.这3种链交织在一起构筑成具有{65.8}拓扑的三维结构.配合物3属单斜晶系P21/c空间群,具有单节点的双层二维结构.Cd(Ⅱ)离子采取七配位的畸变五角双锥体构型,与来自2个1,2-bdc配体的4个氧原子,2个bpp配体的2个氮原子和1个水分子配位.1,2-bdc配体采取双齿螯合/双齿螯合的配位模式将Cd(Ⅱ)离子连接成Cd-(1,2-bdc)-Cd链.bpp配体采取TG构型,连接相邻的Cd(Ⅱ)离子,形成Cd-(bpp)-Cd链.这2种链通过共享Cd(Ⅱ)离子交错排列构筑成二维结构.配合物3显示出强的荧光,最大发射位于408 nm处,对应于配体的π*-π跃迁.不同有机小分子对配合物3的荧光强度有不同程度的影响,苯胺对其有显著的猝灭作用,基于荧光猝灭机理,配合物3可用于选择性检测苯胺分子.     

Interatomic exchange-correlation interaction energy from a measure of quantum theory of atoms in molecules topological bonding: A diatomic case

The potential relations between the measure of topological interatomic bonding—integrals of electron density with respect to internuclear axis over the corresponding quantum theory of atoms in molecules (QTAIM)-defined interatomic surface (IAS)—and interatomic exchange-correlation contributions from the interacting quantum atoms approach are discussed. The quantum chemical computations of 38 equilibrium diatomic systems at different levels of theory (HF, MP2, MP4SDQ, and CCSD) are invoked to support abstract considerations. Parameters of excellent correlations between IAS integrals and interatomic exchange-correlation energy are found by the optimization. The performance of these trends depends on the accuracy of the electronic correlation treatment. The resulting trends are a unique feature of equilibrium states, whereas more complicated dependencies are explored for several systems at non-equilibrium conditions. The relations of established trends with other IAS-based estimations of strength of bonding interactions between topological atoms and issues explored for multiatomic systems are briefly discussed.     

Doubly phenoxo-hydroxo-bridged dicopper(II) complexes: individual contributions of the bridges to antiferromagnetic coupling based on two related biomimetic models for catechol oxidases

This paper describes the synthesis, structure and spectroscopic and magnetic properties of two (μ-phenoxo)(μ-hydroxo)dicopper(II) complexes (1 and 2) which contain similar N,O-donor atoms but with distinct coordination arrangements around the Cu(II) centers. Structural and magnetic studies of 1 and 2 allowed us to evaluate, for the first time, the individual contributions of the {Cu(μ-phenoxo)Cu} and {Cu(μ-hydroxo)Cu} structural units to the antiferromagnetic coupling between the Cu(II) centers in these complexes.     

Electronic packing frustration in complex intermetallic structures: the role of chemical pressure in Ca2Ag7

The assignment of distinct roles to electronics and sterics has a long history in our rationalization of chemical phenomena. Exploratory synthesis in the field of intermetallic compounds challenges this dichotomy with a growing list of phases whose structural chemistry points to an interplay between atomic size effects and orbital interactions. In this paper, we begin with a simple model for how this interdependence may arise in the dense atomic packing of intermetallics: correlations between interatomic distances lead to the inability of a phase to optimize bonds without simultaneously shortening electronically under-supported contacts, a conflict we term electronic packing frustration (EPF). An anticipated consequence of this frustration is the emergence of chemical pressures (CPs) acting on the affected atoms. We develop a theoretical method based on DFT-calibrated μ(2)-Hückel calculations for probing these CP effects. Applying this method to the Ca(2)Ag(7) structure, a variant of the CaCu(5) type with defect planes, reveals its formation is EPF-driven. The defect planes resolve severe CPs surrounding the Ca atoms in a hypothetical CaCu(5)-type CaAg(5) phase. CP analysis also points to a rationale for these results in terms of a CP analogue of the pressure-distance paradox and predicts that the impetus for defect plane insertion is tunable via variations in the electron count.     

Self-Consistent-Field potential-energy surfaces for hydrogen atom pairs within small palladium clusters

An ab initio electronic structure study is presented of hydrogen–hydrogen interactions in an electronic environment perturbed by the presence of palladium atom clusters. In particular, we investigated changes in the interatomic potential when the atomic centers are trapped inside an fcc palladium octahedral hole and when they are separated from each other by a (111) plane of palladium atoms. The (111) plane was modeled with a cluster of three palladium atoms. Self-consistent field (SCF ) level calculations were performed, and palladium atom pseudopotentials were employed to make the systems studied computationally tractable. For pairs of atoms placed within the octahedral hole, various lines of approach were considered [along the (100), (110), and (111) directions]. Lattice deformations and electronic excitations were examined for their effect on the interatomic potential.     

Update of the AIM2000-program for atoms in molecules

The second version of the program package AIM2000 is presented. AIM2000 makes use of the well established theory of atoms in molecules. AIM2000 analyzes the molecular structure and calculates properties of atoms in molecules as well as properties of interatomic surfaces. The program has an interactive, context-sensitive help component and extensive 2D and 3D visualization components.     

Structure and dynamics of model Ag and Pt clusters

The structure and dynamics of model silver and platinum clusters were investigated by performing molecular dynamics calculations with regular quenching along the trajectory. An eigenvector-following routine was used to determine stationary points linking minimum configurations. Clusters of 13 and 14 atoms were studied, using Sutton-Chen potentials suitable for silver and platinum to describe the interatomic interaction. The close relationship between features of the potential energy surface and the dynamic behaviour of the clusters, for example the occurrence of coexistence, is shown. For silver and platinum, very different structural as well as dynamic properties are observed.