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.     

Electron correlations in molecules. III. Strength of electron correlations in localized and aromatic bonds of main-group atoms

We investigate electron correlations within a minimal basis of various chemical bonds formed by second- and third-row atoms and hydrogen. The effects of correlations are characterized by two quantities: (i) intrabond correlation energy ϵ_corr and (ii) the correlation strength parameter Σ. The latter describes the relative suppression of the charge fluctuations within a bond. The quantities ϵ_corr and Σ can be associated with chemical bonds due to the local nature of the correlation phenomenon. It is found that one may distinguish between different classes of chemical bonds which are characterized by similar values of Σ parameter within each class. For instance, all considered bonds between hydrogen and main-group atoms fall into one class. The homopolar bonds formed by the atoms of the third row are characterized by a weaker σ but stronger π correlation strength than the respective bonds of the second row. The strongest correlations are found in homopolar single π bonds of third-row atoms. A particular detailed discussion is given of heteropolar bonds. The electron correlations of aromatic π electrons are found to be considerably weaker than those within the corresponding localized bonds. For the SCF input of the correlation calculation a semi-empirical method is used. The bond orbital approximation allows for a transparent interpretation of the computational results.     

Transferability of interatomic correlation energies

A simple procedure is presented to estimate the interatomic correlation energy of a bond A-B on the basis of intrabond correlations of the homopolar parents A-A and B-B and the bond polarity of A-B. We use a local approach supplemented by a semiempirical mean-field Hamiltonian within the bond orbital approximation. The capability of the interpolation scheme is demonstrated for several molecules formed by main-group atoms.     

Properties of interatomic surfaces: relation to bond energies

A number of properties of interatomic surfaces, as defined by the quantum theory of atoms in molecules (QTAIM), are calculated for approximately 50 molecules. These integrated surface properties are then tested for their ability to correlate and predict bond energies from MP2 atomisation energies. Three surface properties, each with units of energy, are found to show strong correlations with bond energy: single parameter models work well for non-polar bonds, but fail for polar and ionic bonds, where multi-variate methods are required. The local curvature of the interatomic surface is found to be useful this respect, reflecting charge transfer effects.     

van der Waals forces in presence of free charges: an exact derivation from equilibrium quantum correlations

We study interatomic forces in a fluid consisting of a mixture of free charges and neutral atoms in the framework of the quantum many-body problem at nonzero temperature and nonzero density. Of central interest is the interplay between van der Waals forces and screening effects due to free charges. The analysis is carried out in a partially recombined hydrogen plasma in the Saha regime. The effective potentials in the medium between two atoms, or an atom and a charge, or two charges, are determined from the large-distance behavior of equilibrium proton-proton correlations. We show, in a proper low-temperature and low-density scaling limit, that those potentials all decay as r(-6) at large distance r, while the corresponding amplitudes are calculated exactly. In particular, the presence of free charges only causes a partial (nonexponential) screening of the atomic potential, and it does not modify its typical r(-6) decay. That potential reduces to the standard van der Waals form for two atoms in vacuum when the temperature is driven to zero. The analysis is based on first principles: it does not assume preformed atoms and takes into account in a coherent way all effects, quantum mechanical binding, ionization, and collective screening, which originate from the Coulomb potential. Our method relies on the path integral representation of the quantum Coulomb gas.     

石英玻璃分子动力学模拟中的原子电荷转移与系综选择

介绍了SiO2体系分子动力学模拟中的Si、O原子电荷转移问题;采用Morse势函数研究了原子电荷转移对石英玻璃模拟的影响,发现原子电荷转移在影响模型密度的同时,还直接影响着原子的最近邻距离.NPT和NVT系综下的模拟结果对比显示,系综对模型中原子最近邻情况影响不大,但在NVT系综下模拟结果表明实际玻璃中存在的较大的空隙结构,找到了以往模拟中密度结果偏高的原因,提出了一种较好的石英玻璃分子动力学建模的方法.该方法不但解决了在调整电荷时维持原子最近邻距离与保证模型密度之间的矛盾,而且可以很好地描述石英玻璃在远程结构上密度不均、存在较大空隙的无序结构.此外,原子自扩散系数的计算结果展示了空隙结构在石英玻璃扩散性质研究中的作用.     

Strong support effects on the insulator to metal transition in supported Pt clusters as observed by X-ray absorption spectroscopy

The development of a new in situ probe of metallic character in supported metal clusters utilizing X-ray absorption spectroscopy is described. The technique is based on the extent of screening of the core-hole left in the neutral final state after the X-ray absorption. The technique allows for the clear differentiation between local interatomic charge transfer and more delocalized metallic screening. The particle size at the metal-insulator transition is found to depend strongly on the electron richness of the support oxygen atoms (i.e., ionic vs covalent oxides). Pt particles on supports with electron poor oxygen atoms (covalent) show metallic screening for sizes as small as 12 A in diameter. In contrast, on supports with electron rich oxygen atoms (ionic) the Pt particles do not show metallic behavior until around 20 A. The wide variation of previously reported estimates of the particle size at which the insulator to metal transition occurs is explained, giving a consistent picture for the onset of metallic character, and the reasons for the strong support effect.     

Interatomic voids in analysis of computer model structures of liquids and glasses

To analyze the structure of noncrystalline systems (liquids, glasses), it is suggested that the functions to be calculated should include not only the conventional atom-atom radial distribution function and structural factor, but also the same functions for a system of points representing the centers of interatomic voids. The points are located at the nodes of Voronoi polyhedra or, which is equivalent, at the centers of the spheres circumscribed around the Delaunay simplices. The system of points (system {D}) is unambiguously defined by the atomic coordinates and conveys additional information on the structure of the system because each interatomic void is determined by the relative positions of several atoms. Using a homogeneous noncrystalline packing model of atoms and inhomogeneous models derived from it as an example, we demonstrate that system {D} is sensitive to the structural features on medium scales and may be used along with the conventional atom-atom functions to study structural correlations other than short-range order correlations.     

Conformational dependence of electrostatic potential derived charges of a lipid headgroup: Glycerylphosphorylcholine

Atomic monopoles are routinely determined through a least squares fit to molecular electrostatic potentials. We report studies of the variation in atomic monopoles with variation in conformation for the zwitterionic polar head group of lecithins, a common class of lipid. The monopole of one atom, a relatively buried carbon, varied by 1.3 electron units between different conformers. “Exterior” atoms, as seen previously, showed smaller changes in charge and smaller estimated standard deviations. The total charge of local groups of atoms varied less than the charge of individual atoms, indicating that shifts in charge occurred mostly between neighboring atoms. This effect might be reflected in the high correlations seen between charges of many neighboring atoms. These correlations, while present for many logical groupings of atoms (such as within methylene and methyl groups), are curiously absent between some bonded atoms. Monopoles were fit to multiple conformations simultaneously to provide a charge set that could optimally reproduce the electrostatic potential of all the conformers as a means of generating monopoles for molecular dynamics simulations or other studies where conformation varies. In some cases, the charges on chemically equivalent atoms (e.g., the hydrogen atoms in a methyl group) were different by more than their estimated error of fit. These studies lead to the suggestion that a minimum error in reported charges is on the order of 10%. All conformations show that the positive charge of the trimethylalkyl ammonium group is carried by the methyl hydrogens; the total charge on the nine hydrogens is over 2 electron units, counterbalanced by negative monopoles on the carbons. The presence of this diffuse cloud of substantial charge would appear to be a disindicator of the use of a “united” atoms approach for these methyl groups. The effects of the charge variation on intermolecular interactions is also examined.     

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.     

Structure of hydrogenated silicon clusters. Small clusters

The ground state structures of silicon hydride clusters Si_nH_m containing up to 12 silicon atoms are obtained by numerical modeling. The cluster geometry is optimized for a wide set of initial structures using the MINDO/3 approximation for Monte Carlo simulation of interatomic interactions. The energy of the cluster depending on the content of hydrogen is studied, and it is shown that the Si-H and Si-Si bond energies depend little on the cluster size.     

The structure of 1,2-dithioles studied by 13C n.m.r. spectroscopy

The charge separation between the dithiole ring and oxygen in 3-(1′,2′-dithiole-3′-ylidene)-6-methyl-2,3-dihydropyran-2,4-diones and 3-(1′,2′-dithiole-3′-ylidene)-2,3-dihydrobenzo[b] pyran-2,4-diones has been determined by ¹³C and ¹⁹F n.m.r. spectroscopy. By both methods it is found that these compounds are relatively polar. A correlation is established between the ¹³C chemical shift of some carbon atoms and the S2p binding energies measured by e.s.c.a. in the 1,2-dithiole derivatives. This correlation shows that these ¹³C shifts depend on the positive charge taken by the 1,2-dithiole ring and can then constitute a convenient evaluation of this charge.     

Core level shifts of undercoordinated Pt atoms

We present the results of high-energy resolution core level photoelectron spectroscopy experiments paralleled by density functional theory calculations to investigate the electronic structure of highly undercoordinated Pt atoms adsorbed on Pt(111) and its correlation with chemical activity. Pt4f(7/2) core level binding energies corresponding to atoms in different configurations are shown to be very sensitive not only to the local atomic coordination number but also to the interatomic bond lengths. Our results are rationalized by introducing an indicator, the effective coordination, which includes both contributions. The calculated energy center of the valence 5d-band density of states, which is a well known depicter of the surface chemical reactivity, shows a noteworthy correlation with the Pt4f(7/2) core level shifts and with the effective coordination.     

Equatorial contra axial polar substituents. The relation of a chemical reaction to stereochemical substituent constants

The established rates of glycoside hydrolysis reactions were analyzed using free energy relationship plots based on substituent constants that depend on whether the substituent is axial or equatorial. In all cases good correlations were found when assuming either that the transition state had a charged ring-oxygen atom or that it had a charged anomeric carbon atom. The spontaneous hydrolysis of 2,4-dinitrophenyl beta-glycopyranosides and the acidic hydrolysis of methyl beta-D-glycopyranosides were found to give a good correlation, when 100% charge at the ring-oxygen in the transition state of these reactions is assumed. The acidic hydrolysis of methyl alpha-glycopyranosides was found to give good correlations regardless of whether 100% charge at the ring-oxygen or 100% charge at the anomeric carbon was assumed. The findings clearly demonstrate how crucial the stereochemistry of even remote polar substituents is for their electronic effect on chemical reaction.     

Density functional studies of model cerium oxide nanoparticles

Density functional plane-wave calculations have been performed to investigate a series of ceria nanoparticles (CeO2-x)(n), n Ce3+ reduction have been accounted for through the use of an effective on-site Coulomb repulsive interaction within the so-called DFT+U approach. Twelve nanoparticles of up to 2 nm in diameter and of both cuboctahedral and octahedral forms are chosen as representative model systems. Energetic and structural effects of oxygen vacancy formation in these nanoparticles are discussed with respect to those in the bulk and on extended surfaces. We show that the average interatomic distances of the nanoparticles are most significantly affected by the creation of oxygen vacancies. The formation energies of non-stoichiometric nanoparticles (CeO2-x)(n) are found to scale linearly with the average coordination number of Ce atoms; where x < 0 species, containing partially reduced O atoms, are less stable. The stability of octahedral ceria particles at small sizes, and the predicted strong propensity of Ce cations to acquire a reduced state at lower coordinated sites, is supported by interatomic potential-based global optimisations probing the low energy isomers of the Ce19O32 nanoparticle.     

Topological analysis of the molecular charge density and impact sensitivy models of energetic molecules

Important explosives of practical use are composed of nitroaromatic molecules. In this work, we optimized geometries and calculated the electron density of 17 nitroaromatic molecules using the Density Functional Theory (DFT) method. From the DFT one-electron density matrix, we computed the molecular charge densities, thus the electron densities, which were then decomposed into electric multipoles located at the atomic sites of the molecules using the distributed multipole analysis (DMA). The multipoles, which have a direct chemical interpretation, were then used to analyze in details the ground state charge structure of the molecules and to seek for correlations between charge properties and sensitivity of the corresponding energetic material. The DMA multipole moments do not present large variations when the size of the Gaussian basis set is changed; the largest variations occurred in the range 10-15% for the dipole and quadrupole moments of oxygen atoms. The charges on the carbon atoms of the aromatic ring of each molecule become more positive when the number of nitro groups increases and saturate when there are five and six nitro groups. The magnitude and the direction of the dipole moments of the carbon atoms, indicators of site polarization, also depend on the nature of adjacent groups, with the largest dipole value being for C-H bonds. The total magnitude of the quadrupole moment of the aromatic ring carbon atoms indicates a decrease in the delocalized electron density due to an electron-withdrawing effect. Three models for sensitivity of the materials based on the DMA multipoles were proposed. Explosives with large delocalized electron densities in the aromatic ring of the component molecule, expressed by large quadrupole values on the ring carbon atoms, correspond to more insensitive materials. Furthermore, the charges on the nitro groups also influence the impact sensitivity.