Ab initio Hartree–Fock and configuration-interaction treatment of the interaction between two nickel atoms

The interaction between two nickel atoms in the configurations (3d)⁸(4s)² and (3d)⁹ (4s)¹ has been calculated using ab initio methods (Hartree–Fock and configuration interaction). The results of the calculations compare favorably with the optical spectrum. The discrepancy between the calculated and the experimental dissociation energy is discussed, and a new estimate of the dissociation energy is given. The configuration-interaction calculations show that the interaction between the two nickel atoms is of a very complex nature. In spite of this the binding can be interpreted in a simple way. The bond is minly due to the 4sσ_g molecular orbital while the 3d orbitals of the two nuclei are exchange coupled.     

Memory effect on the inelastic interaction of electrons moving parallel to a solid surface

It is generally assumed that two successive inelastic interactions between an electron and a solid are independent of each other. In other words, the electron has no memory of its previous interaction. However, the previous interaction of the electron generates a potential that should influence its succeeding inelastic interaction. The aim of this work is to establish a model to account for the memory effect of an electron between two successive inelastic interactions. On the basis of the dielectric response theory, formulae for differential inverse inelastic mean free paths (DIIMFPs) and inelastic mean free paths (IMFPs) considering the memory effect were derived for electrons moving parallel to a solid surface by solving the Poisson equation and applying suitable boundary conditions. These mean free paths were then calculated with the extended Drude dielectric function for a Cu surface. It was found that the DIIMFP and the IMFP with the memory effect for electron energy E lay between the corresponding values without the memory effect for electron energy E and previous energy E₀. The memory effect increased with increasing electron energy loss, E₀ ? E, in the previous inelastic interaction. Copyright © 2005 John Wiley & Sons, Ltd.     

Modeling of interaction properties of surfaces of phyllosilicates: A theoretical forecast of adsorption isotherms of noble gases at the talc surface

The electrostatic potential and the intensity of the electric field above the isolated layer of the phyllosilicate mineral talc (layer group symmetry C2/m) were computed using the semiempirical INDO /2 method. The electrostatic potential V_c and the intensity of electric field (OVERBAR)E_c, above the surface of semi-infinite crystal were obtained as the sum of the contributions of the infinite number of individual layers. The interaction energy U_int between a noble gas atom and the talc crystal was computed as (a) a pure Lennard-Jones energy U_LJ and (b) the sum of U_LJ and interaction energy with induced dipole moment: U_ind = α|(OVERBAR)E|², where α is the dipole polarizability of the noble gas atom. The one-particle configurational integral was calculated within the classical mechanics limit. Both the free and adsorbed gas phases were assumed to be ideal. The obtained results demonstrate that in the case of uncharged and nonpolar adsorbate and an uncharged surface the electrostatic part of the interaction energy should be included in the total interaction energy. © 1996 John Wiley & Sons, Inc.     

1,2,3-三氮杂苯－(水)3复合物多体相互作用

The interaction between 1,2,3-triazine and three water molecules was studied using density functional theory B3LYP method at 6-31-t＋＋G^＊＊ basis set. Various structures for 1,2,3-triazine-（water）n （n= 1, 2, 3） complex were investigated and the different lower energy structures were reported. Many-body analysis was also carded out to obtain relaxation energy and many-body interaction energy （two, three, and four-body）, and the most stable conformer has the basis set superposition error corrected interaction energy of -- 102.61 kJ/mol. The relaxation energy, two- and three-body interactions have significant contribution to the total interaction energy whereas four-body interaction was very small for 1,2,3-triazine-（water）3 complex.     

The effect of boron nitride nanotubes size on the HArF interaction by NBO and AIM analysis

Three molecules HArF@BNNT(5,0), HArF@BNNT(6,0), and HArF@BNNT(7,0) have been formed by HArF encapsulated in boron nitride nanotubes (BNNTs) with different sizes. Due to the interaction between the HArF and the BNNTs, the H? Ar bond lengths are in a decrease trend, while the Ar? F bond lengths are in an increase trend compared with those of HArF. To investigate the nature of the interaction between H and Ar and the interaction between Ar and F, the quantum theory of “atoms in molecules” was carried out. The Laplacian (?²ρ_b) values of H? Ar suggest that the covalent interaction plays a key role in the H‐Ar interaction. For Ar? F, the results indicate that the Ar‐F interaction has a dominant noncovalent character. Moreover, the results obtained from the ratio of the kinetic‐energy density (G_b) and the potential‐energy density (V_b) (?G_b/V_b) and the total energy density (H_b) are in good agreement with that of ?²ρ_b values. In addition, the results of natural bond orbital charge and electron density difference between the HArF and BNNTs show that less electrons transfer away from the HArF to BNNTs with the gradual increase in the diameters of the BNNTs. © 2014 Wiley Periodicals, Inc.     

Interaction of water with DNA single and double helix in the B conformation

The interaction energy between water and B-DNA in the single and double helix is computed at a number of planar cross sections perpendicular to the helix long axis and for a few cylindrical surfaces enclosing the helix. In addition, Monte Carlo simulations are presented for a small cluster of water around regions of energy minima. On the base of these simulations the structure of water for B-DNA in solution, the quaternary structure of B-DNA, is proposed and discussed. The intermolecular interaction used in the Monte Carlo computation has been derived from ab initio computations of complexes between water and the DNA bases, diethylphosphate, a ribose derivative, and other model compounds.     

Indirect adatom interactions via III–V semiconductor substrates

Substrate-mediated interactions between adatoms on III–V semiconductors are investigated by using the self-consistent Anderson–Newns model in the Hartree–Fock approximation. The Green function formalism of the Dyson equation approach is employed to derive Chebyshev polynomial expressions for the chemisorption energy, interaction energy, and charge transfer, in terms of the adatom separation d. An alternating s- and p-orbital model of GaSb and InAs enabled interacting hydrogen adatoms on their (100) and (111) faces to be studied. As in the metal–substrate case, the chemisorption energy decreased with increasing band widths and adbond energy and, additionally, with increasing band gap. The interaction energy was found to have a d⁻² damping factor for the (100) faces and a d⁻³ factor for the (111) faces, its magnitude being larger for smaller gaps. Self-consistency is shown to play a significant role in interaction energy calculations for small values of d. In the case of charge transfer, its variation with d is purely a self-consistent result. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 377–397, 1998.     

Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes

The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density‐functional calculations. The total interaction energy ΔE^T of the C_4h‐symmetric guanine quartet consisting of Hoogsteen‐type base pairs with two hydrogen bonds between two neighbor bases is −66.07 kcal/mol at the highest level. The uracil quartet with C6 H6O4 interactions between the individual bases has only a small interaction energy of −20.92 kcal mol⁻¹, and the interaction energy of −24.63 kcal/mol for the alternative structure with N3 H3O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25% to all interaction energies. Complexes of metal ions with G‐quartets can be classified into different structure types. The one with Ca²⁺ in the central cavity adopts a C_4h‐symmetric structure with coplanar bases, whereas the energies of the planar and nonplanar Na⁺ complexes are almost identical. The small ions Li⁺, Be²⁺, Cu⁺, and Zn²⁺ prefer a nonplanar S₄‐symmetric structure. The lack of coplanarity prevents probably a stacking of these base quartets. The central cavity is too small for K⁺ ions and, therefore, this ion favors in contrast to all other investigated ions a C₄‐symmetric complex, which is 4.73 kcal/mol more stable than the C_4h‐symmetric one. The distance 1.665 Å between K⁺ and the root‐mean‐square plane of the guanine bases is approximately half of the distance between two stacked G‐quartets. The total interaction energy of alkaline earth ion complexes exceeds those with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen‐bonded biological systems. Compared with the before‐mentioned methods, the HCTH functional leads to longer hydrogen bonds and different relative energies for two U‐quartets. Finally, we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C HO contacts in the uracil quartet. In the G‐quartet, the MMFF94 hydrogen bond distances N2 H22N7 are shorter than the DFT distances, whereas the N1 H1O6 distances are longer. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 109–124, 2001     

Hydrogen–hydrogen interaction in planar biphenyl: A theoretical study based on the interacting quantum atoms and Hirshfeld atomic energy partitioning methods

The nature of H‐H interaction between ortho‐hydrogen atoms in planar biphenyl is investigated by two different atomic energy partitioning methods, namely fractional occupation iterative Hirshfeld (FOHI) and interacting quantum atoms (IQA), and compared with the traditional virial‐based approach of quantum theory of atoms in molecules (QTAIM). In agreement with Bader's hypothesis of H? H bonding, partitioning the atomic energy into intra‐atomic and interatomic terms reveals that there is a net attractive interaction between the ortho‐hydrogens in the planar biphenyl. This falsifies the classical view of steric repulsion between the hydrogens. In addition, in contrast to the traditional QTAIM energy analysis, both FOHI and IQA show that the total atomic energy of the ortho‐hydrogens remains almost constant when they participate in the H‐H interaction. Although, the interatomic part of atomic energy of the hydrogens plays a stabilizing role during the formation of the H? H bond, it is almost compensated by the destabilizing effects of the intra‐atomic parts and consequently, the total energy of the hydrogens remains constant. The trends in the changes of intra‐atomic and interatomic energy terms of ortho‐hydrogens during H? H bond formation are very similar to those observed for the H₂ molecule. © 2014 Wiley Periodicals, Inc.     

Long-range interaction between 1s and 2s or 2p hydrogen atoms

Long-range interaction energy between two hydrogen atoms has been computed in the second order of the perturbation theory. All states of the system arising when one of the atoms is in the 1s and the other in the 2s or 2p state have been considered. The energy represented by a series expansion in inverse powers of the internuclear distance, R, has been computed up to the terms in R^?8. The results are believed to give reliable interaction energies for R > 15 a.u. Accurate interaction energy for two ground-state hydrogen atoms has also been obtained up to the terms in R^?10. Results for the B′ ¹∑ state are employed to discuss the experimental ground-state dissociation energy of H₂, D₂, and HD. For H₂ all values of the dissociation energy obtained from various experimental absorption limits, by using the computed potential energy curve to separate off the effect of rotation, are shown to be satisfactorily consistent. The resulting total energy of H₂ is, however, higher than the most accurate theoretical value.     

Atomic-scale investigation of the interaction between coniferyl alcohol and laccase for lignin degradation using molecular dynamics simulations and spectroscopy

The interaction between coniferyl alcohol (CA) and laccase (LAC) was investigated using molecular dynamics (MD) simulations and spectral experiments. The mode of interaction between CA and LAC was established by MD simulations. The micro-environmental changes, stability and rigidity of the LAC-CA system were assessed by relevant parameters. These parameters include root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg). The calculated binding free energy (ΔG_binding=??19.99?kcal·mol.^?1), the van der waals (VDW) contribution (ΔG_vdw=?23.99?kcal·mol^?1) and the electrostatic energy (ΔG_ele=?23.09?kcal·mol^?1) of LAC-CA system demonstrated that the interaction of LAC-CA was a spontaneous process and the main interaction forces were van der Waal's and electrostatic forces. The values of ΔG_vdw and ΔG_ele were negative, which demonstrated that VDW interactions and electrostatic interactions were favorable for the binding of CA and LAC. The binding constants, thermodynamic parameters, molecular force types and binding distances confirmed the interaction between CA and LAC and further verified the rationality of the theoretical model by spectral experiments. The MD simulations and experimental approaches provide clues for the discovery of new mediators and useful references for the mechanism of microbial degradation of lignin and industrialization of lignocellulose.     

Perturbation theory with an approximate perturbation: The effect of charge overlap on interatomic interactions

The evaluation of interatomic interactions at large separations (R) typically involves neglecting electron exchange, treating the Coulomb interaction between atoms as a perturbation, neglecting third- and higher-order energy contributions, and approximating the Coulomb interaction by a short expansion in spherical harmonics and, usually, powers of R^?1. This last approximation, using an approximate perturbing Hamiltonian to evaluate a second-order perturbed energy, is examined here; error bounds and a simple correction are introduced. Three illustrative applications to the H? H⁺ interaction are given: the error incurred by truncating the spherical-harmonic expansion is bounded, the R^?1 expansion is corrected for the overlap of the “atomic” charge distributions, and the R^?1 expansion is analyzed to see why it works as well as it does.     

Super-Molecular Interaction between Cl and H2O within the Restricted Space of Layered Double Hydroxides

A periodical interaction model of LDHs-Cl-yH₂O has been proposed. The geometry optimization and energy of the layered double hydroxides (LDHs) were calculated using CASTEP/LDA method at the CA-PZ level. The distribution of H₂O in the interlayer and the super-molecular interaction between host layer and guest anion have been investigated by analyzing the geometric parameters, charge population, energy, and density of state (DOS). The results showed that there was a strong super-molecular interaction between the host layer and the guest anion Cl⁻. In the system of LDHs-Cl-yH₂O, the interlayer distance increased gradually then tended to invariableness. And in the process of hydration of LDHs-Cl, hydrogen bonding was superior to electrostatic interaction, and layer-water type hydrogen bonding was a little stronger than anion-water type hydrogen bonding between H₂O and the rest of the structure. When y was 1 or 2, Cl⁻ and the plane of water were parallel to the layer; while y was 3 or 4, distribution of Cl⁻ and water was random. Moreover, the LDHs-Cl-yH₂O would change from ionic crystal to molecular crystal with the increase of number of water molecule. The hydration of LDHs-Cl would achieve a definite saturation state.     

Nonadditivity of the SCF interaction energy in the (LiH)3 complex

The role of nonadditivity of the interaction energy between three LiH molecules was investigated within the SCF ab initio framework. The nonadditive part of the interaction energy is more important in the case of a cyclic structure than in a linear trimer, and is stabilizing in both cases. The value of the ratio of three-body and two-body terms for different points on the energy hypersurface is discussed.     

Long-range molecular interaction coefficients computed from frost-model wave functions

The average long-range interaction energy between two molecules can be written as an inverse asymptotic series in the intermolecular separation distanceR. Using Frost-model wave functions, the dispersion coefficients of the first three (R ^–6,R ^–8,R ^–10 terms in the series are obtained. Coefficients of three- and four-body non-additive interaction energies are also calculated and the form of the dispersion interaction when retardation effects are included is examined.     

Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations

Ab initio MP2/6-31G* interaction energies were calculated for more than 80 geometries of stacked cytosine dimer. Diffuse polarization functions were used to properly cover the dispersion energy. The results of ab initio calculations were compared with those obtained from three electrostatic empirical potential models, constructed as the sum of a Lennard-Jones potential (covering dispersion and repulsion contributions) and the electrostatic term. Point charges and point multipoles of the electrostatic term were also obtained at the MP2/6-31G* level of theory. The point charge MEP model (atomic charges derived from molecular electrostatic potential) satisfactorily reproduced the ab initio data. Addition of π-charges localized below and above the cytosine plane did not affect the calculated energies. The model employing the distributed multipole analysis gave worse agreement with the ab initio data than the MEP approach. The MP2 MEP charges were also derived using larger sets of atomic orbitals: cc-pVDZ, 6-311 + G(2d, p), and aug-cc-pVDZ. Differences between interaction energies calculated using these three sets of point charges and the MP2/6-31G* charges were smaller than 0.8 kcal/mol. The correlated ab initio calculations were also compared with the density functional theory (DFT) method. DFT calculations well reproduced the electrostatic part of interaction energy. They also covered some nonelectrostatic short-range effects which were not reproduced by the empirical potentials. The DFT method does not include the dispersion energy. This energy, approximated by an empirical term, was therefore added to the DFT interaction energy. The resulting interaction energy exhibited an artifact secondary minimum for a 3.9-4.0 vertical separation of bases. This defect is inherent in the DFT functionals, because it is not observed for the Hartree-Fock + dispersion interaction energy.© 1996 John Wiley & Sons, Inc.     

On the Reduction of Copper Oxide

The reduction of CuO with hydrogen has been studied with a temperature programmed reduction technique. According to a proposed reduction mechanism, the reduction was initiated with a interaction between hydrogen and active sites of copper oxide, the rate of the reduction was limited by the diffusion of water from the crystalline. The activation energy of this diffusion is found to be 13Kcal/mol. Reoxidation of copper powder may cause redispersion of the crystalline. The chemical interaction between copper oxide and Cabosil is found very weak.     

β-环糊精与有机胺之间包合作用的理论与实验研究

通过实验和理论计算方法研究了β-环糊精(CD)与乙二胺1及它的三个类似物: 二乙烯三胺2、三乙胺3和乙二胺四乙酸4之间的包合作用. 利用旋光法确定了β-CD与客体分子形成1:1型主–客体包合物, 在298.2 K下测定了包合物在水中的稳定常数(K). 采用半经验PM3方法考察了β-CD与短链脂肪胺1~7、环状脂肪胺8~11以及芳香胺12~13的分子间结合能力, 报道了β-CD与这些客体分子间的包合络合过程并讨论了这些包合体系之间的包合差异性. 变形能和水合能对包合体系的相互作用能的贡献均相当小. β-CD包合物的稳定性取决于主、客体分子之间的尺寸匹配. 对于β-CD与客体1~4形成的包合物而言, 旋光法测定的包合物的K值的顺序与PM3计算得到的包合物络合能绝对值的排序有很好的一致性.