Towards a force field based on density fitting

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.     

Importance of backdonation in [M-(CO)]p+ complexes isoelectronic to [Au-(CO)]+

In this contribution, we study several monocarbonyl-metal complexes in order to unravel the contribution of relativistic effects to the metal-ligand bond length and complexation energy. Using scalar density functional theory (DFT) constrained space orbital variation (CSOV) energy decomposition analysis supplemented by all-electron four-component DFT computations, we describe the dependency of relativistic effects on the orbitals involved in the complexation for the Au(+) isoelectronic series, namely, the fully occupied 5d orbitals and the empty 6s orbitals. We retrieve the well-known sensitivity of gold toward relativity. For platinum and gold, the four-component results illustrate the simultaneous relativistic expansion of the 5d orbitals and the contraction of the 6s orbitals. The consequences of such modifications are evidenced by CSOV computations, which show the importance of both donation and backdonation within such complexes. This peculiar synergy fades away with mercury and thallium for which coordination becomes driven by the accepting 6s orbitals only, which makes the corresponding complexes less sensitive toward the relativistic effects.     

Periodic surface calculations on chemisorption of H2 on a Ni surface

The periodic model of finite surfaces has been employed to investigate the localizability of the chemisorption interaction and to examine the validity of the cluster model. The adsorbate—surface interaction is estimated by the usual perturbation method. The model is applied to chemisorption of hydrogen molecule on a Ni(100) surface. As for the present calculations, the period model is shown to be advantageous over the cluster model in representing both the adsorbate-free surface state and the adsorbate—surface interaction.     

A CSOV study of the difference between HF and DFT intermolecular interaction energy values: the importance of the charge transfer contribution

Intermolecular interaction energy decompositions using the Constrained Space Orbital Variation (CSOV) method are carried out at the Hartree-Fock level on the one hand and using DFT with usual GGA functionals on the other for a number of model complexes to analyze the role of electron correlation in the intermolecular stabilization energy. In addition to the overall stabilization, the results provide information on the variation, with respect to the computational level, of the different contributions to the interaction energy. The complexes studied are the water linear dimer, the N-methylformamide dimer, the nucleic acid base pairs, the benzene-methane and benzene-N2 van der Waals complexes, [Cu+ -(ImH)3]2, where "ImH" stands for the Imidazole ligand, and ImH-Zn++. The variation of the frozen core energy (the sum of the intermolecular electrostatic energy and the Pauli repulsion energy) calculated from the unperturbed orbitals of the interacting entities indicates that the intramolecular correlation contributions can be stabilizing as well as destabilizing, and that general trends can be derived from the results obtained using usual density functionals. The most important difference between the values obtained from HF and DFT computations concerns the charge transfer contribution, which, in most cases, undergoes the largest increase. The physical meaning of these results is discussed. The present work gives reference calculations that might be used to parametrize new correlated molecular mechanics potentials.     

Periodic ab initio approach for the cooperative effect of CH/pi interaction in crystals: relative energy of CH/pi and hydrogen-bonding interactions

The bonding property of the CH/pi interaction in organic crystals has been investigated by the means of a periodic ab initio method. The energy of the CH(sp(2))/pi interaction in crystals, estimated with periodic RHF/6-21G*, showed a reasonable attractive CH(sp(2))/pi interaction owing to a cooperative effect, whereas the results calculated with RHF/cc-pVDZ indicate a negligibly small or repulsive interaction. The relative contribution of the CH(sp(2))/pi interaction to the column packing energy was found to be roughly half of the energy of a conventional hydrogen bond. The calculation of the charge distributions on the aromatic rings participating in the CH(sp(2))/pi interaction in crystals revealed that the atoms were more ionic than those in the gas phase. These theoretical calculations suggest a hydrogen-bonding characteristic for the CH(sp(2))/pi interaction in crystals, which does not occur in solution nor gas phase. We present computational evidence of the existence of the cooperative effect of CH(sp(2))/pi interaction in crystals.     

On the stability of single- and double-stranded DNA helices: The application of the PPT-MCF method on large fragments of DNA

The pseudo-polarization tensor mutually consistent field (PPT -MCF ) method recently introduced [1] has been applied to study the stacking interactions between the nucleotide bases in large periodic B-DNA fragments. The effects on the global and local binding properties caused by replacing one base in the periodic sequence by another base are investigated. The increase in the stability for comparable fragments owing to this base substitution is further enforced in the case of periodic alternating helices. The most important results are that the stacking interaction between two bases is slowly converging with the interbase distance and that the average contribution per base to the binding energy is repulsive. Furthermore, the energetical properties of double helix models in B- and Z-DNA configurations, respectively, consisting of up to five base pairs have been compared. It turns out that the G C G C sequence in Z-DNA is significantly more stable than either in periodic or periodic alternating B-DNA. In these cases the average energy contribution of a single Watson–Crick-type base pair is predicted also to be positive. From the calculations it follows that the double helix is not stabilized owing to the hydrogen bonding between the bases belonging to both strands, in contradiction to most other investigations.     

The implementation of a fast and accurate QM/MM potential method in Amber

Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge density functional tight binding (SCC-DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation.     

Periodic ab initio estimates of the dispersive interaction between molecular nitrogen and a monolayer of hexagonal BN

The ab initio determination of the leading long-range term of pairwise additive dispersive interactions, based on the independent analysis of the response properties of the interacting objects, is here considered in the case where these are part of a periodic system. The interaction of a nitrogen molecule with a thin film of hexagonal BN has been chosen as a case study for identifying some of the problems involved, and for proposing techniques for their solution. In order to validate the results so obtained, the interaction energy between N(2) and a BN monolayer at different distances has been estimated following a totally different approach, namely by performing post-Hartree-Fock (MP2) supercell calculations using the Crystal+Cryscor suite of programs. The results obtained with the two approaches closely agree over a long range, while the limit of validity of the purely dispersive regime can be clearly assessed.     

Comments on the nature of the bonding in oxygenated dinuclear copper enzyme models

The nature of the bonding in model complexes of di-copper metalloenzymes has been analyzed by means of the electronic localization function (ELF) and by the quantum theory of atoms in molecules (QTAIM). The constrained space orbital variations (CSOV) approach has also been used. Density functional theory (DFT) and CASSCF calculations have been carried out on several models of tyrosinase such as the sole Cu2O22+ central core, the Cu2O2(NH3)62+ complex and the Cu2O2(Imidazol)62+ complex. The influence on the central Cu(2)O(2) moiety of both levels of calculation and ligand environment have been discussed. The distinct bonding modes have been characterized for the two major known structures: [Cu(2)(mu-eta(2): eta(2)-O(2))](2+) and [Cu(2)(mu-O(2))](2+). Particular attention has been given to the analysis of the O-O and Cu-O bonds and the nature of the bonding modes has also been analyzed in terms of mesomeric structures. The ELF topological approach shows a significant conservation of the topology between the DFT and CASSCF approaches. Particularly, three-center Cu-O-Cu bonds are observed when the ligands are attached to the central core. At the DFT level, the importance of self interaction effects are emphasized. Although, the DFT approach does not appear to be suitable for the computation of the electronic structure of the isolated Cu(2)O(2) central core, competitive self interaction mechanisms lead to an imperfect but acceptable model when using imidazol ligands. Our results confirm to a certain extent the observations of [M.F. Rode, H.J. Werner, Theoretical Chemistry Accounts 4-5 (2005) 247.] who found a qualitative agreement between B3LYP and localized MRCI calculations when dealing with the Cu(2)O(2) central core with six ammonia ligands.     

Quantum-dot growth simulation on periodic stress of substrate

InAs quantum dots (QDs) are grown on the cleaved edge of an In(x)Ga(1-x)AsGaAs supperlattice experimentally and a good linear alignment of these QDs on the surface of an In(x)Ga(1-x)As layer has been realized. The modulation effects of periodic strain on the substrate are investigated theoretically using a kinetic Monte Carlo method. Our results show that a good alignment of QDs can be achieved when the strain energy reaches 2% of the atomic binding energy. The simulation results are in excellent qualitative agreement with our experiments.     

Density functional theory for molecular and periodic systems using density fitting and continuous fast multipole method: Analytical gradients

A full implementation of analytical energy gradients for molecular and periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian‐type orbitals as basis functions. Its key component is a combination of density fitting (DF) approximation and continuous fast multipole method (CFMM) that allows for an efficient calculation of the Coulomb energy gradient. For exchange‐correlation part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097) is extended to energy gradients. Computational efficiency and asymptotic O(N) scaling behavior of the implementation is demonstrated for various molecular and periodic model systems, with the largest unit cell of hematite containing 640 atoms and 19,072 basis functions. The overall computational effort of energy gradient is comparable to that of the Kohn–Sham matrix formation. © 2016 Wiley Periodicals, Inc.     

乙烷在Pt/γ-Al2O3（001）模型催化剂上吸附行为的理论研究

本文采用密度泛函理论方法和周期性边界条件,考察了Pt原子与γ-Al2O3(001)表面上六种不同位点的相互作用,获得了最稳定吸附位的Pt/γ-Al2O3模型催化剂,建立了Pt原子负载在γ-Al2O3(001)表面的模型催化剂。同时,考查了乙烷分子在Pt/γ-Al2O3模型催化剂上的吸附行为。结果表明,在Pt/γ-Al2O3模型催化剂上,Pt原子转移了部分电子到载体γ-Al2O3。乙烷以分子态形式吸附在Pt/γ-Al2O3模型催化剂上,靠近Pt原子的C-H键受到一定程度地活化。     

考虑次相邻作用的Hückel矩阵的本征值问题

本文用图论方法和差分方程法分别处理了包含次相邻作用的Hückel矩阵的本征值问题。两种方法得到一致的封闭形式的近似解。作为应用, 讨论了次相邻作用对链多烯烃的影响。     

Studies on the structural unit and suspending terminal groups in the quasi-one-dimensional periodic system

Quasi-one-dimensional periodic systems were investigated by the new proposed extrapolation method. The effect of the selection of the different structural units and their spin states on the periodic system was also studied. A quantum chemical calculation investigation of a 28 quasi-one-dimensional periodic system with MNDO (UHF ) and EHMO /ASED –EHCO /ASED was undertaken. Quantum chemical calculation results with the MNDO (UHF ) method showed that the proposed new method could be applied in the situation of the more precise semiempirical method. The selection of the different structural units and their spin states do not affect the extrapolated structural unit energy. The energy of suspending terminal group is generally higher for those with a higher bond order. The interaction energy between the suspending terminal groups generally decreases with the chain length. Comparison between the extrapolation results of EHMO /ASED and those from the crystal orbital calculation of EHCO /ASED indicates their equivalence, thus confirming the validity of the proposed method. © 1995 John Wiley & Sons, Inc.     

Fragment interaction analysis based on local MP2

We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.     

Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach

The graphical unitary group approach has been applied in an efficient implementation of a general multireference configuration interaction (MRCI) method for use with small active molecular orbital spaces in a semiempirical framework. Gradients can be computed analytically for molecular orbitals from a closed-shell or a half-electron open-shell Hartree-Fock calculation. CPU times for single point energy and gradient calculations are reported. The code allows MRCI geometry optimizations of large molecules, as illustrated for the singlet ground state and the four lowest triplet states of fullerene C(76).     

B和N原子掺杂超长(3,3)单壁碳纳米管的从头算研究

用从头算的周期边界条件方法,建立了(3,3)型超长单壁碳纳米管的新模型.使用B3LYP/3-21G方法计算了B和N掺杂纳米管的结构参数、掺杂能量、能带结构以及能隙.研究表明,B和N原子掺杂的(3,3)型单壁碳纳米管具有直接带隙半导体特征,其α轨道计算所得能隙值分别为1.797和2.041 eV.     

Electronic structure and bonding in clusters: Theoretical studies

The electronic structures of small Al _n ,n=5, 9, 13, clusters with bulk geometry are studied using the ab initio Hartree-Fock-LCAO method. The cluster ground states have always multiplicity higher than the lowest possible value. However, the energy difference between ground and lowest low spin state decreases with increasing cluster size. The energy range of the Al _n cluster valence levels is comparable with the width of the occupied part of the 3sp band in bulk Al. The different binding mechanisms that arise when a CO molecule interacts with Al _n clusters in different coordination sites are analyzed in detail with the constrained space orbital variation (CSOV) method. Electrostatic and polarization contributions to the interaction are found to be important. Among charge transfer (donation) contributions π electron transfer from Al _n to CO corresponding to π backbonding is energetically more important than σ electron transfer from CO to Al _n characterizing the σ bond.