Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.     

A hierarchical construction scheme for accurate potential energy surface generation: an application to the F+H2 reaction

We present a hierarchical construction scheme for accurate ab initio potential energy surface generation. The scheme is based on the observation that when molecular configuration changes, the variation in the potential energy difference between different ab initio methods is much smaller than the variation for potential energy itself. This means that it is easier to numerically represent energy difference to achieve a desired accuracy. Because the computational cost for ab initio calculations increases very rapidly with the accuracy, one can gain substantial saving in computational time by constructing a high accurate potential energy surface as a sum of a low accurate surface based on extensive ab initio data points and an energy difference surface for high and low accuracy ab initio methods based on much fewer data points. The new scheme was applied to construct an accurate ground potential energy surface for the FH(2) system using the coupled-cluster method and a very large basis set. The constructed potential energy surface is found to be more accurate on describing the resonance states in the FH(2) and FHD systems than the existing surfaces.     

A new fragment-based approach for calculating electronic excitation energies of large systems

We present a new fragment-based scheme to calculate the excited states of large systems without necessity of a Hartree-Fock (HF) solution of the whole system. This method is based on the implementation of the renormalized excitonic method [M. A. Hajj et al., Phys. Rev. B 72, 224412 (2005)] at ab initio level, which assumes that the excitation of the whole system can be expressed by a linear combination of various local excitations. We decomposed the whole system into several blocks and then constructed the effective Hamiltonians for the intra- and inter-block interactions with block canonical molecular orbitals instead of widely used localized molecular orbitals. Accordingly, we avoided the prerequisite HF solution and the localization procedure of the molecular orbitals in the popular local correlation methods. Test calculations were implemented for hydrogen molecule chains at the full configuration interaction, symmetry adapted cluster/symmetry adapted cluster configuration interaction, HF/configuration interaction singles (CIS) levels and more realistic polyene systems at the HF/CIS level. The calculated vertical excitation energies for lowest excited states are in reasonable accordance with those determined by the calculations of the whole systems with traditional methods, showing that our new fragment-based method can give good estimates for low-lying energy spectra of both weak and moderate interaction systems with economic computational costs.     

On the accuracy of correlation-energy expansions in terms of local increments

The incremental scheme for obtaining the energetic properties of extended systems from wave-function-based ab initio calculations of small (embedded) building blocks, which has been applied to a variety of van der Waals-bound, ionic, and covalent solids in the past few years, is critically reviewed. Its accuracy is assessed by means of model calculations for finite systems, and the prospects for applying it to delocalized systems are given.     

Green functions in the theory of semiconductor surfaces

Electronic properties of a few technologically important semiconductor surfaces, explored in surface Green function calculations, are presented and briefly discussed in comparison with experimental data from high-resolution surface spectroscopy. The emphasis is on results of first-principles calculations employing the local density approximation or the generalized gradient approximation of density functional theory. The systems addressed comprise of the prototype surfaces of the elemental semiconductors diamond and Si, as well as the group IV compound semiconductor SiC. The examples show that surface Green function calculations, as performed by Maria St licka and Sydney Davison in their early work on the surfaces of model systems, such as linear monoatomic chains or the Kronig–Penney model, can nowadays be applied to efficiently evaluate electronic properties of real surfaces. The results of such ab initio Green function calculations are found to be in very good agreement with experimental data.     

Ab initio melting curve of copper by the phase coexistence approach

Ab initio calculations of the melting properties of copper in the pressure range 0-100 GPa are reported. The ab initio total energies and ionic forces of systems representing solid and liquid copper are calculated using the projector augmented wave implementation of density functional theory with the generalized gradient approximation for exchange-correlation energy. An initial approximation to the melting curve is obtained using an empirical reference system based on the embedded-atom model, points on the curve being determined by simulations in which solid and liquid coexist. The approximate melting curve so obtained is corrected using calculated free energy differences between the reference and ab initio system. It is shown that for system-size errors to be rendered negligible in this scheme, careful tuning of the reference system to reproduce ab initio energies is essential. The final melting curve is in satisfactory agreement with extrapolated experimental data available up to 20 GPa, and supports the validity of previous calculations of the melting curve up to 100 GPa.     

Relativistic electronic structure theory

The theoretical and technical foundations are presented for the efficient relativistic electronic structure theories to treat heavy-atomic molecular systems. This review contains two surveys of four-component and two-component quasi-relativistic approaches. First, we review our highly efficient computational scheme for four-component relativistic ab initio molecular orbital (MO) methods over generally contracted spherical harmonic Gaussian-type spinors (GTSs). Illustrative calculations, which are performed with a new four-component relativistic ab initio molecular orbital program package REL4D, clearly show the efficiency of our computational scheme by the Dirac-Hartree-Fock (DHF) and Dirac-Hartree-Fock (DKS) methods. Next, in the two-component quasi-relativistic framework, two relativistic Hamiltonians, RESC and higher order Douglas-Kroll (DK) Hamiltonians, are introduced, and several illustrative calculations are shown. Numerical results for several systems show that good accuracy can be obtained with our third-order DK (DK3) Hamiltonian.     

Ab initio molecular dynamics using hybrid density functionals

Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.     

Molecular dynamics and metadynamics simulations of [2 + 2] photocycloaddition

Triplet state mechanism of [2 + 2] photocycloaddition forming a cyclobutane ring from two ethylenes is investigated in the context of photocatalysis. High‐level ab initio calculations are combined with ab initio adiabatic molecular dynamics and ab initio metadynamics for rare events modeling. In a photocatalytic scheme, a reactant reaches the triplet state either via intersystem crossing (ISC) or triplet sensitization. The model system adopts a biradical structure, which represents energy intersection with the ground state. The system either completes cyclization or undergoes fragmentation into two olefinic units. The potential and free energy surfaces of the cyclobutane/ethylenes system are mapped with multireference approaches describing possible reaction pathways. To obtain a full picture of a double bond photoreactivity, ab initio adiabatic dynamical calculations were used to estimate reaction yields and to model the effects of excess energy. The potential use of density functional theory based approaches for [2 + 2] photocycloaddition was investigated for future simulations and design of realistic photocatalytic systems. Dynamical aspects of [2 + 2] photocycloaddition via a triplet state manifold are investigated by combining ab initio multireference methods and ab initio molecular dynamics and metadynamics. The reaction pathways are studied for a model system of two ethylenes forming a cyclobutane ring to provide a basis for further studies on design of photocatalytic systems.     

A fragment multipole approach to long-range Coulomb interactions in Hartree–Fock calculations on large systems

An efficient ab initio method for electronic structure calculations on extended molecular systems is presented, along with some illustrative applications. A division of the system into subunits allows the interactions to be separated into short- and long-range contributions, leading to a reduction of the computational effort from the original fourth-power size-dependence to one that is approximately quadratic. The short-range contributions to the Fock matrix are obtained in an essentially conventional fashion, while the long-range interactions are evaluated using a two-center multipole expansion formalism. The number of short-range contributions grows only linearly with the number of subunits, while the long-range contributions grow as N². Systematic studies of the computational efforts for systems of up to 99 water molecules organized as one-stranded chains, three-stranded chains, and three-dimensional clusters, as well as alkane chains with up to 69 carbon atoms, have been performed. In these model systems, the overall computational effort grows as N^K where 1 < K < 2.     

Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins

The explicit treatment of polarization as a many-body interaction in condensed-phase systems represents a current problem in empirical force-field development. Although a variety of efficient models for molecular polarization have been suggested, polarizable force fields are still far from common use nowadays. In this work, we consider interactive polarization models employing Thole's short-range damping scheme and assess them for application on polypeptides. Despite the simplicity of the model, we find mean polarizabilities and anisotropies of amino acid side chains in excellent agreement with MP2/cc-pVQZ benchmark calculations. Combined with restrained electrostatic potential (RESP) derived atomic charges, the models are applied in a quantum-mechanical/molecular-mechanical (QM/MM) approach. An iterative scheme is used to establish a self-consistent mutual polarization between the QM and MM moieties. This ansatz is employed to study the influence of the protein polarizability on calculated optical properties of the protonated Schiff base of retinal in rhodopsin (Rh), bacterio-rhodopsin (bR), and pharaonis sensory rhodopsin II (psRII). The shifts of the excitation energy due to the instantaneous polarization response of the protein to the charge transfer on the retinal chromophore are quantified using the high level ab initio multireference spectroscopy-oriented configuration interaction (SORCI) method. The results are compared with those of previously published QM1/QM2/MM models for bR and psRII.     

New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid

We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.     

The determination of intrinsic reaction coordinates by density functional theory

The first implementation of the intrinsic reaction coordinate (IRC ) method within the density functional theory (DFT ) framework is presented. The implementation has been applied to four different types of chemical reactions represented by the isomerization process, HCN ? HNC (A); the S_N2 process, H^? + CH₄ ? CH₄ + H^? (B); the exchange process, H˙ + HX ? HX + H˙ (X ? F,Cl) (C); and the elimination process, C₂H₅Cl ? C₂H₄ + HCl (D). The present study presents for each process optimized structures and calculated harmonic vibrational frequencies for the reactant(s), the transition state, and the product(s) along with the IRC path connecting the stationary points. The calculations were carried out within the local density approximation (LDA ) as well as the LDA/NL scheme where the LDA energy expression is augmented by Perdew's and Becke's nonlocal (NL ) corrections. The LDA and LDA/NL results are compared with each other as well as the best available ab initio calculations and experimental data. For reaction (D), ab initio calculations based on MP 2 geometries and MP 4SDTQ energies have been added due to the lack of accurate published post-HF calculations on this process. A detailed discussion is provided on the efficiency of the IRC algorithms, the relative accuracy of the DFT and ab initio schemes, as well as the reaction mechanisms of the four reactions. It is concluded that the LDA/NL scheme affords the same accuracy as does the MP 4 method. The post-HF methods seem to overestimate activation energies, whereas the corresponding LDA/NL estimates are too low. The LDA activation energies are even lower than the LDA/NL counterparts. The incorporation of the IRC method into the DFT framework provides a promising and reliable tool for probing the chemical reaction path on the potential energy surfaces, even for large-size systems. IRC calculations by ab initio methods of an accuracy similar to the LDA/NL scheme, such as the MP 4 scheme, are not feasible. © John Wiley & Sons, Inc.     

Comparison of the transfer and green matrix methods for the surface problem in periodic chains

For the first time, ab initio Hartree- Fock calculations for the end states of periodic chains are performed with the transfer matrix formalism. The applicability of the method is tested on semi-infinite Li-, LiH-, HF- and H₂O-chains. It is found that the numerical applications of the transfer matrix method in its applied form on the ab initio level have some drawbacks due to the limited number of perturbed end cells which can be taken into account. The comparison with Green matrix (Koster-Slater) calculations shows that the transfer matrix method in its Hartree-Fock version is not faster; this is contrary to the results reported for tight binding model Hamiltonians.     

Molecular mechanics-valence bond method for planar conjugated hydrocarbon cations

We present an extension of the molecular mechanics-valence bond (MMVB) hybrid method to study ground and excited states of planar conjugated hydrocarbon cations. Currently, accurate excited state calculations on these systems are limited to expensive ab initio studies of smaller systems: up to 15 active electrons in 16 pi orbitals with complete active space self-consistent field (CASSCF) theory using high symmetry. The new MMVB extension provides a faster, cheaper treatment to investigate larger cation systems with more than 24 active orbitals. Extension requires both new matrix elements and new parameters: In this paper we present both, for the limited planar case. The scheme is tested for the planar radical cations of benzene, naphthalene, anthracene, and phenanthrene. Calculated MMVB relative energies are in good agreement with CASSCF results for equilibrium geometries on the ground and first excited states, and conical intersections.     

镓原子链的结构稳定性和电子结构

The structural stabilities and electronic structures of Ga atomic chains are studied by the first-principles plane wave pseudopotential method based on the density functional theory. The present calculations show that gallium can form planar chains in linear-, zigzag- and ladder-form one-dimensional structures. The most stable one among the studied structures is the zigzag chain with a unit cell rather close to equilateral triangles with four nearest neighbors, and all the other structures are metastable. The relative structural stability, the energy bands and the charge densities are discussed based on the ab initio calculations and the Jahn-Teller effect.     

分子间相互作用的研究——-价轨道模型势从头算能量分解法

研究分子间相互作用是了解液体,固体性质和结构以及气体性质的关键,也是研究化学和生物化学催化机制及化学反应途径的重要方面.因此,近几年来这个领域的理论和实验研究引起了人们广泛的兴趣并取得了长足的进步.特别值得指出的是Morokuma等提出的基于单行列式从头算的能量分解法,较好地解决了很多体系中分子间相互作用的本质问题,受到了理论化学界的普遍重视.但是这种方法很费计算机时间,对于较大的体系,特别是含有重原子的体系,应用受到了限制.因此简化这种方法,使它能够比较容