Direct computation of second-order SCF properties of large molecules on workstation computers with an application to large carbon clusters

Summary The ab initio SCF computation of second-order properties of large molecules (with 50 atoms or more) on workstation computers is demonstrated for static dipole polarizabilities and nuclear magneting shieldings. The magnetic shieldings are calculated on the basis of gauge including atomic orbitals (GIAO). Algorithmic advances (semi-direct algorithms with efficient integral pre-screening, and use of a quadratically convergent functional for the polarizabilities) are presented together with an illustrative application to the fullerenes C₆₀ and C₇₀.     

Ions in solutions: Determining their polarizabilities from first-principles

Dipole polarizabilities of a series of ions in aqueous solutions are computed from first-principles. The procedure is based on the study of the linear response of the maximally localized Wannier functions to an applied external field, within density functional theory. For most monoatomic cations (Li(+), Na(+), K(+), Rb(+), Mg(2+), Ca(2+) and Sr(2+)) the computed polarizabilities are the same as in the gas phase. For Cs(+) and a series of anions (F(-), Cl(-), Br(-) and I(-)), environmental effects are observed, which reduce the polarizabilities in aqueous solutions with respect to their gas phase values. The polarizabilities of H((aq)) (+), OH((aq)) (-) have also been determined along an ab initio molecular dynamics simulation. We observe that the polarizability of a molecule instantaneously switches upon proton transfer events. Finally, we also computed the polarizability tensor in the case of a strongly anisotropic molecular ion, UO(2) (2+). The results of these calculations will be useful in building interaction potentials that include polarization effects.     

A combined freeze-and-cut strategy for the description of large molecular systems using a localized orbitals approach

A technique to reduce the computational effort in calculating ab initio energies using a localized orbitals approach is presented. By exploiting freeze strategy at the self-consistent field (SCF) level and a cut of the unneeded atomic orbitals, it is possible to perform a localized complete active space (CAS-SCF) calculation on a reduced system. This will open the possibility to perform ab initio treatments on very large molecular systems, provided that the chemically important phenomena happen in a localized zone of the molecule. Two test cases are discussed, to illustrate the performance of the method: the cis-trans interconversion curves for the (7Z)-13 ammoniotridec-7-enoate, which demonstrates the ability of the method to reproduce the interactions between charged groups; and the cisoid-transoid energy barrier for the aldehydic group in the C13 polyenal molecule.     

含双键有机小分子的定域分子轨道的研究

选择22种具有双键的有机小分子(含C、H、O和N原子)作模型分子,应用ab initioSTO-3G和Foster-Boys定域化分子轨道程序,对它们的定域分子轨道进行了研究,得到了定域分子轨道能量,确定了相应分子轨道间的相互作用。对烯类分子的光电子能谱进行了分析,结果较为满意。     

Accuracy of distributed multipoles and polarizabilities: comparison between the LoProp and MpProp models

Localized multipole moments up to the fifth moment as well as localized dipole polarizabilities are calculated with the MpProp and the newly developed LoProp methods for a total of 20 molecules, predominantly derived from amino acids. A comparison of electrostatic potentials calculated from the multipole expansion obtained by the two methods with ab initio results shows that both methods reproduce the electrostatic interaction with an elementary charge with a mean absolute error of approximately 1.5 kJ/mol at contact distance and less than 0.1 kJ/mol at distances 2 A further out when terms up to the octupole moments are included. The polarizabilities are tested with homogenous electric fields and are found to have similar accuracy. The MpProp method gives better multipole moments unless diffuse basis sets are used, whereas LoProp gives better polarizabilities.     

Ab Initio Study on the Anti-HIV Activities of Hydroxyflavones

1 INTRODUCTION AIDS, in other words, Acquired Immunodefici-encysyndrome, is a viral contagious disease withhigh death rate. However, effective treatment againstit has not appeared so far. At present, about 100kinds of natural compounds that could be extractedfrom natural products or artificially synthesized havebeen found to have anti-HIV activities to some ex-tent. They belong to flavonoid, terpenoid, steroid, cou-marin, peptide, alkaloid etc., respectively. Previousstudies show that…     

链烃,环状烃和多面体烃的定域分子轨道研究

采用GAUSSAN 80程序对一系列直链烷烃、环状烃和多面体烷烃进行STO-3G基组下的曲initio计算,在所得非定域分子轨道自洽场结果的基础上,利用Boys方法进行定域化,进而研究了这些分子的定域分子轨道的键弯曲性质、轨道能量和集居数与几何结构之间的关系,用上述结果对一些典型分子的稳定性进行了讨论。     

Polarizable model potential function for nucleic acid bases

A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.     

Ab initio integrated multi-center molecular orbitals method for large cluster systems: total energy and normal vibration

A new computational scheme integrating multi-center ab initio molecular orbitals for determining total energy and normal vibration of large cluster systems is presented. This method can be used to treat large cluster systems such as solvents by quantum mechanics. The geometry parameters, the total energies, the relative energies, and the normal vibrations for four models of water cluster, the hydrated hydronium ion complex, and the transition state of proton transfer are calculated by the present method and are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article is also intended to be used in modeling computer cluster systems using parallel algorithms.     

虚轨道定域化

通过引入虚轨道定域化函数，扩展了集居数的定域化方法，在从头算STO－3G水平上用护展后的方法计算无机小分子、烷烃、卤代烷、醇、胺及共轭烃等，结果表明，定域占据轨道与定域虚轨道的系数和能级分布相似的规律。     

Ab initio and DFT study of the geometric structures and static dipole (hyper)polarizabilities of aromatic anions

The geometries and the static dipole (hyper)polarizabilities (alpha, beta, gamma) of a series of aromatic anions were investigated at the ab initio (HF, MP2, and MP4) and density functional theory DFT (B3LYP) levels of theory. The anions chosen for the present study are the benzenethiolate (Ph-S-), benzenecarboxylate (Ph-CO2-), benzenesulfinate (Ph-SO2-), benzenesulfonate (Ph-SO3-), and 1,3-benzenedicarboxylate (1,3-Ph-(CO2)2(2-)). For benzenethiolate anion, additional alpha, beta, and gamma calculations were performed at the coupled cluster CCSD level with MP2 optimized geometries. The standard diffuse and polarized 6-31+G(d,p) basis set was employed in conjunction to the ab initio and DFT methods. Additional HF calculations were performed with the 6-311++G(3d,3p) basis set for all the anions. The correlated electric properties were evaluated numerically within the formalism of finite field. The optimized geometries were analyzed in terms of the few reports about the phenolate and sulfonate ions. The results show that electron correlation effects on the polarizabilities are very important in all the anion series. Was found that Ph-SO2- is highly polarizable in terms of alpha and beta, and the Ph-S- is the highest second hyperpolarizable in the series. The results of alpha were rationalized in terms of the analysis of the polarization of charge based in Mulliken atomic population and the structural features of the optimized geometries of anions, whereas the large differences in the beta and gamma values in the series were respectively interpreted in terms of the bond length alternation BLA and the separation of charge in the aromatic ring by effects of the substitution. These results allowed us to suggest the benzenesulfinate and benzenethiolate anions as promising candidates that should be incorporated in ionic materials for second and third-order nonlinear optical devices.     

Partitioning of higher multipole polarizabilities: numerical evaluation of transferability

In this work, the partitioning of higher multipole polarizabilities, such as dipole-quadrupole, quadrupole-dipole, and quadrupole-quadrupole polarizabilities, into atomic contributions is studied. Partitioning of higher multipole polarizabilities is necessary in the study of accurate interaction energies where dispersion interactions are of importance. The fractional occupation Hirhsfeld-I (FOHI) method is used to calculate the atomic polarizabilities and is briefly explained together with the methodology for partitioning of the polarizabilities. The atomic multipole polarizabilities are calculated for different sets of molecules, linear alkanes, water clusters, and small organic molecules with different functional groups. It is found that the atomic and group contributions of the dipole and quadrupole polarizabilities are transferable as a function of the functional groups.     

Research in the method of large molecular calculations utilizing transferability of LMO

The localized molecular orbitals of some saturated hydrocarbons and their derivatives have been formed using ab initio method and M. P. [1–2] localization procedure. Two models, SLMO and ELMO , a set of parameters of LMO Fock matrix elements, and a technique called “Group Effect” are proposed. Based on these, we developed a procedure to simulate the ab initio calculations on large molecules. Some test calculations have been done. The results are compared with those of the ab initio method. In general, absolute errors of orbital energies are about 10^?3 a.u., and the relative errors of total energies are about 10^?4. For the original applications, we applied this procedure to some large systems of alkane and their derivatives as well as three Crown-ether compounds. Satisfactory results are obtained.     

Interpolated potential energy surfaces: How accurate do the second derivatives have to be?

A global potential energy surface for the water dimer is constructed using the modified Shepard interpolation scheme of Collins et al. According to this interpolation scheme, the energy at an arbitrary geometry is expressed as a weighted sum of Taylor series expansions from neighboring data points, where the energy and derivative data required are obtained from ab initio calculations. For some ab initio methods, errors are introduced into the second derivative matrix, either by numerical differencing of ab initio energies or numerical integration during the ab initio calculation. Therefore, we test the accuracy required of the second derivative data by truncation of the exact second derivatives to a series of approximate second derivatives, and assess the effect on the results of a quantum diffusion Monte Carlo (QDMC) simulation. Our results show that the calculated zero-point energy and wave function histograms converge to within the numerical uncertainty of the QDMC simulation by inclusion of either three significant figures or three decimal places in the second derivatives.     

Ab initio calculations of dispersion coefficients for nucleic acid base pairs

The results of ab initio calculations of two- and three-body dispersion coefficients for the four most important nucleic acid bases are reported. The isotropic as well as anisotropic coefficients were found by using the time-dependent Hartree-Fock approach and the aug-cc-pVDZ basis set. Single and double excitation coupled-cluster theory with noniterative treatment of triple excitations [CCSD(T)] was used to find the values of static polarizabilities which were subsequently used to estimate the values of the CCSD(T) dispersion coefficients. A comparison of these estimated CCSD(T) dispersion coefficients with coefficients found by using empirical approaches based on atomic contributions revealed that the latter are not reliable.     

Mapping the interaction energy surfaces of cyclic alkanes: evaluating the transferability of an ab initio based potential model

Detailed interaction energy maps are computed for symmetric cyclopropane and tetrahedrane dimer systems using ab initio methods. Interaction energies of cubane and cyclohexane dimers are also reported. The global minimum energy structures of cyclopropane and tetrahedrane systems are both D(3d) structures with energies of -1.850 and -2.171 kcal mol(-1). The ability of NIPE potential model, based on ab initio nonbonding data of neopentane (N), isobutane (I), propane (P), ethane (E) and all their combinations to predict the pair interaction energies of these strained cyclic hydrocarbons is also investigated. The difference between the energies predicted by NIPE and those obtained from the ab initio calculations increases with ring strain In general, NIPE values are in close agreement with the ab initio results for alkane ring structures having low ring strain.     

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 ?. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.     

Polarizable interaction potential for water from coupled cluster calculations. I. Analysis of dimer potential energy surface

A six-dimensional interaction potential for the water dimer has been fitted to ab initio interaction energies computed at 2510 dimer configurations. These energies were obtained by combining the supermolecular second-order energies extrapolated to the complete basis set limit from up to quadruple-zeta quality basis sets with the contribution from the coupled-cluster method including single, double, and noniterative triple excitations computed in a triple-zeta quality basis set. All basis sets were augmented by diffuse functions and supplemented by midbond functions. The energies have been fitted using an analytic form with the induction component represented by a polarizable term, making the potential directly transferable to clusters and the bulk phase. Geometries and energies of stationary points on the potential surface agree well with the results of high-level ab initio geometry optimizations.     

Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.