Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set

In the past, basis sets for use in correlated molecular calculations have largely been taken from single configuration calculations. Recently, Almlof, Taylor, and co‐workers have found that basis sets of natural orbitals derived from correlated atomic calculations (ANOs) provide an excellent description of molecular correlation effects. We report here a careful study of correlation effects in the oxygen atom, establishing that compact sets of primitive Gaussian functions effectively and efficiently describe correlation effects i f the exponents of the functions are optimized in atomic correlated calculations, although the primitive (s p) functions for describing correlation effects can be taken from atomic Hartree–Fock calculations i f the appropriate primitive set is used. Test calculations on oxygen‐containing molecules indicate that these primitive basis sets describe molecular correlation effects as well as the ANO sets of Almlof and Taylor. Guided by the calculations on oxygen, basis sets for use in correlated atomic and molecular calculations were developed for all of the first row atoms from boron through neon and for hydrogen. As in the oxygen atom calculations, it was found that the incremental energy lowerings due to the addition of correlating functions fall into distinct groups. This leads to the concept of c o r r e l a t i o n c o n s i s t e n t b a s i s s e t s, i.e., sets which include all functions in a given group as well as all functions in any higher groups. Correlation consistent sets are given for all of the atoms considered. The most accurate sets determined in this way, [5s4p3d2f1g], consistently yield 99% of the correlation energy obtained with the corresponding ANO sets, even though the latter contains 50% more primitive functions and twice as many primitive polarization functions. It is estimated that this set yields 94%–97% of the total (HF+1+2) correlation energy for the atoms neon through boron.

Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen

We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

/pdf/the-m06-suite-of-density-functionals-for-main-group-1748swzp1l.pdf

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.

General atomic and molecular electronic structure system

Ab initio study of m-benzoquinodimethane

Two of the radicals whose ab initio hyperfine properties exhibited unusually large (30%) deviations from experiment in a recent study of such properties have been reexamined. Inclusion of vibrational averaging effects, MCSCF orbitals and large CI reference spaces resulted in a reduction of the deviation from experiment to 14% for the formaldehyde radical cation. New experimental data on the methoxy radical shows a much larger proton isotropic hyperfine value than previous experimental and theoretical studies. The best current calculations were unable to resolve the discrepancy. The ethyl radical was also included in this study since good experimental beta proton data is available for comparison.

Difficulties in ab initio CI calculations of the hyperfine structure of small radicals

The spin–orbit contribution to the zero‐field splitting (ZFS) in the CH2O 3 A 2(n→π*) state is evaluated using the full Breit–Pauli Hamiltonian. All calculations are carried out at the planar ground state geometry using a double‐zeta plus polarization basis of contracted Gaussian‐lobe functions augmented with diffuse s and p functions. Configuration–interaction wavefunctions, constructed using the 3 A 2 canonical orbitals, are used to describe the 3 A 2 state and all states coupling to it via the spin–orbit Hamiltonian. The excitation energies and oscillator strengths obtained from these wavefunctions are in good agreement with other theoretical calculations and with experiment. Of the 12 states considered in the second‐order perturbation theorytreatment of the spin–orbit interaction, the 1 A 1 ground and the nearby 3 A 1(π→π*) states were the most important. Rydberg states were observed to have very small spin–orbit matrix elements and consequently to have little effect on the ZFS. The spin–orbit contributions to the ZFS parameters D and E were −0.224 and 0.009 cm−1, respectively, which when added to the spin–spin contribution obtained in an earlier paper [S. R. Langhoff, S. T. Elbert, E. R. Davidson, Int. J. Quantum Chem. 7, 999 (1973)] give total values of D=0.314 cm−1 and E=0.04 cm−1. These results are larger than the best experimental results of D=0.141 cm−1 and E=0.02 cm−1, determined by Birss e t a l. [F. W. Birss, R. Y. Dong, and D. A. Ramsay, Chem. Phys. Lett. 18, 11 (1973)] from a rotational analysis of the 0+←0 bands of the 3 A 2←1 A 1 transition. An extensive calculation was also undertaken to assess the degree of convergence in the second‐order perturbation theorytreatment. The contribution of the lowest 100 singlet and triplet states of A 1, B 1, and B 2 symmetry were considered where each state was described by a 100‐term CI wavefunction. This calculation gives a spin–orbit contribution to D of −0.221 cm−1 essentially identical to the previous result providing evidence that the second‐order treatment has indeed converged. The radiative lifetimes of the three sublevels of the triplet state were determined using the same representations for the manifold of electronic states. In the high temperature limit, the radiative lifetime was determined to be between 0.02 and 0.06 sec, somewhat longer than the estimated experimental value of 0.01 sec. The mutual perturbation of the 1 A 1 ground and 3 A 2 states and the perturbation of the 3 A 2 state by the 1 A 1(π→π*) state were determined to be most important in determining the lifetime. These results ensure that the emitted light is polarized primarily along the carbon–oxygen bond in agreement with experiment. A critical examination of the quantitative validity of the numerical results is presented to assess the reliability of the theoretically determined lifetimes.

Abinitio evaluation of the fine structure and radiative lifetime of the 3A2(n→π*) state of formaldehyde

In previous work on the treatment of correlation in molecular systems we have applied a multireference version of second‐order Hylleraas variational perturbation theory. The choice made for the partitioning of H treated the interactions between the correlating functions to infinite order and gave the corrections to the wave function to first order. The method was shown to be accurate in many cases, but became less so when near degeneracies occurred between the reference energy and other eigenvalues of H0. In this article we introduce an effective Hamiltonian method that is analogous to variational perturbation theory, but which is significantly more accurate when near degeneracies are important. This quasidegenerate variational perturbation theory (QDVPT) is an explicitly multireference procedure and treats the entire reference space as a quasidegenerate space. A novel method for solving the QDVPT equations is introduced that avoids explicit construction of the effective Hamiltonian. As a result, the work...

/pdf/quasidegenerate-variational-perturbation-theory-and-the-pybb7r7i5e.pdf

Ernest R. Davidson

Papers

Ab initio study of m-benzoquinodimethane

Difficulties in ab initio CI calculations of the hyperfine structure of small radicals

Abinitio evaluation of the fine structure and radiative lifetime of the 3A2(n→π*) state of formaldehyde

Quasidegenerate Variational Perturbation Theory and the Calculation of First‐Order Properties from Variational Perturbation Theory Wave Functions

The cope rearrangement revisited