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.

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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

Large basis set configuration interaction calculations yield an electron affinity of 0.42 eV for CH2(3B1). Application of an empirical correction, based on the known deficiencies of the basis set and CI method in atomic calculations, suggests that this estimate should be increased to approximately 0.63 eV. This provides futher evidence in favor of a reinterpretation of the photoelectron spectrum work of Zittel et al., which indicated an electron affinity of only 0.210 eV while giving a 3B1–1A1 energy gap of 19.6 kcal/mol.

A theoretical determination of the electron affinity of methylene

We have recently formulated a new approach, named the effective local potential (ELP) method, for calculating local exchange-correlation potentials for orbital-dependent functionals based on minimizing the variance of the difference between a given nonlocal potential and its desired local counterpart [V. N. Staroverov et al., J. Chem. Phys. 125, 081104 (2006)]. Here we show that under a mildly simplifying assumption of frozen molecular orbitals, the equation defining the ELP has a unique analytic solution which is identical with the expression arising in the localized Hartree-Fock (LHF) and common energy denominator approximations (CEDA) to the optimized effective potential. The ELP procedure differs from the CEDA and LHF in that it yields the target potential as an expansion in auxiliary basis functions. We report extensive calculations of atomic and molecular properties using the frozen-orbital ELP method and its iterative generalization to prove that ELP results agree with the corresponding LHF and CEDA values, as they should. Finally, we make the case for extending the iterative frozen-orbital ELP method to full orbital relaxation.

The effective local potential method: implementation for molecules and relation to approximate optimized effective potential techniques.

Hyperpolarizability: Calibration of theoretical methods for chloroform, water, acetonitrile, and p-nitroaniline

A quantitative theory of extended x-ray-absorption fine structure (EXAFS) in diatomic molecules is presented and tested by ab initio calculations in ${\mathrm{Br}}_{2}$. The theory, based on a refinement of conventional EXAFS theory, takes into account (1) an energy-dependent exchange-correlation potential, (2) multielectron excitations, and (3) a single-scattering, spherical-wave expansion. Inelastic processes are included assuming that core-hole excitations and losses in propagation are uncorrelated. We find that a Dirac-Hara exchange potential gives better overall agreement of the EXAFS phase than does the Hedin-Lundqvist potential. The amplitude discrepancy between experiment and single-particle theory can be corrected by adding core-hole lifetime effects, experimental resolution, and multielectron excitations.

Ab initio calculation of extended x-ray-absorption fine structure in Br 2

Molecular beams of monomer HCN and its clusters, generated by supersonic helium expansions, were crossed with the output of an F-center laser operating in the C-H stretching region. The laser was scanned in its low-resolution mode, A v l j 2 = 10 GHz (0.3 cm-I), from 3100 to 3400 cm-I while the molecular beam energy was monitored with a liquid helium cooled bolometer. Excitation spectra of monomer HCN and vibrational photofragmentation spectra of HCN clusters were recorded. Bands associated with unresolved vibration-rotation envelopes were assigned to dimer and trimer transitions. Features corresponding to tetramers and higher polymers were observed but remain unassigned. Under some expansion conditions a photofragmenting solidlike hydrogen cyanide feature was observed. A band corresponding to one of the bound C-H stretching vibrations in the linear trimer was studied under high resolution (15 MHz). For the few comparisons possible, our C-H stretching frequencies are in agreement with other gas-phase measurements. Our results are also consistent with matrix isolation studies when allowances are made for the large solvent shifts possible. Three theoretical approaches were used to predict trends in the C-H stretching frequencies on hydrogen bonding. These are normal-coordinate analysis, a classical electrostatic model, and ab initio quantum mechanics calculations. A critique of these theoretical models is presented. Finally, the observed vibrational predissociation lifetime of the linear trimer is discussed in terms of simple propensity rules.

Ernest R. Davidson

Papers

A theoretical determination of the electron affinity of methylene

The effective local potential method: implementation for molecules and relation to approximate optimized effective potential techniques.

Hyperpolarizability: Calibration of theoretical methods for chloroform, water, acetonitrile, and p-nitroaniline

Ab initio calculation of extended x-ray-absorption fine structure in Br 2

Vibrational spectroscopy of hydrogen cyanide clusters