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

We point out a simplifying but mildly inconsistent assumption of the Perdew-Burke-Ernzerhof (PBE) correlation functional, which should be corrected when evaluating the high-density limit of the PBE energy for nonsinglet systems under uniform density scaling. The discussion also concerns high-density limits of all density functionals that use PBE as an ingredient, including the Tao-Perdew-Staroverov-Scuseria (TPSS) approximation. We revisit the nonrelativistic correlation energies of isoelectronic atomic ions in the limit of infinite nuclear charge and explain small discrepancies between the PBE and TPSS values of these limits existing in the literature.

High-density limit of the Perdew-Burke-Ernzerhof generalized gradient approximation and related density functionals

Molecular electron density distributions in position and momentum space

Potential surfaces have been computed for rotation of the OH groups in C(OH)2 for both the lowest singlet and triplet state. The minima on the singlet surface occur at planar geometries, which represent maxima on the triplet surface. This result is interpreted in terms of different modes of pi electron donation from oxygen being favored in the two states. Evidence is presented that shows pi electron donation is chiefly responsible for making dihydroxycarbene a ground state singlet.

The singlet and triplet state rotational potential surfaces for dihydroxycarbene

Neon matrix ESR and CI theoretical investigation of AlF+; photoionization of AlF from thermal and laser sputtering generation methods

Calculated energy and molecular properties of the ground and low-energy excited states of formamide are presented at the ground state geometry. Satisfactory results are obtained except for the 1ππ* energy which remains too high by 1 eV (which is nevertheless a large improvement over previous calculations). The predicted triplet energies lie at 5.4 eV (3nπ*) and 5.8 eV (3ππ*).

Ernest R. Davidson

Papers

High-density limit of the Perdew-Burke-Ernzerhof generalized gradient approximation and related density functionals

Molecular electron density distributions in position and momentum space

The singlet and triplet state rotational potential surfaces for dihydroxycarbene

Neon matrix ESR and CI theoretical investigation of AlF+; photoionization of AlF from thermal and laser sputtering generation methods

An ab initio study of formamide