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

Hylleraas variational perturbation theory is applied through second order in energy to estimate the correlation energy in several molecular systems. The specific choices for H0 and V which are made lead to equations nearly identical to the multireference linearized coupled‐cluster method of Laidig and Bartlett. The results obtained are in virtually exact agreement where comparisons have been made. Results from test calculations are presented for BeH2, CH2, and C2H4. In addition, the utility of perturbation theory for selecting correlating configurations is examined. This procedure is found to be quite accurate while significantly reducing the size of the system of linear equations to be solved.

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Hylleraas variational perturbation theory: Application to correlation problems in molecular systems

Double cosets are used to reduce the formulas for integrals over symmetry orbitals to unique integrals over atomic orbitals.

Use of double cosets in constructing integrals over symmetry orbitals

Several singlet and triplet potential energy surfaces (PES) for the Bergman cyclization of cis-1,5-hexadiyne-3-ene (1a) have been computed by UDFT, CI, CASCI, CASSCF, and CASMP2 methods. It is found that the first six excited states of 1a can be qualitatively described as linear combinations of the configurations of weakly interacting ethylene and acetylene units. Although the symmetry relaxation from C2ν to C2 makes cyclization of the 13B state Woodward−Hoffmann allowed, it also increases the probability of competing cis−trans isomerization. Hydrogen atom abstraction is another plausible pathway because the terminal alkyne carbons possess a large radical character. In view of the competing processes, we conclude that the Bergman cyclization along the 13B path is unlikely despite its exothermicity (Δ = −42 kcal/mol). Calculations on cyclic analogues of 1a lead to similar conclusions. A less exothermic, but more plausible pathway for photochemical cyclization lies on the 21A PES (Δ = −18 kcal/mol). Compare...

UDFT and MCSCF descriptions of the photochemical Bergman cyclization of enediynes

The B(K) method is compared with conventional Configuration Interaction (CI) and other perturbation methods for the 3B1 and 1A1 states of methylene. Use of Rayleigh-Schroedinger perturbation theory for construction of an effective Hamiltonian is seen to be more accurate for estimating the full CI energy limit.

The B K method: Application to methylene

Emploi de la theorie Jahn-Teller au 2nd ordre pour montrer que les differences d'electronegativite et la conjugaison cyclique peuvent chacune minimiser l'importance de la resonance allylique dans les redicaux libres, bien que la repulsion electronique provoque une resonance importante dans les diradicaux. Confirmation de ces previsions par des calculs MC-SCF et CI sur O(CH 2 ) 2 + et O(CH 2 ) 2

Ernest R. Davidson

Papers

Hylleraas variational perturbation theory: Application to correlation problems in molecular systems

Use of double cosets in constructing integrals over symmetry orbitals

UDFT and MCSCF descriptions of the photochemical Bergman cyclization of enediynes

The B K method: Application to methylene

Allylic resonance - when is it unimportant?