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

Substituent effects on the mechanism of the Cope rearrangement were studied by computing C2h (Cs) cuts through the potential energy surface (PES) for the reaction of 1,5-hexadiene and its di-, tri-, and tetracyano derivatives at the (U)B3LYP/6-31G* and (U)BPW91/6-31G* levels The stabilization of substituted structures along the cuts is discussed in terms of the energies of isodesmic formation from allyl radicals and acetonitrile molecules Cyano groups at C1, C3, and C5 provide a nearly additive stabilization of each point along the Cs cut even though their influence on the geometry is competitive Evaluation of the density of effectively unpaired electrons at various geometries indicates that the radical character of a transition state (TS) is not altered by radical stabilizing substituents as such but depends solely on the interallylic bond length Although the UB3LYP diyl intermediate for the parent compound is plausible when compared to the lowest triplet PES, neither MRPT2 at the UB3LYP geometries n

Transition Regions in the Cope Rearrangement of 1,5-Hexadiene and Its Cyano Derivatives

To be useful in the clinical laboratory, multicomponent fluorescence analysis requires both the rapid measurement of the fluorescence intensity at a variety of excitation and emission wavelengths and the unambiguous reduction of the data by efficient algorithms. The Video Fluorometer, which exploits the multi-channel capability of a low-light-level television sensor to simultaneously acquire excitation and emission spectra, can meet the first requirement. For example, a complete set of emission and excitation spectra for perylene can be obtained in less than 2 s at concentrations of 10(-10) mol/liter. To meet the second need, we present two types of data-reduction strategies: (a)a least-squares fit to the data, with use of the spectra of previously determined compounds likely to be present; and (b)a determination of the eigenvalues and eigenvectors fo the fluorescence matrix, from which the number of components and the possible spectra of each can be estimated. Computer simulations of the least-squares fitting algorithms show that five strongly overlapping components can be determined in the presence of noise with an accuracy of better than 5%. Also, a fluorescent sample containing two species with very similar but unknown spectral properties can be resolved to obtain the spectrum of each.

Multicomponent analysis in clinical chemistry by use of rapid scanning fluorescence spectroscopy.

How robust is present‐day DFT?

Different forms of perturbation theory for the calculation of correlation energy in both closed-and open-shell systems are discussed. For closed-shell systems, Epstein–Nesbet perturbation theory is compared with Moller–Plesset (MP) perturbation theory based on canonical Hartree–Fock orbitals and with MP theory based on internally consistent SCF orbitals. The traditional MP theory gives superior results despite its use of an inferior zeroth-order Hamiltonian. This behavior is rationalized in terms of the larger denominators present in the traditional MP theory. These conclusions are used to support the restricted open-shell perturbation methods proposed recently by Murray and Davidson, and these new methods are compared with spin-restricted Epstein–Nesbet theory and the unrestricted MP (UMP) approach. © 1992 John Wiley & Sons, Inc.

Different forms of perturbation theory for the calculation of the correlation energy

The transition states for single and double methylene group rotation on the singlet trimethylene potential surface have been located at the GVB/6-31G * level of theory, with one pair of electrons correlated. The preference for conrotatory double rotation over single rotation is found to be 0.97 kcal/mol at the GVB level, and is expected to increase slightly with inclusion of additional electron correlation, on the basis of SD-CI calculations on (0,0)- and (0,90)-trimethylene

Ernest R. Davidson

Papers

Transition Regions in the Cope Rearrangement of 1,5-Hexadiene and Its Cyano Derivatives

Multicomponent analysis in clinical chemistry by use of rapid scanning fluorescence spectroscopy.

How robust is present‐day DFT?

Different forms of perturbation theory for the calculation of the correlation energy

Stereomutation of cyclopropane revisited. An ab initio investigation of the potential surface and calculation of secondary isotope effects