Advances in methods and algorithms in a modern quantum chemistry program package
04 Jul 2006-Physical Chemistry Chemical Physics (Royal Society of Chemistry)-Vol. 8, Iss: 27, pp 3172-3191
TL;DR: Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
Abstract: Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
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28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组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�ly.
Abstract: 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。
18,940 citations
TL;DR: Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn, a multifunctional program for wavefunction analysis.
Abstract: Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com.
17,273 citations
TL;DR: The re-optimization of a recently proposed long-range corrected hybrid density functional, omegaB97X-D, to include empirical atom-atom dispersion corrections yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions.
Abstract: We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functional [J.-D. Chai and M. Head-Gordon, J. Chem. Phys., 2008, 128, 084106] to include empirical atom–atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.
9,184 citations
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Abstract: CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.
7,035 citations
Journal Article•
TL;DR: Chai and Head-Gordon as discussed by the authors proposed a long-range corrected (LC) hybrid density functional with Damped Atom-Atom Dispersion corrections, which is called ωB97X-D.
Abstract: Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections Jeng-Da Chai ∗ and Martin Head-Gordon † Department of Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (Dated: June 14, 2008) We report re-optimization of a recently proposed long-range corrected (LC) hybrid density func- tionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent sys- tems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density func- tionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions. I. INTRODUCTION Due to its favorable cost-to-performance ratio, Kohn- Sham density-functional theory (KS-DFT) [1, 2] has be- come the most popular electronic structure theory for large-scale ground-state systems [3–5]. Its extension for treating excited-state systems [6, 7], time-dependent den- sity functional theory (TDDFT), has also been developed to the stage where it is now very widely used. The essential ingredient of KS-DFT, the exchange- correlation energy functional E xc , remains unknown and needs to be approximated. Semi-local gradient-corrected density functionals, though successful in many applica- tions, lead to qualitative failures in some circumstances, where the accurate treatment of non-locality of exchange- correlation hole becomes crucial. These situations occur mostly in the asymptotic regions of molecular systems, such as spurious self-interaction effects upon dissociation [8, 9] and dramatic failures for long-range charge-transfer excitations [10–12]. Widely used hybrid density function- als, like B3LYP [13, 14], do not qualitatively resolve these problems. These self-interaction errors can be qualitatively re- solved using the long-range corrected (LC) hybrid density functionals [15, 16, 18], which employ 100% Hartree-Fock (HF) exchange for long-range electron-electron interac- tions. This is accomplished by a partition of unity, using erf(ωr)/r for long-range (treated by HF exchange) and erfc(ωr)/r for short-range (treated by an exchange func- tional), with the parameter ω controlling the partition- ing. Over the past five years, the LC hybrid scheme has been attracting increasing attention [15] since its compu- tational cost is comparable with standard hybrid func- tionals [13]. However, LC functionals have tended to be inferior to the best hybrids for properties such as ther- mochemistry. ∗ Electronic † Author address: jdchai@berkeley.edu to whom correspondence should be addressed. Electronic address: mhg@cchem.berkeley.edu Recently we have improved the overall accuracy at- tainable with the LC functionals by using a systematic optimization procedure [18]. One important conclusion is that optimizing LC and hybrid functionals with identical numbers of parameters in their GGA exchange and cor- relation terms leads to noticeably better results for all properties using the LC form. The resulting LC func- tional is called ωB97. Further statistically significant improvement results from re-optimizing the entire func- tional with one extra parameter corresponding to an ad- justable fraction of short-range exact exchange, defining the ωB97X functional. Independent test sets covering thermochemistry and non-covalent interactions support these conclusions. However, problems associated with the lack of non-locality of the correlation hole, such as the lack of dispersion interactions (London forces), still remain, as the semi-local correlation functionals cannot capture long-range correlation effects [19, 20]. There have been significant efforts to develop a frame- work that can account for long-range dispersion effects within DFT. Zaremba and Kohn (ZK) [21] derived an exact expression for the second-order dispersion energy in terms of the exact density-density response functions of the two separate systems. To obtain a tractable non- local dispersion functional, Dobson and Dinite (DD) [22] made local density approximations to the ZK response functions. DD’s non-local correlation functional was ob- tained independently [23] by modifying the effective den- sity defined in the earlier work of Rapcewicz and Ashcroft Starting from the formally exact expression of KS- DFT, the adiabatic connection fluctuation-dissipation theorem (ACFDT), for the ground-state exchange- correlation energy, Langreth and co-workers [25] devel- oped a so-called van der Waals density functional (vdW- DF) by making a series of reasonable approximations to yield a computationally tractable scheme. Recently, Becke and Johnson (BJ) developed a series of post-HF correlation models with a novel treatment for dispersion interactions based on the exchange-hole dipole moment [26]. The origin of dispersion claimed in the BJ models was recently questioned by Alonso, and A.
6,345 citations
References
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TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
Abstract: Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact‐exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange‐correlation functional containing local‐spin‐density, gradient, and exact‐exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first‐ and second‐row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
87,732 citations
TL;DR: In this paper, a detailed study of correlation effects in the oxygen atom was conducted, and it was shown that primitive basis sets of primitive Gaussian functions effectively and efficiently describe correlation effects.
Abstract: 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.
26,705 citations
28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组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�ly.
Abstract: 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。
18,940 citations
TL;DR: A description of the ab initio quantum chemistry package GAMESS, which 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.
Abstract: 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.
18,546 citations
15,091 citations