Semi-direct algorithms for the MP2 energy and gradient
TL;DR: In this paper, the authors formulate semi-direct MP2 methods that utilize disk space (which is usually much larger than memory size) for the steps that require most storage, and show that these methods are superior to conventional algorithms despite requiring less disk space.
About: This article is published in Chemical Physics Letters.The article was published on 1990-02-23. It has received 1189 citations till now. The article focuses on the topics: Computer memory & Quartic function.
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TL;DR: In this article, a direct method for evaluating the gradient of the second-order Moller-Plesset (MP2) energy without storing any quartic quantities, such as two-electron repulsion integrals (ERIs), double substitution amplitudes or the two-particle density matrix, was presented.
1,567 citations
22 Jan 2013
TL;DR: Premises of creation of Internet portal designed to provide access to participants of educational and scientific process for the joint creation, consolidation, concentration and rapid spreading of educationaland scientific information resources in its own depository are considered.
Abstract: Premises of creation of Internet portal designed to provide access to participants of educational and scientific process for the joint creation, consolidation, concentration and rapid spreading of educational and scientific information resources in its own depository are considered. CMS-based portal content management systems’ potentiality is investigated. Architecture for Internet portal of MES of Ukraine’s information resources is offered.
969 citations
Additional excerpts
...Методи дослідження – неемпіричні (ab initio) квантово-хімічні розрахункові методи, які реалізовано з використанням програмного пакету «Gaussian’09» [39], а саме – методи функціоналу електронної густини (DFT) – гібридні функціонали B3LYP [40] та M05 [41], метод теорії збурень другого порядку Меллера-Плесета (MP2) [42]; метод STQN локалізації перехідного стану (TS) [43]; розрахунок шляху реакції вздовж її ВКР [44]; методи фізико-хімічної кінетики, які ґрунтуються на теорії перехідного стану [45]; метод спектральної "калориметрії" за Йогансеном [46]; аналіз топології електронної густини за Бейдером (так звана теорія "Атомів у молекулах") [47] із використанням програмного пакету AIMAll [48]; метод оцінки енергії класичних Н-зв’язків за...
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...Для якомога точнішого врахування електронних кореляційних ефектів оптимізація геометрії супроводжувалася так званими розрахунками енергії в одній точці (single point energy calculations) як у вакуумі, так і у розчиннику із ε=4, використовуючи рівень теорії MP2 [42] та базисні набори Попла (Pople’s basis sets of valence triple-ζ quality) [286] та Данінга (Dunning’s cc-type basis sets)...
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...електронної енергії та вільної енергії Гіббса Усі квантово-хімічні розрахунки геометричної, електронної будови та коливальних спектрів (у гармонічному наближенні) досліджуваних об’єктів проведено із використанням програмного пакету «Gaussian’09» [39] на рівнях теорії B3LYP/6-311++G(d,p), B3LYP/6-31G(d,p) [40], M05/6-311++G(2df,pd) [41] та MP2/6-311++G(d,p), MP2/6-31G(d,p) [42], які добре зарекомендували себе для подібного кола задач і об’єктів [282, 283]....
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TL;DR: In this article, a summary of the research work performed so far using high accuracy quantum chemical methods on polyphenolic antioxidant compounds is presented, which represents a further important contribution to elucidation of the beneficial effects on health of these substances.
928 citations
TL;DR: A semi-direct algorithm for eliminating this fifth-order storage is described in this paper, in which small batches of MO integral derivatives are made at a time, their contributions to the MP2 second derivatives are evaluated, and then they are discarded.
799 citations
TL;DR: The purpose of this review is to present the information content of spectroscopic methods, which allow one to focus in on the metalloactive site, define its electronic structure, evaluate the role of the protein in determining geometric and Electronic structure, and elucidate the contributions of electronic structure to function.
Abstract: Approximately one-half of all known protein crystal structures in the protein data bank (PDB) contain metal ion cofactors, which play vital roles in charge neutralization, structure, and function.1,2 These proteins range in size from 5000-107 Da with the metal ion corresponding to only on the order of 0.1 wt % of the molecule. Yet, for a wide range of these metalloproteins, the metal ion and its environment are key to the chemistry as these comprise the active site in catalysis. It is the purpose of this review to present the information content of spectroscopic methods, which allow one to focus in on the metalloactive site (Figure 1), define its electronic structure, evaluate the role of the protein in determining geometric and electronic structure, and elucidate the contributions of electronic structure to function. Metalloproteins are simply metal complexes but with remarkably intricate and complex ligands. The metal ion, clusters of metal ions bridged by oxide or sulfide ligands or equatorially chelated by N-heterocyclic ligands (heme, corrin, etc.), are bound to the protein through one or more of the endogenous ligand lone pair donors in Table 1. Note that for most of the donor groups, this requires deprotonation, and the metal ion competition with the proton for the free base lowers the effective pKA by at least several log units from those intrinsic values listed in Table 1. It is important to emphasize that for a number of the ligands in Tables 1 and 2, in particular phenolate, thiolate, oxo and sulfido, and the N-heterocyclic chelates, the metal complex exhibits extremely intense low energy charge transfer (CT) absorption bands, which reflect highly covalent ligand-metal bonds. These make major contributions to the electronic structure of an active site and can be affected by the geometry of the metal site and the orientation of the ligand-metal bond, which in turn can be influenced by the protein matrix. * To whom correspondence should be addressed. † Department of Chemistry, Stanford University. ‡ Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University. 419 Chem. Rev. 2004, 104, 419−458
753 citations
References
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TL;DR: In this paper, a split-valence extended gaussian basis set was used to obtain the LCAO-MO-SCF energies of closed shell species with two non-hydrogen atoms.
Abstract: Polarization functions are added in two steps to a split-valence extended gaussian basis set: d-type gaussians on the first row atoms C. N, O and F and p-type gaussians on hydrogen. The same d-exponent of 0.8 is found to be satisfactory for these four atoms and the hydrogen p-exponent of 1.1 is adequate in their hydrides. The energy lowering due to d functions is found to depend on the local symmetry around the heavy atom. For the particular basis used, the energy lowerings due to d functions for various environments around the heavy atom are tabulated. These bases are then applied to a set of molecules containing up to two heavy atoms to obtain their LCAO-MO-SCF energies. The mean absolute deviation between theory and experiment (where available) for heats of hydrogenation of closed shell species with two non-hydrogen atoms is 4 kcal/mole for the basis set with full polarization. Estimates of hydrogenation energy errors at the Hartree-Fock limit, based on available calculations, are given.
12,669 citations
TL;DR: TURBOMOLE as discussed by the authors is a program system for SCF that takes full advantage of all discrete point group symmetries and has only modest I/O and background storage requirements.
7,616 citations
TL;DR: In this paper, an efficient algorithm for evaluating the second-order Moller-Plesset (MP2) energy directly from two-electron integrals in the atomic orbital basis, i.e., the integrals are not stored.
2,533 citations
TL;DR: In this article, a direct method for evaluating the gradient of the second-order Moller-Plesset (MP2) energy without storing any quartic quantities, such as two-electron repulsion integrals (ERIs), double substitution amplitudes or the two-particle density matrix, was presented.
1,567 citations
TL;DR: In this article, three improvements on the direct selfconsistent field method are proposed and tested which together increase CPU efficiency by about 50% by selective storage of costly integral batches, improved integral bond for prescreening, and decomposition of the current density matrix into a linear combination of previous density matrices.
Abstract: Three improvements on the direct self‐consistent field method are proposed and tested which together increase CPU‐efficiency by about 50%: (i) selective storage of costly integral batches; (ii) improved integral bond for prescreening; (iii) decomposition of the current density matrix into a linear combination of previous density matrices—for which the two‐electron contributions to the Fock matrix are available—and a remainder ΔD, which is minimized; construction of the current Fock matrix only requires processing of the small ΔD which enhances prescreening.
881 citations