Comparison of the results of AB initio analysis and inverse vibrational problem solution for glyoxal

2000 ◽  
Vol 41 (1) ◽  
pp. 129-134 ◽  
Author(s):  
Yu. N. Panchenko
Keyword(s):  
Ab Initio ◽  
Problem Solution ◽  
Vibrational Problem ◽  
Comparison Of The Results

scholarly journals Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8

2021 ◽  
Author(s):  
Thomas G. Flower ◽  
James H. Hurley
Keyword(s):  
Ab Initio ◽  
Structural Parameters ◽  
Search Model ◽  
Problem Solution ◽  
Molecular Replacement ◽  
Phase Problem ◽  
Search Models ◽  
Sad Phasing ◽  
Predicted Model ◽  
Β Sheet

AbstractThe majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for molecular replacement. The ORF8 protein of SARS-CoV-2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all β-sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.

14N Nuclear Quadrupole Coupling in Heterocyclic Compounds, Part 2. A Comparison of ab initio Calculations and Experimental Results for the Azoles and Azines

1981 ◽  
Vol 36 (1) ◽  
pp. 34-50
Author(s):  
Michael H. Palmer ◽  
Isobel Simpson ◽  
Robert H. Findlay
Keyword(s):  
Ab Initio Calculations ◽  
Ab Initio ◽  
Coupling Constants ◽  
Electric Field Gradients ◽  
Field Gradients ◽  
Double Zeta ◽  
Quadrupole Coupling ◽  
Quadrupole Resonance ◽  
Nuclear Quadrupole ◽  
Comparison Of The Results

Ab initio calculations of double zeta quality have been reported for the conjugated 5- and 6- membered ring heterocycles containing NH and NMe groups. The electric field gradients were calculated and the derived nuclear quadrupole coupling constants (NQCC) compared, both in magnitude and direction, with those obtained by microwave spectroscopy and by nuclear quadrupole resonance. A comparison of the results with those of the corresponding O- and S-heterocycles, and with acyclic compounds has been given, and it was shown that aromaticity considerations were of no relevance to the NQCC values at pyridine-like N; planarity of the N atom at N-1 in the systems 2 c-9 c is responsible for the very low magnitude of Xπ, and this is clearly associated with the level of π-donation from N-1; this is a function of position of the other ring N atoms, and appears to become saturated as the ring positions become predominantly N. In particular three contiguous N atoms seem to have less effect than two N atoms

Ab initio band theory approach to electron energy loss near edge structures

1988 ◽  
Vol 46 ◽  
pp. 506-507
Author(s):  
Xudong Weng ◽  
O.F. Sankey ◽  
Peter Rez
Keyword(s):  
Ab Initio ◽  
Local Density ◽  
Interpolation Method ◽  
Atomic Orbital ◽  
Plane Waves ◽  
Large Set ◽  
Theory Approach ◽  
Band Theory ◽  
Atomic Orbitals ◽  
Pseudopotential Calculations

Single electron band structure techniques have been applied successfully to the interpretation of the near edge structures of metals and other materials. Among various band theories, the linear combination of atomic orbital (LCAO) method is especially simple and interpretable. The commonly used empirical LCAO method is mainly an interpolation method, where the energies and wave functions of atomic orbitals are adjusted in order to fit experimental or more accurately determined electron states. To achieve better accuracy, the size of calculation has to be expanded, for example, to include excited states and more-distant-neighboring atoms. This tends to sacrifice the simplicity and interpretability of the method.In this paper. we adopt an ab initio scheme which incorporates the conceptual advantage of the LCAO method with the accuracy of ab initio pseudopotential calculations. The so called pscudo-atomic-orbitals (PAO's), computed from a free atom within the local-density approximation and the pseudopotential approximation, are used as the basis of expansion, replacing the usually very large set of plane waves in the conventional pseudopotential method. These PAO's however, do not consist of a rigorously complete set of orthonormal states.

An ab initio study of Se-reacted GaAs(0 0 1) surfaces

1998 ◽  
Vol 184-185 (1-2) ◽  
pp. 80-84 ◽  
Author(s):  
W Faschinger
Keyword(s):  
Ab Initio ◽  
Ab Initio Study
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