An ab-initio molecular model of the Scandate cathode

2008 ◽  
Author(s):  
Vasilios Vlahos ◽  
Dane Morgan ◽  
John H. Booske ◽  
Ladislav Turek ◽  
Mark Kirshner ◽  
...  
Keyword(s):  
Ab Initio ◽  
Molecular Model ◽  
Scandate Cathode

scholarly journals Resist Investigation Method using ab initio MO Calculation on basis of Approximation Molecular Model

2017 ◽  
Vol 30 (5) ◽  
pp. 583-589 ◽  
Author(s):  
Shohei Nagata ◽  
Shota Niihara ◽  
Tetsuo Harada ◽  
Takeo Watanabe
Keyword(s):  
Ab Initio ◽  
Molecular Model ◽  
Investigation Method ◽  
Mo Calculation

Synergy among phase-refinement techniques in macromolecular crystallography

2017 ◽  
Vol 73 (11) ◽  
pp. 877-888 ◽  
Author(s):  
Maria Cristina Burla ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Ab Initio ◽  
Electron Density ◽  
Molecular Model ◽  
Experimental Tests ◽  
Protein Chemistry ◽  
Sources Of Information ◽  
Density Maps ◽  
Structure Solution ◽  
Molecular Interpretation ◽  
The Difference

Ab initioand non-ab initiophasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try,viasuitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD–MAD andab initiotechniques.

scholarly journals Predicting dipole orientations in spontelectric methyl formate

2021 ◽  
Vol 75 (3) ◽  
Author(s):  
Christian Kexel ◽  
Andrey V. Solov’yov
Keyword(s):  
Ab Initio ◽  
Predictive Power ◽  
Methyl Formate ◽  
Molecular Model ◽  
Temperature Dependent ◽  
Anomalous Temperature ◽  
Dependent Polarization ◽  
First Time ◽  
Dynamics Method ◽  
Ground State Geometry

Abstract Capturing intermolecular interactions accurately is essential for describing, e.g., morphology of molecular matter on the nanoscale. When it reveals characteristics which are not directly accessible through experiments or ab initio theories, a model here becomes eminently beneficial. In laboratory astrochemistry, the intense study of ices has led i.a. to the exploration of the spontelectric state of nanofilms. Despite its success in biophysics or biochemistry and despite its predictive power, molecular modeling has however not yet been widely deployed for solid-state astrochemistry. In this article, therefore a pertinent hitherto unaddressed problem is tackled by means of the classical molecular-dynamics method, namely the unknown distribution of relative dipole orientations in spontelectric cis-methyl formate (MF). In doing so, from ab initio data, a molecular model is derived which confirms for the first time the anomalous temperature-dependent polarization of MF. These insights thus represent a further step toward understanding spontelectric behavior. Moreover, unprecedented first-principles predictions are reported regarding the ground-state geometry of the MF trimer and tetramer. In conjunction with the study of the binding to carbonaceous substrates, these additional findings can help to exemplarily elucidate molecular ice formation in astrochemical settings. Graphic Abstract

Docking of An Asphaltene Molecular Model on A Fe2O3Surface, An Ab Initio Simulated Annealing

2004 ◽  
Vol 22 (7-8) ◽  
pp. 915-926 ◽  
Author(s):  
F. Alvarez-Ramírez ◽  
I. García-Cruz ◽  
G. Tavizón ◽  
J. M. Martínez-Magadán
Keyword(s):  
Simulated Annealing ◽  
Ab Initio ◽  
Molecular Model

Classification of ab initio models of proteins restored from small-angle X-ray scattering

2018 ◽  
Vol 25 (5) ◽  
pp. 1379-1388 ◽  
Author(s):  
Mao Oide ◽  
Yuki Sekiguchi ◽  
Asahi Fukuda ◽  
Koji Okajima ◽  
Tomotaka Oroguchi ◽  
...  
Keyword(s):  
Ab Initio ◽  
Small Angle ◽  
Structural Information ◽  
Molecular Model ◽  
Dimensional Space ◽  
Principal Component ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

In structure analyses of proteins in solution by using small-angle X-ray scattering (SAXS), the molecular models are restored by using ab initio molecular modeling algorithms. There can be variation among restored models owing to the loss of phase information in the scattering profiles, averaging with regard to the orientation of proteins against the direction of the incident X-ray beam, and also conformational fluctuations. In many cases, a representative molecular model is obtained by averaging models restored in a number of ab initio calculations, which possibly provide nonrealistic models inconsistent with the biological and structural information about the target protein. Here, a protocol for classifying predicted models by multivariate analysis to select probable and realistic models is proposed. In the protocol, each structure model is represented as a point in a hyper-dimensional space describing the shape of the model. Principal component analysis followed by the clustering method is applied to visualize the distribution of the points in the hyper-dimensional space. Then, the classification provides an opportunity to exclude nonrealistic models. The feasibility of the protocol was examined through the application to the SAXS profiles of four proteins.

Toward an alignment of the actin molecule within the actin filament

1983 ◽  
Vol 41 ◽  
pp. 450-451
Author(s):  
P.R. Smith ◽  
W.E. Fowler ◽  
U. Aebi
Keyword(s):  
Actin Filament ◽  
Diffraction Data ◽  
Quantitative Estimate ◽  
Molecular Model ◽  
Quantitative Comparison ◽  
Regulatory Proteins ◽  
Essential Information ◽  
X Ray ◽  
Maximum Resolution ◽  
Lack Of Information

An understanding of the specific interactions of actin with regulatory proteins has been limited by the lack of information about the structure of the actin filament. Molecular actin has been studied in actin-DNase I complexes by single crystal X-ray analysis, to a resolution of about 0.6nm, and in the electron microscope where two dimensional actin sheets have been reconstructed to a maximum resolution of 1.5nm. While these studies have shown something of the structure of individual actin molecules, essential information about the orientation of actin in the filament is still unavailable.The work of Egelman & DeRosier has, however, suggested a method which could be used to provide an initial quantitative estimate of the orientation of actin within the filament. This method involves the quantitative comparison of computed diffraction data from single actin filaments with diffraction data derived from synthetic filaments constructed using the molecular model of actin as a building block. Their preliminary work was conducted using a model consisting of two juxtaposed spheres of equal size.

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.

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