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Christian Jelsch - One of the best experts on this subject based on the ideXlab platform.
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An improved experimental databank of transferable multipolar atom models--ELMAM2. Construction details and applications.
Acta Crystallographica Section A, 2012Co-Authors: Sławomir Domagała, Bertrand Fournier, Dorothee Liebschner, Benoit Guillot, Christian JelschAbstract:ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMAM2 electron-Density Parameters and compared with the former ELMAM database and Density functional theory calculations.
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An improved experimental databank of transferable multipolar atom models – ELMAM2. Construction details and applications
Acta Crystallographica Section A Foundations and Advances, 2012Co-Authors: Sławomir Domagała, Bertrand Fournier, Dorothee Liebschner, Benoit Guillot, Christian JelschAbstract:ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripep-tides and aromatic molecules are calculated using ELMAM2 electron-Density Parameters and compared with the former ELMAM database and Density functional theory calculations.
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2,2′-(Ethane-1,2-diyl)bis[2-(5-bromothiophen-2-yl)-1,3-dioxolane] at 100 K refined using a multipolar atom model
Acta Crystallographica Section C: Crystal Structure Communications, 2011Co-Authors: Maqsood Ahmed, Sajida Noureen, Benoit Guillot, Philippe Gros, Christian JelschAbstract:The title compound, C 16 H 16 Br 2 O 4 S 2 , which is a precursor for the synthesis of oligothiophenes and their substituted homo-logues, was synthesized and its X-ray crystal structure determined at 100 K. The experimental electron-Density Parameters for the available atom types were transferred from the ELMAM2 database. The compound lies about an inversion centre, which coincides with the mid-point of a C—C bond. The molecules in the crystal are linked by several types of weak interactions; the largest contact surfaces are for HÁ Á ÁH and HÁ Á ÁBr. Comment In the recent past, oligothiophenes and their substituted homologues have attracted the attention of the scientific community as they are a promising class of organic semiconductor materials for applications in the production of organic field-effect transistors and as electronic devices (Roncali, 1992). These-conjugated materials have found important applications, for example in organic solar cells (Ma et al.,
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Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Nicolas Muzet, Christian Jelsch, Benoit Guillot, Eduardo Howard, Claude LecomteAbstract:The electron Density and electrostatic potential in an Aldose Reductase holoenzyme complex have been studied by DFT and diffraction methods. Aldose reductase is involved in the reduction of glucose in the polyol pathway using NADPH as a co-factor. The ultra-high resolution of the diffraction data and the low thermal displacement Parameters of the structure allow accurate atomic positions and an experimental charge Density analysis. Based on the X-ray structural data, order-N Density Functional Theory (DFT) calculations have been performed on 711 atoms in the active site of the molecule. The charge Density refinement of the protein was performed with program MoPro using the transferability principle and our database of charge Density Parameters built from crystallographic analyses of peptides and amino acids.
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Structural analysis and multipole modelling of quercetin monohydrate – a quantitative and comparative study
Acta Crystallographica Section B: Structural Science, 2011Co-Authors: Sławomir Domagała, Maqsood Ahmed, Benoit Guillot, Parthapratim Munshi, Christian JelschAbstract:The multipolar atom model, constructed by transferring the charge-Density Parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement Parameters, the residual electron densities and the crystallographic figures of merit. The charge-Density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron Density features very accurately.
Claude Lecomte - One of the best experts on this subject based on the ideXlab platform.
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Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Nicolas Muzet, Christian Jelsch, Benoit Guillot, Eduardo Howard, Claude LecomteAbstract:The electron Density and electrostatic potential in an Aldose Reductase holoenzyme complex have been studied by DFT and diffraction methods. Aldose reductase is involved in the reduction of glucose in the polyol pathway using NADPH as a co-factor. The ultra-high resolution of the diffraction data and the low thermal displacement Parameters of the structure allow accurate atomic positions and an experimental charge Density analysis. Based on the X-ray structural data, order-N Density Functional Theory (DFT) calculations have been performed on 711 atoms in the active site of the molecule. The charge Density refinement of the protein was performed with program MoPro using the transferability principle and our database of charge Density Parameters built from crystallographic analyses of peptides and amino acids.
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Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures
Acta crystallographica. Section D Structural biology, 1998Co-Authors: Christian Jelsch, Virginie Pichon-pesme, Claude Lecomte, André AubryAbstract:Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron Density (parameterized as multipoles) and of the atomic charges. This fine description of the electron Density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole Parameters. A database of such Parameters has been built from charge-Density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-Density multipole Parameters have been transferred and the X-ray structure of a 3_{10} helix octapeptide Ac-Aib_2-L-Lys(Bz)-Aib_2-L-Lys(Bz)-Aib_2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 Å at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-Density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-Density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (Δ B ≃ 0.4 Å2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron Density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement Parameters. The contribution to the diffraction of the different components of the electron Density has also been analyzed. This analysis indicates that the electron-Density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 Å^2). In this case, a non-truncated Fourier synthesis of the deformation Density requires that the diffraction data are available to a resolution better than 0.9 Å.
André Aubry - One of the best experts on this subject based on the ideXlab platform.
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Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures
Acta crystallographica. Section D Structural biology, 1998Co-Authors: Christian Jelsch, Virginie Pichon-pesme, Claude Lecomte, André AubryAbstract:Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron Density (parameterized as multipoles) and of the atomic charges. This fine description of the electron Density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole Parameters. A database of such Parameters has been built from charge-Density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-Density multipole Parameters have been transferred and the X-ray structure of a 3_{10} helix octapeptide Ac-Aib_2-L-Lys(Bz)-Aib_2-L-Lys(Bz)-Aib_2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 Å at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-Density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-Density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (Δ B ≃ 0.4 Å2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron Density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement Parameters. The contribution to the diffraction of the different components of the electron Density has also been analyzed. This analysis indicates that the electron-Density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 Å^2). In this case, a non-truncated Fourier synthesis of the deformation Density requires that the diffraction data are available to a resolution better than 0.9 Å.
Xibing Li - One of the best experts on this subject based on the ideXlab platform.
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investigation on the linear energy storage and dissipation laws of rock materials under uniaxial compression
Rock Mechanics and Rock Engineering, 2019Co-Authors: Fengqiang Gong, Xibing LiAbstract:To investigate the energy evolution characteristics of rock materials under uniaxial compression, the single-cyclic loading–unloading uniaxial compression tests of four rock materials (Qingshan granite, Yellow sandstone, Longdong limestone and Black sandstone) were conducted under five unloading stress levels. The stress–strain curves and failure characteristics of rock specimens under the single-cyclic loading–unloading uniaxial compression tests basically corresponded with those of under uniaxial compression, which indicates that single-cyclic loading–unloading has minimal effects on the variations in the loading–deformation response of rocks. The input energy Density, elastic energy Density and dissipated energy Density of four rocks under five unloading stress levels were calculated using the graphical integration method, and variation characteristics of those three energy Density Parameters with different unloading stress levels were explored. The results show that all three energy Density Parameters above increased nonlinearly with increasing unloading stress level as quadratic polynomial functions. Meanwhile, both the elastic and dissipated energy Density increased linearly when the input energy Density increased, and the linear energy storage and dissipation laws for rock materials were observed. Furthermore, a linear relationship between the dissipated and elastic energy Density was also proposed. Using the linear energy storage or dissipation law, the elastic and dissipated energy Density at any stress levels can be calculated, and the internal elastic (or dissipated) energy Density at peak compressive strength (the peak elastic and dissipated energy Density for short) can be obtained. The ratio of the elastic energy Density to dissipated energy Density with increasing input energy Density was investigated using a new method, and the results show that this ratio tends to be constant at the peak compressive strength of rock specimens.
Paweł Ogonowski - One of the best experts on this subject based on the ideXlab platform.
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APPLICATION OF THE STRAIN ENERGY Density PARAMETER FOR ESTIMATION OF MULTIAXIAL FATIGUE LIFE OF SINTERED STEELS WITH STRESS CONCENTRATORS
Journal of Theoretical and Applied Mechanics, 2009Co-Authors: Tadeusz Łagoda, Cetin Morris Sonsino, Paweł OgonowskiAbstract:This paper presents fatigue test results of a Fe-Cu sintered alloy (1.5% Cu) and three types of Fe-Cu-Ni sintered alloys (2% Cu, 2.5% Ni). Fe-Cu-Ni sintered alloys were produced under different compaction pressures and sintering temperatures. Round specimens with fillet notches were subjected to a constant amplitude pure bending, pure torsion and a combined in-phase and out-of-phase $ (\delta=90^{\circ}$) bending with torsion. All results have been described by the criterion of the strain energy Density parameter on the critical plane. It was assumed that the fatigue life is influenced by a linear combination of normal and strain energy Density Parameters with the coefficients that refer to the calculated plane. In particular, it allowed one to compute fatigue lives sufficiently comparable to the experimental ones.
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Fatigue life estimation of notched specimens under bending and torsion with strain energy Density parameter
Journal of Theoretical and Applied Mechanics, 2007Co-Authors: Tadeusz Łagoda, Paweł OgonowskiAbstract:This paper presents an energy damage parameter based on the critical plane under a complex loading state and stress concentration. Two criteria including combinations of the normal and shear strain energy Density Parameters have been proposed. The plane in which the normal or shear strain energy Density parameter reaches its maximum is assumed to be the critical plane. The predictions of the proposed model have been compared with constant amplitude fatigue tests under combined proportional bending and torsion carried out on ring-notched specimens made of 42CrMo4V steel.