Ab initio calculation of the electron density of tetraazatetraoxatricyclotetradecane: an explanation for the deficiency of charge density in certain covalent bonds

1987 ◽  
Vol 109 (25) ◽  
pp. 7617-7623 ◽  
Author(s):  
Kathryn L. Kunze ◽  
Michael B. Hall
Keyword(s):  
Charge Density ◽  
Ab Initio ◽  
Electron Density ◽  
Ab Initio Calculation ◽  
Covalent Bonds

scholarly journals A theoretical-electron-density databank using a model of real and virtual spherical atoms

2017 ◽  
Vol 73 (4) ◽  
pp. 610-625 ◽  
Author(s):  
Ayoub Nassour ◽  
Slawomir Domagala ◽  
Benoit Guillot ◽  
Theo Leduc ◽  
Claude Lecomte ◽  
...  
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Density Functional ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Ligand Complex ◽  
Urea Molecule ◽  
Covalent Bonds ◽  
Similar Chemical ◽  
Chemical Groups

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

scholarly journals Transferability of Multipole Charge-Density Parameters: Application to Very High Resolution Oligopeptide and Protein Structures

1998 ◽  
Vol 54 (6) ◽  
pp. 1306-1318 ◽  
Author(s):  
Christian Jelsch ◽  
Virginie Pichon-Pesme ◽  
Claude Lecomte ◽  
André Aubry
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Diffraction Data ◽  
Protein Structures ◽  
Fourier Synthesis ◽  
Covalent Bonds ◽  
X Ray ◽  
Density Peaks ◽  
Deformation Electron Density ◽  
Temperature Factors

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 (\Delta 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.

AB INITIO CALCULATION OF THE ELECTRONIC AND MECHANICAL PROPERTIES OF TRANSITION METALS AND THEIR NITRIDES

2004 ◽  
Vol 18 (07n08) ◽  
pp. 281-289 ◽  
Author(s):  
CHENG-BIN LI ◽  
MING-KAI LI ◽  
FU-QING LIU ◽  
XIANG-JUN FAN
Keyword(s):  
Mechanical Properties ◽  
Transition Metals ◽  
Ab Initio Calculations ◽  
Charge Density ◽  
Ab Initio ◽  
Electronic Properties ◽  
Density Of States ◽  
Ab Initio Calculation ◽  
Structural And Electronic Properties

The results of ab initio calculations of the bulk moduli (B0) and related structural and electronic properties of selected transition metals and their nitrides are presented. There is a correlation between B0 and valence charge density. B0 does not vary monotonically with the addition of d electrons. Charge density and density of states (DOS) plots enable us to explain it.

An efficient linear scaling method for ab initio calculation of electron density of proteins

2004 ◽  
Vol 394 (4-6) ◽  
pp. 293-297 ◽  
Author(s):  
Ai M. Gao ◽  
Da W. Zhang ◽  
John Z.H. Zhang ◽  
Yingkai Zhang
Keyword(s):  
Ab Initio ◽  
Electron Density ◽  
Ab Initio Calculation ◽  
Linear Scaling ◽  
Scaling Method

Features of Valence Electron Density Distribution in Zr–H and Zr–He

2015 ◽  
Vol 1084 ◽  
pp. 241-245 ◽  
Author(s):  
Oksana V. Lopatina ◽  
Leonid A. Svyatkin ◽  
Yury M. Koroteev ◽  
Ivan P. Chernov
Keyword(s):  
Density Distribution ◽  
Charge Density ◽  
Ab Initio ◽  
Electron Density ◽  
Coordination Sphere ◽  
Electronic Structures ◽  
Electron Density Distribution ◽  
Valence Electron ◽  
Valence Electron Density ◽  
Host Metal

Ab initio calculations of electronic structures of Zr–H and Zr–He systems have been done. The influence of hydrogen or helium impurities on the electron density distribution of the host metal has been considered. Extremely inhomogeneous redistribution of the metal valence charge density within the first coordination sphere of the impurity was found. The character of the observed anisotropy depends on the impurity type.

scholarly journals Charge-density analysis and electrostatic properties of a new hybrid compound

2014 ◽  
Vol 70 (a1) ◽  
pp. C285-C285
Author(s):  
Noureddine Dadda ◽  
Amani Direm ◽  
Benoit Guillot ◽  
Christian Jelsch ◽  
Nourredine Bnelai-cherif
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Density Functional ◽  
Lone Pair ◽  
Theoretical Data ◽  
Density Functional Theory Calculations ◽  
Biologically Active ◽  
Hybrid Compound ◽  
Covalent Bonds ◽  
Additional Charges

2-carboxy-4-methylaniline is a biologically active molecule serving as a pharmaceutical intermediate [1]. We've synthesized, studied and refined the crystal structure of its derivative 2-carboxy-4-methylanilinium chloride monohydrate using three different electron-density models. In the first model, the ELMAM2 multipolar electron-density database [2] was transferred to the molecule. Theoretical structure factors were also computed from periodic density functional theory calculations [3] and yielded, after multipolar-atoms refinement, the second charge-density model. An alternative electron-density modelling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites, was used in the third model in the refinement versus the theoretical data. The crystallographic refinements, structural properties, electron-density distributions and molecular electrostatic potentials obtained from the different charge-density models were compared.

scholarly journals Charge-density analysis using multipolar atom and spherical charge models: 2-methyl-1,3-cyclopentanedione, a compound displaying a resonance-assisted hydrogen bond

2014 ◽  
Vol 70 (2) ◽  
pp. 197-211 ◽  
Author(s):  
Ayoub Nassour ◽  
Maciej Kubicki ◽  
Jonathan Wright ◽  
Teresa Borowiak ◽  
Grzegorz Dutkiewicz ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Charge Density ◽  
Electron Density ◽  
Dipole Moments ◽  
Lone Pair ◽  
Covalent Bonds ◽  
Density Maps ◽  
Structure Factors ◽  
Density Analysis ◽  
Additional Charges

The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 Å resolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen–Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O—H...O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C—C=C—OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.

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