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 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 Experimental and theoretical charge density of DL-alanyl-methionine

2001 ◽  
Vol 57 (4) ◽  
pp. 567-578 ◽  
Author(s):  
Régis Guillot ◽  
Nicolas Muzet ◽  
Slimane Dahaoui ◽  
Claude Lecomte ◽  
Christian Jelsch
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Carbonyl Oxygen ◽  
Intramolecular Interactions ◽  
Geometrical Parameters ◽  
Covalent Bonds ◽  
Area Detector ◽  
Lone Pairs

X-ray diffraction data up to d = 0.50 Å resolution have been collected at 100 K for a DL-alanyl-methionine single crystal using a CCD area detector. Multipolar crystallographic refinement was carried out and the electron density of the molecule has been analyzed. The deformation electron density around the S atom reveals two lone pairs with an sp 3 hybridization and agrees with the results of density functional theory calculations. The topological properties of the covalent bonds and of the hydrogen bonds have been investigated. Two weak polar intramolecular interactions of the type C5 (pentagonal cyclic structure) have unfavorable geometrical parameters for hydrogen bonds and are devoid of critical points. The two electron lone pairs of the carbonyl oxygen appear asymmetric in the experimental deformation density. This could be attributed to the different strength of the hydrogen bond and intramolecular polar interaction involving the carbonyl oxygen. In the ab-initio-derived deformation maps, the asymmetry of the electron doublets is reproduced only very partially.

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.

scholarly journals Adenine as a Halogen Bond Acceptor: A Combined Experimental and DFT Study

Crystals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 224 ◽  
Author(s):  
Yannick Roselló ◽  
Mónica Benito ◽  
Elies Molins ◽  
Miquel Barceló-Oliver ◽  
Antonio Frontera
Keyword(s):  
Density Functional ◽  
Halogen Bond ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Adenine Ring ◽  
Bonding Interaction ◽  
Donor Ability ◽  
Adenine Derivative

In this work, we report the cocrystallization of N9-ethyladenine with 1,2,4,5-tetrafluoro-3,6-diiodobenzene (TFDIB), a classical XB donor. As far as our knowledge extends, this is the first cocrystal reported to date where an adenine derivative acts as a halogen bond acceptor. In the solid state, each adenine ring forms two centrosymmetric H-bonded dimers: one using N1···HA6–N6 and the other N7···HB6–N6. Therefore, only N3 is available as a halogen bond acceptor that, indeed, establishes an N···I halogen bonding interaction with TFDIB. The H-bonded dimers and halogen bonds have been investigated via DFT (Density Functional Theory) calculations and the Bader’s Quantum Theory of Atoms In Molecules (QTAIM) method at the B3LYP/6-311+G* level of theory. The influence of H-bonding interactions on the lone pair donor ability of N3 has also been analyzed using the molecular electrostatic potential (MEP) surface calculations.

scholarly journals Expression and interactions of stereochemically active lone pairs and their relation to structural distortions and thermal conductivity

IUCrJ ◽  
2020 ◽  
Vol 7 (3) ◽  
pp. 480-489 ◽  
Author(s):  
Kasper Tolborg ◽  
Carlo Gatti ◽  
Bo B. Iversen
Keyword(s):  
Thermal Conductivity ◽  
Density Functional ◽  
Lone Pair ◽  
Density Functional Theory Calculations ◽  
Orbital Interaction ◽  
Void Space ◽  
Metal Compounds ◽  
Bond Angles ◽  
Lone Pairs ◽  
Bonding Effect

In chemistry, stereochemically active lone pairs are typically described as an important non-bonding effect, and recent interest has centred on understanding the derived effect of lone pair expression on physical properties such as thermal conductivity. To manipulate such properties, it is essential to understand the conditions that lead to lone pair expression and provide a quantitative chemical description of their identity to allow comparison between systems. Here, density functional theory calculations are used first to establish the presence of stereochemically active lone pairs on antimony in the archetypical chalcogenide MnSb2O4. The lone pairs are formed through a similar mechanism to those in binary post-transition metal compounds in an oxidation state of two less than their main group number [e.g. Pb(II) and Sb(III)], where the degree of orbital interaction (covalency) determines the expression of the lone pair. In MnSb2O4 the Sb lone pairs interact through a void space in the crystal structure, and their their mutual repulsion is minimized by introducing a deflection angle. This angle increases significantly with decreasing Sb—Sb distance introduced by simulating high pressure, thus showing the highly destabilizing nature of the lone pair interactions. Analysis of the chemical bonding in MnSb2O4 shows that it is dominated by polar covalent interactions with significant contributions both from charge accumulation in the bonding regions and from charge transfer. A database search of related ternary chalcogenide structures shows that, for structures with a lone pair (SbX 3 units), the degree of lone pair expression is largely determined by whether the antimony–chalcogen units are connected or not, suggesting a cooperative effect. Isolated SbX 3 units have larger X—Sb—X bond angles and therefore weaker lone pair expression than connected units. Since increased lone pair expression is equivalent to an increased orbital interaction (covalent bonding), which typically leads to increased heat conduction, this can explain the previously established correlation between larger bond angles and lower thermal conductivity. Thus, it appears that for these chalcogenides, lone pair expression and thermal conductivity may be related through the degree of covalency of the system.

Structure and electron density of oxysulfide Sm2Ti2S2O4.9, a visible-light-responsive photocatalyst

2008 ◽  
Vol 64 (3) ◽  
pp. 291-298 ◽  
Author(s):  
Masatomo Yashima ◽  
Kiyonori Ogisu ◽  
Kazunari Domen
Keyword(s):  
Dft Calculations ◽  
Visible Light ◽  
Valence Band ◽  
Electron Density ◽  
Diffraction Data ◽  
Density Functional ◽  
Oxygen Deficiency ◽  
Covalent Bonds ◽  
Synchrotron Powder Diffraction ◽  
Visible Wavelengths

We report the crystal structure and electron density of samarium titanium oxysulfide, Sm2Ti2S2O4.9, photocatalyst obtained through the Rietveld analysis, maximum-entropy method (MEM) and MEM-based pattern fitting of the high-resolution synchrotron powder diffraction data taken at 298.7 K. The Sm2Ti2S2O4.9 has a tetragonal structure with the space group I4/mmm. Refined occupancy factors at the `equatorial' O1 and `apical' O2 sites were 0.994 (3) and 0.944 (12), respectively, which strongly suggest oxygen deficiency at the O2 site. Electron-density analyses based on the synchrotron diffraction data of Sm2Ti2S2O4.9 in combination with density-functional theory (DFT) calculations of stoichiometric Sm2Ti2S2O5 reveal covalent bonds between Ti and O atoms, while the Sm and S atoms are more ionic. The presence of S 3p and O 2p orbitals results in increased dispersion of the valence band, raising the top of the valence band and making the material active at visible wavelengths. The present DFT calculations of stoichiometric Sm2Ti2S2O5 indicate the possibility of overall splitting of water, although Sm2Ti2S2O4.9 works as a visible-light-responsive photocatalyst in aqueous solutions only in the presence of sacrificial electron donors or acceptors. The oxygen deficiency and cocatalyst seem to be factors affecting the catalytic activity.

Density functional theory study of bis(imino) N-heterocyclic carbene iron(II) complexes

2014 ◽  
Vol 92 (10) ◽  
pp. 925-931 ◽  
Author(s):  
Jameel Al Thagfi ◽  
Gino G. Lavoie
Keyword(s):  
Density Functional Theory ◽  
Electron Density ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Iron Complexes ◽  
Relative Energy ◽  
Iron Complex ◽  
Geometrical Parameters ◽  
Functional Theory ◽  
Imine Group

Density functional theory calculations at the B3LYP/DGDZVP and UB3LYP/TZVP levels were performed on 1,3-bis[1-(2,6-dimethylphenylimino)ethyl]imidazolium and on the corresponding imidazol-2-ylidene iron(II) dichloride complex, respectively. The resulting geometrical parameters of the optimized structures were in good agreement with previously reported X-ray structures. The ground state for the high-spin (quintet multiplicity) iron complex is 82.4 kJ/mol lower in energy compared to the low-spin (triplet) configuration, in agreement with magnetic susceptibility measurements. Further calculations were carried out on related benzimidazol-2-ylidene and pyrimidin-2-ylidene ligands and on the corresponding iron complexes to gain insight into their electronic properties and reactivities. The energy of the highest occupied and lowest unoccupied molecular orbitals of all three carbenes suggests that the pyrimidin-2-ylidene and the benzimidazol-2-ylidene are the best σ-donor and best π-acceptor, respectively. Using those results, the metal center in the pyrimidin-2-ylidene iron dichloride complex was predicted to bear the highest electron density. This was supported by the high relative energy of its highest occupied molecular orbital compared to that of the corresponding imidazole-2-ylidene and benzimidazol-2-ylidene iron complexes. The electrostatic potential maps of all three metal complexes furthermore indicated a marked decrease in electron density for the coordinated imine group, supporting a greater reactivity towards nucleophiles.

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.

scholarly journals Experimental and theoretical charge density distribution in Pigment Yellow 101

2015 ◽  
Vol 17 (6) ◽  
pp. 4677-4686 ◽  
Author(s):  
Jonathan J. Du ◽  
Linda Váradi ◽  
Jinlong Tan ◽  
Yiliang Zhao ◽  
Paul W. Groundwater ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Distribution ◽  
Charge Density ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
X Ray Diffraction ◽  
Charge Density Distribution ◽  
Functional Theory ◽  
X Ray ◽  
Multipole Refinement

The charge density distribution in 2,2′-dihydroxy-1,1′-naphthalazine (Pigment Yellow 101; P.Y.101) has been determined using high-resolution X-ray diffraction and multipole refinement, along with density functional theory calculations.

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