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 Stabilization of N-, N,N-, N,N′-methylated and unsubstituted simple amidine salts by multifurcated hydrogen bonds

2006 ◽  
Vol 20 (4) ◽  
pp. 169-176 ◽  
Author(s):  
Jarosław Spychała
Keyword(s):  
Chemical Shift ◽  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
2D Nmr ◽  
Biological Properties ◽  
Carbonyl Oxygen ◽  
Relative Strength ◽  
Intramolecular Interactions ◽  
Covalent Bonds ◽  
Natural Isotopic Abundance

In the light of the usefulness of amidines in medicinal chemistry, this paper considers the effects on biological properties and chemical reactivities of organic molecules affected by intramolecular interactions. The study of chemical shifts has been an important source of information on the electronic structure of amidine salts and their ability to form non-covalent bonds with nucleic acids. The NMR and IR results demonstrate that hydrogen bonds are a force for promoting chemical reactions. The thymine O2 carbonyl oxygen in a close proximity to the amidinium cation does interact with the appropriately spaced amidinium NH donor moieties. The1H-15N 2D NMR (GHSQC and GHMBC) spectra with natural isotopic abundance of15N fully confirm the intramolecular character of the bonds. A rule able to estimate the relative strength of the new multifurcated hydrogen bonds is given. The appearance of the ΔδNHchemical shift differences near zero is due to the strong intramolecular interactions. The strength of the H-bond donation by acetamidines is reflected in the N–H dissociation/recombination process (positive charge shift has been invoked to explain other effects on benzamidines). The temperature dependence of chemical shift for the amidine NH protons in dimethyl sulfoxide solutions is herein discussed.

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 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 Crystal structure of atazanavir, C38H52N6O7

2020 ◽  
Vol 35 (2) ◽  
pp. 129-135
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Hydroxyl Group ◽  
Amide Nitrogen ◽  
Classical Hydrogen Bond ◽  
Intramolecular Hydrogen ◽  
Atazanavir Sulfate

The crystal structure of atazanavir has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Atazanavir crystallizes in space group P21 (#4) with a = 15.33545(7), b = 5.90396(3), c = 21.56949(13) Å, β = 96.2923(4)°, V = 1941.134(11) Å3, and Z = 2. Despite being labeled as “atazanavir sulfate”, the commercial reagent sample consisted of atazanavir free base. The structure consists of an array of extended-conformation molecules parallel to the ac-plane. Although the atazanavir molecule contains only four classical hydrogen bond donors, hydrogen bonding is, surprisingly, important to the crystal energy. Both intra- and intermolecular hydrogen bonds are significant. The hydroxyl group forms bifurcated intramolecular hydrogen bonds to a carbonyl oxygen atom and an amide nitrogen. Several amide nitrogens act as donors to the hydroxyl group and carbonyl oxygen atoms. An amide nitrogen acts as a donor to another amide nitrogen. Several methyl, methylene, methyne, and phenyl hydrogens participate in hydrogen bonds to carbonyl oxygens, an amide nitrogen, and the pyridine nitrogen. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1426.

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.

Crystal structure of rivastigmine hydrogen tartrate Form I (Exelon®), C14H23N2O2(C4H5O6)

2016 ◽  
Vol 31 (2) ◽  
pp. 97-103 ◽  
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Strong Hydrogen Bond ◽  
Hydroxyl Groups ◽  
A Chain ◽  
Tartrate Anion

The crystal structure of rivastigmine hydrogen tartrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rivastigmine hydrogen tartrate crystallizes in space group P21 (#4) with a = 17.538 34(5), b = 8.326 89(2), c = 7.261 11(2) Å, β = 98.7999(2)°, V = 1047.929(4) Å3, and Z = 2. The un-ionized end of the hydrogen tartrate anions forms a very strong hydrogen bond with the ionized end of another anion to form a chain. The ammonium group of the rivastigmine cation forms a strong discrete hydrogen bond with the carbonyl oxygen atom of the un-ionized end of the tartrate anion. These hydrogen bonds form a corrugated network in the bc-plane. Both hydroxyl groups of the tartrate anion form intramolecular O–H⋯O hydrogen bonds. Several C–H⋯O hydrogen bonds appear to contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1501.

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.

A DFT-D study on the stability and intramolecular interactions of the salts of 1,2,3- and 1,2,4-triazoles

2014 ◽  
Vol 92 (11) ◽  
pp. 1111-1117
Author(s):  
Xueli Zhang ◽  
Xuedong Gong
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Energy Gap ◽  
Lattice Energy ◽  
Intramolecular Interactions ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Formation Reaction ◽  
The Stability ◽  
Intramolecular Hydrogen

Nitrogen-rich 1,2,4-triazole (1) and 1,2,3-triazole (2) react as bases with the oxygen-rich acids HNO3 (a), HN(NO2)2 (b), and HClO4 (c) to produce energetic salts (1a, 1b, and 1c and 2a, 2b, and 2c, respectively) potentially applicable to composite explosives and propellants. In this study, these salts were studied with the dispersion-corrected density functional theory. For the isomers such as 1a and 2a, the more negative ΔrGm of the formation reaction leads to a higher thermally stable salt. The ability to form intramolecular hydrogen bonds predicted with the quantum theory of atoms in molecules has the order of 2 > 1. Different hydrogen bonds result in different second-order perturbation energies, redshifts in IR, and electron density differences. The charge transfer, binding energy, dispersion energy, lattice energy, and energy gap between frontier orbits in the salts of 1 are larger than those of 2, which is helpful for stabilizing the former, and 1 is more obviously stabilized than 2 by formation of salts. Different conformations of 1 and 2 hardly affect the frontier orbital distributions. Base 1 is a more preferred base than 2 to form salts.

The mechanism of 1,3-dipolar cycloaddition reactions of cyclopropanes and nitrones — A theoretical study

2005 ◽  
Vol 83 (10) ◽  
pp. 1752-1767 ◽  
Author(s):  
D Wanapun ◽  
K A Van Gorp ◽  
N J Mosey ◽  
M A Kerr ◽  
T K Woo
Keyword(s):  
Lewis Acid ◽  
Density Functional ◽  
Cycloaddition Reaction ◽  
Acid Catalyst ◽  
Density Functional Theory Calculations ◽  
Reaction Rates ◽  
Carbonyl Oxygen ◽  
Dipolar Cycloaddition ◽  
Similar Reaction ◽  
Lewis Acid Catalyst

The 1,3-dipolar cycloaddition reaction of cyclopropanes and nitrones to give tetrahydro-1,2-oxazine has been studied with density functional theory calculations at the B3LYP/6-31+G(d,p) level of theory. Realistic substituents were modelled including those at the 2-, 3-, 4-, and 6-positions of the final oxazine ring product. The strained σ bond of the cyclopropane was found to play the role of an alkene in a conventional [3+2] dipolar cycloaddition. Two distinct, but similar, reaction mechanisms were found — an asymmetric concerted pathway and a stepwise zwitterionic pathway. The reaction barriers of the two pathways were nearly identical, differing by less than ~1 kcal/mol, no matter what the substituents were. The effect of a Lewis acid catalyst was examined and found to have a very large effect on the calculated barriers through coordination to the carbonyl oxygen atoms of the diester substituents on the cyclopropane. The reaction barrier was found to decrease by as much as ~19 kcal/mol when using a BF3 molecule as a model for the Lewis acid catalyst. Solvent effects and the nature of the regiospecificity of the reaction were also examined. Trends in the calculated barriers for the reaction were in good agreement with available trends in the reaction rates measured experimentally. Key words: 1,3-dipolar cycloaddition, cyclopropane, nitrone, tetrahydro-1,2-oxazines, ab initio quantum chemistry, mechanism.

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