scholarly journals Numerical computation of critical properties and atomic basins from three-dimensional grid electron densities

2003 ◽  
Vol 36 (1) ◽  
pp. 65-73 ◽  
Author(s):  
C. Katan ◽  
P. Rabiller ◽  
C. Lecomte ◽  
M. Guezo ◽  
V. Oison ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Software Package ◽  
Topological Analysis ◽  
Hessian Matrix ◽  
Three Dimensional ◽  
Chemical Bonds ◽  
Critical Properties ◽  
Electron Densities ◽  
Atomic Properties ◽  
Intermolecular Contacts

InteGriTyis a software package that performs topological analysis following the AIM (atoms in molecules) approach on electron densities given on three-dimensional grids. Tricubic interpolation is used to obtain the density, its gradient and the Hessian matrix at any required position. Critical points and integrated atomic properties have been derived from theoretical densities calculated for the compounds NaCl and TTF–2,5Cl2BQ (tetrathiafulvalene–2,5-dichlorobenzoquinone), thus covering the different kinds of chemical bonds: ionic, covalent, hydrogen bonds and other intermolecular contacts.

EDMA: a computer program for topological analysis of discrete electron densities

2012 ◽  
Vol 45 (3) ◽  
pp. 575-580 ◽  
Author(s):  
Lukáš Palatinus ◽  
Siriyara Jagannatha Prathapa ◽  
Sander van Smaalen
Keyword(s):  
Computer Program ◽  
Electron Density ◽  
Critical Points ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Real Space ◽  
Principal Curvatures ◽  
Electron Densities ◽  
Structure Solution ◽  
Aperiodic Crystals

EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.

Topological analysis of experimental electron densities

1999 ◽  
Vol 32 (2) ◽  
pp. 210-217 ◽  
Author(s):  
Mohamed Souhassou ◽  
Robert H. Blessing
Keyword(s):  
Amino Acid ◽  
Crystal Structures ◽  
Electron Density ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Electron Densities ◽  
Acid Crystal ◽  
Density Distributions ◽  
Amino Acid Crystal ◽  
Experimental Electron Density

Practical computing algorithms are described for analysing the topology of experimental electron density distributions represented as either three-dimensional grid densities or multipolar pseudoatom superpositions. The algorithms are implemented in the programNEWPROP, results from which are illustrated with applications to twoN-acetyl,C-methylamide blocked amino acid crystal structures.

Weak Hydrogen Bonds in the Molecular Packing of N-Tetraalkyl Terephthalamides

2011 ◽  
Vol 66 (4) ◽  
pp. 397-406
Author(s):  
Peter G. Jones ◽  
Piotr Kuś
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Ring Plane ◽  
Hydrogen Atoms ◽  
Hydrogen Bond System ◽  
Layer Structures ◽  
Weak Hydrogen Bonds ◽  
Intermolecular Contacts ◽  
Bond System ◽  
Great Complexity

We present the structures of eight terephthaldiamides, seven of which (1 - 7) are fully substituted at both nitrogens and so cannot form classical hydrogen bonds. The structure of N,N´-dimethyl- N,N´-diphenylterephthalamide (7) represents a new polymorph. Where possible, the molecules tend to exhibit inversion symmetry. The amide groups are rotated significantly out of the central aromatic plane, by 33° to 84° (average 54°). The carbonyl carbon of the amide group may lie significantly (ca. 0.1 - 0.2 Å ) out of the aromatic ring plane. The packing patterns exploit those types of contact still available, namely C-H· · ·O (especially) and C-H· · ·π. The smaller substituents in general lead to simpler packing patterns such as layer structures; more complex substituents can lead to three-dimensional patterns of great complexity. The central ring tends to play less of a role as the substituents become larger. Phenyl substituents often use their para hydrogen atoms to form intermolecular contacts, presumably because they are sterically more exposed. One terephthaldiamide (8) with two NHR groups forms a mixed “classical and weak” bifurcated (N-H, o-C-H)· · ·O hydrogen bond system.

Tricarbonyl(η5-formylcyclopentadienyl)manganese(I) and tricarbonyl(η5-formylcyclopentadienyl)rhenium(I) containing short π(CO)...π(CO) and π(CO)...π interactions

2012 ◽  
Vol 68 (3) ◽  
pp. m69-m72 ◽  
Author(s):  
Alexander S. Romanov ◽  
Gary F. Angles ◽  
Mikhail Yu. Antipin ◽  
Tatiana V. Timofeeva
Keyword(s):  
Hydrogen Bonds ◽  
Carbonyl Group ◽  
Three Dimensional ◽  
The Other ◽  
Carbonyl Groups ◽  
Π Interactions ◽  
Dimensional Network ◽  
Intermolecular Contacts

The structures of tricarbonyl(formylcyclopentadienyl)manganese(I), [Mn(C6H5O)(CO)3], (I), and tricarbonyl(formylcyclopentadienyl)rhenium(I), [Re(C6H5O)(CO)3], (II), were determined at 100 K. Compounds (I) and (II) both possess a carbonyl group in atransposition relative to the substituted C atom of the cyclopentadienyl ring, while the other two carbonyl groups are in almost eclipsed positions relative to their attached C atoms. Analysis of the intermolecular contacts reveals that the molecules in both compounds form stacks due to short attractive π(CO)...π(CO) and π(CO)...π interactions, along the crystallographiccaxis for (I) and along the [201] direction for (II). Symmetry-related stacks are bound to each other by weak intermolecular C—H...O hydrogen bonds, leading to the formation of the three-dimensional network.

scholarly journals Conformational flexibility in amidophosphoesters: a CSD analysis completed with two new crystal structures of (C6H5O)2P(O)X [X = NHC7H13 and N(CH2C6H5)2]

2020 ◽  
Vol 76 (1) ◽  
pp. 104-116
Author(s):  
Banafsheh Vahdani Alviri ◽  
Mehrdad Pourayoubi ◽  
Abdul Ajees Abdul Salam ◽  
Marek Nečas ◽  
Arie van der Lee ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Intramolecular Interactions ◽  
Large Contribution ◽  
Scanning Calorimetry ◽  
Π Interactions ◽  
Intermolecular Contacts ◽  
Phenyl Rings ◽  
Dsc Analyses

The crystal structures of diphenyl (cycloheptylamido)phosphate, C19H24NO3P or (C6H5O)2P(O)(NHC7H13), (I), and diphenyl (dibenzylamido)phosphate, C26H24NO3P or (C6H5O)2P(O)[N(CH2C6H5)2], (II), are reported. The NHC7H13 group in (I) provides two significant hydrogen-donor sites in N—H...O and C—H...O hydrogen bonds, needed for a one-dimensional hydrogen-bond pattern along [100] in the crystal, while (II), with a (C6H5CH2)2N moiety, lacks these hydrogen bonds, but its three-dimensional supramolecular structure is mediated by C—H...π interactions. The conformational behaviour of the phenyl rings in (I), (II) and analogous structures from the Cambridge Structural Database (CSD) were studied in terms of flexibility, volume of the other group attached to phosphorus and packing forces. From this study, synclinal (±sc), anticlinal (±ac) and antiperiplanar (±ap) conformations were found to occur. In the structure of (II), there is an intramolecular C ortho —H...O interaction that imposes a +sc conformation for the phenyl ring involved. For the structures from the CSD, the +sc and ±ap conformations appear to be mainly imposed by similar C ortho —H...O intramolecular interactions. The large contribution of the C...H/H...C contacts (32.3%) in the two-dimensional fingerprint plots of (II) is a result of the C—H...π interactions. The differential scanning calorimetry (DSC) analyses exhibit peak temperatures (T m) at 109 and 81 °C for (I) and (II), respectively, which agree with the strengths of the intermolecular contacts and the melting points.

scholarly journals The nature of the chemical bond in oxyanionic crystals based on QTAIM topological analysis of electron densities

RSC Advances ◽  
2019 ◽  
Vol 9 (21) ◽  
pp. 12020-12033 ◽  
Author(s):  
Dmitry V. Korabel'nikov ◽  
Yuriy N. Zhuravlev
Keyword(s):  
Hydrogen Bonds ◽  
Chemical Bond ◽  
Topological Analysis ◽  
Electron Densities

The QTAIM topological analysis of the calculated electron densities in oxyanionic crystals revealed the covalency criteria for metal–oxygen and hydrogen bonds.

scholarly journals 2-Methyl-4-(4-nitrophenyl)but-3-yn-2-ol: crystal structure, Hirshfeld surface analysis and computational chemistry study

2019 ◽  
Vol 75 (8) ◽  
pp. 1232-1238 ◽  
Author(s):  
Ignez Caracelli ◽  
Julio Zukerman-Schpector ◽  
Ricardo S. Schwab ◽  
Everton M. da Silva ◽  
Mukesh M. Jotani ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Computational Chemistry ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
The Other ◽  
Dispersion Forces ◽  
Prominent Feature ◽  
Compound C ◽  
Intermolecular Contacts ◽  
A Site

The di-substituted acetylene residue in the title compound, C11H11NO3, is capped at either end by di-methylhydroxy and 4-nitrobenzene groups; the nitro substituent is close to co-planar with the ring to which it is attached [dihedral angle = 9.4 (3)°]. The most prominent feature of the molecular packing is the formation, via hydroxy-O—H...O(hydroxy) hydrogen bonds, of hexameric clusters about a site of symmetry \overline{3}. The aggregates are sustained by 12-membered {...OH}6 synthons and have the shape of a flattened chair. The clusters are connected into a three-dimensional architecture by benzene-C—H...O(nitro) interactions, involving both nitro-O atoms. The aforementioned interactions are readily identified in the calculated Hirshfeld surface. Computational chemistry indicates there is a significant energy, primarily electrostatic in nature, associated with the hydroxy-O—H...O(hydroxy) hydrogen bonds. Dispersion forces are more important in the other identified but, weaker intermolecular contacts.

scholarly journals Influence of Multiple & Cooperative Hydrogen Bonding on the Acidity of Polyhydroxylated Piperidines: Electron Density Topological Analysis

2021 ◽  
Author(s):  
Marjan Jebeli Javan
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Gas Phase ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Solution Phase ◽  
Hydroxyl Group ◽  
Hydroxyl Groups ◽  
Gas Phase Acidity ◽  
Polarized Continuum Model

Abstract Hydrogen bonds are the presiding concepts for arranging the three-dimensional forms of biological molecules like proteins, carbohydrates and nucleic acids, and acts as guides for proton transfer reactions. Gas-phase acidity and pKa calculations in dimethyl sulfoxide on a line of polyhydroxylated piperidines specify that multiple hydrogen bonds lead to enhance acidities.The gas-phase acidity (GPA) of polyhydroxylated piperidines was investigated by MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) method. For each structure, varied primary and secondary hydroxyl groups were deprotonated. The natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses have also been used to realize the character of the hydrogen bonding interactions in these compounds. The results show by adding each hydroxyl group, ΔHacid in the gas phase (it becomes less endothermic) and pKa value in the solution phase was decreased. Therefore, intramolecular hydrogen bonds lead to enhance the acid strength. In both the gas phase and solution phase, the β-Nojrimycin-OH2 (β-1-OH2) was found to be the most acidic compound with calculated gas-phase acidity (GPA) of 349.4 kcal.mol-1 and the pKa value of 22.0 (8.0 pKa units more acidic than 1-propanol).It was also shown, applying the polarized continuum model (PCM), there is a superior linear correlation with the gas phase acidities (GPAs) of polyhydroxylated piperidines and their calculated pKa (DMSO) values.

scholarly journals Bis(9-aminoacridinium) bis(pyridine-2,6-dicarboxylato)zincate(II) trihydrate

2012 ◽  
Vol 68 (4) ◽  
pp. m355-m356
Author(s):  
M. Mirzaei ◽  
H. Eshtiagh-Hosseini ◽  
E. Eydizadeh ◽  
Z. Yousefi ◽  
K. Molčanov
Keyword(s):  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Distorted Octahedron ◽  
Compound C ◽  
Π Stacking ◽  
Dimensional Network ◽  
Intermolecular Contacts ◽  
The Mean

In the title compound, (C13H11N2)2[Zn(C7H3NO4)2]·3H2O, the ZnIIion is six-coordinated with the N4O2donor set being a distorted octahedron through two almost perpendicular (r.m.s. deviation of ligand atoms from the mean plane is 0.057 Å) tridentate pyridine-2,6-dicarboxylate ligands [dihedral angle between the ligands = 86.06 (4)°]. The charge is compensated by two 9-aminoacridinium cations protonated on the ring N atom. A variety of intermolecular contacts, such as ion–ion, N—H...O and O—H...O hydrogen bonds, and π–π stacking [centroid–centroid distances = 3.4907 (9)–4.1128 (8) Å], between cations and between anions, play important roles in the formation of the three-dimensional network.

The Nature of Chemical Bonds in the Tetragonal Polymorph of InTe. First‐Principles Based Topological Analysis

2021 ◽  
Author(s):  
Aleksey V. Kovalenko ◽  
Andrei V. Bandura ◽  
Dmitry D. Kuruch ◽  
Sergey I. Lukyanov ◽  
Robert A. Evarestov
Keyword(s):  
First Principles ◽  
Topological Analysis ◽  
Chemical Bonds
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