A topological analysis of the interion interactions of tetraphenylphosphonium squarate

2006 ◽  
Vol 84 (5) ◽  
pp. 804-811 ◽  
Author(s):  
David Wolstenholme ◽  
Manuel AS Aquino ◽  
T Stanley Cameron ◽  
Joseph D Ferrara ◽  
Katherine N Robertson
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Critical Points ◽  
Topological Analysis ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Multipole Refinement ◽  
Diverse Interactions

The tetraphenylphosphonium squarate salt crystallizes with a number of diverse interactions, which all have the potential to be classified as hydrogen bonds. The squarate anions are found as dimers linked by O-H···O interactions. The multipole refinement of the tetraphenylphosphonium squarate was performed using the Hansen–Coppens model followed by topological analysis of its intermolecular interactions. A total of 28 interactions were found among the symmetry related molecules, which include a number of C-H···Cπ, C-H···O, and C-H···H-C interactions, along with the O-H···O interaction. With the criteria for hydrogen bonding proposed by Popelier and Koch, it is possible to determine which of these interactions are hydrogen bonds and which are van der Waals interactions. Both linear and exponentially dependent correlations can be seen for the properties of the bond critical points involving the intermolecular interactions that fulfill these criteria. All this leads to a better understanding of the role that hydrogen bonds play in the formation of small organic compounds.Key words: electron density, multiple refinement, hydrogen bonds.

Intra- and intermolecular interactions in small bioactive molecules: cooperative features from experimental and theoretical charge-density analysis

2006 ◽  
Vol 62 (4) ◽  
pp. 612-626 ◽  
Author(s):  
Parthapratim Munshi ◽  
Tayur N. Guru Row
Keyword(s):  
Salicylic Acid ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Van Der Waals Interactions ◽  
Bioactive Molecules ◽  
Topological Features ◽  
Weak Intermolecular Interactions

The topological features of the charge densities, ρ(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of `Atoms In Molecules'. The roles of interactions such as C—H...O, C—H...S, C—H...π and π...π have been investigated quantitatively in the presence of strong hydrogen bonds such as O—H...O, N—H...O and N—H...S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S...S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug–receptor recognition.

scholarly journals Crystal structure and halogen–hydrogen bonding of a Delépine reaction intermediate

2021 ◽  
Vol 77 (1) ◽  
pp. 1-4
Author(s):  
David Z. T. Mulrooney ◽  
Helge Müller-Bunz ◽  
Tony D. Keene
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Van Der Waals ◽  
Hirshfeld Surface ◽  
Van Der Waals Interactions ◽  
Hirshfeld Surface Analysis ◽  
Space Group ◽  
Molecular Salt

The reaction of 1,5-dibromopentane with urotropine results in crystals of the title molecular salt, 5-bromourotropinium bromide [systematic name: 1-(5-bromopentyl)-3,5,7-triaza-1-azoniatricyclo[3.3.1.13,7]decane bromide], C11H22BrN4 +·Br− (1), crystallizing in space group P21/n. The packing in compound 1 is directed mainly by H...H van der Waals interactions and C—H...Br hydrogen bonds, as revealed by Hirshfeld surface analysis. Comparison with literature examples of alkylurotropinium halides shows that the interactions in 1 are consistent with those in other bromides and simple chloride and iodide species.

Topological analysis of the electron density in hydrogen bonds

1999 ◽  
Vol 55 (4) ◽  
pp. 563-572 ◽  
Author(s):  
E. Espinosa ◽  
M. Souhassou ◽  
H. Lachekar ◽  
C. Lecomte
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Positive Curvature ◽  
Topological Analysis ◽  
Peptide Bonds ◽  
X Ray ◽  
Systematic Relationships ◽  
Experimental Electron Density

Topological analysis of the experimental electron density ρ(r) in hydrogen-bonding regions has been carried out for a large number of organic compounds using different multipole models and techniques. Relevant systematic relationships between topological properties at the critical points and the usual geometric parameters are pointed out. Results involving X-ray data only and joint X-ray and neutron data, as well as special hydrogen bonding cases (symmetric, bifurcated, peptide bonds, etc.) are included and analysed in the same framework. A new classification of hydrogen bonds using the positive curvature of the electron density at the critical point [\lambda_3({\bf r}_{\rm CP})] is proposed.

scholarly journals Pixel calculations using Orca or GAUSSIAN for electron density automated within the Oscail package

2021 ◽  
Vol 54 (5) ◽  
Author(s):  
Patrick McArdle
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Electron Density ◽  
Intermolecular Interactions ◽  
Lattice Energy ◽  
Van Der Waals Interactions ◽  
Rational Basis ◽  
Simple Analysis ◽  
Crystal Lattice Energy ◽  
Hydrogen Bonding Interactions

Many discussions of the intermolecular interactions in crystal structures concentrate almost exclusively on an analysis of hydrogen bonding. A simple analysis of atom–atom distances is all that is required to detect and analyse hydrogen bonding. However, for typical small-molecule organic crystal structures, hydrogen-bonding interactions are often responsible for less than 50% of the crystal lattice energy. It is more difficult to analyse intermolecular interactions based on van der Waals interactions. The Pixel program can calculate and partition intermolecular energies into Coulombic, polarization, dispersion and repulsion energies, and help put crystal structure discussions onto a rational basis. This Windows PC implementation of Pixel within the Oscail package requires minimal setup and can automatically use GAUSSIAN or Orca for the calculation of electron density.

Biotransformation, spectroscopic investigation, crystal structure and electrostatic properties of 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate studied using transferred electron-density parameters

2018 ◽  
Vol 74 (5) ◽  
pp. 534-541 ◽  
Author(s):  
Ammara Shahid ◽  
Ambreen Aziz ◽  
Sajida Noureen ◽  
Maqsood Ahmed ◽  
Sammer Yousuf ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Van Der Waals Interactions ◽  
Estradiol Valerate ◽  
Spectrometric Analysis ◽  
Spectroscopic Techniques ◽  
Charge Delocalization ◽  
Atom Model ◽  
Network Of Hydrogen Bonds

The biologically transformed product of estradiol valerate, namely 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate, C18H22O3·H2O, has been investigated using UV–Vis, IR, 1H and 13C NMR spectroscopic techniques, as well as by mass spectrometric analysis. Its crystal structure was determined using single-crystal X-ray diffraction based on data collected at 100 K. The structure was refined using the independent atom model (IAM) and the transferred electron-density parameters from the ELMAM2 database. The structure is stabilized by a network of hydrogen bonds and van der Waals interactions. The topology of the hydrogen bonds has been analyzed by the Bader theory of `Atoms in Molecules' framework. The molecular electrostatic potential for the transferred multipolar atom model reveals an asymmetric character of the charge distribution across the molecule due to a substantial charge delocalization within the molecule. The molecular dipole moment was also calculated, which shows that the molecule has a strongly polar character.

Tetrakis[(1-phenyltetrazol-5-yl)sulfanylmethyl]methane

2007 ◽  
Vol 63 (3) ◽  
pp. o1145-o1147 ◽  
Author(s):  
Alexander S. Lyakhov ◽  
Marina V. Zatsepina ◽  
Tatiana V. Artamonova ◽  
Pavel N. Gaponik ◽  
Grigorii I. Koldobskii
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Rotation Axis ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Π Interactions ◽  
Compound C

The title compound, C33H28N16S4, prepared by the divergent method, presents a core unit for further synthesis of tetrazole-containing dendrimers. The central C atom lies on a crystallographic twofold rotation axis. π–π Interactions and weak non-classical C—H...N hydrogen bonds are responsible for the formation of layers parallel to the bc plane, with van der Waals interactions between them.

scholarly journals Manganese Fluorene Phosphonates: Formation of Isolated Chains

Inorganics ◽  
2018 ◽  
Vol 6 (3) ◽  
pp. 92 ◽  
Author(s):  
Clarisse Bloyet ◽  
Jean-Michel Rueff ◽  
Vincent Caignaert ◽  
Bernard Raveau ◽  
Jean-François Lohier ◽  
...  
Keyword(s):  
Magnetic Susceptibility ◽  
Hydrogen Bonds ◽  
Phosphonic Acid ◽  
Van Der Waals ◽  
Exchange Interactions ◽  
Van Der Waals Interactions ◽  
Antiferromagnetic Exchange ◽  
Hydrothermal Conditions ◽  
Hirshfeld Surfaces ◽  
Nitrate Tetrahydrate

9,9-dimethylfluorenyl-2-phosphonic acid 1 was reacted with manganese nitrate tetrahydrate to produce under hydrothermal conditions the crystalline manganese phosphonate Mn(H2O)2[O2(OH)PC15H13]2·2H2O which crystallize in the P21/c space group. This compound is a rare example of Mn-phosphonate material featuring isolated chains. The interactions between these chains containing the 9,9-dimethylfluorenyl moieties, result from Van der Waals interactions involving the fluorene ligands and C···H–C hydrogen bonds as revealed by Hirshfeld Surfaces. This material features antiferromagnetic exchange interactions as revealed by the magnetic susceptibility as a function of the temperature.

Competition and cooperativity of hydrogen-bonding and tetrel-bonding interactions involving triethylene diamine (DABCO), H2O and CO2 in air

2020 ◽  
Vol 44 (6) ◽  
pp. 2328-2338 ◽  
Author(s):  
Jianming Yang ◽  
Qinwei Yu ◽  
Fang-Ling Yang ◽  
Ka Lu ◽  
Chao-Xian Yan ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Tetrel Bond

Triethylene diamine (DABCO) can interact with H2O and CO2 in air to form dimeric and trimeric complexes via hydrogen bond, tetrel bond as well as van der Waals interactions.

Sign in / Sign up

Export Citation Format

Share Document