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.

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.

scholarly journals A computational study on how structure influences the optical properties in model crystal structures of amyloid fibrils

2017 ◽  
Vol 19 (5) ◽  
pp. 4030-4040 ◽  
Author(s):  
Luca Grisanti ◽  
Dorothea Pinotsi ◽  
Ralph Gebauer ◽  
Gabriele S. Kaminski Schierle ◽  
Ali A. Hassanali
Keyword(s):  
Optical Properties ◽  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Crystal Structures ◽  
Amyloid Fibrils ◽  
Computational Study ◽  
Model Systems ◽  
Hydrogen Bonding Interactions ◽  
Model Crystal ◽  
Different Types

Different types of hydrogen bonding interactions that occur in amyloids model systems and molecular factors that control the susceptibility of the protons to undergo proton transfer and how this couples to the optical properties.

A two-dimensional silver(I) coordination polymer constructed from 4-aminophenylarsonate and triphenylphosphane: poly[[(μ3-4-aminophenylarsonato-κ3N:O:O)(triphenylphosphane-κP)silver(I)] monohydrate]

2015 ◽  
Vol 71 (4) ◽  
pp. 258-261 ◽  
Author(s):  
Zu-Ping Xiao ◽  
Meng Wen ◽  
Chun-Ya Wang ◽  
Xi-He Huang
Keyword(s):  
Hydrogen Bonding ◽  
Coordination Mode ◽  
Aqueous Ammonia ◽  
Van Der Waals Interactions ◽  
Water Molecules ◽  
Stacking Interactions ◽  
Two Dimensional ◽  
Solvent Water ◽  
Hydrogen Bonding Interactions ◽  
Amine Groups

The title compound, {[Ag(C6H7AsNO3)(C18H15P)]·H2O}n, has been synthesized from the reaction of 4-aminophenylarsonic acid with silver nitrate, in aqueous ammonia, with the addition of triphenylphosphane (PPh3). The AgIcentre is four-coordinated by one amino N atom, one PPh3P atom and two arsonate O atoms, forming a severely distorted [AgNPO2] tetrahedron. Two AgI-centred tetrahedra are held together to produce a dinuclear [Ag2O2N2P2] unit by sharing an O–O edge. 4-Aminophenylarsonate (Hapa−) adopts a μ3-κ3N:O:O-tridentate coordination mode connecting two dinuclear units, resulting in a neutral [Ag(Hapa)(PPh3)]nlayer lying parallel to the (10\overline{1}) plane. The PPh3ligands are suspended on both sides of the [Ag(Hapa)(PPh3)]nlayer, displaying up and down orientations. There is anR22(8) hydrogen-bonded dimer involving two arsonate groups from two Hapa−ligands related by a centre of inversion. Additionally, there are hydrogen-bonding interactions involving the solvent water molecules and the arsonate and amine groups of the Hapa−ligands, and weak π–π stacking interactions within the [Ag(Hapa)(PPh3)]nlayer. These two-dimensional layers are further assembled by weak van der Waals interactions to form the final architecture.

scholarly journals Crystal structures ofN′-aminopyridine-2-carboximidamide andN′-{[1-(pyridin-2-yl)ethylidene]amino}pyridine-2-carboximidamide

2017 ◽  
Vol 73 (7) ◽  
pp. 1021-1025
Author(s):  
Francois Eya'ane Meva ◽  
Timothy John Prior ◽  
David John Evans ◽  
Emmanuel Roland Mang
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Dimensional Chain ◽  
Two Dimensional ◽  
One Dimensional ◽  
Bond Lengths ◽  
Hydrogen Bonding Interactions ◽  
Hydrogen Bonding Network

The crystal structures ofN′-aminopyridine-2-carboximidamide (C6H8N4),1, andN′-{[1-(pyridin-2-yl)ethylidene]amino}pyridine-2-carboximidamide (C13H13N5),2, are described. The non-H atoms in compound1are nearly planar (r.m.s. deviation from planarity = 0.0108 Å), while2is twisted about the central N—N bond by 17.8 (2)°. Both molecules are linked by intermolecular N—H...N hydrogen-bonding interactions;1forms a two-dimensional hydrogen-bonding network and for2the network is a one-dimensional chain. The bond lengths of these molecules are similar to those in other literature reports of azine and diimine systems.

scholarly journals Crystal Structures of Four Novel Thiophene/Phenyl-piperidine Hybrid Chalcones

2014 ◽  
Vol 70 (a1) ◽  
pp. C1020-C1020
Author(s):  
Masood Parvez ◽  
Muhammad Bakhtiar ◽  
Muhammad Baqir ◽  
Muhammad Zia-ur-Rehman
Keyword(s):  
Hydrogen Bonding ◽  
Pharmaceutical Industry ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Benzene Ring ◽  
Drug Targets ◽  
Important Class ◽  
Hydrogen Bonding Interactions ◽  
Benzene Rings ◽  
Type C

Chalcones constitute an important class of bioactive drug targets in the pharmaceutical industry that includes anti-ulcerative drug sofalcone. In continuation of our work, the crystal structures of four closely related 1-phenyl-piperidine based chalcones will be presented. I: C19 H21NOS, MW = 311.43, T = 173(2) K, λ = 0.71073 Å, Orthorhombic, P b c a, a = 10.1045(4), b = 10.5358(4), c = 30.6337(12) Å, V = 3261.2(2) Å3, Z = 8, Dc = 1.269 Mg/m3, F (000) = 1328, R [I>2σ(I)] = 0.059. II: C18H19NOS, MW = 297.40, T = 173(2) K, λ = 1.54178 Å, Orthorhombic, P b c a, a = 8.9236(2), b = 11.0227(2), c = 30.8168(6) Å, V = 3031.21(11) Å3 Z = 8, Dc = 1.303 Mg/m3, F (000) = 1264, R [I>2σ(I)] = 0.035. III: C18H19NOS, MW = 297.40, T = 173(2) K, λ = 1.54178 Å, Orthorhombic, P b c a, a = 8.82990(10), b = 11.0061(2), c = 31.2106(5) Å, V = 3033.13(8) Å3, Z = 8, Dc = 1.303 Mg/m3, F (000) = 1264, R [I>2σ(I)] = 0.048. IV: C18H18ClNOS, MW = 331.84, T = 173(2) K, λ = 0.71073 Å, Monoclinic, P 21/c, a = 14.1037(4), b = 11.3153(3), c = 10.1290(2) Å, β = 101.1367(14)0, V = 1586.02(7) Å3, Z = 4, Dc = 1.390 Mg/m3, F (000) = 696, R [I>2σ(I)] = 0.038. The crystals of I, II and III are isomorphous. In all structures, the piperidine rings are in chair conformations, thiophene rings are essentially planar and the C=C bonds in the prop-2-en-1-one fragment adopt E-conformation. All crystal structures are devoid of any classical hydrogen bonds. However, non-classical hydrogen bonding interactions of the type C---H...O in compounds II, III and IV link the molecules into chains extended along the b-axis. Moreover, C---H...Cg interactions involving thiophene rings in I and III and benzene ring in IV and π...π interactions between benzene rings lying about inversion centers are present in II and III.

scholarly journals Crystal structures of three complexes of zinc chloride with tri-tert-butylphosphane

2016 ◽  
Vol 72 (1) ◽  
pp. 35-39 ◽  
Author(s):  
Aaron D. Finke ◽  
Danielle L. Gray ◽  
Jeffrey S. Moore
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Zinc Chloride ◽  
Chloride Complex ◽  
Lewis Base ◽  
Ambient Conditions ◽  
Hydrogen Bonding Interactions ◽  
Complex Forms ◽  
Cl Atoms

Under anhydrous conditions and in the absence of a Lewis-base solvent, a zinc chloride complex with tri-tert-butylphosphane as the μ-bridged dimer is formed,viz.di-μ-chlorido-bis[chloridobis(tri-tert-butylphosphane)zinc], [ZnCl4(C12H27P)2], (1), which features a nearly square-shaped (ZnCl)2cyclic core and whose Cl atoms interact weakly with C—H groups on the phosphane ligand. In the presence of THF, monomeric dichlorido(tetrahydrofuran-κO)(tri-tert-butylphosphane-κP)zinc, [ZnCl2(C4H8O)(C12H27P)] or [P(tBu3)(THF)ZnCl2], (2), is formed. This slightly distorted tetrahedral Zn complex has weak C—H...Cl interactions between the Cl atoms and phosphane and THF C—H groups. Under ambient conditions, the hydrolysed complex tri-tert-butylphosphonium aquatrichloridozincate 1,2-dichloroethane monosolvate, (C12H28P)[ZnCl3(H2O)]·C2H4Cl2or [HPtBu3]+[(H2O)ZnCl3]−·C2H4Cl2, (3), is formed. This complex forms chains of [(H2O)ZnCl3]−anions from hydrogen-bonding interactions between the water H atoms and Cl atoms that propagate along thebaxis.

THE EFFECT OF SUBSTITUTION ON STRUCTURE, INTRAMOLECULAR HYDROGEN BONDING STRENGTH, ELECTRON DENSITY AND RESONANCE IN 3-AMINO 2-IMINOMETHYL ACRYL ALDEHYDE

2012 ◽  
Vol 11 (05) ◽  
pp. 925-939 ◽  
Author(s):  
HEIDAR RAISSI ◽  
MAHDI YOOSEFIAN ◽  
FARIBA MOLLANIA ◽  
FARZANEH FARZAD
Keyword(s):  
Hydrogen Bonding ◽  
Electron Density ◽  
Population Analysis ◽  
Intramolecular Hydrogen Bonding ◽  
Analysis Data ◽  
Covalent Character ◽  
Hydrogen Bonding Interactions ◽  
Hydrogen Bond Strength ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonding Strength

B3LYP/6-311++G** calculations have been carried out to simulate the influence of substitutions in position R1 and R2 of 3-amino 2-iminomethyl acryl aldehyde on intramolecular hydrogen bond strength. The following substituents are taken into considerations: CN, NO2, Cl, F, CH3, CHO, NH2, C2H5, SH, SCH3, CF3 and CH3CO and their vibrational frequencies are calculated at the same level of theory. Quantum theory of "Atoms in Molecules" and Natural Bond Orbitals method were applied to analyzed H-bond interactions. The electron density (ρ) and Laplacian (∇2ρ) properties, estimated by AIM calculations, indicate that N⋯H bond possesses low ρ and positive ∇2ρ values which are in agreement with electrostatic character of the HBs, whereas N–H bonds have covalent character (∇2ρ < 0). Natural population analysis data, the electron density and Laplacian properties, as well as, ν (N-H) and γ (N-H) have been used to evaluate the hydrogen bonding interactions.

scholarly journals Crystal structures of chlorido[dihydroxybis(1-iminoethoxy)]arsanido-κ3 N,As,N′]platinum(II) and of a polymorph of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II)

2020 ◽  
Vol 76 (2) ◽  
pp. 180-185
Author(s):  
Nina R. Marogoa ◽  
D.V. Kama ◽  
Hendrik G. Visser ◽  
M. Schutte-Smith
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Donor Ligands ◽  
Intermolecular Hydrogen Bonding ◽  
Π Interactions ◽  
Hydrogen Bonding Interactions ◽  
Oxygen Donor ◽  
Dimensional Network

Each central platinum(II) atom in the crystal structures of chlorido[dihydroxybis(1-iminoethoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C4H10AsN2O4)Cl] (1), and of chlorido[dihydroxybis(1-iminopropoxy)arsanido-κ3 N,As,N′]platinum(II), [Pt(C6H14AsN2O4)Cl] (2), is coordinated by two nitrogen donor atoms, a chlorido ligand and to arsenic, which, in turn, is coordinated by two oxygen donor ligands, two hydroxyl ligands and the platinum(II) atom. The square-planar and trigonal–bipyramidal coordination environments around platinum and arsenic, respectively, are significantly distorted with the largest outliers being 173.90 (13) and 106.98 (14)° for platinum and arsenic in (1), and 173.20 (14)° and 94.20 (9)° for (2), respectively. One intramolecular and four classical intermolecular hydrogen-bonding interactions are observed in the crystal structure of (1), which give rise to an infinite three-dimensional network. A similar situation (one intramolecular and four classical intermolecular hydrogen-bonding interactions) is observed in the crystal structure of (2). Various π-interactions are present in (1) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.7225 (7) Å, and between the centroids of five-membered (Pt, As, C, N, O) rings of neighbouring molecules with distances of 3.7456 (4) and 3.7960 (6) Å. Likewise, weak π-interactions are observed in (2) between the platinum(II) atom and the centroid of one of the five-membered rings formed by Pt, As, C, N, O with a distance of 3.8213 (2) Å, as well as between the Cl atom and the centroid of a symmetry-related five-membered ring with a distance of 3.8252 (12) Å. Differences between (2) and the reported polymorph [Miodragović et al. (2013). Angew. Chem. Int. Ed. 52, 10749–10752] are discussed.

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