A comparison between predicted and measured structural parameters in symmetric hydrogen bonds

1981 ◽  
Vol 11 (5-6) ◽  
pp. 167-172 ◽  
Author(s):  
Mizuhiko Ichikawa
Keyword(s):  
Hydrogen Bonds ◽  
Structural Parameters

On the structural diversity anions coordinate to the butterfly-shaped [(R2Sn)3O(OH)2]2+ cations and vice versa

2014 ◽  
Vol 92 (6) ◽  
pp. 496-507 ◽  
Author(s):  
Hans Reuter ◽  
Hilko Wilberts
Keyword(s):  
Hydrogen Bonds ◽  
Iodine Atom ◽  
Structural Parameters ◽  
Structural Diversity ◽  
Hydroxyl Groups ◽  
Equatorial Position ◽  
Chelating Ligands ◽  
Trigonal Bipyramidal Coordination ◽  
Trigonal Bipyramidal ◽  
Oxygen Framework

The syntheses and crystal structures of [(t-Bu2Sn)3O(OH)2]CO3·3MeOH, 1a, [(t-Bu2Sn)3O(OH)2]CO3·3H2O·acetone, 1b, [(t-Bu2Sn)3O(OH)2][I]2·[(t-Bu2Sn(OH)I]2·2DMSO, 1c, and [(Cy2Sn)3O(OH)2][I]2·2DMSO, 2a, all containing the trinuclear [(R2Sn)3O(OH)2]2+ ion have been described. The butterfly shape of this cation is derived from two annulated, four-membered tin–oxygen rings with a central μ3-oxygen atom and trigonal-bipyramidally coordinated tin atom both belonging to both rings and two μ2-hydroxyl groups and two outer, four-fold coordinated tin atoms. In 1a and 1b, the carbonate anions interact with the outer tin atoms of the cations as bidentate chelating ligands in the classical syn–syn coordination mode, and vice versa. In this way, both outer tin atoms expand their coordination sphere from four to five, with the consequence that bond angles and lengths within the cation are determined by the axial and equatorial position of the oxygen atoms within the trigonal-bipyramidal coordination on all three tin atoms. 1c consists of two different building units, an up to now unknown hydroxide iodide of composition [(t-Bu2Sn(OH)I]2 with hydrogen-bonded DMSO molecules and a [(t-Bu2Sn)3O(OH)2]2+ cation with one coordinated and one isolated, via hydrogen bonds connected iodine ion. The hydroxide iodine is built up of two five-fold coordinated tin atoms linked via two hydroxyl groups with exocyclic iodine atoms occupying axial positions at the trigonal-biypramidally coordinated tin atoms. The unprecedented coordination of the iodine ion to the [(t-Bu2Sn)3O(OH)2]2+ cation takes place between both outer tin atoms, resulting in a five-fold, trigonal-bipyramidal coordination at these tin atoms, too. Structural parameters within the so-formed [(t-Bu2Sn)3O(OH)2I]+ complex are very similar to those of 1a and 1b, with the exception of a significant lengthening of the tin–oxygen bonds opposite to the bridging iodine atom. 2a represents the first example of the [(R2Sn)3O(OH)2]2+ cation without R = t-butyl, so far. In the solid, it consists of two crystallographic independent [(Cy2Sn)3O(OH)2][I]2 building units, each connected to two DMSO molecules via hydrogen bonds. Both building units are very similar with respect to their conformation. Each of the iodine anions coordinates with only one of the two outer tin atoms, one in an inwards, one in an outwards to the tin-oxygen framework directed position. These tin atoms are therefore also trigonal-bipyramidally coordinated as in 1a−1c, but because of steric reasons one of the trigonal-bipyramids has changed its orientation within the tin–oxygen framework, accompanied by enormous changes of bond lengths and angles therein.

Formation and distortion of iodidoantimonates(III): the first isolated [SbI6]3−octahedron

2017 ◽  
Vol 73 (3) ◽  
pp. 432-442 ◽  
Author(s):  
Maciej Bujak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Structural Parameters ◽  
Hybrid Structure ◽  
Organic Hybrid ◽  
Hydrogen Bond Interactions ◽  
Different Types ◽  
Spatial Dimensions ◽  
Induced Changes

The ability to intentionally construct, through different types of interactions, inorganic–organic hybrid materials with desired properties is the main goal of inorganic crystal engineering. The primary deformation, related to intrinsic interactions within inorganic substructure, and the secondary deformation, mainly caused by the hydrogen bond interactions, are both responsible for polyhedral distortions of halogenidoantimonates(III) with organic cations. The evolution of structural parameters, in particular the Sb—I secondary- and O/N/C—H...I hydrogen bonds, as a function of temperature assists in understanding the contribution of those two distortion factors to the irregularity of [SbI6]3−polyhedra. In tris(piperazine-1,4-diium) bis[hexaiodidoantimonate(III)] pentahydrate, (C4H12N2)3[SbI6]2·5H2O (TPBHP), where the isolated [SbI6]3–units were found, distortion is governed only by O/N/C—H...I hydrogen bonds, whereas in piperazine-1,4-diium bis[tetraiodidoantimonate(III)] tetrahydrate, (C4H12N2)[SbI4]2·4H2O (PBTT), both primary and O—H...I secondary factors cause the deformation of one-dimensional [{SbI4}n]n−chains. The larger in spatial dimensions piperazine-1,4-diium cations, in contrast to the smaller water of crystallization molecules, do not significantly contribute to the octahedral distortion, especially in PBTT. The formation of isolated [SbI6]3−ions in TPBHP is the result of specific second coordination sphere hydrogen bond interactions that stabilize the hybrid structure and simultaneously effectively separate and prevent [SbI6]3−units from mutual interactions. The temperature-induced changes, further supported by the analysis of data retrieved from the Cambridge Structural Database, illustrate the significance of both primary and secondary distortion factors on the deformation of octahedra. Also, a comparison of packing features in the studied hybrids with those in the non-metal containing piperazine-1,4-diium diiodide diiodine (C4H12N2)I2·I2(PDD) confirms the importance and hierarchy of different types of interactions.

scholarly journals Toward a uniform description of hydrogen bonds and halogen bonds: correlations of interaction energies with various geometric, electronic and topological parameters

RSC Advances ◽  
2017 ◽  
Vol 7 (17) ◽  
pp. 10295-10305 ◽  
Author(s):  
Jian-Wei Zou ◽  
Meilan Huang ◽  
Gui-Xiang Hu ◽  
Yong-Jun Jiang
Keyword(s):  
Hydrogen Bonds ◽  
Structural Parameters ◽  
Interaction Energies ◽  
Halogen Bonds ◽  
Topological Parameters

Correlations between interaction energies and various structural parameters were established to reveal the differences between hydrogen bonds and halogen bonds.

scholarly journals TheZ′ = 12 superstructure of Λ-cobalt(III) sepulchrate trinitrate governed by C—H...O hydrogen bonds

2016 ◽  
Vol 72 (3) ◽  
pp. 372-380 ◽  
Author(s):  
Somnath Dey ◽  
Andreas Schönleber ◽  
Swastik Mondal ◽  
Siriyara Jagannatha Prathapa ◽  
Sander van Smaalen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Hydrogen Bonds ◽  
Room Temperature ◽  
Structural Parameters ◽  
Molecular Packing ◽  
Nitrate Group ◽  
Structural Variations ◽  
Monoclinic Symmetry ◽  
Low Temperature Crystal Structure

Λ-Cobalt(III) sepulchrate trinitrate crystallizes inP6322 withZ= 2 (Z′ = 1/6) at room temperature. Slabs perpendicular to the hexagonal axis comprise molecules Co(sepulchrate) alternating with nitrate groupsAandB. Coordinated by six sepulchrate molecules, highly disordered nitrate groupsCare accommodated between the slabs. Here we report the fully ordered, low-temperature crystal structure of Co(sep)(NO3)3. It is found to be a high-Z′ structure withZ′ = 12 of the 12-fold 6a_{h}\times\sqrt{3}b_{h}\times c_{h} superstructure with monoclinic symmetryP21(cunique). Correlations between structural parameters are effectively removed by refinements within the superspace approach. Superstructure formation is governed by a densification of the packing in conjunction with ordering of nitrate groupC, the latter assuming different orientations for each of theZ′ = 12 independent copies in the superstructure. The Co(sep) moiety exhibits small structural variations over its 12 independent copies, while orientations of nitrate groupsAandBvary less than the orientations of the nitrate groupCdo. Molecular packing in the superstructure is found to be determined by short C—H...H—C contacts, with H...H distances of 2.2–2.3 Å, and by short C—H...O contacts, with H...O distances down to 2.2 Å. These contacts presumably represent weak C—H...O hydrogen bonds, but in any case they prevent further densification of the structure and strengthening of weak N—H...O hydrogen bonds with observed H...O distances of 2.4–2.6 Å.

scholarly journals Isostructural Inorganic–Organic Piperazine-1,4-diium Chlorido- and Bromidoantimonate(III) Monohydrates: Octahedral Distortions and Hydrogen Bonds

Molecules ◽  
2020 ◽  
Vol 25 (6) ◽  
pp. 1361
Author(s):  
Maciej Bujak ◽  
Dawid Siodłak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ligand Exchange ◽  
Structural Parameters ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Bond Interactions ◽  
Hybrid Crystals ◽  
Structural Database ◽  
Hydrogen Bonded Systems

Halogenidoantimonate(III) monohydrates of the (C4H12N2)[SbX5]·H2O (X = Cl, 1 or Br, 2) formula, crystallizing in the same monoclinic space group of P21/n, are isostructural, with an isostructurality index close to 99%. The single crystal X-ray diffraction data do not show any indication of phase transition in cooling these crystals from room temperature to 85 K. Both hybrid crystals are built up from [SbX6]3– octahedra that are joined together by a common edge forming isolated bioctahedral [Sb2X10]4– units, piperazine-1,4-diium (C4H12N2)2+ cations and water of crystallization molecules. These structural components are joined together by related but somewhat different O/N/C–H···X and N–H···O hydrogen bonded systems. The evolution of structural parameters, notably the secondary Sb–X bonds along with the associated X/Sb–Sb/X–X/Sb angles and O/N/C–H···X hydrogen bonds, as a function of ligand exchange and temperature, along with their influence on the irregularity of [SbX6]3– octahedra, was determined. The comparison of packing features and hydrogen bond parameters, additionally supported by the Hirshfeld surface analysis and data retrieved from the Cambridge Structural Database, demonstrates the hierarchy and importance of hydrogen bond interactions that influence the irregularity of single [SbX6]3– units.

Synthesis, Structure and Spectroscopy of a New Polyiodide in the α,ω-Diazaniumalkane Iodide/Iodine System

2012 ◽  
Vol 67 (5) ◽  
pp. 447-451 ◽  
Author(s):  
Guido J. Reiss ◽  
Martin van Megen
Keyword(s):  
Raman Spectroscopy ◽  
Hydrogen Bonds ◽  
Excellent Agreement ◽  
Title Compound ◽  
Structural Parameters ◽  
Three Dimensional ◽  
Monoclinic Space Group ◽  
Spectroscopic Methods ◽  
Trans Conformation ◽  
X Ray

The reaction of 1,4-diaminobutane with hydroiodic acid in the presence of iodine yields the title compound 1,4-diazaniumbutane tetraiodide, C4H14N2I4 (1). The title compound has been structurally characterized by crystallographic and spectroscopic methods (Raman and IR). 1is built up by centrosymmetric 1,4-diazaniumbutane cations in all-trans conformation and linear I42- anions. Both, cations and anions are located on centers of inversion (2/m) in the monoclinic space group C2/m. The hydrogen bonds between the azanium groups and the terminal iodine atoms of the I42- anions lead to a three-dimensional framework. The structural parameters of the tetraiodide anion, derived from X-ray crystallographic data are in excellent agreement with the results from Raman spectroscopy. The Raman and IR data for the analogous a,w-diazaniumalkane tetraiodide salts (H3N-(CH2)6-NH3)I4 (2) and (H3N-(CH2)7-NH3)I4 (3) are reported, and the structures of 1, 2and 3are compared.

scholarly journals Crystal structures and the Hirshfeld surface analysis of (E)-4-nitro-N′-(o-chloro, o- and p-methylbenzylidene)benzenesulfonohydrazides

2018 ◽  
Vol 74 (12) ◽  
pp. 1710-1716
Author(s):  
Akshatha R. Salian ◽  
Sabine Foro ◽  
B. Thimme Gowda
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Parameters ◽  
Three Dimensional ◽  
Monoclinic Crystal ◽  
Torsion Angles ◽  
Axis Direction ◽  
Hydrogen Bonding Interactions ◽  
Torsional Angles

The crystal structures of (E)-N′-(2-chlorobenzylidene)-4-nitrobenzenesulfonohydrazide, C13H10ClN3O4S (I), (E)-N′-(2-methylbenzylidene)-4-nitrobenzenesulfonohydrazide, C14H13N3O4S (II), and (E)-N′-(4-methylbenzylidene)-4-nitrobenzenesulfonohydrazide monohydrate, C14H13N3O4S·H2O (III), have been synthesized, characterized and their crystal structures determined to study the effects of the nature and sites of substitutions on the structural parameters and the hydrogen-bonding interactions. All three compounds crystallize in the monoclinic crystal system, with space group P21 for (I) and P21/c for (II) and (III). Compound (III) crystallizes as a monohydrate. All three compounds adopt an E configuration around the C=N bond. The molecules are bent at the S atom with C—S—N—N torsion angles of −59.0 (3), 58.0 (2) and −70.2 (1)° in (I), (II) and (III), respectively. The sulfonohydrazide parts are also non-linear, as is evident from the S—N—N—C torsional angles of 159.3 (3), −164.2 (1) and 152.3 (1)° in (I), (II) and (III), respectively, while the hydrazide parts are almost planar with the N—N=C—C torsion angles being −179.1 (3)° in (I), 176.7 (2)° in (II) and 175.0 (2)° in (III). The 4-nitro-substituted phenylsulfonyl and 2/4-substituted benzylidene rings are inclined to each other by 81.1 (1)° in (I), 81.4 (1)° in (II) and 74.4 (1)° in (III). The compounds show differences in hydrogen-bonding interactions. In the crystal of (I), molecules are linked via N—H...O hydrogen bonds, forming C(4) chains along the a-axis direction that are interconnected by weak C—H...O hydrogen bonds, generating layers parallel to the ac plane. In the crystal of (II), the amino H atom shows bifurcated N—H...O(O) hydrogen bonding with both O atoms of the nitro group generating C(9) chains along the b-axis direction. The chains are linked by weak C—H...O hydrogen bonds, forming a three-dimensional framework. In the crystal of (III), molecules are linked by Ow—H...O, N—H...Ow and C—H...O hydrogen bonds, forming layers lying parallel to the bc plane. The fingerprint plots generated for the three compounds show that for (I) and (II) the O...H/H...O contacts make the largest contributions, while for the para-substituted compound (III), H...H contacts are the major contributors to the Hirshfeld surfaces.

scholarly journals A Theoretical Study of Hydrogen-Bonded Complexes of Ethylene Glycol, Thioglycol and Dithioglycol with Water

2021 ◽  
Vol 34 (1) ◽  
pp. 169-182
Author(s):  
Ruchi Kohli ◽  
Rupinder Preet Kaur
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Ethylene Glycol ◽  
Structural Parameters ◽  
Intermolecular Hydrogen Bond ◽  
Basis Set ◽  
Interaction Energies ◽  
Orbital Theory ◽  
Hydrogen Bond Formation

In the present study, a theoretical analysis of hydrogen bond formation of ethylene glycol, thioglycol, dithioglycol with single water molecule has been performed based on structural parameters of optimized geometries, interaction energies, deformation energies, orbital analysis and charge transfer. ab initio molecular orbital theory (MP2) method in conjunction with 6-31+G* basis set has been employed. Twelve aggregates of the selected molecules with water have been optimized at MP2/6-31+G* level and analyzed for intramolecular and intermolecular hydrogen bond interactions. The evaluated interaction energies suggest aggregates have hydrogen bonds of weak to moderate strength. Although the aggregates are primarily stabilized by conventional hydrogen bond donors and acceptors, yet C-H···O, S-H···O, O-H···S, etc. untraditional hydrogen bonds also contribute to stabilize many aggregates. The hydrogen bonding involving sulfur in the aggregates of thioglycol and dithioglycol is disfavoured electrostatically but favoured by charge transfer. Natural bond orbital (NBO) analysis has been employed to understand the role of electron delocalizations, bond polarizations, charge transfer, etc. as contributors to stabilization energy.

scholarly journals Crystal structure and Hirshfeld surface analysis of (E)-N′-[4-(piperidin-1-yl)benzylidene]arylsulfonohydrazides

2018 ◽  
Vol 74 (12) ◽  
pp. 1826-1832
Author(s):  
Nikhila Pai ◽  
Sabine Foro ◽  
B. Thimme Gowda
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Structural Parameters ◽  
Hirshfeld Surface ◽  
Two Dimensional ◽  
Asymmetric Unit ◽  
Monoclinic Crystal ◽  
Space Groups ◽  
Unit Cells ◽  
Independent Molecules

The crystal structures and Hirshfeld surface analyses of three Schiff bases, namely (E)-N′-[4-(piperidin-1-yl)benzylidene]benzenesulfonohydrazide, C18H21N3O2S, (I), (E)-4-methyl-N′-[4-(piperidin-1-yl)benzylidene]benzenesulfonohydrazide, C19H23N3O2S, (II), and (E)-4-chloro-N′-[4-(piperidin-1-yl)benzylidene]benzenesulfonohydrazide, C18H20ClN3O2S, (III), derived from arylsulfonohydrazides and 4-(piperidin-4-yl)benzaldehyde have been analysed to investigate the effect of substituents on the structural parameters. All three structures crystallize in monoclinic crystal systems, in the space groups P21/c for (I) and (II), and C2/c for (III). Compound (III) contains two independent molecules in the asymmetric unit and sixteen molecules per unit cell, while (I) and (II) both have one and four molecules, respectively, in their asymmetric units and unit cells. In all cases, the central part of the molecule is twisted at the S atom. In the crystals, the molecules are linked via N—H...O hydrogen bonds, forming chains. Two-dimensional fingerprint plots of various interatomic contacts show that the major contributions are from H...H interactions.

A THEORETICAL STUDY ABOUT THE ELECTRONIC COOPERATIVE EFFECT ON HYDROCYANIDE CHAINS USING DFT CALCULATIONS AND AIM TOPOLOGICAL PARAMETERS

2008 ◽  
Vol 07 (02) ◽  
pp. 247-256 ◽  
Author(s):  
BOAZ GALDINO DE OLIVEIRA ◽  
REGIANE DE CÁSSIA MARITAN UGULINO DE ARAÚJO ◽  
VERNECK MAIA SOARES ◽  
MOZART NEVES RAMOS
Keyword(s):  
Hydrogen Bonds ◽  
Theoretical Study ◽  
Structural Parameters ◽  
Cooperative Effect ◽  
Topological Properties ◽  
Electronic Density ◽  
Topological Parameters ◽  
Electronic Densities ◽  
Atoms In Molecules Theory ◽  
Excessive Number

A theoretical investigation about the cooperative effect on ( HCN )n homo and ( HCN )n ⋯ HF heterochains was performed in terms of structural parameters and topological properties obtained in concordance with the protocol of Bader's atoms in molecules theory. Initially, the hydrogen bonding distances, electronic densities, and Laplacian descriptors were used to characterize small ( HCN )n and ( HCN )n ⋯ HF chains formed by n = 2–4 units of HCN . Hydrogen bond distances and distribution of charge density have revealed that the cooperative effect on ( HCN )n ⋯ HF heterochains is ruled by the polarity of the extreme hydrofluoric acid species. Furthermore, we investigated larger homo and heterochain systems formed by n = 2–8 molecules of HCN . In this insight, the drastic polarized effect caused by HF molecule which was considered very substantial at prior, in fact is seriously limited by an excessive number of HCN molecules connected to the heterochain. This leads to a stabilization of the ( N ⋯ HF ) hydrogen bonds with invariable electronic density in the range of [Formula: see text]. In this stage and henceforth, the cooperative effect is re-established with n = 4 molecules of HCN . Thereby, the electronic density of the hydrogen bonds become unaltered within the ( HCN )n ⋯ HF heterochains.

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