scholarly journals The Effect of Deoxyfluorination on Intermolecular Interactions in the Crystal Structures of 1,6-Anhydro-2,3-epimino-hexopyranoses

Molecules ◽  
2022 ◽  
Vol 27 (1) ◽  
pp. 278
Author(s):  
Martin Jakubec ◽  
Ivana Císařová ◽  
Jindřich Karban ◽  
Jan Sýkora
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Hydroxy Group ◽  
Single Molecule ◽  
Electrostatic Interactions ◽  
Fluorine Atom ◽  
Weak Interactions ◽  
Qualitative Evaluation ◽  
Hydrogen Atoms

The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-Fax and C4-Feq epimines presented here.

Directional Weak Intermolecular Interactions: σ-Hole Bonding

2010 ◽  
Vol 63 (12) ◽  
pp. 1598 ◽  
Author(s):  
Jane S. Murray ◽  
Kevin E. Riley ◽  
Peter Politzer ◽  
Timothy Clark
Keyword(s):  
Hydrogen Bonding ◽  
Intermolecular Interactions ◽  
Electrostatic Potential ◽  
Crystal Engineering ◽  
Molecular Electrostatic Potential ◽  
Weak Interactions ◽  
Halogen Bonding ◽  
Donor Atom ◽  
Weak Intermolecular Interactions ◽  
Special Case

The prototypical directional weak interactions, hydrogen bonding and σ-hole bonding (including the special case of halogen bonding) are reviewed in a united picture that depends on the anisotropic nature of the molecular electrostatic potential around the donor atom. Qualitative descriptions of the effects that lead to these anisotropic distributions are given and examples of the importance of σ-hole bonding in crystal engineering and biological systems are discussed.

Structural and Spectral Studies of 2-Pyridineformamide Thiosemicarbazone and its Complexes Prepared with Zinc Halides

2000 ◽  
Vol 55 (6) ◽  
pp. 511-518 ◽  
Author(s):  
Alfonso Castiñeiras ◽  
Isabel Garcia ◽  
Elena Bermejo ◽  
Douglas X. West
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Trigonal Bipyramid ◽  
Spectral Studies ◽  
Hydrogen Atoms ◽  
Pyridyl Nitrogen ◽  
Imine Nitrogen

Reduction of 2-cyanopyridine by sodium in dry methanol in presence of thiosemicarbazide produces 2-pyridineformamide thiosemicarbazone, HAm4DH. The crystal structure of HAm4DH, which has a number of intermolecular interactions involving its five NH hydrogen atoms, has been solved. Crystal structures of the complexes prepared by reaction of HAm4DH with zinc(II) chloride, bromide and iodide have also been obtained. Neutral HAm4DH is coordinated via the pyridyl nitrogen, imine nitrogen and thione sulfur atoms, and each complex is five-coordinate with two halogen ligands. The structures of the three complexes are best described as square pyramidal with [Zn(HAm4DH)l2] having the largest distortion toward a trigonal bipyramid.

Different supramolecular architectures mediated by different weak interactions in the crystals of three N-aryl-2,5-dimethoxybenzenesulfonamides

2017 ◽  
Vol 73 (10) ◽  
pp. 833-844 ◽  
Author(s):  
K. Shakuntala ◽  
S. Naveen ◽  
N. K. Lokanath ◽  
P. A. Suchetan ◽  
M. Abdoh
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Shape Index ◽  
Intramolecular Interactions ◽  
Molecular Conformations ◽  
Supramolecular Architectures ◽  
The Relationship

The synthesis and evaluation of the pharmacological activities of molecules containing the sulfonamide moiety have attracted interest as these compounds are important pharmacophores. The crystal structures of three closely related N-aryl-2,5-dimethoxybenzenesulfonamides, namely N-(2,3-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (I), N-(2,4-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (II), and N-(2,4-dimethylphenyl)-2,5-dimethoxybenzenesulfonamide, C16H19NO4S, (III), are described. The asymmetric unit of (I) consists of two symmetry-independent molecules, while those of (II) and (III) contain one molecule each. The molecular conformations are stabilized by different intramolecular interactions, viz. C—H...O interactions in (I), N—H...Cl and C—H...O interactions in (II), and C—H...O interactions in (III). The crystals of the three compounds display different supramolecular architectures built by various weak intermolecular interactions of the types C—H...O, C—H...Cl, C—H...π(aryl), π(aryl)–π(aryl) and Cl...Cl. A detailed Hirshfeld surface analysis of these compounds has also been conducted in order to understand the relationship between the crystal structures. The d norm and shape-index surfaces of (I)–(III) support the presence of various intermolecular interactions in the three structures. Analysis of the fingerprint plots reveals that the greatest contribution to the Hirshfeld surfaces is from H...H contacts, followed by H...O/O...H contacts. In addition, comparisons are made with the structures of some related compounds. Putative N—H...O hydrogen bonds are observed in 29 of the 30 reported structures, wherein the N—H...O hydrogen bonds form either C(4) chain motifs or R 2 2(8) rings. Further comparison reveals that the characteristics of the N—H...O hydrogen-bond motifs, the presence of other interactions and the resultant supramolecular architecture is largely decided by the position of the substituents on the benzenesulfonyl ring, with the nature and position of the substituents on the aniline ring exerting little effect. On the other hand, the crystal structures of (I)–(III) display several weak interactions other than the common N—H...O hydrogen bonds, resulting in supramolecular architectures varying from one- to three-dimensional depending on the nature and position of the substituents on the aniline ring.

Supramolecular networks of 10-(2-hydroxyethyl)acridin-9(10H)-one and 10-(2-chloroethyl)acridin-9(10H)-one

2013 ◽  
Vol 69 (3) ◽  
pp. 289-292
Author(s):  
Chang-Shuai He ◽  
Lu-Fang Liu ◽  
Lei Guo ◽  
Jian-Zhong Wu
Keyword(s):  
Hydrogen Bonding ◽  
Melting Point ◽  
Intermolecular Interactions ◽  
Hydroxy Group ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Π Stacking ◽  
Chlorine Substituent ◽  
Supramolecular Networks

Both 10-(2-hydroxyethyl)acridin-9(10H)-one, C15H13NO2, and 10-(2-chloroethyl)acridin-9(10H)-one, C15H12ClNO, have monoclinic (P21/c) symmetry and supramolecular three-dimensional networks. But the differences in the intermolecular interactions displayed by the hydroxy group and the chlorine substituent lead to stronger intermolecular π-stacking interactions and hydrogen bonding, and hence a significantly higher melting point for the former.

Diphenyl(2-hydroxy-phenyl)phosphine and its Trimethylsilyl Ether as Ligands for Gold(I) Complexes

1999 ◽  
Vol 54 (1) ◽  
pp. 30-37 ◽  
Author(s):  
Christian Hollatz ◽  
Annette Schier ◽  
Hubert Schmidbaur
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Spectroscopic Data ◽  
Trimethylsilyl Ether ◽  
Chloro Complex

Diphenyl(2-hydroxy-phenyl)phosphine was introduced as a ligand for gold(I) halides and pentafluorophenyl gold(I) in order to probe the interplay of intra- and intermolecular interactions based on aurophilic (Au· · ·Au) and hydrogen bonding. 1:1 complexes of the type Ph2(2-HO-C6H4)P-Au-X with X = Cl, Br, C6F5 have been prepared and characterized by analytical and spectroscopic data. The crystal structure of the chloro complex (1) has been determined. In the lattice the molecules form dimers through O-H· · ·Cl hydrogen bonds. Au· · ·Au contacts are ruled out by steric congestion. Reaction of 1 with triethylamine yields a 1:1 adduct with O-H· · ·NEt3 hydrogen bonding. The trimethylsilyl ether of the title ligand also forms 1:1 complexes with AuCl, AuBr, Aul, and AuC6F5. The crystal structures of the chloro (5) and iodo (7) compound have been determined. In both cases the lattices are built from monomers which show only minor differences in their conformations. The silylether groups are not acting as intra- or intermolecular donor functions to the gold atoms.

Comparison of hydrogen bonds and diverse weak interactions of the nitro group in 2-methyl-4-nitroanilinium nitrate, bisulfate and two hexafluoridosilicates: elementary graph-set approach

2016 ◽  
Vol 72 (6) ◽  
pp. 916-926 ◽  
Author(s):  
Marek Daszkiewicz ◽  
Agnieszka Mielcarek
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Nitro Group ◽  
Weak Interactions ◽  
Gradual Expansion ◽  
Graph Set ◽  
Mathematical Relations ◽  
Elementary Graph ◽  
Bonding Patterns

Crystal structures of (H2m4na)NO3(1), (H2m4na)HSO4(2), (H2m4na)2SiF6(3) and (H2m4na)2SiF6·2H2O (4), where 2m4na = 2-methyl-4-nitroaniline, are presented. Two layers of interactions occur in the structures, N—H...O/F hydrogen bonds and interactions with the nitro group. Although diverse, hydrogen-bonding patterns are compared with each other by means of interrelations among elementary graph-set descriptors and descriptors of hydrogen-bonding patterns. Using mathematical relations, the gradual expansion of the ring patterns was shown in the crystal structures. Parallel and perpendicular arranged nitro groups form weak π(N)NO2...π(O)NO2and π(N)NO2...ONO2interactions, respectively. The πNO2...πringinteraction has an impact to the stabilization of parallel oriented nitro groups. Generally, weak interactions constructed by the nitro group occur in the studied crystals as follows: π(N)NO2...π(O)NO2, πring...πring, C—H...O (1); π(N)NO2...π(O)NO2, π(N)NO2...ONO2(2); π(N)NO2...π(O)NO2, π(N)NO2...ONO2(3); C—H...O (4).

scholarly journals Crystal structures offac-tricarbonylchlorido(6,6′-dihydroxy-2,2′-bipyridine)rhenium(I) tetrahydrofuran monosolvate andfac-bromidotricarbonyl(6,6′-dihydroxy-2,2′-bipyridine)manganese(I) tetrahydrofuran monosolvate

2016 ◽  
Vol 72 (8) ◽  
pp. 1201-1205
Author(s):  
Sheri Lense ◽  
Nicholas A. Piro ◽  
Scott W. Kassel ◽  
Andrew Wildish ◽  
Brent Jeffery
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Hydroxy Group ◽  
Metal Ion ◽  
Solvent Molecule ◽  
Intramolecular Hydrogen Bonding ◽  
Distorted Octahedral Geometry ◽  
Halide Ligand ◽  
Bipyridine Ligand ◽  
Intramolecular Hydrogen

The structures of two facially coordinated Group VII metal complexes,fac-[ReCl(C10H8N2O2)(CO)3]·C4H8O (I·THF) andfac-[MnBr(C10H8N2O2)(CO)3]·C4H8O (II·THF), are reported. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ligand, and a 6,6′-dihydroxy-2,2′-bipyridine ligand in a distorted octahedral geometry. Both complexes co-crystallize with a non-coordinating tetrahydrofuran (THF) solvent molecule and exhibit intermolecular but not intramolecular hydrogen bonding. In both crystal structures, chains of complexes are formed due to intermolecular hydrogen bonding between a hydroxy group from the 6,6′-dihydroxy-2,2′-bipyridine ligand and the halide ligand from a neighboring complex. The THF molecule is hydrogen bonded to the remaining hydroxy group.

scholarly journals Two polymorphs oftrans-[3-(3-nitrophenyl)oxiran-2-yl](phenyl)methanone

2016 ◽  
Vol 72 (7) ◽  
pp. 1054-1059
Author(s):  
Fred H. Greenberg ◽  
Alexander Y. Nazarenko
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Title Compound ◽  
Compound C ◽  
Polymorphic Forms

The title compound, C15H11NO4, crystallizes in two polymorphic forms, centrosymmetric monoclinic and chiral orthorhombic. The geometry of the molecules in the two polymorphs is slightly different, possibly due to intermolecular interactions. There are no classical hydrogen bonding in these two structures. However, a number of C—H...O intermolecular interactions, involving both O atoms of the nitro as well the benzoyl groups, stabilize the crystal structures.

Two-dimensional condensation of nucleobases: A comparative study of halogen derivatives of cytosine

2009 ◽  
Vol 74 (11-12) ◽  
pp. 1611-1622 ◽  
Author(s):  
Lukáš Fojt ◽  
Vladimír Vetterl ◽  
Thomas Doneux
Keyword(s):  
Hydrogen Bonding ◽  
Intermolecular Interactions ◽  
Electrostatic Interactions ◽  
Dispersion Forces ◽  
Two Dimensional ◽  
Electrode Surfaces ◽  
Different Types ◽  
Self Association ◽  
Derivatives Of ◽  
Third Derivative

The high ability of self-association of nucleic acid components leads to a two-dimensional (2D) condensation at electrode surfaces. The driving force of the process resides in the intermolecular interactions, such as dispersion forces, hydrogen bonding or electrostatic interactions. In this study, the condensation of 5-halogen cytosine derivatives (5-fluorocytosine, 5-bromocytosine and 5-iodocytosine) at the hanging mercury drop electrode was investigated to evaluate the influence of the different types of intermolecular interactions in the phenomenon. All of these derivatives form 2D capacitance pits, but in distinct conditions of pH, concentrations and temperature. Dispersion forces are identified as the main contributor to the 2D condensation of 5-iodocytosine, while for 5-fluorocytosine this is hydrogen bonding in hemiprotonated dimers. The third derivative, 5-bromocytosine, is an intermediate case between the two formers.

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