The CH/π Hydrogen Bond: An Important Molecular Force in Controlling the Crystal Conformation of Organic Compounds and Three-Dimensional Structure of Biopolymers

2006 ◽  
pp. 255-302 ◽  
Author(s):  
Motohiro Nishio ◽  
Yoji Umezawa
Keyword(s):  
Hydrogen Bond ◽  
Organic Compounds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Molecular Force

scholarly journals 4-(Pyrimidin-2-yl)piperazin-1-ium (E)-3-carboxyprop-2-enoate

2014 ◽  
Vol 70 (6) ◽  
pp. o702-o703 ◽  
Author(s):  
Thammarse S. Yamuna ◽  
Manpreet Kaur ◽  
Jerry P. Jasinski ◽  
H. S. Yathirajan
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Intermolecular Hydrogen Bond ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Axis Direction ◽  
Π Interactions ◽  
Centroid Distance

In the cation of the title salt, C8H13N4+·C4H3O4−, the piperazinium ring adopts a slightly distorteded chair conformation. In the crystal, a single strong O—H...O intermolecular hydrogen bond links the anions, forming chains along thec-axis direction. The chains of anions are linked by the cations,viaN—H...O hydrogen bonds, forming sheets parallel to (100). These layers are linked by weak C—H...O hydrogen bonds, forming a three-dimensional structure. In addition, there are weak π–π interactions [centroid–centroid distance = 3.820 (9) Å] present involving inversion-related pyrimidine rings.

scholarly journals 3,4-Difluoro-2-hydroxybenzoic acid

2014 ◽  
Vol 70 (5) ◽  
pp. o519-o519 ◽  
Author(s):  
Bhaskarachar Ravi Kiran ◽  
Bandrehalli Siddagangaiah Palakshamurthy ◽  
Giriyapura R. Vijayakumar ◽  
Hebbur Shivamurthy Bharath
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Hydroxybenzoic Acid ◽  
Stacking Interactions ◽  
Three Dimensional Structure ◽  
Compound C ◽  
Centroid Distance

In the title compound, C7H4F2O3, an intramolecular O—H...O hydrogen bond is observed. In the crystal, inversion dimers linked by pairs of O—H...O hydrogen bonds generateR22(8) ring motifs. These dimers are linked by C—H...O and C—H...F hydrogen bonds, forming sheets lying parallel to (30-1). The sheets are linked by aromatic π–π stacking interactions [inter-centroid distance = 3.7817 (9) Å], forming a three-dimensional structure.

scholarly journals Syntheses and crystal structures of a new pyrazine dicarboxamide ligand, N 2,N 3-bis(quinolin-8-yl)pyrazine-2,3-dicarboxamide, and of a copper perchlorate binuclear complex

2020 ◽  
Vol 76 (3) ◽  
pp. 332-338
Author(s):  
Dilovan S. Cati ◽  
Helen Stoeckli-Evans
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Copper Atom ◽  
Binuclear Complex ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Pyramidal Geometry ◽  
Difference Fourier ◽  
Square Pyramidal Geometry

The title pyrazine dicarboxamide ligand, N 2,N 3-bis(quinolin-8-yl)pyrazine-2,3-dicarboxamide (H2L1), C24H16N6O2, has a twisted conformation with the outer quinoline groups being inclined to the central pyrazine ring by 9.00 (6) and 78.67 (5)°, and by 79.94 (4)° to each other. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming layers parallel to the (10\overline{1}) plane, which are in turn linked by offset π–π interactions [intercentroid distances 3.4779 (9) and 3.6526 (8) Å], forming a supramolecular three-dimensional structure. Reaction of the ligand H2L1 with Cu(ClO4)2 in acetonitrile leads to the formation of the binuclear complex, [μ-(3-{hydroxy[(quinolin-8-yl)imino]methyl}pyrazin-2-yl)[(quinolin-8-yl)imino]methanolato]bis[diacetonitrilecopper(II)] tris(perchlorate) acetonitrile disolvate, [Cu2(C24H15N6O2)(CH3CN)4](ClO4)3·2CH3CN or [Cu2(HL1−)(CH3CN)4](ClO4)3·2CH3CN (I). In the cation of complex I, the ligand coordinates to the copper(II) atoms in a bis-tridentate fashion. A resonance-assisted O—H...O hydrogen bond is present in the ligand; the position of this H atom was located in a difference-Fourier map. Both copper(II) atoms are fivefold coordinate, being ligated by three N atoms of the ligand and by the N atoms of two acetonitrile molecules. The first copper atom has a perfect square-pyramidal geometry while the second copper atom has a distorted shape. In the crystal, the cation and perchlorate anions are linked by a number of C—H...O hydrogen bonds, forming a supramolecular three-dimensional structure.

scholarly journals Reinvestigation of the crystal structure ofN-(4-chlorobenzylidene)-2-hydroxyaniline: a three-dimensional structure containing O—H...N, O—H...O and C—H...π(arene) hydrogen bonds

2018 ◽  
Vol 74 (3) ◽  
pp. 376-379 ◽  
Author(s):  
Marisiddaiah Girisha ◽  
Hemmige S. Yathirajan ◽  
Ravindranath S. Rathore ◽  
Christopher Glidewell
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Compound C ◽  
Related Compounds

The molecule of the title compound, C13H10ClNO, (I), which contains an intramolecular O—H...N hydrogen bond, is almost planar: the dihedral angle between the two aryl rings is only 3.31 (9)°. The molecules of (I) are linked into sheets by two C—H...π(arene) hydrogen bonds and the sheets are linked into a three-dimensional structure by O—H...O hydrogen bonds. Comparisons are made with the structures of a number of related compounds.

scholarly journals MOLTRA-II. New three dimensional descriptors of the hydrogen bond

2018 ◽  
Vol 1 (3) ◽  
pp. e00069 ◽  
Author(s):  
S.V. Trepalin ◽  
A.V. Yarkov ◽  
O.A. Raevsky
Keyword(s):  
Hydrogen Bond ◽  
Surface Area ◽  
Management System ◽  
Three Dimensional ◽  
Optimal Structure ◽  
Dimensional Structure ◽  
Chemical Databases ◽  
Polar Surface Area ◽  
Polar Surface ◽  
Three Dimensional Structure

The program MOLTRA-II, created on the basis of the CHEmical Databases management system CHED, is supplemented by the possibility of calculating new descriptors based on the three-dimensional structure and hydrogen bond parameters. The program calculates PSA descriptors (Polar Surface Area), OSA (Optimal Structure Area) and energy of the hydrogen bond.

The 1:1 adduct of triphenylsilanol and 4,4′-bipyridyl, and three pairwise-concomitant triclinic polymorphs of the 4:1 adduct having Z′ = 0.5, 1 and 4

2003 ◽  
Vol 59 (2) ◽  
pp. 277-286 ◽  
Author(s):  
Katharine F. Bowes ◽  
George Ferguson ◽  
Alan J. Lough ◽  
Christopher Glidewell
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Methanol Solution ◽  
Dimensional Structure ◽  
Triclinic Space Group ◽  
Space Group ◽  
Three Dimensional Structure ◽  
Phenyl Rings ◽  
Hydrogen Bonded

Crystallization from methanol solution of mixtures of triphenylsilanol and 4,4′-bipyridyl has given a 1:1 adduct (I), Ph3SiOH·C10H8N2, and three polymorphic 4:1 adducts (II)–(IV), (Ph3SiOH)4·C10H8N2. In (I), the components are linked by a single O—H...N hydrogen bond and by a number of C—H...π(arene) hydrogen bonds to form a continuous three-dimensional structure. Compounds (II)–(IV) are all triclinic, space group P\bar 1, with Z′ values of 0.5, 1 and 4, respectively. The basic hydrogen-bonded aggregate is the same in each of (II)–(IV), having a pair of silanol molecules linked to the bipyridyl via O—N...N hydrogen bonds and a further pair of silanol molecules linked to the first pair via O—H...O hydrogen bonds. In (II) there is just one such aggregate lying across a centre of inversion (Z′ = 0.5) and in (III) there are two such aggregates, both lying across centres of inversion (Z′ = 2 × 0.5 = 1). In (IV) there are six independent aggregates of this type, four of which lie across centres of inversion and two of which lie in general positions, so that Z′ = (4 × 0.5) + 2 = 4. While the components in (I) are fully ordered, each of (II)–(IV) exhibits extensive disorder involving both the bipyridyl units and the phenyl rings of the silanol components.

scholarly journals The crystal structure of a new ferrocenyl P,N ligand: 1-[(2,2-dimethylhydrazin-1-ylidene)methyl]-1′-(diphenylphosphorothioyl)ferrocene

2018 ◽  
Vol 74 (2) ◽  
pp. 133-136
Author(s):  
Toma Nardjes Mouas ◽  
Jean-Claude Daran ◽  
Hocine Merazig ◽  
Eric Manoury
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Asymmetric Unit ◽  
Three Dimensional Structure ◽  
Π Interactions ◽  
Independent Molecules

The asymmetric unit of the title compound, [Fe(C8H11N2)(C17H14PS)], contains two independent molecules (A and B) with very similar conformations. Each molecule is built up from a ferrocene unit substituted in the 1 and 1′ positions by a protected sulfur diphenylphosphine and by a dimethylhydrazine, –C(H)=N—N(CH3)2, fragment. The two independent molecules are linked by a C—H...N hydrogen bond. In the crystal, the A–B dimer is linked by a pair of C—H...S hydrogen bonds, forming a centrosymmetric four-molecule arrangement. These units are linked by C—H...π interactions, forming a supramolecular three-dimensional structure.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

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