Investigation of intermolecular hydrogen bond interactions in crystalline l-Cysteine by DFT calculations of the oxygen-17, nitrogen-14, and hydrogen-2 EFG tensors and AIM analysis

2009 ◽  
Vol 141 (1) ◽  
pp. 49-58 ◽  
Author(s):  
Ahmad G. Nozad ◽  
Sakineh Meftah ◽  
Mohammad H. Ghasemi ◽  
Roya A. Kiyani ◽  
Mustafa Aghazadeh
Keyword(s):  
Hydrogen Bond ◽  
Dft Calculations ◽  
Intermolecular Hydrogen Bond ◽  
Aim Analysis ◽  
Hydrogen Bond Interactions

Di-μ-2-sulfonatobenzoato-bis[aqua(1,10-phenanthroline)copper(II)] trihydrate

2006 ◽  
Vol 62 (4) ◽  
pp. m875-m877
Author(s):  
Wei-Bing Zhang ◽  
Shuang-Di Ruan ◽  
Shu-Juan Zhu ◽  
Hong-Ping Xiao ◽  
Sai-Ya Ye
Keyword(s):  
Hydrogen Bond ◽  
Network Structure ◽  
Title Compound ◽  
Intermolecular Hydrogen Bond ◽  
Two Dimensional ◽  
Bridging Ligands ◽  
Pyramidal Geometry ◽  
Hydrogen Bond Interactions ◽  
Dimensional Network ◽  
Square Pyramidal Geometry

In the title compound, [Cu2(C7H4O5S)2(C12H8N2)2(H2O)2]·3H2O, each copper(II) atom is coordinated by two N atoms from one 1,10-phenanthroline molecule, two carboxylate O atoms from two 2-sulfonatobenzoato dianions and one aqua O atom in a distorted square pyramidal geometry. The 2-sulfonatobenzoato dianions function as μ2-bridging ligands in the formation of a dinuclear complex. Intermolecular hydrogen-bond interactions link the dinuclear units into a two-dimensional network structure.

Synthesis of ReItricarbonyl complexes with various sulfur- and oxygen-donating ligands: crystal structures of two ReIdinuclear structures bridged by S atoms

2018 ◽  
Vol 74 (10) ◽  
pp. 1116-1122
Author(s):  
Pheello I. Nkoe ◽  
Hendrik G. Visser ◽  
Chantel Swart ◽  
Alice Brink ◽  
Marietjie Schutte-Smith
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Synthesis And Characterization ◽  
X Ray Diffraction ◽  
Metal Centre ◽  
Pyridine Ligand ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Mononuclear Complexes

The synthesis and characterization of two dinuclear complexes, namelyfac-hexacarbonyl-1κ3C,2κ3C-(pyridine-1κN)[μ-2,2′-sulfanediyldi(ethanethiolato)-1κ2S1,S3:2κ3S1,S2,S3]dirhenium(I), [Re2(C4H8S3)(C5H5N)(CO)6], (1), and tetraethylammoniumfac-tris(μ-2-methoxybenzenethiolato-κ2S:S)bis[tricarbonylrhenium(I)], (C8H20N)[Re2(C7H7OS)3(CO)6], (2), together with two mononuclear complexes, namely (2,2′-bithiophene-5-carboxylic acid-κ2S,S′)bromidotricarbonylrhenium(I), (3), and bromidotricarbonyl(methyl benzo[b]thiophene-2-carboxylate-κ2O,S)rhenium(I), (4), are reported. Crystals of (1) and (2) were characterized by X-ray diffraction. The crystal structure of (1) revealed two Re—S—Re bridges. The thioether S atom only bonds to one of the ReImetal centres, while the geometry of the second ReImetal centre is completed by a pyridine ligand. The structure of (2) is characterized by three S-atom bridges and an Re...Re nonbonding distance of 3.4879 (5) Å, which is shorter than the distance found for (1) [3.7996 (6)/3.7963 (6) Å], but still clearly a nonbonding distance. Complex (1) is stabilized by six intermolecular hydrogen-bond interactions and an O...O interaction, while (2) is stabilized by two intermolecular hydrogen-bond interactions and two O...π interactions.

Intermolecular hydrogen bond interactions in N-carboxymethyl chitosan and nH2O: DFT and NBO studies

2020 ◽  
Author(s):  
Beti Safitri ◽  
Dwi Hudiyanti ◽  
Marlyn Dian Laksitorini ◽  
Nurwarrohman Andre Sasongko ◽  
Parsaoran Siahaan
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Carboxymethyl Chitosan ◽  
Hydrogen Bond Interactions

scholarly journals Interactions of Aggregating Peptides Probed by IR-UV Action Spectroscopy

2018 ◽  
Author(s):  
Sjors Bakels ◽  
E.M. Meijer ◽  
Mart Greuell ◽  
Sebastiaan Porskamp ◽  
George Rouwhorst ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Self Assembly ◽  
Intermolecular Hydrogen Bond ◽  
Beta Sheet ◽  
Dispersion Interactions ◽  
Intramolecular Hydrogen Bonds ◽  
Action Spectroscopy ◽  
Hydrogen Bond Interactions ◽  
Intramolecular Hydrogen

Peptide aggregation, the self-assembly of peptides into structured beta-sheet fibril structures, is driven by a combination of intra- and intermolecular interactions. Here, the interplay between intramolecular and formed inter-sheet hydrogen bonds and the effect of dispersion interactions on the formation of neutral, isolated, peptide dimers is studied by infrared action spectroscopy. Therefore, four different homo- and hetereogeneous dimers formed from three different alanine-based model peptides have been studied under controlled and isolated conditions. The peptides differ from one another in the presence and location of a UV chromophore containing cap on either the C- or N-terminus. Conformations of the monomers of the peptides direct the final dimer structure: strongly hydrogen bonded or folded structures result in weakly bound dimers. Here the intramolecular hydrogen bonds are favored over new intermolecular hydrogen bond interactions. In contrast, linearly folded monomers are the ideal template to form parallel beta-sheet type structures. The weak intramolecular hydrogen bonds present in the linear monomers are replaced by the stronger inter-sheet hydrogen bond interactions. The influence of π-π disperion interactions on the structure of the dimer is minimal, the phenyl rings have the tendency to fold away from the peptide backbone to favour intermolecular hydrogen bond interactions. Quantum chemical calculations confirm our experimental observations.

scholarly journals New Insights Into the Structure of Hydroxylated and Alkylated Glycols: A Comparative X-ray Diffraction, Raman and Molecular Dynamics Study of Ethane-1,2-Diol, 2-Methoxyethan-1-ol and 1,2-Dimethoxy Ethane

2020 ◽  
Author(s):  
Lorenzo Gontrani ◽  
Pietro Tagliatesta ◽  
Antonio Agresti ◽  
Sara Pescetelli ◽  
Marilena Carbone
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Room Temperature ◽  
Intermolecular Hydrogen Bond ◽  
Hydroxyl Groups ◽  
Gauche Conformation ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Diffraction Patterns ◽  
Intramolecular Hydrogen

In this study, we report a detailed experimental and theoretical investigation of three glycols, namely ethane-1,2-diol, 2-methoxyethan-1-ol and 1,2-dimethoxy ethane. For the first time, the X-Ray spectra of the latter two liquids was measured at room temperature, and they were compared with the newly measured spectrum of ethane-1,2-diol. The experimental diffraction patterns were interpreted very satisfactorily with molecular dynamics calculations, and suggest that in liquid ethane-1,2-diol most molecules are found in gauche conformation, with intramolecular hydrogen bond between the two hydroxyl groups. Intramolecular H-bonds are established in the mono-alkylated diol, but the interaction is weaker. The EDXD study also evidences strong intermolecular hydrogen-bond interactions, with short O···O correlations in both systems, while longer methyl-methyl interactions are found in 1,2-dimethoxy ethane. X-Ray studies are complemented by micro Raman investigations at room temperature and at 80°C, that confirm the conformational analysis predicted by X-Ray experiments and simulations.

Bis(2-nitrophenyl) selenide, bis(2-aminophenyl) selenide and bis(2-aminophenyl) telluride: structural and theoretical analysis

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Raju Saravanan ◽  
Harkesh B. Singh ◽  
Ray J. Butcher
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Weak Interactions ◽  
Intermolecular Hydrogen Bond ◽  
Three Dimensional ◽  
Molecular Structures ◽  
Aim Analysis ◽  
Hydrogen Bond Interaction ◽  
Dimensional Array ◽  
Pyramidal Geometry

Three organoselenium and organotellurium compounds containing ortho substitutents, namely, bis(2-nitrophenyl) selenide, C12H8N2O4Se, 2, bis(2-aminophenyl) selenide, C12H12N2Se, 3, and bis(2-aminophenyl) telluride, C12H12N2Te, 7, have been investigated by both structural and theoretical methods. In the structures of all three compounds, there are intramolecular contacts between both Se and Te with the ortho substituents. In the case of 2, this is achieved by rotation of the nitro group from the arene plane. For 3, both amino groups exhibit pyramidal geometry and are involved in intramolecular N—H...Se interactions, with one also participating in intermolecular N—H...N hydrogen bonding. While 3 and 7 are structurally similar, there are some significant differences. In addition to both intramolecular N—H...Te interactions and intermolecular N—H...N hydrogen bonding, 7 also exhibits intramolecular N—H...N hydrogen bonding. In the packing of these molecules, for 2, there are weak intermolecular C—H...O contacts and these, along with the O...N interactions mentioned above, link the molecules into a three-dimensional array. For 3, in addition to the N—H...N and N—H...Se interactions, there are also weak intermolecular C—H...Se interactions, which also link the molecules into a three-dimensional array. On the other hand, 7 shows intermolecular N—H...N interactions linking the molecules into R 2 2(16) centrosymmetric dimers. In the theoretical studies, for compound 2, AIM (atoms in molecules) analysis revealed critical points in the Se...O interactions with values of 0.017 and 0.026 a.u. These values are suggestive of weak interactions present between Se and O atoms. For 3 and 7, the molecular structures displayed intramolecular, as well as intermolecular, hydrogen-bond interactions of the N—H...N type. The strength of this hydrogen-bond interaction was calculated by AIM analysis. Here, the intermolecular (N—H...N) hydrogen bond is stronger than the intramolecular hydrogen bond. This was confirmed by the electron densities for 3 and 7 [ρ(r) = 0.015 and 0.011, respectively].

(4-Pyridyl)methyl N-phenylthiocarbamate

2006 ◽  
Vol 62 (7) ◽  
pp. o2852-o2853 ◽  
Author(s):  
Hai-Lian Xiao ◽  
Ke-Fei Wang ◽  
Fang-Fang Jian
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bond ◽  
Title Compound ◽  
Intermolecular Hydrogen Bond ◽  
Phenyl Isothiocyanate ◽  
Dioxane Solution ◽  
Asymmetric Unit ◽  
Hydrogen Bond Interactions ◽  
Compound C ◽  
Independent Molecules

The title compound, C13H12N2OS, was prepared by the reaction of (4-pyridyl)methanol with phenyl isothiocyanate and NaOH in a 1,4-dioxane solution. The asymmetric unit contains two independent molecules. The molecular structure and packing are stabilized by N—H...N intermolecular hydrogen-bond interactions and C—H...π interactions.

scholarly journals Chloropentaphenyldisiloxane—Model Study on Intermolecular Interactions in the Crystal Structure of a Monofunctionalized Disiloxane

Chemistry ◽  
2021 ◽  
Vol 3 (2) ◽  
pp. 444-453
Author(s):  
Jonathan O. Bauer ◽  
Tobias Götz
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Molecular Model ◽  
Intermolecular Hydrogen Bond ◽  
Model Systems ◽  
Materials Chemistry ◽  
Hydrogen Bond Interactions ◽  
Model Study

Small functional siloxane units have gained great interest as molecular model systems for mimicking more complex silicate structures both in nature and in materials chemistry. The crystal structure of chloropentaphenyldisiloxane, which was synthesized for the first time, was elucidated by single-crystal X-ray diffraction analysis. The molecular crystal packing was studied in detail using state-of-the-art Hirshfeld surface analysis together with a two-dimensional fingerprint mapping of the intermolecular interactions. It was found that the phenyl C–H bonds act as donors for both weak C–H···π and C–H···Cl hydrogen bond interactions. The influence of intramolecular Si–O–Si bond parameters on the acceptor capability of functional groups in intermolecular hydrogen bond interactions is discussed.

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