Theoretical exploration of the cooperative effect in NMF–NMF–amino acid residue hydrogen bonding system

2008 ◽  
Vol 10 (36) ◽  
pp. 5607 ◽  
Author(s):  
Xichen Li ◽  
Wenlan Liu ◽  
Kening Sun ◽  
Yan Wang ◽  
Hongwei Tan ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Cooperative Effect ◽  
Bonding System ◽  
Hydrogen Bonding System

CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?

2009 ◽  
Vol 08 (04) ◽  
pp. 691-711 ◽  
Author(s):  
FENG FENG ◽  
HUAN WANG ◽  
WEI-HAI FANG ◽  
JIAN-GUO YU
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Density Functional ◽  
Biological Systems ◽  
Binding Energies ◽  
Semiempirical Model ◽  
Hydrogen Bonded Systems ◽  
High Level ◽  
Hydrogen Bonded

A modified semiempirical model named RM1BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

Ethylenediammonium thiophene-2,5-dicarboxylate dihydrate, an acid–base complex with a three-dimensional hydrogen-bonding system

2006 ◽  
Vol 62 (7) ◽  
pp. o2951-o2952 ◽  
Author(s):  
Si-Min Wu ◽  
Ming Li ◽  
Jiang-Feng Xiang ◽  
Liang-Jie Yuan ◽  
Ju-Tang Sun
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Water Molecules ◽  
Inversion Center ◽  
Acid Base ◽  
Special Position ◽  
Compound C ◽  
Bonding System ◽  
Hydrogen Bonding System

The crystal structure of the title compound, C2H10N2 2+·C6H2O4S2−·2H2O, is built of ethylenediammonium dications, occupying a special position on an inversion center, thiophene-2,5-dicarboxylate dianions, in a special position on the twofold axis, and water molecules in general positions. All residues are involved in an extensive hydrogen-bonding system, which links them into a three-dimensional supramolecular arrangement.

Structure of Hydrated Copper(II) Colchiceine

1999 ◽  
Vol 52 (4) ◽  
pp. 333 ◽  
Author(s):  
Maureen F. Mackay ◽  
Robert W. Gable ◽  
James D. Morrison ◽  
Lothar O. Satzke
Keyword(s):  
Hydrogen Bonding ◽  
Copper Atom ◽  
Three Dimensional ◽  
Water Molecules ◽  
R Factor ◽  
Bonding System ◽  
Dimensional Network ◽  
Square Planar ◽  
Hydrogen Bonding System ◽  
C 50

Hydrated crystals of copper(II) colchiceine belong to the tetragonal space group P 432I2 with a 13·415(1), c 50·169(8) Å and Z 8. The structure has been refined to a conventional R factor of 0·077 for 4560 observed data. The tropolonic oxygens from two colchiceine molecules are coordinated to the copper atom in this bis-chelated complex to form a square planar arrangement. The sites of three of the waters are clearly defined, but the others are disordered over seven partially occupied sites. An intricate hydrogen-bonding system links the complex and water molecules into a three-dimensional network in the crystal.

The impact on the ring related vibrational frequencies of pyridine of hydrogen bonds with haloforms – a topology perspective

2019 ◽  
Vol 21 (4) ◽  
pp. 1724-1736 ◽  
Author(s):  
Enrico Benassi ◽  
Kamila Akhmetova ◽  
Haiyan Fan
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Ring Structure ◽  
Vibrational Frequencies ◽  
Bonding System ◽  
Hydrogen Bonding System ◽  
The Impact

An intermolecular ring structure is identified for the hydrogen bonding system of pyridine and haloforms.

A correlation study between hydrogen-bonded network and gelation ability of three galactose derivatives

CrystEngComm ◽  
2015 ◽  
Vol 17 (17) ◽  
pp. 3345-3353 ◽  
Author(s):  
Somnath Mukherjee ◽  
G. Rama Krishna ◽  
Balaram Mukhopadhyay ◽  
C. Malla Reddy
Keyword(s):  
Hydrogen Bonding ◽  
Correlation Study ◽  
Bonding System ◽  
Hydrogen Bonding System ◽  
Hydrogen Bonding Network ◽  
Hydrogen Bonded

The hydrogen bonding network in the crystals of the three saccharides was correlated with their gelling ability or inability, and unexpectedly, a 2D hydrogen-bonded system was found to show efficient gelation, whereas a 1D hydrogen bonding system was a nongelator.

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