Insight into structure, stability and hydrogen bond in complexes of guanine and thymine at the molecular level using computational chemical method

2021 ◽  
Vol 11 (1) ◽  
pp. 127-134
Author(s):  
Nhung Ngo Thi Hong ◽  
Huong Dau Thi Thu ◽  
Trung Nguyen Tien
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Energy Surface ◽  
Covalent Bond ◽  
Electrostatic Energy ◽  
Substantial Contribution ◽  
Structure Stability ◽  
Dispersion Terms ◽  
Insight Into

Nine stable structures of complexes formed by interaction of guanine with thymine were located on potential energy surface at B3LYP/6-311++G(2d,2p). The complexes are quite stable with interaction energy from -5,8 to -17,7 kcal.mol-1. Strength of complexes are contributed by hydrogen bonds, in which a pivotal role of N−H×××O/N overcoming C−H×××O/N hydrogen bond, up to to 3.5 times, determines stabilization of complexes investigated. It is found that polarity of N/C−H covalent bond over proton affinity of N/O site governs stability of hydrogen bond in the complexes. The obtained results show that the N/C−H×××O/N red-shifting hydrogen bonds occur in all complexes, and a larger magnitude of an elongation of N−H compared C-H bond length accompanied by a decrease of its stretching frequency is detected in the N/C−H×××O/N hydrogen bond upon complexation. The SAPT2+ analysis indicates the substantial contribution of attractive electrostatic energy versus the induction and dispersion terms in stabilizing the complexes.

Structural role of hydrogen bond networks in amino acid–acid systems. (I) The network with highly polarizable OHO hydrogen bonds in sarcosine–methanesulfonic acid (2:1) crystal

2008 ◽  
Vol 351 (1-3) ◽  
pp. 99-105 ◽  
Author(s):  
Marek Ilczyszyn ◽  
Dorota Chwaleba ◽  
Krzysztof Mierzwicki ◽  
Maria M. Ilczyszyn
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Methanesulfonic Acid ◽  
Structural Role ◽  
Hydrogen Bond Networks ◽  
Acid Acid

scholarly journals On the Role of Hydrogen Bond Strength and Charge Transfer of a Diels-Alder Reaction On-Water: Semiempirical and Free Energy Calculations.

2021 ◽  
Author(s):  
Andrés Henao Aristizàbal ◽  
Yomna Gohar ◽  
René Whilhelm ◽  
Thomas D. Kühne
Keyword(s):  
Hydrogen Bond ◽  
Free Energy ◽  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Alder Reaction ◽  
Free Energy Calculations ◽  
Diels Alder ◽  
Diels Alder Reaction

Accelerated chemistry at the interface with water has received increasing attention. The mechanisms behind the enhanced reactivity On-Water are not yet clear. In this work we use a Langevin scheme in the spirit of second generation Car-Parrinello to accelerate the second-order density functional Tight-Binding (DFTB2) method in order to investigate the free energy of two Diels-Alder reaction On-Water: the cycloaddition between cyclopentadiene and ethyl cinnamate or thionocinnamate. The only difference between the reactants is the substitution of a carbonyl oxygen for a thiocarbonyl sulfur, making possible the distinction between them as strong and weak hydrogen-bond acceptors. We find a different mechanism for the reaction during the transition states and uncover the role of hydrogen bonds along with the reaction path. Our results suggest that acceleration of Diels-Alder reactions do not arise from an increased number of hydrogen bonds at the transition state and charge transfer plays a significant role. However, the presence of water and hydrogen-bonds is determinant for the catalysis of these reactions.

scholarly journals The role of nitro groups in the binding of nitroaromatics to protein MOPC 315

1978 ◽  
Vol 173 (3) ◽  
pp. 713-722 ◽  
Author(s):  
P Gettins ◽  
D Givol ◽  
R A Dwek
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Fluorescence Quenching ◽  
Nitro Group ◽  
Protein Interactions ◽  
Chemical Shifts ◽  
Binding Constants

Two series of dinitrophenyl haptens, in which chlorine replaces one or both nitro groups, were used to investigate, by a combination of high-resolution 1H n.m.r. and fluorescence quenching, the presence of groups in the combining site of protein MOPC 315, which form hydrogen bonds to the aromatic-ring substituents of the hapten. The large differences in binding constants on successive replacement of nitro groups were shown to be due to specific hapten-substituent-protein interactions by (a) showing that there was little difference in the interaction between these haptens and 3-methylindole (a model for the residue tryptophan-93L with which the hapten stacks in protein MOPC 315), (b) proving by 1H n.m.r. that the mode of hapten binding is constant and (c) showing that the differences in Kd were consistent with the relative hydrogen-bonding capacities of chlorine and the nitro moiety. In this way it was established that each nitro group forms a hydrogen bond. Furthermore, from consideration of the 1H n.m.r. chemical shifts of several dinitrophenyl haptens and their trinitrophenyl analogues, it was shown that there is no distortion of the o-nitro group on binding to the variable fragment of protein MOPC 315.

Role of strong intramolecular N—H...N hydrogen bonds in determining the conformation of adenosine-receptor antagonists

2006 ◽  
Vol 62 (4) ◽  
pp. 634-641 ◽  
Author(s):  
Valeria Ferretti ◽  
Loretta Pretto ◽  
Mojgan Aghazadeh Tabrizi ◽  
Paola Gilli
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Adenosine Receptors ◽  
Systematic Investigation ◽  
New Drugs ◽  
Receptor Subtypes ◽  
Pyrimidine Derivatives ◽  
Planar Conformation ◽  
Chemical Class

Over the last few years many efforts have been devoted to the discovery of new adenosine antagonists which can selectively bind to one of the four adenosine receptors, called A1, A2A, A2B and A3, in order to develop new drugs with few side effects. The present paper reports the crystal structures of four newly synthesized antagonists belonging to the chemical class of pyrazolo-triazolo-pyrimidine derivatives, which display good affinity and selectivity properties towards the A2A or A3 receptor subtypes. These molecules assume an overall planar conformation due to the formation of strong intramolecular N—H...N hydrogen bonds. A systematic investigation on molecules containing the ureidic —NH—C(=O,S)—NH—C=N— fragment has shown that the formation of such interactions is a common feature for this class of compounds. The associated energy, evaluated through DFT calculations, is some 50.24 kJ mol−1, leading to the conclusion that the hydrogen bond, and consequently the planar conformation, is retained not only in the solid state but also in solution during the interaction of the molecule with its receptor.

The emerging role of hydrogen bond interactions in polyglutamine structure, stability and association

Soft Matter ◽  
2013 ◽  
Vol 9 (8) ◽  
pp. 2359-2364 ◽  
Author(s):  
Natasha H. Rhys ◽  
Lorna Dougan
Keyword(s):  
Hydrogen Bond ◽  
Structure Stability ◽  
Hydrogen Bond Interactions

Structure of a proteolytically resistant analogue of (NLys)5SFTI-1 in complex with trypsin: evidence for the direct participation of the Ser214 carbonyl group in serine protease-mediated proteolysis

2014 ◽  
Vol 70 (3) ◽  
pp. 668-675 ◽  
Author(s):  
Szymon Krzywda ◽  
Mariusz Jaskolski ◽  
Krzysztof Rolka ◽  
Maciej J. Stawikowski
Keyword(s):  
Hydrogen Bond ◽  
Carbonyl Group ◽  
Serine Proteases ◽  
Peptide Ligands ◽  
Protein Protein Interaction ◽  
Proteolytic Resistance ◽  
Structural Differences ◽  
Natural Inhibitor ◽  
Insight Into

Peptide–peptoid hybrids are found to be potent inhibitors of serine proteases. These engineered peptidomimetics benefit from both types of units of the biopolymeric structure: the natural inhibitor part serves as a good binding template, while the P1-positioned peptoid component provides complete resistance towards proteolysis. In this report, the mechanism of proteolytic resistance of a P1 peptoid-containing analogue is postulated based on the crystal structure of the (NLys)5-modified sunflower trypsin inhibitor SFTI-1 in complex with bovine trypsin solved at 1.29 Å resolution. The structural differences between the (NLys)5SFTI-1–trypsin complex and the native SFTI-1–trypsin complex are surprisingly small and reveal the key role of the carbonyl group of the Ser214 residue of the enzyme, which is crucial for binding of the inhibitor and plays a crucial role in proteolysis mediated by serine proteases. The incorporatedNLys5 peptoid residue prevents Ser214 from forming a hydrogen bond to the P1 residue, and in turn Gln192 does not form a hydrogen bond to the carbonyl group of the P2 residue. It also increases the distance between the Ser214 carbonyl group and the Ser195 residue, thus preventing proteolysis. The hybrid inhibitor structure reported here provides insight into protein–protein interaction, which can be efficiently and selectively probed with the use of peptoids incorporated within endogenous peptide ligands.

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