Energetics of Hydrogen Bond Networks in RNA:  Hydrogen Bonds Surrounding G+1 and U42 Are the Major Determinants for the Tertiary Structure Stability of the Hairpin Ribozyme†

Biochemistry ◽  
2002 ◽  
Vol 41 (48) ◽  
pp. 14095-14102 ◽  
Author(s):  
Dagmar Klostermeier ◽  
David P. Millar
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Tertiary Structure ◽  
Structure Stability ◽  
Hairpin Ribozyme ◽  
Hydrogen Bond Networks

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.

Hydrogen-Bond Networks: Strengths of Different Types of Hydrogen Bonds and An Alternative to the Low Barrier Hydrogen-Bond Proposal

2013 ◽  
Vol 135 (47) ◽  
pp. 17919-17924 ◽  
Author(s):  
Alireza Shokri ◽  
Yanping Wang ◽  
George A. O’Doherty ◽  
Xue-Bin Wang ◽  
Steven R. Kass
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Hydrogen Bond Networks ◽  
Different Types

Kinetic behaviour investigations and crystal structure of nitric acid dihydrate

2001 ◽  
Vol 57 (1) ◽  
pp. 27-35 ◽  
Author(s):  
N. Lebrun ◽  
F. Mahe ◽  
J. Lamiot ◽  
M. Foulon ◽  
J. C. Petit ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Nitric Acid ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Three Dimensional ◽  
Thermal Conditions ◽  
Kinetic Behaviour ◽  
Hydrogen Bond Networks ◽  
Atomic Distance

X-ray powder diffraction experiments are performed to prove the possible crystallization of nitric acid dihydrate (HNO3·2H2O, further denoted NAD) and to determine the best thermal conditions for growing a single crystal. It is shown that the kinetic behaviour of NAD strongly depends on the preliminary thermal treatment. One good single crystal obtained by an in situ adapted Bridgman method procedure enabled determination of the crystal structure. The intensities of diffracted lines with h odd are all very weak. The H atom of nitric acid is delocalized to one water molecule leading to an association of equimolar nitrate (NO3 −) and an H5O2 + ionic group. The asymmetric unit contains two such molecules. These two molecules are related by a pseudo a/2 translation (with a 0.3 Å mean atomic distance difference), except for one H atom of the water molecules (0.86 Å) because of their different orientations in the two molecules. The two molecules, linked by very strong hydrogen bonds, are arranged in layers. Two layers which are linked by weaker hydrogen bonds are approximately oriented along the c axis. The structure may be described by translations of this set of two layers along the c axis without hydrogen bonds leading to a two-dimensional hydrogen-bond network. The structures of the monohydrate (NAM) and trihydrate (NAT) are re-determined for comparisons. These structures may be described by one- and three-dimensional hydrogen-bond networks, respectively.

scholarly journals Short hydrogen bonds enhance nonaromatic protein-related fluorescence

2021 ◽  
Vol 118 (21) ◽  
pp. e2020389118
Author(s):  
Amberley D. Stephens ◽  
Muhammad Nawaz Qaisrani ◽  
Michael T. Ruggiero ◽  
Gonzalo Díaz Mirón ◽  
Uriel N. Morzan ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Transition Probabilities ◽  
Ab Initio Molecular Dynamics ◽  
Single Amino Acid ◽  
Hydrogen Bond Networks ◽  
Short Hydrogen Bond ◽  
Photoactive Materials ◽  
Dynamics Simulations ◽  
Short Hydrogen Bonds

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

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