scholarly journals Defining the Bounds of Chemical Coupling Between Covalent and Hydrogen-bonds in Small Water Clusters

2021 ◽  
Author(s):  
Zi Li ◽  
Yong Yang ◽  
Xing Nie ◽  
Tianlv Xu ◽  
Steven Kirk ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Clusters ◽  
Covalent Bond ◽  
Covalent Bonds ◽  
Bond Path ◽  
Small Water ◽  
Chemical Coupling ◽  
Chemical Character ◽  
Sigma Bond

We seek to determine the two-way transfer of chemical character due to the coupling occurring between hydrogen-bonds and covalent-bonds known to account for the unusual strength of hydrogen-bonds in water. We have provided a vector-based quantification of the chemical character of uncoupled hydrogen-bonds and covalent-bonds and then determined the effects of two-way coupling consistent with the total local energy density H(rb) < 0 for hydrogen-bonds. We have calculated the precessions Kʹ of the eigenvectors around the bond-path for the Ehrenfest Force F(r) and compared with the corresponding QTAIM Kʹ. In doing so we explain why the Ehrenfest Force F(r) provides insights into the coupling between the hydrogen and covalent bonds whilst QTAIM cannot. Conditions for favorable transfer of electron momentum from the hydrogen atom of a sigma bond to the hydrogen-bond are found, with excellent agreement with the hydrogen-bond BCP and covalent-bond BCP separations providing the theoretical bounds for coupling.

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.

scholarly journals Electronic origin of the dependence of hydrogen bond strengths on nearest-neighbor and next-nearest-neighbor hydrogen bonds in polyhedral water clusters (H2O)n, n = 8, 20 and 24

2016 ◽  
Vol 18 (29) ◽  
pp. 19746-19756 ◽  
Author(s):  
Suehiro Iwata ◽  
Dai Akase ◽  
Misako Aida ◽  
Sotiris S. Xantheas
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Nearest Neighbor ◽  
Water Clusters ◽  
Hydrogen Donor ◽  
Donor And Acceptor ◽  
Bond Strengths

Comparison of the sum of the characteristic factors for some of the typical hydrogen donor and acceptor pairs with the CT term/kJ mol−1 (the upper value) and the O⋯O distance/in cubic (H2O)8.

An explanation of the unusual strength of the hydrogen bond in small water clusters

2020 ◽  
Vol 120 (19) ◽  
Author(s):  
Shuman Li ◽  
Alireza Azizi ◽  
Steven R. Kirk ◽  
Samantha Jenkins
Keyword(s):  
Hydrogen Bond ◽  
Water Clusters ◽  
Small Water

Sub-THz specific relaxation times of hydrogen bond oscillations in E.coli thioredoxin. Molecular dynamics and statistical analysis

2014 ◽  
Vol 171 ◽  
pp. 179-193 ◽  
Author(s):  
Tatiana Globus ◽  
Igor Sizov ◽  
Boris Gelmont
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Relaxation Time ◽  
Hydrogen Bonds ◽  
Spectral Resolution ◽  
Relaxation Times ◽  
Low Frequency ◽  
Thz Spectroscopy ◽  
Vibrational Modes ◽  
Covalent Bonds

Hydrogen bonds (H-bonds) in biological macromolecules are important for the molecular structure and functions. Since interactions via hydrogen bonds are weaker than covalent bonds, it can be expected that atomic movements involving H-bonds have low frequency vibrational modes. Sub-Terahertz (sub-THz) vibrational spectroscopy that combines measurements with molecular dynamics (MD) computational prediction has been demonstrated as a promising approach for biological molecule characterization. Multiple resonance absorption lines have been reported. The knowledge of relaxation times of atomic oscillations is critical for the successful application of THz spectroscopy for hydrogen bond characterization. The purpose of this work is to use atomic oscillations in the 0.35–0.7 THz range, found from molecular dynamic (MD) simulations of E.coli thioredoxin (2TRX), to study relaxation dynamics of two intra-molecular H-bonds, O⋯H–N and O⋯H–C. Two different complimentary techniques are used in this study, one is the analysis of the statistical distribution of relaxation time and dissipation factor values relevant to low frequency oscillations, and the second is the analysis of the autocorrelation function of low frequency quasi-periodic movements. By studying hydrogen bond atomic displacements, it was found that the atoms are involved in a number of collective oscillations, which are characterized by different relaxation time scales ranging from 2–3 ps to more than 150 ps. The existence of long lasting relaxation processes opens the possibility to directly observe and study H-bond vibrational modes in sub-THz absorption spectra of bio-molecules if measured with an appropriate spectral resolution. The results of measurements using a recently developed frequency domain spectroscopic sensor with a spectral resolution of 1 GHz confirm the MD analysis.

scholarly journals An Explanation of the Unusual Strength of the Hydrogen-Bond in Small Water Clusters

Authorea ◽  
2020 ◽  
Author(s):  
Shuman Li ◽  
Alireza Azizi ◽  
Steven Kirk ◽  
Samantha Jenkins
Keyword(s):  
Hydrogen Bond ◽  
Water Clusters ◽  
Small Water

Bonding Analysis of Water Clusters Using Quasi-Atomic Orbitals

2021 ◽  
Author(s):  
Jorge L Galvez Vallejo ◽  
Juan Duchimaza Heredia ◽  
Mark Gordon
Keyword(s):  
Hydrogen Bonds ◽  
Water Clusters ◽  
Atomic Orbital ◽  
Atomic Orbitals ◽  
Bonding Analysis ◽  
Small Water

The quasi-atomic orbital (QUAO) bonding analysis introduced by Ruedenberg and co-workers is used to develop an understanding of the hydrogen bonds in small water clusters, from the dimer through the...

Hydrogen-Bond Distances to Halide Ions in Organic and Organometallic Crystal Structures: Up-to-date Database Study

1998 ◽  
Vol 54 (4) ◽  
pp. 456-463 ◽  
Author(s):  
T. Steiner
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Bond Distance ◽  
Covalent Bond ◽  
Chloride Ions ◽  
Halide Ions ◽  
Iodide Ions ◽  
Data Volume ◽  
Geometrical Data

Geometrical data on hydrogen bonds to halide ions are compiled from the currently available crystal structures. Hydrogen bonds from 25 donor types to fluoride, chloride, bromide and iodide ions are considered. Compared with earlier compilations, the increased data volume allows a finer subdivision of O—H and N—H donors, and the donors C—H, S—H and P—H can be included. For a given donor type, the hydrogen-bond distance typically increases by over 0.5 Å from fluoride to chloride, 0.15 Å from chloride to bromide and 0.25 Å from bromide to iodide acceptors. The strongest of the C—H donors considered, chloroform, forms hydrogen bonds with chloride ions with an average H...Cl separation of only 2.39 Å and an average C...Cl separation of 3.42 Å. The lengthening of the N—H covalent bond in hydrogen bonds to chloride ions is quantified from neutron diffraction data.

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