An ab initio Study on the Hydrogen Bond Energies of Nucleic Acid Basepairs: Adenine-Uracil Watson-Crick and Guanine-Uracil Wobble Basepairs

Heterocycles ◽  
2000 ◽  
Vol 52 (3) ◽  
pp. 1047 ◽  
Author(s):  
Tadafumi Uchimaru ◽  
Shun-ichi Kawahara
Keyword(s):  
Hydrogen Bond ◽  
Nucleic Acid ◽  
Ab Initio ◽  
Ab Initio Study ◽  
Bond Energies ◽  
Hydrogen Bond Energies

Ab initio studies of the vibrational spectra of some hydrogen-bonded complexes of fluoroacetylene

2010 ◽  
Vol 88 (8) ◽  
pp. 716-724 ◽  
Author(s):  
Ponnadurai Ramasami ◽  
Thomas A. Ford
Keyword(s):  
Hydrogen Bond ◽  
Ab Initio ◽  
Vibrational Spectra ◽  
Molecular Structures ◽  
Stationary Points ◽  
Bond Energies ◽  
Length Changes ◽  
Hydrogen Bond Energies ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Ab initio molecular orbital theory has been used to compute the properties of a number of hydrogen-bonded complexes between fluoroacetylene as proton donor and ammonia, water, hydrogen fluoride, phosphine, hydrogen sulfide, and hydrogen chloride as proton acceptors. The properties considered were the vibrational spectra, the molecular structures, the hydrogen-bond energies, and the electron densities, and one of the aims of the study was to ascertain whether there was any evidence of blue-shifting hydrogen-bond character in the complexes formed. The adducts with NH3, H2O, PH3, and H2S were of the conventional CH···X kind (X = N, O, P, S), with hydrogen-bond energies decreasing in the order NH3 > H2O > PH3 ≈ H2S. Those formed with HF and HCl showed the presence of three alternative structures; in addition to the CH···F(Cl) complexes, adducts of the F(Cl)H···F and F(Cl)H···π type were also found to be stationary points on the potential energy surfaces, with stabilities in the order F(Cl)H···π > CH···F(Cl) > F(Cl)H···F. The hydrogen-bond energies of the CH···X series correlated with the gas-phase basicities of the proton acceptors; moreover, the CH bond-length changes, the wavenumber shifts, the complex–monomer infrared intensity ratios of the CH stretching modes, and the amounts of charge transferred on complex formation were all found to track with the hydrogen-bond energies. All those properties considered here are consistent with the formation of red-shifting hydrogen bonds, to the exclusion of the blue-shifting alternatives.

Contributions to Silicon-Hydrogen Bond-Stretching Frequency in Amorphous Si Alloys

1992 ◽  
Vol 258 ◽  
Author(s):  
Z. Jing ◽  
J. L. Whitten ◽  
G. Lucovsky
Keyword(s):  
Experimental Data ◽  
Hydrogen Bond ◽  
Dielectric Constant ◽  
Ab Initio ◽  
Effective Dielectric Constant ◽  
Bond Energies ◽  
Calculated Frequency ◽  
Bond Stretching ◽  
Amorphous Si ◽  
Good Agreement

ABSTRACTWe have performed ab initio calculations and determined the bond-energies and vibrational frequencies of Si-H groups that are: i) attached to Si-atoms as their immediate, and also more distant neighbors; and ii) attached to three O-atoms as their immediate neighbors, but are connected to an all Si-atom matrix. These arrangements simulate bonding geometries on Si surfaces, and the calculated frequency for i) is in good agreement with that of an Si-H group on an Si surface. To compare these results with a-Si:H alloys it is necessary to take into account an additional factor: the effective dielectric constant of the host. We show how to do this, demonstrating the way results of the ab initio calculations should then be compared with experimental data.

Cooperative interaction between hydrogen bond and N···Y interactions (Y = H, Li, F, Cl, and Br): a comparative study

2015 ◽  
Vol 93 (6) ◽  
pp. 626-631
Author(s):  
Zahra Fallah Ebrahimi ◽  
Mehdi D. Esrafili ◽  
Esmail Vessally
Keyword(s):  
Hydrogen Bond ◽  
Comparative Study ◽  
Ab Initio ◽  
Halogen Bond ◽  
Cooperative Interaction ◽  
Ab Initio Study ◽  
Absolute Value ◽  
Lithium Bond ◽  
Cooperative Energy

A comparative ab initio study is performed to investigate the cooperativity between the N···H hydrogen bond and the N···Y interactions in XCN···HCN···YCN complexes, where X = H, F, and Y = H, Li, F, Cl, and Br. To understand the properties of the systems better, the corresponding dimers are also studied. It is found that the lithium bond has a larger influence on the hydrogen bond than vice versa. The shortening of the N···H distances in the trimers is dependent on the strength of the H···Y interactions and they become larger in the order lithium bond > hydrogen bond > halogen bond. The estimated values of cooperative energy Ecoop are all negative with much larger Ecoop in absolute value for the systems including lithium.

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