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The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics.

Guillaumes L, Simon S, Fonseca Guerra C - ChemistryOpen (2015)

Bottom Line: In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine-thymine (AT) DNA base pairs.Removing the aromatic rings of either A or T has no effect on the Watson-Crick bond strength.Bonding analyses based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor-acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

View Article: PubMed Central - PubMed

Affiliation: Institut de Química Computacional i Catàlisi, Departament de Química, Universitat de Girona 17071, Girona, Spain).

ABSTRACT
Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine-thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson-Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp (2) to sp (3), does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor-acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

No MeSH data available.


Molecular orbital diagram with the most pronounced donor–acceptor interactions in the N6(H)⋅⋅⋅O4 and N1⋅⋅⋅(H)N3 hydrogen bonds between adenine and thymine.
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fig03: Molecular orbital diagram with the most pronounced donor–acceptor interactions in the N6(H)⋅⋅⋅O4 and N1⋅⋅⋅(H)N3 hydrogen bonds between adenine and thymine.

Mentions: Next, we consider the possibility of charge-transfer interactions in the σ-electron system. Figure 3 displays the basic features in the electronic structures of the DNA bases A and T that lead to the donor–acceptor orbital interactions: a lone pair on a proton-acceptor nitrogen or oxygen atom pointing toward and donating charge into the unoccupied σ* orbital of an N−H group of the other base. This leads to the formation of a weak covalent bond which is σLP+σ*N−H bond. For a complete description of the covalent component in the hydrogen bonds of AT, see ref. 5a.


The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics.

Guillaumes L, Simon S, Fonseca Guerra C - ChemistryOpen (2015)

Molecular orbital diagram with the most pronounced donor–acceptor interactions in the N6(H)⋅⋅⋅O4 and N1⋅⋅⋅(H)N3 hydrogen bonds between adenine and thymine.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4522182&req=5

fig03: Molecular orbital diagram with the most pronounced donor–acceptor interactions in the N6(H)⋅⋅⋅O4 and N1⋅⋅⋅(H)N3 hydrogen bonds between adenine and thymine.
Mentions: Next, we consider the possibility of charge-transfer interactions in the σ-electron system. Figure 3 displays the basic features in the electronic structures of the DNA bases A and T that lead to the donor–acceptor orbital interactions: a lone pair on a proton-acceptor nitrogen or oxygen atom pointing toward and donating charge into the unoccupied σ* orbital of an N−H group of the other base. This leads to the formation of a weak covalent bond which is σLP+σ*N−H bond. For a complete description of the covalent component in the hydrogen bonds of AT, see ref. 5a.

Bottom Line: In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine-thymine (AT) DNA base pairs.Removing the aromatic rings of either A or T has no effect on the Watson-Crick bond strength.Bonding analyses based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor-acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

View Article: PubMed Central - PubMed

Affiliation: Institut de Química Computacional i Catàlisi, Departament de Química, Universitat de Girona 17071, Girona, Spain).

ABSTRACT
Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine-thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson-Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp (2) to sp (3), does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor-acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

No MeSH data available.