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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.


Hydrogen-bond distances (in Å) and energies (in kcal mol−1) for adenine–thymine (AT) and its smaller analogs at the BLYP-D3(BJ)/TZ2P level of theory.
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fig01: Hydrogen-bond distances (in Å) and energies (in kcal mol−1) for adenine–thymine (AT) and its smaller analogs at the BLYP-D3(BJ)/TZ2P level of theory.

Mentions: To study the importance of the π electrons and aromaticity on the hydrogen bonds of the DNA base pair AT, we have investigated computationally all the possible dimers of A and its smaller mimics A′ and A“ with T and its smaller mimics T′ and T”. The hydrogen-bond distances and energies calculated at the BLYP-D3(BJ)/TZ2P level of theory for the possible dimers (AT, AT′, AT“, A′T, A′T′, A′T”, A“T, A”T′, and A“T”) are shown in Figure 1. The optimal structures of these dimers have been obtained in CS symmetry, and C1 symmetry for monomers.


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)

Hydrogen-bond distances (in Å) and energies (in kcal mol−1) for adenine–thymine (AT) and its smaller analogs at the BLYP-D3(BJ)/TZ2P level of theory.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig01: Hydrogen-bond distances (in Å) and energies (in kcal mol−1) for adenine–thymine (AT) and its smaller analogs at the BLYP-D3(BJ)/TZ2P level of theory.
Mentions: To study the importance of the π electrons and aromaticity on the hydrogen bonds of the DNA base pair AT, we have investigated computationally all the possible dimers of A and its smaller mimics A′ and A“ with T and its smaller mimics T′ and T”. The hydrogen-bond distances and energies calculated at the BLYP-D3(BJ)/TZ2P level of theory for the possible dimers (AT, AT′, AT“, A′T, A′T′, A′T”, A“T, A”T′, and A“T”) are shown in Figure 1. The optimal structures of these dimers have been obtained in CS symmetry, and C1 symmetry for monomers.

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.