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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.


VDD atomic charges (in me−) of the prepared monomers (see [Eq. (5)]).
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fig02: VDD atomic charges (in me−) of the prepared monomers (see [Eq. (5)]).

Mentions: Previously, we shown that A and T are electronically complementary, that is, the proton- acceptor atoms have a negative charge whereas the corresponding protons they face are all positively charged. This is also the case for the smaller mimics of A and T (as can be seen in Figure 2). The differences in charge of the atoms N1 and H6 for A, A′, and A“, and of H3 and O4 for T, T′, and T” are small, as expected from the small differences in hydrogen-bond energies and lengths.


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)

VDD atomic charges (in me−) of the prepared monomers (see [Eq. (5)]).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig02: VDD atomic charges (in me−) of the prepared monomers (see [Eq. (5)]).
Mentions: Previously, we shown that A and T are electronically complementary, that is, the proton- acceptor atoms have a negative charge whereas the corresponding protons they face are all positively charged. This is also the case for the smaller mimics of A and T (as can be seen in Figure 2). The differences in charge of the atoms N1 and H6 for A, A′, and A“, and of H3 and O4 for T, T′, and T” are small, as expected from the small differences in hydrogen-bond energies and lengths.

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.