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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.


Adenine (A) and its smaller analogs (A′ and A“) and Thymine (T) and its smaller analogs (T′ and T”).
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sch02: Adenine (A) and its smaller analogs (A′ and A“) and Thymine (T) and its smaller analogs (T′ and T”).

Mentions: In the present paper, we study the resonance assistance to the hydrogen bonds of AT and its smaller analogs (see Scheme 2), because the Lewis structure of AT in Scheme 1 as proposed by Gilli et al.3 suggests that the smaller mimic can also give the same resonance assistance. Also, our previous work on the Watson–Crick base pairs based on high-level density functional theory (DFT) computations,5a showed that the hydrogen bonds affected mainly the atomic charges of the blue part in Scheme 1. However, the resonance of the π electrons encompasses a larger part of the adenine nucleobase as can be seen in the lower (green) part of Scheme 1, suggesting that we can remove the 5-membered ring of the purine base, but we cannot remove the 6-membered ring. For the pyrimidine base, the resonance structures suggest that we need to incorporate all frontier atoms.


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)

Adenine (A) and its smaller analogs (A′ and A“) and Thymine (T) and its smaller analogs (T′ and T”).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

sch02: Adenine (A) and its smaller analogs (A′ and A“) and Thymine (T) and its smaller analogs (T′ and T”).
Mentions: In the present paper, we study the resonance assistance to the hydrogen bonds of AT and its smaller analogs (see Scheme 2), because the Lewis structure of AT in Scheme 1 as proposed by Gilli et al.3 suggests that the smaller mimic can also give the same resonance assistance. Also, our previous work on the Watson–Crick base pairs based on high-level density functional theory (DFT) computations,5a showed that the hydrogen bonds affected mainly the atomic charges of the blue part in Scheme 1. However, the resonance of the π electrons encompasses a larger part of the adenine nucleobase as can be seen in the lower (green) part of Scheme 1, suggesting that we can remove the 5-membered ring of the purine base, but we cannot remove the 6-membered ring. For the pyrimidine base, the resonance structures suggest that we need to incorporate all frontier atoms.

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.