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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.


Atomic Voronoi deformation density (VDD) charges (in me−) for front atoms in A“T” and a“t”.
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fig08: Atomic Voronoi deformation density (VDD) charges (in me−) for front atoms in A“T” and a“t”.

Mentions: This part will address this question if the hydrogen donor and acceptor atoms need to be sp2-hybridzed atoms by comparing A“T” (sp2) to a“t” (sp3), see Figure 8. The latter exists in the chair and boat conformation and, in analogy to cyclohexane, the chair conformation is 4.8 kcal mol−1 lower in energy (see Supporting Information). The hydrogen-bond energy of the sp2-hybridized A“T” is 7.9 kcal mol−1 stronger bound than its saturated equivalent (see Table 2). This cannot be attributed to the π electrons as the π polarization in the sp2-hybridized A“T” amounts only to −1.9 kcal mol−1 (see Table 1). At the equilibrium structures, all the bonding components of the interaction energy, ΔEoi and ΔVelstat, are smaller for a“t”, than for A“T”, but the Pauli repulsion is also smaller in the case of a“t”.


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)

Atomic Voronoi deformation density (VDD) charges (in me−) for front atoms in A“T” and a“t”.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig08: Atomic Voronoi deformation density (VDD) charges (in me−) for front atoms in A“T” and a“t”.
Mentions: This part will address this question if the hydrogen donor and acceptor atoms need to be sp2-hybridzed atoms by comparing A“T” (sp2) to a“t” (sp3), see Figure 8. The latter exists in the chair and boat conformation and, in analogy to cyclohexane, the chair conformation is 4.8 kcal mol−1 lower in energy (see Supporting Information). The hydrogen-bond energy of the sp2-hybridized A“T” is 7.9 kcal mol−1 stronger bound than its saturated equivalent (see Table 2). This cannot be attributed to the π electrons as the π polarization in the sp2-hybridized A“T” amounts only to −1.9 kcal mol−1 (see Table 1). At the equilibrium structures, all the bonding components of the interaction energy, ΔEoi and ΔVelstat, are smaller for a“t”, than for A“T”, but the Pauli repulsion is also smaller in the case of a“t”.

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.