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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.


Voronoi deformation density (VDD) atomic charges (ΔQπA,oi, in me−) associated with the formation of the different dimers. The contributions stemming from the π electrons are given.
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fig07: Voronoi deformation density (VDD) atomic charges (ΔQπA,oi, in me−) associated with the formation of the different dimers. The contributions stemming from the π electrons are given.

Mentions: The σ and π charge rearrangements for the nine dimers are depicted in Figure 6 and 7 respectively. The ΔQσA,oi values reveal a clear charge-transfer picture for AT and its equivalents: negative charge is lost on the electron-donor atoms, whereas there is a significant accumulation of negative charge on the nitrogen atoms of the electron-accepting N−H bonds (see Figure 6). The π-electron density of the bases is polarized in such a way that the build-up of charge arising from charge-transfer interactions in the σ system is counteracted and compensated: the electron-donor atoms gain π density and the nitrogen atoms of the electron-accepting N−H bonds lose π density (compare ΔQσA,oi and ΔQπA,oi in Figure 6 and 7). This π charge rearrangement is in agreement with the Lewis structure proposed by Gilli et al.3 (see Scheme 1). The charge rearrangements for T“ are somewhat smaller than for T and T′, which is in line with the weaker orbital interactions for T”. Furthermore, we see that the charge rearrangements in σ and π electronic systems do not depend on the aromatic ring.


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)

Voronoi deformation density (VDD) atomic charges (ΔQπA,oi, in me−) associated with the formation of the different dimers. The contributions stemming from the π electrons are given.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig07: Voronoi deformation density (VDD) atomic charges (ΔQπA,oi, in me−) associated with the formation of the different dimers. The contributions stemming from the π electrons are given.
Mentions: The σ and π charge rearrangements for the nine dimers are depicted in Figure 6 and 7 respectively. The ΔQσA,oi values reveal a clear charge-transfer picture for AT and its equivalents: negative charge is lost on the electron-donor atoms, whereas there is a significant accumulation of negative charge on the nitrogen atoms of the electron-accepting N−H bonds (see Figure 6). The π-electron density of the bases is polarized in such a way that the build-up of charge arising from charge-transfer interactions in the σ system is counteracted and compensated: the electron-donor atoms gain π density and the nitrogen atoms of the electron-accepting N−H bonds lose π density (compare ΔQσA,oi and ΔQπA,oi in Figure 6 and 7). This π charge rearrangement is in agreement with the Lewis structure proposed by Gilli et al.3 (see Scheme 1). The charge rearrangements for T“ are somewhat smaller than for T and T′, which is in line with the weaker orbital interactions for T”. Furthermore, we see that the charge rearrangements in σ and π electronic systems do not depend on the aromatic ring.

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.