Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

Villani, Giovanni

doi:10.1002/cphc.201200971

Cited by 16 publications

(30 citation statements)

References 65 publications

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“…[43][44][45] in the optimized geometries of my previous paper [43][44][45] . After the addition of one or two methyl groups on the A or C bases, all geometries of these systems are reoptimized.…”

Section: Methodsmentioning

confidence: 94%

Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs

Villani

2015

J. Phys. Chem. B

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The effects of the addition of one (hemimethylation) or two (methylation) methyl groups on the 10 different couples of base pairs of DNA (three dimers of A-T, three of C-G, and four mixed A-T and C-G complexes) has been studied. Changes in the main static properties (energy, structure, atomic charges) and dynamics (movement of hydrogen atoms from one base to the other) have been considered and analyzed. The results of this study support the idea that the quantitative effects of the methylation of these complexes depend on the specific system under consideration and on the H-bridge studied. In any case, some general behavior can be highlighted. In particular, the relationship between the transfer of hydrogen atoms between the bases (with the possible generation of mutation points) and the methylation can be schematized in the two most important methylated bases: adenine and cytosine. A different behavior has been found in these two cases, and we suggest that this could be related to the different amounts of these methylated systems in prokaryotes and eukaryotes. In particular, this different behavior could explain why adenine methylation is present mainly in the bacteria and cytosine methylation is present in more complex organisms.

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Section: Methodsmentioning

confidence: 94%

Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs

Villani

2015

J. Phys. Chem. B

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“…WBIs have been used to quantify the bonding interaction between molecules in covalently bound atoms and non‐covalent interactions, included π‐stacking interactions . To evaluate the inter‐ring density, the total WBI (TWBI) was calculated as the sum over all atom‐atom inter‐ring pairwise interactions (Equation ).…”

Section: Theoretical Methodsmentioning

confidence: 99%

“…(1) WBIs have been used to quantify the bonding interaction between molecules in covalently bound atoms and non-covalent interactions, included p-stacking interactions. [37][38][39] To evaluate the inter-ring density, the total WBI (TWBI) was calculated as the sum over all atom-atom interring pairwise interactions (Equation 2). Basis set dependencies in the WBI have been sparsely reported in the literature [40] and were found when diffuse functions were included, therefore TWBI analyses were limited to aug-cc-pVDZ in the following study.…”

Section: Stmentioning

confidence: 99%

Interpreting geometric preferences in π‐stacking interactions through molecular orbital analysis

Lutz

Bayse

2017

Int J of Quantum Chemistry

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The preference of π‐stacking interactions for parallel‐displaced (PD) and twisted (TW) conformations over the fully eclipsed sandwich (S) in small π‐stacked dimers of benzene, pyridine, pyrimidine, 1,3,5‐trifluorobenzene, and hexafluorobenzene are examined in terms of enhancement of the inter‐ring density through mixing of the monomer orbitals (MOs). PD and/or TW conformations are consistent with a non‐zero “stack bond order” (SBO), defined in analogy to the bond order of conventional MO theory, as the difference in the occupation of bonding and antibonding π‐type dimer MOs. In the S conformation, the equal number of bonding and antibonding MOs cancel overall stack bonding character between the monomers for an SBO of zero and an overall repulsive interaction. PD from the S shifts the character of at least one antibonding combination of monomer π‐type MOs with nodes perpendicular to the coordinate for PD to bonding, leading to an attractive nonzero SBO. The inter‐ring density measured through the Wiberg bond index analysis shows an enhancement at the PD conformations consistent with greater interpenetration of the monomer densities. This intuitive bonding model for π‐stacking interactions is complementary to highly accurate calculations of π‐stacking energies and allows a predictive understanding of relative stability using cheaper quantum chemical methods.

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“…(46–50) Various high-level quantum mechanical (e.g., post-Hartree Fock) methods can very accurately capture features that depend on, for example, electron correlation and dispersion effects, (51, 52) but due to computational expense, most investigations have so far utilized small model systems, containing only one or two base pairs, designed to capture specific effects (e.g., π-stacking, (53, 54) hydrogen bonding, (55) sterics/shape (56) , electrostatics), (51, 57, 58) rather than the combination of these effects that is manifested experimentally. Proper modeling of these combined effects are no small task, and ongoing efforts have been led by the Šponer and Hobza laboratories for both RNA and DNA systems, among others.…”

Section: Available Computational Methodsmentioning

confidence: 99%

Computational Approaches to Predicting the Impact of Novel Bases on RNA Structure and Stability

et al. 2013

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The use of computational modelling techniques to gain insight into nucleobase interactions has been a challenging endeavor to date. Accurate treatment requires the tackling of many challenges, but also holds the promise of great rewards. The development of effective computational approaches to predict the binding affinities of nucleobases and analogs can, for example, streamline the process of developing novel nucleobase modifications, which should facilitate the development of new RNAi-based therapeutics, for example. This brief review focuses on available computational approaches to predicting base pairing affinity in RNA-based contexts such as nucleobase-nucleobase interactions in duplexes and nucleobase-protein interactions. The challenges associated with such modelling along with potential future directions for the field are highlighted.

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Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

Cited by 16 publications

References 65 publications

Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs

Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs

Interpreting geometric preferences in π‐stacking interactions through molecular orbital analysis

Computational Approaches to Predicting the Impact of Novel Bases on RNA Structure and Stability

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