The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

Ebrahimi, Ali; Habibi‐Khorassani, Sayyed Mostafa; Delarami, Hojat Samareh; Esmaeeli, Hadi

doi:10.1007/s10822-010-9348-2

Cited by 23 publications

(17 citation statements)

References 42 publications

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“…Hydrogen bonds are due to electrostatic interactions with significant contributions of charge‐transfer and polarization effects 28–30. Methyl groups are electron donors, which can both strengthen or weaken hydrogen bonding between nucleobases, depending on the specific hydrogen‐bond configuration 31–33. Furthermore, the polarizability of a molecule is increased when a methyl group is present.…”

Section: Resultsmentioning

confidence: 99%

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Bald

Wang

Dong

et al. 2011

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Methylation of DNA nucleobases is an important control mechanism in biology applied, for example, in the regulation of gene expression. The effect of methylation on the intermolecular interactions between guanine molecules is studied through an interplay between scanning tunneling microscopy (STM) and density functional theory with empirical dispersion correction (DFT-D). The present STM and DFT-D results show that methylation of guanine can have subtle effects on the hydrogen-bond strength with a strong dependence on the position of methylation. It is demonstrated that the methylation of DNA nucleobases is a precise means to tune intermolecular interactions and consequently enables very specific recognition of DNA methylation by enzymes. This scheme is used to generate four different types of artificial 2D nanostructures from methylated guanine. For instance, a 2D guanine windmill motif that is stabilized by cooperative hydrogen bonding is revealed. It forms by self-assembly on a graphite surface under ambient conditions at the liquid-solid interface when the hydrogen-bonding donor at the N1 site of guanine is blocked by a methyl group.

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Section: Resultsmentioning

confidence: 99%

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Bald

Wang

Dong

et al. 2011

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“…A-T versus G-C. The energy of an individual H-bond has been evaluated by several approaches: (1) in the (presumed) absence of other intermolecular interactions as a bonding energy of the H-bonded complex [2]; (2) through calculations of inter-residue compliance constants for all possible X-HÁÁÁY contacts [3]; (3) by application of an atom replacement procedure [4]; (4) using the ELM (Espinosa, Lecomte, Molins) equation [5] to estimate of the individual OÁÁÁH energy, whereas NÁÁÁH ones obtained from the difference in the total binding energy between the two monomers and the energies of the remaining OÁÁÁH interactions [6] (5) utilizing the obtained relationship between the dissociation energy of the individual intermolecular interactions and the electron density at the H-bond critical point, obtained for symmetrical complexes with two identical N-HÁÁÁO H-bonds [7,8]; (6) an application of the Natural Bond Orbital (NBO) concept to intermolecular interactions [9]. All these methods were described in more detail as well as their results compared in our previous paper [9].…”

Section: Introductionmentioning

confidence: 99%

Correlations of NBO energies of individual hydrogen bonds in nucleic acid base pairs with some QTAIM parameters

2015

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DNA and RNA base-pairs are the most important systems containing multiple hydrogen bonds. Characterizing the energy of individual intermolecular interactions in such systems is vital and still an open problem that has been tackled here within the framework of the natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) theories. In the NBO language, energy of an individual H-bond depends on the interaction of the n Y , r* XH , and r XH orbitals directly involved in H-bonding. A partial charge transfer between donor (n Y) and acceptor (r* XH) orbitals provides a substantial bonding contribution to the energies of the H-bonds, and in the end, the H-bonded complexes. It is accompanied with a repulsive contribution due to the proximity of the n Y and r XH orbitals. Energies of the individual H-bonds, resulting from addition of the both terms, were correlated with several parameters, provided by the QTAIM analysis which has also been extensively used to characterize the hydrogen bond. The calculations were performed for the G-C and AT Watson-Crick base pairs, their substituted derivatives (by one of two substituents, NH 3 ? or OH 2 ?), A-U occurring in RNA and a wobble pair G-U. The best correlations were found for the NBO energy with the electron density and the potential energy density at H-bond critical points. The correlations held for the heterogeneous samples of HBs of different types, i.e. N-HÁÁÁO, N-HÁÁÁN, and C-HÁÁÁO, occurring simultaneously in DNA base pairs.

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“…In the second one, the individual HB energies (∆E HB ) were estimated using the electron densities (ρ) calculated using the AIM method at the H-bond critical points (HBCPs) on the basis of the following equation [51][52][53].…”

Section: Computational Details and Methodologymentioning

confidence: 99%

Theoretical insight to intermolecular hydrogen bond interactions between methyl N-(2-pyridyl) carbamate and acetic acid: substituent effects, cooperativity and energy decomposition analysis

Chalanchi

Ebrahimi

Nowroozi

2019

BCC

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In the present work, the hydrogen bond (HB) interactions between substituted syn and anti rotamers of methyl N-(2-pyridyl) carbamate and acetic acid were investigated using quantum mechanical (QM) calculations. The rotamers have two typical active sites to form hydrogen bonds with acetic acid, such that four stable complexes are found on the potential energy surface. The complexes in which the oxygen atom of carbamate acts as proton acceptor are stabilized by EWSs and are destabilized by EDSs. The trend in the effects of substituents is reversed in the other two complexes, in which the nitrogen atom of ring is involved in the interaction. According to energy data, the substituent effects on the interaction energy can be expressed by Hammett constants. The natural resonance theory (NRT) model was used to investigate the charge distribution on the carbamate group and to discuss the interaction energies. The individual HB energies were estimated to evaluate their cooperative contributions on the interaction energies of the complexes. In addition, the localized molecular orbital energy decomposition analyses (LMO-EDA) demonstrate that the electrostatic interactions are the most important stabilizing components of interactions.

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The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine–thymine and guanine–cytosine base pairs

Cited by 23 publications

References 42 publications

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Control of Self‐Assembled 2D Nanostructures by Methylation of Guanine

Correlations of NBO energies of individual hydrogen bonds in nucleic acid base pairs with some QTAIM parameters

Theoretical insight to intermolecular hydrogen bond interactions between methyl N-(2-pyridyl) carbamate and acetic acid: substituent effects, cooperativity and energy decomposition analysis

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