Substituent effects of R (R=CH3, CH3O, F and NO2) on the A:T and C:G base pairs: a theoretical study

Meng, Fancui; Liu, Chengbu; Xu, Weifeng

doi:10.1016/s0009-2614(03)00590-6

Cited by 21 publications

(21 citation statements)

References 19 publications

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“…The difference in flexibility between adenine-thymine (A-T) and guanine-cytosine (G-C) base pairs may be an additional factor for molecular recognition during the binding of other molecules to DNA, especially in the case of intercalation processes [7,8]. Several ab initio molecular orbital studies on the substitution effect on hydrogen-bond formation energy of adenine-uracile-X (A-U-X), X-adenine-uracile (X-A-U), guanine-cytosine-X (G-C-X), and X-guanine-cytosine (X-G-C) base pairs have already been reported by Kawahara et al [9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

“…Usually, the cytosine derivatives possessing an ED group form a more stable pair with guanine (in comparison with G-C) and the guanine derivatives possessing an EW group form a more stable pair with cytosine (in comparison with G-C). In addition, the adenine derivatives possessing an EW group and the thymine derivatives possessing an ED group form more stable pairs with the thymine and adenine bases, respectively (in comparison with A-T) [8]. Although many studies were performed on the effects of substituents on the total binding energies and the geometries of the G-C and A-T base pairs [8,36], but no studies were done on the effects of substituents on the individual H-bond energies.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, the adenine derivatives possessing an EW group and the thymine derivatives possessing an ED group form more stable pairs with the thymine and adenine bases, respectively (in comparison with A-T) [8]. Although many studies were performed on the effects of substituents on the total binding energies and the geometries of the G-C and A-T base pairs [8,36], but no studies were done on the effects of substituents on the individual H-bond energies. In this work, we have investigated the substituent effects on the individual hydrogen bond energies in the A-T and G-C base pairs (see Fig.…”

Section: Introductionmentioning

confidence: 99%

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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

Ebrahimi

Habibi‐Khorassani

Delarami

et al. 2010

J Comput Aided Mol Des

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The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO(2)) increase the total binding energy (DeltaE) of X-G-C derivatives and the electron donating (ED) substituent (CH(3)) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH(3) in the 1 position and F in the 5 position, which in both cases the DeltaE value decreases negligibly small. With minor exceptions (X=8-CH(3), 8-F, and 9-NO(2)), both ED and EW substituents increase slightly the DeltaE values of X-A-T derivatives. The individual HB energies (E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO(2) substituted derivative in each case.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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

Ebrahimi

Habibi‐Khorassani

Delarami

et al. 2010

J Comput Aided Mol Des

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“…Kawahara et al [21], Bickelhaupt et al [33][34][35], and Meng et al [40][41][42] examined by theoretical computations the effect of substituents on the hydrogen bonding of modified DNA base pairs. Bickelhaupt et al [35,39] investigated how the strength and length of hydrogen bonds is influenced by the introduction of F, Cl, and Br substituents at position 8 in the purine (Scheme 1) and at position 6 of the pyrimidine nucleobases.…”

Section: Introductionmentioning

confidence: 99%

“…The same authors analyzed in particular [34] the impact of substituents (NH, NH 2 , NH 3 + , O -, OH, and OH 2 + ) at position 8 in the purine ring and in position 6 in the pyrimidine cycle on interaction energies for hydrogen-bonded complexes of substituted guanines with cytosine derivatives. Meng et al [40][41][42] investigated the effect of CH 3 , CH 3 O, F, and NO 2 substituents on the adenine-thymine base pairing. Popelier et al [43] examined by theoretical DFT computations at the B3LYP/6-311+G(2d,p) level the effects of 42 substituents on the interaction energy of the cytosine-guanine base pairs.…”

Section: Introductionmentioning

confidence: 99%

Effects of structural variations on the hydrogen bond pairing between adenine derivatives and thymine

Nikolova¹,

Galabov²

2015

Maced. J. Chem. Chem. Eng.

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The hydrogen bonding between substituted adenines and thymine was investigated by density functional theory computations at the B3LYP/6-311+G(2d,2p) level. The effect of 20 different polar substituents at position 8 in adenine was examined in detail. Three different theoretical parameters, reflecting the electrostatics at the atoms involved in hydrogen bonding, were applied. An excellent correlation between electrostatic potentials at the bonding atoms in the monomer adenines and interaction energies was derived (Eqn. 2). It can be employed in designing bioactive adenine derivatives that are able to bind with a finely adjusted strength to thymine bioreceptor sites. NBO and Hirshfeld atomic charges are found to be less successful as reactivity predictors in these interactions.Keywords: DNA base pair; adenine; thymine; hydrogen bonding; electrostatic potential; atomic charges ЕФЕКТИ НА СТРУКТУРНИТЕ ВАРИЈАЦИИ ВРЗ СПАРУВАЊЕТО НА АДЕНИНСКИ ДЕРИВАТИ И ТИМИН СО ПОМОШ НА ВОДОРОДНО СВРЗУВАЊЕИстражувано е водородното сврзување помеѓу супституирани аденини и тимин со помош на пресметки според теоријата за функционал на електронската густина на нивото B3LYP/6-311+G(2d,2p). Детално е изучуван ефектот на 20 различни поларни супституенти на аденин во позицијата 8. Применети се три различни теоретски параметри кои ја рефлектираат електростатиката на атомите вклучени во водородното сврзување. Добиена е одлична корелација помеѓу електростатските потенцијали на сврзувачките атоми во мономерните аденини и интеракционите енергии (р-ка 2). Тоа може да се примени при дизајнирање на биоактивни аденински деривати кои можат да се сврзат со фино нагодена јачина со тиминските биорецепторски сајтови. Најдено е дека т.н. NBO и Хиршфилдовите (Hirshfeld) атомски полнежи се помалку успешни како претскажувачи на реактивноста во овие интеракции.Клучни зборови: ДНК базен пар; аденин; тимин; водородно сврзување; електростатски потенцијал; атомски полнежи  Dedicated to Academician Gligor Jovanovski on the occasion of his 70 th birthday.

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An Electron Density Source‐Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States^†

et al. 2018

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The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc.

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Substituent effects of R (R=CH3, CH3O, F and NO2) on the A:T and C:G base pairs: a theoretical study

Cited by 21 publications

References 19 publications

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

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

Effects of structural variations on the hydrogen bond pairing between adenine derivatives and thymine

An Electron Density Source‐Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States^†

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Substituent effects of R (R=CH3, CH3O, F and NO2) on the A:T and C:G base pairs: a theoretical study

Cited by 21 publications

References 19 publications

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

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

Effects of structural variations on the hydrogen bond pairing between adenine derivatives and thymine

An Electron Density Source‐Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†

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An Electron Density Source‐Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States^†