Estimation of individual binding energies in some dimers involving multiple hydrogen bonds using topological properties of electron charge density

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

doi:10.1016/j.chemphys.2009.09.013

Cited by 36 publications

(30 citation statements)

References 35 publications

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“…In the previous work [35], we used linear, quadratic and exponential relations to estimate the individual DE HB s by fitting several parameters, such that the DE -P DE HB value converged to zero (where DE are the total binding energy and DE HB s are the individual binding energies). The procedure has also been employed in the present study.…”

Section: Computational Details and Methodsologymentioning

confidence: 99%

“…Although many theoretical studies performed on the total hydrogen bond energy of the Watson-Crick type base pairs, especially the A-T and G-C base pairs [5,10,16,[25][26][27][28][29][30][31], a few studies performed on the individual hydrogen bond energies [32][33][34][35]. Asensio et al [32] evaluated the cooperative hydrogen bonding in the A-T and G-C base pairs.…”

Section: Introductionmentioning

confidence: 99%

“…Grunenberg estimated the relative strength of each HB in A-T and G-C using the compliance constants [33]. In previous work [35], we evaluated the strength of individual HBs for several complexes with multiple HBs, including A-T and G-C, using the electron densities q calculated by atoms in molecules (AIM) method at the bond critical points (BCPs). The electron-donating (ED) and electron-withdrawing (EW) groups change the binding energies of the A-T and G-C base pairs.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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: Computational Details and Methodsologymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Self Cite

View full text Add to dashboard Cite

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“…Herein, the estimation of E HB s was performed on the basis of an exponential relation between BCP and E HB by fitting several parameters, such that the DE-AEE HB value (where DE is the total binding energy and E HB s are individual H-bond energies) converged to zero [60,61].…”

Section: Methodsmentioning

confidence: 99%

Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR, NBO and AIM analyses

Ebrahimi

Habibi‐Khorassani

2011

Molecular Physics

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Protonation increases the total binding energy of the 8-oxoguanine-cytosine (8OG:C) base pair by 60-70% at the B3LYP/6-311þþG(d, p) level of theory. It changes the individual H-bond energies, estimated from electron charge densities at bond critical points, by 1.16 to À16.41 kcal mol À1 . The individual H-bond energies and the two bond X-Y spin-spin coupling constants ( 2h J X-Y ) increase with protonation where 8OG behaves as an H-bond donor; the reverse is true for the H-bonds in which the 8OG unit acts as an H-bond acceptor. Similar to 2h J X-Y , the value of 1h J O-H (a one-bond H Á Á Á Y spin-spin coupling constant) is distance dependent and in linear correlation with the O Á Á Á H distance, but the 1h J N-H values are independent of the N-H distance and the PSO term is the predominant portion in it. The 1 J X-H spin-spin coupling constant is dominated by the negative FC term for all hydrogen bonds, although the PSO term is the best to investigate the behaviour of 1 J X-H across the X-H Á Y H-bond.

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“…?G(d,p) basis set [16,17] was used. It has been demonstrated that B3LYP of theory is very reliable for predicting hydrogen bonding interactions [18][19][20][21]. First, the geometries of the isolated cysteine and propanoic acid monomers were fully optimized.…”

Section: Computational Detailsmentioning

confidence: 99%

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

Huang

Dai

2010

Struct Chem

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The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311??G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine-propanoic acid (Cys-Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra-and inter-molecular H-bonds have been found in Cys-Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of CysProp complexes. The strongest H-bonds (O2H A ÁÁÁO1 B and O2H A ÁÁÁO1 B ) exist in the most stable Cys-Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (q) of BCP and H-bond length as well as the Fock matrix element (F ij ) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.

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Estimation of individual binding energies in some dimers involving multiple hydrogen bonds using topological properties of electron charge density

Cited by 36 publications

References 35 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

Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR, NBO and AIM analyses

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

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