Study of the hydrogen bond in different orientations of adenine-thymine base pairs: An ab initio study

Monajjemi, Majid; Chahkandi, Behzad; Zare, Kazem; Amiri, Ali

doi:10.1007/s10541-005-0123-2

Cited by 12 publications

(13 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Dependence of the Optimized Geometry of the AT Base Pair on the Level of Theory. The available data in the literature 20,22,[81][82][83][84][85][86][87][88] for the X • • • Y distances of the AT base pair studied by Hartree-Fock (HF), B3LYP, BP86, and post-SCF [MP2, RI-MP2] theories with different basis sets are listed in Table 1 for comparison.…”

Section: Resultsmentioning

confidence: 99%

Red-Shifted Hydrogen Bonds and Blue-Shifted van der Waals Contact in the Standard Watson−Crick Adenine−Thymine Base Pair

Zhou

Qiu

2009

J. Phys. Chem. A

View full text Add to dashboard Cite

Standard Watson-Crick adenine-thymine (AT) base pair has been investigated by using the B3LYP functional with 6-31G(d, p) basis set, at which level of theory the geometrical characteristics of the AT base pair are the best in agreement with the experiment. It exhibits simultaneously red-shifted N-H...O and N-H...N hydrogen bonds as well as a blue-shifted C-H...O contact. AIM analysis suggests that the blue-shifted C-H...O contact exists as van der Waals interaction, and the electron density rho that reflects the strength of a bond has been used to explain the red- and blue-shifted. By means of NBO analysis, we report a method to estimate the effect of hyperconjugation quantitatively, which combines the electron density in the X-H (X = N, C) sigma bonding orbital with that in the sigma* antibonding orbital. The effect of structural reorganization on the origins of the red- and blue-shifted has been considered by the partial optimization, its behavior on the X-H (X = N, C) bond is quite different. Rehybridization and repolarization models are employed, and they act as bond-shortening effects. The competition between the electrostatic attractions and Pauli/nucleus repulsions is present in the two typical red-shifted N-H...O and N-H...N hydrogen bonds as well as in the blue-shifted C-H...O van der Waals contact. Electrostatic attraction between H and Y atoms (Y = O, N) is an important reason for the red shift, while the nucleus-nucleus repulsion between H and O atoms may be a factor leading to the C-H bond contraction and its blue shift. The electric field effect induced by the acceptor O atom on the C-H bond is also discussed.

show abstract

Section: Resultsmentioning

confidence: 99%

Red-Shifted Hydrogen Bonds and Blue-Shifted van der Waals Contact in the Standard Watson−Crick Adenine−Thymine Base Pair

Zhou

Qiu

2009

J. Phys. Chem. A

View full text Add to dashboard Cite

show abstract

“…Specifically, the calculations use the TZVP basis set 26 and the B3LYP functional, which contains the B3 exchange functional 27 and the gradient‐corrected LYP correlation functional 28. The adequacy of this hybrid functional in describing hydrogen bonds in molecular systems has been shown numerous times in the literature 29–31. The nature of all optimized structures, monomers and donor–acceptor complexes has been confirmed by analytical frequency calculations.…”

Section: Computational Detailsmentioning

confidence: 97%

The role of hydrogen bonds in protein–ligand interactions. DFT calculations in 1,3‐dihydrobenzimidazole‐2 thione derivatives with glycinamide as model HIV RT inhibitors

Kretschmer

Kinzel

González

2011

Int J of Quantum Chemistry

View full text Add to dashboard Cite

ABSTRACT:The structures, redshifts, binding energies, Bader analysis, and sharedelectron numbers (SENs) of 1,3-dihydrobenzimidazole-2-thione (DBS) derivatives hydrogen bonded to glycinamide were calculated by the means of DFT methods. The DBS-glycinamide complex serves as a model for human immunodeficiency virus reverse transcriptase inhibitors of the N-dimethylallyl-6-methyl-4,5,6,7-tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepin-2(1H)-thione family. A correlation between experimental Gibbs free energies, associated biological activities and the energy of the hydrogen bond obtained with the SEN method showed a linear relationship for different substitution patterns. Our results suggest that efficient inhibitors are those substituted in the 8-position with electron-withdrawing small substituents.

show abstract

“…The Onsager-SCRF was that it permitted one to directly exploit almost all of the computational facilities of the Gaussian packages .For this reason, and for its very limited computational cost , it is still in use by people not requiring an accurate description of salvation effects but just a guess or a qualitative correction to the values obtained for the isolated molecule. Users must be aware of the limitations of the approach,of the unphysical deformation of the solute charge distribution it may induce, and of other shortcomings specific of the approach, such as the lack of salvation for solutes with zero permanent dipole [65][66] . In the Onsager method, the solute molecule is placed in a spherical cavity of radius a 0 surrounded by a continuum with constant dielectric properties 67 .…”

Section: Methodsmentioning

confidence: 99%

The interaction of single walled carbon nanotube (SWCNT) with phospholipids membrane: in point view of solvent effect

Elsagh¹,

Jalilian²,

Ilkhani³

2015

Orient. J. Chem

View full text Add to dashboard Cite

Nature provides us with a very large number of channels or nano-pores embedded in cell membranes. The function of channels is to allow selectivity and specificity for a Variety of molecular species transport across the cell membrane. These channels,included : a)ligand-gated channels) voltage-gated channels, c)Second messenger gated channels, d)mechanic sensitive channels) Gap junctions: porins not gated [1][2][3][4][5][6][7] . ORIENTAL JOURNAL OF CHEMISTRY ABSTRACTIn this research, we have studied the structural properties of phospholipids, surrounding single-walled carbon nanotube (SWCNT, by using ab-inition and molecular dynamics simulation. Carbon nanotubes (SWCNTs) are very common in medical research and are being highly studied in the fields of biosensing methods for disease treatment and efficient drug delivery and health monitoring. The transportation of SWCNT through the cell membrane widely investigated because of many advantages. Because of the differences among force fields, the energy of a molecule calculated using two different force fields will not be the same. In this study difference in force field illustrated by comparing the energy of calculated by using force fields, MM+, Amber and OPLS. The quantum Mechanics (QM) calculations were carried out with the GAUSSIAN 09 program based on density functional theory (DFT) at B1LYP/6-31G* level. In our recent study the electronic structure of open-end of SWCNT and transportation of SWCNT through the phospholipids in skin cell membrane have been discussedfor both vacuum and solvent media.

show abstract

Study of the hydrogen bond in different orientations of adenine-thymine base pairs: An ab initio study

Cited by 12 publications

References 39 publications

Red-Shifted Hydrogen Bonds and Blue-Shifted van der Waals Contact in the Standard Watson−Crick Adenine−Thymine Base Pair

Red-Shifted Hydrogen Bonds and Blue-Shifted van der Waals Contact in the Standard Watson−Crick Adenine−Thymine Base Pair

The role of hydrogen bonds in protein–ligand interactions. DFT calculations in 1,3‐dihydrobenzimidazole‐2 thione derivatives with glycinamide as model HIV RT inhibitors

The interaction of single walled carbon nanotube (SWCNT) with phospholipids membrane: in point view of solvent effect

Contact Info

Product

Resources

About