Study of the hydrogen bond in different orientations of adenine-thymine base pairs: an ab initio study
Yazarlar (4)
Prof. Dr. Majıd MONAJJEMI Islamic Azad University, İran
B Chahkandi Islamic Azad University, İran
K Zare Islamic Azad University, İran
A Amiri Islamic Azad University, İran
| Makale Türü | Özgün Makale (ESCI dergilerinde yayınlanan tam makale) | ||
| Dergi Adı | Biochemistry Moscow | ||
| Dergi ISSN | 0006-2979 Wos Dergi Scopus Dergi | ||
| Makale Dili | İngilizce | Basım Tarihi | 03-2005 |
| Cilt / Sayı / Sayfa | 70 / 3 / 366–376 | DOI | 10.1007/s10541-005-0123-2 |
| Makale Linki | http://www.scopus.com/inward/record.url?eid=2-s2.0-17544367685&partnerID=MN8TOARS | ||
| Özet |
| In order to gain deeper insight into structure, charge distribution, and energies of A-T base pairs, we have performed quantum chemical ab initio and density functional calculations at the HF (Hartree-Fock) and B3LYP levels with 3-21G*, 6-31G*, 6-31G**, and 6-31++G**basis sets. The calculated donor-acceptor atom distances in the Watson-Crick A-T base pair are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. In addition, for further correction of interaction energies between adenine and thymine, the basis set superposition error (BSSE) associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. In the Watson-Crick A-T base pair there is a good agreement between theory and experimental results. The distances for (N2...H23-N19), (N8-H13...O24), and (C1...O18) are 2.84, 2.94, and 3.63 Å, respectively, at B3LYP/6-31G**level, which is in good agreement with experimental results (2.82, 2.98, and 3.52 Å). Interaction energy of the Watson-Crick A-T base pair is -13.90 and -10.24 kcal/mol at B3LYP/6-31G**and HF/6-31G**levels, respectively. The interaction energy of model (9) A-T base pair is larger than others, -18.28 and -17.26 kcal/mol, and for model (2) is the smallest value, -13.53 and -13.03 kcal/mol, at B3LYP/6-31G* *and B3LYP/6-31++G**levels, respectively. The computed B3LYP/6-31G**bond enthalpies for Watson-Crick A-T pairs of -14.4 kcal/mol agree well with the experimental results of -12.1 kcal/mol deviating by as little as -2.3 kcal/mol. The BSSE of some cases is large (9.85 kcal/mol) and some is quite small (0.6 kcal/mol). © 2005 Pleiades Publishing Inc. |
| Anahtar Kelimeler |
| Ab initio | B3LYP | Hydrogen bonding | Watson-Crick base pairs |
BM Sürdürülebilir Kalkınma Amaçları
| Atıf Sayıları | |
| Web of Science | 12 |
| Scopus | 9 |
| Scopus | 21 |