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Titolo:
Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes
Autore:
Meyer, M; Steinke, T; Brandl, M; Suhnel, J;
Indirizzi:
Konrad Zuse Zentrum Informat Tech Berlin, D-14195 Berlin, Germany Konrad Zuse Zentrum Informat Tech Berlin Berlin Germany D-14195 Germany Inst Mol Biotechnol, D-07745 Jena, Germany Inst Mol Biotechnol Jena Germany D-07745 otechnol, D-07745 Jena, Germany
Titolo Testata:
JOURNAL OF COMPUTATIONAL CHEMISTRY
fascicolo: 1, volume: 22, anno: 2001,
pagine: 109 - 124
SICI:
0192-8651(20010115)22:1<109:DFSOGA>2.0.ZU;2-D
Fonte:
ISI
Lingua:
ENG
Soggetto:
RELATIVISTIC EFFECTIVE POTENTIALS; MOLECULAR-ORBITAL METHODS; AB-INITIO CALCULATIONS; ACID BASE-PAIRS; METAL-CATIONS; BASIS-SETS; HYDROGEN-BOND; FORCE FIELD; DNA BASES; C-H...O;
Keywords:
density functional theory; effective core potential; hydrogen bond; guanine; uracil; metal ion; C-H...O interaction;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
64
Recensione:
Indirizzi per estratti:
Indirizzo: Meyer, M Konrad Zuse Zentrum Informat Tech Berlin, Takustr 7, D-14195 Berlin, Germany Konrad Zuse Zentrum Informat Tech Berlin Takustr 7 Berlin Germany D-14195
Citazione:
M. Meyer et al., "Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes", J COMPUT CH, 22(1), 2001, pp. 109-124

Abstract

The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density-functional calculations. The total interaction energy DeltaE(T) of the C(4)h-symmetric guanine quartet consisting of Hoogsteen-type base pairs with two hydrogen bonds between two neighbor bases is -66.07 kcal/mol at the highest level. The uracil quartet withC6-H6 . . . O4 interactions between the individual bases has only a small interaction energy of -20.92 kcal mol(-1), and the interaction energy of -24.63 kcal/mol for the alternative structure with N3-H3 . . . O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10; and 25% to all interaction energies. Complexes of metal ions with G-quartets can be classified into different structure types. The one with Ca2+ in the central cavity adopts a C-4h-symmetric structure with coplanar bases,whereas the energies of the planar and nonplanar Naf complexes are almost identical. The small ions Li+, Be2+, Cu+, and Zn2+ prefer a nonplanar S-4-symmetric structure. The lack of coplanarity prevents probably a stacking ofthese base quartets. The central cavity is too small for K+ ions and, therefore, this ion favors in contrast to all other investigated ions a C-4-symmetric complex, which is 4.73 kcal/mol more stable than the C-4h-symmetric one. The distance 1.665 Angstrom between K+ and the root-mean-square plane of the guanine bases is approximately half of the distance between two stacked G-quartets. The total interaction energy of alkaline earth ion complexes exceeds those with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen-bonded biological systems. Compared with thebefore-mentioned methods, the HCTH functional leads to longer hydrogen bonds and different relative energies for two U-quartets. Finally, we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C-H . . .O contacts in the uracil quartet. In the G-quartet, the MMFF94 hydrogen bond distances N2--H22 . . . N7 are shorter than the DET distances, whereas the N1-H1 . . . O6distances are longer. (C) 2000 John Wiley & Sons, Inc.

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Documento generato il 18/09/20 alle ore 17:23:32