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Titolo:
Geometrical and vibrational properties of nucleic acid constituents interacting with explicit water molecules as analyzed by density functional theory calculation. 1. Uracil+n(w)H(2)O (n(w)=1,...,7)
Autore:
Gaigeot, MP; Ghomi, M;
Indirizzi:
Univ Paris 06, UPRESA CNRS 7033, Lab Physicochim Biomol & Cellulaire, F-75252 Paris 05, France Univ Paris 06 Paris France 05 mol & Cellulaire, F-75252 Paris 05, France
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY B
fascicolo: 21, volume: 105, anno: 2001,
pagine: 5007 - 5017
SICI:
1520-6106(20010531)105:21<5007:GAVPON>2.0.ZU;2-E
Fonte:
ISI
Lingua:
ENG
Soggetto:
NEUTRON INELASTIC-SCATTERING; MECHANICAL FORCE-FIELDS; GROUND-STATE PROPERTIES; URACIL-WATER; AB-INITIO; OPTICAL SPECTROSCOPIES; IMINO PROTON; BASES; RNA; HYDRATION;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
46
Recensione:
Indirizzi per estratti:
Indirizzo: Ghomi, M Univ Paris 06, UPRESA CNRS 7033, Lab Physicochim Biomol & Cellulaire, CaseCourrier 138,4 Pl Jussieu, F-75252 Paris 05, France Univ Paris 06 Case Courrier 138,4 Pl Jussieu Paris France 05 nce
Citazione:
M.P. Gaigeot e M. Ghomi, "Geometrical and vibrational properties of nucleic acid constituents interacting with explicit water molecules as analyzed by density functional theory calculation. 1. Uracil+n(w)H(2)O (n(w)=1,...,7)", J PHYS CH B, 105(21), 2001, pp. 5007-5017

Abstract

To analyze the preferential sites of interaction of water molecules with uracil (RNA base) through the first hydration shell, we resorted to density functional theory (DFT) calculations by means of B3LYP exchange and correlation functionals. The effect of two different basis sets with and without diffuse orbitals, i.e., 6-31G* and 6-31++G*, respectively, has been studied on the energetics, as well as on the geometrical and vibrational properties, of the studied compounds. Water molecules have been gradually placed in an average plane containing uracil, and their number (n(w)) was varied from 1 to 7. For a given value of n(w), different possible interaction sites of water molecule(s) with respect to the base have been taken into consideration. The results obtained from this investigation allowed us to estimate theenergy difference separating optimized configurations by taking into account both electronic and vibrational energies. The most energetically favorable configurations for a given n(w) value were then used in further calculations with higher n(w) values. It has been shown that the most energeticallyfavorable supermolecular configurations found with large number of n(w) contain water dimers and water trimers. Geometrical parameters of uracil, water molecules, and hydrated uracil have been discussed in detail. Calculatedvibrational modes for uracil and hydrated uracil (uracil + 7H(2)O) have been compared with those previously analyzed by optical spectroscopy.

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Documento generato il 02/04/20 alle ore 18:47:20