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Titolo:
A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
Autore:
Cui, Q; Elstner, M; Kaxiras, E; Frauenheim, T; Karplus, M;
Indirizzi:
Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA Harvard UnivCambridge MA USA 02138 & Chem Biol, Cambridge, MA 02138 USA Harvard Univ, Dept Phys, Cambridge, MA 02138 USA Harvard Univ Cambridge MA USA 02138 v, Dept Phys, Cambridge, MA 02138 USA Univ Gesamthsch Paderborn, Dept Theoret Phys, D-33098 Paderborn, Germany Univ Gesamthsch Paderborn Paderborn Germany D-33098 8 Paderborn, Germany Univ Strasbourg 1, ISIS, Lab Chim Biophys, F-67000 Strasbourg, France UnivStrasbourg 1 Strasbourg France F-67000 , F-67000 Strasbourg, France Univ Oxford, New Chem Lab, Oxford OX1 3QT, England Univ Oxford Oxford England OX1 3QT New Chem Lab, Oxford OX1 3QT, England
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY B
fascicolo: 2, volume: 105, anno: 2001,
pagine: 569 - 585
SICI:
1520-6106(20010118)105:2<569:AQIOTS>2.0.ZU;2-3
Fonte:
ISI
Lingua:
ENG
Soggetto:
ALANINE-BASED PEPTIDES; MOLECULAR-DYNAMICS SIMULATIONS; ELECTRON-SPIN-RESONANCE; ALPHA-HELIX; COMBINED QUANTUM; HYBRID QUANTUM; BIOLOGICAL MACROMOLECULES; CONFIGURATION-INTERACTION; GEOMETRY OPTIMIZATION; COMPUTER-SIMULATION;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
91
Recensione:
Indirizzi per estratti:
Indirizzo: Karplus, M Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA Harvard Univ Cambridge MA USA 02138 l, Cambridge, MA 02138 USA
Citazione:
Q. Cui et al., "A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method", J PHYS CH B, 105(2), 2001, pp. 569-585

Abstract

A quantum mechanical/molecular mechanical (QM/MM) approach based on an approximate density functional theory, the so-called self-consistent charge density functional tight binding (SCC-DFTB) method, has been implemented in the CHARMM program and tested on a number of systems of biological interest. In the gas phase, SCC-DFTB gives reliable energetics for models of the triosephosphate isomerase (TIM) catalyzed reactions. The rms errors in the energetics compared to B3LYP/6-31+G(d,p) are about 2-4 kcal/mol; this is to becontrasted with AM1, where the corresponding errors are 9-11 kcal/mol. Themethod also gives accurate vibrational frequencies. For the TIM reactions in the presence of the enzyme, the overall SCC-DFTB/CHARMM results are in somewhat worse agreement with the B3LYP/6-31+G(d,p)/CHARMM values; the rms error in the energies is 5.3 kcal/mol. Single-point B3LYP/CHARMM energies atthe SCC-DFTB/CHARMM optimized structures were found to be very similar to the full B3LYP/CHARMM values. The relative stabilities of the alpha (R) and3(10) conformations of penta- and octaalanine peptides were studied with minimization and molecular dynamics simulations in vacuum and in solution. Although CHARMM and SCC-DFTB give qualitative different results in the gas phase (the latter is in approximate agreement with previous B3LYP calculations), similar behavior was found in aqueous solution simulations with CHARMMand SCC-DFTB/CHARMM. The 310 conformation was not found to be stable, and converted to the alpha (R) form in about 15 ps. The cia conformation was stable in the simulation with both SCC-DFTB/CHARMM and CHARMM. The i,i+3 CO HN distances in the CIR conformation were shorter with the SCC-DFTB method (2.58 Angstrom) than with CHARMM (3.13 Angstrom). With SCC-DFTB/CHARMM, significant populations with i,i+3 CO.. HN distances near 2.25 Angstrom, particularly for the residues at the termini, were found. This can be related to the conclusion from NMR spectroscopy that the 310 configuration contributesfor alanine rich peptides, especially at the termini.

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Documento generato il 11/07/20 alle ore 11:04:44