CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.

Details

Serval ID
serval:BIB_42ED2EDA0DF1
Type
Article: article from journal or magazin.
Collection
Publications
Title
CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.
Journal
Journal of Chemical Physics
Author(s)
Montero-Cabrera L.A., Röhrig U., Padrón-Garcia J.A., Crespo-Otero R., Montero-Alejo A.L., Garcia de la Vega J.M., Chergui M., Rothlisberger U.
ISSN
0021-9606 (Print)
ISSN-L
0021-9606
Publication state
Published
Issued date
2007
Peer-reviewed
Oui
Volume
127
Number
14
Pages
145102
Language
english
Abstract
Very large molecular systems can be calculated with the so called CNDOL approximate Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term named CNDOL/21 shows great consistency and easier SCF convergence when used together with an appropriate function for charge repulsion energies that is derived from traditional formulas. It is possible to obtain a priori molecular orbitals and electron excitation properties after the configuration interaction of single excited determinants with reliability, maintaining interpretative possibilities even being a simplified Hamiltonian. Tests with some unequivocal gas phase maxima of simple molecules (benzene, furfural, acetaldehyde, hexyl alcohol, methyl amine, 2,5 dimethyl 2,4 hexadiene, and ethyl sulfide) ratify the general quality of this approach in comparison with other methods. The calculation of large systems as porphine in gas phase and a model of the complete retinal binding pocket in rhodopsin with 622 basis functions on 280 atoms at the quantum mechanical level show reliability leading to a resulting first allowed transition in 483 nm, very similar to the known experimental value of 500 nm of "dark state." In this very important case, our model gives a central role in this excitation to a charge transfer from the neighboring Glu(-) counterion to the retinaldehyde polyene chain. Tests with gas phase maxima of some important molecules corroborate the reliability of CNDOL/2 Hamiltonians.
Keywords
Binding Sites, Computational Biology/methods, Electronics, Gases, Models, Chemical, Polyenes/chemistry, Porphyrins/chemistry, Quantum Theory, Retinaldehyde/chemistry, Rhodopsin/chemistry, Thermodynamics
Pubmed
Web of science
Create date
30/10/2015 10:17
Last modification date
20/08/2019 14:45
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