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

• Published in: The Journal of chemical physics 2007-10, Vol.127 (14), p.145102-145102
• Main Authors: Montero-Cabrera, Luis Alberto, Röhrig, Ute, Padrón-Garcia, Juan A, Crespo-Otero, Rachel, Montero-Alejo, Ana L, Garcia de la Vega, José M, Chergui, Majed, Rothlisberger, Ursula
• Format: Article
• Language: English
• Subjects: Binding Sites; Computational Biology - methods; Electronics; Gases; Models, Chemical; Polyenes - chemistry; Porphyrins - chemistry; Quantum Theory; Retinaldehyde - chemistry; Rhodopsin - chemistry; Thermodynamics
• ISSN: 0021-9606; 1089-7690
• DOI: 10.1063/1.2761869

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.