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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 101 (1999), S. 180-185 
    ISSN: 1432-2234
    Keywords: Key words: Density functional theory ; Proton ; translocation ; Photocycle ; Opsin shift
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The effects of the amino acid side chains of the binding pocket of bacteriorhodopsin (bR) and of a water molecule on the structure of the retinal Schiff base have been studied using Becke3LYP/6-31G* level of density functional theory. A model protonated Schiff base structure including six conjugated double bonds and methyl substituents was optimized in the presence of several amino acid side chains and of a water molecule, separately. The Schiff base structure was also calculated in the form of a neutral species. At each optimized complex geometry the atomic charges of the model Schiff base were calculated using Mulliken population analysis. In agreement with previously proposed counterion(s) of the protonated retinal Schiff base in bR, the results show that Asp85 and Asp212, which are present in the form of negatively charged groups, have significantly large effects on the structure and electronic configuration of both unprotonated and protonated model Schiff bases. The presence of a water molecule in the vicinity of the Schiff base demonstrates significant effects which are comparable to those of aspartate groups. Other side chains studied did not show any significant effect in this direction. Apart from the aspartate groups and the water molecule, in none of the other complexes studied are the atomic charges and the bond alternation of the model Schiff base significantly influenced by the presence of the neighboring amino acids.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1572-8951
    Keywords: Water dimer ; PES ; DFT ; B3PW91 ; ab initio
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Conventional ab initio and density functional methods with extended basis sets were employed in the study of a path on the water-dimer potential energy surface. The results show that density functional methods do depend strongly on the type of exchange-correlation potential employed, as well as on the quality of the basis sets – similarly to conventional ab initio methods – and on the density of the grid. Gradient-corrected methods behave, as expected, better than uncorrected ones, the Becke–Lee–Yang–Parr (BLYP) potential being the one that gives the best results. However, too large chemical- and hydrogen-bond lengths and absolute energies, as well as too small relative total and correlation energies demonstrate that even BLYP calculations with a relative large basis set are not good as MP2 calculations of the same size. Adiabatically connected functionals (ACM), represented in this work by B3PW91, provide an improvement on the whole surface.
    Type of Medium: Electronic Resource
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