Exploring the potential energy surface of retinal, a comparison of the performance of different methods

Abstract

The ground state structure of retinal has been investigated. We found that DFT and CASSCF produce different results for the bond length alternation in a model system of retinal. Quantum mechanics/molecular mechanics calculations including the closest surrounding amino acids have been performed, using DFT and CASSCF to calculate the structure of retinal in the protein cavity. The planarity of the retinal molecule is affected by the surrounding protein. DFT and CASSCF produce different twist angles. The difference between CASSCF and DFT appears to be related to the positively charged nitrogen of the Schiff base, which leads to different pi-bond orders produced by the two methods.

Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin

“…7,31 However, it is important to note that the weaker bond-length alternation predicted by DFT QM/ MM models of the complete system (i.e., with a fully relaxed retinyl chromophore and surrounding protein environment) is in very good agreement with a recent double-quantum solid-state NMR study 32 (see open circles in Figure 7). The reduction in bond-length alternation near the Schiff base linkage might be attributed to partial delocalization of the net positive charge in the pSB since such a delocalization of positive charge is expected to reduce the bond order of CC double bonds.…”

“…1,2,[5][6][7] Recent breakthroughs in X-ray crystallography 5,[8][9][10] have made significant contributions toward a complete atomistic description of the protein structure. However, even with these important advances in X-ray crystallography, the resolution remains insufficient to unequivocally define the parts functionally important to the chromophore binding site.…”

“…1,2,[5][6][7][20][21][22] In particular, recent DFT QM/MM studies 1,2 have addressed the elucidation of chromophoreopsin interactions responsible for phototransduction and energy storage through 11-cis/all-trans isomerization, a problem that has been largely elusive to first-principles examinations. Some of the fundamental questions are as follows: What are the molecular rearrangements responsible for 11-cis/all-trans isomerization in the rhodopsin binding pocket?…”

Computational Photobiology and Beyond

“…For PSB11 and PSBAT these levels yield significantly different BLA values. Blomgren et al [42] have proposed that this difference originates from the dynamic electron correlation which is (partially) included in DFT functionals. The changes in the BLA computed for PSB11 are also reflected in the magnitude of the twisting of the C6-C7 single bond with respect to the backbone (see Fig.…”

Ab initio molecular orbital theory: a tool for THz spectroscopic investigation

“…A number of other more advanced quantum mechanical methods have been used recently. 23,26,61 Examples include multiconfiguration self-consistent field theories, density functional theory and the consistent force-field method. We have chosen to use ab initio techniques, in the first instance, which are well documented, easy to use and widely available.…”