Fig. 1: Structure and scope of Arch-3zero.
From: Rhodopsin charge diffusion computations disclose contrasting color-tuning mechanisms
A Schematic structure of a microbial rhodopsin with an all-trans chromophore and a counterion located near its Schiff base. B Left. Subsystems of Arch-3zero before counterion configuration and geometry optimizations. Center and right. Illustration of the negative charge optimization process. The blue (i.e., negative) color representing the D222 charge is transferred to other residues during the optimization and then affects geometrical relaxation. C ESP generated by shielding a central negative charge (charges and bond length parameters are from acetone, described at the HF/6-31G* level of theory). The initial ESP given in red is diffuse (top blue line) or localized (bottom orange line) after shortening and elongating the dipole bond length, respectively. D The effect seen in C is qualitatively replicated (green lines) by delocalizing of a single central negative charge spanning the same blue and orange line limits by changing the charge fraction (X).
