. Author manuscript; available in PMC: 2010 Apr 13.

Published in final edited form as: J Phys Chem Lett. 2010 Jan 21;1(3):668–672. doi: 10.1021/jz100026k

Table 1.

Comparison of Distances from the PSB Nitrogen Atom to the Side Chain Oxygen Atom of the Asn87, Tyr111, and Glu180 Residues between the Optimized QM/MM Wildtype (WT), Demethyl (DM), and Deprotonated (SBR^cip, SBR^cidp) Retinal Geometries^a

distance (Ǻ)	QM/MM-optimized structures
distance (Ǻ)	WT	DM	SBR^cip	SBR^cidp
OH (Tyr111) ↔ N (PSBR)	3.41	3.47	3.49	3.51
OD1 (Asn87) ↔ N (PSBR)	3.93	2.78	3.84	3.79
OE2 (Glu180) ↔ N (PSBR)	4.29	4.55	4.55	4.55
C5 ↔ SBN⁺/SBN	10.61	10.23	10.84	10.83
A-DBL	1.365	1.359	1.348	1.347
A-SBL	1.432	1.427	1.454	1.457
BLA	0.067	0.068	0.106	0.100

A-DBL refers to the average double bond length. A-SBL refers to the average single bond length. BLA refers to the bond length alternation, which is A-SBL minus A-DBL. Details of the geometric parameters are given in the Supporting Information.