The planarity of the polyene chain of the retinal chromophore in bacteriorhodopsin is studied using molecular dynamics simulation techniques and applying different force-field parameters and starting crystal structures. The largest deviations from a planar structure are observed for the C(13)==C(14) and C(15)==N(16) double bonds in the retinal Schiff base structure. The other dihedral angles along the polyene chain of the chromophore, although having lower torsional barriers in some cases, do not significantly deviate from the planar structure. The results of the simulations of different mutants of the pigment show that, among the studied amino acids of the binding pocket, the side chain of Trp-86 has the largest impact on the planarity of retinal, and the mutation of this amino acid to alanine leads to chromophore planarity. Deletion of the methyl C(20), removal of a water molecule hydrogen-bonded to H(15), or mutation of other amino acids to alanine did not show any significant influence on the distortion of the chromophore. The results from the present study suggest the importance of the bulky residue of Trp-86 in the isomerization process, in both ground and excited states of the chromophore, and in fine-tuning of the pK(a) of the retinal protonated Schiff base in bacteriorhodopsin. The dark adaptation of the pigment and the last step of the bacteriorhodopsin photocycle imply low barriers against the rotation of the double bonds in the Schiff base region. The twisted double bonds found in the present study are consistent with the proposed mechanism of these ground state isomerization events.

No abstract

The microscopic longitudinal elastic modulus, deviations from Hooke’s law, the maximum of the retractive force and tensile strength are calculated for single infinite polyethylene chains using a first principle crystal orbital method and including electron correlation effects by perturbation theory. The best theoretical value of the modulus is 334 GPa at the single-particle level and 276 GPa including correlation. Significant deviations from Hooke’s law start at small deformations and amount to 30%–40% at ε=0.10–0.15. The maximum of the retractive force is f=0.814 mdyn at ε=0.38 and f=0.631 mdyn at ε=0.31, using restricted or unrestricted Hartree–Fock states as zeroth-order wave functions for perturbation theory, respectively. The corresponding maxima of the microscopic tensile strength are at 44.6 and 34.2 GPa, respectively.