Molecular dynamics simulations of native ubiquinone-10 binding in the photosynthetic reaction center of Rhodobacter sphaeroides are presented that support the theory that the neutral and radical anionic quinones Q B and Q B •bind in different locations. The differences in binding are attributed to differing protonation states of the nearby amino acids GLU L212 and ASP L213. Q B binding at the "dark-adapted" Q B site observed by Stowell et al. is most consistent with protonation of GLU L212. Q B •binding at the experimentally observed "light-adapted" Q B •site is consistent only with protonation of both GLU L212 and ASP L213. The experimentally established pH dependence of electron-transfer rate, combined with our MD results, implies that protonation of ASP L213 must occur before electron transfer. Additionally, the molecular dynamics results suggest that movement of the semiquinone anion Q B •between sites (for different amino acid protonation states) is spontaneous near room temperature and cannot by itself account for the higher of two experimentally observed activation energies for electron transfer from Q A to Q B .

The hybrid Hartree−Fock/density functional B3LYP has been used to predict a variety of properties of 1,4-naphthoquinone, 2-methyl-1,4-naphthoquinone, 2,3-dimethyl-1,4-naphthoquinone, and 9,10-anthraquinone, as well as their radical anions. Geometries and spin properties show good agreement with experiment. The calculated adiabatic electron affinities show excellent agreement with previously determined experimental values, where available. An electron affinity of 1.63 eV is predicted for 2,3-dimethyl-1,4-naphthoquinone. A complete analysis of the vibrational spectra of each neutral molecule is provided and compared with available experimental and previous theoretical results. In each case, the CO antisymmetric stretching vibration is found to be slightly higher in frequency than the CO symmetric stretch. The first full analysis of the vibrational spectra of each of the radical anions is presented, and a comparison is made with the spectra of the neutral molecules. It is found that B3LYP/6-31G(d) theory consistently overestimates vibrational frequencies by 4−5%, in agreement with previous tests, but also does an excellent job of predicting the correct relative ordering of vibrational modes. Unrestricted Hartree−Fock geometries and frequencies are also provided for comparison.

1,l,-Biisoquinoline)bis(2,2,-bipyridine)ruthenium(II) bis(hexafluorophosphate) (2) exists as an ~3:1 mixture of its two diastereomeric forms in acetone solutions at 25 °C. The major isomer, ( , / , )-2, crystallizes in the monoclinic space group C2/c with Z = 8, a = 29.12(1), b = 18.593(7), and c = 17.85(1) Á, ß = 127.81(4)°, R = 0.053, and Rv = 0.062 at 25 °C. As expected, the 1,1'-biisoquinoline ligand is nonplanar, which is a result of a transannular steric interaction between Hg and Hg-. Diastereomerically pure samples of 2 were found to isomerize rapidly in solution at room temperature in the absence of light to give a thermodynamic mixture of the two diastereomers. The rate data for the latter equilibrium at 80 °C are K = 2.89, fc(6amaj-»6am¡n) = 12.7(3) s™1, and fc(6amjn-»6amaj) = 36.6(9) s™1. The activation parameters were determined in the temperature range of 50-90 °C: * (maj-min) = 68.7 kJ mol-1, A5*(maj-»min) = -21 J K™1 mol™1, Aff*(min-»maj) = 66.1 kJ mol™1, and AS*(min-maj) = -38 J K™1 mol™1. Spin saturation transfer (SST), spin inversion transfer (SIT), and two-dimensional exchange spectroscopy (2D EXSY) NMR experiments using 2 and its 2,2'-bipyridine-dg analogue demonstrate that the interconversion of the two diastereomers is the result of an intramolecular process of C2 symmetry that does not change the cis/trans relationship between the 1,1'-biisoquinoline and 2,2'-bipyridine ligands. Irregular mechanisms that involve breaking just one of the ruthenium-isoquinoline bonds have been ruled out because the rate of isomerization of a water-soluble derivative of 2, / -( / -1,1 '-biisoquinoline)bis(2,2'-bipyridine)ruthenium(II) dichloride, is essentially the same in D20 containing 1 M LiCl (fc(6amaj-*6am¡") = 5.7(2) s™1) and 1 M DC1 (/:(6amaj-6amin) = 7.1(1) s™1) at 80 °C. We therefore conclude that interconversion of the two diastereoisomers of 2 takes place by a regular mechanism that involves atropisomerization of the 2-1,1 '-biisoquinoline ligand via a syn transition state.

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