Modeling the bacterial photosynthetic reaction center. 4. The structural, electrochemical, and hydrogen-bonding properties of 22 mutants of Rhodobacter sphaeroides.

Site-directed mutagenesis has been employed by a number of groups to produce mutants of bacterial photosynthetic reaction centers, with the aim of tuning their operation by modifying hydrogen-bond patterns in the close vicinity of the "special pair" of bacteriochlorophylls P identical with P(L)P(M). Direct X-ray structural measurements of the consequences of mutation are rare. Attention has mostly focused on effects on properties such as carbonyl stretching frequencies and midpoint potentials to infer indirectly the induced structural modifications. In this work, the structures of 22 mutants of Rhodobacter sphaeroides have been calculated using a mixed quantum-mechanical molecular-mechanical method by modifying the known structure of the wild type. We determine (i) the orientation of the 2a-acetyl groups in the wild type, FY(M197), and FH(M197) series mutants of the neutral and oxidized reaction center, (ii) the structure of the FY(M197) mutant and possible water penetration near the special pair, (iii) that significant protein chain distortions are required to assemble some M160 series mutants (LS(M160), LN(M160), LQ(M160), and LH(M160) are considered), (iv) that there is competition for hydrogen-bonding between the 9-keto and 10a-ester groups for the introduced histidine in LH(L131) mutants, (v) that the observed midpoint potential of P for HL(M202) heterodimer mutants, including one involving also LH(M160), can be correlated with the change of electrostatic potential experienced at P(L), (vi) that hydrogen-bond cleavage may sometimes be induced by oxidation of the special pair, (vii) that the OH group of tyrosine M210 points away from P(M), and (viii) that competitive hydrogen-bonding effects determine the change in properties of NL(L166) and NH(L166) mutants. A new technique is introduced for the determination of ionization energies at the Koopmans level from QM/MM calculations, and protein-induced Stark effects on vibrational frequencies are considered.

Protonation-induced paramagnetism. Structures and stabilities of six- and seven-coordinate complexes of Os(II) in singlet and triplet states: a density functional study.

Li, Yeh, and Taube in 1993 (J. Am. Chem. Soc. 1993, 115, 10384) synthesized a number of complexes which can be formally regarded as protonated Os(II) species. Some of these were paramagnetic, in contrast to the diamagnetism of the closed shell 5d(6) Os(II) ions. This intriguing phenomenon is investigated theoretically using density functional theory. The geometries, stabilities, and electronic structures of a series of six- and seven-coordinate osmium complexes were studied in gas phase and aqueous solution using the B3P86 functional, in conjunction with the isodensity-polarized continuum model of solvation. The general formula for these complexes is [Os(NH(3))(4)H(L(1)(x)())(m)()(L(2)(y)())(n)()](()(x)()(+)(y)()(+3)+), where L(1) and L(2) = H(2)O, NH(3), CH(3)OH, CH(3)CN, Cl(-), and CN(-), which could be regarded as protonated Os(II) species or hydrides of Os(IV), although according to this work the osmium-hydrogen interaction is best described as a covalent Os(III)-H bond, in which the hydrogen is near-neutral. The ground states are generally found to be singlets, with low-lying triplet excited states. Solvation tends to favor the singlet states by as much as approximately 18 kcal mol(-)(1) in the 3+ ions, an effect which is proportional to the corresponding difference in molecular volumes. To have realistic estimates of the importance of spin-orbit coupling in these systems, the spin-orbit energy corrections were computed for triplet [Os(NH(3))(4)](2+), [Os(NH(3))(4)H](3+), and [Os(NH(3))(4)H(H(2)O)](3+), along with gas-phase Os and its ions as well as [Os(H(2)O)(6)](3+). The seven-coordinate triplet-state complex [Os(NH(3))(5)H(CH(3)OH)](3+), which had been successfully isolated by Li, Yeh, and Taube, is predicted to be a stable six-coordinate complex which strongly binds to a methanol molecule in the second coordination shell. The calculations further suggest that the singlet-triplet splitting would be very small, a few kilocalories per mole at most. The geometries and the electronic structures of the complexes are interpreted and rationalized in terms of Pauling's hybridization model in conjunction with conventional ligand field theory that effectively precludes the existence of true seven-coordinate triplet-state complexes of the above formula.

Modeling the bacterial photosynthetic reaction center 3: interpretation of effects of site-directed mutagenesis on the special-pair midpoint potential.

Interpretation of changes in midpoint potential of the "special pair" in bacterial photosynthetic reaction centers caused by site-directed mutagenesis is discussed in terms of a simple tight-binding model which relates them to concomitant variations in spin distribution between the two bacteriochlorophyll molecules of the special pair. Our analysis improves on previous similar ones by Allen and co-workers [Artz, K., Williams, J. C., Allen, J. P., Lendzian, F., Rautter, J., and Lubitz, W. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 13582; Ivancich, A., Artz, K., Williams, J. C., Allen, J. P., and Mattioli, T. A. (1998) Biochemistry 37, 11812] in that it is both more complete, including electron-phonon coupling, and more accurate. It is applied to analyze data for a series of M160 mutants of Rhodobacter sphaeroides, yielding a value of 0.18+/-0.03 eV for the electronic coupling energy between the highest occupied levels of the two bacteriochlorophylls in the wild-type and a value of the energy offset E(o) between the highest occupied molecular orbitals of the L and M bacteriochlorophylls of 0.14+/-0.03 eV. For a mutant in which the electron hole in the special pair cation is located entirely on the reactive (L) side, a potential of 641+/-30 mV with respect to the normal hydrogen electrode is predicted. This agrees well with the average value ca. 650 mV observed for the heterodimer mutant HL(M202) in which the bacteriochlorophyll on the unreactive M side has been replaced by a bacteriopheophytin, causing extensive charge localization. However, the deduced coupling is found to be very sensitive to small changes in the assumptions used in the model, and various important chemical effects remain to be included.

Towards efficient molecular wires and switches: the Brooker ions.

In search of materials which may function as molecular wires or switches, analytical models have suggested that the Brooker ions should be particularly interesting. We study them in detail using ab initio, semi-empirical and specially-designed empirical techniques, predicting molecular geometries, charge distributions, and conductivities. Provided molecular symmetry is maintained, odd polyenes and Brooker ions NH2-(CH)+ 2n - 1 - NH2 are shown to conduct significantly better than even polyenes, but the advantage becomes a simple multiplicative factor once solitons form (chains of length ca 20 A). Symmetry lowering is predicted to dramatically decrease the conductivity but introduces the possibility that the Brooker ions may function as molecular switches, having greatly enhanced, switchable, non-linear optical properties.