Youngdo Won

Spectroscopy and electron transfer dynamics of the bacterial photosynthetic reaction center

Article de synthese traitant du centre reactionnel des Bacteries photosynthetiques. Sont decrites la structure des chromophones de Rsp. viridis (bacteriopheophytine et bacteriochlorophylle), obtenue par cristallographie aux RX, leurs proprietes photophysiques, leur organisation spatiale et leur comportement dynamique. Des modeles theoriques representant les transferts electroniques et les accepteurs-donneurs sont proposes

Pseudospectral generalized valence‐bond calculations: Application to methylene, ethylene, and silylene

The pseudospectral (PS) method for self‐consistent‐field calculations is extended for use in generalized valence‐bond calculations and is used to calculate singlet–triplet excitation energies in methylene, silylene, and ethylene molecules and bond dissociation and twisting energies in ethylene. We find that the PS calculations lead to an accuracy in total energies of ≤0.1 kcal/mol and excitation energies to ≤0.01 kcal/mol for all systems. With effective core potentials on Si, we find greatly improved accuracy for PS.

On the viability of the superexchange mechanism in the primary charge separation step of bacterial photosynthesis

Abstract We investigate the feasibility of participation of the intermediate bacteriochlorophyll of the reaction center via a superexchange mechanism in the primary charge separation process of bacterial photosynthesis. When an internal charge transfer state of the special pair is incorporated into the theoretical model, an adequate rate of electron transfer can be attained without creating a discrepancy in the calculated singlet-triplet splitting of the charge-separated radical pair state, in contrast to results obtained by R.A. Marcus (Chem. Phys. Lett. 133 (1988) 471–477) without the internal charge transfer state.

Pseudospectral Hartree–Fock calculations on glycine

The pseudospectral method for Hartree–Fock calculations is applied to the glycine molecule, a test case with 100 basis functions. Several algorithmic improvements are reported, including a Newton–Raphson convergence scheme, Fock matrix updating, a multigrid technique, and optional recalculation of integrals. The pseudospectral method is shown to accurately reproduce the Roothaan–Hall relative and total energies for three conformations of glycine. Timing results show the pseudospectral code to be substantially faster than conventional Hartree–Fock codes.

Pseudospectral Hartree-Fock gradient calculations

Techniques for the calculation of analytic first derivatives of the Hartree–Fock energy are reported, within the context of the pseudospectral ab initio method. Using these gradients, geometry optimization is carried out on several molecules at the 6‐31 G** level. The resultant geometries are compared to those from conventional ab initio molecular‐orbital calculations, and it is shown that bond lengths agree to within 0.003 A, while bond angles are within 1°.

Exciton interactions in synthetic porphyrin dimers.

The Soret absorption spectra of six synthetic rigid porphyrin dimers whose crystal structures have been determined are simulated using simple exciton theory. The objective is to test the validity of the point dipole and associated approximations; the electronic interaction parameters are thus calculated using data obtained from the monomer spectra, with no adjustable parameters. Satisfactory agreement between theory and experiment is obtained for one class of dimers but not for a second. This poses a challenge for semiempirical electronic structure methods as to whether improvements over the point dipole calculations can be obtained.

PHOTOCHEMICAL CHARGE SEPARATION IN PHOTOSYNTHETIC REACTION CENTERS

The basic facts and outstanding issues concerning reaction center structure and charge separation dynamics are first summarized. Various theoretical modeling efforts are then presented, classified by the type of approach taken. Recent experimental work is then described, focusing on three types of experiments (electric field, holeburning, and various investigations of genetically modified RCs)

Numerical tests of a generalized multilevel vibronic coupling formalism

An approximate matrix continued fraction method for calculating optical line shapes of molecular systems with multilevel excited state manifolds is compared with converged basis set results. It is shown that the theory gives correct spectral envelopes for all parameter values studied.

Role of Charge Transfer States of the Special Pair in Primary Photosynthetic Charge Separation

We propose a model for primary charge separation in the reaction centers of photosynthetic bacteria based upon an internal charge transfer state of the special pair dimer. In our model, this state serves as a trigger for primary electron transfer, linking the excited state of the special pair (with which it is nearly in resonance) to a superexchange pathway coupled to the initial bacteriopheophytin acceptor. The recombination reaction is not similarly facilitated because the charge transfer state is not close in energy to the ground state; this could be a key factor in explaining the high quantum yield of the primary electron transfer event. The model provides a qualitative explanation for three important experimental measurements (Stark effect, photochemical holeburning, singlet-triplet splitting of the charge separated species) on the reaction center. In addition, its predictions are in excellent accord with recent studies of a genetically modified reaction center in which one bacteriochlorophyll molecule of the special pair is changed to a pheophytin. For this system, one can directly observe the proposed charge transfer state participating in the electron transfer kinetics, located at an energy compatible with our model calculations.

Temperature Dependence of the Longwavelength Absorption Band of the Reaction Center of Rhodopseudomonas viridis

In a series of previous papers(1,2), we have constructed a vibronic coupling model for the excited states of the chromophores in the reaction center (RC) of photosynthetic bacteria. The model has been used to compute various optical properties (absorption, circular dichroism, polarized absorption, holeburning spectra) of the reaction center pigments; a particular focus has been investigation of the low energy Q y exciton component of the special pair bacteriochlorophylls. Many of the intramolecular vibrational parameters (frequencies, excited state geometry shifts) are obtained a priori from monomer experiments, reducing the parametric flexibility associated with phenomenological lineshape functions. Good agreement with experiment has been obtained by varying a limited set of electronic parameters and by including an intermolecular mode for the special pair dimer P.