A stochastic surrogate Hamiltonian approach of coherent and incoherent exciton transport in the Fenna-Matthews-Olson complex

The capture and transduction of energy in biological systems is clearly necessary for life, and nature has evolved remarkable macromolecular entities to serve these purposes. The Fenna-Matthews-Olson (FMO) complex serves as an intermediate to transfer the energy from the chlorosome to the special pairs of different photo systems. Recent observations have both suggested the importance of coherent exciton transport within the FMO and motivated an elegant and appropriate theoretical construct for interpreting these observations. Here we employ a different approach to exciton transport in a relaxing environment, one based on the stochastic surrogate Hamiltonian method. With it, we calculate the quantum trajectories through the FMO complex both for the model involving seven bacteriochlorophylls that has been used before, and for one involving an eighth bacteriochlorophyll, which has been observed in some new and very important structural work. We find that in both systems, efficient energy transfer to the ultimate receptor occurs, but that because of the placement of, and energy relaxation among, the different bacteriochlorophyll subunits in the FMO complex, the importance of coherent oscillation that was discussed extensively for the seven site system is far less striking for the eight site system, effectively because of the weak mixing between the initial site and the remainder of the system. We suggest that the relevant spectral densities can be determinative for the energy transport route and may provide a new way to enhance energy transfer in artificial devices.     

Correlated intermolecular coupling fluctuations in photosynthetic complexes

The functioning and efficiency of natural photosynthetic complexes is strongly influenced by their embedding in a noisy protein environment, which can even serve to enhance the transport efficiency. Interactions with the environment induce fluctuations of the transition energies and couplings between the chlorophyll molecules, and due to the fact that different fluctuations will partially be caused by the same environmental factors, correlations between the various fluctuations will occur. We argue that fluctuations of the couplings should, in general, not be neglected, as these have a considerable impact on population transfer rates, decoherence rates, and the efficiency of photosynthetic complexes. Furthermore, while correlations between transition energy fluctuations have been studied, we provide the first quantitative study of the effect of correlations between coupling fluctuations and transition energy fluctuations, and of correlations between the various coupling fluctuations. It is shown that these additional correlations typically lead to changes in interchromophore transfer rates and population oscillations and can lead to a limited enhancement of the light harvesting efficiency.     

Influence of environment on proton-transfer mechanisms in model triads from theoretical calculations

We have carried out theoretical calculations to analyze molecular interactions and proton transfer mechanisms in the formate–imidazole–water system, which may be considered the simplest model of catalytic triads in serine proteases. Computations were carried out at the density functional theory level. The effect of a dielectric environment on energy surfaces is considered using a polarizable continuum model and the self-consistent reaction field approach. The role played by inertial and noninertial polarization of this environment is emphasized. Nonequilibrium solvation effects have been estimated. The results show that there are different reaction mechanisms, concerted or stepwise, that may be competitive, depending on the nature of the molecular environment. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1675–1688, 1998     

Theoretical studies on effective metal-to-ligand charge transfer characteristics of novel ruthenium dyes for dye sensitized solar cells

The development of ruthenium dye-sensitizers with highly effective metal-to-ligand charge transfer (MLCT) characteristics and narrowed transition energy gaps are essential for the new generation of dye-sensitized solar cells. Here, we designed a novel anchoring ligand by inserting the cyanovinyl-branches inside the anchoring ligands of selected highly efficient dye-sensitizers and studied their intrinsic optical properties using theoretical methods. Our calculated results show that the designed ruthenium dyes provide good performances as sensitizers compared to the selected efficient dyes, because of their red-shift in the UV–visible absorption spectra with an increase in the absorption intensity, smaller energy gaps and thereby enhancing MLCT transitions. We found that, the designed anchoring ligand acts as an efficient “electron-acceptor” which boosts electron-transfer from a –NCS ligand to this ligand via a Ru-bridge, thus providing a way to lower the transition energy gap and enhance the MLCT transitions.     

A Complex Comprising a Cyanine Dye Rotaxane and a Porphyrin Nanoring as a Model Light‐Harvesting System

A nanoring‐rotaxane supramolecular assembly with a Cy7 cyanine dye (hexamethylindotricarbocyanine) threaded along the axis of the nanoring was synthesized as a model for the energy transfer between the light‐harvesting complex LH1 and the reaction center in purple bacteria photosynthesis. The complex displays efficient energy transfer from the central cyanine dye to the surrounding zinc porphyrin nanoring. We present a theoretical model that reproduces the absorption spectrum of the nanoring and quantifies the excitonic coupling between the nanoring and the central dye, thereby explaining the efficient energy transfer and demonstrating similarity with structurally related natural light‐harvesting systems.     

A Complex Comprising a Cyanine Dye Rotaxane and a Porphyrin Nanoring as a Model Light-Harvesting System

A nanoring-rotaxane supramolecular assembly with a Cy7 cyanine dye (hexamethylindotricarbocyanine) threaded along the axis of the nanoring was synthesized as a model for the energy transfer between the light-harvesting complex LH1 and the reaction center in purple bacteria photosynthesis. The complex displays efficient energy transfer from the central cyanine dye to the surrounding zinc porphyrin nanoring. We present a theoretical model that reproduces the absorption spectrum of the nanoring and quantifies the excitonic coupling between the nanoring and the central dye, thereby explaining the efficient energy transfer and demonstrating similarity with structurally related natural light-harvesting systems.     

Potential dependence of step and kink energies on Au(100) electrodes in sulfuric acid

Using electrochemical STM we studied monolayer high Au islands on Au(100) electrodes in sulfuric acid as a function of the electrode potential. We made use of theoretical and experimental methods recently developed for UHV experiments on metal islands. It is demonstrated that these models are likewise applicable to islands on metal electrodes in a liquid environment. From a quantitative analysis of the equilibrium island shape and of the island shape fluctuations we determined the step free energy (line tension) as a function of orientation and the kink energy, and the dependence of these quantities on the electrode potential. In a first approach to a theoretical understanding the electrostatic contributions to the line tension are considered. It is concluded that these contributions should add significantly to the observed variation with the potential. This fails however to provide essential features of the experimental result.     

Energy transfer in the nanostar: the role of coulombic coupling and dynamics

We present a theoretical investigation of energy transfer in the phenylene ethynelene dendrimer known as the nanostar. Data from extensive molecular dynamics simulations are used to model the dynamical effects caused by torsional motion of the phenyl groups. We compare rate constants for energy transfer between the two-ring chromophore and the three-ring chromophore obtained via the F?rster model, the ideal dipole approximation (IDA), and the transition density cube (TDC) method, which has as its limit an exact representation of the Coulombic coupling. We find that the rate constants obtained with the TDC are extremely sensitive to the phenyl group rotation, whereas the constants computed with the F?rster model and the IDA are not. The implications of these results for the interpretation of recent pump-probe experiments on the nanostar are discussed in detail. Finally, we predict the temperature dependence of the rate constant for energy transfer.     

Excited state dynamics in photosynthetic reaction center and light harvesting complex 1

Key to efficient harvesting of sunlight in photosynthesis is the first energy conversion process in which electronic excitation establishes a trans-membrane charge gradient. This conversion is accomplished by the photosynthetic reaction center (RC) that is, in case of the purple photosynthetic bacterium Rhodobacter sphaeroides studied here, surrounded by light harvesting complex 1 (LH1). The RC employs six pigment molecules to initiate the conversion: four bacteriochlorophylls and two bacteriopheophytins. The excited states of these pigments interact very strongly and are simultaneously influenced by the surrounding thermal protein environment. Likewise, LH1 employs 32 bacteriochlorophylls influenced in their excited state dynamics by strong interaction between the pigments and by interaction with the protein environment. Modeling the excited state dynamics in the RC as well as in LH1 requires theoretical methods, which account for both pigment-pigment interaction and pigment-environment interaction. In the present study we describe the excitation dynamics within a RC and excitation transfer between light harvesting complex 1 (LH1) and RC, employing the hierarchical equation of motion method. For this purpose a set of model parameters that reproduce RC as well as LH1 spectra and observed oscillatory excitation dynamics in the RC is suggested. We find that the environment has a significant effect on LH1-RC excitation transfer and that excitation transfers incoherently between LH1 and RC.     

State-to-state rotational rate constants for CO + He: infrared double resonance measurements and simulation of the data using the SAPT theoretical potential energy surface

An extensive data set of 54 time-resolved pump-probe measurements was used to examine CO + He rotational energy transfer within the CO v = 2 rotational manifold. Rotational levels in the range Ji = 2-9 were excited and collisional energy transfer of population to the levels Jf = 1-10 was monitored. The resulting data set was analyzed by fitting to numerical solutions of the master equation. State-to-state rate constant matrices were generated using fitting law functions and ab initio theoretical calculations that employed the SAPT potential energy surface of Heijmen et al. [J. Chem. Phys. 107, 9921 (1997)]. Fitting laws based on the modified exponential gap (MEG), statistical power exponential gap (SPEG), and energy corrected sudden with exponential power (ECS-EP) models all yielded acceptable simulations of the kinetic data, as did the theoretical rate constants. However, the latter were unique in their ability to reproduce both our kinetic data and the pressure broadening coefficients for CO + He. These results provide an impressive demonstration of the quality of the symmetry adapted perturbation theory (SAPT) potential energy surface.     

Elastic/inelastic and charge transfer collisions of H++H2 at collision energies of 4.67, 6, 7.3, and 10 eV

Quantum mechanical studies of vibrational and rotational state-resolved differential cross sections, integral cross sections, and transition probabilities for both the elastic/inelastic and charge transfer processes have been carried out at collision energies of 4.67, 6, 7.3, and 10 eV using the vibrational close-coupling rotational infinite-order sudden approach. The dynamics has been performed employing our newly obtained quasidiabatic potential energy surfaces which were generated using ab initio procedures and Dunning's correlation-consistent-polarized quadrupole zeta basis set. The present theoretical results for elastic/inelastic processes provide an overall excellent agreement with the available experimental data and they are also found to be almost similar to that obtained in earlier theoretical results using the ground electronic potential energy surface, lending credence to the accuracy and reliability of the quasidiabatic potential energy surfaces. The results for the complementary charge transfer processes are also presented at these energies.     

Dependence of charge transfer reorganization energy on carrier localisation in organic molecular crystals

Taking the organic molecular material dithiophene-tetrathiafulvalene (DT-TTF) as an example of a high mobility organic molecular material, we use density functional calculations to calculate the dependency of the reorganization energy associated with charge carrier transport on: (i) the geometric and electronic responsiveness of the local molecular crystal environment, and, (ii) the local spatial extent of the charge carrier. We find that in our most realistic extended models the charge transfer reorganization energy is strongly dependent on carrier localization. In particular, whereas highly localized carriers are found to be highly susceptible to their charge transfer efficiency being affected by changes in the local crystal environment, more delocalized carriers are better able to maintain their low reorganization energies. Considering that maintaining a relatively small charge transfer reorganization energy magnitude is an important factor in achieving high carrier mobilities, we suggest that those materials better able to sustain carriers with short-range thermally resistant intermolecular delocalisation should be sought for device applications.     

INVESTIGATIONS ON THE FLUORESCENCE CONCENTRATION QUENCHING OF FLAVOMONONUCLEOTIDE IN GLYCERINE-WATER SOLUTIONS

We measured concentration changes of the fluorescence quantum yield eta/eta 0 of flavomononucleotide (FMN) in glycerine-water solutions of various viscosities. The results obtained show that FMN dimers are traps for the exciting light energy as well as the energy transferred non-radiatively. Very good agreement between the experimental and theoretical eta/eta 0 results was obtained. It has been shown that in the investigated solutions non-radiative energy transfer from monomers to dimers takes place, preceded by the migration of energy. It has been stated that no monomer quenching occurs in these solutions. The contribution of the individual fluorescence concentration quenching mechanisms has been determined.     

Ufasomes as Plausible Carriers for Horizontal Gene Transfer

In this article, we propose ufasomes as carriers for the horizontal transfer of genes from plants. “Ufasome” is an abbreviation for unsaturated fatty acid liposomes, which are generated at specific pH. The formation of ufasomes is believed to occur due to associative interaction in mixtures of fully ionized and unionized fatty acids at pH > 7.0. In past, ufasomes have been widely considered as pre-biotic models for cellular compartments. Using same principles, in the present work, we provide a theoretical treatise presenting ufasomes as carriers for horizontal transfer of engineered genes from plants to either soil-microbes or to environment.