Juha Linnanto

Quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes

The present review describes the use of quantum chemical methods in estimation of structures and electronic transition energies of photosynthetic pigments in vacuum, in solution and imbedded in proteins. Monomeric Mg-porphyrins, chlorophylls and bacteriochlorophylls and their solvent 1:1 and 1:2 complexes were studied. Calculations were performed for Mg-porphyrin, Mg-chlorin, Mg-bacteriochlorin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), d and bacteriochlorophylls a, b, c, d, e, f, g, h, plus several homologues. Geometries were optimised with PM3, PM3/CISD, PM5, ab initio HF (6-31G*/6-311G**) and density functional B3LYP (6-31G*/6-311G**) methods. Spectroscopic transition energies were calculated with ZINDO/S CIS, PM3 CIS, PM3 CISD, ab initio CIS, time-dependent HF and time-dependent B3LYP methods. Estimates for experimental transition energies were obtained from linear correlations of the calculated transition energies of 1:1 solvent complexes against experimentally recorded solution energies (scaling). According to the calculations in five-coordinated solvent complexes the magnesium atom lies out of the porphyrin plane, while in six-coordinated complexes the porphyrin is nearly planar. Charge densities on magnesium and nitrogen atoms were strongly dependent on the computational method deployed. Several dark states of low oscillator strength below the main Soret band were predicted for solvent complexes and chlorophylls and bacteriochlorophylls in protein environment. Such states, though not yet identified experimentally, might serve as intermediate states for excitation energy transfer in photosynthetic complexes. Q(y), Q(x) and Soret transition energies were found to depend on the orientation of the acetyl group and external pressure. A method to estimate site energies and dimeric interaction energies and to simulate absorption and CD spectra of photosynthetic complexes is described. Simulations for the light harvesting complexes Rhodospirillum molischianum, chlorosomes of Chlorobium tepidum and Chloroflexus aurantiacus, and LHC-II of Spinacia oleracea are presented as examples.

A model of the protein–pigment baseplate complex in chlorosomes of photosynthetic green bacteria

In contrast to photosynthetic reaction centers, which share the same structural architecture, more variety is found in the light-harvesting antenna systems of phototrophic organisms. The largest antenna system described, so far, is the chlorosome found in anoxygenic green bacteria, as well as in a recently discovered aerobic phototroph. Chlorosomes are the only antenna system, in which the major light-harvesting pigments are organized in self-assembled supramolecular aggregates rather than on protein scaffolds. This unique feature is believed to explain why some green bacteria are able to carry out photosynthesis at very low light intensities. Encasing the chlorosome pigments is a protein-lipid monolayer including an additional antenna complex: the baseplate, a two-dimensional paracrystalline structure containing the chlorosome protein CsmA and bacteriochlorophyll a (BChl a). In this article, we review current knowledge of the baseplate antenna complex, which physically and functionally connects the chlorosome pigments to the reaction centers via the Fenna–Matthews–Olson protein, with special emphasis on the well-studied green sulfur bacterium Chlorobaculum tepidum (previously Chlorobium tepidum). A possible role for the baseplate in the biogenesis of chlorosomes is discussed. In the final part, we present a structural model of the baseplate through combination of a recent NMR structure of CsmA and simulation of circular dichroism and optical spectra for the CsmA–BChl a complex.

Investigation on chlorosomal antenna geometries: tube, lamella and spiral-type self-aggregates

Molecular mechanics calculations and exciton theory have been used to study pigment organization in chlorosomes of green bacteria. Single and double rod, multiple concentric rod, lamella, and Archimedean spiral macrostructures of bacteriochlorophyll c molecules were created and their spectral properties evaluated. The effects of length, width, diameter, and curvature of the macrostructures as well as orientations of monomeric transition dipole moment vectors on the spectral properties of the aggregates were studied. Calculated absorption, linear dichroism, and polarization dependent fluorescence-excitation spectra of the studied long macrostructures were practically identical, but circular dichroism spectra turned out to be very sensitive to geometry and monomeric transition dipole moment orientations of the aggregates. The simulations for long multiple rod and spiral-type macrostructures, observed in recent high-resolution electron microscopy images (Oostergetel et al., FEBS Lett 581:5435–5439, 2007) gave shapes of circular dichroism spectra observed experimentally for chlorosomes. It was shown that the ratio of total circular dichroism intensity to integrated absorption of the Qy transition is a good measure of degree of tubular structures in the chlorosomes. Calculations suggest that the broad Qy line width of chlorosomes of sulfur bacteria could be due to (1) different orientations of the transition moment vectors in multi-walled rod structures or (2) a variety of Bchl-aggregate structures in the chlorosomes.

Mirror symmetry and vibrational structure in optical spectra of chlorophyll a

The absorption and fluorescence emission spectra of chlorophyll a in different organic solvents where the central Mg atom is either penta- or hexacoordinated have been studied using conventional and selective spectroscopy methods at ambient and cryogenic temperatures. A breakdown of the basic model mirror-symmetry rule in relation to the lowest-energy Q(y) transitions was observed due to Franck-Condon and Hertzberg-Teller interactions. Detailed vibrational structure in the ground electronic state, virtually independent of the Mg coordination state, was revealed by hole-burning fluorescence line-narrowing technique. The total Huang-Rhys factor associated with the linear vibronic coupling strength of the solvent collective vibrations and the local chlorophyll a intramolecular vibrations is equal to 0.53+/-0.07 in fluorescence and to 0.39+/-0.05 in absorption. The electron-phonon coupling part was also found to depend on the excitation wavelength within the inhomogeneously broadened absorption origin band, its average value being S(ph) approximately = 0.38. All these numbers qualify for the weak vibronic coupling. A comparison of the conjugate Q(y) absorption and fluorescence emission spectra as well as the temperature dependence of the absorption spectra allowed unambiguous locating of the still controversial Q(x) absorption band position for penta- and hexacoordinated chlorophyll a species. The basic experimental findings have been qualitatively supported by semiempirical quantum chemical calculations.

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results

The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium‐bacteriochlorin, magnesium‐chlorin, magnesium‐porphin, mesochlorophyll a, chlorophylls a, b, c1, c2, c3, and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree‐Fock/6‐31G* ab initio and density functional B3LYP/6‐31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c1, and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self‐consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6‐31G* or Hartree‐Fock/6‐31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree‐Fock/6‐31G* and B3LYP/6‐31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin‐like molecules.

Spectroscopic properties of Mg-chlorin, Mg-porphin and chlorophylls a, b, c1, c2, c3 and d studied by semi-empirical and ab initio MO/CI methods

The semi-empirical and ab initio molecular orbital/configuration interaction (MO/CI) methods were used to study spectroscopic properties of chlorophylls a, b, c1, c2, c3 and d and magnesium porphin and magnesium chlorin. Energy minimisation at the PM3 level of all chlorophylls put the magnesium atom away from the centre and above the porphyrin ring and the atomic charges on the nitrogen atoms became positive. At the ab initio HF/6-31G* level of calculation the magnesium is centrally located in the porphyrin plane and the atomic charge on the magnesium atom is positive and that on the surrounding nitrogens negative. Three CI methods used, ZINDO/S CIS (15,15), PM3 CISD (5,5) and ab initio CIS (5,5)/6-31G*, obeyed linear correlation between the experimentally observed and calculated spectroscopic transition energies. The PM3 CISD (5,5) method gave best estimates of Qy, Qx and the Soret transition energies, but predicted oscillator strengths poorly. The ZINDO/S CIS (15,15) method gave best results in the overall simulation of the absorption spectra of chlorophylls, both intensities and wavelengths. The effect of solvent co-ordination on the excited states of chlorophyll a and chlorophyll b was also studied. Calculations predict solvent induced spectroscopic shifts of the Qx and Soret transitions but leave the Qy transition almost unshifted. This is a result of solvent-induced energy level shifts and charge redistribution on the magnesium atom of chlorophylls in the excited states. The results are discussed with reference to spectroscopic properties of chlorophylls in solution, chlorophylls in aggregates and in photosynthetic light-harvesting antenna.

Excitation Energy Transfer in Isolated Chlorosomes from Chlorobaculum tepidum and Prosthecochloris aestuarii

Excitation energy transfer in chlorosomes from photosynthetic green sulfur bacteria, Chlorobaculum (Cba.) tepidum and Prosthecochloris (Pst.) aestuarii, have been studied at room temperature by time‐resolved femtosecond transient absorption spectroscopy. Bleach rise times from 117 to 270 fs resolved for both chlorosomes reflect extremely efficient intrachlorosomal energy transfer. Bleach relaxation times, from 1 to 3 ps and 25 to 35 ps, probed at 758 nm were tentatively assigned to intrachlorosomal energy transfer based on amplitude changes of the global fits and model calculations. The anisotropy decay constant of about 1 ps resolved at 807 nm probe wavelength for the chlorosomes from Chloroflexus aurantiacus, Pst. aestuarii and Cba. tepidum was related to energy transfer between bacteriochlorophyll a molecules of the baseplate and partly to intrachlorosomal energy transfer. The longer anisotropy components 6.6, 8.8 and 12.1 ps resolved for the three chlorosomes, respectively, were assigned to chlorosome to baseplate energy transfer. Global fits of magic‐angle data also revealed longer chlorosome to baseplate energy transfer components from 95 to 135 ps, in accord with results from simulations.

Challenges facing an understanding of the nature of low-energy excited states in photosynthesis

While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.

Exciton Description of Chlorosome to Baseplate Excitation Energy Transfer in Filamentous Anoxygenic Phototrophs and Green Sulfur Bacteria

A description of intra-chlorosome and from chlorosome to baseplate excitation energy transfer in green sulfur bacteria and in filamentous anoxygenic phototrophs is presented. Various shapes and sizes, single and multiwalled tubes, cylindrical spirals and lamellae of the antenna elements mimicking pigment organization in chlorosomes were generated by using molecular mechanics calculations, and the absorption, LD, and CD spectra of these were predicted by using exciton theory. Calculated absorption and LD spectra were similar for all modeled antenna structures; on the contrary, CD spectra turned out to be sensitive to the size and pigment orientations in the antenna. It was observed that, bringing two tubular antennae at close enough interaction distance, the exciton density of the lowest energy state became localized on pigments facing each other in the antenna dimer. Calculations predicted for stacked tubular antenna elements extremely fast, faster than 500 fs, intra-chlorosome energy transfer toward the baseplates in the direction perpendicular to the chlorosome long axis. Downhill excitation energy transfer according to our model is driven by interactions of the antennae with their immediate surroundings. Energy transfer from the chlorosome to the baseplate, consisting of 2D lattices of monomeric and dimeric bacteriochlorophyll a molecules, was predicted to occur in 5-15 ps, in agreement with experimental findings. Advancement of excitation through a double tube antenna stack, a model for antenna element organization in chlorosomes of green sulfur bacteria, to a monomeric baseplate was visualized in space and in time.

Quantum Chemical Simulations of Excited-State Absorption Spectra of Photosynthetic Bacterial Reaction Center and Antenna Complexes

The semiempirical ZINDO/S CIS configuration interaction method has been used to study the ground- and excited-state absorption spectra of wild type and heterodimer M202HL reaction centers from purple bacterium Rhodobacter sphaeroides as well as of peripheral LH2 and LH3 light harvesting complexes from purple bacterium Rhodopseudomonas acidophila. The calculations well reproduce the experimentally observed excited-state absorption spectra between 1000 and 17,000 cm(-1), despite the necessarily limited number of chromophores and protein subunits involved in the calculations. The electron density analysis reveals that the charge transfer between adjacent chromophores dominates the excited-state absorption spectra. Clear spectroscopic differences observed between the wild type and heterodimer reaction centers as well as between the LH2 and LH3 antenna complexes arise from differences in the energy level manifolds of the complexes, particularly those of the charge transfer states. The calculations also imply that the lowest excited state of the bacterial reaction centers has charge transfer character that is related to charge transfer within the special pair and between the special pair and the accessory bacteriochlorophyll of the photosynthetically active electron transfer branch.