Bacteriochlorophyll and chlorophyll molecules are crucial building blocks of the photosynthetic apparatus in bacteria, algae, and plants. Embedded in transmembrane protein complexes, they are responsible for the primary processes of photosynthesis: excitation energy and charge transfer. Here, we use ab initio many-body perturbation theory within the GW approximation and Bethe–Salpeter equation (BSE) approach to calculate the electronic structure and optical excitations of bacteriochlorophylls a , b , c , d , and e and chlorophylls a and b . We systematically study the effects of the structure, basis set size, partial self-consistency in GW , and the underlying exchange–correlation approximation and compare our calculations with results from time-dependent density functional theory, multireference RASPT2, and experimental literature results. We find that optical excitations calculated with GW +BSE are in excellent agreement with experimental data, with an average deviation of less than 100 meV for the first three bright excitations of the entire family of (bacterio)chlorophylls. Contrary to state-of-the-art time-dependent density functional theory (TDDFT) with an optimally tuned range-separated hybrid functional, this accuracy is achieved in a parameter-free approach. Moreover, GW +BSE predicts the energy differences between the low-energy excitations correctly and eliminates spurious charge transfer states that TDDFT with (semi)local approximations is known to produce. Our study provides accurate reference results and highlights the potential of the GW +BSE approach for the simulation of larger pigment complexes.

Methylene blue [3,7-Bis(di-methylamino) phenothiazin-5-ium chloride] is a phenothiazine dye with applications as a sensitizer for photodynamic therapy, photoantimicrobials, and dye-sensitized solar cells. Time-dependent density functional theory (TDDFT), based on (semi)local and global hybrid exchange-correlation functionals, fails to correctly describe its spectral features due to known limitations for describing optical excitations of π-conjugated systems. Here, we use TDDFT with a non-empirical optimally tuned range-separated hybrid functional to explore the optical excitations of gas phase and solvated methylene blue. We compute solvated configurations using molecular dynamics and an iterative procedure to account for explicit solute polarization. We rationalize and validate that by extrapolating the optimized range separation parameter to an infinite amount of solvating molecules, the optical gap of methylene blue is well described. Moreover, this method allows us to resolve contributions from solvent–solute intermolecular interactions and dielectric screening. We validate our results by comparing them to first-principles calculations based on the GW+Bethe–Salpeter equation approach and experiment. Vibronic calculations using TDDFT and the generating function method account for the spectra’s subbands and bring the computed transition energies to within 0.15 eV of the experimental data. This methodology is expected to perform equivalently well for describing solvated spectra of π-conjugated systems.

Evolutionary algorithm is combined with full-potential ab-initio calculations to investigate conformational space of (MoS 2 ) n and (MoSe 2 ) n (n = 1 − 10) nanoclusters and to identify the lowest energy structural isomers of these systems. It is argued that within both BLYP and PBE functionals, these nanoclusters favor sandwiched planar configurations, similar to their ideal planar sheets. The second order difference in total energy (∆ 2 E) of the lowest energy isomers are computed to estimate the abundance of the clusters at different sizes and to determine the magic sizes of (MoS 2 ) n and (MoSe 2 ) n nanoclusters. In order to investigate the electronic properties of nanoclusters, their energy gap is calculated by several methods, including hybrid functionals (B3LYP and PBE0), GW approach, and ∆scf method. At the end, the vibrational modes of the lowest lying isomers are calculated by using the force constants method and the IR active modes of the systems are identified. The vibrational spectra are used to calculate the Helmholtz free energy of the systems and then to investigate abundance of the nanoclusters at finite temperatures. arXiv:1710.00052v1 [cond-mat.mtrl-sci]

In purple bacteria, the fundamental charge-separation step that drives the conversion of radiation energy into chemical energy proceeds along one branch - the A branch - of a heterodimeric pigment-protein complex, the reaction center. Here, we use first principles time-dependent density functional theory (TDDFT) with an optimally-tuned range-separated hybrid functional to investigate the electronic and excited-state structure of the primary six pigments in the reaction center of \textit{Rhodobacter sphaeroides}. By explicitly including amino-acid residues surrounding these six pigments in our TDDFT calculations, we systematically study the effect of the protein environment on energy and charge-transfer excitations. Our calculations show that a forward charge transfer into the A branch is significantly lower in energy than the first charge transfer into the B branch, in agreement with the unidirectional charge transfer observed experimentally. We further show that inclusion of the protein environment redshifts this excitation significantly, allowing for energy transfer from the coupled $Q_x$ excitations. Through analysis of transition and difference densities, we demonstrate that most of the $Q$-band excitations are strongly delocalized over several pigments and that both their spatial delocalization and charge-transfer character determine how strongly affected they are by thermally-activated molecular vibrations. Our results suggest a mechanism for charge-transfer in this bacterial reaction center and pave the way for further first-principles investigations of the interplay between delocalized excited states, vibronic coupling, and the role of the protein environment of this and other complex light-harvesting systems.

Photoinduced charge-transfer excitations are key to understand the primary processes of natural photosynthesis and for designing photovoltaic and photocatalytic devices. In this paper, we use Bacteriochlorophyll dimers extracted from the light harvesting apparatus and reaction center of a photosynthetic purple bacterium as model systems to study such excitations using first-principles numerical simulation methods. We distinguish four different regimes of intermolecular coupling, ranging from very weakly coupled to strongly coupled, and identify the factors that determine the energy and character of charge-transfer excitations in each case. We also construct an artificial dimer to systematically study the effects of intermolecular distance and orientation on charge-transfer excitations, as well as the impact of molecular vibrations on these excitations. Our results provide design rules for tailoring charge-transfer excitations in Bacteriochloropylls and related photoactive molecules, and highlight the importance of including charge-transfer excitations in accurate models of the excited-state structure and dynamics of Bacteriochlorophyll aggregates.