Electronic Coherence Dephasing in Excitonic Molecular Complexes: Role of Markov and Secular Approximations

We compare four different types of equations of motion for reduced density matrix of a system of molecular excitons interacting with thermodynamic bath. All four equations are of second order in the linear system-bath interaction Hamiltonian, with different approximations applied in their derivation. In particular we compare time-nonlocal equations obtained from so-called Nakajima-Zwanzig identity and the time-local equations resulting from the partial ordering prescription of the cummulant expansion. In each of these equations we alternatively apply secular approximation to decouple population and coherence dynamics from each other. We focus on the dynamics of intraband electronic coherences of the excitonic system which can be traced by coherent two-dimensional spectroscopy. We discuss the applicability of the four relaxation theories to simulations of population and coherence dynamics, and identify features of the two-dimensional coherent spectrum that allow us to distinguish time-nonlocal effects.Comment: 14 pages, 8 figure

Band gap engineering in penta-graphene by substitutional doping: first-principles calculations

Using density functional theory, we study the structure, electronic properties and partial charges of a new carbon allotrope-penta-graphene (PG)-substitutionally doped by Si, B and N. We found that the electronic bandgap of PG can be tuned down to 0.2 eV due to carbon substitutions. However, the value of the band gap depends on the type and location of the dopants. For example, the strongest reduction of the band gap is obtained for Si substitutions on the top (bottom) plane of PG, whereas the substitution in the middle plane of PG has a smaller effect on the band gap of the material. Surface termination with fluorine and hydroxyl groups results in an increase of the band gap together with considerable changes in electronic and atomic partial charge distribution in the system. Our findings, which are robust against the use of different exchange- correlation functionals, indicate the possibility of tuning the bandgap of the material to make it suitable for optoelectronic and photovoltaic applications

Watching the acetylene vinylidene intramolecular reaction in real time

It is a long-standing dream of scientists to capture the ultra-fast dynamics of molecular or chemical reactions in real time and to make a molecular movie. With free-electron lasers delivering extreme ultraviolet (XUV) light at unprecedented intensities, in combination with pump-probe schemes, it is now possible to visualize structural changes on the femtosecond time scale in photo-excited molecules. In hydrocarbons the absorption of a single photon may trigger the migration of a hydrogen atom within the molecule. Here, such a reaction was filmed in acetylene molecules (C2H2) showing a partial migration of one of the protons along the carbon backbone which is consistent with dynamics calculations on ab initio potential energy surfaces. Our approach opens attractive perspectives and potential applications for a large variety of XUV-induced ultra-fast phenomena in molecules relevant to physics, chemistry, and biology

Structure-based simulation of linear optical spectra of the CP43 core antenna of photosystem II

The linear optical spectra (absorbance, linear dichroism, circular dichroism, fluorescence) of the CP43 (PsbC) antenna of the photosystem II core complex (PSIIcc) pertaining to the S(0) → S(1) (Q(Y)) transitions of the chlorophyll (Chl) a pigments are simulated by applying a combined quantum chemical/electrostatic method to obtain excitonic couplings and local transition energies (site energies) on the basis of the 2.9 Å resolution crystal structure (Guskov et al., Nat Struct Mol Biol 16:334-342, 2009). The electrostatic calculations identify three Chls with low site energies (Chls 35, 37, and 45 in the nomenclature of Loll et al. (Nature 438:1040-1044, 2005). A refined simulation of experimental spectra of isolated CP43 suggests a modified set of site energies within 143 cm(-1) of the directly calculated values (root mean square deviation: 80 cm(-1)). In the refined set, energy sinks are at Chls 37, 43, and 45 in agreement with earlier fitting results (Raszewski and Renger, J Am Chem Soc 130:4431-4446, 2008). The present structure-based simulations reveal that a large part of the redshift of Chl 37 is due to a digalactosyldiacylglycerol lipid. This finding suggests a new role for lipids in PSIIcc, namely the tuning of optical spectra and the creation of an excitation energy funnel towards the reaction center. The analysis of electrostatic pigment-protein interactions is used to identify amino acid residues that are of potential interest for an experimental approach to an assignment of site energies and energy sinks by site-directed mutagenesis

Structure-based modeling of energy transfer in photosynthesis

We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment–protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton–vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion