Photoinduced non-adiabatic energy transfer pathways in dendrimer building blocks.

The efficiency of the intramolecular energy transfer in light harvesting dendrimers is determined by their well-defined architecture with high degree of order. After photoexcitation, through-space and through-bond energy transfer mechanisms can take place, involving vectorial exciton migration among different chromophores within dendrimer highly branched structures. Their inherent intramolecular energy gradient depends on how the multiple chromophoric units have been assembled, subject to their inter-connects, spatial distances, and orientations. Herein, we compare the photoinduced nonadiabatic molecular dynamics simulations performed on a set of different combinations of a chain of linked dendrimer building blocks composed of two-, three-, and four-ring linear polyphenylene chromophoric units. The calculations are performed with the recently developed ab initio multiple cloning-time dependent diabatic basis implementation of the Multiconfigurational Ehrenfest (MCE) approach. Despite differences in short time relaxation pathways and different initial exciton localization, at longer time scales, electronic relaxation rates and exciton final redistributions are very similar for all combinations. Unlike the systems composed of two building blocks, considered previously, for the larger 3 block systems here we observe that bifurcation of the wave function accounted by cloning is important. In all the systems considered in this work, at the time scale of few hundreds of femtoseconds, cloning enhances the electronic energy relaxation by ∼13% compared to that of the MCE method without cloning. Thus, accurate description of quantum effects is essential for understanding of the energy exchange in dendrimers both at short and long time scales.

Vibronic Quantum Beating between Electronic Excited States in a Heterodimer.

Energy transfer in multichromophoric molecules can be affected by coherences that are induced by the electronic and vibrational couplings between chromophore units. Coherent electron-vibrational dynamics can persist at the subpicosecond time scale even at room temperature. Furthermore, wave-like localized-delocalized motions of the electronic wave function can be modulated by vibrations that actively participate in the intermolecular energy transfer process. Herein, nonadiabatic excited state molecular dynamics simulations have been performed on a rigid synthetic heterodimer that has been proposed as a simplified model for investigating the role and mechanism of coherent energy transfer in multichromophoric systems. Both surface hopping (SH) and Ehrenfest approaches (EHR) have been considered. After photoexcitation of the system at room temperature, EHR simulations reveal an ultrafast beating of electronic populations between the two lowest electronic states. These oscillations are not observed at low temperature and have vibrational origins. Furthermore, they cannot be reproduced using SH approach. This periodic behavior of electronic populations induces oscillations in the spatial localization of the electronic transition density between monomers. Vibrations whose frequencies are near-resonant with energy difference between the two lowest electronic excited states are in the range of the electronic population beating, and they are the ones that contribute the most to the coherent dynamics of these electronic transitions.

Improved density functional theory/electrostatic calculation of the His291 protonation state in cytochrome C oxidase: self-consistent charges for solvation energy calculation.

The protonation state of His291 in cytochrome c oxidase (CcO), a ligand to the Cu(B) center of the enzyme, has been recently studied in this group by using combined density functional theory (DFT)/electrostatic (QM/MM) calculations. On the basis of these calculations, a model of the proton pumping mechanism of CcO has been proposed. Due to certain technical difficulties, the procedure used in the previous calculation to find partial atomic charges of the QM system for the solvation energy evaluation was not entirely satisfactory; i.e., it was not self-consistent. Here, we describe a procedure that resolves the problem and report on the improved calculations of the protonation state of the His residue. The new procedure fits the protein and reaction field potentials in the region of the QM system with artificial point charges placed on a surface of a sphere surrounding the QM system and a few charges inside the sphere and allows one to perform DFT calculations that involve an inhomogeneous dielectric environment in a self-consistent way. The procedure improves the accuracy of calculations in comparison with previous work. The improved results show, however, that although the absolute energies change significantly the relative energies of the protonated and deprotonated states of His291 remain close to the previously reported ones and therefore do not change significantly the pK(a) values reported earlier. Therefore, our new improved calculations support for the proposed His291 model of the CcO pump.

Stable fourfold configurations for small vacancy clusters in silicon from ab initio calculations.

Using density-functional-theory calculations, we have identified new stable configurations for tri-, tetra-, and pentavacancies in silicon. These new configurations consist of combinations of a ring hexavacancy with three, two, or one interstitial atoms, respectively, such that all atoms remain fourfold. As a result, their formation energies are lower by 0.6, 1.0, and 0.6 eV, respectively, than the "part of a hexagonal ring" configurations, believed until now to be the lowest-energy states.