Ab initio adiabatic study of the AgH system

In the framework of the Born–Oppenheimer (BO) method, we illustrate our ab-initio spectroscopic study of the of silver hydride molecule. The calculation of 48 electrons for this system is very difficult, so we have been employed a pseudo-potential (P.P) to reduce the big number of electrons to two electrons of valence, which is proposed by Barthelat and Durant. This allowed us to make a configuration interaction (CI). The potential energy curves (PECs) and the spectroscopic constants of AgH have been investigated for Σ+, Π and Δ symmetries. We have been determined the permanent and transition dipole moments (PDM and TDM), the vibrational energies levels and their spacing. We compared our results with the available experimental and theoretical results in the literature. We found a good accordance with the experimental and theoretical data that builds a validation of the choice of our approach.

Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes

Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.

Substituent Effects on the Solubility and Electronic Properties of the Cyanine Dye Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations

The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of withdrawing substituents (W-W pairs) exhibiting the most negative solvation energies, suggesting dyes with W-W pairs are more soluble than others. With respect to pristine Cy5, the transition dipole moment was relatively unaffected upon substitution while numerous W-W pairs and pairs of donating and withdrawing substituents (D-W pairs) enhanced the static dipole difference. The increase in static dipole difference was correlated with an increase in the magnitude of the sum of the Hammett constants of the substituents on the dye. The results of this study provide insight into how specific substituents affect Cy5 monomers and which pairs can be used to engineer dyes with desired properties.

Spectroscopic study of the Electronic Properties of AgH

In this study, we describe our ab-initio study of the molecule of silver hydride AgH in the framework of the Born-Oppenheimer (BO) approximation.This molecule is composed of 48 electrons so the calculation of all electrons is very difficult. To solve this problem, we have been used a pseudo-potential (P.P),which is proposed by Barthelat and Durant allow reducing the number of electrons to two electrons of valence. This allowed usto perform a configuration interaction (CI). We have been determined the potential energy curves (PECs) and the spectroscopic constants for all symmetries Σ+, Π and Δ of AgH. The permanent and transition dipole moments (PDM and TDM), the vibrational energies levels and their spacing have been determined.We compared our results with the available theoretical and experimental studies in the literature. We found a good agreement with the theoretical and experimental results, which builds a validation of the choice of our method.

Directionality of light absorption and emission in representative fluorescent proteins

Fluorescent molecules are like antennas: The rate at which they absorb light depends on their orientation with respect to the incoming light wave, and the apparent intensity of their emission depends on their orientation with respect to the observer. However, the directions along which the most important fluorescent molecules in biology, fluorescent proteins (FPs), absorb and emit light are generally not known. Our optical and X-ray investigations of FP crystals have now allowed us to determine the molecular orientations of the excitation and emission transition dipole moments in the FPs mTurquoise2, eGFP, and mCherry, and the photoconvertible FP mEos4b. Our results will allow using FP directionality in studies of molecular and biological processes, but also in development of novel bioengineering and bioelectronics applications.