Theoretical description of protein field effects on electronic excitations of biological chromophores

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems

Electron scattering from molecules and molecular aggregates of biological relevance

In this Topical Review we survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. We briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptides and other biomolecules. The applications of the data obtained is briefly described as well as future required developments

Multiple scattering approach to elastic electron collisions with molecular clusters

We revisit our multiple-scattering method to treat low energy elastic electron collisions with (H2O)2. Calculations are performed for different geometries of the water dimer with different dipole moments. The effect of the dipole moment of the cluster is analysed. The elastic cross sections are compared to R-matrix results. Good agreement is found above 1 eV for all geometries. Results conrm the validity of the technique

Plasma–liquid interactions: a review and roadmap

Plasma–liquid interactions represent a growing interdisciplinary area of research involving plasma science, fluid dynamics, heat and mass transfer, photolysis, multiphase chemistry and aerosol science. This review provides an assessment of the state-of-the-art of this multidisciplinary area and identifies the key research challenges. The developments in diagnostics, modeling and further extensions of cross section and reaction rate databases that are necessary to address these challenges are discussed. The review focusses on non-equilibrium plasmas

On the description of the environment polarization response to electronic transitions

This paper addresses the issue of accurately describing the structures and properties of electronically excited systems embedded in an environment, through multiscale approaches combining quantum-mechanical (QM) and polarizable classical representations of the system and environment, respectively. Such approaches represent an efficient strategy and allow to effectively study the excited states of molecular systems in the condensed phase, still maintaining the computational efficiency and the physical reliability of the ground-state calculations. The most important theoretical and computational aspects of the coupling between the QM system and the polarizable environment are presented and discussed. Even if these approaches already reached an evident degree of maturity, they can still be subject to further development, in order to achieve their full potential. This perspective presents an overview of the state of the art of these strategies, showing the fields of applicability and indicating the current limitations, which need to be overcome in future developments

Computed vibrational excitation of CF₄ by low-energy electrons and positrons: Comparing calculations and experiments

Quantum calculations for the excitation of the asymmetric modes of the CF4 target gas, 3 and 4, by impact of low-energy electrons and positrons are carried out in the energy range around 1 eV and are compared with recent experimental findings. The similarities and differences between the two types of projectiles, and the two different modes, are analyzed and discussed vis à vis the present accord with the experimental result

Electron attachment to molecules in a cluster environment

Low-energy dissociative electron attachment (DEA) to the CF2Cl2 and CF3Cl molecules in a water cluster environment is investigated theoretically. Calculations are performed for the water trimer and water hexamer. It is shown that the DEA cross section is strongly enhanced when the attaching molecule is embedded in a water cluster, and that this cross section grows as the number of water molecules in the cluster increases. This growth is explained by a trapping effect that is due to multiple scattering by water molecules while the electron is trapped in the cluster environment. The trapping increases the resonance lifetime and the negative ion survival probability. This confirms qualitatively existing experiments on electron attachment to the CF2Cl2 molecule placed on the surface of H2O ice. The DEA cross sections are shown to be very sensitive to the position of the attaching molecule within the cluster and the orientation of the electron beam relative to the cluster

Quantum mechanical study of the solvent-dependence of electronic energy transfer rates in a Bodipy closely-spaced dyad

TheabilityofFo ̈rstertheorytodescribeelectronicenergytransferrates,andtheirsolvent-dependence, have been studied theoretically in a series of 15 solvents of varying degrees of polarity for a rigid closely-spaced dyad, constituted by two boron dipyrromethene dyes, which was recently studied experimentally by Harriman & Ziessel, Photochem. Photobiol. Sci., 2010, 9, 960. We use time-dependent density functional theory calculations coupled to the polarizable continuum model to analyse the solvent-dependence of the spectroscopic and energy transfer properties of the system. This methodology allows us to examine the impact of the solvent on both electronic (solvent screening) and structural (dipole separation and orientation) factors by consistently incorporating solvent effects in the determination of molecular geometries, transition densities, and electronic couplings. In addition, we analyse the impact of bridge-mediated contributions to the electronic interaction between the dyes. We are therefore able to assess whether a Fo ̈ rster-type point-dipole approximation is valid for the molecular system studied

Control of Coherences and Optical Responses of Pigment-Protein Complexes by Plasmonic Nanoantennae

The key for light-harvesting in pigment-protein complexes are molecular excitons, delocalized excited states comprising a superposition of excitations at different molecular sites. There is experimental evidence that the optical response due to such excitons can be largely affected by plasmonic nanoantennae. Here we employ a multiscale approach combining time-dependent density functional theory and polarizable classical models to study the optical behavior of the LH2 complex present in bacteria when interacting with a gold nanorod. The simulation not only reproduces the experiments but also explains their molecular origin. By tuning the chromophoric unit and selectively switching on/off the excitonic interactions, as well as by exploring different setups, we clearly show that the dramatic enhancement in the optical response, unexpectedly, is not accompanied by changes in the coherences. Instead polarization effects are dominant. These results can be used to design an optimal control of the light-harvesting process through plasmonic nanoantennae

Theoretical Investigation of the Mechanism and Dynamics of Intramolecular Coherent Resonance Energy Transfer in Soft Molecules: A Case Study of Dithia-anthracenophane

A computational study is conducted on dithia-anthracenophane (DTA), for which there is experimental evidence for coherent resonance energy transfer dynamics, and on dimethylanthracene (DMA), a molecule representing the energy donor and the acceptor in DTA. Electronic excitation energies are calculated by configuration interaction singles (CIS) and time-dependent density functional theory (TDDFT) methods and are compared to experimental ones. Electronic coupling constants are calculated between two DMAs embedded into the ground-state structure of DTA employing methods based on transition densities. The resulting values of electronic coupling provide a more consistent interpretation of experiments than those based on one-half the level spacing of DTA excitation energies. Solvation effects are studied based on the polarizable continuum model (PCM). Solvent-induced polarization and screening effects are shown to make opposite contributions, and the net electronic coupling is little different from the value in a vacuum. The likelihood of coherent population transfer is assessed on the basis of a recently developed theory of coherent resonance energy transfer. The time scale of bath is shown to have an important role in sustaining the quantum coherence. The combination of quantum chemical and dynamical data suggests that the electronic coupling in DTA is in the range of 50-100 cm-1. The presence of oscillatory excitation population dynamics can be understood from the picture of polaronic excitation moderately dressed with dispersive vibrational modes. The effect of torsional modulation on the excitation energies of DTA and electronic coupling is examined on the basis of optimized structures with the torsional angle constrained. The result suggests that inelastic effect due to torsional motion cannot be disregarded in DTA