Combining classical molecular dynamics and quantum mechanical methods for the description of electronic excitations: The case of carotenoids.

Carotenoids are important actors both in light-harvesting (LH) and in photoprotection functions of photosynthetic pigment-protein complexes. A deep theoretical investigation of this multiple role is still missing owing to the difficulty of describing the delicate interplay between electronic and nuclear degrees of freedom. A possible strategy is to combine accurate quantum mechanical (QM) methods with classical molecular dynamics. To do this, however, accurate force-fields (FF) are necessary. This article presents a new FF for the different carotenoids present in LH complexes of plants. The results show that all the important structural properties described by the new FF are in very good agreement with QM reference values. This increased accuracy in the simulation of the structural fluctuations is also reflected in the description of excited states. Both the energy order and the different nature of the lowest singlet states are preserved during the dynamics when the new FF is used, whereas an unphysical mixing is found when a standard FF is used.

Limits and potentials of quantum chemical methods in modelling photosynthetic antennae.

Advances in electronic spectroscopies with femtosecond time resolution have provided new information on the excitonic processes taking place during the energy conversion in natural photosynthetic antennae. This has promoted the development of new theoretical protocols aiming at accurately describing the properties and mechanisms of exciton formation and relaxation. In this perspective, we provide an overview of the quantum chemical based approaches, trying to underline both the potentials of the methods and their weaknesses. In particular three main aspects will be analysed, the quantum mechanical description of excitonic parameters (site energies and couplings), the incorporation of environmental effects on these parameters through hybrid quantum/classical approaches, and the modelling of the dynamical coupling among such parameters and the vibrations of the pigment-protein complex.

Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II.

Light-harvesting pigment-protein complexes (PPC) represent the fundamental units through which the photosynthetic organisms absorb sunlight and funnel the energy to the reaction centre for carrying out the primary energy conversion reactions of photosynthesis. Here we apply a multiscale computational strategy to a specific PPC present in the photosystem II of plants and algae (CP29) to investigate in what detail should the environment effects due to protein and membrane/solvent be included for an accurate description of optical spectra. We find that a refinement of the crystal structure is needed before any meaningful quantum chemical calculations of pigment transition energies can be performed. For this purpose we apply classical molecular dynamics simulations of the PPC within its natural environment and we perform ab initio computations of the exciton Hamiltonian of the complex, including the environment either implicitly by the polarizable continuum model (PCM) or explicitly using the polarizable QM/MM methodology (MMPol). However, PCM essentially leads to an unspecific redshift of all transition energies, and MMPol is able to reveal site-specific changes in the optical properties of the pigments. Based on the latter and the excitonic couplings obtained within a polarizable QM/MM methodology, optical spectra are calculated, which are in good qualitative agreement with experimental data. A weakness of the approach is however found in the overestimation of the fluctuations of the excitonic parameters of the pigments along the MD trajectory. An explanation for such a finding in terms of the limits of the force fields commonly used for protein cofactors is presented and discussed.

Plasmon enhanced light harvesting: multiscale modeling of the FMO protein coupled with gold nanoparticles.

Plasmonic systems, such as metal nanoparticles, are becoming increasingly important in spectroscopies and devices because of their ability to enhance, even by several orders of magnitude, the photophysical properties of neighboring systems. In particular, it has been shown both theoretically and experimentally that combining nanoplasmonic devices with natural light-harvesting proteins substantially increases the fluorescence and absorption properties of the system. This kind of biohybrid device can have important applications in the characterization and design of efficient light-harvesting systems. In the present work, the FMO light-harvesting protein was combined with gold nanoparticles of different sizes, and its photophysical properties were characterized using a multiscale quantum-mechanical classical-polarizable and continuum model (QM/MMPol/PCM). By optimal tuning of the plasmon resonance of the metal nanoparticles, fluorescence enhancements of up to 2 orders of magnitude were observed. Orientation effects were found to be crucial: amplifications by factors of up to 300 were observed for the absorption process, while the radiative decay of the emitting state increased at most by a factor of 10, mostly as a result of poor alignment of the emitting state with the considered metal aggregates. Despite being a limiting factor for high-fluorescence-enhancement devices, the strong orientation dependence may represent an important feature of the natural light-harvesting system that could allow selective enhancement of a specific excited state of the complex.

Molecular basis of the exciton-phonon interactions in the PE545 light-harvesting complex.

Long-lived quantum coherences observed in several photosynthetic pigment-protein complexes at low and at room temperatures have generated a heated debate over the impact that the coupling of electronic excitations to molecular vibrations of the relevant actors (pigments, proteins and solvents) has on the excitation energy transfer process. In this work, we use a combined MD and QM/MMPol strategy to investigate the exciton-phonon interactions in the PE545 light-harvesting complex by computing the spectral densities for each pigment and analyzing their consequences in the exciton dynamics. Insights into the origin of relevant peaks, as well as their differences among individual pigments, are provided by correlating them with normal modes obtained from a quasi-harmonic analysis of the motions sampled by the pigments in the complex. Our results indicate that both the protein and the solvent significantly modulate the intramolecular vibrations of the pigments thus playing an important role in promoting or suppressing certain exciton-phonon interactions. We also find that these low-frequency features are largely smoothed out when the spectral density is averaged over the complex, something difficult to avoid in experiments that underscores the need to combine theory and experiment to understand the origin of quantum coherence in photosynthetic light-harvesting.

Theoretical characterization of charge transport in one-dimensional collinear arrays of organic conjugated molecules.

A great deal of interest has recently focused on host-guest systems consisting of one-dimensional collinear arrays of conjugated molecules encapsulated in the channels of organic or inorganic matrices. Such architectures allow for controlled charge and energy migration processes between the interacting guest molecules and are thus attractive in the field of organic electronics. In this context, we characterize here at a quantum-chemical level the molecular parameters governing charge transport in the hopping regime in 1D arrays built with different types of molecules. We investigate the influence of several parameters (such as the symmetry of the molecule, the presence of terminal substituents, and the molecular size) and define on that basis the molecular features required to maximize the charge carrier mobility within the channels. In particular, we demonstrate that a strong localization of the molecular orbitals in push-pull compounds is generally detrimental to the charge transport properties.

Alignment and relaxation dynamics of dye molecules in host-guest inclusion compounds as probed by dielectric spectroscopy.

The alignment and relaxation dynamics of a polar dye molecule, N,N-dimethyl-4(4-nitrophenylazo)aniline (DNAA), in zeolite L and perhydrotriphenylene (PHTP) channels were investigated by means of a combination of optical, dielectric, and quantum-chemical methods. Both the zeolite L and PHTP channels enable the dye molecules to align along the channel axis. An amplified net dipole moment of DNAA in PHTP is observed and attributed to enhanced 1D close alignment of dye molecules. In zeolite L channels, a concentration gradient is found with aggregation at the channel entrances. The dynamics of the dye in zeolite L channels reveals localized conical rotational fluctuation modes following Arrhenius-type activation with energy of 0.31 eV, which we assign to small noninteracting fluctuating polar units of the dyes being loosely aligned or isolated. Unlike zeolite L, relaxations in PHTP are characterized by cooperative wobbling motions interpreted as increased intermolecular dipole interaction due to a closely packed one-dimensional array. Temperature-dependent activation energies of 0.25 eV below 0 degrees C and 0.37 eV at ambient temperature reflect the role of the soft channel walls in the activation process.

Spatial control of 3D energy transfer in supramolecular nanostructured host-guest architectures.

Systematic control of 3D energy transfer (ET) dynamics is achieved in supramolecular nanostructured host-guest systems using spacer-functionalized guest chromophores. Quantum chemistry-based Monte Carlo simulations reveal the strong impact of the spacer length on the ET dynamics, efficiency, and dimensionality. Remarkably high exciton diffusion lengths demonstrate that there is ample scope for optimizing oligomeric or polymeric optoelectronic devices.

On the origin of small band gaps in alternating thiophene-thienopyrazine oligomers.

We have studied experimentally and theoretically the optical and electrochemical properties of small band gap oligo(7,7'-bis(thiophen-2-yl)-5,5'-bisthieno[3,4-b]pyrazine)s with alternating blocks of bithiophene units and bisthienopyrazine units up to a total length of 16 units. The optical absorptions of the ground state, the triplet excited state, and the corresponding radical cation have been identified and shift to lower energy with increasing chain length. The optical absorption correlates well with quantum chemical calculations and the electrochemical band gap. We show that reduction of the band gap with chain length results from a significant rise of the HOMO level and a moderate reduction of the LUMO energy. Comparison of the chain length dependence of the transition energy at maximum absorption (Emax) and of the redox potentials with previously published data on oligothiophenes and related mixed thiophene-thienopyrazine oligomers shows that the reduction of Emax is more easily induced by increasing the number of thienopyrazine units than by extending the chain, mainly because thienopyrazine is both a better donor and a better acceptor than thiophene. Strong interactions between neighboring thienopyrazine units, with some possible admixing of quinoid character, are the main cause of the small band gap in these oligomers.

An oligomer study on small band gap polymers.

Small band gap polymers may increase the energy conversion efficiency of polymer solar cells by increased absorption of sunlight. Here we present a combined experimental and theoretical study on the optical and electrochemical properties of a series of well-defined, lengthy, small band gap oligo(5,7-bis(thiophen-2-yl)thieno[3,4-b]pyrazine)s ( E g = 1.50 eV) having alternating donor and acceptor units. The optical absorptions of the ground state, triplet excited state, radical cation, and dication are identified and found to shift to lower energy with increasing chain length. The reduction of the band gap in these alternating small band gap oligomers mainly results from an increase of the highest occupied molecular orbital (HOMO) level. The S 1-T 1 singlet-triplet splitting is reduced from approximately 0.9 eV from the trimeric monomer to -0.5 eV for the pentamer. This significant exchange energy is consistent with the fact that both the HOMO and the lowest unoccupied molecular orbital (LUMO) remain distributed over virtually all units, rather than being localized on the D and A units.

Increasing Photovoltaic Performance of an Organic Cationic Chromophore by Anion Exchange.

A symmetrical cyanine dye chromophore is modified with different counteranions to study the effect on crystal packing, polarizability, thermal stability, optical properties, light absorbing layer morphology, and organic photovoltaic (OPV) device parameters. Four sulfonate-based anions and the bulky bistriflylimide anion are introduced to the 2-[5-(1,3-dihydro-1,3,3-trimethyl-2H-indol-2-ylidene)-1,3-pentadien-1-yl]-1,3,3-trimethyl-3H-indolium chromophore using an Amberlyst A26 (OH- form) anion exchanger. Anionic charge distribution clearly correlates with device performance, whereby an average efficiency of 2% was reached in a standard bilayer organic solar. Evidence is given that the negative charge of the anion distributed over a large number of atoms is significantly more important than the size of the organic moieties of the sulfonate charge carrying group. This provides a clear strategy for future design of more efficient cyanine dyes for OPV applications.

Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation.

We present the mathematical derivation and the computational implementation of the analytical geometry derivatives for a polarizable QM/MM model (QM/MMPol). In the adopted QM/MMPol model, the focused part is treated at QM level of theory, while the remaining part (the environment) is described classically as a set of fixed charges and induced dipoles. The implementation is performed within the ONIOM procedure, resulting in a polarizable embedding scheme, which can be applied to solvated and embedded systems and combined with different polarizable force fields available in the literature. Two test cases characterized by strong hydrogen-bond and dipole-dipole interactions, respectively, are used to validate the method with respect to the nonpolarizable one. Finally, an application to geometry optimization of the chromophore of Rhodopsin is presented to investigate the impact of including mutual polarization between the QM and the classical parts in conjugated systems.

Substrate-induced variations of molecular packing, dynamics, and intermolecular electronic couplings in pentacene monolayers on the amorphous silica dielectric.

Charge-carrier transport in thin-film organic field-effect transistors takes place within the first (few) molecular layer(s) of the active organic material in contact with the gate dielectric. Here, we use atomistic molecular dynamics simulations to evaluate how interactions with bare amorphous silica surfaces that vary in terms of surface potential influence the molecular packing and dynamics of a monolayer pentacene film. The results indicate that the long axis of the pentacene molecules has a non-negligible tilt angle away from the surface normal. Grazing-incidence X-ray diffraction patterns for these models are calculated, and we discuss notable differences in the shapes of the Bragg rods as a function of the molecular packing, also in relation to previously published experimental reports. Intermolecular electronic couplings (transfer integrals) evaluated for the monolayers show marked differences compared to bulk crystal calculations, a result that points to the importance of fully considering the molecular packing environment in charge-carrier mobility models for organic electronic materials.

Spatial and Electronic Correlations in the PE545 Light-Harvesting Complex.

The recent discovery of long-lasting quantum coherence effects in photosynthetic pigment-protein complexes has challenged our view of the role that protein motions play in light-harvesting processes. Several groups have suggested that correlated fluctuations involving the pigments site energies and couplings could be at the origin of such unexpected behavior. Here we combine molecular dynamics simulations with quantum mechanics/molecular mechanics calculations to analyze the degree of correlated fluctuations in the PE545 complex of Rhodomonas sp. strain CS24. We find that correlations between the motions of the chromophores, which are significantly assisted by the water solvent, do not translate into appreciable site energy correlations but do lead to significant cross-correlations of energies and couplings. Such behavior, not observed in a recent study on the Fenna-Mathews-Olson complex, seems to provide phycobiliproteins with an additional fundamental mechanism to control quantum coherence and light-harvesting efficiency compared with chlorophyll-containing complexes.

Electronic properties and supramolecular organization of terminal bis(alkylethynyl)-substituted benzodithiophenes.

Benzodithiophene (BDT) was symmetrically bisubstituted in the terminal positions with five different alkynes C≡C-(C(n)H(2n+1)) with n = 4, 6, 8, 10, 12. The materials were characterized as potential materials for field-effect transistor applications. Electrochemical measurements in solution and photophysical measurements in solution and in the solid state, together with UV photoelectron spectroscopy in air and quantum-chemical calculations, elucidate the nature of the frontier orbitals and of the excited states as well as their deactivation pathways. Structural information on the molecular assembly in the solid state, both at room temperature and at elevated temperatures, is obtained by a combination of DSC, polarized optical microscopy, and 2D-WAXS, which point to the crystallinity of the compounds in all phases and reveal π-stacking arrangements independently of the length of the alkyl side chains.