Optical excitations of chlorophyll a and b monomers and dimers

Combined Multireference-Multiscale Approach to the Description of Photosynthetic Reaction Centers

A first-principles description of the primary photochemical processes that drive photosynthesis and sustain life on our planet remains one of the grand challenges of modern science. Recent research established that explicit incorporation of protein electrostatics in excited-state calculations of photosynthetic pigments, achieved for example with quantum-mechanics/molecular-mechanics (QM/MM) approaches, is essential for a meaningful description of the properties and function of pigment-protein complexes. Although time-dependent density functional theory has been used productively so far in QM/MM approaches for the study of such systems, this methodology has limitations. Here we pursue for the first time a QM/MM description of the reaction center in the principal enzyme of oxygenic photosynthesis, Photosystem II, using multireference wave function theory for the high-level QM region. We identify best practices and establish guidelines regarding the rational choice of active space and appropriate state-averaging for the efficient and reliable use of complete active space self-consistent field (CASSCF) and the N-electron valence state perturbation theory (NEVPT2) in the prediction of low-lying excited states of chlorophyll and pheophytin pigments. Given that the Gouterman orbitals are inadequate as a minimal active space, we define specific minimal and extended active spaces for the NEVPT2 description of electronic states that fall within the Q and B bands. Subsequently, we apply our multireference-QM/MM protocol to the description of all pigments in the reaction center of Photosystem II. The calculations reproduce the electrochromic shifts induced by the protein matrix and the ordering of site energies consistent with the identity of the primary donor (ChlD1) and the experimentally known asymmetric and directional electron transfer. The optimized protocol sets the stage for future multireference treatments of multiple pigments, and hence for multireference studies of charge separation, while it is transferable to the study of any photoactive embedded tetrapyrrole system.

Total absorption spectrum of benzene aggregates obtained from two different approaches

CONTEXT

The study of molecular aggregation effects on the electronic spectrum is essential for the development of optoelectronic devices. However, investigating the entire valence absorption spectrum of aggregates using quantum mechanical methods is a challenging task. In this work, we perform systematic simulations of the absorption spectrum of benzene molecular clusters up to 35 eV applying two approaches based on time-dependent density functional theory. The results show that depending on the dimer packing, different energy shifts occur for the symmetry allowed [Formula: see text] transition, in comparison to the monomer. The transition intensity increases for the band around 6 eV for larger aggregates from the monomer to dimers and tetramer, indicating the occurrence of the symmetry forbidden (in [Formula: see text] point group) [Formula: see text] [Formula: see text] transition. The benzene crystal exhibits a large redshift following the experimental spectrum. Also, the continuum regions of all spectra show a good agreement with the experiments both in gas and solid phases.

METHODS

Geometry optimization of the monomer was carried out with Gaussian 09 software using the PBE0/def2-TZVP level of theory. We used dimers and tetramer molecular geometries extracted from the experimental crystal structure. The absorption spectra were directly obtained by the Liouville-Lanczos TDDFT approach with plane waves basis set or indirectly by TDDFT pseudo-spectra calculated in a [Formula: see text] basis followed by analytic continuation procedure to obtain complex polarizability. The former is available at Quantum ESPRESSO, and the latter was calculated using Gaussian 09 with the post-processing performed with a code previously developed in our group.

Physicochemical, antioxidant properties of carotenoids and its optoelectronic and interaction studies with chlorophyll pigments

The physicochemical and antioxidant properties of seven carotenoids: antheraxanthin, β-carotene, neoxanthin, peridinin, violaxanthin, xanthrophyll and zeaxanthin were studied by theoretical means. Then the Optoelectronic properties and interaction of chlorophyll-carotenoid complexes are analysed by TDDFT and IGMPLOT. Global reactivity descriptors for carotenoids and chlorophyll (Chla, Chlb) are calculated via conceptual density functional theory (CDFT). The higher HOMO-LUMO (HL) gap indicated structural stability of carotenoid, chlorophyll and chlorophyll-carotenoid complexes. The chemical hardness for carotenoids and Chlorophyll is found to be lower in the solvent medium than in the gas phase. Results showed that carotenoids can be used as good reactive nucleophile due to lower µ and ω. As proton affinities (PAs) are much lower than the bond dissociation enthalpies (BDEs), it is anticipated that direct antioxidant activity in these carotenoids is mainly due to the sequential proton loss electron transfer (SPLET) mechanism with dominant solvent effects. Also lower PAs of carotenoid suggest that antioxidant activity by the SPLET mechanism should be a result of a balance between proclivities to transfer protons. Reaction rate constant with Transition-State Theory (TST) were estimated for carotenoid-Chlorophyll complexes in gas phase. Time dependent Density Functional Theory (TDDFT) showed that all the chlorophyll (Chla, Chlb)-carotenoid complexes show absorption wavelength in the visible region. The lower S1-T1 adiabatic energy gap indicated ISC transition from S1 to T1 state.

Accurate Computation of the Absorption Spectrum of Chlorophyll a with Pair Natural Orbital Coupled Cluster Methods

The ability to accurately compute low-energy excited states of chlorophylls is critically important for understanding the vital roles they play in light harvesting, energy transfer, and photosynthetic charge separation. The challenge for quantum chemical methods arises both from the intrinsic complexity of the electronic structure problem and, in the case of biological models, from the need to account for protein–pigment interactions. In this work, we report electronic structure calculations of unprecedented accuracy for the low-energy excited states in the Q and B bands of chlorophyll a. This is achieved by using the newly developed domain-based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD) in combination with sufficiently large and flexible basis sets. The results of our DLPNO–STEOM-CCSD calculations are compared with more approximate approaches. The results demonstrate that, in contrast to time-dependent density functional theory, the DLPNO–STEOM-CCSD method provides a balanced performance for both absorption bands. In addition to vertical excitation energies, we have calculated the vibronic spectrum for the Q and B bands through a combination of DLPNO–STEOM-CCSD and ground-state density functional theory frequency calculations. These results serve as a basis for comparison with gas-phase experiments.

Color tuning of chlorophyll a and b pigments revealed from gas-phase spectroscopy

Chlorophyll (Chl) pigments are responsible for vital mechanisms in photosynthetic proteins: light harvesting, energy transfer and charge separation. A complex interplay between the Chl molecule and its microenvironment determines its transition energy. Interactions such as excitonic coupling with one or more pigments (Chls or carotenoids), axial ligation to the magnesium center, or electrostatic interactions between Chl and nearby amino-acid residues all influence the photophysical properties. Here we use time-resolved photodissociation action spectroscopy to determine transition energies of Chla/b complexes in vacuo to directly compare the impact of a negatively charged axial ligand (formate) to that of exciton coupling between two Chls. Experiments carried out at the electrostatic ion storage ring ELISA allow dissociation to be sampled on hundreds of milliseconds time scale. Absorption-band maxima of Chla-formate complexes are found at 433 ± 4 nm/2.86 ± 0.03 eV (Soret band) and in the region 654-675 nm/1.84-1.90 eV (Q band) and those of Chla dimers tagged by a quaternary ammonium ion at 419 ± 5 nm/2.96 ± 0.04 eV (Soret band) and 647 nm/1.92 eV (Q band). The axial ligand strongly affects the Chla transition energies causing redshifts of 0.21 eV of the Soret band and 0.04-0.1 eV of the Q band compared to Chla tagged by a quaternary ammonium. Slightly smaller shifts were found in case of Chlb. The redshifts are approximately twice that induced by excitonic coupling between two Chlas, also tagged by a quaternary ammonium ion. Axial ligation brings the absorption by isolated Chls very close to that of photosynthetic proteins.

LCAO-TDDFT-k-: spectroscopy in the optical limit

Understanding, optimizing, and controlling the optical absorption process, exciton gemination, and electron-hole separation and conduction in low dimensional systems is a fundamental problem in materials science. However, robust and efficient methods capable of modelling the optical absorbance of low dimensional macromolecular systems and providing physical insight into the processes involved have remained elusive. We employ a highly efficient linear combination of atomic orbitals (LCAOs) representation of the Kohn-Sham (KS) orbitals within time dependent density functional theory (TDDFT) in the reciprocal space (k) and frequency (ω) domains, as implemented within our LCAO-TDDFT-k-ωcode, applying eithera prioriora posteriorithe derivative discontinuity correction of the exchange functional Δxto the KS eigenenergies as a scissors operator. In so doing we are able to provide a semi-quantitative description of the photoabsorption cross section, conductivity, and dielectric function for prototypical 0D, 1D, 2D, and 3D systems within the optical limit (‖q‖ → 0+) as compared to both available measurements and from solving the Bethe-Salpeter equation with quasiparticleG0W0eigenvalues (G0W0-BSE). Specifically, we consider 0D fullerene (C60), 1D metallic (10, 0) and semiconducting (10, 10) single-walled carbon nanotubes, 2D graphene (Gr) and phosphorene (Pn), and 3D rutile (R-TiO2) and anatase (A-TiO2). For each system, we also employ the spatially and energetically resolved electron-hole spectral density to provide direct physical insight into the nature of their optical excitations. These results demonstrate the reliability, applicability, efficiency, and robustness of our LCAO-TDDFT-k-ωcode, and open the pathway to the computational design of macromolecular systems for optoelectronic, photovoltaic, and photocatalytic applicationsin silico.

Conductivity models for electron energy loss spectroscopy of graphene in a scanning transmission electron microscope with high energy resolution

Recent advancements in the energy resolution and probing capabilities of monochromated electron-beam spectroscopy instruments have made this experimental technique increasingly useful for investigating and understanding the plasmonic, photonic, and electronic properties of graphene-enhanced systems. We develop herein an empirical model for the in-plane conductivity of doped monolayer graphene, comparing with ab initio data from the terahertz (THz) to the upper range of frequencies accessible with the valence electron energy loss spectroscopy (VEELS). Along with our ab initio data, this model is employed to calculate the energy loss spectra using a relativistic formulation, allowing us to analyze the effects that different electron beam parameters have on the response of graphene in a monochromated scanning transmission electron microscope setup. In particular, we explore the effects of reducing the collection angle of scattered electrons, thereby deducing a computational procedure for extracting the real and imaginary parts of the optical conductivity of graphene layers from VEELS measurements. Our modeling ultimately provides insight into how the optoelectronic properties of graphene are expected to manifest in the VEELS obtained via monochromated beams, with the effects of graphene doping, the excitation of its plasmon-polaritons, and relativistic contributions included comprehensively.