Assignment of the Q-bands of the chlorophylls: coherence loss via Qx - Qy mixing

Molecular interactions of photosystem I and ZIF-8 in bio-nanohybrid materials

Bio-nanohybrid devices featuring natural photocatalysts bound to a nanostructure hold great promise in the search for sustainable energy conversion. One of the major challenges of integrating biological systems is protecting them against harsh environmental conditions while retaining, or ideally enhancing their photophysical properties. In this mainly computational work we investigate an assembly of cyanobacterial photosystem I (PS I) embedded in a metal-organic framework (MOF), namely the zeolitic imidazolate framework ZIF-8. This complex has been reported experimentally [Bennett et al., Nanoscale Adv., 2019, 1, 94] but so far the molecular interactions between PS I and the MOF remained elusive. We show via absorption spectroscopy that PS I remains intact throughout the encapsulation-release cycle. Molecular dynamics (MD) simulations further confirm that the encapsulation has no noticeable structural impact on the photosystem. However, the MOF building blocks frequently coordinate to the Mg2+ ions of chlorophylls in the periphery of the antenna complex. High-level quantum mechanical calculations reveal charge-transfer interactions, which affect the excitonic network and thereby may reversibly change the fluorescence properties of PS I. Nevertheless, our results highlight the stability of PS I in the MOF, as the reaction center remains unimpeded by the heterogeneous environment, paving the way for applications in the foreseeable future.

Calculation of quasi-diabatic states within the DFT/MRCI(2) framework: The QD-DFT/MRCI(2) method

We describe a procedure for the calculation of quasi-diabatic states within the recently introduced DFT/MRCI(2) framework [S. P. Neville and M. S. Schuurman, J. Chem. Phys. 157, 164103 (2022)]. Based on an effective Hamiltonian formalism, the proposed procedure, which we term QD-DFT/MRCI(2), has the advantageous characteristics of being simultaneously highly efficient and effectively black box in nature while directly yielding both quasi-diabatic potentials and wave functions of high quality. The accuracy and efficiency of the QD-DFT/MRCI(2) formalism are demonstrated via the simulation of the vibronic absorption spectra of furan and chlorophyll a.

Vibronic Coupling Drives the Ultrafast Internal Conversion in a Functionalized Free-Base Porphyrin

Internal conversion (IC) is a common radiationless transition in polyatomic molecules. Theory predicts that molecular vibrations assist IC between excited states, and ultrafast experiments can provide insight into their structure-function relationship. Here we elucidate the dynamics of the vibrational modes driving the IC process within the Q band of a functionalized porphyrin molecule. Through a combination of ultrafast multidimensional spectroscopies and theoretical modeling, we observe a 60 fs Qy-Qx IC and demonstrate that it is driven by the interplay among multiple high-frequency modes. Notably, we identify 1510 cm-1 as the leading tuning mode that brings the porphyrin to an optimal geometry for energy surface crossing. By employing coherent wave packet analysis, we highlight a set of short-lived vibrations (1200-1400 cm-1), promoting the IC within ≈60 fs. Furthermore, we identify one coupling mode (1350 cm-1) that is responsible for vibronic mixing within the Q states. Our findings indicate that porphyrin-core functionalization modulates IC effectively, offering new opportunities in photocatalysis and optoelectronics.

Two-Dimensional Electronic Spectroscopy Characterization of Fucoxanthin-Chlorophyll Protein Reveals Excitonic Carotenoid-Chlorophyll Interactions

Fucoxanthin Chlorophyll Protein (FCP) is a Light Harvesting Complex found in diatoms and brown algae. It is particularly interesting for its efficiency in capturing the blue-green part of the light spectrum due to the presence of specific chromophores (fucoxanthin, chlorophyll a, and chlorophyll c). Recently, the crystallographic structure of FCP was solved, revealing the 3D arrangement of the pigments in the protein scaffold. While this information is helpful for interpreting the spectroscopic features of FCP, it has also raised new questions about the potential interactions between fucoxanthin and chlorophyll c. These interactions were suggested by their spatial closeness but have never been experimentally observed. To investigate this possible interaction mechanism, in this work, two-dimensional electronic spectroscopy (2DES) has been applied to study the ultrafast relaxation dynamics of FCP. The experiments captured an instantaneous delocalization of the excitation among fucoxanthin and chlorophyll c, suggesting the presence of a non-negligible coupling between the chromophores.

Full visible range two-dimensional electronic spectroscopy with high time resolution

Two-dimensional electronic spectroscopy (2DES) is a powerful method to study coherent and incoherent interactions and dynamics in complex quantum systems by correlating excitation and detection energies in a nonlinear spectroscopy experiment. Such dynamics can be probed with a time resolution limited only by the duration of the employed laser pulses and in a spectral range defined by the pulse spectrum. In the blue spectral range (<500 nm), the generation of sufficiently broadband ultrashort pulses with pulse durations of 10 fs or less has been challenging so far. Here, we present a 2DES setup based on a hollow-core fiber supercontinuum covering the full visible range (400-700 nm). Pulse compression via custom-made chirped mirrors yields a time resolution of <10 fs. The broad spectral coverage, in particular the extension of the pulse spectra into the blue spectral range, unlocks new possibilities for coherent investigations of blue-light absorbing and multichromophoric compounds, as demonstrated by a 2DES measurement of chlorophyll a.

Signatures of intramolecular vibrational and vibronic Q[Formula: see text]-Q[Formula: see text] coupling effects in absorption and CD spectra of chlorophyll dimers

An electron-vibrational coupling model that includes the vibronic (non-adiabatic) coupling between the Q[Formula: see text] and Q[Formula: see text] transitions of chlorophyll (Chl), created by Reimers and coworkers (Scientific Rep. 3, 2761, 2013) is extended here to chlorophyll dimers with interchlorophyll excitonic coupling. The model is applied to a Chl a dimer of the water-soluble chlorophyll binding protein (WSCP). As for isolated chlorophyll, the vibronic coupling is found to have a strong influence on the high-frequency vibrational sideband in the absorption spectrum, giving rise to a band splitting. In contrast, in the CD spectrum the interplay of vibronic coupling and static disorder leads to a strong suppression of the vibrational sideband in excellent agreement with the experimental data. The conservative nature of the CD spectrum in the low-energy region is found to be caused by a delicate balance of the intermonomer excitonic coupling between the purely electronic Q[Formula: see text] transition and the Q[Formula: see text] transition involving intramolecular vibrational excitations on one hand and the coupling to higher-energy electronic transitions on the other hand.

Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations

Cyanobacterial photosystem I (PSI) is one of the most efficient photosynthetic machineries found in nature. Due to the large scale and complexity of the system, the energy transfer mechanism from the antenna complex to the reaction center is still not fully understood. A central element is the accurate evaluation of the individual chlorophyll excitation energies (site energies). Such an evaluation must include a detailed treatment of site specific environmental influences on structural and electrostatic properties, but also their evolution in the temporal domain, because of the dynamic nature of the energy transfer process. In this work, we calculate the site energies of all 96 chlorophylls in a membrane-embedded model of PSI. The employed hybrid QM/MM approach using the multireference DFT/MRCI method in the QM region allows to obtain accurate site energies under explicit consideration of the natural environment. We identify energy traps and barriers in the antenna complex and discuss their implications for energy transfer to the reaction center. Going beyond previous studies, our model also accounts for the molecular dynamics of the full trimeric PSI complex. Via statistical analysis we show that the thermal fluctuations of single chlorophylls prevent the formation of a single prominent energy funnel within the antenna complex. These findings are also supported by a dipole exciton model. We conclude that energy transfer pathways may form only transiently at physiological temperatures, as thermal fluctuations overcome energy barriers. The set of site energies provided in this work sets the stage for theoretical and experimental studies on the highly efficient energy transfer mechanisms in PSI.

Synchronization of opening and closing of two gramicidin A channels pulled together by a linker: possible relevance to channel clustering

The linear 15-mer peptide gramicidin A (gA) produced by Bacillus brevis is known to form the simplest natural ion channel in lipid membranes representing a head-to-head transmembrane dimer. Its incorporation into a planar lipid bilayer manifests itself in regular electrical current transitions. If two gA subunits are tightly connected by a water-soluble, flexible linker of a certain length, the current transitions become heterogeneous: in a part of them, the amplitude is almost twofold higher than that of a single channel, thereby demonstrating the synchronous opening of two single channels. The lifetime, i.e. the open-state duration, of this dual channel is by several orders of magnitude longer than that of the single channel. Here, we used the ideas of the theory of excitons to hypothesize about the mechanism of synchronous opening and closing of two adjacent channels. Two independent (uncoupled) single channels can be described by two independent conformational coordinates q1 and q2, while two closely located channels can exhibit collective behavior, if the coupling between them produces mixing of the individual states (q1,0) and (0,q2). We suppose that a similar phenomenon can occur not only with synthetic derivatives of gA, but also with such natural channel-forming peptide antibiotics and toxins as alamethicin and syringomycin. In particular, channel clustering observed with these peptides may be also associated with formation of collective conductance states, resulting from mixing of their monomeric states, which allows us to explain the fact that clusters of these channels transmit ions and nonelectrolytes of the same size as the original single channels.

Extracting the excitonic Hamiltonian of a chlorophyll dimer from broadband two-dimensional electronic spectroscopy

We apply Frenkel exciton theory to model the entire Q-band of a tightly bound chlorophyll dimer inspired by the photosynthetic reaction center of photosystem II. The potential of broadband two-dimensional electronic spectroscopy experiment spanning the Q_x and Q_y regions to extract the parameters of the model dimer Hamiltonian is examined through theoretical simulations of the experiment. We find that the local nature of Q_x excitation enables identification of molecular properties of the delocalized Q_y excitons. Specifically, we demonstrate that the cross-peak region, where excitation energy is resonant with Q_y while detection is at Q_x, contains specific spectral signatures that can reveal the full real-space molecular Hamiltonian, a task that is impossible by considering the Q_y transitions alone. System-bath coupling and site energy disorder in realistic systems may limit the resolution of these spectral signatures due to spectral congestion.

Quasiparticle Self-Consistent GW-Bethe-Salpeter Equation Calculations for Large Chromophoric Systems

The GW-Bethe–Salpeter equation (BSE) method is promising for calculating the low-lying excitonic states of molecular systems. However, so far it has only been applied to rather small molecules and in the commonly implemented diagonal approximations to the electronic self-energy, it depends on a mean-field starting point. We describe here an implementation of the self-consistent and starting-point-independent quasiparticle self-consistent (qsGW)-BSE approach, which is suitable for calculations on large molecules. We herein show that eigenvalue-only self-consistency can lead to an unfaithful description of some excitonic states for chlorophyll dimers while the qsGW-BSE vertical excitation energies (VEEs) are in excellent agreement with spectroscopic experiments for chlorophyll monomers and dimers measured in the gas phase. Furthermore, VEEs from time-dependent density functional theory calculations tend to disagree with experimental values and using different range-separated hybrid (RSH) kernels does change the VEEs by up to 0.5 eV. We use the new qsGW-BSE implementation to calculate the lowest excitation energies of the six chromophores of the photosystem II (PSII) reaction center (RC) with nearly 2000 correlated electrons. Using more than 11,000 (6000) basis functions, the calculation could be completed in less than 5 (2) days on a single modern compute node. In agreement with previous TD-DFT calculations using RSH kernels on models that also do not include environmental effects, our qsGW-BSE calculations only yield states with local characters in the low-energy spectrum of the hexameric complex. Earlier works with RSH kernels have demonstrated that the protein environment facilitates the experimentally observed interchromophoric charge transfer. Therefore, future research will need to combine correlation effects beyond TD-DFT with an explicit treatment of environmental electrostatics.

Comparative Absorption Dynamics of the Singlet Excited States of Chlorophylls a and d

Transient absorption dynamics of chlorophylls a and d dissolved in tetrahydrofuran was measured by the broadband femtosecond laser pump-probe spectroscopy in a spectral range from 400 to 870 nm. The absorption spectra of the excited S₁ singlet states of chlorophylls a and d were recorded, and the dynamics of the of the Q_y band shift of the stimulated emission (Stokes shift of fluorescence) was determined in a time range from 60 fs to 4 ps. The kinetics of the intramolecular conversion Q_x→Q_y (electronic transition S₂→S₁) was measured; the characteristic relaxation time was 54 ± 3 and 45 ± 9 fs for chlorophylls a and d, respectively.

Inactivation Mechanism of Algal Chlorophyll by Allelochemical Quercetin

Cyanobacteria harmful algal blooms (CyanoHABs) are a global concern. Application of allelochemicals is a promising solution for cyanobacteria control, due to its high efficiency, low cost and ecological safety. Flavonoids (natural polyphenols produced by aquatic plants) are reported capable of effectively inhibiting the growth of algae; however, the molecular mechanism of algae chlorophyll inactivation is still unclear. In this study, quercetin was used as a typical flavonoid, to investigate the inactivation effect of allelochemical on Microcystis aeruginosa chlorophyll a. The absorption and fluorescence spectra showed that chlorophyll reacted with quercetin to form pheophytin, and the formation rate of pheophytin increased with increasing quercetin concentration (1 × 10^-5-1 × 10^-2 M). FTIR spectra and DFT calculation showed that Mg²⁺ complexed with the 3-OH and 4-C = O groups in the quercetin ring C so that chlorophyll was inactivated due to the loss of Mg²⁺ ions. Overall, this study revealed that quercetin inactivated chlorophyll a of cyanobacteria by capturing Mg²⁺ ions, providing insights into the molecular mechanisms of algal bloom control by allelochemicals.

Iron oxide@chlorophyll clustered nanoparticles eliminate bladder cancer by photodynamic immunotherapy-initiated ferroptosis and immunostimulation

The escape of bladder cancer from immunosurveillance causes monotherapy to exhibit poor efficacy; therefore, designing a multifunctional nanoparticle that boosts programmed cell death and immunoactivation has potential as a treatment strategy. Herein, we developed a facile one-pot coprecipitation reaction to fabricate cluster-structured nanoparticles (CNPs) assembled from Fe₃O₄ and iron chlorophyll (Chl/Fe) photosensitizers. This nanoassembled CNP, as a multifunctional theranostic agent, could perform red-NIR fluorescence and change the redox balance by the photoinduction of reactive oxygen species (ROS) and attenuate iron-mediated lipid peroxidation by the induction of a Fenton-like reaction. The intravesical instillation of Fe₃O₄@Chl/Fe CNPs modified with 4-carboxyphenylboronic acid (CPBA) may target the BC wall through glycoproteins in the BC cavity, allowing local killing of cancer cells by photodynamic therapy (PDT)-induced singlet oxygen and causing chemodynamic therapy (CDT)-mediated ferroptosis. An interesting possibility is reprogramming of the tumor microenvironment from immunosuppressive to immunostimulatory after PDT-CDT treatment, which was demonstrated by the reduction of PD-L1 (lower “off” signal to the effector immune cells), IDO-1, TGF-β, and M2-like macrophages and the induction of CD8⁺ T cells on BC sections. Moreover, the intravesical instillation of Fe₃O₄@Chl/Fe CNPs may enhance the large-area distribution on the BC wall, improving antitumor efficacy and increasing survival rates from 0 to 91.7%. Our theranostic CNPs not only demonstrated combined PDT-CDT-induced cytotoxicity, ROS production, and ferroptosis to facilitate treatment efficacy but also opened up new horizons for eliminating the immunosuppressive effect by simultaneous PDT-CDT.

Bethe-Salpeter equation insights into the photo-absorption function and exciton structure of chlorophyll a and b in light-harvesting complex II

The photo-absorption process and the excitation of chlorophyll (Chl) is the primary and essential step of photosynthesis in green plants. By solving the Bethe-Salpeter equation (BSE) on top of the GW approximation within ab initio many-body perturbation theory, we calculate the photo-absorption function and the excitons structure of Chl a and b in their in vivo conformations as measured by X-ray diffraction in the light-harvesting complex (LHC) II. BSE optical absorption spectra are in good agreement with the experiment and we discuss residual discrepancies. The experimental evidence of multiple Chla forms in vivo is explained by BSE. The Chla and Chlb BSE exciton wavefunctions present important charge-transfer differences on the Soret band. Q excitons are almost identical, apart from charge (both electron and hole) localization on the Chlb C7 aldheide formyl group, absent on the Chla methyl C7, that is exactly the group where the two chlorophylls differ.

Characterizing Mode Anharmonicity and Huang-Rhys Factors Using Models of Femtosecond Coherence Spectra

Femtosecond laser pulses readily produce coherent quantum beats in transient-absorption spectra. These oscillatory signals often arise from molecular vibrations and therefore may contain information about the excited-state potential energy surface near the Franck-Condon region. Here, by fitting the measured spectra of two laser dyes to microscopic models of femtosecond coherence spectra (FCS) arising from molecular vibrations, we classify coherent quantum-beat signals as fundamentals or overtones and quantify their Huang-Rhys factors and anharmonicity values. We discuss the extracted Huang-Rhys factors in the context of quantum-chemical computations. This work solidifies the use of FCS for analysis of coherent quantum beats arising from molecular vibrations, which will aid studies of molecular aggregates and photosynthetic proteins.

Structure-based model of fucoxanthin-chlorophyll protein complex: Calculations of chlorophyll electronic couplings

Diatoms are a group of marine algae that are responsible for a significant part of global oxygen production. Adapted to life in an aqueous environment dominated by the blue-green light, their major light-harvesting antennae-fucoxanthin-chlorophyll protein complexes (FCPs)-exhibit different pigment compositions than of plants. Despite extensive experimental studies, until recently the theoretical description of excitation energy dynamics in these complexes was limited by the lack of high-resolution structural data. In this work, we use the recently resolved crystallographic information of the FCP complex from Phaeodactylum tricornutum diatom [Wang et al., Science 363, 6427 (2019)] and quantum chemistry-based calculations to evaluate the chlorophyll transition dipole moments, atomic transition charges from electrostatic potential, and the inter-chlorophyll couplings in this complex. The obtained structure-based excitonic couplings form the foundation for any modeling of stationary or time-resolved spectroscopic data. We also calculate the inter-pigment Förster energy transfer rates and identify two quickly equilibrating chlorophyll clusters.

Molecular mechanisms of light harvesting in the minor antenna CP29 in near-native membrane lipidic environment

CP29, a chlorophyll a/ b-xanthophyll binding protein, bridges energy transfer between the major LHCII antenna complexes and photosystem II reaction centers. It hosts one of the two identified quenching sites, making it crucial for regulated photoprotection mechanisms. Until now, the photophysics of CP29 has been studied on the purified protein in detergent solutions since spectrally overlapping signals affect in vivo measurements. However, the protein in detergent assumes non-native conformations compared to its physiological state in the thylakoid membrane. Here, we report a detailed photophysical study on CP29 inserted in discoidal lipid bilayers, known as nanodiscs, which mimic the native membrane environment. Using picosecond time-resolved fluorescence and femtosecond transient absorption (TA), we observed shortening of the Chl fluorescence lifetime with a decrease of the carotenoid triplet formation yield for CP29 in nanodiscs as compared to the protein in detergent. Global analysis of TA data suggests a 1Chl* quenching mechanism dependent on excitation energy transfer to a carotenoid dark state, likely the proposed S*, which is believed to be formed due to a carotenoid conformational change affecting the S1 state. We suggest that the accessibility of the S* state in different local environments plays a key role in determining the quenching of Chl excited states. In vivo, non-photochemical quenching is activated by de-epoxidation of violaxanthin into zeaxanthin. CP29-zeaxanthin in nanodiscs further shortens the Chl lifetime, which underlines the critical role of zeaxanthin in modulating photoprotection activity.

Light Emission from Vibronic Polaritons in Coupled Metalloporphyrin-Multimode Cavity Systems

In this study, we explore how one can use cavity polariton formation and a non-Condon vibronic coupling mechanism to form a type of hybrid light-matter state we denote as Herzberg-Teller (HT) vibronic polaritons. We use simple models to define the basic characteristics of these hybrid light-matter excitations including their dispersive energies. Experimentally, we find evidence of HT polaritons in the light emission spectra from copper(II) tetraphenylporphyrin (CuTPP) molecules strongly coupled to both single and multimode Fabry-Perot resonator structures. For specific resonator designs, we find evidence of significant enhancement of light emission from a short-lived sing-doublet state of CuTPP, which couples to a higher energy singlet state via a non-Condon vibronic mechanism. The results of a two-state model support the conclusion that this enhancement and the temperature-dependent dispersion of the light emission peak energy stem from radiative relaxation into cavity photon states dressed by collective vibrations of the molecules participating in polariton formation. These results show how researchers can leverage the complex interplay of electronic and nuclear degrees of freedom in light absorbing molecules to form a vaster array of coherent light-matter states and potentially transform platforms in optoelectronic and photocatalytic technologies.

Two-dimensional electronic spectroscopy of the Qx to Qy relaxation of chlorophylls a in photosystem II core complex

Using two-dimensional electronic spectroscopy, we measured the Qx to Qy transfer dynamics of the chlorophyll a (Chl a) manifold in the photosystem II (PSII) monomeric core complex from Arabidopsis thaliana. A PSII monomeric core consists of 35 Chls a and no Chl b, thus allowing for a clear window to study Chl a Qx dynamics in a large pigment-protein complex. Initial excitation in the Qx band results in a transfer to the Qy band in less than 60 fs. Upon the ultrafast transfer, regardless of the excitation frequency within the Qx band, the quasi-transient absorption spectra are very similar. This observation indicates that Chl a’s Qx to Qy transfer is not frequency selective. Using a simple model, we determined that this is not due to the lifetime broadening of the ultrafast transfer but predominantly due to a lack of correlation between the PSII core complex’s Chl a Qx and Qy bands. We suggest the origin to be the intrinsic loss of correlation during the Qx to Qy internal conversion as observed in previous studies of molecular Chl a dissolved in solvents.

Towards a quantitative description of excitonic couplings in photosynthetic pigment-protein complexes: quantum chemistry driven multiscale approaches

A structure-based quantitative calculation of excitonic couplings between photosynthetic pigments has to describe the dynamical polarization of the protein/solvent environment of the pigments, giving rise to reaction field and screening effects. Here, this challenging problem is approached by combining the fragment molecular orbital (FMO) method with the polarizable continuum model (PCM). The method is applied to compute excitonic couplings between chlorophyll a (Chl a) pigments of the water-soluble chlorophyll-binding protein (WSCP). By calibrating the vacuum dipole strength of the 0-0 transition of the Chl a chromophores according to experimental data, an excellent agreement between calculated and experimental linear absorption and circular dichroism spectra of WSCP is obtained. The effect of the mutual polarization of the pigment ground states is calculated to be very small. The simple Poisson-Transition-charge-from-Electrostatic-potential (Poisson-TrEsp) method is found to accurately describe the screening part of the excitonic coupling, obtained with FMO/PCM. Taking into account that the reaction field effects of the latter method can be described by a scalar constant leads to an improvement of Poisson-TrEsp that is expected to provide the basis for simple and realistic calculations of optical spectra and energy transfer in photosynthetic light-harvesting complexes. In addition, we present an expression for the estimation of Huang-Rhys factors of high-frequency pigment vibrations from experimental fluorescence line-narrowing spectra that takes into account the redistribution of oscillator strength by the interpigment excitonic coupling. Application to WSCP results in corrected Huang-Rhys factors that are less than one third of the original values obtained by the standard electronic two-state analysis that neglects the above redistribution. These factors are important for the estimation of the dipole strength of the 0-0 transition of the chromophores and for the development of calculation schemes for the spectral density of the exciton-vibrational coupling.

Vibrational Modes Promoting Exciton Relaxation in the B850 Band of LH2

Exciton relaxation dynamics in multichromophore systems are often modeled using Redfield theory, where bath fluctuations mediate the relaxation among the exciton eigenstates. Identifying the vibrational or phonon modes that are implicated in exciton relaxation allows more detailed understanding of exciton dynamics. Here we focus on a well-studied light-harvesting II complex (LH2) isolated from the photosynthetic purple bacterium Rhodoblastus acidophilus strain 10050. Using two synchronized mode-locked lasers, we carried out a polarization-dependent two-dimensional electronic spectroscopy (2DES) study of an ultrafast exciton relaxation in the B850 band of LH2. 2DES data with different polarization configurations enable us to investigate the exciton relaxation between the k = ±1 exciton states. Then, we identify vibrational modes coupled to the exciton relaxation by analyzing the coherent wavepackets in the 2DES signals. Focusing on the coherent vibrational wavepackets, the data suggest that certain symmetry-breaking modes of monomeric units play a key role in exciton relaxation.

Density functionals with asymptotic-potential corrections are required for the simulation of spectroscopic properties of materials

Five effects of correction of the asymptotic potential error in density functionals are identified that significantly improve calculated properties of molecular excited states involving charge-transfer character. Newly developed materials-science computational methods are used to demonstrate how these effects manifest in materials spectroscopy. Connection is made considering chlorophyll-a as a paradigm for molecular spectroscopy, 22 iconic materials as paradigms for 3D materials spectroscopy, and the VN - defect in hexagonal boron nitride as an example of the spectroscopy of defects in 2D materials pertaining to nanophotonics. Defects can equally be thought of as being "molecular" and "materials" in nature and hence bridge the relms of molecular and materials spectroscopies. It is concluded that the density functional HSE06, currently considered as the standard for accurate calculations of materials spectroscopy, should be replaced, in most instances, by the computationally similar but asymptotically corrected CAM-B3LYP functional, with some specific functionals for materials-use only providing further improvements.

Antibacterial Nanoparticles with Natural Photosensitizers Extracted from Spinach Leaves

We prepared antibacterial polystyrene nanoparticles (NPs) with natural photosensitizers from chlorophyll (Chl) extract via a simple nanoprecipitation method using the same solvent for dissolution of the polystyrene matrix and extraction of Chls from spinach leaves. A high photo-oxidation and antibacterial effect was demonstrated on Escherichia coli and was based on the photogeneration of singlet oxygen O₂(¹Δ_g), which was directly monitored by NIR luminescence measurements and indirectly verified using a chemical trap. The photoactivity of NPs was triggered by visible light, with enhanced red absorption by Chls. To reduce the quenching effect of carotenoids (β-carotene, lutein, etc.) in the Chl extract, diluted and/or preirradiated samples, in which the photo-oxidized carotenoids lose their quenching effect, were used for preparation of the NPs. For enhanced photo-oxidation and antibacterial effects, a sulfonated polystyrene matrix was used for preparation of a stable dispersion of sulfonated NPs, with the quenching effect of carotenoids being suppressed.

Femtosecond anisotropy excitation spectroscopy to disentangle the Qx and Qy absorption in chlorophyll a

Femtosecond anisotropy excitation spectroscopy is a powerful tool for unraveling contributions of electronic transitions. Here, we applied it to chlorophyll a, identifying the contribution of Qx and Qy transitions within its absorption spectrum.

Q-Band relaxation in chlorophyll: new insights from multireference quantum dynamics

The ultrafast relaxation within the Q-bands of chlorophyll plays a crucial role in photosynthetic light-harvesting. We investigate this process via nuclear and electronic quantum dynamics on multireference potential energy surfaces.

Ultrafast energy transfer between lipid-linked chromophores and plant light-harvesting complex II

Light-Harvesting Complex II (LHCII) is a membrane protein found in plant chloroplasts that has the crucial role of absorbing solar energy and subsequently performing excitation energy transfer to the reaction centre subunits of Photosystem II. LHCII provides strong absorption of blue and red light, however, it has minimal absorption in the green spectral region where solar irradiance is maximal. In a recent proof-of-principle study, we enhanced the absorption in this spectral range by developing a biohybrid system where LHCII proteins together with lipid-linked Texas Red (TR) chromophores were assembled into lipid membrane vesicles. The utility of these systems was limited by significant LHCII quenching due to protein-protein interactions and heterogeneous lipid structures. Here, we organise TR and LHCII into a lipid nanodisc, which provides a homogeneous, well-controlled platform to study the interactions between TR molecules and single LHCII complexes. Fluorescence spectroscopy determined that TR-to-LHCII energy transfer has an efficiency of at least 60%, resulting in a 262% enhancement of LHCII fluorescence in the 525-625 nm range, two-fold greater than in the previous system. Ultrafast transient absorption spectroscopy revealed two time constants of 3.7 and 128 ps for TR-to-LHCII energy transfer. Structural modelling and theoretical calculations indicate that these timescales correspond to TR-lipids that are loosely- or tightly-associated with the protein, respectively, with estimated TR-to-LHCII separations of ∼3.5 nm and ∼1 nm. Overall, we demonstrate that a nanodisc-based biohybrid system provides an idealised platform to explore the photophysical interactions between extrinsic chromophores and membrane proteins with potential applications in understanding more complex natural or artificial photosynthetic systems.

Accurate prediction of the properties of materials using the CAM-B3LYP density functional

Density functionals with asymptotic corrections to the long-range potential provide entry-level methods for calculations on molecules that can sustain charge transfer, but similar applications in materials science are rare. We describe an implementation of the CAM-B3LYP range-separated functional within the Vienna Ab-initio Simulation Package (VASP) framework, together with its analytical functional derivatives. Results obtained for eight representative materials: aluminum, diamond, graphene, silicon, NaCl, MgO, 2D h-BN, and 3D h-BN, indicate that CAM-B3LYP predictions embody mean-absolute deviations (MAD) compared to HSE06 that are reduced by a factor of six for lattice parameters, four for quasiparticle band gaps, three for the lowest optical excitation energies, and six for exciton binding energies. Further, CAM-B3LYP appears competitive compared to ab initio G₀ W₀ and Bethe-Salpeter equation approaches. The CAM-B3LYP implementation in VASP was verified by comparison of optimized geometries and reaction energies for isolated molecules taken from the ACCDB database, evaluated in large periodic unit cells, to analogous results obtained using Gaussian basis sets. Using standard GW pseudopotentials and energy cutoffs for the plane-wave calculations and the aug-cc-pV5Z basis set for the atomic-basis ones, the MAD in energy for 1738 chemical reactions was 0.34 kcal mol^-1 , while for 480 unique bond lengths this was 0.0036 Å; these values reduced to 0.28 kcal mol^-1 (largest error 0.94 kcal mol^-1 ) and 0.0009 Å by increasing the plane-wave cutoff energy to 850 eV.

Unraveling the internal conversion process within the Q-bands of a chlorophyll-like-system through surface-hopping molecular dynamics simulations

The non-radiative relaxation process within the Q-bands of chlorophylls represents a crucial preliminary step during the photosynthetic mechanism. Despite several experimental and theoretical efforts performed in order to clarify the complex dynamics characterizing this stage, a complete understanding of this mechanism is still far to be reached. In this study, non-adiabatic excited-state molecular dynamic simulations have been performed to model the non-radiative process within the Q-bands for a model system of chlorophylls. This system has been considered in the gas phase and then, to have a more representative picture of the environment, with implicit and mixed implicit-explicit solvation models. In the first part of this analysis, absorption spectra have been simulated for each model in order to guide the setup for the non-adiabatic excited-state molecular dynamic simulations. Then, non-adiabatic excited-state molecular dynamic simulations have been performed on a large set of independent trajectories and the population of the Q_x and Q_y states has been computed as the average of all the trajectories, estimating the rate constant for the process. Finally, with the aim of investigating the possible role played by the solvent in the Q_x-Q_y crossing mechanism, an essential dynamic analysis has been performed on the generated data, allowing one to find the most important motions during the simulated dynamics.

Chlorophyll excitation energies and structural stability of the CP47 antenna of photosystem II: a case study in the first-principles simulation of light-harvesting complexes

Natural photosynthesis relies on light harvesting and excitation energy transfer by specialized pigment-protein complexes. Their structure and the electronic properties of the embedded chromophores define the mechanisms of energy transfer. An important example of a pigment-protein complex is CP47, one of the integral antennae of the oxygen-evolving photosystem II (PSII) that is responsible for efficient excitation energy transfer to the PSII reaction center. The charge-transfer excitation induced among coupled reaction center chromophores resolves into charge separation that initiates the electron transfer cascade driving oxygenic photosynthesis. Mapping the distribution of site energies among the 16 chlorophyll molecules of CP47 is essential for understanding excitation energy transfer and overall antenna function. In this work, we demonstrate a multiscale quantum mechanics/molecular mechanics (QM/MM) approach utilizing full time-dependent density functional theory with modern range-separated functionals to compute for the first time the excitation energies of all CP47 chlorophylls in a complete membrane-embedded cyanobacterial PSII dimer. The results quantify the electrostatic effect of the protein on the site energies of CP47 chlorophylls, providing a high-level quantum chemical excitation profile of CP47 within a complete computational model of "near-native" cyanobacterial PSII. The ranking of site energies and the identity of the most red-shifted chlorophylls (B3, followed by B1) differ from previous hypotheses in the literature and provide an alternative basis for evaluating past approaches and semiempirically fitted sets. Given that a lot of experimental studies on CP47 and other light-harvesting complexes utilize extracted samples, we employ molecular dynamics simulations of isolated CP47 to identify which parts of the polypeptide are most destabilized and which pigments are most perturbed when the antenna complex is extracted from PSII. We demonstrate that large parts of the isolated complex rapidly refold to non-native conformations and that certain pigments (such as chlorophyll B1 and β-carotene h1) are so destabilized that they are probably lost upon extraction of CP47 from PSII. The results suggest that the properties of isolated CP47 are not representative of the native complexed antenna. The insights obtained from CP47 are generalizable, with important implications for the information content of experimental studies on biological light-harvesting antenna systems.

Utilization of blue-green light by chlorosomes from the photosynthetic bacterium Chloroflexus aurantiacus: Ultrafast excitation energy conversion and transfer

Chlorosomes of photosynthetic green bacteria are unique molecular assemblies providing efficient light harvesting followed by multi-step transfer of excitation energy to reaction centers. In each chlorosome, 10⁴-10⁵ bacteriochlorophyll (BChl) c/d/e molecules are organized by self-assembly into high-ordered aggregates. We studied the early-time dynamics of the excitation energy flow and energy conversion in chlorosomes isolated from Chloroflexus (Cfx.) aurantiacus bacteria by pump-probe spectroscopy with 30-fs temporal resolution at room temperature. Both the S₂ state of carotenoids (Cars) and the Soret states of BChl c were excited at ~490 nm, and absorption changes were probed at 400-900 nm. A global analysis of spectroscopy data revealed that the excitation energy transfer (EET) from Cars to BChl c aggregates occurred within ~100 fs, and the Soret → Q energy conversion in BChl c occurred faster within ~40 fs. This conclusion was confirmed by a detailed comparison of the early exciton dynamics in chlorosomes with different content of Cars. These processes are accompanied by excitonic and vibrational relaxation within 100-270 fs. The well-known EET from BChl c to the baseplate BChl a proceeded on a ps time-scale. We showed that the S₁ state of Cars does not participate in EET. We discussed the possible presence (or absence) of an intermediate state that might mediates the Soret → Q_y internal conversion in chlorosomal BChl c. We discussed a possible relationship between the observed exciton dynamics and the structural heterogeneity of chlorosomes.

Observing the Fluctuation Dynamics of Dative Bonds Using Two-Dimensional Electronic Spectroscopy

We perform two-dimensional electronic spectroscopy on chlorophyll (Chl) a and b molecules in aprotic solvents of different Lewis basicity. By analyzing the ultrafast spectral diffusion dynamics of the Q_y transition, we show that a certain timescale of the spectral diffusion dynamics is affected by the solvents' Lewis basicity. Control experiments with Chlorin-e6-a Chl molecule analog-and ab initio time-dependent density functional theory calculations confirm that we are directly probing the fluctuation dynamics of the dative bond between the solvent's lone pair and the Mg²⁺ center in Chls that is responsible for the Lewis basicity. The observation is indicative of dative bond length and angular fluctuations with timescales ranging between ∼30 and 150 ps and the dative bond-strength-dependent perturbation on the Q_y transition frequency of Chls.

Asymmetry in the Q y Fluorescence and Absorption Spectra of Chlorophyll a Pertaining to Exciton Dynamics

Significant asymmetry found between the high-resolution Q_y emission and absorption spectra of chlorophyll-a is herein explained, providing basic information needed to understand photosynthetic exciton transport and photochemical reactions. The Q_y spectral asymmetry in chlorophyll has previously been masked by interference in absorption from the nearby Q_x transition, but this effect has recently been removed using extensive quantum spectral simulations or else by analytical inversion of absorption and magnetic circular dichroism data, allowing high-resolution absorption information to be accurately determined from fluorescence-excitation spectra. To compliment this, here, we measure and thoroughly analyze the high-resolution differential fluorescence line narrowing spectra of chlorophyll-a in trimethylamine and in 1-propanol. The results show that vibrational frequencies often change little between absorption and emission, yet large changes in line intensities are found, this effect also being strongly solvent dependent. Among other effects, the analysis in terms of four basic patterns of Duschinsky-rotation matrix elements, obtained using CAM-B3LYP calculations, predicts that a chlorophyll-a molecule excited into a specific vibrational level, may, without phase loss or energy relaxation, reemit the light over a spectral bandwidth exceeding 1,000 cm⁻¹ (0.13 eV) to influence exciton-transport dynamics.

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.

Establishment of the Qy Absorption Spectrum of Chlorophyll a Extending to Near-Infrared

A weak absorption tail related to the Q_y singlet electronic transition of solvated chlorophyll a is discovered using sensitive anti-Stokes fluorescence excitation spectroscopy. The quasi-exponentially decreasing tail was, at ambient temperature, readily observable as far as -2400 cm^-1 from the absorption peak and at relative intensity of 10^-7. The tail also weakened rapidly upon cooling the sample, implying its basic thermally activated nature. The shape of the spectrum as well as its temperature dependence were qualitatively well reproduced by quantum chemical calculations involving the pigment intramolecular vibrational modes, their overtones, and pairwise combination modes, but no intermolecular/solvent modes. A similar tail was observed earlier in the case of bacteriochlorophyll a, suggesting generality of this phenomenon. Long vibronic red tails are, thus, expected to exist in all pigments of light-harvesting relevance at physiological temperatures.

Relaxation Dynamics of Chlorophyll b in the Sub-ps Ultrafast Timescale Measured by 2D Electronic Spectroscopy

A thorough characterization of the early time sub-100 fs relaxation dynamics of biologically relevant chromophores is of crucial importance for a complete understanding of the mechanisms regulating the ultrafast dynamics of the relaxation processes in more complex multichromophoric light-harvesting systems. While chlorophyll a has already been the object of several investigations, little has been reported on chlorophyll b, despite its pivotal role in many functionalities of photosynthetic proteins. Here the relaxation dynamics of chlorophyll b in the ultrafast regime have been characterized using 2D electronic spectroscopy. The comparison of experimental measurements performed at room temperature and 77 K allows the mechanisms and the dynamics of the sub-100 fs relaxation dynamics to be characterized, including spectral diffusion and fast internal conversion assisted by a specific set of vibrational modes.

Single-photon emitters in hexagonal boron nitride: a review of progress

This report summarizes progress made in understanding properties such as zero-phonon-line energies, emission and absorption polarizations, electron-phonon couplings, strain tuning and hyperfine coupling of single photon emitters in hexagonal boron nitride. The primary aims of this research are to discover the chemical nature of the emitting centres and to facilitate deployment in device applications. Critical analyses of the experimental literature and data interpretation, as well as theoretical approaches used to predict properties, are made. In particular, computational and theoretical limitations and challenges are discussed, with a range of suggestions made to overcome these limitations, striving to achieve realistic predictions concerning the nature of emitting centers. A symbiotic relationship is required in which calculations focus on properties that can easily be measured, whilst experiments deliver results in a form facilitating mass-produced calculations.

Uncovering dark multichromophoric states in Peridinin-Chlorophyll-Protein

It has long been recognized that visible light harvesting in Peridinin-Chlorophyll-Protein is driven by the interplay between the bright (S2) and dark (S1) states of peridinin (carotenoid), along with the lowest-lying bright (Qy) and dark (Qx) states of chlorophyll-a. Here, we analyse a chromophore cluster in the crystal structure of Peridinin-Chlorophyll-Protein, in particular, a peridinin-peridinin and a peridinin-chlorophyll-a dimer, and present quantum chemical evidence for excited states that exist beyond the confines of single peridinin and chlorophyll chromophores. These dark multichromophoric states, emanating from the intermolecular packing native to Peridinin-Chlorophyll-Protein, include a correlated triplet pair comprising neighbouring peridinin excitations and a charge-transfer interaction between peridinin and the adjacent chlorophyll-a. We surmise that such dark multichromophoric states may explain two spectral mysteries in light-harvesting pigments: the sub-200-fs singlet fission observed in carotenoid aggregates, and the sub-200-fs chlorophyll-a hole generation in Peridinin-Chlorophyll-Protein.

Characterization of a novel herbicide and antibiotic-resistant Chlorella sp. with an extensive extracellular matrix

A herbicide and antibiotic-resistant microalgal strain, isolated from a eutrophic site at Giofyros river (Heraklion, Crete, Greece) was extensively characterized. In the presence of relatively high concentrations of common photosynthesis inhibitors (DCMU and atrazine), as well as various antibiotics (spectinomycin, kanamycin, and chloramphenicol), the green microalga was able to increase its biomass in approximately equal levels compared to the control. Despite the high concentrations of the inhibitors, photosynthetic efficiency and chlorophyll a amount per dry cell biomass were comparable to those of control cultures in almost all cases. 18S rDNA analysis showed that this microalga belongs to the Chlorella genus. Optical and electron microscopy studies revealed the presence of an extensive extracellular matrix (EM) that surrounds the cells and plays an important role in colony formation and cell-cell interactions. Fourier transform infrared spectroscopy provided evidence that the EM consists of a polysaccharide. This matrix could be separated from the cells with a simple centrifugation. Depending on growth conditions, the dry cell biomass of this Chlorella strain was found to contain 35-39% proteins and 27-42% carbohydrates. The results of this study have demonstrated that the EM plays a protective role for cell homeostasis maintenance against the various chemical agents. This green microalga is a suitable candidate for further studies regarding sustainable biomass production in waste waters for a series of applications.

How the Protein Environment Can Tune the Energy, the Coupling, and the Ultrafast Dynamics of Interacting Chlorophylls: The Example of the Water-Soluble Chlorophyll Protein

The interplay between active molecules and the protein environment in light-harvesting complexes tunes the photophysics and the dynamical properties of pigment-protein complexes in a subtle way, which is not fully understood. Here we characterized the photophysics and the ultrafast dynamics of four variants of the water-soluble chlorophyll protein (WSCP) as an ideal model system to study the behavior of strongly interacting chlorophylls. We found that when coordinated by the WSCP protein, the presence of the formyl group in chlorophyll b replacing the methyl group in chlorophyll a strongly affects the exciton energy and the dynamics of the system, opening up the possibility of tuning the photophysics and the transport properties of multichromophores by engineering specific interactions with the surroundings.

On the excitation dependence of fluorescence spectra of meso-tetrapyridyl zinc (II) porphyrin and its relation with hydrogen bonding and outlying decoration

Zinc porphyrins are potential candidates for boosting the advancement of various technological applications, including those exploring the molecule's radiative emissions. In this work, the excitation dependence of fluorescence spectra from 5,10,15,20-meso-tetrapyridyl zinc(II) porphyrin dissolved in a binary solvent mixture of CHCl₃: MeOH, is reported. Important modifications in the profiles of the fluorescence bands are observed after exciting the molecules in a broad wavelength range from 350 to 565 nm. We attribute such modifications to the existence of two distinct relaxation pathways, related to two quasi-degenerated potential energy surfaces (PES) in the ZnTPyP's first excited state whose population rates changes for different excitation wavelengths. We also observed that by changing the CHCl₃:MeOH proportion in the binary mixture, a quenching mechanism mediated by the MeOH hydrogen bondings and ZnTPyP takes place, which allows for tuning the excitation dependence of the aforementioned relaxations pathways. Moreover, our data confirm that the addition of outlying RuCl(dppb)(bipy) ruthenium complex linked to the pyridyl moieties of the ZnTPyP ring is also an excellent strategy to modify the excitation dependence of the fluorescence relaxation pathways.

Vibronic structure of photosynthetic pigments probed by polarized two-dimensional electronic spectroscopy and ab initio calculations

Bacteriochlorophyll a (Bchl a) and chlorophyll a (Chl a) play important roles as light absorbers in photosynthetic antennae and participate in the initial charge-separation steps in photosynthetic reaction centers. Despite decades of study, questions remain about the interplay of electronic and vibrational states within the Q-band and its effect on the photoexcited dynamics. Here we report results of polarized two-dimensional electronic spectroscopic measurements, performed on penta-coordinated Bchl a and Chl a and their interpretation based on state-of-the-art time-dependent density functional theory calculations and vibrational mode analysis for spectral shapes. We find that the Q-band of Bchl a is comprised of two independent bands, that are assigned following the Gouterman model to Q x and Q y states with orthogonal transition dipole moments. However, we measure the angle to be ∼75°, a finding that is confirmed by ab initio calculations. The internal conversion rate constant from Q x to Q y is found to be 11 ps-1. Unlike Bchl a, the Q-band of Chl a contains three distinct peaks with different polarizations. Ab initio calculations trace these features back to a spectral overlap between two electronic transitions and their vibrational replicas. The smaller energy gap and the mixing of vibronic states result in faster internal conversion rate constants of 38-50 ps-1. We analyze the spectra of penta-coordinated Bchl a and Chl a to highlight the interplay between low-lying vibronic states and their relationship to photoinduced relaxation. Our findings shed new light on the photoexcited dynamics in photosynthetic systems where these chromophores are primary pigments.

Higher Order Vibronic Sidebands of Chlorophyll a and Bacteriochlorophyll a for Enhanced Excitation Energy Transfer and Light Harvesting

Optical absorption and fluorescence spectra of molecules in condensed phases often show extensive sidebands. Originating from electron-vibrational and electron-phonon couplings, these spectral tails bear important information on the dynamics of electronic states and processes the molecules are involved in. The vibronic sidebands observed in conjugate Q_y absorption and fluorescence spectra of chlorophyll a and bacteriochlorophyll a are relatively weak, characterized by the total Huang-Rhys factor which is less than one. Therefore, it is widely considered that only fundamental intramolecular modes are responsible for their formation. Here, we provide evidence for extra-long and structured fluorescence tails of chlorophyll a and bacteriochlorophyll a as far as 4000 cm^-1 from respective spectral origins, far beyond the frequency range of fundamental modes. According to quantum chemical simulations, these sidebands extending to ∼960 nm in chlorophyll a and ∼1140 nm in bacteriochlorophyll a into the infrared part of the optical spectrum are mainly contributed to by vibrational overtones of the fundamental modes. Because energy transfer and relaxation processes generally depend on vibronic overlap integrals, these findings potentially contribute to better understanding of many vital photo-induced phenomena, including photosynthetic light harvesting.