Protein Matrix Control of Reaction Center Excitation in Photosystem II

Femtosecond optical studies of the primary charge separation reactions in far-red photosystem II from Synechococcus sp. PCC 7335

Primary processes of light energy conversion by Photosystem II (PSII) were studied using femtosecond broadband pump-probe absorption difference spectroscopy. Transient absorption changes of core complexes isolated from the cyanobacterium Synechococcus sp. PCC 7335 grown under far-red light (FRL-PSII) were compared with the canonical Chl a containing spinach PSII core complexes upon excitation into the red edge of the Qy band. Absorption changes of FRL-PSII were monitored at 278 K in the 400-800 nm spectral range on a timescale of 0.1-500 ps upon selective excitation at 740 nm of four chlorophyll (Chl) f molecules in the light harvesting antenna, or of one Chl d molecule at the ChlD1 position in the reaction center (RC) upon pumping at 710 nm. Numerical analysis of absorption changes and assessment of the energy levels of the presumed ion-radical states made it possible to identify PD1+ChlD1- as the predominant primary charge-separated radical pair, the formation of which upon selective excitation of Chl d has an apparent time of ∼1.6 ps. Electron transfer to the secondary acceptor pheophytin PheoD1 has an apparent time of ∼7 ps with a variety of excitation wavelengths. The energy redistribution between Chl a and Chl f in the antenna occurs within 1 ps, whereas the energy migration from Chl f to the RC occurs mostly with lifetimes of 60 and 400 ps. Potentiometric analysis suggests that in canonical PSII, PD1+ChlD1- can be partially formed from the excited (PD1ChlD1)* state.

Oxygenic Photosynthesis in Far-Red Light: Strategies and Mechanisms

Oxygenic photosynthesis, the process that converts light energy into chemical energy, is traditionally associated with the absorption of visible light by chlorophyll molecules. However, recent studies have revealed a growing number of organisms capable of using far-red light (700-800 nm) to drive oxygenic photosynthesis. This phenomenon challenges the conventional understanding of the limits of this process. In this review, we briefly introduce the organisms that exhibit far-red photosynthesis and explore the different strategies they employ to harvest far-red light. We discuss the modifications of photosynthetic complexes and their impact on the delivery of excitation energy to photochemical centers and on overall photochemical efficiency. Finally, we examine the solutions employed to drive electron transport and water oxidation using relatively low-energy photons. The findings discussed here not only expand our knowledge of the remarkable adaptation capacities of photosynthetic organisms but also offer insights into the potential for enhancing light capture in crops.

A Vision for the Future of Multiscale Modeling

The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.

Excitation landscape of the CP43 photosynthetic antenna complex from multiscale simulations

Photosystem II (PSII), the principal enzyme of oxygenic photosynthesis, contains two integral light harvesting proteins (CP43 and CP47) that bind chlorophylls and carotenoids. The two intrinsic antennae play crucial roles in excitation energy transfer and photoprotection. CP43 interacts most closely with the reaction center of PSII, specifically with the branch of the reaction center (D1) that is responsible for primary charge separation and electron transfer. Deciphering the function of CP43 requires detailed atomic-level insights into the properties of the embedded pigments. To advance this goal, we employ a range of multiscale computational approaches to determine the site energies and excitonic profile of CP43 chlorophylls, using large all-atom models of a membrane-bound PSII monomer. In addition to time-dependent density functional theory (TD-DFT) used in the context of a quantum-mechanics/molecular-mechanics setup (QM/MM), we present a thorough analysis using the perturbed matrix method (PMM), which enables us to utilize information from long-timescale molecular dynamics simulations of native PSII-complexed CP43. The excited state energetics and excitonic couplings have both similarities and differences compared with previous experimental fits and theoretical calculations. Both static TD-DFT and dynamic PMM results indicate a layered distribution of site energies and reveal specific groups of chlorophylls that have shared contributions to low-energy excitations. Importantly, the contribution to the lowest energy exciton does not arise from the same chlorophylls at each system configuration, but rather changes as a function of conformational dynamics. An unexpected finding is the identification of a low-energy charge-transfer excited state within CP43 that involves a lumenal (C2) and the central (C10) chlorophyll of the complex. The results provide a refined basis for structure-based interpretation of spectroscopic observations and for further deciphering excitation energy transfer in oxygenic photosynthesis.

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. We illustrate PigmentHunter's capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna-Matthews-Olson protein, and ring deformation in photosystems I and II.

Stabilization of Charge-Transfer Excited States in Biological Systems: A Computational Focus on the Special Pair in Photosystem II Reaction Centers

Charge-transfer (CT) excited states play an important role in many biological processes. However, many computational approaches often inadequately address the equilibration effects of nuclear and environmental degrees of freedom on these states. One prominent example of systems in which CT states are of utmost importance is reaction centers (RC) in photosystems. Here we use a multiscale approach combined with time-dependent density functional theory to explore the lowest CT excited state of the special pair PD1-PD2 in the Photosystem II-RC of a cyanobacterium. We find that the nonequilibrium CT excited state resides near the Soret band, making an exciton the lowest-energy excited state. However, accounting for nuclear and state-specific dielectric equilibration along the CT potential energy surface (PES), the CT state PD1--PD2+ stabilizes energetically below the excitonic state. This underscores the crucial role of state-specific solvation in mapping the PES of CT states, as demonstrated in a simplified dimer model.

Fluorescence quenching in aggregates of fucoxanthin-chlorophyll protein complexes: Interplay of fluorescing and dark states

Diatoms, a major group of algae, account for about a quarter of the global primary production on Earth. These photosynthetic organisms face significant challenges due to light intensity variations in their underwater habitat. To avoid photodamage, they have developed very efficient non-photochemical quenching (NPQ) mechanisms. These mechanisms originate in their light-harvesting antenna - the fucoxanthin-chlorophyll protein (FCP) complexes. Spectroscopic studies of NPQ in vivo are often hindered by strongly overlapping signals from the photosystems and their antennae. Fortunately, in vitro FCP aggregates constitute a useful model system to study fluorescence (FL) quenching in diatoms. In this work, we present streak-camera FL measurements on FCPa and FCPb complexes, isolated from a centric diatom Cyclotella meneghiniana, and their aggregates. We find that spectra of non-aggregated FCP are dominated by a single fluorescing species, but the FL spectra of FCP aggregates additionally contain contributions from a redshifted emissive state. We relate this red state to a charge transfer state between chlorophyll c and chlorophyll a molecules. The FL quenching, on the other hand, is due to an additional dark state that involves incoherent energy transfer to the fucoxanthin carotenoids. Overall, the global picture of energy transfer and quenching in FCP aggregates is very similar to that of major light-harvesting complexes in higher plants (LHCII), but microscopic details between FCPs and LHCIIs differ significantly.

Multistate, Polarizable QM/MM Embedding Scheme Based on the Direct Reaction Field Method: Solvatochromic Shifts, Analytical Gradients and Optimizations of Conical Intersections in Solution

We recently introduced a polarizable embedding scheme based on an integral-exact reformulation of the direct reaction field method (IEDRF) that accounts for the differential solvation of ground and excited states in QM/MM simulations. The polarization and dispersion interactions between the quantum-mechanical (QM) and molecular-mechanical (MM) regions are described by the DRF Hamiltonian, while the Pauli repulsion between explicitly treated QM electrons and the implicit electron density around MM atoms is modeled with effective core potentials. A single Hamiltonian is used for all electronic states so that Born-Oppenheimer states belonging to the same geometry are orthogonal and state crossings are well-defined. In this work, we describe the implementation of the method using graphical processing unit acceleration in TeraChem, where it is combined with multiple electronic structure methods, including Hartree-Fock, time-dependent density functional theory, and complete active space self-consistent field. In contrast with older implementations of the DRF method, integrals of the polarization operators are evaluated exactly. Expressions for ingredients needed to construct analytical gradients and nonadiabatic coupling vectors are derived and tested by optimizing a conical intersection between two excited states in the presence of a polarizable solvent shell. The method is applied to estimate the solvent shifts of absorption energies of a series of donor-acceptor dyes having low-lying charge-transfer states. Even for a nonpolar solvent such as n-hexane, the inclusion of its static polarizability leads to non-negligible shifts that improve the agreement to essentially quantitative levels (0.03 eV) with full-system calculations. Good agreement with the positions of the experimental absorption maxima measured in solution is also observed.

Short-Range Effects in the Special Pair of Photosystem II Reaction Centers: The Nonconservative Nature of Circular Dichroism

Photosystem II reaction centers extract electrons from water, providing the basis of oxygenic life on earth. Among the light-sensitive pigments of the reaction center, a central chlorophyll a dimer, known as the special pair, so far has escaped a complete theoretical characterization of its excited state properties. The close proximity of the special pair pigments gives rise to short-range effects that comprise a coupling between local and charge transfer (CT) excited states as well as other intermolecular quantum effects. Using a multiscale simulation and a diabatization technique, we show that the coupling to CT states is responsible for 45% of the excitonic coupling in the special pair. The other short-range effects cause a nonconservative nature of the circular dichroism spectrum of the reaction center by effectively rotating the electric transition dipole moments of the special pair pigments inverting and strongly enhancing their intrinsic rotational strength.

Reaction Center Excitation in Photosystem II: From Multiscale Modeling to Functional Principles

Oxygenic photosynthesis is the fundamental energy-converting process that utilizes sunlight to generate molecular oxygen and the organic compounds that sustain life. Protein-pigment complexes harvest light and transfer excitation energy to specialized pigment assemblies, reaction centers (RC), where electron transfer cascades are initiated. A molecular-level understanding of the primary events is indispensable for elucidating the principles of natural photosynthesis and enabling development of bioinspired technologies. The primary enzyme in oxygenic photosynthesis is Photosystem II (PSII), a membrane-embedded multisubunit complex, that catalyzes the light-driven oxidation of water. The RC of PSII consists of four chlorophyll a and two pheophytin a pigments symmetrically arranged along two core polypeptides; only one branch participates in electron transfer. Despite decades of research, fundamental questions remain, including the origin of this functional asymmetry, the nature of primary charge-transfer states and the identity of the initial electron donor, the origin of the capability of PSII to enact charge separation with far-red photons, i.e., beyond the "red limit" where individual chlorophylls absorb, and the role of protein conformational dynamics in modulating charge-separation pathways.In this Account, we highlight developments in quantum-chemistry based excited-state computations for multipigment assemblies and the refinement of protocols for computing protein-induced electrochromic shifts and charge-transfer excitations calibrated with modern local correlation coupled cluster methods. We emphasize the importance of multiscale atomistic quantum-mechanics/molecular-mechanics and large-scale molecular dynamics simulations, which enabled direct and accurate modeling of primary processes in RC excitation at the quantum mechanical level.Our findings show how differential protein electrostatics enable spectral tuning of RC pigments and generate functional asymmetry in PSII. A chlorophyll pigment on the active branch (ChlD1) has the lowest site energy in PSII and is the primary electron donor. The complete absence of low-lying charge-transfer states within the central pair of chlorophylls excludes a long-held assumption about the initial charge separation. Instead, we identify two primary charge separation pathways, both with the same pheophytin acceptor (PheoD1): a fast pathway with ChlD1 as the primary electron donor (short-range charge-separation) and a slow pathway with PD1PD2 as the initial donor (long-range charge separation). The low-energy spectrum is dominated by two states with significant charge-transfer character, ChlD1δ+PheoD1δ- and PD1δ+PheoD1δ-. The conformational dynamics of PSII allows these charge-transfer states to span wide energy ranges, pushing oxygenic photosynthesis beyond the "red limit". These results provide a quantum mechanical picture of the primary events in the RC of oxygenic photosynthesis, forming a solid basis for interpreting experimental observations and for extending photosynthesis research in new directions.

Triplet states in the reaction center of Photosystem II

In oxygenic photosynthesis sunlight is harvested and funneled as excitation energy into the reaction center (RC) of Photosystem II (PSII), the site of primary charge separation that initiates the photosynthetic electron transfer chain. The chlorophyll ChlD1 pigment of the RC is the primary electron donor, forming a charge-separated radical pair with the vicinal pheophytin PheoD1 (ChlD1+PheoD1-). To avert charge recombination, the electron is further transferred to plastoquinone QA, whereas the hole relaxes to a central pair of chlorophylls (PD1PD2), subsequently driving water oxidation. Spin-triplet states can form within the RC when forward electron transfer is inhibited or back reactions are favored. This can lead to formation of singlet dioxygen, with potential deleterious effects. Here we investigate the nature and properties of triplet states within the PSII RC using a multiscale quantum-mechanics/molecular-mechanics (QM/MM) approach. The low-energy spectrum of excited singlet and triplet states, of both local and charge-transfer nature, is compared using range-separated time-dependent density functional theory (TD-DFT). We further compute electron paramagnetic resonance properties (zero-field splitting parameters and hyperfine coupling constants) of relaxed triplet states and compare them with available experimental data. Moreover, the electrostatic modulation of excited state energetics and redox properties of RC pigments by the semiquinone QA- is described. The results provide a detailed electronic-level understanding of triplet states within the PSII RC and form a refined basis for discussing primary and secondary electron transfer, charge recombination pathways, and possible photoprotection mechanisms in PSII.

Multiscale QM/MM modelling of catalytic systems with ChemShell

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

Solar energy conversion by photosystem II: principles and structures

Photosynthetic water oxidation by Photosystem II (PSII) is a fascinating process because it sustains life on Earth and serves as a blue print for scalable synthetic catalysts required for renewable energy applications. The biophysical, computational, and structural description of this process, which started more than 50 years ago, has made tremendous progress over the past two decades, with its high-resolution crystal structures being available not only of the dark-stable state of PSII, but of all the semi-stable reaction intermediates and even some transient states. Here, we summarize the current knowledge on PSII with emphasis on the basic principles that govern the conversion of light energy to chemical energy in PSII, as well as on the illustration of the molecular structures that enable these reactions. The important remaining questions regarding the mechanism of biological water oxidation are highlighted, and one possible pathway for this fundamental reaction is described at a molecular level.

Charge separation in the photosystem II reaction center resolved by multispectral two-dimensional electronic spectroscopy

The photosystem II reaction center (PSII RC) performs the primary energy conversion steps of oxygenic photosynthesis. While the PSII RC has been studied extensively, the similar time scales of energy transfer and charge separation and the severely overlapping pigment transitions in the Q_y region have led to multiple models of its charge separation mechanism and excitonic structure. Here, we combine two-dimensional electronic spectroscopy (2DES) with a continuum probe and two-dimensional electronic vibrational spectroscopy (2DEV) to study the cyt b559-D1D2 PSII RC at 77 K. This multispectral combination correlates the overlapping Q_y excitons with distinct anion and pigment-specific Q_x and mid-infrared transitions to resolve the charge separation mechanism and excitonic structure. Through extensive simultaneous analysis of the multispectral 2D data, we find that charge separation proceeds on multiple time scales from a delocalized excited state via a single pathway in which Pheo_D1 is the primary electron acceptor, while Chl_D1 and P_D1 act in concert as the primary electron donor.

Understanding Primary Charge Separation in the Heliobacterial Reaction Center

The homodimeric reaction center of heliobacteria retains features of the ancestral reaction center and can thus provide insights into the evolution of photosynthesis. Primary charge separation is expected to proceed in a two-step mechanism along either of the two reaction center branches. We reveal the first charge-separation step from first-principles calculations based on time-dependent density functional theory with an optimally tuned range-separated hybrid and ab initio Born-Oppenheimer molecular dynamics: the electron is most likely localized on the electron transfer cofactor 3 (EC3, OH-chlorophyll a), and the hole on the adjacent EC2. Including substantial parts of the surrounding protein environment into the calculations shows that a distinct structural mechanism is decisive for the relative energetic positioning of the electronic excitations: specific charged amino acids in the vicinity of EC3 lower the energy of charge-transfer excitations and thus facilitate efficient charge separation. These results are discussed considering recent experimental insights.

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.

Alternative Fast and Slow Primary Charge-Separation Pathways in Photosystem II

Photosystem-II (PSII) is a multi-subunit protein complex that harvests sunlight to perform oxygenic photosynthesis. Initial light-activated charge separation takes place at a reaction centre consisting of four chlorophylls and two pheophytins. Understanding the processes following light excitation remains elusive due to spectral congestion, the ultrafast nature, and multi-component behaviour of the charge-separation process. Here, using advanced computational multiscale approaches which take into account the large-scale configurational flexibility of the system, we identify two possible primary pathways to radical-pair formation that differ by three orders of magnitude in their kinetics. The fast (short-range) pathway is dominant, but the existence of an alternative slow (long-range) charge-separation pathway hints at the evolution of redundancy that may serve other purposes, adaptive or protective, related to formation of the unique oxidative species that drives water oxidation in PSII.

Quantum mechanical analysis of excitation energy transfer couplings in photosystem II

We evaluated excitation energy transfer (EET) coupling (J) between all pairs of chlorophylls (Chls) and pheophytins (Pheos) in the protein environment of photosystem II based on the time-dependent density functional theory with a quantum mechanical/molecular mechanics approach. In the reaction center, the EET coupling between Chls PD1 and PD2 is weaker (|J(PD1/PD2)| = 79 cm-1), irrespective of a short edge-to-edge distance of 3.6 Å (Mg-to-Mg distance of 8.1 Å), than the couplings between PD1 and the accessory ChlD1 (|J(PD1/ChlD2)| = 104 cm-1) and between PD2 and ChlD2 (|J(PD2/ChlD1)| = 101 cm-1), suggesting that PD1 and PD2 are two monomeric Chls rather than a "special pair". There exist strongly coupled Chl pairs (|J| > ∼100 cm-1) in the CP47 and CP43 core antennas, which may be candidates for the red-shifted Chls observed in spectroscopic studies. In CP47 and CP43, Chls ligated to CP47-His26 and CP43-His56, which are located in the middle layer of the thylakoid membrane, play a role in the "hub" that mediates the EET from the lumenal to stromal layers. In the stromal layer, Chls ligated to CP47-His466, CP43-His441, and CP43-His444 mediate the EET from CP47 to ChlD2/PheoD2 and from CP43 to ChlD1/PheoD1 in the reaction center. Thus, the excitation energy from both CP47 and CP43 can always be utilized for the charge-separation reaction in the reaction center.

Functional Water Networks in Fully Hydrated Photosystem II

Water channels and networks within photosystem II (PSII) of oxygenic photosynthesis are critical for enzyme structure and function. They control substrate delivery to the oxygen-evolving center and mediate proton transfer at both the oxidative and reductive endpoints. Current views on PSII hydration are derived from protein crystallography, but structural information may be compromised by sample dehydration and technical limitations. Here, we simulate the physiological hydration structure of a cyanobacterial PSII model following a thorough hydration procedure and large-scale unconstrained all-atom molecular dynamics enabled by massively parallel simulations. We show that crystallographic models of PSII are moderately to severely dehydrated and that this problem is particularly acute for models derived from X-ray free electron laser (XFEL) serial femtosecond crystallography. We present a fully hydrated representation of cyanobacterial PSII and map all water channels, both static and dynamic, associated with the electron donor and acceptor sides. Among them, we describe a series of transient channels and the attendant conformational gating role of protein components. On the acceptor side, we characterize a channel system that is absent from existing crystallographic models but is likely functionally important for the reduction of the terminal electron acceptor plastoquinone Q_B. The results of the present work build a foundation for properly (re)evaluating crystallographic models and for eliciting new insights into PSII structure and function.

Conical Intersections in Solution with Polarizable Embedding: Integral-Exact Direct Reaction Field

A common strategy to exploring the properties and reactivity of complex systems is to use quantum mechanics/molecular mechanics (QM/MM) embedding, wherein a QM region is defined and treated with electronic structure theory, and the remainder of the system is treated with a force field. Important to the description of electronic excited states, especially those of charge-transfer character, is the treatment of the coupling between the QM and MM subsystems. The state of the art is to use a polarizable force field for the MM region and mutually couple the QM wavefunction and MM induced dipoles, in addition to the usual electrostatic embedding, yielding a polarizable embedding (QM/MM-Pol) approach. However, we showed previously that current popular QM/MM-Pol approaches exhibit issues of root flipping and/or incorrect descriptions of electronic crossings in multistate calculations [J. Chem. Theory Comput. 14, 2137 (2018)]. Here, we demonstrate a solution to these problems with an integral-exact reformulation of the direct reaction field approach of Thole and Van Duijnen (QM/MM-IEDRF). The resulting embedding potential includes one- and two-electron operators and many-body dipole-induced dipole interactions and thus includes a natural description of the screening of electron-electron interactions by the MM induced dipoles. Pauli repulsion from the environment is mimicked by effective core potentials on the MM atoms. Inherent to the DRF approach is the assumption that MM dipoles respond instantaneously to the positions of the QM electrons; therefore, dispersion interactions are captured approximately. All electronic states are eigenfunctions of the same Hamiltonian, while the polarization induced in the environment and the associated energetic stabilization are unique to each state. This allows for a consistent definition of transition properties and state crossings. We demonstrate QM/MM-IEDRF by exploring the influence of a (polarizable) inert xenon matrix environment on the conical intersection underlying the photoisomerization of ethylene.

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.

Effects of Novel Photosynthetic Inhibitor [CuL2]Br2 Complex on Photosystem II Activity in Spinach

The effects of the novel [CuL₂]Br₂ complex (L = bis{4H-1,3,5-triazino [2,1-b]benzothiazole-2-amine,4-(2-imidazole)}copper(II) bromide complex) on the photosystem II (PSII) activity of PSII membranes isolated from spinach were studied. The absence of photosynthetic oxygen evolution by PSII membranes without artificial electron acceptors, but in the presence of [CuL₂]Br₂, has shown that it is not able to act as a PSII electron acceptor. In the presence of artificial electron acceptors, [CuL₂]Br₂ inhibits photosynthetic oxygen evolution. [CuL₂]Br₂ also suppresses the photoinduced changes of the PSII chlorophyll fluorescence yield (F_V) related to the photoreduction of the primary quinone electron acceptor, Q_A. The inhibition of both characteristic PSII reactions depends on [CuL₂]Br₂ concentration. At all studied concentrations of [CuL₂]Br₂, the decrease in the F_M level occurs exclusively due to a decrease in Fv. [CuL₂]Br₂ causes neither changes in the F₀ level nor the retardation of the photoinduced rise in F_M, which characterizes the efficiency of the electron supply from the donor-side components to Q_A through the PSII reaction center (RC). Artificial electron donors (sodium ascorbate, DPC, Mn²⁺) do not cancel the inhibitory effect of [CuL₂]Br₂. The dependences of the inhibitory efficiency of the studied reactions of PSII on [CuL₂]Br₂ complex concentration practically coincide. The inhibition constant Ki is about 16 µM, and logKi is 4.8. As [CuL₂]Br₂ does not change the aromatic amino acids’ intrinsic fluorescence of the PSII protein components, it can be proposed that [CuL₂]Br₂ has no significant effect on the native state of PSII proteins. The results obtained in the present study are compared to the literature data concerning the inhibitory effects of PSII Cu(II) aqua ions and Cu(II)-organic complexes.

Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model

In this work, a set of 12-6-4 force fields (FFs) parameters were developed for the actinyl molecular cations, AnO2n+ (n = 1, 2), from uranium to plutonium for classical molecular dynamics (MD) for four water models: TIP3P, SPC/E, OPC3, and TIP4Pew. Such a non-bonded potential model taking into account the induced dipole between the metallic center and the surrounding molecules has shown better performances for various cations than the classic 12-6 non-bonded potentials. The parametrization method proposed elsewhere for metallic cations has been extended to these molecular cations. In contrast to the actinyl 12-6 FFs from the literature, the new models reproduce correctly both solvation and thermodynamic properties, thanks to the inclusion of the induced dipole term (C4). The transferability of such force fields was assessed by performing MD simulations of carbonato actinyl species, which are highly implicated in actinide migration or actinide extraction from seawater. A highly satisfying agreement was found when comparing the EXAFS signals computed from our MD simulation to the experimental ones. The set of FFs developed here opens new possibilities for the study of actinide chemistry.

Modulations in Chlorophyll a Fluorescence Based on Intensity and Spectral Variations of Light

Photosynthetic efficiency is significantly affected by both qualitative and quantitative changes during light exposure. The properties of light have a profound effect on electron transport and energy absorption in photochemical reactions. In addition, fluctuations in light intensity and variations in the spectrum can lead to a decrease in photosystem II efficiency. These features necessitate the use of a simple and suitable tool called chlorophyll a fluorescence to study photosynthetic reactions as a function of the aforementioned variables. This research implies that chlorophyll a fluorescence data can be used to determine precise light conditions that help photoautotrophic organisms optimally function.

Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry

Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue‐absorbing proteorhodopsin (BPR) and green‐absorbing proteorhodopsin (GPR). This blue/green color‐shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C₁₄−C₁₅ bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts.

The initial charge separation step in oxygenic photosynthesis

Photosystem II is crucial for life on Earth as it provides oxygen as a result of photoinduced electron transfer and water splitting reactions. The excited state dynamics of the photosystem II-reaction center (PSII-RC) has been a matter of vivid debate because the absorption spectra of the embedded chromophores significantly overlap and hence it is extremely difficult to distinguish transients. Here, we report the two-dimensional electronic-vibrational spectroscopic study of the PSII-RC. The simultaneous resolution along both the visible excitation and infrared detection axis is crucial in allowing for the character of the excitonic states and interplay between them to be clearly distinguished. In particular, this work demonstrates that the mixed exciton-charge transfer state, previously proposed to be responsible for the far-red light operation of photosynthesis, is characterized by the Chl_D1⁺Phe radical pair and can be directly prepared upon photoexcitation. Further, we find that the initial electron acceptor in the PSII-RC is Phe, rather than P_D1, regardless of excitation wavelength.

The photosystem II reaction center (PSII-RC) is a model system to understand the initial steps of photosynthesis, but its excited state dynamics is difficult to disentangle with most spectroscopic methods. Here the authors perform a two-dimensional electronic-vibrational spectroscopic study of PSII-RC, providing detailed insight into such dynamics and into the mechanism of charge separation.

The Electronic Origin of Far-Red-Light-Driven Oxygenic Photosynthesis

Photosystem‐II uses sunlight to trigger charge separation and catalyze water oxidation. Intrinsic properties of chlorophyll a pigments define a natural “red limit” of photosynthesis at ≈680 nm. Nevertheless, charge separation can be triggered with far‐red photons up to 800 nm, without altering the nature of light‐harvesting pigments. Here we identify the electronic origin of this remarkable phenomenon using quantum chemical and multiscale simulations on a native Photosystem‐II model. We find that the reaction center is preorganized for charge separation in the far‐red region by specific chlorophyll–pheophytin pairs, potentially bypassing the light‐harvesting apparatus. Charge transfer can occur along two distinct pathways with one and the same pheophytin acceptor (Pheo_D1). The identity of the donor chlorophyll (Chl_D1 or P_D1) is wavelength‐dependent and conformational dynamics broaden the sampling of the far‐red region by the two charge‐transfer states. The two pathways rationalize spectroscopic observations and underpin designed extensions of the photosynthetically active radiation limit.

Enhancement of DNAzymatic activity using iterative in silico maturation

Enhancement of DNZymatic activity using a combined iterative in silico and in vitro method as a cheaper and more stable alternative to antibodies or enzymes.

Electrostatic profiling of photosynthetic pigments: implications for directed spectral tuning

Photosynthetic pigment-protein complexes harvest solar energy with a high quantum efficiency. Protein scaffolds are known to tune the spectral properties of embedded pigments principally through structured electrostatic environments. Although the physical nature of electrostatic tuning is straightforward, the precise spatial principles of electrostatic preorganization remain poorly explored for different protein matrices and incompletely characterized with respect to the intrinsic properties of different photosynthetic pigments. In this work, we study the electronic structure features associated with the lowest excited state of a series of eight naturally occurring (bacterio)chlorophylls and pheophytins to describe the precise topological differences in electrostatic potentials and hence determine intrinsic differences in the expected mode and impact of electrostatic tuning. The difference electrostatic potentials between the ground and first excited states are used as fingerprints. Both the spatial profile and the propensity for spectral tuning are found to be unique for each pigment, indicating spatially and directionally distinct modes of electrostatic tuning. The results define a specific partitioning of the protein matrix around each pigment as an aid to identify regions with a maximal impact on spectral tuning and have direct implications for dimensionality reduction in protein design and engineering. Thus, a quantum mechanical basis is provided for understanding, predicting, and ultimately designing sequence-modified or pigment-exchanged biological systems, as suggested for selected examples of pigment-reconstituted proteins.

Shedding Light on Primary Donors in Photosynthetic Reaction Centers

Chlorophylls (Chl)s exist in a variety of flavors and are ubiquitous in both the energy and electron transfer processes of photosynthesis. The functions they perform often occur on the ultrafast (fs-ns) time scale and until recently, these have been difficult to measure in real time. Further, the complexity of the binding pockets and the resulting protein-matrix effects that alter the respective electronic properties have rendered theoretical modeling of these states difficult. Recent advances in experimental methodology, computational modeling, and emergence of new reaction center (RC) structures have renewed interest in these processes and allowed researchers to elucidate previously ambiguous functions of Chls and related pheophytins. This is complemented by a wealth of experimental data obtained from decades of prior research. Studying the electronic properties of Chl molecules has advanced our understanding of both the nature of the primary charge separation and subsequent electron transfer processes of RCs. In this review, we examine the structures of primary electron donors in Type I and Type II RCs in relation to the vast body of spectroscopic research that has been performed on them to date. Further, we present density functional theory calculations on each oxidized primary donor to study both their electronic properties and our ability to model experimental spectroscopic data. This allows us to directly compare the electronic properties of hetero- and homodimeric RCs.

A dimeric chlorophyll electron acceptor differentiates type I from type II photosynthetic reaction centers

This research addresses one of the most compelling issues in the field of photosynthesis, namely, the role of the accessory chlorophyll molecules in primary charge separation. Using a combination of empirical and computational methods, we demonstrate that the primary acceptor of photosystem (PS) I is a dimer of accessory and secondary chlorophyll molecules, Chl_2A and Chl_3A, with an asymmetric electron charge density distribution. The incorporation of highly coupled donors and acceptors in PS I allows for extensive delocalization that prolongs the lifetime of the charge-separated state, providing for high quantum efficiency. The discovery of this motif has widespread implications ranging from the evolution of naturally occurring reaction centers to the development of a new generation of highly efficient artificial photosynthetic systems.

Video abstract

Phthalocyanine as a Bioinspired Model for Chlorophyll f-Containing Photosystem II Drives Photosynthesis into the Far-Red Region

The textbook explanation that P₆₈₀ pigments are the red limit to drive oxygenic photosynthesis must be reconsidered by the recent discovery that chlorophyll f (Chlf)-containing Photosystem II (PSII) absorbing at 727 nm can drive water oxidation. Two different families of unsymmetrically substituted Zn phthalocyanines (Pc) absorbing in the 700-800 nm spectral window and containing a fused imidazole-phenyl substituent or a fused imidazole-hydroxyphenyl group have been synthetized and characterized as a bioinspired model of the Chlf/Tyrosine_Z /Histidine₁₉₀ cofactors of PSII. Transient absorption studies in the presence of an electron acceptor and irradiating in the far-red region evidenced an intramolecular electron transfer process. Visible and FT-IR signatures indicate the formation of a hydrogen-bonded phenoxyl radical in ZnPc II-OH. This study sets the foundation for the utilization of a broader spectral window for multi-electronic catalytic processes with one of the most robust and efficient dyes.

The origin of unidirectional charge separation in photosynthetic reaction centers: nonadiabatic quantum dynamics of exciton and charge in pigment-protein complexes

Exciton charge separation in photosynthetic reaction centers from purple bacteria (PbRC) and photosystem II (PSII) occurs exclusively along one of the two pseudo-symmetric branches (active branch) of pigment-protein complexes. The microscopic origin of unidirectional charge separation in photosynthesis remains controversial. Here we elucidate the essential factors leading to unidirectional charge separation in PbRC and PSII, using nonadiabatic quantum dynamics calculations in conjunction with time-dependent density functional theory (TDDFT) with the quantum mechanics/molecular mechanics/polarizable continuum model (QM/MM/PCM) method. This approach accounts for energetics, electronic coupling, and vibronic coupling of the pigment excited states under electrostatic interactions and polarization of whole protein environments. The calculated time constants of charge separation along the active branches of PbRC and PSII are similar to those observed in time-resolved spectroscopic experiments. In PbRC, Tyr-M210 near the accessary bacteriochlorophyll reduces the energy of the intermediate state and drastically accelerates charge separation overcoming the electron-hole interaction. Remarkably, even though both the active and inactive branches in PSII can accept excitons from light-harvesting complexes, charge separation in the inactive branch is prevented by a weak electronic coupling due to symmetry-breaking of the chlorophyll configurations. The exciton in the inactive branch in PSII can be transferred to the active branch via direct and indirect pathways. Subsequently, the ultrafast electron transfer to pheophytin in the active branch prevents exciton back transfer to the inactive branch, thereby achieving unidirectional charge separation.

Two-dimensional HYSCORE spectroscopy reveals a histidine imidazole as the axial ligand to Chl3A in the M688HPsaA genetic variant of Photosystem I

Recent studies on Photosystem I (PS I) have shown that the six core chlorophyll a molecules are highly coupled, allowing for efficient creation and stabilization of the charge-separated state. One area of particular interest is the identity and function of the primary acceptor, A₀, as the factors that influence its ultrafast processes and redox properties are not yet fully elucidated. It was recently shown that A₀ exists as a dimer of the closely-spaced Chl₂/Chl₃ molecules wherein the reduced A₀^- state has an asymmetric distribution of electron spin density that favors Chl₃. Previous experimental work in which this ligand was changed to a hard base (histidine, M688H_PsaA) revealed severely impacted electron transfer processes at both the A₀ and A₁ acceptors; molecular dynamics simulations further suggested two distinct conformations of PS I in which the His residue coordinates and forms a hydrogen bond to the A₀ and A₁ cofactors, respectively. In this study, we have applied 2D HYSCORE spectroscopy in conjunction with molecular dynamics simulations and density functional theory calculations to the study of the M688H_PsaA variant. Analysis of the hyperfine parameters demonstrates that the His imidazole serves as the axial ligand to the central Mg²⁺ ion in Chl_3A in the M688H_PsaA variant. Although the change in ligand identity does not alter delocalization of electron density over the Chl₂/Chl₃ dimer, a small shift in the asymmetry of delocalization, coupled with the electron withdrawing properties of the ligand, most likely accounts for the inhibition of forward electron transfer in the His-ligated conformation.

How Can We Predict Accurate Electrochromic Shifts for Biochromophores? A Case Study on the Photosynthetic Reaction Center

Protein-embedded chromophores are responsible for light harvesting, excitation energy transfer, and charge separation in photosynthesis. A critical part of the photosynthetic apparatus are reaction centers (RCs), which comprise groups of (bacterio)chlorophyll and (bacterio)pheophytin molecules that transform the excitation energy derived from light absorption into charge separation. The lowest excitation energies of individual pigments (site energies) are key for understanding photosynthetic systems, and form a prime target for quantum chemistry. A major theoretical challenge is to accurately describe the electrochromic (Stark) shifts in site energies produced by the inhomogeneous electric field of the protein matrix. Here, we present large-scale quantum mechanics/molecular mechanics calculations of electrochromic shifts for the RC chromophores of photosystem II (PSII) using various quantum chemical methods evaluated against the 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). We show that certain range-separated density functionals (ωΒ97, ωΒ97X-V, ωΒ2PLYP, and LC-BLYP) correctly reproduce RC site energy shifts with time-dependent density functional theory (TD-DFT). The popular CAM-B3LYP functional underestimates the shifts and is not recommended. Global hybrid functionals are too insensitive to the environment and should be avoided, while nonhybrid functionals are strictly nonapplicable. Among the applicable approximate coupled cluster methods, the canonical versions of CC2 and ADC(2) were found to deviate significantly from the reference results both for the description of the lowest excited state and for the electrochromic shifts. By contrast, their spin-component-scaled (SCS) and particularly the scale-opposite-spin (SOS) variants compare well with the reference DLPNO-STEOM-CCSD and the best range-separated DFT methods. The emergence of RC excitation asymmetry is discussed in terms of intrinsic and protein electrostatic potentials. In addition, we evaluate a minimal structural scaffold of PSII, the D1-D2-CytB559 RC complex often employed in experimental studies, and show that it would have the same site energy distribution of RC chromophores as the full PSII supercomplex, but only under the unlikely conditions that the core protein organization and cofactor arrangement remain identical to those of the intact enzyme.

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.

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.