Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event

Exploring the Light-Emitting Agents in Renilla Luciferases by an Effective QM/MM Approach

Bioluminescence is a fascinating natural phenomenon, wherein organisms produce light through specific biochemical reactions. Among these organisms, Renilla luciferase (RLuc) derived from the sea pansy Renilla reniformis is notable for its blue light emission and has potential applications in bioluminescent tagging. Our study focuses on RLuc8, a variant of RLuc with eight amino acid substitutions. Recent studies have shown that the luminescent emitter coelenteramide can adopt multiple protonation states, which may be influenced by nearby residues at the enzyme's active site, demonstrating a complex interplay between protein structure and bioluminescence. Herein, using the quantum mechanical consistent force field method and the semimacroscopic protein dipole-Langevin dipole method with linear response approximation, we show that the phenolate state of coelenteramide in RLuc8 is the primary light-emitting species in agreement with experimental results. Our calculations also suggest that the proton transfer (PT) from neutral coelenteramide to Asp162 plays a crucial role in the bioluminescence process. Additionally, we reproduced the observed emission maximum for the amide anion in RLuc8-D120A and the pyrazine anion in the presence of a Na+ counterion in RLuc8-D162A, suggesting that these are the primary emitters. Furthermore, our calculations on the neutral emitter in the engineered AncFT-D160A enzyme, structurally akin to RLuc8-D162A but with a considerably blue-shifted emission peak, aligned with the observed data, possibly explaining the variance in emission peaks. Overall, this study demonstrates an effective approach to investigate chromophores' bimolecular states while incorporating the PT process in emission spectra calculations, contributing valuable insights for future studies of PT in photoproteins.

Unique Vibrational Characteristics and Structures of the Photoexcited Retinal Chromophore in Ion-Pumping Rhodopsins

Photoisomerization of an all-trans-retinal chromophore triggers ion transport in microbial ion-pumping rhodopsins. Understanding chromophore structures in the electronically excited (S1) state provides insights into the structural evolution on the potential energy surface of the photoexcited state. In this study, we examined the structure of the S1-state chromophore in Natronomonas pharaonis halorhodopsin (NpHR), a chloride ion-pumping rhodopsin, using time-resolved resonance Raman spectroscopy. The spectral patterns of the S1-state chromophore were completely different from those of the ground-state chromophore, resulting from unique vibrational characteristics and the structure of the S1 state. Mode assignments were based on a combination of deuteration shifts of the Raman bands and hybrid quantum mechanics-molecular mechanics calculations. The present observations suggest a weakened bond alternation in the π conjugation system. A strong hydrogen-out-of-plane bending band was observed in the Raman spectra of the S1-state chromophore in NpHR, indicating a twisted polyene structure. Similar frequency shifts for the C═N/C═C and C-C stretching modes of the S1-state chromophore in NpHR were observed in the Raman spectra of sodium ion-pumping and proton-pumping rhodopsins, suggesting that these unique features are common to the S1 states of ion-pumping rhodopsins.

Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.

Quantum-classical simulations of rhodopsin reveal excited-state population splitting and its effects on quantum efficiency

The activation of rhodopsin, the light-sensitive G-protein coupled receptor responsible for dim-light vision in vertebrates, is driven by an ultrafast excited-state double-bond isomerization with a quantum efficiency of almost 70%. The origin of such light sensitivity is not understood and a key question is whether in-phase nuclear motion controls the quantum efficiency value. Here, we use hundreds of quantum-classical trajectories to show that, 15 femtoseconds after light absorption, a degeneracy between the reactive excited state and a neighboring state causes the splitting of the rhodopsin population into subpopulations. These subpopulations propagate with different velocities and lead to distinct contributions to the quantum efficiency. We also show that such splitting is modulated by protein electrostatics, thus linking amino-acid sequence variations to quantum efficiency modulation. Finally, we discuss how such a linkage that in principle could be exploited to achieve higher quantum efficiencies, would simultaneously increase the receptor thermal noise leading to a trade-off that may have played a role in rhodopsin evolution.

Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives

We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.

Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. Here we briefly outline the challenges associated with such computations and review the progress made in this field.

Acid-base equilibrium of the chromophore counterion results in distinct photoisomerization reactivity in the primary event of proteorhodopsin

Proteorhodopsin (PR) is a proton-pumping rhodopsin, and it is known to exhibit a multi-phasic decay of the excited-state population in the primary process. So far, this complex excited-state decay has been attributed to the branching of the relaxation pathway on the excited-state potential energy surface. However, a recent ultrafast spectroscopic study on a sodium-pumping rhodopsin suggested that such a complex decay may originate from the heterogeneity in the ground state due to the acid-base equilibrium of the counterion of the protonated retinal Schiff base (PRSB). In this study, we studied the excited-state dynamics of PR at pH 11 and 4, in which the counterion of the PRSB, Asp97, is completely deprotonated and protonated, respectively. The obtained time-resolved absorption data revealed that the excited-state lifetime is decisively governed by the protonation state of Asp97, and the photoisomerization of the PRSB chromophore proceeds faster and more efficiently when Asp97 is deprotonated. This conclusion was further supported by high similarity of the excited-state dynamics between PR at pH 4 and the D97N mutant in which Asp97 is replaced with neutral Asn. The results of this study suggest that the protonation state of the PRSB counterion plays a decisive role in determining the excited-state dynamics and the photoisomerization reactivity of rhodopsins in general, by making a significant influence on the exited-state potential energy surface of the PRSB chromophore.

Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins

Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.

Conical Intersections at the Nanoscale: Molecular Ideas for Materials

The ability to predict and describe nonradiative processes in molecules via the identification and characterization of conical intersections is one of the greatest recent successes of theoretical chemistry. Only recently, however, has this concept been extended to materials science, where nonradiative recombination limits the efficiencies of materials for various optoelectronic applications. In this review, we present recent advances in the theoretical study of conical intersections in semiconductor nanomaterials. After briefly introducing conical intersections, we argue that specific defects in materials can induce conical intersections between the ground and first excited electronic states, thus introducing pathways for nonradiative recombination. We present recent developments in theoretical methods, computational tools, and chemical intuition for the prediction of such defect-induced conical intersections. Through examples in various nanomaterials, we illustrate the significance of conical intersections for nanoscience. We also discuss challenges facing research in this area and opportunities for progress.

Charge Transfer Driven Structural Relaxation in a Push-Pull Azobenzene Dye-Semiconductor Complex

Photoexcited structural dynamics in azo-compounds may differ fundamentally whether the push-pull photochromic azo-compound is isolated or forms a heterogeneous charge transfer complex, due to a sudden oxidation of the chromophore. Herein, we use a quantum-classical self-consistent approach that incorporates nonadiabatic excited-state electronic quantum dynamics into molecular mechanics to study the photoexcited dynamics of the push-pull azo-compound para-Methyl Red in the gas phase and sensitizing the (101) anatase surface of TiO₂. We find that the photoinduced S₂/S₀ trans-to- cis isomerization of para-Methyl Red in the gas phase occurs through a pedal-like torsion around the ϕ_CNNC dihedral angle, without evidence to support the inversion mechanism, likewise in the parent azobenzene molecule. However, the photoexcited structural relaxation of the charge transfer complex para-Methyl Red/TiO₂ contrasts essentially with the isolated azo-compounds. Immediately after photoexcitation, the excited electron flows into the TiO₂ conduction band, with an injection time constant of ≃5 fs, and no indication of isomerization is observed during the 1.5 ps simulations. Instead, a strong vibronic relaxation occurs that excites the NN stretching mode of the azo-group, which is ultimately ascribed to the NA relaxation, and delocalization, of the hole wavepacket.

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.

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

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

Active site structure and absorption spectrum of channelrhodopsin-2 wild-type and C128T mutant

We show by extensive ground state and absorption spectra simulations that the channelrhodopsin-2 active site samples three different hydrogen-bonding patterns.

In spite of considerable interest, the active site of channelrhodopsin still lacks a detailed atomistic description, the understanding of which could strongly enhance the development of novel optogenetics tools. We present a computational study combining different state-of-the-art techniques, including hybrid quantum mechanics/molecular mechanics schemes and high-level quantum chemical methods, to properly describe the hydrogen-bonding pattern between the retinal chromophore and its counterions in channelrhodopsin-2 Wild-Type and C128T mutant. Especially, we show by extensive ground state dynamics that the active site, containing a glutamic acid (E123) and a water molecule, is highly dynamic, sampling three different hydrogen-bonding patterns. This results in a broad absorption spectrum that is representative of the different structural motifs found. A comparison with bacteriorhodopsin, characterized by a pentagonal hydrogen-bonded active site structure, elucidates their different absorption properties.

Theoretical Studies on the Color-Tuning Mechanism in Retinal Proteins

The excited states of the three retinal proteins, bovine rhodopsin (Rh), bacteriorhodopsin (bR), and sensory rhodopsin II (sRII) were studied using the symmetry-adapted cluster-configuration interaction (SAC-CI) and combined quantum mechanical and molecular mechanical (QM/MM) methods. The computed absorption energies are in good agreement with the experimental ones for all three proteins. The spectral tuning mechanism was analyzed in terms of three contributions:  molecular structures of the chromophore in the binding pockets, electrostatic (ES) interaction of the chromophore with the surrounding protein environment, and quantum-mechanical effect between the chromophore and the counterion group. This analysis provided an insight into the mechanism of the large blue-shifts in the absorption peak position of Rh and sRII from that of bR. Protein ES effect is primarily important both in Rh and in sRII, and the structure effect is secondary important in Rh. The quantum-mechanical interaction between the chromophore and the counterion is very important for quantitative reproduction of the excitation energy. These results indicate that the present approach is useful for studying the absorption spectra and the mechanism of the color tuning in the retinal proteins.

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities

We have developed automatic methods to calculate multipoles and anisotropic polarizabilities for all atoms and bond centers in a protein and to include such a model in the calculation of electronic properties at any level of quantum mechanical theory. This approach is applied for the calculation of the electronic spectra of retinal in rhodopsin at the CASPT2//CASSCF level (second-order multiconfigurational perturbation theory) for the wild-type protein, as well as two mutants and isorhodopsin in QM/MM structures based on two crystal structures. We also perform a detailed investigation of the importance and distance dependence of the multipoles and the polarizabilities for both the absolute and the relative absorption energies. It is shown that the model of the surrounding protein strongly influences the spectrum and that different models give widely different results. For example, the Amber 1994 and 2003 force fields give excitation energies that differ by up to 16 kJ/mol. For accurate excitation energies, multipoles up to quadrupoles and anisotropic polarizabilities are needed. However, interactions with residues more than 10 Å from the chromophore can be treated with a standard polarizable force field without any dipoles or quadrupoles.

Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy

We review the most recent experimental and computational efforts aimed at exposing the very early phases of the ultrafast isomerization in visual Rhodopsins and we discuss future advanced experiments and calculations.

Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins

Comparative modeling and ab initio multiconfigurational quantum chemistry are combined to investigate the reactivity of the human nonvisual photoreceptor melanopsin. It is found that both the thermal and photochemical isomerization of the melanopsin 11-cis retinal chromophore occur via a space-saving mechanism involving the unidirectional, counterclockwise twisting of the =C11H-C12H= moiety with respect to its Lys340-linked frame as proposed by Warshel for visual pigments [Warshel A (1976) Nature 260(5553):679-683]. A comparison with the mechanisms documented for vertebrate (bovine) and invertebrate (squid) visual photoreceptors shows that such a mechanism is not affected by the diversity of the three chromophore cavities. Despite such invariance, trajectory computations indicate that although all receptors display less than 100 fs excited state dynamics, human melanopsin decays from the excited state ∼40 fs earlier than bovine rhodopsin. Some diversity is also found in the energy barriers controlling thermal isomerization. Human melanopsin features the highest computed barrier which appears to be ∼2.5 kcal mol(-1) higher than that of bovine rhodopsin. When assuming the validity of both the reaction speed/quantum yield correlation discussed by Warshel, Mathies and coworkers [Weiss RM, Warshel A (1979) J Am Chem Soc 101:6131-6133; Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1991) Science 254(5030):412-415] and of a relationship between thermal isomerization rate and thermal activation of the photocycle, melanopsin turns out to be a highly sensitive pigment consistent with the low number of melanopsin-containing cells found in the retina and with the extraretina location of melanopsin in nonmammalian vertebrates.

Ultrafast photochemistry of anabaena sensory rhodopsin: experiment and theory

Light induced isomerization of the retinal chromophore activates biological function in all retinal protein (RP) driving processes such as ion-pumping, vertebrate vision and phototaxis in organisms as primitive as archea, or as complex as mammals. This process and its consecutive reactions have been the focus of experimental and theoretical research for decades. The aim of this review is to demonstrate how the experimental and theoretical research efforts can now be combined to reach a more comprehensive understanding of the excited state process on the molecular level. Using the Anabaena Sensory Rhodopsin as an example we will show how contemporary time-resolved spectroscopy and recently implemented excited state QM/MM methods consistently describe photochemistry in retinal proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

QuanPol: a full spectrum and seamless QM/MM program

The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. The QM methods include Hartree-Fock method, density functional theory method (DFT), generalized valence bond theory method, multiconfiguration self-consistent field method, Møller-Plesset perturbation theory method, and time-dependent DFT method. The induced dipoles of the MM atoms and the induced surface charges of the continuum solvation model are self-consistently and variationally determined together with the QM wavefunction. The MM force field methods can be user specified, or a standard force field such as MMFF94, Chemistry at Harvard Molecular Mechanics (CHARMM), Assisted Model Building with Energy Refinement (AMBER), and Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). Analytic gradients for all of these methods are implemented so geometry optimization and molecular dynamics (MD) simulation can be performed. MD free energy perturbation and umbrella sampling methods are also implemented.

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, while generally agreeing in predicting the correct location of the absorption maximum, they often reached contradicting conclusions on how the environment tunes the spectrum. To address this controversial issue, we combine here a thorough structural and dynamical characterization of rhodopsin with a careful validation of its excited-state properties via the use of a wide range of state-of-the-art quantum chemical approaches including various flavors of time-dependent density functional theory (TDDFT), different multireference perturbative schemes (CASPT2 and NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, we obtain a comprehensive structural description of the chromophore-protein system and sample a wide range of thermally accessible configurations. We show that, in order to obtain reliable excitation properties, it is crucial to employ a sufficient number of representative configurations of the system. In fact, the common use of a single, ad hoc structure can easily lead to an incorrect model and an agreement with experimental absorption spectra due to cancelation of errors. Finally, we show that, to properly account for polarization effects on the chromophore and to quench the large blue-shift induced by the counterion on the excitation energies, it is necessary to adopt an enhanced description of the protein environment as given by a large quantum region including as many as 250 atoms.

Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment

The nonadiabatic photodynamics of the all-trans-2,4-pentadiene-iminium cation (protonated Schiff base 3, PSB3) and the all-trans-3-methyl-2,4-pentadiene-iminium cation (MePSB3) were investigated in the gas phase and in polar (aqueous) and nonpolar (n-hexane) solutions by means of surface hopping using a multireference configuration-interaction (MRCI) quantum mechanical/molecular mechanics (QM/MM) level. Spectra, lifetimes for radiationless deactivation to the ground state, and structural and electronic parameters are compared. A strong influence of the polar solvent on the location of the crossing seam, in particular in the bond length alternation (BLA) coordinate, is found. Additionally, inclusion of the polar solvent changes the orientation of the intersection cone from sloped in the gas phase to peaked, thus enhancing considerably its efficiency for deactivation of the molecular system to the ground state. These factors cause, especially for MePSB3, a substantial decrease in the lifetime of the excited state despite the steric inhibition by the solvent.

Electrostatically guided dynamics--the root of fidelity in a promiscuous terpene synthase?

Terpene cyclases are responsible for the initial cyclization cascade in the multistep synthesis of more than 60,000 known natural products. This abundance of compounds is generated using a very limited pool of substrates based on linear isoprenoids. The astounding chemodiversity obtained by terpene cyclases suggests a tremendous catalytic challenge to these often promiscuous enzymes. In the current study we present a detailed mechanistic view of the biosynthesis of the monoterpene bornyl diphosphate (BPP) from geranyl diphosphate by BPP synthase using state of the art simulation methods. We identify the bornyl cation as an enzyme-induced bifurcation point on the multidimensional free energy surface, connecting between the product BPP and the side product camphene. Chemical dynamics simulations suggest that the active site diphosphate moiety steers reaction trajectories toward product formation. Nonetheless, chemical dynamics is not precise enough for exclusive product formation, providing a rationale for the lack of fidelity in this promiscuous terpene cyclase.

The effect of protein environment on photoexcitation properties of retinal

Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.

Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems

Recent years have witnessed an explosion in computational power, leading to attempts to model ever more complex systems. Nevertheless, there remain cases for which the use of brute-force computer simulations is clearly not the solution. In such cases, great benefit can be obtained from the use of physically sound simplifications. The introduction of such coarse graining can be traced back to the early usage of a simplified model in studies of proteins. Since then, the field has progressed tremendously. In this review, we cover both key developments in the field and potential future directions. Additionally, particular emphasis is given to two general approaches, namely the renormalization and reference potential approaches, which allow one to move back and forth between the coarse-grained (CG) and full models, as these approaches provide the foundation for CG modeling of complex systems.

Vibrational motions associated with primary processes in bacteriorhodopsin studied by coherent infrared emission spectroscopy

The primary energetic processes driving the functional proton pump of bacteriorhodopsin take place in the form of complex molecular dynamic events after excitation of the retinal chromophore into the Franck-Condon state. These early events include a strong electronic polarization, skeletal stretching, and all-trans-to-13-cis isomerization upon formation of the J intermediate. The effectiveness of the photoreaction is ensured by a conical intersection between the electronic excited and ground states, providing highly nonadiabatic coupling to nuclear motions. Here, we study real-time vibrational coherences associated with these motions by analyzing light-induced infrared emission from oriented purple membranes in the 750-1400 cm(-)(1) region. The experimental technique applied is based on second-order femtosecond difference frequency generation on macroscopically ordered samples that also yield information on phase and direction of the underlying motions. Concerted use of several analysis methods resulted in the isolation and characterization of seven different vibrational modes, assigned as C-C stretches, out-of-plane methyl rocks, and hydrogen out-of-plane wags, whereas no in-plane H rock was found. Based on their lifetimes and several other criteria, we deduce that the majority of the observed modes take place on the potential energy surface of the excited electronic state. In particular, the direction sensitivity provides experimental evidence for large intermediate distortions of the retinal plane during the excited-state isomerization process.

Multiscale modeling of biological functions

Recent years have witnessed a tremendous explosion in computational power, which in turn has resulted in great progress in the complexity of the biological and chemical problems that can be addressed by means of all-atom simulations. Despite this, however, our computational time is not infinite, and in fact many of the key problems of the field were resolved long before the existence of the current levels of computational power. This review will start by presenting a brief historical overview of the use of multiscale simulations in biology, and then present some key developments in the field, highlighting several cases where the use of a physically sound simplification is clearly superior to a brute-force approach. Finally, some potential future directions will be discussed.

First-principles calculation of electronic spectra of light-harvesting complex II

We report on a fully quantum chemical investigation of important structural and environmental effects on the site energies of chlorophyll pigments in green-plant light-harvesting complex II (LHC II). Among the tested factors are technical and structural aspects as well as effects of neighboring residues and exciton couplings in the chlorophyll network. By employing a subsystem time-dependent density functional theory (TDDFT) approach based on the frozen density embedding (FDE) method we are able to determine site energies and electronic couplings separately in a systematic way. This approach allows us to treat much larger systems in a quantum chemical way than would be feasible with a conventional density functional theory. Based on this method, we have simulated a series of mutagenesis experiments to investigate the effect of a lack of one pigment in the chlorophyll network on the excitation properties of the other pigments. From these calculations, we can conclude that conformational changes within the chlorophyll molecules, direct interactions with neighboring residues, and interactions with other chlorophyll pigments can lead to non-negligible changes in excitation energies. All of these factors are important when site energies shall be calculated with high accuracy. Moreover, the redistribution of the oscillator strengths due to exciton coupling has a large impact on the calculated absorption spectra. This indicates that modeling mutagenesis experiments requires us to consider the entire set of chlorophyll molecules in the wild type and in the mutant, rather than just considering the missing chlorophyll pigment. An analysis of the mixing of particular excitations and the coupling elements in the FDEc calculation indicates that some pigments in the chlorophyll network act as bridges which mediate the interaction between other pigments. These bridges are also supported by the calculations on the "mutants" lacking the bridging pigment.