Modeling the bacterial photosynthetic reaction center. VII. Full simulation of the intervalence hole–transfer absorption spectrum of the special-pair radical cation

Coherent Two-Dimensional and Broadband Electronic Spectroscopies

Over the past few decades, coherent broadband spectroscopy has been widely used to improve our understanding of ultrafast processes (e.g., photoinduced electron transfer, proton transfer, and proton-coupled electron transfer reactions) at femtosecond resolution. The advances in femtosecond laser technology along with the development of nonlinear multidimensional spectroscopy enabled further insights into ultrafast energy transfer and carrier relaxation processes in complex biological and material systems. New discoveries and interpretations have led to improved design principles for optimizing the photophysical properties of various artificial systems. In this review, we first provide a detailed theoretical framework of both coherent broadband and two-dimensional electronic spectroscopy (2DES). We then discuss a selection of experimental approaches and considerations of 2DES along with best practices for data processing and analysis. Finally, we review several examples where coherent broadband and 2DES were employed to reveal mechanisms of photoinitiated ultrafast processes in molecular, biological, and material systems. We end the review with a brief perspective on the future of the experimental techniques themselves and their potential to answer an even greater range of scientific questions.

Mutation H(M202)L does not lead to the formation of a heterodimer of the primary electron donor in reaction centers of Rhodobacter sphaeroides when combined with mutation I(M206)H

In photosynthetic reaction centers (RCs) of purple bacteria, conserved histidine residues [His L173 and His M202 in Rhodobacter (Rba.) sphaeroides] are known to serve as fifth axial ligands to the central Mg atom of the bacteriochlorophyll (BChl) molecules (P_A and P_B, respectively) that constitute the homodimer (BChl/BChl) primary electron donor P. In a number of previous studies, it has been found that replacing these residues with leucine, which cannot serve as a ligand to the Mg ion of BChl, leads to the assembly of heterodimer RCs with P represented by the BChl/BPheo pair. Here, we show that a homodimer P is assembled in Rba. sphaeroides RCs if the mutation H(M202)L is combined with the mutation of isoleucine to histidine at position M206 located in the immediate vicinity of P_B. The resulting mutant H(M202)L/I(M206)H RCs are characterized using pigment analysis, redox titration, and a number of spectroscopic methods. It is shown that, compared to wild-type RCs, the double mutation causes significant changes in the absorption spectrum of the P homodimer and the electronic structure of the radical cation P⁺, but has only minor effect on the pigment composition, the P/P⁺ midpoint potential, and the initial electron-transfer reaction. The results are discussed in terms of the nature of the axial ligand to the Mg of P_B in mutant H(M202)L/I(M206)H RCs and the possibility of His M202 participation in the previously proposed through-bond route for electron transfer from the excited state P* to the monomeric BChl B_A in wild-type RCs.

Spectral and Photochemical Properties of Rhodobacter sphaeroides R-26 Reaction Center Films in Vacuum

Using absorption spectroscopy in the visible/near-IR and mid-IR regions, spectral and photochemical properties of isolated reaction centers (RCs) from Rhodobacter sphaeroides R-26 were studied in dried films on the inorganic support surface (quartz or CaF₂ plates) under vacuum dehydration conditions (10^-2 or 7·10^-5 mm Hg). Three detergents, N,N-dimethyldodecylamine N-oxide (LDAO), Triton X-100 (TX100), and n-dodecyl-β-D-maltoside (DM), were tested for their ability to stabilize the RC-detergent complexes in the vacuum-dried state. It was shown that in the presence of LDAO, RC complexes underwent destruction in vacuum. In contrast, DM provided an environment that minimized irreversible disruptive changes in the RCs in vacuum. The effects of vacuum dehydration on the RC-DM films included a small increase in the content of α-helices in the RC protein, a short-wavelength reversible shift in the optical transitions of pigments, and minor changes in the electronic structure of the P⁺ dimer. The films retained their photochemical activity upon excitation with high-intensity light (200 mW/cm²). TX100 also helped to maintain spectral and functional properties of the RCs in vacuum; however, in this case, the stabilizing effect was less pronounced than in the presence of DM, especially, at high detergent concentrations. The results are discussed within the framework of a model suggesting that the detergent-protein interactions and the properties of detergent micelles play a dominant role in maintaining the structure of the RCs upon vacuum dehydration of the RC complexes. The obtained data can be useful for developing hybrid photoconverting systems based on bacterial RCs.

Effect of Leucine M196 Substitution by Histidine on Electronic Structure of the Primary Electron Donor and Electron Transfer in Reaction Centers from Rhodobacter sphaeroides

In our recent X-ray study, we demonstrated that substitution of the natural leucine residue M196 with histidine in the reaction center (RC) from Rhodobacter (Rba.) sphaeroides leads to formation of a close contact between the genetically introduced histidine and the primary electron donor P (bacteriochlorophylls (BChls) P_A and P_B dimer) creating a novel pigment-protein interaction that is not observed in native RCs. In the present work, the possible nature of this novel interaction and its effects on the electronic properties of P and the photochemical charge separation in isolated mutant RCs L(M196)H are investigated at room temperature using steady-state absorption spectroscopy, light-induced difference FTIR spectroscopy, and femtosecond transient absorption spectroscopy. The results are compared with the data obtained for the RCs from Rba. sphaeroides pseudo-wild type strain. It is shown that the L(M196)H mutation results in a decrease in intensity and broadening of the long-wavelength Q_y absorption band of P at ~865 nm. Due to the mutation, there is also weakening of the electronic coupling between BChls in the radical cation P⁺ and increase in the positive charge localization on the P_A molecule. Despite the significant perturbations of the electronic structure of P, the mutant RCs retain high electron transfer rates and quantum yield of the P⁺Q_A^- state (Q_A is the primary quinone acceptor), which is close to the one observed in the native RCs. Comparison of our results with the literature data suggests that the imidazole group of histidine M196 forms a π-hydrogen bond with the π-electron system of the P_B molecule in the P dimer. It is likely that the specific (T-shaped) spatial organization of the π-hydrogen interaction and its potential heterogeneity in relation to the bonding energy is, at least partially, the reason that this type of interaction between the protein and the pigment and quinone cofactors is not realized in the native RCs.

Electron-vibration entanglement in the Born-Oppenheimer description of chemical reactions and spectroscopy

Entanglement is sometimes regarded as the quintessential measure of the quantum nature of a system and its significance for the understanding of coupled electronic and vibrational motions in molecules has been conjectured. Previously, we considered the entanglement developed in a spatially localized diabatic basis representation of the electronic states, considering design rules for qubits in a low-temperature chemical quantum computer. We extend this to consider the entanglement developed during high-energy processes. We also consider the entanglement developed using adiabatic electronic basis, providing a novel way for interpreting effects of the breakdown of the Born-Oppenheimer (BO) approximation. We consider: (i) BO entanglement in the ground-state wavefunction relevant to equilibrium thermodynamics, (ii) BO entanglement associated with low-energy wavefunctions relevant to infrared and tunneling spectroscopies, (iii) BO entanglement in high-energy eigenfunctions relevant to chemical reaction processes, and (iv) BO entanglement developed during reactive wavepacket dynamics. A two-state single-mode diabatic model descriptive of a wide range of chemical phenomena is used for this purpose. The entanglement developed by BO breakdown correlates simply with the diameter of the cusp introduced by the BO approximation, and a hierarchy appears between the various BO-breakdown correction terms, with the first-derivative correction being more important than the second-derivative correction which is more important than the diagonal correction. This simplicity is in contrast to the complexity of BO-breakdown effects on thermodynamic, spectroscopic, and kinetic properties. Further, processes poorly treated at the BO level that appear adequately treated using the Born-Huang adiabatic approximation are found to have properties that can only be described using a non-adiabatic description. For the entanglement developed between diabatic electronic states and the nuclear motion, qualitatively differently behavior is found compared to traditional properties of the density matrix and hence entanglement provides new information about system properties. For chemical reactions, this type of entanglement simply builds up as the transition-state region is crossed. It is robust to small changes in parameter values and is therefore more attractive for making quantum qubits than is the related fragile ground-state entanglement, provided that coherent motion at the transition state can be sustained.

Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology

David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.

Non-adiabatic effects in thermochemistry, spectroscopy and kinetics: the general importance of all three Born–Oppenheimer breakdown corrections

Analytical and numerical solutions describing Born–Oppenheimer breakdown in a simple, widely applicable, model depict shortcomings in modern computational methods.

Dynamical theory of primary processes of charge separation in the photosynthetic reaction center

A dynamical theory has been developed for primary separation of charges in the course of photosynthesis. The theory deals with both hopping and superexchange transfer mechanisms. Dynamics of electron transfer from dimeric bacteriochlorophyll to quinone has been calculated. The results obtained agree with experimental data and provide a unified explanation of both the hierarchy of the transfer time in the photosynthetic reaction center and the phenomenon of coherent oscillations accompanying the transfer process.

EPR, ENDOR, and special TRIPLE measurements of P(*+) in wild type and modified reaction centers from Rb. sphaeroides

The influence of the protein environment on the primary electron donor, P, a bacteriochlorophyll a dimer, of reaction centers from Rhodobacter sphaeroides, has been investigated using electron paramagnetic resonance and electron nuclear double resonance spectroscopy. These techniques were used to probe the effects on P that are due to alteration of three amino acid residues, His L168, Asn L170, and Asn M199. The introduction of Glu at L168, Asp at L170, or Asp at M199 changes the oxidation/reduction midpoint potential of P in a pH-dependent manner (Williams et al. (2001) Biochemistry 40, 15403-15407). For the double mutant His L168 to Glu and Asn at L170 to Asp, excitation results in electron transfer along the A-side branch of cofactors at pH 7.2, but at pH 9.5, a long-lived state involving B-side cofactors is produced (Haffa et al. (2004) J Phys Chem B 108, 4-7). Using electron paramagnetic resonance spectroscopy, the mutants with alterations of each of the three individual residues and a double mutant, with changes at L168 and L170, were found to have increased linewidths of 10.1-11.0 G compared to the linewidth of 9.6 G for wild type. The Special TRIPLE spectra were pH dependent, and at pH 8, the introduction of aspartate at L170 increased the spin density ratio, rho (L)/rho (M), to 6.1 while an aspartate at the symmetry related position, M199, decreased the ratio to 0.7 compared to the value of 2.1 for wild type. These results indicate that the energy of the two halves of P changes by about 100 meV due to the mutations and are consistent with the interpretation that electrostatic interactions involving these amino acid residues contribute to the switch in pathway of electron transfer.

Towards a comprehensive model for the electronic and vibrational structure of the Creutz-Taube ion

Since the synthesis of the Creutz-Taube ion, the nature of its charge localization has been of immense scientific interest, this molecule providing a model system for the understanding of the operation of biological photosynthetic and electron-transfer processes. However, recent work has shown that its nature remains an open question. Many systems of this type, including photosynthetic reaction centres, are of current research interest, and thereby the Creutz-Taube ion provides an important chemical paradigm: the key point of interest is the details of how such molecules behave. We lay the groundwork for the construction of a comprehensive model for its chemical and spectroscopic properties. Advances are described in some of the required areas including: simulation of electronic absorption spectra; quantitative depiction of the large interaction of the ion's electronic description with solvent motions; and the physics of Ru-NH3 spectator-mode vibrations. We show that details of the solvent electron-phonon coupling are critical in the interpretation of the spectator-mode vibrations, as these strongly mix with solvent motions when 0.75<2J/lambda<1. In this regime, a double-well potential exists which does not support localized zero-point vibration, and many observed properties of the Creutz-Taube ion are shown to be consistent with the hypothesis that the ion has this character.

Stark spectroscopy of mixed-valence systems

Many mixed-valence systems involve two or more states with different electric dipole moments whose magnitudes depend upon the charge transfer distance and the degree of delocalization; these systems can be interconverted by excitation of an intervalence charge transfer transition. Stark spectroscopy involves the interaction between the change in dipole moment of a transition and an electric field, so the Stark spectra of mixed-valence systems are expected to provide quantitative information on the degree of delocalization. In limiting cases, a classical Stark analysis can be used, but in intermediate cases the analysis is much more complex because the field affects not only the band position but also the intrinsic bandshape. Such non-classical Stark effects lead to widely different bandshapes. Several examples of both classes are discussed. Because electric fields are applied to immobilized samples, complications arise from inhomogeneous broadening, along with other effects that limit our ability to extract unique parameters in some cases. In the case of the radical cation of the special pair in photosynthetic reaction centres, where the mixed-valence system is in a very complex but structurally well-defined environment, a detailed analysis can be performed.

Pressure-induced spectral changes for the special-pair radical cation of the bacterial photosynthetic reaction center

The effect of pressure up to 6 kbars on the near to mid infrared absorption spectrum (7500-14,300 cm(-1) or 1333-700 nm) of the oxidized reaction center of Rhodobacter sphaeroides is measured and interpreted using density-functional B3LYP, INDO, and PM5 calculations. Two weak electronic transition origins at approximately 8010 and approximately 10,210 cm(-1) are unambiguously identified. The first transition is assigned to a Qy tripdoublet band that involves, in the localized description of the excitation, a triplet absorption on one of the bacteriochlorophyll molecules (PM) in the reaction center's special pair intensified by the presence of a radical cation on the other (PL). While most chlorophyll transition energies decrease significantly with increasing pressure, the tripdoublet band is found to be almost pressure insensitive. This difference is attributed to the additional increase in the tripdoublet-band energy accompanying compression of the pi-stacked special pair. The second band could either be the anticipated second Qy tripdoublet state, a Qx tripdoublet state, or a state involving excitation from a low-lying doubly occupied orbital to the half-occupied cationic orbital. A variety of absorption bands that are also resolved in the 8300-9600 cm(-1) region are assigned as vibrational structure associated with the first tripdoublet absorption. These sidebands are composites that are shown by the calculations to comprise many unresolved individual modes; while the calculated pressure sensitivity of each individual mode is small, the calculated pressure dependence of the combined sideband structure is qualitatively similar to the observed pressure dependence, preventing the positive identification of possible additional electronic transitions in this spectral region.

Charge Delocalization in the Special-Pair Radical Cation of Mutant Reaction Centers of Rhodobacter sphaeroides from Stark Spectra and Nonadiabatic Spectral Simulations

Stark and absorption spectra for the hole-transfer band of the bacteriochlorophyll special pair in the wild-type and L131LH, M160LH, and L131LH/M160LH mutants of the bacterial reaction center of Rhodobacter sphaeroides are presented, along with extensive analyses based on nonadiabatic spectral simulations. Dramatic changes in the Stark spectra are induced by the mutations, changes that are readily interpreted in terms of the redox-energy asymmetry and degree of charge localization in the special-pair radical cation. The effect of mutagenesis on key properties such as the electronic coupling within the special pair and the reorganization energy associated with intervalence hole transfer are determined for the first time. Results for the L131LH and M160LH/L131LH mutants indicate that these species can be considered as influencing the special pair primarily through modulation of the redox asymmetry, as is usually conceptualized, but M160LH is shown to develop a wide range of effects that can be interpreted in terms of significant mutation-induced structural changes in and around the special pair. The nonadiabatic spectra simulations are performed using both a simple two-state 1-mode and an extensive four-state 70-mode model, which includes the descriptions of additional electronic states and explicitly treats the major vibrational modes involved. Excellent agreement between the two simulation approaches is obtained. The simple model is shown to reproduce key features of the Stark effect of the main intervalence transition, while the extensive model quantitatively reproduces most features of the observed spectra for both the electronic and the phase-phonon regions, thus giving a more comprehensive description of the effect of the mutations on the properties of the special-pair radical cation. These results for a series of closely related mixed-valence complexes show that the Stark spectra provide a sensitive indicator for the properties of the mixed-valence complexes and should serve as an instructive example on the application of nonadiabatic simulations to the study of mixed-valence complexes in general as well as other chemical systems akin to the photosynthetic special pair.

First Singlet (n,π*) Excited State of Hydrogen-Bonded Complexes between Water and Pyrimidine

Hydrogen bonds from water to excited-state formaldehyde and from water to excited-state pyridine have been shown to display novel motifs to traditional hydrogen bonds involving ground states, with, in particular for H2O:pyridine, strong interactions involving the electron-rich pi cloud dominating the (n,pi) excited state. We investigate H2O:pyrimidine and various dihydrated species and reveal another motif, one in which the hydrogen bonding can dramatically alter the electronic structure of the excited state. Such effects are rare for ground-state interactions for which hydrogen bonding usually acts to merely perturb the electronic structure of the participating molecules. It arises as the (n,pi*) excitation of isolated pyrimidine is delocalized over both nitrogens but asymmetric hydrogen bonding causes it to localize on just the noninteracting atom. As a result, the excited-state hydrogen bond in H2O:pyrimidine is suprisingly very similar to the ground-state structure. These results lead to an improved understanding of the spectroscopy of pyrimidine in liquid water, and to the prediction that stable excited-state hydrogen bonds in H2O:pyrimidine should be observable, despite failure of experiments to actually do so. They also provide a simple model for the intricate control over primary charge separation in photosynthesis exerted by hydrogen bonding, and for solvent-induced electron localization in symmetric mixed-valence complexes. All conclusions are based on strong parallels found between the results of calculations performed using density-functional theory (DFT) and time-dependent DFT (TDDFT), complete-active-space self-consistent-field (CASSCF) with second-order perturbation-theory correction (CASPT2) theory, and equation-of-motion coupled cluster (EOM-CCSD) theory, calculations that are verified through detailed comparison of computed properties with experimental data for both the isolated molecules and the ground-state hydrogen bond.

A Unified Description of the Electrochemical, Charge Distribution, and Spectroscopic Properties of the Special-Pair Radical Cation in Bacterial Photosynthesis

We apply our four-state 70-vibration vibronic-coupling model for the properties of the photosynthetic special-pair radical cation to: (1) interpret the observed correlations between the midpoint potential and the distribution of spin density between the two bacteriochlorophylls for 30 mutants of Rhodobacter sphaeroides, (2) interpret the observed average intervalence hole-transfer absorption energies as a function of spin density for six mutants, and (3) simulate the recently obtained intervalence electroabsorption Stark spectrum of the wild-type reaction center. While three new parameters describing the location of the sites of mutation with respect to the special pair are required to describe the midpoint-potential data, a priori predictions are made for the transition energies and the Stark spectrum. In general, excellent predictions are made of the observed quantities, with deviations being typically of the order of twice the experimental uncertainties. A unified description of many chemical and spectroscopic properties of the bacterial reaction center is thus provided. Central to the analysis is the assumption that the perturbations made to the reaction center, either via mutations of protein residues or by application of an external electric field, act only to independently modify the oxidation potentials of the two halves of the special pair and hence the redox asymmetry E0. While this appears to be a good approximation, clear evidence is presented that effects of mutation can be more extensive than what is allowed for. A thorough set of analytical equations describing the observed properties is obtained using the Born-Oppenheimer adiabatic approximation. These equations are generally appropriate for intervalence charge-transfer problems and include, for the first time, full treatment of both symmetric and antisymmetric vibrational motions. The limits of validity of the adiabatic approach to the full nonadiabatic problem are obtained.

Molecular Electronics: From Basic Chemical Principles to Photosynthesis to Steady-State Through-Molecule Conductivity to Computer Architectures

Molecular electronics offers many possibilities for the development of electronic devices beyond the limit of silicon technology. Its basic ideas and history are reviewed, and a central aspect of the delocalization of electrons across molecules and junctions is examined. Analogies between key processes affecting steady-state through-molecule conduction and equilibrium geometric and spectroscopic properties of paradigm molecules, such as hydrogen, ammonia, benzene, and the Creutz–Taube ion are drawn, and the mechanisms by which control can be exerted over molecular-electronic processes during biological photosynthesis are examined. Ab initio molecular dynamics and simulations of conductivity are then presented for carbon nanotube flanged to gold(111), and device characteristics are calculated for a molecular shift register clocked by two gold electrodes.