Modelling the bacterial photosynthetic reaction center. VI. Use of density-functional theory to determine the nature of the vibronic coupling between the four lowest-energy electronic states of the special-pair radical cation

Electron-Vibration Entanglement of Resonating Dimers in Quantum Transport

Electron transport in a single molecule resulting from the superposition of its vibronic states depends on the coupling strength with the metallic leads. However, dynamical coherence and Fermionic correlation in molecule-molecule and molecule-lead coupling necessitates a critical approach to treat the current and its noise level, especially in the presence of a variable external bias for temperature-dependent conduction. Primarily, this work is a generalization of the theoretical approach of the atomic dimers to incorporate the effect of vibrational modes in current and conductance characteristics. The variation of current and differential conductance due to the external bias reveals a vibrational Coulomb blockade structure corresponding to the functioning vibrational mode in the system. The numerical demonstration for a diverse class of molecules generically shows that electron-vibration interaction can quantitatively predict the nature of coherent electron transport and current noise. Secondly, an attempt has been made to illustrate the effect of magnitude of coherence-induced noise suppression of current as a signature of electron-vibration entanglement. Finally, temperature-dependent conductance of the molecular junction in dimer structure has been estimated along with the peak shifts due to the applied gate voltage.

A unified diabatic description for electron transfer reactions, isomerization reactions, proton transfer reactions, and aromaticity

A way is found for describing general chemical reactions using diabatic multi-state and “twin-state” models. (Image adapted with permission from https://www.flickr.com/photos/cybaea/64638988/).

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.

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.

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.

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.