Linear response in theory of electron transfer reactions as an alternative to the molecular harmonic oscillator model

PyCTRAMER: A Python package for charge transfer rate constant of condensed-phase systems from Marcus theory to Fermi's golden rule

In this work, we introduce PyCTRAMER, a comprehensive Python package designed for calculating charge transfer (CT) rate constants in disordered condensed-phase systems at finite temperatures, such as organic photovoltaic (OPV) materials. PyCTRAMER is a restructured and enriched version of the CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory) package [Tinnin et al. J. Chem. Phys. 154, 214108 (2021)], enabling the computation of the Marcus CT rate constant and the six levels of the linearized semiclassical approximations of Fermi's golden rule (FGR) rate constant. It supports various types of intramolecular and intermolecular CT transitions from the excitonic states to CT state. Integrating quantum chemistry calculations, all-atom molecular dynamics (MD) simulations, spin-boson model construction, and rate constant calculations, PyCTRAMER offers an automatic workflow for handling photoinduced CT processes in explicit solvent environments and interfacial CT in amorphous donor/acceptor blends. The package also provides versatile tools for individual workflow steps, including electronic state analysis, state-specific force field construction, MD simulations, and spin-boson model construction from energy trajectories. We demonstrate the software's capabilities through two examples, highlighting both intramolecular and intermolecular CT processes in prototypical OPV systems.

First-Principles Modeling of the Absorption Spectrum of Crystal Violet in Solution: The Importance of Environmentally Driven Symmetry Breaking

Theoretical spectroscopy plays a crucial role in understanding the properties of the materials and molecules. One of the most promising methods for computing optical spectra of chromophores embedded in complex environments from the first principles is the cumulant approach, where both (generally anharmonic) vibrational degrees of freedom and environmental interactions are explicitly accounted for. In this work, we verify the capabilities of the cumulant approach in describing the effect of complex environmental interactions on linear absorption spectra by studying Crystal Violet (CV) in different solvents. The experimental absorption spectrum of CV strongly depends on the nature of the solvent, indicating strong coupling to the condensed-phase environment. We demonstrate that these changes in absorption line shape are driven by an increased splitting between absorption bands of two low-lying excited states that is caused by a breaking of the D3 symmetry of the molecule and that in polar solvents, this symmetry breaking is mainly driven by electrostatic interactions with the condensed-phase environment rather than distortion of the structure of the molecule, in contrast with conclusions reached in a number of previous studies. Our results reveal the importance of explicitly including a counterion in the calculations in nonpolar solvents due to electrostatic interactions between CV and the ion. In polar solvents, these interactions are strongly reduced due to solvent screening effects, thus minimizing the symmetry breaking. Computed spectra in methanol are found to be in reasonable agreement with the experiment, demonstrating the strengths of the outlined approach in modeling strong environmental interactions.

All-Atom Photoinduced Charge Transfer Dynamics in Condensed Phase via Multistate Nonlinear-Response Instantaneous Marcus Theory

Photoinduced charge transfer (CT) in the condensed phase is an essential component in solar energy conversion, but it is challenging to simulate such a process on the all-atom level. The traditional Marcus theory has been utilized for obtaining CT rate constants between pairs of electronic states but cannot account for the nonequilibrium effects due to the initial nuclear preparation. The recently proposed instantaneous Marcus theory (IMT) and its nonlinear-response formulation allow for incorporating the nonequilibrium nuclear relaxation to electronic transition between two states after the photoexcitation from the equilibrium ground state and provide the time-dependent rate coefficient. In this work, we extend the nonlinear-response IMT method for treating photoinduced CT among general multiple electronic states and demonstrate it in the organic photovoltaic carotenoid-porphyrin-fullerene triad dissolved in explicit tetrahydrofuran solvent. All-atom molecular dynamics simulations were employed to obtain the time correlation functions of energy gaps, which were used to generate the IMT-required time-dependent averages and variances of the relevant energy gaps. Our calculations show that the multistate IMT could capture the significant nonequilibrium effects due to the initial nuclear state preparation, and this is corroborated by the substantial differences between the population dynamics predicted by the multistate IMT and the Marcus theory, where the Marcus theory underestimates the population transfer. The population dynamics by multistate IMT is also shown to have a better agreement with the all-atom nonadiabatic mapping dynamics than the Marcus theory does. Because the multistate nonlinear-response IMT is straightforward and cost-effective in implementation and accounts for the nonequilibrium nuclear effects, we believe this method offers a practical strategy for studying charge transfer dynamics in complex condensed-phase systems.

Instantaneous Marcus theory for photoinduced charge transfer dynamics in multistate harmonic model systems

Modeling the dynamics of photoinduced charge transfer (CT) in condensed phases presents challenges due to complicated many-body interactions and the quantum nature of electronic transitions. While traditional Marcus theory is a robust method for calculating CT rate constants between electronic states, it cannot account for the nonequilibrium effects arising from the initial nuclear state preparation. In this study, we employ the instantaneous Marcus theory (IMT) to simulate photoinduced CT dynamics. IMT incorporates nonequilibrium structural relaxation following a vertical photoexcitation from the equilibrated ground state, yielding a time-dependent rate coefficient. The multistate harmonic (MSH) model Hamiltonian characterizes an organic photovoltaic carotenoid-porphyrin-fullerene triad dissolved in explicit tetrahydrofuran solvent, constructed by mapping all-atom inputs from molecular dynamics simulations. Our calculations reveal that the electronic population dynamics of the MSH models obtained with IMT agree with the more accurate quantum-mechanical nonequilibrium Fermi's golden rule. This alignment suggests that IMT provides a practical approach to understanding nonadiabatic CT dynamics in condensed-phase systems.

Beyond the Condon limit: Condensed phase optical spectra from atomistic simulations

While dark transitions made bright by molecular motions determine the optoelectronic properties of many materials, simulating such non-Condon effects in condensed phase spectroscopy remains a fundamental challenge. We derive a Gaussian theory to predict and analyze condensed phase optical spectra beyond the Condon limit. Our theory introduces novel quantities that encode how nuclear motions modulate the energy gap and transition dipole of electronic transitions in the form of spectral densities. By formulating the theory through a statistical framework of thermal averages and fluctuations, we circumvent the limitations of widely used microscopically harmonic theories, allowing us to tackle systems with generally anharmonic atomistic interactions and non-Condon fluctuations of arbitrary strength. We show how to calculate these spectral densities using first-principles simulations, capturing realistic molecular interactions and incorporating finite-temperature, disorder, and dynamical effects. Our theory accurately predicts the spectra of systems known to exhibit strong non-Condon effects (phenolate in various solvents) and reveals distinct mechanisms for electronic peak splitting: timescale separation of modes that tune non-Condon effects and spectral interference from correlated energy gap and transition dipole fluctuations. We further introduce analysis tools to identify how intramolecular vibrations, solute-solvent interactions, and environmental polarization effects impact dark transitions. Moreover, we prove an upper bound on the strength of cross correlated energy gap and transition dipole fluctuations, thereby elucidating a simple condition that a system must follow for our theory to accurately predict its spectrum.

Cation-induced changes in the inner- and outer-sphere mechanisms of electrocatalytic CO2 reduction

The underlying mechanism of cation effects on CO2RR remains debated. Herein, we study cation effects by simulating both outer-sphere electron transfer (OS-ET) and inner-sphere electron transfer (IS-ET) pathways during CO2RR via constrained density functional theory molecular dynamics (cDFT-MD) and slow-growth DFT-MD (SG-DFT-MD), respectively. Our results show without any cations, only OS-ET is feasible with a barrier of 1.21 eV. In the presence of K+ (Li+), OS-ET shows a very high barrier of 2.93 eV (4.15 eV) thus being prohibited. However, cations promote CO2 activation through IS-ET with the barrier of only 0.61 eV (K+) and 0.91 eV (Li+), generating the key intermediate (adsorbed CO[Formula: see text]). Without cations, CO2-to-CO[Formula: see text](ads) conversion cannot proceed. Our findings reveal cation effects arise from short-range Coulomb interactions with reaction intermediates. These results disclose that cations modulate the inner- and outer-sphere pathways of CO2RR, offering substantial insights on the cation specificity in the initial CO2RR steps.

Modified Fermi's golden rule rate expressions

Fermi's golden rule (FGR) serves as the basis for many expressions of spectroscopic observables and quantum transition rates. The utility of FGR has been demonstrated through decades of experimental confirmation. However, there still remain important cases where the evaluation of a FGR rate is ambiguous or ill-defined. Examples are cases where the rate has divergent terms due to the sparsity in the density of final states or time dependent fluctuations of system Hamiltonians. Strictly speaking, assumptions of FGR are no longer valid for such cases. However, it is still possible to define modified FGR rate expressions that are useful as effective rates. The resulting modified FGR rate expressions resolve a long standing ambiguity often encountered in using FGR and offer more reliable ways to model general rate processes. Simple model calculations illustrate the utility and implications of new rate expressions.

Quantum dynamical effects of vibrational strong coupling in chemical reactivity

Recent experiments suggest that ground state chemical reactivity can be modified when placing molecular systems inside infrared cavities where molecular vibrations are strongly coupled to electromagnetic radiation. This phenomenon lacks a firm theoretical explanation. Here, we employ an exact quantum dynamics approach to investigate a model of cavity-modified chemical reactions in the condensed phase. The model contains the coupling of the reaction coordinate to a generic solvent, cavity coupling to either the reaction coordinate or a non-reactive mode, and the coupling of the cavity to lossy modes. Thus, many of the most important features needed for realistic modeling of the cavity modification of chemical reactions are included. We find that when a molecule is coupled to an optical cavity it is essential to treat the problem quantum mechanically to obtain a quantitative account of alterations to reactivity. We find sizable and sharp changes in the rate constant that are associated with quantum mechanical state splittings and resonances. The features that emerge from our simulations are closer to those observed in experiments than are previous calculations, even for realistically small values of coupling and cavity loss. This work highlights the importance of a fully quantum treatment of vibrational polariton chemistry.

A Gaussian field approach to the planar electric double layer structures in electrolyte solutions

In this work, the planar, electric, double-layer structures of non-polarizable electrodes in electrolyte solutions are studied with Gaussian field theory. A response function with two Yukawa functions is used to capture the electrostatic response of the electrolyte solution, from which the modified response function in the planar symmetry is derived analytically. The modified response function is further used to evaluate the induced charge density and the electrostatic potential near an electrode. The Gaussian field theory, combined with a two-Yukawa response function, can reproduce the oscillatory decay behavior of the electric potentials in concentrated electrolyte solutions. When the exact sum rules for the bulk electrolyte solutions and the electric double layers are used as constraints to determine the parameters of the response function, the Gaussian field theory could at least partly capture the nonlinear response effect of the surface charge density. Comparison with results for a planar electrode with fixed surface charge densities from molecular simulations demonstrates the validity of Gaussian field theory.

Resonant Cavity Modification of Ground-State Chemical Kinetics

Recent experiments have suggested that ground-state chemical kinetics can be suppressed or enhanced by coupling molecular vibrations with a cavity radiation mode. Here, we develop an analytical rate theory for cavity-modified chemical kinetics based on the Pollak-Grabert-Hänggi theory. Unlike previous work, our theory covers the complete range of solvent friction values, from the energy-diffusion-limited to the spatial-diffusion-limited regimes. We show that chemical kinetics is enhanced when bath friction is weak and suppressed when bath friction is strong. For weak bath friction, the resonant photon frequency (at which the maximum modification of the chemical rate is achieved) is close to the reactant well. In the strong friction limit, the resonant photon frequency is instead close to the barrier frequency. Finally, we observe that rate changes as a function of the photon frequency are much sharper and more sizable in the weak friction limit than in the strong friction limit.

Semiclassical Modified Redfield and Generalized Förster Theories of Exciton Relaxation/Transfer in Light-Harvesting Complexes: The Quest for the Principle of Detailed Balance

A conceptual problem of transfer theories that use a semiclassical description of the electron-vibrational coupling is the neglect of the correlation between momenta and coordinates of nuclei. In the Redfield theory of exciton relaxation, this neglect leads to a violation of the principle of detailed balance; equal “uphill” and “downhill” transfer rate constants are obtained. Here, we investigate how this result depends on nuclear reorganization effects, neglected in Redfield but taken into account in the modified Redfield theory. These reorganization effects, resulting from a partial localization of excited states, are found to promote a preferential “downhill” relaxation of excitation energy. However, for realistic spectral densities of light-harvesting antennae in photosynthesis, the reorganization effects are too small to compensate for the missing coordinate–momentum uncertainty. For weaker excitonic couplings as they occur between domains of strongly coupled pigments, we find the principle of detailed balance to be fulfilled in a semiclassical variant of the generalized Förster theory. A qualitatively correct description of the transfer is obtained with this theory at a significantly lower computational cost as with the quantum generalized Förster theory. Larger deviations between the two theories are expected for large energy gaps as they occur in complexes with chemically different pigments.

Three-state harmonic models for photoinduced charge transfer

A widely used strategy for simulating the charge transfer between donor and acceptor electronic states in an all-atom anharmonic condensed-phase system is based on invoking linear response theory to describe the system in terms of an effective spin-boson model Hamiltonian. Extending this strategy to photoinduced charge transfer processes requires also taking into consideration the ground electronic state in addition to the excited donor and acceptor electronic states. In this paper, we revisit the problem of describing such nonequilibrium processes in terms of an effective three-state harmonic model. We do so within the framework of nonequilibrium Fermi's golden rule (NE-FGR) in the context of photoinduced charge transfer in the carotenoid-porphyrin-C₆₀ (CPC₆₀) molecular triad dissolved in explicit tetrahydrofuran (THF). To this end, we consider different ways for obtaining a three-state harmonic model from the equilibrium autocorrelation functions of the donor-acceptor, donor-ground, and acceptor-ground energy gaps, as obtained from all-atom molecular dynamics simulations of the CPC₆₀/THF system. The quantum-mechanically exact time-dependent NE-FGR rate coefficients for two different charge transfer processes in two different triad conformations are then calculated using the effective three-state model Hamiltonians as well as a hierarchy of more approximate expressions that lead to the instantaneous Marcus theory limit. Our results show that the photoinduced charge transfer in CPC₆₀/THF can be described accurately by the effective harmonic three-state models and that nuclear quantum effects are small in this system.

Multiscale Models for Light-Driven Processes

Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes.

Linear-Response and Nonlinear-Response Formulations of the Instantaneous Marcus Theory for Nonequilibrium Photoinduced Charge Transfer

Instantaneous Marcus theory (IMT) offers a way for capturing the time-dependent charge transfer (CT) rate coefficient in nonequilibrium photoinduced CT processes, where the system was photoexcited from its equilibrated ground state vertically to the excitonic state, followed by an electronic transition to the CT state. As derived from the linearized semiclassical nonequilibrium Fermi's golden rule (LSC NE-FGR), the original IMT requires expensive all-atom nonequilibrium molecular dynamics (NEMD) simulations. In this work, we propose computationally efficient linear-response and nonlinear-response formulations for IMT rate calculations, which only require equilibrium molecular dynamics simulations. The linear- and nonlinear-response IMT methods were tested to predict the transient behavior in the photoinduced CT dynamics of the carotenoid-porphyrin-C₆₀ molecular triad solvated in explicit tetrahydrofuran. Our result demonstrated that the nonlinear-response IMT is in excellent agreement with the benchmark NEMD for all cases investigated here, whereas the linear-response IMT predicts the correct trend for all cases but overestimates the transient CT rate in one case involving a significant nonequilibrium relaxation. This mild breakdown of linear-response IMT is due to neglecting the higher-order terms in the exact nonlinear-response IMT. Taking advantage of time translational symmetry, the linear- and nonlinear-response approaches were demonstrated to be able to reduce the computational cost by 80% and 60% compared with NEMD simulations, respectively. Thus, we highly recommend the readily applicable and accurate nonlinear-response IMT approach for simulating nonequilibrium CT processes in complex molecular systems in the condensed phase.

Insights into Photosynthetic Energy Transfer Gained from Free-Energy Structure: Coherent Transport, Incoherent Hopping, and Vibrational Assistance Revisited

Giant strides in ultrashort laser pulse technology have enabled real-time observation of dynamical processes in complex molecular systems. Specifically, the discovery of oscillatory transients in the two-dimensional electronic spectra of photosynthetic systems stimulated a number of theoretical investigations exploring the possible physical mechanisms of the remarkable quantum efficiency of light harvesting processes. In this work, we revisit the elementary aspects of environment-induced fluctuations in the involved electronic energies and present a simple way to understand energy flow with the intuitive picture of relaxation in a funnel-type free-energy landscape. The presented free-energy description of energy transfer reveals that typical photosynthetic systems operate in an almost barrierless regime. The approach also provides insights into the distinction between coherent and incoherent energy transfer and the criteria by which the necessity of the vibrational assistance is considered.

Computational modeling of charge hopping dynamics along a disordered one-dimensional wire with energy gradients in quantum environments

This computational study investigates the effects of energy gradients on charge hopping dynamics along a one-dimensional chain of discrete sites coupled to quantum bath, which is modeled at the level of Pauli master equation (PME). This study also assesses the performance of different approximations for the hopping rates. Three different methods for solving the PME, a fourth order Runge-Kutta method, numerical diagonalization of the rate matrix followed by analytic propagation, and kinetic Monte Carlo simulation method, are tested and confirmed to produce virtually identical values of time dependent mean square displacement, diffusion constant, and mobility. Five different rate expressions, exact numerical evaluation of Fermi's Golden Rule (FGR) rate, stationary phase interpolation (SPI) approximation, semiclassical approximation, classical Marcus rate, and Miller-Abrahams rate, are tested to help understand the effects of approximations in representing quantum environments in the presence of energy gradients. The results based on direct numerical evaluation of FGR rate exhibit transition from diffusive to non-diffusive behavior with the increase in the gradient and show that the charge transport in the quantum bath is more sensitive to the magnitude of the gradient and the disorder than in the classical bath. Among all the four approximations for the hopping rates, the SPI approximation is confirmed to work best overall. A comparison of two different methods to calculate the mobility identifies drift motion of the population distribution as the major source of non-diffusive behavior and provides more reliable information on the contribution of quantum bath.

Reorganization energies and spectral densities for electron transfer problems in charge transport materials

Various contributions to the outer reorganization energy of an electron transfer system and their theoretical and computational aspects have been discussed.

Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems

Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment-protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics.

The modeling of the absorption lineshape for embedded molecules through a polarizable QM/MM approach

We present a polarizable QM/MM strategy to simulate the absorption line shape of chromophores embedded in complex matrices, including both homogeneous and inhomogeneous broadening.

Confinement Effects on an Electron Transfer Reaction in Nanoporous Carbon Electrodes

Nanoconfinement generally leads to a drastic effect on the physical and chemical properties of ionic liquids. Here we investigate how the electrochemical reactivity in such media may be impacted inside of nanoporous carbon electrodes. To this end, we study a simple electron transfer reaction using molecular dynamics simulations. The electrodes are held at constant electric potential by allowing the atomic charges on the carbon atoms to fluctuate. We show that the Fe³⁺/Fe²⁺ couple dissolved in an ionic liquid exhibits a deviation with respect to Marcus theory. This behavior is rationalized by the stabilization of a solvation state of the Fe³⁺ cation in the disordered nanoporous electrode that is not observed in the bulk. The simulation results are fitted with a recently proposed two solvation state model, which allows us to estimate the effect of such a deviation on the kinetics of electron transfer inside of nanoporous electrodes.

Stochastic simulation of anharmonic dissipation. I. Linear response regime

Over decades, the theoretical study of the quantum dissipative dynamics was mainly based on the linear dissipation model. The study of the nonlinear dissipative dynamics in condensed phases, where there exist an infinite number of bath modes, is extremely difficult even if not impossible. This work put forward a stochastic scheme for the simulation of the nonlinear dissipative dynamics. In the linear response regime, the second-order cumulant expansion becomes exact to reproduce the effect of the bath on the evolution of the reduced system. Consequently, a Hermitian stochastic Liouville equation is derived without explicit treatment of the bath. Stochastic simulations for an anharmonic model illustrate that the dynamics dissipated by anharmonic bath exhibits substantial difference on temperature dependence compared to that with the Caldeira-Leggett model.

From charge transport parameters to charge mobility in organic semiconductors through multiscale simulation

This review introduces the development and application of a multiscale approach to assess the charge mobility for organic semiconductors, which combines quantum chemistry, Kinetic Monte Carlo (KMC), and molecular dynamics (MD) simulations. This approach is especially applicable in describing a large class of organic semiconductors with intermolecular electronic coupling (V) much less than intramolecular charge reorganization energy (λ), a situation where the band description fails obviously. The charge transport is modeled as successive charge hopping from one molecule to another. We highlight the quantum nuclear tunneling effect in the charge transfer, beyond the semiclassical Marcus theory. Such an effect is essential for interpreting the "paradoxical" experimental finding that optical measurement indicated "local charge" while electrical measurement indicated "bandlike". Coupled MD and KMC simulations demonstrated that the dynamic disorder caused by intermolecular vibration has negligible effect on the carrier mobility. We further apply the approach for molecular design of n-type materials and for rationalization of experimental results. The charge reorganization energy is analyzed through decomposition into internal coordinates relaxation, so that chemical structure contributions to the intramolecular electron-phonon interaction are revealed and give helpful indication to reduce the charge reorganization energy.

Photophysical investigations on supramolecular fullerene/phthalocyanine charge transfer interactions in solution

The photophysical features of non-covalently linked fullerenes C60 and C70 with a designed free-base phthalocyanine, namely, 2,3,9,10,16,17,23,24-octakis-(octyloxy)-29H,31H-phthalocyanine (1) have been investigated employing various spectroscopic tools like UV-vis absorption spectrophotometry, steady state and time resolved fluorescence along with proton NMR measurements in toluene. The ground state interaction between fullerenes and 1 is nicely demonstrated with the appearance of well defined charge transfer absorption bands in the visible region of the electronic spectra. Steady state fluorescence experiment reveals efficient quenching of the excited singlet state of 1 in presence of both C60 and C70. The average values of binding constants for the non-covalent complexes of C60 and C70 with 1 are determined to be ~18,150 and ~32,000 dm(3) mol(-1), respectively. The magnitude of K suggests that 1 preferentially binds C70 in comparison to C60 although average value of selectivity in binding is measured to be low (~1.75). Time resolved emission measurements establish photoinduced energy transfer from the excited singlet state of 1 to fullerene in toluene. Measurements of free energy of electron transfer and free energy of radical ion-pair formation elicit that C70/1 complex is stabilized more in comparison to C60/1 complex regarding generation of charge-separated state. Proton NMR studies provide very good support in favor of effective ground state complexation between fullerenes and 1. Semi empirical theoretical calculations on fullerene/1 systems in vacuo substantiate the stronger binding between C70 and 1 in comparison to C60/1 system in terms of heat of formation value of the respective complexes, and determine the orientation of bound guest (here C70) towards the plane of 1 during complexation.

Understanding photosynthetic light-harvesting: a bottom up theoretical approach

We discuss a bottom up approach for modeling photosynthetic light-harvesting. Methods are reviewed for a full structure-based parameterization of the Hamiltonian of pigment-protein complexes (PPCs). These parameters comprise (i) the local transition energies of the pigments in their binding sites in the protein, the site energies; (ii) the couplings between optical transitions of the pigments, the excitonic couplings; and (iii) the spectral density characterizing the dynamic modulation of pigment transition energies and excitonic couplings by protein vibrations. Starting with quantum mechanics perturbation theory, we provide a microscopic foundation for the standard PPC Hamiltonian and relate the expressions obtained for its matrix elements to quantities that can be calculated with classical molecular mechanics/electrostatics approaches including the whole PPC in atomic detail and using charge and transition densities obtained with quantum chemical calculations on the isolated building blocks of the PPC. In the second part of this perspective, the Hamiltonian is utilized to describe the quantum dynamics of excitons. Situations are discussed that differ in the relative strength of excitonic and exciton-vibrational coupling. The predictive power of the approaches is demonstrated in application to different PPCs, and challenges for future work are outlined.

Normal mode analysis of the spectral density of the Fenna-Matthews-Olson light-harvesting protein: how the protein dissipates the excess energy of excitons

We report a method for the structure-based calculation of the spectral density of the pigment-protein coupling in light-harvesting complexes that combines normal-mode analysis with the charge density coupling (CDC) and transition charge from electrostatic potential (TrEsp) methods for the computation of site energies and excitonic couplings, respectively. The method is applied to the Fenna-Matthews-Olson (FMO) protein in order to investigate the influence of the different parts of the spectral density as well as correlations among these contributions on the energy transfer dynamics and on the temperature-dependent decay of coherences. The fluctuations and correlations in excitonic couplings as well as the correlations between coupling and site energy fluctuations are found to be 1 order of magnitude smaller in amplitude than the site energy fluctuations. Despite considerable amplitudes of that part of the spectral density which contains correlations in site energy fluctuations, the effect of these correlations on the exciton population dynamics and dephasing of coherences is negligible. The inhomogeneous charge distribution of the protein, which causes variations in local pigment-protein coupling constants of the normal modes, is responsible for this effect. It is seen thereby that the same building principle that is used by nature to create an excitation energy funnel in the FMO protein also allows for efficient dissipation of the excitons' excess energy.

Influence of temperature on coherent dynamics of a two-level system immersed in a dissipative spin bath

The quantum dynamics of a two-level system coupled to an Ohmic spin bath is studied by means of the perturbation approach based on a unitary transformation. A scattering function xi(k) is introduced in the transformation to take into account quantum fluctuations. By the master equation within the Born approximation, nonequilibrium dynamics quantities are calculated. The method works well for the coupling constant 0<alpha<alpha(c) and a finite bare tunneling Delta. It is found that (i) only at zero temperature with small coupling or moderate one does the spin-spin-bath model display identical behavior as the well-known spin-boson-bath model; (ii) in comparison with the known results of spin-boson-bath model, the coherence-incoherence transition point, which occurs at alpha(c)=12[1+etaDelta/omega(c)], is temperature independent; and (iii) the nonequilibrium correlation function P(t)=tau(z)(t), evolves without temperature dependence, while tau(x)(t) depends on temperature. Both P(t) and tau(x)(t) not only satisfy their initial conditions, respectively, and also have correct long time limits. Besides, the Shiba relation and sum rule are exactly satisfied in the coherent regime for this method. Our results show that increasing temperature does not help the system suppress decoherence in the coherent regime, i.e., finite temperature does not favor the coherent dynamics in this regime. Thus, the finite-temperature dynamics induced by two kinds of baths (spin-bath and boson-bath) exhibit distinctly different physics.

Closed-form expressions of quantum electron transfer rate based on the stationary-phase approximation

Closed-form rate expressions are derived on the basis of the stationary-phase approximation for the Fermi golden rule expression of the quantum electron-transfer (ET) rate. First, on the basis of approximate solutions of the stationary-phase points near DeltaG = 0, -lambda, and lambda, where DeltaG is the reaction free energy and lambda is the reorganization energy, three closed-form rate expressions are derived, which are respectively valid near each value of DeltaG. Numerical tests for a model Ohmic spectral density with an exponential cutoff demonstrate good performance of the derived expressions in the respective regions of their validity. In particular, the expression near DeltaG = -lambda, which differs from the semiclassical approximation only by a prefactor quadratic in DeltaG, works substantially better than the latter. Then, a unified formula is suggested, which interpolates the three approximate expressions and serves as a good approximation in all three regions. We have also demonstrated that the interpolation formula can serve as a good quantitative means for understanding the temperature dependence of the quantum ET rate.

Theoretical study of ultrafast heterogeneous electron transfer reactions at dye-semiconductor interfaces: coumarin 343 at titanium oxide

A theoretical study of photoinduced heterogeneous electron transfer in the dye-semiconductor system coumarin 343-TiO(2) is presented. The study is based on a generic model for heterogeneous electron transfer reactions, which takes into account the coupling of the electronic states to the nuclear degrees of freedom of coumarin 343 as well as to the surrounding solvent. The quantum dynamics of the electron injection process is simulated employing the recently proposed multilayer formulation of the multiconfiguration time-dependent Hartree method. The results reveal an ultrafast injection dynamics of the electron from the photoexcited donor state into the conduction band of the semiconductor. Furthermore, the mutual influence of electronic injection dynamics and nuclear motion is analyzed in some detail. The analysis shows that--depending on the time scale of nuclear motion--electronic vibrational coupling can result in electron transfer driven by coherent vibrational motion or vibrational motion induced by ultrafast electron transfer.

Quantum Dynamical Simulation of Electron-Transfer Reactions in an Anharmonic Environment

The multilayer multiconfiguration time-dependent Hartree theory is applied to study the quantum dynamics of ultrafast electron-transfer reactions in a condensed-phase environment with anharmonic potential functions. Effects of anharmonicity for both the nuclear degrees of freedom of the environment and the intramolecular vibrational degrees of freedom are investigated. Whereas the former can in principle be mapped to a fictitious harmonic bath, the latter cannot be represented in this way and, thus, go beyond the commonly employed linear response approximation. Numerical examples are presented to illustrate these findings.

Enzymatic catalysis and transfers in solution. I. Theory and computations, a unified view

The transfer of hydride, proton, or H atom between substrate and cofactor in enzymes has been extensively studied for many systems, both experimentally and computationally. A simple equation for the reaction rate, an analog of an equation obtained earlier for electron transfer rates, is obtained, but now containing an approximate analytic expression for the bond rupture-bond forming feature of these H transfers. A "symmetrization," of the potential energy surfaces is again introduced [R. A. Marcus, J. Chem. Phys. 43, 679 (1965); J. Phys. Chem. 72, 891 (1968)], together with Gaussian fluctuations of the remaining coordinates of the enzyme and solution needed for reaching the transition state. Combining the two expressions for the changes in the difference of the two bond lengths of the substrate-cofactor subsystem and in the fluctuation coordinates of the protein leading to the transition state, an expression is obtained for the free energy barrier. To this end a two-dimensional reaction space (m,n) is used that contains the relative coordinates of the H in the reactants, the heavy atoms to which it is bonded, and the protein/solution reorganization coordinate, all leading to the transition state. The resulting expression may serve to characterize in terms of specific parameters (two "reorganization" terms, thermodynamics, and work terms), experimental and computational data for different enzymes, and different cofactor-substrate systems. A related characterization was used for electron transfers. To isolate these factors from nuclear tunneling, when the H-tunneling effect is large, use of deuterium and tritium transfers is of course helpful, although tunneling has frequently and understandably dominated the discussions. A functional form is suggested for the dependence of the deuterium kinetic isotope effect (KIE) on DeltaG degrees and a different form for the 13C KIE. Pressure effects on deuterium and 13C KIEs are also discussed. Although formulated for a one-step transfer of a light particle in an enzyme, the results would also apply to single-step transfers of other atoms and groups in enzymes and in solution.

Summarizing lecture: factors influencing enzymatic H-transfers, analysis of nuclear tunnelling isotope effects and thermodynamic versus specific effects

In the articles in this Discussion, a wide variety of topics are treated, including reorganization energy, initially introduced for electron transfers ('environmentally assisted tunnelling'), nuclear tunnelling, H/D and 12C/13C kinetic isotope effects (KIEs), the effect of changes of distal and nearby amino acid residues using site-directed mutagenesis, and dynamics versus statistical effects. A coordinate-free form of semi-classical theory is used to examine topics on data such as tunnelling versus 'over-the-barrier' paths and temperature and pressure effects on KIEs. The multidimensional semi-classical theory includes classically allowed and classically forbidden transitions. More generally, we address the question of relating kinetic to thermodynamic factors, as in the electron transfer field, so learning about specific versus thermodynamic effects in enzyme catalysis and KIEs.

On the microscopic theory of polar solvation dynamics

A microscopic model of the time-resolved Stokes shift is developed. The model calculates the solvation dynamics by combining the atomic resolution of the solute structure with dipolar dynamics from the polarization structure factors of the homogeneous solvent. Calculations are made for coumarin 153 and quinoxaline optical dyes with atomic geometries and charge distributions taken from quantum calculations. Stokes shift dynamics is calculated and compared to experiment in high-temperature acetonitrile and methanol and in low-temperature 2-methyl-tetrahydrofurane using dielectric relaxation data from experiment.