Photoexcited Electron Transfer: Short-Time Dynamics and Turnover Control by Dephasing, Relaxation, and Mixing

Sub-100-fs energy transfer in coenzyme NADH is a coherent process assisted by a charge-transfer state

Excitation energy transfer (EET) is a key photoinduced process in biological chromophoric assemblies. Here we investigate the factors which can drive EET into efficient ultrafast sub-ps regimes. We demonstrate how a coherent transport of electronic population could facilitate this in water solvated NADH coenzyme and uncover the role of an intermediate dark charge-transfer state. High temporal resolution ultrafast optical spectroscopy gives a 54±11 fs time constant for the EET process. Nonadiabatic quantum dynamical simulations computed through the time-evolution of multidimensional wavepackets suggest that the population transfer is mediated by photoexcited molecular vibrations due to strong coupling between the electronic states. The polar aqueous solvent environment leads to the active participation of a dark charge transfer state, accelerating the vibronically coherent EET process in favorably stacked conformers and solvent cavities. Our work demonstrates how the interplay of structural and environmental factors leads to diverse pathways for the EET process in flexible heterodimers and provides general insights relevant for coherent EET processes in stacked multichromophoric aggregates like DNA strands.

Time-resolved spectra of I2 in a krypton crystal by G-MCTDH simulations: nonadiabatic dynamics, dissipation and environment driven decoherence

Time- and frequency-resolved pump-probe spectra of I₂ in a krypton crystal are calculated and analyzed using high-dimensional multi-state quantum dynamics by the Gaussian-based multi-configuration time-dependent Hartree (G-MCTDH) method.

Ultrafast structural rearrangement dynamics induced by the photodetachment of phenoxide in aqueous solution

The elementary processes that accompany the interaction of ionizing radiation with biologically relevant molecules are of fundamental importance. However, the ultrafast structural rearrangement dynamics induced by the ionization of biomolecules in aqueous solution remain hitherto unknown. Here, we employ femtosecond optical pump-probe spectroscopy to elucidate the vibrational wave packet dynamics that follow the photodetachment of phenoxide, a structural mimic of tyrosine, in aqueous solution. Photodetachment of phenoxide leads to wave packet dynamics of the phenoxyl radical along 12 different vibrational modes. Eight of the modes are totally symmetric and support structural rearrangement upon electron ejection. Comparison to a previous photodetachment study of phenoxide in the gas phase reveals the important role played by the solvent environment in driving ultrafast structural reorganization induced by ionizing radiation. This work provides insight into the ultrafast molecular dynamics that follow the interaction of ionizing radiation with molecules in aqueous solution.

The interaction of biomolecules with ionizing radiation induces structural changes which are still largely unknown. The authors use femtosecond wave packet spectroscopy to observe ultrafast structural dynamics that follow the photodetachment of phenoxide in aqueous solution.

Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes

Scanning tunneling microscope break junction measurements are used to examine how the molecular conductance of nucleic acids depends on the composition of their backbone and the linker group to the electrodes. Molecular conductances of 10 base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a heteroduplex of DNA/aeg-PNA with identical nucleobase sequence were measured. The molecular conductance was found to vary by 12 to 13 times with the change in backbone. Computational studies show that the molecular conductance differences between nucleic acids of different backbones correlate with differences in backbone structural flexibility. The molecular conductance was also measured for duplexes connected to the electrode through two different linkers, one directly to the backbone and one directly to the nucleobase stack. While the linker causes an order-of-magnitude increase in the overall conductance for a particular duplex, the differences in the electrical conductance with backbone composition are preserved. The highest molecular conductance value, 0.06G₀, was measured for aeg-PNA duplexes with a base stack linker. These findings reveal an important new strategy for creating longer and more complex electroactive, nucleic acid assemblies.

Theoretical aspects of femtosecond double-pump single-molecule spectroscopy. I. Weak-field regime

We present a theoretical description of double-pump femtosecond single-molecule signals with fluorescence detection.

Quantum heat engines and refrigerators: continuous devices

Quantum thermodynamics supplies a consistent description of quantum heat engines and refrigerators up to a single few-level system coupled to the environment. Once the environment is split into three (a hot, cold, and work reservoir), a heat engine can operate. The device converts the positive gain into power, with the gain obtained from population inversion between the components of the device. Reversing the operation transforms the device into a quantum refrigerator. The quantum tricycle, a device connected by three external leads to three heat reservoirs, is used as a template for engines and refrigerators. The equation of motion for the heat currents and power can be derived from first principles. Only a global description of the coupling of the device to the reservoirs is consistent with the first and second laws of thermodynamics. Optimization of the devices leads to a balanced set of parameters in which the couplings to the three reservoirs are of the same order and the external driving field is in resonance. When analyzing refrigerators, one needs to devote special attention to a dynamical version of the third law of thermodynamics. Bounds on the rate of cooling when Tc→0 are obtained by optimizing the cooling current. All refrigerators as Tc→0 show universal behavior. The dynamical version of the third law imposes restrictions on the scaling as Tc→0 of the relaxation rate γc and heat capacity cV of the cold bath.

Primary Photonic Processes in Energy Harvesting: Quantum Dynamical Analysis of Exciton Energy Transfer over Three-Dimensional Dendrimeric Geometries

In molecular solar energy harvesting systems, quantum mechanical features may be apparent in the physical processes involved in the acquisition and migration of photon energy. With a sharply declining distance-dependence in transfer efficiency, the excitation energy generally takes a large number of steps en route to the site of its utilization; quantum features are rapidly dissipated in an essentially stochastic process. In the case of engineered dendrimeric polymers, each such step usually takes the form of an inward hop between chromophores in neighboring generation shells. A physically intuitive, structure-determined adjacency matrix formulation of the energy flow affords insights into the key harvesting and inward funneling processes. A numerical method based on this analytic approach has now been developed and is able to deliver results on significantly larger dendrimeric polymers, with the help of large multi-processor computers. Central to this study is the interpretation of key features such as the relevance of a spectroscopic gradient and the presence of traps or irregularities due to conformational changes and folding. With the objective of fine-tune the funneling process, this model now allows the incorporation of parameters derived from quantum chemical calculations, affording new insights into the detailed operation of the harvesting process in a variety of dendrimer systems.

Molecular theory and simulation of coherence transfer in metal carbonyls and its signature on multidimensional infrared spectra

We present a general and comprehensive theoretical and computational framework for modeling ultrafast multidimensional infrared spectra of a vibrational excitonic system in liquid solution. Within this framework, we describe the dynamics of the system in terms of a quantum master equation that can account for population relaxation, dephasing, coherence-to-coherence transfer, and coherence-to-population transfer. A unique feature of our approach is that, in principle, it does not rely on any adjustable fitting parameters. More specifically, the anharmonic vibrational Hamiltonian is derived from ab initio electronic structure theory, and the system-bath coupling is expressed explicitly in terms of liquid degrees of freedom whose dynamics can be obtained via molecular dynamics simulations. The applicability of the new approach is demonstrated by employing it to model the recently observed signatures of coherence transfer in the two-dimensional spectra of dimanganese decacarbonyl in liquid cyclohexane. The results agree well with experiment and shed new light on the nature of the molecular interactions and dynamics underlying the spectra and the interplay between dark and bright states, their level of degeneracy, and the nature of their interactions with the solvent.

Molecular dynamics simulations of porphyrin-dendrimer systems: toward modeling electron transfer in solution

We have performed computational simulations of porphyrin-dendrimer systems--a cationic porphyrin electrostatically associated to a negatively charged dendrimer--using the method of classical molecular dynamics (MD) with an atomistic force field. Previous experimental studies have shown a strong quenching effect of the porphyrin fluorescence that was assigned to electron transfer (ET) from the dendrimer's tertiary amines (Paulo, P. M. R.; Costa, S. M. B. J. Phys. Chem. B 2005, 109, 13928). In the present contribution, we evaluate computationally the role of the porphyrin-dendrimer conformation in the development of a statistical distribution of ET rates through its dependence on the donor-acceptor distance. We started from simulations without explicit solvent to obtain trajectories of the donor-acceptor distance and the respective time-averaged distributions for two dendrimer sizes and different initial configurations of the porphyrin-dendrimer pair. By introducing explicit solvent (water) in our simulations, we were able to estimate the reorganization energy of the medium for the systems with the dendrimer of smaller size. The values obtained are in the range 0.6-1.5 eV and show a linear dependence with the inverse of the donor-acceptor distance, which can be explained by a two-phase dielectric continuum model taking into account the medium heterogeneity provided by the dendrimer organic core. Dielectric relaxation accompanying ET was evaluated from the simulations with explicit solvent showing fast decay times of some tens of femtoseconds and slow decay times in the range of hundreds of femtoseconds to a few picoseconds. The variations of the slow relaxation times reflect the heterogeneity of the dendrimer donor sites which add to the complexity of ET kinetics as inferred from the experimental fluorescence decays.

Ab Initio Prediction of Tryptophan Fluorescence Quenching by Protein Electric Field Enabled Electron Transfer

We report quantum mechanical-molecular mechanical (QM-MM) predictions of fluorescence quantum yields for 20 tryptophans in 17 proteins, whose yields span the range from 0.01 to 0.3, using ab initio computed coupling matrix elements for photoinduced electron transfer from the 1La excited indole ring to a local backbone amide. The average coupling elements span the range 140-1000 cm-1, depending on tryptophan rotamer conformation. The matrix elements were from the singles configuration interaction matrix, and were largely insensitive to which of the three basis sets was used. Large fluctuations were seen on the time scale of tens of femtoseconds, caused primarily by side chain and backbone torsional variations for 150 ps of dynamics at 300 K. The largest coupling occurs for the chi1 = -60 degrees rotamer and is purely through-bond. There is no apparent correlation between the coupling magnitude and quantum yield, which is still dominated by energy gap and reorganization energy. The source of error bars for predicted quenching rates using the weak coupling golden rule may be due to inaccurate averaged Franck-Condon weighted densities because of inadequate simulation times and parameters and/or to failure of the weak coupled golden rule used in these predictions because of the broad distribution of Landau-Zener probabilities arising from the large variable coupling.

Symmetry-adapted-cluster/symmetry-adapted-cluster configuration interaction methodology extended to giant molecular systems: ring molecular crystals

The symmetry adapted cluster (SAC)/symmetry adapted cluster configuration interaction (SAC-CI) methodology for the ground, excited, ionized, and electron-attached states of molecules was extended to giant molecular systems. The size extensivity of energy and the size intensivity of excitation energy are very important for doing quantitative chemical studies of giant molecular systems and are designed to be satisfied in the present giant SAC/SAC-CI method. The first extension was made to giant molecular crystals composed of the same molecular species. The reference wave function was defined by introducing monomer-localized canonical molecular orbitals (ml-CMO's), which were obtained from the Hartree-Fock orbitals of a tetramer or a larger oligomer within the electrostatic field of the other part of the crystal. In the SAC/SAC-CI calculations, all the necessary integrals were obtained after the integral transformation with the ml-CMO's of the neighboring dimer. Only singles and doubles excitations within each neighboring dimer were considered as linked operators, and perturbation selection was done to choose only important operators. Almost all the important unlinked terms generated from the selected linked operators were included: the unlinked terms are important for keeping size extensivity and size intensivity. Some test calculations were carried out for the ring crystals of up to 10 000-mer, confirming the size extensivity and size intensivity of the calculated results and the efficiency of the giant method in comparison with the standard method available in GAUSSIAN 03. Then, the method was applied to the ring crystals of ethylene and water 50-mers, and formaldehyde 50-, 100-, and 500-mers. The potential energy curves of the ground state and the polarization and electron-transfer-type excited states were calculated for the intermonomer distances of 2.8-100 A. Several interesting behaviors were reported, showing the potentiality of the present giant SAC/SAC-CI method for molecular engineering.

Nonequilibrium quantum dynamics in the condensed phase via the generalized quantum master equation

The Nakajima-Zwanzig generalized quantum master equation provides a general, and formally exact, prescription for simulating the reduced dynamics of a quantum system coupled to a quantum bath. In this equation, the memory kernel accounts for the influence of the bath on the system's dynamics, and the inhomogeneous term accounts for initial system-bath correlations. In this paper, we propose a new approach for calculating the memory kernel and inhomogeneous term for arbitrary initial state and system-bath coupling. The memory kernel and inhomogeneous term are obtained by numerically solving a single inhomogeneous Volterra equation of the second kind for each. The new approach can accommodate a very wide range of projection operators, and requires projection-free two-time correlation functions as input. An application to the case of a two-state system with diagonal coupling to an arbitrary bath is described in detail. Finally, the utility and self-consistency of the formalism are demonstrated by an explicit calculation on a spin-boson model.

Electron transfer mechanism and the locality of the system-bath interaction: A comparison of local, semilocal, and pure dephasing models

We simulate the effects of two types of dephasing processes, a nonlocal dephasing of system eigenstates and a dephasing of semilocal eigenstates, on the rate and mechanism of electron transfer (eT) through a series of donor-bridge-acceptor systems, D-B(N)-A, where N is the number of identical bridge units. Our analytical and numerical results show that pure dephasing, defined as the perturbation of system eigenstates through the system-bath interaction, does not disrupt coherent eT because it induces no localization; electron transfer may proceed through superexchange in a system undergoing only pure dephasing. A more physically reasonable description may be obtained via a system-bath interaction that reflects the perturbation of more local electronic structure by local nuclear distortions and dipole interactions. The degree of locality of this interaction is guided by the structure of the system Hamiltonian and by the nature of the measurement performed on the system (i.e., the nature of the environment). We compare our result from this "semilocal" model with an even more local phenomenological dephasing model. We calculate electron transfer rate by obtaining nonequilibrium steady-state solutions for the elements of a reduced density matrix; a semigroup formalism is used to write down the dissipative part of the equation of motion.

Dissipative dynamics of a system passing through a conical intersection: Ultrafast pump-probe observables

The dynamics of a system incorporating a conical intersection, in the presence of a dissipative environment, is studied with the purpose of identifying observable ultrafast spectroscopic signatures. A model system consisting of two vibronically coupled electronic states with two nuclear degrees of freedom is constructed. Dissipation is treated by two different methods, Lindblad semigroup formalism and the surrogate Hamiltonian approach. Pump-probe experimental expectation values such as transient emission and transient absorption are calculated and compared to the adiabatic and diabatic population transfer. The ultrafast population transfer reflecting the conical intersection is not mirrored in transient absorption measurements such as the recovery of the bleach. Emission from the excited state can be suppressed on the ultrafast time scale, but the existence of a conical intersection is only one of the possible mechanisms that can provide ultrafast damping of emission.

Transient Phenomena in Time- and Frequency-Gated Spontaneous Emission

The effect of overlapping pump and gate pulses on time- and frequency-gated spontaneous emission spectra is explored for a model of material dynamics that accounts for strong nonadiabatic and electron-vibrational coupling effects, vibrational relaxation, and optical dephasing, thus representing characteristic features of photoinduced excited-state dynamics in large molecules in the gas phase or in condensed phases. The behaviors of the sequential, coherent, and doorway-window contributions to the spontaneous emission spectrum are studied separately. The interrelation between the sequential and coherent contributions is demonstrated to be sensitive to the carrier frequencies of the pump and gate pulses and also to the optical dephasing rate, opening the possibility of an experimental determination of the latter. The coherent contribution is shown to dominate the spectrum at specific emission frequencies.

Time- and frequency-resolved fluorescence spectra of nonadiabatic dissipative systems: What photons can tell us

The monitoring of the excited-state dynamics by time- and frequency-resolved spontaneous emission spectroscopy has been studied in detail for a model exhibiting an excited-state curve crossing. The model represents characteristic aspects of the photoinduced ultrafast dynamics in large molecules in the gas or condensed phases and accounts for strong nonadiabatic and electron-vibrational coupling effects, as well as for vibrational relaxation and optical dephasing. A comprehensive overview of the dependence of spontaneous emission spectra on the characteristics of the excitation and detection processes (such as carrier frequencies, pump/gate pulse durations, as well as optical dephasing) is presented. A systematic comparison of ideal spectra, which provide simultaneously perfect time and frequency resolution and thus contain maximal information on the system dynamics, with actually measurable time- and frequency-gated spectra has been carried out. The calculations of real time- and frequency-gated spectra demonstrate that complementary information on the excited-state dynamics can be extracted when the duration of the gate pulse is varied.

A semiclassical generalized quantum master equation for an arbitrary system-bath coupling

The Nakajima-Zwanzig generalized quantum master equation (GQME) provides a general, and formally exact, prescription for simulating the reduced dynamics of a quantum system coupled to a, possibly anharmonic, quantum bath. In this equation, a memory kernel superoperator accounts for the influence of the bath on the dynamics of the system. In a previous paper [Q. Shi and E. Geva, J. Chem. Phys. 119, 12045 (2003)] we proposed a new approach to calculating the memory kernel, in the case of arbitrary system-bath coupling. Within this approach, the memory kernel is obtained by solving a set of two integral equations, which requires a new type of two-time system-dependent bath correlation functions as input. In the present paper, we consider the application of the linearized semiclassical (LSC) approximation for calculating those correlation functions, and subsequently the memory kernel. The new approach is tested on a benchmark spin-boson model. Application of the LSC approximation for calculating the relatively short-lived memory kernel, followed by a numerically exact solution of the GQME, is found to provide an accurate description of the relaxation dynamics. The success of the proposed LSC-GQME methodology is contrasted with the failure of both the direct application of the LSC approximation and the weak coupling treatment to provide an accurate description of the dynamics, for the same model, except at very short times. The feasibility of the new methodology to anharmonic systems is also demonstrated in the case of a two level system coupled to a chain of Lennard-Jones atoms.

Quantum anti-zeno acceleration of a chemical reaction

Evidence of acceleration of a chemical reaction in a condensed phase due to the quantum anti-Zeno effect is presented by a quantum-mechanical calculation. The acceleration is caused by electronic decoherence. The mechanism clearly indicates the anti-Zeno effect and involves both delocalization of the electronic dynamics and a feedback loop by coupling to vibrations. Believed to be the first established example of the quantum anti-Zeno effect in chemistry, the observed phenomenon suggests the possibility of quantum control of chemical reactivity by choice of solvent.

Electrochromic detection of a coherent component in the formation of the charge pair P(+)H(L)(-) in bacterial reaction centers

We demonstrate coupling of an intraprotein electron transfer reaction to coherent vibrational motions. The kinetics of charge separation toward the radical pair state P(+)H(L)(-) were studied in reaction centers of Rhodobacter sphaeroides at 15 K. The electrochromic shift of the bacteriochlorophyll monomers is the most prominent spectral feature associated with this charge displacement. The newly reported absolute absorption spectrum of the P(+)H(L)(-) state is discussed in terms of this shift. In wild-type reaction centers, the rise kinetics of the electrochromic shift display a small but significant 30 cm(-)(1) periodic modulation (period of approximately 1 ps). This modulation is also present in FL181Y mutant reaction centers, where overall charge separation is somewhat more rapid than in the wild-type reaction center. In contrast, in YM210L mutant reaction centers, where the charge separation is much slower, the modulation is absent. The conclusion that the motion along the reaction coordinate has a 30 cm(-)(1) coherent component is discussed in light of possible mechanisms of electron transfer.