Chirped Laser Pulse Control of Vibronic Wavepackets and Energy Transfer in Phycocyanin 645.

Photosynthetic organisms use light-harvesting complexes to increase the spectrum of light that they absorb from solar photons. Recent ultrafast spectroscopic studies have revealed that efficient (sub-ps) energy transfer is mediated by vibronic coherence in the phycobiliprotein phycocyanin 645 (PC645). Here, we report studies that employ broadband pump-probe spectroscopy with linearly chirped excitation pulses to further investigate the relationship between vibronic state preparation and energy transfer dynamics in PC645. Negatively chirped pulse excitation is found to enhance wavepackets of a high-frequency mode (1580 cm-1) and increase the rate of downhill energy transfer, while on the other hand, positively chirped pulses suppress these oscillatory features and decrease this rate. Model calculations incorporating the influence of the chirped pump pulse are used to understand its effect on initial state preparation. These results provide mechanistic insight into how the overall nonequilibrium rate of energy transfer is influenced by initial state preparation.

Exciton polaron formation and hot-carrier relaxation in rigid Dion-Jacobson-type two-dimensional perovskites.

The efficiency of two-dimensional Dion-Jacobson-type materials relies on the complex interplay between electronic and lattice dynamics; however, questions remain about the functional role of exciton-phonon interactions. Here we establish the robust polaronic nature of the excitons in these materials at room temperature by combining ultrafast spectroscopy and electronic structure calculations. We show that polaronic distortion is associated with low-frequency (30-60 cm-1) lead iodide octahedral lattice motions. More importantly, we discover how targeted ligand modification of this two-dimensional perovskite structure manipulates exciton-phonon coupling, exciton polaron population and carrier cooling. At high excitation density, stronger exciton-phonon coupling increases the hot-carrier lifetime, forming a hot-phonon bottleneck. Our study provides detailed insight into the exciton-phonon coupling and its role in carrier cooling in two-dimensional perovskites relevant for developing emerging hybrid semiconductor materials with tailored properties.

Trajectory Ensemble Methods Provide Single-Molecule Statistics for Quantum Dynamical Systems.

The emergence of experiments capable of probing quantum dynamics at the single-molecule level requires the development of new theoretical tools capable of simulating and analyzing these dynamics beyond an ensemble-averaged description. In this article, we present an efficient method for sampling and simulating the dynamics of the individual quantum systems that make up an ensemble and apply it to study the nonequilibrium dynamics of the ubiquitous spin-boson model. We generate an ensemble of single-system trajectories, and we analyze this trajectory ensemble using tools from classical statistical mechanics. Our results demonstrate that the dynamics of quantum coherence is highly heterogeneous at the single-system level due to variations in the initial bath configuration, which significantly affects the transient exchange of coherence between the system and its bath. We observe that single systems tend to retain coherence over time scales longer than that of the ensemble. We also compute a novel thermodynamic entanglement entropy that quantifies a thermodynamic driving force favoring system-bath entanglement.

Influence of solution phase environmental heterogeneity and fluctuations on vibronic spectra: Perylene diimide molecular chromophore complexes in solution.

Ensembles of ab initio parameterized Frenkel-exciton model Hamiltonians for different perylene diimide dimer systems are used, together with various dissipative quantum dynamics approaches, to study the influence of the solvation environment and fluctuations in chromophore relative orientation and packing on the vibronic spectra of two different dimer systems: a π-stacked dimer in aqueous solution in which the relative chromophore geometry is strongly confined by a phosphate bridge and a side-by-side dimer in dichloromethane involving a more flexible alkyne bridge that allows quasi-free rotation of the chromophores relative to one another. These entirely first-principles calculations are found to accurately reproduce the main features of the experimental absorption spectra, providing a detailed mechanistic understanding of how the structural fluctuations and environmental interactions influence the vibronic dynamics and spectroscopy of solutions of these multi-chromophore complexes.

Analytic and numerical vibronic spectra from quasi-classical trajectory ensembles.

The truncated Wigner approximation to quantum dynamics in phase space is explored in the context of computing vibronic line shapes for monomer linear optical spectra. We consider multiple model potential forms including a shifted harmonic oscillator with both equal and unequal frequencies on the ground and excited state potentials as well as a shifted Morse potential model. For the equal-frequency shifted harmonic oscillator model, we derive an analytic expression for the exact vibronic line shape that emphasizes the importance of using a quantum mechanical distribution of phase space initial conditions. For the unequal-frequency shifted harmonic oscillator model, we are no longer able to obtain an exact expression for the vibronic line shape in terms of independent deterministic classical trajectories. We show how one can rigorously account for corrections to the truncated Wigner approximation through nonlinear responses of the line shape function to momentum fluctuations along a classical trajectory and demonstrate the qualitative improvement in the resulting spectrum when the leading-order quantum correction is included. Finally, we numerically simulate absorption spectra of a highly anharmonic shifted Morse potential model. We find that, while finite quantization and the dissociation limit are captured with reasonable accuracy, there is a qualitative breakdown of the quasi-classical trajectory ensemble's ability to describe the vibronic line shape when the relative shift in Morse potentials becomes large. The work presented here provides clarity on the origin of unphysical negative features known to contaminate absorption spectra computed with quasi-classical trajectory ensembles.

Modeling Nonperturbative Field-Driven Vibronic Dynamics: Selective State Preparation and Nonlinear Spectroscopy.

The partially linearized density matrix formalism for nonadiabatic dynamics is adapted to incorporate a classical external electromagentic field into the system Hamiltonian. This advancement encompasses the possibility of describing field-driven dynamics and computing a variety of linear and nonlinear spectroscopic signals beyond the perturbative limit. The capabilities of the developed approach are demonstrated on a simple two-state vibronic model coupled to a bath, for which we (a) perform an exhaustive search in the field parameter space for optimal state preparation and (b) compute time-resolved transient absorption spectroscopy to monitor the effect of different pulse shapes on measurable experimental signals. While no restrictions on the form of the field have to be assumed, we focus here on Gaussian shaped (linearly) chirped pulses.

Quantum biology revisited.

Photosynthesis is a highly optimized process from which valuable lessons can be learned about the operating principles in nature. Its primary steps involve energy transport operating near theoretical quantum limits in efficiency. Recently, extensive research was motivated by the hypothesis that nature used quantum coherences to direct energy transfer. This body of work, a cornerstone for the field of quantum biology, rests on the interpretation of small-amplitude oscillations in two-dimensional electronic spectra of photosynthetic complexes. This Review discusses recent work reexamining these claims and demonstrates that interexciton coherences are too short lived to have any functional significance in photosynthetic energy transfer. Instead, the observed long-lived coherences originate from impulsively excited vibrations, generally observed in femtosecond spectroscopy. These efforts, collectively, lead to a more detailed understanding of the quantum aspects of dissipation. Nature, rather than trying to avoid dissipation, exploits it via engineering of exciton-bath interaction to create efficient energy flow.

Thermal transport in model copper-polyethylene interfaces.

Thermal transport through model copper-polyethylene interfaces is studied using two-temperature nonequilibrium molecular dynamics. This approach treats electronic and phonon contributions to the thermal transport in the metallic region, but only phonon mediated transport is assumed in the polymer. Results are compared with nonequilibrium molecular dynamics simulations of heat transport in which only phonon contributions are incorporated. The influence of the phase of the polymer component (crystalline, amorphous, and lamella) and, where relevant, its orientation relative to the metallic interface structure is explored. These computational studies suggest that the thermal conductivity of the metal-polymer interface can be more than 40 times greater when the polymer chains of the lamella are oriented perpendicular to the interface than the situation when the interface is formed by an amorphous polymer or a crystalline polymer phase in which the chains orient parallel to the interface. The simulations suggest that the phonon contribution to the thermal conductivity of the copper region can be increased by as much as a factor of three when coupling between the electrons and phonons in the metal region is incorporated. This, combined with the explicit inclusion of the purely electronic component of the thermal transport in the metal region, can lead to a substantial increase in the heat flux promoted by the interface while maintaining a constant temperature drop. These simulation results have important implications for designing materials that have excellent electrical insulation properties but can also be highly effective in heat conduction.

Multi-level description of the vibronic dynamics of open quantum systems.

A new approximate coherent state path integral approach, which enables accurate and efficient dynamical treatment of model Hamiltonians that incorporate excited electronic states of multiple chromophores that are coupled to discrete high frequency harmonic vibrational modes, is presented. The approach is based on the mapping Hamiltonian formalism for the electronic states together with semiclassical coherent state expressions for the forward and backward propagators describing the quantum bath modes. The density matrix dynamics is propagated in the full coherent state basis for the electronic mapping and discrete vibrational mode oscillators using ensembles of weighted trajectories. An effective scheme for projecting the ensemble onto selected vibronic basis states is presented enabling the evolution of the reduced system density matrix to be monitored as well as exploring the importance of selected vibronic relaxation pathways in the multichromophore system dynamics. The approach is demonstrated for simple model Hamiltonians, and we show how this coherent state density matrix propagation approach for high frequency discrete harmonic vibrational modes can be combined with partial linearized density matrix propagation to treat an additional continuum bath of low frequency environmental modes that could, in principle, include anharmonicity.

Variety, the spice of life and essential for robustness in excitation energy transfer in light-harvesting complexes.

For over a decade there has been some significant excitement and speculation that quantum effects may be important in the excitation energy transport process in the light harvesting complexes of certain bacteria and algae, in particular via the Fenna-Matthews-Olsen (FMO) complex. Whilst the excitement may have waned somewhat with the realisation that the observed long-lived oscillations in two-dimensional electronic spectra of FMO are probably due to vibronic coherences, it remains a question whether these coherences may play any important role. We review our recent work showing how important the site-to-site variation in coupling between chloroplasts in FMO and their protein scaffold environment is for energy transport in FMO and investigate the role of vibronic modes in this transport. Whilst the effects of vibronic excitations seem modest for FMO, we show that for bilin-based pigment-protein complexes of marine algae, in particular PC645, the site-dependent vibronic excitations seem essential for robust excitation energy transport, which may again open the door for important quantum effects to be important in these photosynthetic complexes.

Asymmetric Synthesis of Griffipavixanthone Employing a Chiral Phosphoric Acid-Catalyzed Cycloaddition.

Asymmetric synthesis of the biologically active xanthone dimer griffipavixanthone is reported along with its absolute stereochemistry determination. Synthesis of the natural product is accomplished via dimerization of a p-quinone methide using a chiral phosphoric acid catalyst to afford a protected precursor in excellent diastereo- and enantioselectivity. Mechanistic studies, including an unbiased computational investigation of chiral ion-pairs using parallel tempering, were performed in order to probe the mode of asymmetric induction.

Communication: Symmetrical quasi-classical analysis of linear optical spectroscopy.

The symmetrical quasi-classical approach for propagation of a many degree of freedom density matrix is explored in the context of computing linear spectra. Calculations on a simple two state model for which exact results are available suggest that the approach gives a qualitative description of peak positions, relative amplitudes, and line broadening. Short time details in the computed dipole autocorrelation function result in exaggerated tails in the spectrum.

Semiclassical Path Integral Calculation of Nonlinear Optical Spectroscopy.

Computation of nonlinear optical response functions allows for an in-depth connection between theory and experiment. Experimentally recorded spectra provide a high density of information, but to objectively disentangle overlapping signals and to reach a detailed and reliable understanding of the system dynamics, measurements must be integrated with theoretical approaches. Here, we present a new, highly accurate and efficient trajectory-based semiclassical path integral method for computing higher order nonlinear optical response functions for non-Markovian open quantum systems. The approach is, in principle, applicable to general Hamiltonians and does not require any restrictions on the form of the intrasystem or system-bath couplings. This method is systematically improvable and is shown to be valid in parameter regimes where perturbation theory-based methods qualitatively breakdown. As a test of the methodology presented here, we study a system-bath model for a coupled dimer for which we compare against numerically exact results and standard approximate perturbation theory-based calculations. Additionally, we study a monomer with discrete vibronic states that serves as the starting point for future investigation of vibronic signatures in nonlinear electronic spectroscopy.

First-Principles Models for Biological Light-Harvesting: Phycobiliprotein Complexes from Cryptophyte Algae.

There have been numerous efforts, both experimental and theoretical, that have attempted to parametrize model Hamiltonians to describe excited state energy transfer in photosynthetic light harvesting systems. The Frenkel exciton model, with its set of electronically coupled two level chromophores that are each linearly coupled to dissipative baths of harmonic oscillators, has become the workhorse of this field. The challenges to parametrizing such Hamiltonians have been their uniqueness, and physical interpretation. Here we present a computational approach that uses accurate first-principles electronic structure methods to compute unique model parameters for a collection of local minima that are sampled with molecular dynamics and QM geometry optimization enabling the construction of an ensemble of local models that captures fluctuations as these systems move between local basins of inherent structure. The accuracy, robustness, and reliability of the approach is demonstrated in an application to the phycobiliprotein light harvesting complexes from cryptophyte algae. Our computed Hamiltonian ensemble provides a first-principles description of inhomogeneous broadening processes, and a standard approximate non-Markovian reduced density matrix dynamics description is used to estimate lifetime broadening contributions to the spectral line shape arising from electronic-vibrational coupling. Despite the overbroadening arising from this approximate line shape theory, we demonstrate that our model Hamiltonian ensemble approach is able to provide a reliable fully first-principles method for computation of spectra and can distinguish the influence of different chromophore protonation states in experimental results. A key feature in the dynamics of these systems is the excitation of intrachromophore vibrations upon electronic excitation and energy transfer. We demonstrate that the Hamiltonian ensemble approach provides a reliable first-principles description of these contributions that have been detailed in recent broad-band pump-probe and two-dimensional electronic spectroscopy experiments.

Using coherence to enhance function in chemical and biophysical systems.

Coherence phenomena arise from interference, or the addition, of wave-like amplitudes with fixed phase differences. Although coherence has been shown to yield transformative ways for improving function, advances have been confined to pristine matter and coherence was considered fragile. However, recent evidence of coherence in chemical and biological systems suggests that the phenomena are robust and can survive in the face of disorder and noise. Here we survey the state of recent discoveries, present viewpoints that suggest that coherence can be used in complex chemical systems, and discuss the role of coherence as a design element in realizing function.

How flexible is a protein: simple estimates using FRET microscopy.

Flexible proteins are frequently used to link subunits of larger complexes in various contexts, for instance, in the construction of unimolecular sensors used in FRET microscopy, and fusion proteins. How flexible such linkers are can be an important question in the overall design of the complex, and yet sometimes suprisingly difficult to establish. Such difficulties can arise because the actual flexibility of a protein depends significantly on its interactions with the solvent, and when the local environment is a subcellular compartment, even the conditions of the solvent, may not be known. In this communication we propose a simple numerical procedure through which the flexibility of such proteins can be extracted from FRET based microscopy data.

Challenges facing an understanding of the nature of low-energy excited states in photosynthesis.

While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.

Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes.

An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation.

Semiclassical Path Integral Dynamics: Photosynthetic Energy Transfer with Realistic Environment Interactions.

This article reviews recent progress in the theoretical modeling of excitation energy transfer (EET) processes in natural light harvesting complexes. The iterative partial linearized density matrix path-integral propagation approach, which involves both forward and backward propagation of electronic degrees of freedom together with a linearized, short-time approximation for the nuclear degrees of freedom, provides an accurate and efficient way to model the nonadiabatic quantum dynamics at the heart of these EET processes. Combined with a recently developed chromophore-protein interaction model that incorporates both accurate ab initio descriptions of intracomplex vibrations and chromophore-protein interactions treated with atomistic detail, these simulation tools are beginning to unravel the detailed EET pathways and relaxation dynamics in light harvesting complexes.

Transport properties of pristine few-layer black phosphorus by van der Waals passivation in an inert atmosphere.

Ultrathin black phosphorus is a two-dimensional semiconductor with a sizeable band gap. Its excellent electronic properties make it attractive for applications in transistor, logic and optoelectronic devices. However, it is also the first widely investigated two-dimensional material to undergo degradation upon exposure to ambient air. Therefore a passivation method is required to study the intrinsic material properties, understand how oxidation affects the physical properties and enable applications of phosphorene. Here we demonstrate that atomically thin graphene and hexagonal boron nitride can be used for passivation of ultrathin black phosphorus. We report that few-layer pristine black phosphorus channels passivated in an inert gas environment, without any prior exposure to air, exhibit greatly improved n-type charge transport resulting in symmetric electron and hole transconductance characteristics.