Quantum biology revisited

Correlated Lattice Fluctuations in CsPbBr3 Quantum Dots Give Rise to Long-Lived Electronic Coherence

Electronic coherence is central to numerous areas of science, from quantum biology to quantum materials. In quantum materials, lead-halide perovskite (LHP) quantum dots (QDs) have been shown to support electronic coherence through observation of coherent single-photon emission and superfluorescence arising from spatial coherence at low temperatures. In contrast, direct measurement of temporal coherence between exciton states has been lacking. Here, we employ coherent multi-dimensional spectroscopy to observe an electronic coherence between exciton states in CsPbBr3 QDs that is long-lived at room temperature, surviving nearly three times longer than the electronic dephasing time. This observation of a long-lived electronic coherence at room temperature points to nearly perfectly correlated lattice fluctuations for each excitonic state in the superposition. These experiments reveal that the properties of LHP QDs extend to lattice dynamics that give rise to correlated fluctuations in the basis exciton states, a process that may next be optimized by design.

Machine Learning for Video Classification Enables Quantifying Intermolecular Couplings from Simulated Time-Evolved Multidimensional Spectra

Signals in two-dimensional electronic spectroscopy (2DES) encode information about electronic, vibrational, and vibronic couplings in molecular structures. However, chemical information is often difficult to extract. Here, we use a (2+1)-dimensional convolutional neural network ((2+1)D-CNN) to map simulated 2DES spectra to their underlying electronic couplings. The (2+1)D-CNN approach, in contrast to lower-dimensional network architectures, can access all of the time and frequency dimensions in the 2DES signal. We find that the (2+1)D-CNN algorithm classifies regimes of Coulombic couplings in dimers with a 10-fold cross-validation accuracy of (96.2 ± 1.0)%. By examining the optimized filters within the CNN, we find that the (2+1)D-CNN learns from frequency-domain peaks in 2DES spectra and their time evolution (including quantum beating). We also generate and analyze class-activation maps (CAMs) to reveal which features of the spectroscopic data are most important for the (2+1)D-CNN classifications. These studies provide an ML approach to address inverse problems in multidimensional spectroscopy and provide strategies to better understand how chemical information is encoded in spectroscopic data.

Distinguishing packing configurations of molecular dimers using excited-state absorption peaks in two-dimensional electronic spectra

Packing conformations of molecular aggregates are known to strongly influence the locations and intensities of spectral peaks. Here, we develop the third-order nonlinear spectroscopy signals for a purely electronic model of a molecular dimer, which is a prototype aggregate system. The model-which focuses on excited-state absorption (ESA) pathways in two-dimensional electronic spectra-reveals that orientational averaging leads to diagnostic ESA peak locations for H- and J-dimers. We constructed DNA-templated dimers of cyanine molecules as representative systems and used ultrabroadband two-dimensional electronic spectroscopy measurements to support the predicted signatures arising from the theoretical model. Fitting of steady-state spectra supports the assigned packing conformations. The results elucidate how ESA peaks can be diagnostic spectral signatures of packing conformation. This work lays the foundation for future studies that can include the complicating effects of vibronic states and additional electronic levels.

Nuclear quantum effects explain chemiosmosis: The power of the proton

ATP is a universal bio-currency, with chemiosmosis the metabolic mint by which currency is printed. Chemiosmosis leverages a membrane potential and ion gradient, typically a proton gradient, to generate ATP. The current chemiosmotic hypothesis is both cannon and dogma. However, there are obstacles to the unqualified and uncritical acceptance of this model. Intriguingly the proton is sufficiently small to exhibit quantum phenomena of wave-particle duality, often thought the exclusive prerogative of smaller subcellular particles. Evidence shows that chemiosmosis is by necessity critically dependent upon these nuclear quantum effects (NQE) of hydrogen, most notably as a proton. It is well established scientific orthodoxy that protons in water and hydrogen atoms of water molecules exhibit quantum phenomena. The effect is amplified by the hydrogen bonding and juxta-membrane location of protons in mitochondria and chloroplasts. NQE explains the otherwise inexplicable features of chemiosmosis, including the paucity of protons, the rate of proton movement and ATP genesis in otherwise subliminal proton motive forces and thus functionality of alkaliphiles. It also accounts for the efficiencies of chemiosmosis reported at greater than 100% in certain contexts, which violates the second law of thermodynamics under the paradigm of classical physics. Mitochondria may have evolved to exploit quantum biology with notable features such as dimeric ATP synthases adumbrating the first double-slip experiment with the protons. The dramatic global deceleration of mitochondrial chemiosmosis and all cellular function following proton substitution with its heavier isotopes, deuterium and tritium: "deuteruction", is testimony to the primacy of nuclear quantum effects in this Quantum Chemiosmosis. Indeed the speed of evolution itself and its inexorable route to homeothermy may be due to the power of nuclear quantum effects of the smallest nucleus, the proton. The atom that is almost nothing was selected to bring about the most important processes and complex manifestations of life.

Nonadiabatic Field: A Conceptually Novel Approach for Nonadiabatic Quantum Molecular Dynamics

Reliable trajectory-based nonadiabatic quantum dynamics methods at the atomic/molecular level are critical for the practical understanding and rational design of many important processes in real large/complex systems, where the quantum dynamical behavior of electrons and that of nuclei are coupled. The paper reports latest progress of nonadiabatic field (NaF), a conceptually novel approach for nonadiabatic quantum dynamics with independent trajectories. Substantially different from the mainstreams of Ehrenfest-like dynamics and surface hopping methods, the nuclear force in NaF involves the nonadiabatic force arising from the nonadiabatic coupling between different electronic states, in addition to the adiabatic force contributed by a single adiabatic electronic state. NaF is capable of faithfully describing the interplay between electronic and nuclear motion in a broad regime, which covers where the relevant electronic states keep coupled in a wide range or all the time and where the bifurcation characteristic of nuclear motion is essential. NaF is derived from the exact generalized phase space formulation with coordinate-momentum variables, where constraint phase space (CPS) is employed for discrete electronic-state degrees of freedom (DOFs) and infinite Wigner phase space is used for continuous nuclear DOFs. We propose efficient integrators for the equations of motion of NaF in both adiabatic and diabatic representations. Since the formalism in the CPS formulation is not unique, NaF can in principle be implemented with various phase space representations of the time correlation function (TCF) for the time-dependent property. They are applied to a suite of representative gas-phase and condensed-phase benchmark models where numerically exact results are available for comparison. It is shown that NaF is relatively insensitive to the phase space representation of the electronic TCF and will be a potential tool for practical and reliable simulations of the quantum mechanical behavior of both electronic and nuclear dynamics of nonadiabatic transition processes in real systems.

Ultrafast Dynamics in Flavocytochrome C by Using Transient Absorption and Femtosecond Fluorescence Lifetime Spectroscopy

Flavocytochrome c sulfide dehydrogenase (FCC) is an important enzyme of sulfur metabolism in sulfur-oxidizing bacteria, and its catalytic properties have been extensively studied. However, the ultrafast dynamics of FCC is not well understood. We present ultrafast transient absorption and fluorescence spectroscopy measurements to unravel the early events upon excitation of the heme and flavin chromophores embedded in the flavocytochrome c (FccAB) from the bacterium Thiocapsa roseopersicina. The fluorescence kinetics of FccAB suggests that the majority of the photoexcited species decay nonradiatively within the first few picoseconds. Transient absorption spectroscopy supports these findings by suggesting two major dynamic processes in FccAB, internal conversion occurring in about 400 fs and the vibrational cooling occurring in about 4 ps, mostly affecting the heme moiety.

High-Frequency Tails in Spectral Densities

Recent advances in numerically exact quantum dynamics methods have brought the dream of accurately modeling the dynamics of chemically complex open systems within reach. Path-integral-based methods, hierarchical equations of motion, and quantum analog simulators all require the spectral density (SD) of the environment to describe its effect on the system. Here, we focus on the decoherence dynamics of electronically excited species in solution in the common case where nonradiative electronic relaxation dominates and is much slower than electronic dephasing. We show that the computed relaxation rate is highly sensitive to the choice of SD representation─such as the Drude-Lorentz or Brownian modes─or strategy used to capture the main SD features, even when early-time dephasing dynamics remains robust. The key reason is that electronic relaxation is dominated by the resonant contribution from the high-frequency tails of the SD, which are orders of magnitude weaker than the main features of the SD and can vary significantly between strategies. This finding highlights an important, yet overlooked, numerical challenge: obtaining an accurate SD requires capturing its structure over several orders of magnitude to ensure correct decoherence dynamics at both early and late times. To address this, we provide a simple transformation that recovers the correct relaxation rates in quantum simulations constrained by algorithmic or physical limitations on the shape of the SD. Our findings enable a comparison of different numerically exact simulation methods and expand the capabilities of analog simulations of open quantum dynamics.

Dependence of energy relaxation and vibrational coherence on the location of light-harvesting chromoproteins in photosynthetic antenna protein complexes

Phycobilisomes are antenna protein complexes in cyanobacteria and red algae. In phycobilisomes, energy transfer is unidirectional with an extremely high quantum efficiency close to unity. We investigate intraprotein energy relaxation and quantum coherence of constituent chromoproteins of allophycocyanin (APC) and two kinds of C-phycocyanin (CPC) in phycobilisomes using two-dimensional electronic spectroscopy. These chromoproteins produced by an Escherichia coli expression system have similar adjacent pairs of pigments α84 and β84, which are excited to delocalized exciton states. However, the kinetics and coherence of exciton states are significantly different from each other. Even CPCs with almost the same molecular structure display different 2D spectra when the locations in the phycobilisome are different. The spectra of the inner CPC in the phycobilisome are red-shifted relative to that of the outer one. This may promote the efficient and unidirectional energy transfer to the APC core. We observe low-frequency coherent vibrational motion of ∼200 cm-1 with large amplitude and a decay time of 200 fs. The wave packet motion involving energy relaxation and oscillatory motions on the potential energy surface of the exciton state is clearly visualized using beat-frequency-resolved 2D-ES.

Exciton Transfer Simulations in a Light-Harvesting 2 Complex Reveal the Transient Delocalization Mechanism

The striking efficiency of exciton transfer in light-harvesting (LH) complexes has remained a topic of debate since the revision of the long-held role of electronic coherences. To address this issue, we have developed a neural network for the pigments in the LH2 complex of Rhodospirillum molischianum that allows nonadiabatic molecular dynamic (NAMD) simulations of exciton transfer in a coupled quantum mechanical/molecular mechanics (QM/MM) embedding. The calculated exciton occupations are averaged over hundreds of trajectories, each lasting several picoseconds. We have obtained transitions within the B800 and B850 rings that agree well with the experimental results, indicating an incoherent hopping process in the B800 ring and a more delocalized transfer in the B850 subsystem. The reorganization energies and excitonic couplings are comparable to each other, indicating that the "transient delocalization" transport model is the underlying cause of the highly efficient exciton transport in the B850 ring. This phenomenon can be attributed to a localized exciton that shows occasional large delocalization events. Our results indicate that the reason for the striking efficiency is the unusual electronic property of bacteriochlorophyll, manifested in minimal inner and outer sphere reorganization energies.

Bioelectrical synchronization of Picea abies during a solar eclipse

Regular light-dark cycles greatly affect organisms, and events like eclipses induce distinctive physiological and behavioural shifts. While well documented in animals, plant behaviour during eclipses remains largely unexplored. Here, we monitored multiple spruce trees to assess their individual and collective bioelectrical responses to a solar eclipse. Trees anticipated the eclipse, synchronizing their bioelectrical behaviour hours in advance. Older trees displayed greater anticipatory behaviour with early time-asymmetry and entropy increases. These results reveal a relationship between trees, shaped by individual age and physiology as well as collective history. This highlights the significance of synchrony in plants, offering new insights into coordinated behaviours in nature.

Quantum life science: biological nano quantum sensors, quantum technology-based hyperpolarized MRI/NMR, quantum biology, and quantum biotechnology

The emerging field of quantum life science combines principles from quantum physics and biology to study fundamental life processes at the molecular level. Quantum mechanics, which describes the properties of small particles, can help explain how quantum phenomena such as tunnelling, superposition, and entanglement may play a role in biological systems. However, capturing these effects in living systems is a formidable challenge, as it involves dealing with dissipation and decoherence caused by the surrounding environment. We overview the current status of the quantum life sciences from technologies and topics in quantum biology. Technologies such as biological nano quantum sensors, quantum technology-based hyperpolarized MRI/NMR, high-speed 2D electronic spectrometers, and computer simulations are being developed to address these challenges. These interdisciplinary fields have the potential to revolutionize our understanding of living organisms and lead to advancements in genetics, molecular biology, medicine, and bioengineering.

Diffractive Imaging of Transient Electronic Coherences in Molecules with Electron Vortices

Direct imaging of transient electronic coherences in molecules has been challenging, with the potential to control electron motions and influence reaction outcomes. We propose a novel time-resolved vortex electron diffraction technique to spatially resolve transient electronic coherences in isolated molecules. By analyzing helical dichroism diffraction signals, the contribution of electronic populations cancels out, isolating the purely electronic coherence signals. This allows direct monitoring of the time evolution and decoherence of transient electronic coherences in molecules.

Internal State Cooling of an Atom with Thermal Light

A near-minimal instance of optical cooling is experimentally presented, wherein the internal-state entropy of a single atom is reduced more than twofold by illuminating it with broadband, incoherent light. Since the rate of optical pumping by a thermal state increases monotonically with its temperature, the cooling power in this scenario increases with higher thermal occupation, an example of a phenomenon known as cooling by heating. In contrast to optical pumping using coherent, narrow-band laser light, here, we perform the same task with fiber-coupled, broadband sunlight, the brightest laboratory-accessible source of continuous blackbody radiation.

Investigation of quantum trajectories in photosynthetic light harvesting through a quantum stochastic approach

In natural photosynthesis systems, pigment-protein complexes harvest the photon from sunlight with near-unity quantum efficiency. These complexes show incredible properties that cannot be merely extrapolated from knowledge of their composition. Additionally, the environment perturbing the light-harvesting process significantly affects the mechanism of photosynthesis. This research investigates the photosystem II reaction center (PSII RC) from a new perspective which considers the restricted path of the exciton transfer, in the photosynthesis system, as a quantum trajectory picture with the quantum continuous measurement. In this work, the corridor path of exciton transfer dynamics satisfies the equation of motion, as the spin dynamics, which consists of precession, relaxation, and random force rapidly fluctuating spin splitting arising from the bath. Moreover, the width of the corridor is an important factor for restricting path dynamics resulting in the localization and decoherence phenomenon. Our method is to analyze exciton transfer dynamics through paths on the Bloch sphere, in order to investigate the propagating states in accordance with the weight functional which depends on the coupling parameter between the system and environment as the phonon bath. Our results show that the paths outside the width of the corridor have a considerably lower weight functional and decoherence functional than those inside the width. Therefore, the degrees of localization, the weight functional, and the decoherence functional are related. Furthermore, the simulation reveals three characteristics of exciton transfer: gradual transfer, no transfer, and rapid transfer, relying significantly on the coupling between the system and phonons.

Electronic-vibrational resonance damping time-dependent photosynthetic energy transfer acceleration revealed by 2D electronic spectroscopy

The effects of damping time of electronic-vibrational resonance modes on energy transfer in photosynthetic light-harvesting systems are examined. Using the hierarchical equations of motion (HEOM) method, we simulate the linear absorption and two-dimensional electronic spectra (2DES) for a dimer model based on bottleneck sites in the light-harvesting complex of photosystem II. A site-dependent spectral density is incorporated, with only the low-energy site being coupled to the resonance mode. Similar patterns are observed in linear absorption spectra and early time 2DES for various damping times, owing to the weak coupling strength. However, notable differences emerge in the dynamics of the high-energy diagonal and cross-peaks in the 2DES. It is found that the coupling of electronic-vibrational resonance modes accelerates the energy transfer process, with rates being increased as the damping time is extended, but the impact becomes negligible when the damping time exceeds a certain threshold. To evaluate the reliability of the perturbation method, the modified Redfield (MR) method is employed to simulate 2DES under the same conditions. The results from the MR method are aligned with those obtained from the HEOM method, but the MR method predicts faster dynamics.

Improved Description of Environment and Vibronic Effects with Electrostatically Embedded ML Potentials

Incorporation of environment and vibronic effects in simulations of optical spectra and excited state dynamics is commonly done by combining molecular dynamics with excited state calculations, which allows to estimate the spectral density describing the frequency-dependent system-bath coupling strength. The need for efficient sampling, however, usually leads to the adoption of classical force fields despite well-known inaccuracies due to the mismatch with the excited state method. Here, we present a multiscale strategy that overcomes this limitation by combining EMLE simulations based on electrostatically embedded ML potentials with the QM/MMPol polarizable embedding model to compute the excited states and spectral density of 3-methyl-indole, the chromophoric moiety of tryptophan that mediates a variety of important biological functions, in the gas phase, in water solution, and in the human serum albumin protein. Our protocol provides highly accurate results that faithfully reproduce their ab initio QM/MM counterparts, thus paving the way for accurate investigations on the interrelation between the time scales of biological motion and the photophysics of tryptophan and other biosystems.

NSF NeXUS: A New Model for Accessing the Frontiers of Ultrafast Science

NSF NeXUS is an open-access user facility that enables observation of electron motion with sub-femtosecond time resolution, angstrom spatial resolution, and element-specific spectral resolution.

Diverse Transient Chiral Dynamics in Evolutionary Distinct Photosynthetic Reaction Centers

The evolution of photosynthetic reaction centers (RCs) from anoxygenic bacteria to higher-order oxygenic cynobacteria and plants highlights a remarkable journey of structural and functional diversification as an adaptation to environmental conditions. The role of chirality in these centers is important, influencing the arrangement and function of key molecules involved in photosynthesis. Investigating the role of chirality may provide a deeper understanding of photosynthesis and the evolutionary history of life on Earth. In this study, we explore chirality-related energy transfer in two evolutionarily distinct RCs: one from the anoxygenic purple sulfur bacterium Thermochromatium tepidum (BRC) and the other from the oxygenic cyanobacterium Thermosynechococcus vulcanus (PSII RC), utilizing two-dimensional electronic spectroscopy (2DES). By employing circularly polarized laser pulses, we can extract transient chiral dynamics within these RCs, offering a detailed view of their chiral contribution to energy transfer processes. We also compute traditional 2DES and compare these results with spectra related to circular dichroism. Our findings indicate that two-dimensional circular dichroism spectroscopy effectively reveals chiral dynamics, emphasizing the structural symmetries of pigments and their interactions with associated proteins. Despite having similar pigment-protein architectures, the BRC and PSII RC exhibit significantly different chiral dynamics on an ultrafast time scale. In the BRC, the complex contributions of pigments such as BChM, BPhL, BCh, and PM to key excitonic states lead to more pronounced chiral features and dynamic behavior. In contrast, the PSII RC, although significantly influenced by ChlD1 and ChlD2, shows less complex chiral effects and more subdued chiral dynamics. Notably, the PSII RC demonstrates a faster decay of coherence to localized excitonic populations compared to the BRC, which may represent an adaptive mechanism to minimize oxidative stress in oxygenic photosystems. By examining and comparing the chiral excitonic interactions and dynamics of BRC and PSII RC, this study offers valuable insights into the mechanisms of photosynthetic complexes. These findings could contribute to understanding how the functional optimization of photosynthetic proteins in ultrafast time scales is linked to biological evolution.

Application of the Time-Domain Multichromophoric Fluorescence Resonant Energy Transfer Method in the NISE Programme

We present the implementation of the time-domain multichromophoric fluorescence resonant energy transfer (TC-MCFRET) approach in the numerical integration of the Schrödinger equation (NISE) program. This method enables the efficient simulation of incoherent energy transfer between distinct segments within large and complex molecular systems, such as photosynthetic complexes. Our approach incorporates a segmentation protocol to divide these systems into manageable components and a modified thermal correction to ensure detailed balance. The implementation allows us to calculate the energy transfer rate in the NISE program systematically and easily. To validate our method, we applied it to a range of test cases, including parallel linear aggregates and biologically relevant systems like the B850 rings from LH2 and the Fenna-Matthews-Olson complex. Our results show excellent agreement with previous studies, demonstrating the accuracy and efficiency of our TD-MCFRET method. We anticipate that this approach will be widely applicable to the calculation of energy transfer rates in other large molecular systems and will pave the way for future simulations of multidimensional electronic spectra.

Systematic study of the role of dissipative environment in regulating entanglement and exciton delocalization in the Fenna-Matthews-Olson complex

In this article, we perform a systematic study of the global entanglement and exciton coherence length dynamics in natural light-harvesting system Fenna-Matthews-Olson (FMO) complex across various parameters of a dissipative environment from low to high temperatures, weak to strong system-environment coupling, and non-Markovian environments. A nonperturbative numerically exact hierarchical equations of motions method is employed to obtain the dynamics of the system. We found that entanglement is driven primarily by the strength of interaction between the system and environment, and it is modulated by the interplay between temperature and non-Markovianity. In contrast, coherence length is found to be insensitive to non-Markovianity. In agreement with previous studies, we do not observe a direct correlation between global entanglement and the efficiency of the excitation energy transfer in the FMO complex. As a new result, we found that the coherence length dynamics is correlated with the excitation energy transfer dynamics.

Tunneling Times in an Asymmetric Harmonic Double-Well with Application to Electron Transfers in Biological Macromolecules

Tunneling times were calculated in electron transfer processes using an asymmetric harmonic double-well model. The simplicity of a direct variational calculation in the approximate solution of the Schrödinger equation, along with the interpretation of tunneling times within the probabilistic framework of a two-level system, allows for the efficient and accurate determination of tunneling times with minimal computational cost. These calculations were applied to electron transfer processes in the study of the photosynthetic reaction center and in the context of catalysis in UV-induced DNA lesion repair and are in agreement with the experimental, computational, and theoretical results with which they were compared. It was seen that the donor-acceptor distance needed to be adjusted for closer agreement between the calculated and experimentally observed times. However, the adjusted values for this distance remain close to those reported in the literature.

Intramolecular charge transfer and the function of vibronic excitons in photosynthetic light harvesting

A widely discussed explanation for the prevalence of pairs or clusters of closely spaced electronic chromophores in photosynthetic light-harvesting proteins is the presence of ultrafast and highly directional excitation energy transfer pathways mediated by vibronic excitons, the delocalized optical excitations derived from mixing of the electronic and vibrational states of the chromophores. We discuss herein the hypothesis that internal conversion processes between exciton states on the <100 fs timescale are possible when the excitonic potential energy surfaces are controlled by the vibrational modes that induce charge transfer character in a strongly coupled system of chromophores. We discuss two examples, the peridinin-chlorophyll protein from marine dinoflagellates and the intact phycobilisome from cyanobacteria, in which the intramolecular charge-transfer (ICT) character arising from out-of-plane distortion of the conjugation of carotenoid or bilin chromophores also results in localization of the initially delocalized optical excitation on the vibrational timescale. Tuning of the ground state conformations of the chromophores to manipulate their ICT character provides a natural photoregulatory mechanism, which would control the overall quantum yield of excitation energy transfer by turning on and off the delocalized character of the optical excitations.

Self-consistent approach to the dynamics of excitation energy transfer in multichromophoric systems

Computationally tractable and reliable, albeit approximate, methods for studying exciton transport in molecular aggregates immersed in structured bosonic environments have been actively developed. Going beyond the lowest-order (Born) approximation for the memory kernel of the quantum master equation typically results in complicated and possibly divergent expressions. Starting from the memory kernel in the Born approximation, and recognizing the quantum master equation as the Dyson equation of Green's functions theory, we formulate the self-consistent Born approximation to resum the memory-kernel perturbation series in powers of the exciton-environment interaction. Our formulation is in the Liouville space and frequency domain and handles arbitrary exciton-environment spectral densities. In a molecular dimer coupled to an overdamped oscillator environment, we conclude that the self-consistent cycle significantly improves the Born-approximation energy-transfer dynamics. The dynamics in the self-consistent Born approximation agree well with the solutions of hierarchical equations of motion over a wide range of parameters, including the most challenging regimes of strong exciton-environment interactions, slow environments, and low temperatures. This is rationalized by the analytical considerations of coherence-dephasing dynamics in the pure-dephasing model. We find that the self-consistent Born approximation is good (poor) at describing energy transfer modulated by an underdamped vibration resonant (off-resonant) with the exciton energy gap. Nevertheless, it reasonably describes exciton dynamics in the seven-site model of the Fenna-Matthews-Olson complex in a realistic environment comprising both an overdamped continuum and underdamped vibrations.

Electronic dynamics created at conical intersections and its dephasing in aqueous solution

A dynamical rearrangement in the electronic structure of a molecule can be driven by different phenomena, including nuclear motion, electronic coherence or electron correlation. Recording such electronic dynamics and identifying its fate in an aqueous solution has remained a challenge. Here, we reveal the electronic dynamics induced by electronic relaxation through conical intersections in both isolated and solvated pyrazine molecules using X-ray spectroscopy. We show that the ensuing created dynamics corresponds to a cyclic rearrangement of the electronic structure around the aromatic ring. Furthermore, we found that such electronic dynamics were entirely suppressed when pyrazine was dissolved in water. Our observations confirm that conical intersections can create electronic dynamics that are not directly excited by the pump pulse and that aqueous solvation can dephase them in less than 40 fs. These results have implications for the investigation of electronic dynamics created during light-induced molecular dynamics and shed light on their susceptibility to aqueous solvation.

Coherence in Chemistry: Foundations and Frontiers

Coherence refers to correlations in waves. Because matter has a wave-particle nature, it is unsurprising that coherence has deep connections with the most contemporary issues in chemistry research (e.g., energy harvesting, femtosecond spectroscopy, molecular qubits and more). But what does the word "coherence" really mean in the context of molecules and other quantum systems? We provide a review of key concepts, definitions, and methodologies, surrounding coherence phenomena in chemistry, and we describe how the terms "coherence" and "quantum coherence" refer to many different phenomena in chemistry. Moreover, we show how these notions are related to the concept of an interference pattern. Coherence phenomena are indeed complex, and ambiguous definitions may spawn confusion. By describing the many definitions and contexts for coherence in the molecular sciences, we aim to enhance understanding and communication in this broad and active area of chemistry.

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies - two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy - and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

Fluorescence-Detected Two-Dimensional Electronic Spectroscopy of a Single Molecule

Single-molecule fluorescence spectroscopy is a powerful method that avoids ensemble averaging, but its temporal resolution is limited by the fluorescence lifetime to nanoseconds at most. At the ensemble level, two-dimensional spectroscopy provides insight into ultrafast femtosecond processes, such as energy transfer and line broadening, even beyond the Fourier limit, by correlating pump and probe spectra. Here, we combine these two techniques and demonstrate coherent 2D spectroscopy of individual dibenzoterrylene (DBT) molecules at room temperature. We excite the molecule in a confocal microscope with a phase-modulated train of femtosecond pulses and detect the emitted fluorescence with single-photon counting detectors. Using a phase-sensitive detection scheme, we were able to measure the nonlinear 2D spectra of most of the DBT molecules that we studied. Our method is applicable to a wide range of single emitters and opens new avenues for understanding energy transfer in single quantum objects on ultrafast time scales.

OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors

Non-Markovian dynamics arising from the strong coupling of a system to a structured environment is essential in many applications of quantum mechanics and emerging technologies. Deriving an accurate description of general quantum dynamics including memory effects is, however, a demanding task, prohibitive to standard analytical or direct numerical approaches. We present a major release of our open source software package, OQuPy (Open Quantum System in Python), which provides several recently developed numerical methods that address this challenging task. It utilizes the process tensor approach to open quantum systems (OQS) in which a single map, the process tensor, captures all possible effects of an environment on the system. The representation of the process tensor in a tensor network form allows for an exact yet highly efficient description of non-Markovian OQS (NM-OQS). The OQuPy package provides methods to (1) compute the dynamics and multi-time correlations of quantum systems coupled to single and multiple environments, (2) optimize control protocols for NM-OQS, (3) simulate interacting chains of NM-OQS, and (4) compute the mean-field dynamics of an ensemble of NM-OQS coupled to a common central system. Our aim is to provide an easily accessible and extensible tool for researchers of OQS in fields such as quantum chemistry, quantum sensing, and quantum information.

Pushing the limits of ultrafast diffraction: Imaging quantum coherences in isolated molecules

Quantum coherence governs the outcome and efficiency of photochemical reactions and ultrafast molecular dynamics. Recent ultrafast gas-phase X-ray scattering and electron diffraction have enabled the observation of femtosecond nuclear dynamics driven by vibrational coherence. However, probing attosecond electron dynamics and coupled electron-nuclear dynamics remains challenging. This article discusses advances in ultrafast X-ray scattering and electron diffraction, highlighting their potential to resolve attosecond charge migration and vibronic coupling at conical intersections. Novel techniques, such as X-ray scattering with orbital angular momentum beams and combined X-ray and electron diffraction, promise to selectively probe coherence contributions and visualize charge migration in real-space. These emerging methods could further our understanding of coherence effects in chemical reactions.

Semiclassical dynamics in Wigner phase space II: Nonadiabatic hybrid Wigner dynamics

We present an approximate semiclassical (SC) framework for mixed quantized dynamics in Wigner phase space in a two-part series. In the first article, we introduced the Adiabatic Hybrid Wigner Dynamics (AHWD) method that allows for a few important "system" degrees of freedom to be quantized using high-level double Herman-Kluk SC theory while describing the rest (the "bath") using classical-limit linearized SC theory. In this second article, we extend our hybrid Wigner dynamics to nonadiabatic processes. The resulting Nonadiabatic Hybrid Wigner Dynamics (NHWD) has two variants that differ in the choice of degrees of freedom to be quantized. Specifically, we introduce NHWD(E) where only the electronic state variables are quantized and the NHWD(V) where both electronic state variables and a handful of strongly coupled nuclear modes are quantized. We show that while NHWD(E) proves accurate for a wide range of scattering models and spin-boson models, systems where a few nuclear modes are strongly coupled to electronic states require NHWD(V) to accurately capture the long-time dynamics. Taken together, we show that AHWD and NHWD represent a new framework for SC simulations of high-dimensional systems with significant quantum effects.

Photoelectrochemical Two-Dimensional Electronic Spectroscopy (PEC2DES) of Photosystem I: Charge Separation Dynamics Hidden in a Multichromophoric Landscape

We present a nonlinear spectroelectrochemical technique to investigate photosynthetic protein complexes. The PEC2DES setup combines photoelectrochemical detection (PEC) that selectively probes the protein photogenerated charges output with two-dimensional electronic spectroscopy (2DES) excitation that spreads the nonlinear optical response of the system in an excitation-detection map. PEC allows us to distinguish the contribution of charge separation (CS) from other de-excitation pathways, whereas 2DES allows us to disentangle congested spectral bands and evaluate the exciton dynamics (decays and coherences) of the photosystem complex. We have developed in operando phase-modulated 2DES by measuring the photoelectrochemical reaction rate in a biohybrid electrode functionalized with a plant photosystem complex I-light harvesting complex I (PSI-LHCI) layer. Optimizing the photoelectrochemical current signal yields reliable linear spectra unequivocally associated with PSI-LHCI. The 2DES signal is validated by nonlinear features like the characteristic vibrational coherence at 750 cm-1. However, no energy transfer dynamics is observed within the 450 fs experimental window. These intriguing results are discussed in the context of incoherent mixing resulting in reduced nonlinear contrast for multichromophoric complexes, such as the 160 chlorophyll PSI. The presented PEC2DES method identifies generated charges unlike purely optical 2DES and opens the way to probe the CS channel in multichromophoric complexes.

Distinct vibrational motions promote disparate excited-state decay pathways in cofacial perylenediimide dimers

A complex interplay of structural, electronic, and vibrational degrees of freedom underpins the fate of molecular excited states. Organic assemblies exhibit a myriad of excited-state decay processes, such as symmetry-breaking charge separation (SB-CS), excimer (EX) formation, singlet fission, and energy transfer. Recent studies of cofacial and slip-stacked perylene-3,4:9,10-bis(dicarboximide) (PDI) multimers demonstrate that slight variations in core substituents and H- or J-type aggregation can determine whether the system follows an SB-CS pathway or an EX one. However, questions regarding the relative importance of structural properties and molecular vibrations in driving the excited-state dynamics remain. Here, we use a combination of two-dimensional electronic spectroscopy, femtosecond stimulated Raman spectroscopy, and quantum chemistry computations to compare the photophysics of two PDI dimers. The dimer with 1,7-bis(pyrrolidin-1'-yl) substituents (5PDI2) undergoes ultrafast SB-CS from a photoexcited mixed state, while the dimer with bis-1,7-(3',5'-di-t-butylphenoxy) substituents (PPDI2) rapidly forms an EX state. Examination of their quantum beating features reveals that SB-CS in 5PDI2 is driven by the collective vibronic coupling of two or more excited-state vibrations. In contrast, we observe signatures of low-frequency vibrational coherence transfer during EX formation by PPDI2, which aligns with several previous studies. We conclude that key electronic and structural differences between 5PDI2 and PPDI2 determine their markedly different photophysics.

TD-DMRG Study of Exciton Dynamics with both Thermal and Static Disorders for Fenna-Matthews-Olson Complex

Photosynthesis is a fundamental process that converts solar energy into chemical energy. Understanding the microscopic mechanisms of energy transfer in photosynthetic systems is crucial for the development of novel optoelectronic materials. Simulating these processes poses significant challenges due to the intricate interactions between electrons and phonons, compounded by static disorder. In this work, we present a numerically nearly exact study using the time-dependent density matrix renormalization group (TD-DMRG) method to simulate the quantum dynamics of the Fenna-Matthews-Olson (FMO) complex considering an eight-site model with both thermal and static disorders. We employ the thermo-field dynamics formalism for temperature effects. We merge all electronic interactions into one large matrix product state (MPS) site, boosting accuracy efficiently without increasing complexity. Previous combined experimental and computational studies indicated that the static disorders range from 30 to 90 cm-1 for different FMO sites. We employ a Gaussian distribution and the auxiliary bosonic operator approach to consider the static disorder in our TD-DMRG algorithm. We investigate the impact of different initial excitation sites, temperatures, and degrees of static disorder on the exciton dynamics and temporal coherence. It is found that under the influence of the experimentally determined static disorder strength, the exciton population evolution shows a non-negligible difference at zero temperature, while it is hardly affected at room temperature.

Frequency-Dependent Vibronic Effects in Steady State Energy Transport

The interplay between electronic and intramolecular high-frequency vibrational degrees of freedom is ubiquitous in natural light-harvesting systems. Recent studies have indicated that an intramolecular vibrational donor-acceptor frequency difference can enhance energy transport. Here, we analyze the extent to which different intramolecular donor-acceptor vibrational frequencies affect excitation energy transport in the natural nonequilibrium steady state configuration. Comments are included on the less physical equilibrium case for comparison with the literature. It is found that for constant Huang-Rhys factors, whereas the acceptor population increases in the equilibrium case when the intramolecular vibrational frequency of the acceptor exceeds that of the donor, this increase is negligible for the nonequilibrium steady state. Therefore, these changes in acceptor population do not significantly enhance energy transport in the nonequilibrium steady state for the natural scenario of incoherent light excitation with biologically relevant parameters of typical photosynthetic complexes. Insight about a potential mechanism to optimize energy transfer in the nonequilibrium steady state based on increasing the harvesting time at the reaction center is analyzed.

Persistence of Correlations in Neurotransmitter Transport through the Synaptic Cleft

The "quantum brain" proposal can revolutionize our understanding of cognition if proven valid. The core of the most common "quantum brain" mechanism is the appearance of correlated neuron triggering induced by quantum correlations between ions. In this work, we examine the preservation of the correlations created in the pre-synaptic neurons through the transfer of neurotransmitters across the synaptic cleft, a critical ingredient for the validity of the "quantum brain" hypothesis. We simulated the transport of two neurotransmitters at two different clefts, with the only assumption that they start simultaneously, and determined the difference in their first passage times. We show that in physiological conditions, the correlations are persistent even if the parameters of the two neurons are different.

Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna-Matthews-Olson complex

A trajectory surface hopping approach, which uses machine learning to speed up the most time-consuming steps, has been adopted to investigate the exciton transfer in light-harvesting systems. The present neural networks achieve high accuracy in predicting both Coulomb couplings and excitation energies. The latter are predicted taking into account the environment of the pigments. Direct simulation of exciton dynamics through light-harvesting complexes on significant time scales is usually challenging due to the coupled motion of nuclear and electronic degrees of freedom in these rather large systems containing several relatively large pigments. In the present approach, however, we are able to evaluate a statistically significant number of non-adiabatic molecular dynamics trajectories with respect to exciton delocalization and exciton paths. The formalism is applied to the Fenna-Matthews-Olson complex of green sulfur bacteria, which transfers energy from the light-harvesting chlorosome to the reaction center with astonishing efficiency. The system has been studied experimentally and theoretically for decades. In total, we were able to simulate non-adiabatically more than 30 ns, sampling also the relevant space of parameters within their uncertainty. Our simulations show that the driving force supplied by the energy landscape resulting from electrostatic tuning is sufficient to funnel the energy towards site 3, from where it can be transferred to the reaction center. However, the high efficiency of transfer within a picosecond timescale can be attributed to the rather unusual properties of the BChl a molecules, resulting in very low inner and outer-sphere reorganization energies, not matched by any other organic molecule, e.g., used in organic electronics. A comparison with electron and exciton transfer in organic materials is particularly illuminating, suggesting a mechanism to explain the comparably high transfer efficiency.

Memory effects in the efficiency control of energy transfer under incoherent light excitation in noisy environments

Fluctuations in energy gap and coupling constants between chromophores can play an important role in absorption and energy transfer across a collection of two-level systems. In photosynthesis, light-induced quantum coherence can affect the efficiency of energy transfer to the designated "trap" state. Theoretically, the interplay between fluctuations and coherence has been studied often, employing either a Markovian or a perturbative approximation. In this study, we depart from these approaches to incorporate memory effects by using Kubo's quantum stochastic Liouville equation. We introduce the effects of decay of the created excitation (to the ground state) on the desired propagation and trapping that provides a direction of flow of the excitation. In the presence of light-induced pumping, we establish a relation between the efficiency, the mean survival time, and the correlation decay time of the bath-induced fluctuations. A decrease in the steady-state coherence during the transition from the non-Markovian regime to the Markovian limit results in a decrease in efficiency. As in the well-known Haken-Strobl model, the ratio of the square of fluctuation strength to the rate plays a critical role in determining the mechanism of energy transfer and in shaping the characteristics of the efficiency profile. We recover a connection between the transfer flux and the imaginary part of coherences in both equilibrium and excited bath states, in both correlated and uncorrelated bath models. We uncover a non-monotonic dependence of efficiency on site energy heterogeneity for both correlated and uncorrelated bath models.

Transient Chiral Dynamics in the Fenna-Matthews-Olson Complex Revealed by Two-Dimensional Circular Dichroism Spectroscopy

Chirality plays a pivotal role across scientific disciplines with profound implications spanning light-matter interactions, molecular recognition, and natural evolutionary processes. This study delves into the active influence of molecular chirality on exciton energy transfer within photosynthetic protein complexes, focusing on the Fenna-Matthews-Olson (FMO) complex. Employing two-dimensional circular dichroism (2DCD) spectroscopy, we investigate the transient chiral dynamics of excitons during energy transfer processes within the FMO complex. Our approach, incorporating pulse information into population dynamics based on the third-order response function, facilitates the calculation of 2DCD spectra and dynamics. This enables the extraction of chiral contributions to excitonic energy transfer and the examination of electronic wave functions. We demonstrate that 2DCD spectra offer excitation energies that are better resolved than those from conventional two-dimensional electronic spectroscopy. These findings deepen our understanding of exciton energy transfer mechanisms in natural photosynthesis, emphasizing the potential of 2DCD spectroscopy as a powerful tool for unraveling the chiral contribution to exciton dynamics.

Nonadiabatic molecular dynamics with subsystem density functional theory: application to crystalline pentacene

In this work, we report the development and assessment of the nonadiabatic molecular dynamics approach with the electronic structure calculations based on the linearly scaling subsystem density functional method. The approach is implemented in an open-source embedded Quantum Espresso/Libra software specially designed for nonadiabatic dynamics simulations in extended systems. As proof of the applicability of this method to large condensed-matter systems, we examine the dynamics of nonradiative relaxation of excess excitation energy in pentacene crystals with the simulation supercells containing more than 600 atoms. We find that increased structural disorder observed in larger supercell models induces larger nonadiabatic couplings of electronic states and accelerates the relaxation dynamics of excited states. We conduct a comparative analysis of several quantum-classical trajectory surface hopping schemes, including two new methods proposed in this work (revised decoherence-induced surface hopping and instantaneous decoherence at frustrated hops). Most of the tested schemes suggest fast energy relaxation occurring with the timescales in the 0.7-2.0 ps range, but they significantly overestimate the ground state recovery rates. Only the modified simplified decay of mixing approach yields a notably slower relaxation timescales of 8-14 ps, with a significantly inhibited ground state recovery.

Exciton annihilation and diffusion length in disordered multichromophoric nanoparticles

Efficient exciton transport is the essential property of natural and synthetic light-harvesting (LH) devices. Here we investigate exciton transport properties in LH organic polymer nanoparticles (ONPs) of 40 nm diameter. The ONPs are loaded with a rhodamine B dye derivative and bulky counterion, enabling dye loadings as high as 0.3 M, while preserving fluorescence quantum yields larger than 30%. We use time-resolved fluorescence spectroscopy to monitor exciton-exciton annihilation (EEA) kinetics within the ONPs dispersed in water. We demonstrate that unlike the common practice for photoluminescence investigations of EEA, the non-uniform intensity profile of the excitation light pulse must be taken into account to analyse reliably intensity-dependent population dynamics. Alternatively, a simple confocal detection scheme is demonstrated, which enables (i) retrieving the correct value for the bimolecular EEA rate which would otherwise be underestimated by a typical factor of three, and (ii) revealing minor EEA by-products otherwise unnoticed. Considering the ONPs as homogeneous rigid solutions of weakly interacting dyes, we postulate an incoherent exciton hoping mechanism to infer a diffusion constant exceeding 0.003 cm2 s-1 and a diffusion length as large as 70 nm. This work demonstrates the success of the present ONP design strategy at engineering efficient exciton transport in disordered multichromophoric systems.

Probing the design principles of photosynthetic systems through fluorescence noise measurement

Elucidating the energetic processes which govern photosynthesis, the engine of life on earth, are an essential goal both for fundamental research and for cutting-edge biotechnological applications. Fluorescent signal of photosynthetic markers has long been utilised in this endeavour. In this research we demonstrate the use of fluorescent noise analysis to reveal further layers of intricacy in photosynthetic energy transfer. While noise is a common tool analysing dynamics in physics and engineering, its application in biology has thus far been limited. Here, a distinct behaviour in photosynthetic pigments across various chemical and biological environments is measured. These changes seem to elucidate quantum effects governing the generation of oxidative radicals. Although our method offers insights, it is important to note that the interpretation should be further validated expertly to support as conclusive theory. This innovative method is simple, non-invasive, and immediate, making it a promising tool to uncover further, more complex energetic events in photosynthesis, with potential uses in environmental monitoring, agriculture, and food-tech.

Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence

After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.

Protein Effects on the Excitation Energies and Exciton Dynamics of the CP24 Antenna Complex

In this study, the site energy fluctuations, energy transfer dynamics, and some spectroscopic properties of the minor light-harvesting complex CP24 in a membrane environment were determined. For this purpose, a 3 μs-long classical molecular dynamics simulation was performed for the CP24 complex. Furthermore, using the density functional tight binding/molecular mechanics molecular dynamics (DFTB/MM MD) approach, we performed excited state calculations for the chlorophyll a and chlorophyll b molecules in the complex starting from five different positions of the MD trajectory. During the extended simulations, we observed variations in the site energies of the different sets as a result of the fluctuating protein environment. In particular, a water coordination to Chl-b 608 occurred only after about 1 μs in the simulations, demonstrating dynamic changes in the environment of this pigment. From the classical and the DFTB/MM MD simulations, spectral densities and the (time-dependent) Hamiltonian of the complex were determined. Based on these results, three independent strongly coupled chlorophyll clusters were revealed within the complex. In addition, absorption and fluorescence spectra were determined together with the exciton relaxation dynamics, which reasonably well agrees with experimental time scales.

Bexcitonics: Quasiparticle approach to open quantum dynamics

We develop a quasiparticle approach to capture the dynamics of open quantum systems coupled to bosonic thermal baths of arbitrary complexity based on the Hierarchical Equations of Motion (HEOM). This is done by generalizing the HEOM dynamics and mapping it into that of the system in interaction with a few bosonic fictitious quasiparticles that we call bexcitons. Bexcitons arise from a decomposition of the bath correlation function into discrete features. Specifically, bexciton creation and annihilation couple the auxiliary density matrices in the HEOM. The approach provides a systematic strategy to construct exact quantum master equations that include the system-bath coupling to all orders even for non-Markovian environments. Specifically, by introducing different metrics and representations for the bexcitons it is possible to straightforwardly generate different variants of the HEOM, demonstrating that all these variants share a common underlying quasiparticle picture. Bexcitonic properties, while unphysical, offer a coarse-grained view of the correlated system-bath dynamics and its numerical convergence. For instance, we use it to analyze the instability of the HEOM when the bath is composed of underdamped oscillators and show that it leads to the creation of highly excited bexcitons. The bexcitonic picture can also be used to develop more efficient approaches to propagate the HEOM. As an example, we use the particle-like nature of the bexcitons to introduce mode-combination of bexcitons in both number and coordinate representation that uses the multi-configuration time-dependent Hartree to efficiently propagate the HEOM dynamics.

Theory of 2D electronic spectroscopy of water soluble chlorophyll-binding protein (WSCP): Signatures of Chl b derivate

We investigate how electronic excitations and subsequent dissipative dynamics in the water soluble chlorophyll-binding protein (WSCP) are connected to features in two-dimensional (2D) electronic spectra, thereby comparing results from our theoretical approach with experimental data from the literature. Our calculations rely on third-order response functions, which we derived from a second-order cumulant expansion of the dissipative dynamics involving the partial ordering prescription, assuming a fast vibrational relaxation in the potential energy surfaces of excitons. Depending on whether the WSCP complex containing a tetrameric arrangement of pigments composed of two dimers with weak excitonic coupling between them binds the chlorophyll variant Chl a or Chl b, the resulting linear absorption and circular dichroism spectra and particularly the 2D spectra exhibit substantial differences in line shapes. These differences between Chl a WSCP and Chl b WSCP cannot be explained by the slightly modified excitonic couplings within the two variants. In the case of Chl a WSCP, the assumption of equivalent dimer subunits facilitates a reproduction of substantial features from the experiment by the calculations. In contrast, for Chl b WSCP, we have to assume that the sample, in addition to Chl b dimers, contains a small but distinct fraction of chemically modified Chl b pigments. The existence of such Chl b derivates has been proposed by Pieper et al. [J. Phys. Chem. B 115, 4042 (2011)] based on low-temperature absorption and hole-burning spectroscopy. Here, we provide independent evidence.

Near-atomic-resolution structure of J-aggregated helical light-harvesting nanotubes

Cryo-electron microscopy has delivered a resolution revolution for biological self-assemblies, yet only a handful of structures have been solved for synthetic supramolecular materials. Particularly for chromophore supramolecular aggregates, high-resolution structures are necessary for understanding and modulating the long-range excitonic coupling. Here, we present a 3.3 Å structure of prototypical biomimetic light-harvesting nanotubes derived from an amphiphilic cyanine dye (C8S3-Cl). Helical 3D reconstruction directly visualizes the chromophore packing that controls the excitonic properties. Our structure clearly shows a brick layer arrangement, revising the previously hypothesized herringbone arrangement. Furthermore, we identify a new non-biological supramolecular motif-interlocking sulfonates-that may be responsible for the slip-stacked packing and J-aggregate nature of the light-harvesting nanotubes. This work shows how independently obtained native-state structures complement photophysical measurements and will enable accurate understanding of (excitonic) structure-function properties, informing materials design for light-harvesting chromophore aggregates.

Seeking a quantum advantage with trapped-ion quantum simulations of condensed-phase chemical dynamics

Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond the reach of current classical-digital simulation. To identify a 'quantum advantage' for these simulations, performance analysis of both analog-quantum simulation on noisy hardware and classical-digital algorithms is needed. In this Review, we make a comparison between a noisy analog trapped-ion simulator and a few choice classical-digital methods on simulating the dynamics of a model molecular Hamiltonian with linear vibronic coupling. We describe several simple Hamiltonians that are commonly used to model molecular systems, which can be simulated with existing or emerging trapped-ion hardware. These Hamiltonians may serve as stepping stones towards the use of trapped-ion simulators for systems beyond the reach of classical-digital methods. Finally, we identify dynamical regimes in which classical-digital simulations seem to have the weakest performance with respect to analog-quantum simulations. These regimes may provide the lowest hanging fruit to make the most of potential quantum advantages.

Theoretical model of femtosecond coherence spectroscopy of vibronic excitons in molecular aggregates

When used as pump pulses in transient absorption spectroscopy measurements, femtosecond laser pulses can produce oscillatory signals known as quantum beats. The quantum beats arise from coherent superpositions of the states of the sample and are best studied in the Fourier domain using Femtosecond Coherence Spectroscopy (FCS), which consists of one-dimensional amplitude and phase plots of a specified oscillation frequency as a function of the detection frequency. Prior works have shown ubiquitous amplitude nodes and π phase shifts in FCS from excited-state vibrational wavepackets in monomer samples. However, the FCS arising from vibronic-exciton states in molecular aggregates have not been studied theoretically. Here, we use a model of vibronic-exciton states in molecular dimers based on displaced harmonic oscillators to simulate FCS for dimers in two important cases. Simulations reveal distinct spectral signatures of excited-state vibronic-exciton coherences in molecular dimers that may be used to distinguish them from monomer vibrational coherences. A salient result is that, for certain relative orientations of the transition dipoles, the key resonance condition between the electronic coupling and the frequency of the vibrational mode may yield strong enhancement of the quantum-beat amplitude and, perhaps, also cause a significant decrease of the oscillation frequency to a value far lower than the vibrational frequency. Future studies using these results will lead to new insights into the excited-state coherences generated in photosynthetic pigment-protein complexes.

A Many-Body Perspective of Nuclear Quantum Effects in Aqueous Clusters

Nuclear quantum effects play an important role in the structure and thermodynamics of aqueous systems. By performing a many-body expansion with nuclear-electronic orbital (NEO) theory, we show that proton quantization can give rise to significant energetic contributions for many-body interactions spanning several molecules in single-point energy calculations of water clusters. Although zero-point motion produces a large increase in energy at the one-body level, nuclear quantum effects serve to stabilize higher-order molecular interactions. These results are significant because they demonstrate that nuclear quantum effects play a nontrivial role in many-body interactions of aqueous systems. Our approach also provides a pathway for incorporating nuclear quantum effects into water potential energy surfaces. The NEO approach is advantageous for many-body expansion analyses because it includes nuclear quantum effects directly in the energies.

Quantum information scrambling and chemical reactions

The ultimate regularity of quantum mechanics creates a tension with the assumption of classical chaos used in many of our pictures of chemical reaction dynamics. Out-of-time-order correlators (OTOCs) provide a quantum analog to the Lyapunov exponents that characterize classical chaotic motion. Maldacena, Shenker, and Stanford have suggested a fundamental quantum bound for the rate of information scrambling, which resembles a limit suggested by Herzfeld for chemical reaction rates. Here, we use OTOCs to study model reactions based on a double-well reaction coordinate coupled to anharmonic oscillators or to a continuum oscillator bath. Upon cooling, as one enters the tunneling regime where the reaction rate does not strongly depend on temperature, the quantum Lyapunov exponent can approach the scrambling bound and the effective reaction rate obtained from a population correlation function can approach the Herzfeld limit on reaction rates: Tunneling increases scrambling by expanding the state space available to the system. The coupling of a dissipative continuum bath to the reaction coordinate reduces the scrambling rate obtained from the early-time OTOC, thus making the scrambling bound harder to reach, in the same way that friction is known to lower the temperature at which thermally activated barrier crossing goes over to the low-temperature activationless tunneling regime. Thus, chemical reactions entering the tunneling regime can be information scramblers as powerful as the black holes to which the quantum Lyapunov exponent bound has usually been applied.