Coherent multidimensional optical spectroscopy of excitons in molecular aggregates; quasiparticle versus supermolecule perspectives

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.

Cross Peaks on Two-Dimensional Optical Spectra Arising from Quantum Cross-Correlation Functions

Cross peaks on 2D optical spectra are indicative of interactions between molecular excitonic states. Currently, the two conventional assignments of cross peaks are direct coupling and population transfer between excitonic states. Here, we show that there is another possible source of cross peaks. We theoretically demonstrate that for a model comprising two nondirectly interacting excitons or two-level systems (TLSs), cross peaks can arise if there is a complex-valued or quantum frequency-gap cross-correlation function between the two TLSs. Considering only real-valued or classical cross-correlation functions will result in no cross peaks. We derive and validate the mathematical expressions describing such cross peaks. We then simulate the 2D electronic spectra of an example model system comprising nondirectly interacting TLSs whose quantum cross-correlation functions arise from coupling to a common overdamped Brownian oscillator mode. We show that there are clear observational differences between such quantum correlation cross peaks with conventional direct coupling and population transfer cross peaks.

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.

Signatures of exciton-exciton annihilation in 2DES spectra including up to six-wave mixing processes

Two-dimensional electronic spectroscopy (2DES) is a powerful spectroscopic tool that allows us to study the dynamics of excited states. Exciton-exciton annihilation is at least a fifth order process, which corresponds to intrachromophoric internal conversion from the double-excited high-energy chromophoric state into the single-excited state of the same chromophore. At high excitation intensities, this effect becomes apparent in standard 2DES and can be inspected via high order nK1⃗-nK2⃗+K3⃗ nonlinear processes. We calculate 2DES based on K1⃗-K2⃗+K3⃗ and 2K1⃗-2K2⃗+K3⃗ wave mixing processes to reveal exciton-exciton annihilation (EEA) induced exciton symmetry breaking, which occurs at high excitation intensities. We present the general theory that captures all these processes for bosonic and paulionic quasiparticles in a unified way and demonstrate that the NEEs can be easily utilized for highly nonlinear two-dimensional spectra calculations by employing phase cycling for separating various phase matching conditions. The approach predicts various excitonic third- to fifth-order features; however, due to high excitation intensities, contributions of different order processes become comparable and overlap, i.e., the signals no longer can be associated with well-defined order-to-the-field contributions. In addition, EEA leads to breaking of the exciton symmetries, thus enabling population of dark excitons. Such effects are due to the local nature of the EEA process.

Interconnection between Polarization-Detected and Population-Detected Signals: Theoretical Results and Ab Initio Simulations

Most of spectroscopic signals are specified by the nonlinear laser-induced polarization. In recent years, population-detection of signals becomes a trend in femtosecond spectroscopy. Polarization-detected (PD) and population-detected signals are fundamentally different, because they are determined by photoinduced processes acting on disparate time scales. In this work, we consider the fluorescence-detected (FD) N-wave-mixing (NWM) signal as a representative example of population-detected signals, derive a rigorous expression for this signal, and discuss its approximate variants suitable for numerical simulations. This leads us to the definition of the phenomenological FD (PFD) signal, which contains as a special case all definitions of FD signals available in the literature. Then we formulate and prove the population-polarization equivalence (PPE) theorem, which states that PFD NWM signals produced by (possibly strong) laser pulses can be evaluated as conventional PD signals in which the effective polarization is determined by the PFD transition dipole moment operator. We use the PPE theorem for the construction of the ab initio protocol for the simulation of PFD 4WM signals. As an example, we calculate electronic two-dimensional (2D) PFD spectra of the gas-phase pyrazine and compare them with the corresponding PD 2D spectra.

Elucidating phonon dephasing mechanisms in layered perovskites with coherent Raman spectroscopies

Organic-inorganic hybrid perovskite quantum wells exhibit electronic structures with properties intermediate between those of inorganic semiconductors and molecular crystals. In these systems, periodic layers of organic spacer molecules occupy the interstitial spaces between perovskite sheets, thereby confining electronic excitations to two dimensions. Here, we investigate spectroscopic line broadening mechanisms for phonons coupled to excitons in lead-iodide layered perovskites with phenyl ethyl ammonium (PEA) and azobenzene ethyl ammonium (AzoEA) spacer cations. Using a modified Elliot line shape analysis for the absorbance and photoluminescence spectra, polaron binding energies of 11.2 and 17.5 meV are calculated for (PEA)2PbI4 and (AzoEA)2PbI4, respectively. To determine whether the polaron stabilization processes influence the dephasing mechanisms of coupled phonons, five-pulse coherent Raman spectroscopies are applied to the two systems under electronically resonant conditions. The prominence of inhomogeneous line broadening mechanisms detected in (AzoEA)2PbI4 suggests that thermal fluctuations involving the deformable organic phase broaden the distributions of phonon frequencies within the quantum wells. In addition, our data indicate that polaron stabilization primarily involves photoinduced reorganization of the organic phases for both systems, whereas the impulsively excited phonons represent less than 10% of the total polaron binding energy. The signal generation mechanisms associated with our fifth-order coherent Raman experiments are explored with a perturbative model in which cumulant expansions are used to account for time-coincident vibrational dephasing and polaron stabilization processes.

Unraveling the excitonics of light emission from metal-halide perovskite quantum dots

Metal halide semicondictor perovskites have been under intense investigation for their promise in light absorptive applications like photovoltaics. They have more recently experienced interest for their promise in light emissive applications. A key aspect of perovskites is their glassy, ionic lattice that exhibits dynamical disorder. One possible result of this dynamical disorder is their strong coupling between electronic and lattice degrees of freedom which may confer remarkable properties for light emission such as defect tolerance. How does the system, comprised of excitons, couple to the bath, comprised of lattice modes? How does this system-bath interaction give rise to novel light emissive properties and how do these properties give insight into the nature of these materials? We review recent work from this group in which time-resolved photoluminescence spectroscopy is used to reveal such insights. Based upon a fast time resolution of 3 ps, energy resolution, and temperature dependence, a wide variety of insights are gleaned. These insights include: lattice contributions to the emission linewidths, multiexciton formation, hot carrier cooling, excitonic fine structure, single dot superradiance, and a breakdown of the Condon approximation, all due to complex structural dynamics in these materials.

Probing the Effect of Mutations on Light Harvesting in CP29 by Transient Absorption and First-Principles Simulations

Natural light harvesting is exceptionally efficient thanks to the local energy funnel created within light-harvesting complexes (LHCs). To understand the design principles underlying energy transport in LHCs, ultrafast spectroscopy is often complemented by mutational studies that introduce perturbations into the excitonic structure of the natural complexes. However, such studies may fall short of identifying all excitation energy transfer (EET) pathways and their changes upon mutation. Here, we show that a synergistic combination of first-principles calculations and ultrafast spectroscopy can give unprecedented insight into the EET pathways occurring within LHCs. We measured the transient absorption spectra of the minor CP29 complex of plants and of two mutants, systematically mapping the kinetic components seen in experiments to the simulated exciton dynamics. With our combined strategy, we show that EET in CP29 is surprisingly robust to the changes in the exciton states induced by mutations, explaining the versatility of plant LHCs.

Insights into Energy Transfer in Light-Harvesting Complex II Through Machine-Learning Assisted Simulations

Light-harvesting complex II (LHCII) is the major antenna of higher plants. Energy transfer processes taking place inside its aggregate of chlorophylls have been experimentally investigated with time-resolved techniques, but a complete understanding of the most relevant energy transfer pathways and relative characteristic times remains elusive. Theoretical models to disentangle experimental data in LHCII have long been challenged by the large size and complex nature of the system. Here, we show that a fully first-principles approach combining molecular dynamics and machine learning can be successfully used to reproduce transient absorption spectra and characterize the EET pathways and the involved times.

Scaling Law for Kasha's Rule in Photoexcited Molecular Aggregates

We study the photophysics of molecular aggregates from a quantum optics perspective, with emphasis on deriving scaling laws for the fast nonradiative relaxation of collective electronic excitations, referred to as Kasha's rule. Aggregates exhibit an energetically broad manifold of collective states with delocalized electronic excitations originating from near-field dipole-dipole exchanges between neighboring monomers. Photoexcitation at optical wavelengths, much larger than the monomer-monomer average separation, addresses almost exclusively symmetric collective states, which for an arrangement known as H-aggregate show an upward hypsochromic shift. The extremely fast subsequent nonradiative relaxation via intramolecular vibrational modes populates lower energy, subradiant states, resulting in effective inhibition of fluorescence. Our analytical treatment allows for the derivation of an approximate scaling law of this relaxation process, linear in the number of available low-energy vibrational modes and directly proportional to the dipole-dipole interaction strength between neighboring monomers.

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.

Artificial-Intelligence-Based Surrogate Solution of Dissipative Quantum Dynamics: Physics-Informed Reconstruction of the Universal Propagator

The accurate (or even approximate) solution of the equations that govern the dynamics of dissipative quantum systems remains a challenging task in quantum science. While several algorithms have been designed to solve those equations with different degrees of flexibility, they rely mainly on highly expensive iterative schemes. Most recently, deep neural networks have been used for quantum dynamics, but current architectures are highly dependent on the physics of the particular system and usually limited to population dynamics. Here we introduce an artificial-intelligence-based surrogate model that solves dissipative quantum dynamics by parametrizing quantum propagators as Fourier neural operators, which we train using both data set and physics-informed loss functions. Compared with conventional algorithms, our quantum neural propagator avoids time-consuming iterations and provides a universal superoperator that can be used to evolve any initial quantum state for arbitrarily long times. To illustrate the wide applicability of the approach, we employ our quantum neural propagator to compute the population dynamics and time-correlation functions of the Fenna-Matthews-Olson complex.

Multidimensional high-harmonic echo spectroscopy: Resolving coherent electron dynamics in the EUV regime

We theoretically propose a multidimensional high-harmonic echo spectroscopy technique which utilizes strong optical fields to resolve coherent electron dynamics spanning an energy range of multiple electronvolts. Using our recently developed semi-perturbative approach, we can describe the coherent valence electron dynamics driven by a sequence of phase-matched and well-separated short few-cycle strong infrared laser pulses. The recombination of tunnel-ionized electrons by each pulse coherently populates the valence states of a molecule, which allows for a direct observation of its dynamics via the high harmonic echo signal. The broad bandwidth of the effective dipole between valence states originated from the strong-field excitation results in nontrivial ultra-delayed partial rephasing echo, which is not observed in standard two-dimensional optical spectroscopic techniques in a two-level molecular systems. We demonstrate the results of simulations for the anionic molecular system and show that the ultrafast valence electron dynamics can be well captured with femtosecond resolution.

Time-Resolved X-ray Absorption Spectroscopy: An MCTDH Quantum Dynamics Protocol

Expressions for linear and nonlinear spectroscopy simulation in the X-ray window in which the time evolution of a photoexcited molecular system is treated via quantum dynamics are derived. By leveraging on the peculiar properties of core-excited/ionized states, first- and third-order response functions are recast in the limit of time-scale separation between the extremely short core-state lifetime and the (comparably longer) electronic-state transfer and nuclear vibrational motion. This work is a natural extension of Segatta et al. (J. Chem. Theory Comput. 2023, 19, 2075-2091), in which some of the present authors coupled MCTDH quantum dynamics to spectroscopy simulation at different levels of sophistication. Full quantum dynamics and approximate expressions are compared by simulating X-ray transient absorption spectroscopy at the carbon K-edge in the pyrene molecule.

Intraband Exciton Transitions in Photosynthetic Complexes Revealed by Novel Five-Wave-Mixing Spectroscopy

We calculate the χ(4) optical response of an oriented photosystem II reaction center of purple bacteria described by the Frenkel exciton model using nonlinear exciton equations (NEE). This approach treats each chromophore as an anharmonic oscillator and provides an intuitive quasiparticle picture of nonlinear spectroscopic signals of interacting excitons. It provides a computationally powerful description of nonlinear spectroscopic signals that avoids complete diagonalization of the total Hamiltonian. Expressions for the second- and the fourth-order nonlinear signals are derived. The NEE have been successfully employed in the past to describe even-order-wave-mixing. Here, we extend them to aggregates with broken inversion symmetries. Even-order susceptibilities require the introduction of permanent dipoles, which allow to directly probe low-frequency intraband transitions of excitons.

Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers

Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining considerable interest. New methods to improve the rigidity of the DNA scaffold and thus the stability of the molecular dye aggregates to encourage exciton delocalization are desired. In these dye-DNA constructs, one potential way to increase the stability of the aggregates is to create an additional covalent bond via photo-cross-linking reactions between thymines in the DNA scaffold. Specifically, we report an approach to increase the yield of photo-cross-linking reaction between thymines in the core of a DNA Holliday junction while limiting the damage from UV irradiation to DNA. We investigated the effect of the distance between thymines on the photo-cross-linking reaction yields by using linkers with different lengths to tether the dyes to the DNA templates. By comprehensively evaluating the photo-cross-linking reaction yields of dye-DNA aggregates using linkers with different lengths, we conclude that interstrand thymines tend to photo-cross-link more efficiently with short linkers. A higher cross-linking yield was achieved due to the shorter intermolecular distance between thymines influenced by strong dye-dye interactions. Our method establishes the possibility of improving the stability of DNA-scaffolded dye aggregates, thereby expanding their use in exciton-based applications such as light harvesting, nanoscale computing, quantum computing, and optoelectronics.

First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex

The dynamics of delocalized excitons in light-harvesting complexes (LHCs) can be investigated using different experimental techniques, and transient absorption (TA) spectroscopy is one of the most valuable methods for this purpose. A careful interpretation of TA spectra is essential for the clarification of excitation energy transfer (EET) processes occurring during light-harvesting. However, even in the simplest LHCs, a physical model is needed to interpret transient spectra as the number of EET processes occurring at the same time is very large to be disentangled from measurements alone. Physical EET models are commonly built by fittings of the microscopic exciton Hamiltonians and exciton-vibrational parameters, an approach that can lead to biases. Here, we present a first-principles strategy to simulate EET and transient absorption spectra in LHCs, combining molecular dynamics and accurate multiscale quantum chemical calculations to obtain an independent estimate of the excitonic structure of the complex. The microscopic parameters thus obtained are then used in EET simulations to obtain the population dynamics and the related spectroscopic signature. We apply this approach to the CP29 minor antenna complex of plants for which we follow the EET dynamics and transient spectra after excitation in the chlorophyll b region. Our calculations reproduce all the main features observed in the transient absorption spectra and provide independent insight on the excited-state dynamics of CP29. The approach presented here lays the groundwork for the accurate simulation of EET and unbiased interpretation of transient spectra in multichromophoric systems.

Three-Dimensional Rotational Averaging Using Irreducible Sets of Linearly Independent Fundamental Isotropic Cartesian Tensors: A Computational Approach

The theoretical formulation of linear and nonlinear molecular spectroscopies applied to isotropic samples (e.g., liquid or gas solutions) goes through a fundamental step known as the rotational averaging of Cartesian tensors. Rotational averaging of Cartesian tensors is a mathematical procedure from which the expressions for the rotationally invariant observables (e.g., rates or intensities), associated with a given spectroscopic process, can be found. In this work, the mathematical/computational procedure for finding the rotational averages of Cartesian tensors of any rank n, which is based on the use of the fundamental isotropic Cartesian tensors (FICTs), is discussed. Moreover, for the first time, a heuristic computational method for finding a set of linearly independent FICTs is proposed. The procedure has been tested for 2 ≤ n ≤ 12, where most of the linear and nonlinear molecular spectroscopies apply (e.g., one-photon and multiphoton absorption, emission, electronic circular dichroism, Raman optical activity, coherent and incoherent mth-harmonic generation, etc.). Finally, it is shown how this computational procedure can be extended for n > 12.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.

Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer

A bacteriochlorophyll a (Bchla) dimer is a basic functional unit in the LH1 and LH2 photosynthetic pigment-protein antenna complexes of purple bacteria, where an ordered, close arrangement of Bchla pigments-secured by noncovalent bonding to a protein template-enables exciton delocalization at room temperature. Stable and tunable synthetic analogs of this key photosynthetic subunit could lead to facile engineering of exciton-based systems such as in artificial photosynthesis, organic optoelectronics, and molecular quantum computing. Here, using a combination of synthesis and theory, we demonstrate that exciton delocalization can be achieved in a dimer of a synthetic bacteriochlorin (BC) featuring stability, high structural modularity, and spectral properties advantageous for exciton-based devices. The BC dimer was covalently templated by DNA, a stable and highly programmable scaffold. To achieve exciton delocalization in the absence of pigment-protein interactions critical for the Bchla dimer, we relied on the strong transition dipole moment in BC enabled by two auxochromes along the Qy transition, and omitting the central metal and isocyclic ring. The spectral properties of the synthetic "free" BC closely resembled those of Bchla in an organic solvent. Applying spectroscopic modeling, the exciton delocalization in the DNA-templated BC dimer was evaluated by extracting the excitonic hopping parameter, J to be 214 cm-1 (26.6 meV). For comparison, the same method applied to the natural protein-templated Bchla dimer yielded J of 286 cm-1 (35.5 meV). The smaller value of J in the BC dimer likely arose from the partial bacteriochlorin intercalation and the difference in medium effect between DNA and protein.

Galván I, Alavi A, Aleotti F, Aquilante F, Autschbach J, Avagliano D, Baiardi A, Bao JJ, Battaglia S, Birnoschi L, Blanco-González A, Bokarev SI, Broer R, Cacciari R, Calio PB, Carlson RK, Carvalho Couto R, Cerdán L, Chibotaru LF, Chilton NF, Church JR, Conti I, Coriani S, Cuéllar-Zuquin J, Daoud RE, Dattani N, Decleva P, de Graaf C, Delcey M, De Vico L, Dobrautz W, Dong SS, Feng R, Ferré N, Filatov(Gulak) M, Gagliardi L, Garavelli M, González L, Guan Y, Guo M, Hennefarth MR, Hermes MR, Hoyer CE, Huix-Rotllant M, Jaiswal VK, Kaiser A, Kaliakin DS, Khamesian M, King DS, Kochetov V, Krośnicki M, Kumaar AA, Larsson ED, Lehtola S, Lepetit MB, Lischka H, López Ríos P, Lundberg M, Ma D, Mai S, Marquetand P, Merritt ICD, Montorsi F, Mörchen M, Nenov A, Nguyen VHA, Nishimoto Y, Oakley MS, Olivucci M, Oppel M, Padula D, Pandharkar R, Phung QM, Plasser F, Raggi G, Rebolini E, Reiher M, Rivalta I, Roca-Sanjuán D, Romig T, Safari AA, Sánchez-Mansilla A, Sand AM, Schapiro I, Scott TR, Segarra-Martí J, Segatta F, Sergentu DC, Sharma P, Shepard R, Shu Y, Staab JK, Straatsma TP, Sørensen LK, Tenorio BNC, Truhlar DG, Ungur L, Vacher M, Veryazov V, Voß TA, Weser O, Wu D, Yang X, Yarkony D, Zhou C, Zobel JP, Lindh R. The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

Machine Learning Approach Based on a Range-Corrected Deep Potential Model for Efficient Vibrational Frequency Computation

As an ensemble average result, vibrational spectrum simulation can be time-consuming with high accuracy methods. We present a machine learning approach based on the range-corrected deep potential (DPRc) model to improve the computing efficiency. The DPRc method divides the system into "probe region" and "solvent region"; "solvent-solvent" interactions are not counted in the neural network. We applied the approach to two systems: formic acid C═O stretching and MeCN C≡N stretching vibrational frequency shifts in water. All data sets were prepared using the quantum vibration perturbation approach. Effects of different region divisions, one-body correction, cut range, and training data size were tested. The model with a single-molecule "probe region" showed stable accuracy; it ran roughly 10 times faster than regular deep potential and reduced the training time by about four. The approach is efficient, easy to apply, and extendable to calculating various spectra.

Double-quantum spectroscopy of dense atomic vapors: Interplay between Doppler and self-broadenings

In this article, we present a simulation study of the linear and nonlinear spectroscopy of dense atomic vapors. Motivated by recent experiments, we focus on double quantum spectroscopy, which directly probes dipole-dipole interactions. By explicitly including thermal velocity, we show that temperature has an important impact on the self-broadening mechanisms of the linear and nonlinear spectra. We also provide analytical expressions for the response functions in the short time limit using the two-body approximation, which shows that double quantum spectroscopy for atomic vapors directly probes the transition amplitude of the electronic excitation between two atoms. We also propose an expression for the double quantum spectrum that includes the effect of Doppler broadening, and we discuss the effect of density on the spectrum. We show that when Doppler broadening is negligible compared to self-broadening, the double quantum spectrum scales with the atomic density, while when Doppler broadening dominates, it scales as the square of the density.

Enhancing the FRET by tuning the bandgap of acceptor ternary ZnCdS quantum dots

In this article, we report the band gap tuning of ternary ZnCdS quantum dots (QDs) by varying the concentration of the capping ligand, mercaptoacetic acid (MAA). The functionalization of QDs leads to the control of their size and band gap due to the quantum confinement effect, causing blue shift in the absorption and photoluminescence (PL) spectra with a gradual change in the concentration of the capping ligand from 0.5 to 2.5 M. Ensulizole (2-phenylbenzimidazole-5-sulfonic acid) is an important organic ultraviolet (UV) filter that is frequently used in sunscreen cosmetics. An effective overlapping of the PL spectrum of ensulizole and the absorption spectrum of QDs with 2.5 M MAA is achieved. A formidable decrease in the PL intensity and the PL lifetime of ensulizole promotes an efficient Förster resonance energy transfer (FRET) from sunscreen ensulizole to the QDs. The magnitude of the FRET efficiency (E) is ∼70%. This very high value of E is the signature of the existence of a very fast energy transfer process from ensulizole to the MAA functionalized ZnCdS QDs. The dyad system consisting of ZnCdS QDs and ensulizole sunscreen can serve as a prototype model to develop a better understanding of the photochemistry of ensulizole and consequently the formulation of more efficient sunscreen cosmetics.

Ab initio simulation of peak evolutions and beating maps for electronic two-dimensional signals of a polyatomic chromophore

By employing the doorway-window (DW) on-the-fly simulation protocol, we performed ab initio simulations of peak evolutions and beating maps of electronic two-dimensional (2D) spectra of a polyatomic molecule in the gas phase. As the system under study, we chose pyrazine, which is a paradigmatic example of photodynamics dominated by conical intersections (CIs). From the technical perspective, we demonstrate that the DW protocol is a numerically efficient methodology suitable for simulations of 2D spectra for a wide range of excitation/detection frequencies and population times. From the information content perspective, we show that peak evolutions and beating maps not only reveal timescales of transitions through CIs but also pinpoint the most relevant coupling and tuning modes active at these CIs.

Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach

In this paper, we present dyadic adaptive HOPS (DadHOPS), a new method for calculating linear absorption spectra for large molecular aggregates. This method combines the adaptive HOPS (adHOPS) framework, which uses locality to improve computational scaling, with the dyadic HOPS method previously developed to calculate linear and nonlinear spectroscopic signals. To construct a local representation of dyadic HOPS, we introduce an initial state decomposition that reconstructs the linear absorption spectra from a sum over locally excited initial conditions. We demonstrate the sum over initial conditions can be efficiently Monte Carlo sampled and that the corresponding calculations achieve size-invariant [i.e., O(1)] scaling for sufficiently large aggregates while trivially incorporating static disorder in the Hamiltonian. We present calculations on the photosystem I core complex to explore the behavior of the initial state decomposition in complex molecular aggregates as well as proof-of-concept DadHOPS calculations on an artificial molecular aggregate inspired by perylene bis-imide to demonstrate the size-invariance of the method.

Transient chiral dynamics revealed by two-dimensional circular dichroism spectroscopy

Chirality has been considered as one of the key factors in the evolution of life in nature. It is important to uncover how chiral potentials of molecular systems play vital role in fundamental photochemical processes. Here, we investigate the role of chirality in photoinduced energy transfer in a model dimeric system, where the monomers are excitonically coupled. To observe transient chiral dynamics and energy transfer, we employ circularly polarized laser pulses in two-dimensional electronic spectroscopy to construct the two-dimensional circular dichroism (2DCD) spectral maps. Tracking time-resolved peak magnitudes in 2DCD spectra allows one to identify chirality induced population dynamics. The dynamics of energy transfer is revealed by the time-resolved kinetics of cross peaks. However, the differential signal of 2DCD spectra shows the magnitude of cross peaks is dramatically reduced at initial waiting time, which indicates the weak chiral interactions between two monomers. The downhill energy transfer is resolved by presenting a strong magnitude of cross peak in 2DCD spectra after long waiting time. The chiral contribution towards coherent and incoherent energy-transfer pathways in the model dimer system is further examined via control of excitonic couplings between two monomers. Applications are made to study the energy-transfer process in the Fenna-Matthews-Olson complex. Our work uncovers the potential of 2DCD spectroscopy to resolve the chiral-induced interactions and population transfers in excitonically coupled systems.

Pulse overlap artifacts and double quantum coherence spectroscopy

The double quantum coherence (DQC) signal in nonlinear spectroscopy gives information about the many-body correlation effects not easily available by other methods. The signal is short-lived, consequently, a significant part of it is generated during the pulse overlap. Since the signal is at two times the laser frequency, one may intuitively expect that the pulse overlap-related artifacts are filtered out by the Fourier transform. Here, we show that this is not the case. We perform explicit calculations of phase-modulated two-pulse experiments of a two-level system where the DQC is impossible. Still, we obtain a significant signal at the modulation frequency, which corresponds to the DQC, while the Fourier transform over the pulse delay shows a double frequency. We repeat the calculations with a three-level system where the true DQC signal occurs. We conclude that with realistic dephasing times, the pulse-overlap artifact can be significantly stronger than the DQC signal. Our results call for great care when analyzing such experiments. As a rule of thumb, we recommend that only delays larger than 1.5 times the pulse length should be used.

Nonlinear Molecular Electronic Spectroscopy via MCTDH Quantum Dynamics: From Exact to Approximate Expressions

We present an accurate and efficient approach to computing the linear and nonlinear optical spectroscopy of a closed quantum system subject to impulsive interactions with an incident electromagnetic field. It incorporates the effect of ultrafast nonadiabatic dynamics by means of explicit numerical propagation of the nuclear wave packet. The fundamental expressions for the evaluation of first- and higher-order response functions are recast in a general form that can be used with any quantum dynamics code capable of computing the overlap of nuclear wave packets evolving in different states. Here we present the evaluation of these expressions with the multiconfiguration time-dependent Hartree (MCTDH) method. Application is made to pyrene, excited to its lowest bright excited state S₂ which exhibits a sub-100-fs nonadiabatic decay to a dark state S₁. The system is described by a linear vibronic coupling Hamiltonian, parametrized with multiconfiguration electronic structure methods. We show that the ultrafast nonadiabatic dynamics can have a remarkable effect on the spectral line shapes that goes beyond simple lifetime broadening. Furthermore, a widely employed approximate expression based on the time scale separation of dephasing and population relaxation is recast in the same theoretical framework. Application to pyrene shows the range of validity of such approximations.

The hierarchy of Davydov's Ansätze: From guesswork to numerically "exact" many-body wave functions

This Perspective presents an overview of the development of the hierarchy of Davydov's Ansätze and a few of their applications in many-body problems in computational chemical physics. Davydov's solitons originated in the investigation of vibrational energy transport in proteins in the 1970s. Momentum-space projection of these solitary waves turned up to be accurate variational ground-state wave functions for the extended Holstein molecular crystal model, lending unambiguous evidence to the absence of formal quantum phase transitions in Holstein systems. The multiple Davydov Ansätze have been proposed, with increasing Ansatz multiplicity, as incremental improvements of their single-Ansatz parents. For a given Hamiltonian, the time-dependent variational formalism is utilized to extract accurate dynamic and spectroscopic properties using Davydov's Ansätze as its trial states. A quantity proven to disappear for large multiplicities, the Ansatz relative deviation is introduced to quantify how closely the Schrödinger equation is obeyed. Three finite-temperature extensions to the time-dependent variation scheme are elaborated, i.e., the Monte Carlo importance sampling, the method of thermofield dynamics, and the method of displaced number states. To demonstrate the versatility of the methodology, this Perspective provides applications of Davydov's Ansätze to the generalized Holstein Hamiltonian, variants of the spin-boson model, and systems of cavity-assisted singlet fission, where accurate dynamic and spectroscopic properties of the many-body systems are given by the Davydov trial states.

Simulation of two-dimensional infrared Raman spectroscopy with application to proteins

Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.

Characterization of excited states in time-dependent density functional theory using localized molecular orbitals

Localized molecular orbitals are often used for the analysis of chemical bonds, but they can also serve to efficiently and comprehensibly compute linear response properties. While conventional canonical molecular orbitals provide an adequate basis for the treatment of excited states, a chemically meaningful identification of the different excited-state processes is difficult within such a delocalized orbital basis. In this work, starting from an initial set of supermolecular canonical molecular orbitals, we provide a simple one-step top-down embedding procedure for generating a set of orbitals, which are localized in terms of the supermolecule but delocalized over each subsystem composing the supermolecule. Using an orbital partitioning scheme based on such sets of localized orbitals, we further present a procedure for the construction of local excitations and charge-transfer states within the linear response framework of time-dependent density functional theory (TDDFT). This procedure provides direct access to approximate diabatic excitation energies and, under the Tamm-Dancoff approximation, also their corresponding electronic couplings-quantities that are of primary importance in modeling energy transfer processes in complex biological systems. Our approach is compared with a recently developed diabatization procedure based on subsystem TDDFT using projection operators, which leads to a similar set of working equations. Although both of these methods differ in the general localization strategies adopted and the type of basis functions (Slaters vs Gaussians) employed, an overall decent agreement is obtained.

Extracting the excitonic Hamiltonian of a chlorophyll dimer from broadband two-dimensional electronic spectroscopy

We apply Frenkel exciton theory to model the entire Q-band of a tightly bound chlorophyll dimer inspired by the photosynthetic reaction center of photosystem II. The potential of broadband two-dimensional electronic spectroscopy experiment spanning the Q_x and Q_y regions to extract the parameters of the model dimer Hamiltonian is examined through theoretical simulations of the experiment. We find that the local nature of Q_x excitation enables identification of molecular properties of the delocalized Q_y excitons. Specifically, we demonstrate that the cross-peak region, where excitation energy is resonant with Q_y while detection is at Q_x, contains specific spectral signatures that can reveal the full real-space molecular Hamiltonian, a task that is impossible by considering the Q_y transitions alone. System-bath coupling and site energy disorder in realistic systems may limit the resolution of these spectral signatures due to spectral congestion.

femtoPro: virtual-reality interactive training simulator of an ultrafast laser laboratory

The huge field of optics and photonics research and development is in constant demand of well-trained experts. However, it is challenging to teach efficiently the setup process of complicated optical experiments due to limited hardware availability and eye-safety concerns, in particular, in the case of femtosecond lasers. We have developed an interactive simulation of an ultrafast laser laboratory ("femtoPro") for teaching and training, implementing physical models for the calculation and visualization of Gaussian laser beam propagation, ultrashort optical pulses, their modulation by typical optical elements, and linear as well as nonlinear light-matter interaction. This facilitates the setup and simulated measurement procedure, in virtual reality (VR) and at real-time speeds, of various typical optical arrangements and spectroscopy schemes such as telescopes, interferometers, or pulse characterization. femtoPro can be employed to supplement academic teaching in connection with regular courses in optics or spectroscopy, to train future scientists and engineers in the field of (ultrafast) optics in practical skills, to communicate to other researchers how to set up and align a particular experiment, to "test-build" and simulate new designs of optical setups, to simulate ultrafast spectroscopy data, to offer practical exercises to high-school students, and to reach out to the general public.

Equation-of-Motion Methods for the Calculation of Femtosecond Time-Resolved 4-Wave-Mixing and N-Wave-Mixing Signals

Femtosecond nonlinear spectroscopy is the main tool for the time-resolved detection of photophysical and photochemical processes. Since most systems of chemical interest are rather complex, theoretical support is indispensable for the extraction of the intrinsic system dynamics from the detected spectroscopic responses. There exist two alternative theoretical formalisms for the calculation of spectroscopic signals, the nonlinear response-function (NRF) approach and the spectroscopic equation-of-motion (EOM) approach. In the NRF formalism, the system-field interaction is assumed to be sufficiently weak and is treated in lowest-order perturbation theory for each laser pulse interacting with the sample. The conceptual alternative to the NRF method is the extraction of the spectroscopic signals from the solutions of quantum mechanical, semiclassical, or quasiclassical EOMs which govern the time evolution of the material system interacting with the radiation field of the laser pulses. The NRF formalism and its applications to a broad range of material systems and spectroscopic signals have been comprehensively reviewed in the literature. This article provides a detailed review of the suite of EOM methods, including applications to 4-wave-mixing and N-wave-mixing signals detected with weak or strong fields. Under certain circumstances, the spectroscopic EOM methods may be more efficient than the NRF method for the computation of various nonlinear spectroscopic signals.

Taming Quantum Noise for Efficient Low Temperature Simulations of Open Quantum Systems

The hierarchical equations of motion (HEOM), derived from the exact Feynman-Vernon path integral, is one of the most powerful numerical methods to simulate the dynamics of open quantum systems. Its applicability has so far been limited to specific forms of spectral reservoir distributions and relatively elevated temperatures. Here we solve this problem and introduce an effective treatment of quantum noise in frequency space by systematically clustering higher order Matsubara poles, equivalent to an optimized rational decomposition. This leads to an elegant extension of the HEOM to arbitrary temperatures and very general reservoirs in combination with efficiency, high accuracy, and long-time stability. Moreover, the technique can directly be implemented in other approaches such as Green's function, stochastic, and pseudomode formulations. As one highly nontrivial application, for the subohmic spin-boson model at vanishing temperature the Shiba relation is quantitatively verified which predicts the long-time decay of correlation functions.

Molecular Chirality and Its Monitoring by Ultrafast X-ray Pulses

Major advances in X-ray sources including the development of circularly polarized and orbital angular momentum pulses make it possible to probe matter chirality at unprecedented energy regimes and with Ångström and femtosecond spatiotemporal resolutions. We survey the theory of stationary and time-resolved nonlinear chiral measurements that can be carried out in the X-ray regime using tabletop X-ray sources or large scale (XFEL, synchrotron) facilities. A variety of possible signals and their information content are discussed.

Calculating non-linear response functions for multi-dimensional electronic spectroscopy using dyadic non-Markovian quantum state diffusion

We present a methodology for simulating multi-dimensional electronic spectra of molecular aggregates with coupling of electronic excitation to a structured environment using the stochastic non-Markovian quantum state diffusion (NMQSD) method in combination with perturbation theory for the response functions. A crucial aspect of our approach is that we propagate the NMQSD equation in a doubled system Hilbert space, but with the same noise. We demonstrate that our approach shows fast convergence with respect to the number of stochastic trajectories, providing a promising technique for numerical calculation of two-dimensional electronic spectra of large molecular aggregates.

Vibrational response functions for multidimensional electronic spectroscopy in the adiabatic regime: A coherent-state approach

Multi-dimensional spectroscopy represents a particularly insightful tool for investigating the interplay of nuclear and electronic dynamics, which plays an important role in a number of photophysical processes and photochemical reactions. Here, we present a coherent state representation of the vibronic dynamics and of the resulting response functions for the widely used linearly displaced harmonic oscillator model. Analytical expressions are initially derived for the case of third-order response functions in an N-level system, with ground state initialization of the oscillator (zero-temperature limit). The results are then generalized to the case of Mth order response functions, with arbitrary M. The formal derivation is translated into a simple recipe, whereby the explicit analytical expressions of the response functions can be derived directly from the Feynman diagrams. We further generalize to the whole set of initial coherent states, which form an overcomplete basis. This allows one, in principle, to derive the dependence of the response functions on arbitrary initial states of the vibrational modes and is here applied to the case of thermal states. Finally, a non-Hermitian Hamiltonian approach is used to include in the above expressions the effect of vibrational relaxation.

Gaussian process regression for absorption spectra analysis of molecular dimers

A common task is the determination of system parameters from spectroscopy, where one compares the experimental spectrum with calculated spectra, that depend on the desired parameters. Here we discuss an approach based on a machine learning technique, where the parameters for the numerical calculations are chosen from Gaussian Process Regression (GPR). This approach does not only quickly converge to an optimal parameter set, but in addition provides information about the complete parameter space, which allows for example to identify extended parameter regions where numerical spectra are consistent with the experimental one. We consider as example dimers of organic molecules and aim at extracting in particular the interaction between the monomers, and their mutual orientation. We find that indeed the GPR gives reliable results which are in agreement with direct calculations of these parameters using quantum chemical methods.

Unique Signatures of Topological Phases in Two-Dimensional THz Spectroscopy

We develop a microscopic theory for the two-dimensional (2D) spectroscopy of one-dimensional topological superconductors. We consider a ring geometry of an archetypal topological superconductor with periodic boundary conditions, bypassing energy-specific differences caused by topologically protected or trivial boundary modes that are hard to distinguish. We show numerically and analytically that the cross-peak structure of the 2D spectra carries unique signatures of the topological phases of the chain. Our work reveals how 2D spectroscopy can identify topological phases in bulk properties.

Excitonic Nature of Carotenoid–Phthalocyanine Dyads and Its Role in Transient Absorption Spectra

Artificial carotenoid–tetrapyrrole dyads have been extensively used as model systems to understand the quenching mechanisms that occur in light-harvesting complexes during nonphotochemical quenching. In particular, dyads containing a carotenoid covalently linked to a zinc phthalocyanine have been studied by transient absorption spectroscopy, and the observed signals have been interpreted in terms of an excitonically coupled state involving the lowest excited states of the two fragments. If present, such excitonic delocalization would have significant implications on the mechanism of nonphotochemical quenching. Here, we use quantum chemical calculations to show that this delocalization is not needed to reproduce the transient absorption spectra. On the contrary, the observed signals can be explained through excitonic couplings in the higher-energy manifold of states. We also argue that the covalent linkage between the two fragments allows for electronic communications, which complicates the analysis of the spectra based on two independent but coupled moieties. These findings call for a more thorough reassessment of the photophysics in these dyads and its implications in the context of natural nonphotochemical quenching.

Machine learning recognition of protein secondary structures based on two-dimensional spectroscopic descriptors

Protein secondary structure discrimination is crucial for understanding their biological function. It is not generally possible to invert spectroscopic data to yield the structure. We present a machine learning protocol which uses two-dimensional UV (2DUV) spectra as pattern recognition descriptors, aiming at automated protein secondary structure determination from spectroscopic features. Accurate secondary structure recognition is obtained for homologous (97%) and nonhomologous (91%) protein segments, randomly selected from simulated model datasets. The advantage of 2DUV descriptors over one-dimensional linear absorption and circular dichroism spectra lies in the cross-peak information that reflects interactions between local regions of the protein. Thanks to their ultrafast (∼200 fs) nature, 2DUV measurements can be used in the future to probe conformational variations in the course of protein dynamics.

Simulation of absorption spectra of molecular aggregates: A hierarchy of stochastic pure state approach

Simulation of spectroscopic observables for molecular aggregates with strong and structured coupling of electronic excitation to vibrational degrees of freedom is an important but challenging task. The Hierarchy of Pure States (HOPS) provides a formally exact solution based on local, stochastic trajectories. Exploiting the localization of HOPS for the simulation of absorption spectra in large aggregates requires a formulation in terms of normalized trajectories. Here, we provide a normalized dyadic equation where the ket- and bra-states are propagated in different electronic Hilbert spaces. This work opens the door to applying adaptive HOPS methods for the simulation of absorption spectra.

The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol

The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.

Dynamics of Excitons in Conjugated Molecules and Organic Semiconductor Systems

The exciton, an excited electron-hole pair bound by Coulomb attraction, plays a key role in photophysics of organic molecules and drives practically important phenomena such as photoinduced mechanical motions of a molecule, photochemical conversions, energy transfer, generation of free charge carriers, etc. Its behavior in extended π-conjugated molecules and disordered organic films is very different and very rich compared with exciton behavior in inorganic semiconductor crystals. Due to the high degree of variability of organic systems themselves, the exciton not only exerts changes on molecules that carry it but undergoes its own changes during all phases of its lifetime, that is, birth, conversion and transport, and decay. The goal of this review is to give a systematic and comprehensive view on exciton behavior in π-conjugated molecules and molecular assemblies at all phases of exciton evolution with emphasis on rates typical for this dynamic picture and various consequences of the above dynamics. To uncover the rich variety of exciton behavior, details of exciton formation, exciton transport, exciton energy conversion, direct and reverse intersystem crossing, and radiative and nonradiative decay are considered in different systems, where these processes lead to or are influenced by static and dynamic disorder, charge distribution symmetry breaking, photoinduced reactions, electron and proton transfer, structural rearrangements, exciton coupling with vibrations and intermediate particles, and exciton dissociation and annihilation as well.

Searching for a Unique Exciton Model of Photosynthetic Pigment–Protein Complexes: Photosystem II Reaction Center Study by Differential Evolution

Studying the optical properties of photosynthetic pigment–protein complexes (PPCs) in the visible light range, both experimentally and theoretically, is one of the ways of gaining knowledge about the function of the photosynthetic machinery of living species. To simulate the PPC optical response, it is necessary to use semiclassical theories describing the effect of external fields–matter interaction, energy migration in molecular crystals, and electron–phonon coupling. In this paper, we report the results of photosystem II reaction center (PSIIRC) linear optical response simulations. Applying the multimode Brownian oscillator model and the theory of molecular excitons, we have demonstrated that the absorption, circular and linear dichroism, and steady-state fluorescence of PSIIRC can be accurately fitted with the help of differential evolution (DE), the multiparametric evolutionary optimization algorithm. To explore the effectiveness of DE, we used the simulated experimental data as the target functions instead of those actually measured. Only 2 of 10 DE strategies have shown the best performance of the optimization algorithm. With the best tuning parameters of DE/rand-to-best/1/exp strategy determined from the strategy tests, we found the exact solution for the PSIIRC exciton model and fitted the spectra with a reasonable convergence rate.

Correlated spectral fluctuations quantified by line shape analysis of fifth-order two-dimensional electronic spectra

Correlated spectral fluctuations were suggested to coordinate excitation transport inside natural light harvesting complexes. We demonstrate the capacities of 2D line shapes from fifth-order coherent electronic signals (R5-2D) to report on such fluctuations in molecular aggregates and present a stochastic approach to fluctuations in correlated site and bi-exciton binding energies in the optical dynamics of Frenkel excitons. The model is applied to R5-2D line shapes of a homodimer, and we show that the peak tilt dynamics are a measure for site energy disorder, inter-site correlation, and the strength of bi-exciton binding energy fluctuations.

Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates

Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn-Renger-May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm-1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.