Spectral line shapes in linear absorption and two-dimensional spectroscopy with skewed frequency distributions

Farag, Marwa H.; Hoenders, B.J.; Knoester, Jasper; Jansen, Thomas L. C.

doi:10.1063/1.4985665

Cited by 13 publications

(5 citation statements)

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“…The response function formulation presented above is still valid, but they need to be evaluated explicitly including the resulting non-Gaussian fluctuations. [111][112][113][114][115][116][117][118][119][120] In these cases, the numerical integration of the Schrödinger equation (NISE) 121 and the non-linear exciton propagation (NEP) algorithms 122 should be of use. 110…”

Section: () F T T −mentioning

confidence: 99%

“…When the vibrational modes are spectators in chemical reactions, the Gaussian approximation , making the foundation of the line-broadening function breaks down. The response function formulation presented above is still valid, but they need to be evaluated explicitly including the resulting non-Gaussian fluctuations. − In these cases, the numerical integration of the Schrödinger equation (NISE) and the nonlinear exciton propagation (NEP) algorithms should be of use …”

Section: Brief Theoretical Account Of Vibrational Spectroscopymentioning

confidence: 99%

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Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

et al. 2020

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Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and inter-protein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an allencompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semi-empirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository website (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-theart multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

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Section: () F T T −mentioning

confidence: 99%

Section: Brief Theoretical Account Of Vibrational Spectroscopymentioning

confidence: 99%

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

et al. 2020

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“…It is worth noting that the approach here presented is not necessarily limited to the second‐order cumulant expansion. By computing higher‐order correlators, it may be possible to model cases where the frequency fluctuations strongly deviate from Gaussian statistics . Also, from the point of view of algorithm design, some improvements have to be done in the optimization of the code for the QM/MM MD simulations, exploiting modern parallel computing technologies, which would allow much faster simulations on systems of the same size of that presented in this tutorial, or larger ones.…”

Section: Discussionmentioning

confidence: 99%

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

Loco

Cupellini

2018

Int J of Quantum Chemistry

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In this tutorial review, we focus on a multiscale method to compute the electronic absorption line shape of molecular dyes embedded in a biological environment. To treat the coupling of the electronic excitations with the nuclear degrees of freedom of the system, we use the spectral density (SD) of the exciton-phonon coupling computed from a Born-Oppenheimer molecular dynamics, which takes into account the effect of the biological environment on the dye's nuclear and electronic degrees of freedom. The theoretical basis of the approach is given, as well as a comprehensive description of the computational protocol for the extraction of the energy gap autocorrelation function evaluating the electronic excitation along the classical trajectory. Furthermore a benchmark application from a recently published study is presented as an example of how the derived SD can be used in computational spectroscopy to accurately simulate the absorption lineshape, including both vibronic and temperature effects. K E Y W O R D S absorption lineshape, spectral density, QM/MM molecular dynamics 1 | INTRODUCTIONThe accurate modeling of electronic absorption spectra is a fundamental tool to understand and complement experimental data. Experimental and computational techniques are widely used to identify molecular species and to predict environment effects on the molecular response and photochemistry.From a computational point of view, many different approaches have been exploited in theoretical spectroscopy. [1][2][3][4] The most basic one applied to the simulation of absorption spectra, is based on the computation of the excitation energies of a dye in the ground-state equilibrium geometry, including, if necessary, the solvent effects with an implicit model 5-8 or within an atomistic approach. 9-16 These vertical excitation energies are then compared to the maxima of the corresponding experimental absorption bands. This approach is commonly used, even to benchmark the level of theory for excited-state simulations against experiments. 17 However, comparison of vertical excitation energies can easily become inadequate when accurate estimations of the absorption spectrum are needed. 1 The coupling of electronic transitions to nuclear degrees of freedom (DOFs), for example, generates a characteristic vibronic progression, and can result in an asymmetrical lineshape even when the vibronic structure is hidden in homogeneous and inhomogeneous broadening. 18 Other factors, such as the configurations sampled by the chromophore and the finite lifetime of the excited state, contribute to the spectral shape.For molecules in condensed phase, peaks positions and intensities in the absorption spectra are also affected by the interactions with the inhomogeneous environment, owing to the many different configurations that the solvent adopts around the molecule. The resulting spectra are thus broadened by the many possible solvatochromic shifts.A method able to reproduce both peak positions and line shapes would be of crucial importance to the computatio...

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“…The advantage of the quantum-classical method is that we can investigate the dynamics of model systems with a realistic size and geometry of extensive molecular aggregates. Additionally, this method is not constrained to harmonic bath dynamics and allows us to include the effect of anharmonicities often seen in, for example, hydrogen-bonding systems, which can have significant consequences on the two-dimensional spectra. , The presence of very delocalized exciton states in chlorosomes ensures their robustness to perturbations from localized intramolecular vibrations, which require a quantum description and justifies the approximation of the bath with classical trajectories. Previous studies comparing the applied quantum-classical approach with a full quantum treatment for model systems, where the full quantum treatment is possible, demonstrate the need to be cautious with the interpretation of thermalization dynamics. , …”

Section: Methodsmentioning

confidence: 99%

Ultrafast Anisotropy Decay Reveals Structure and Energy Transfer in Supramolecular Aggregates

Erić,

Castro,

et al. 2023

J. Phys. Chem. B

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Chlorosomes from green bacteria perform the most efficient light capture and energy transfer, as observed among natural light-harvesting antennae. Hence, their unique functional properties inspire developments in artificial light-harvesting and molecular optoelectronics. We examine two distinct organizations of the molecular building blocks as proposed in the literature, demonstrating how these organizations alter light capture and energy transfer, which can serve as a mechanism that the bacteria utilize to adapt to changes in light conditions. Spectral simulations of polarization-resolved two-dimensional electronic spectra unravel how changes in the helicity of chlorosomal aggregates alter energy transfer. We show that ultrafast anisotropy decay presents a spectral signature that reveals contrasting energy pathways in different chlorosomes.

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Spectral line shapes in linear absorption and two-dimensional spectroscopy with skewed frequency distributions

Cited by 13 publications

References 67 publications

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Modeling the absorption lineshape of embedded systems from molecular dynamics: A tutorial review

Ultrafast Anisotropy Decay Reveals Structure and Energy Transfer in Supramolecular Aggregates

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