Two-Dimensional Spectroscopy Is Being Used to Address Core Scientific Questions in Biology and Materials Science

Petti, Megan K.; Lomont, Justin P.; Maj, Michał; Zanni, Martin T.

doi:10.1021/acs.jpcb.7b11370

Cited by 77 publications

(60 citation statements)

References 127 publications

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“…The proliferation of two-dimensional optical spectroscopy (2DOS) has revolutionised research into the structure and dynamics of chemical systems. [1][2][3] The detection of coherent quantum superpositions can identify electronic couplings and the existence of excitonic states, as well as vibronic couplings and the motions of nuclear wavepackets on a potential energy surface. 4,5 The study of such coherences requires the use of ultrafast spectroscopic techniques, where 2DOS provides a means of differentiating individual coherence pathways.…”

Section: Introductionmentioning

confidence: 99%

Spectral Filtering as a Tool for Two-Dimensional Spectroscopy: A Theoretical Model

et al. 2018

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Two-dimensional optical spectroscopy is a powerful technique for the probing of coherent quantum superpositions. Recently, the finite width of the laser spectrum has been employed to selectively tune experiments for the study of particular coherences. This involves the exclusion of certain transition frequencies, which results in the elimination of specific Liouville pathways. The rigorous analysis of such experiments requires the use of ever more sophisticated theoretical models for the optical spectroscopy of electronic and vibronic systems. Here we develop a nonimpulsive and non-Markovian model, which combines an explicit definition of the laser spectrum, via the equation of motion-phase matching approach (EOM-PMA), with the hierarchical equations of motion (HEOM). This theoretical framework is capable of simulating the 2D spectroscopy of vibronic systems with low frequency modes, coupled to environments of intermediate and slower time scales. In order to demonstrate the spectral filtering of vibronic coherences, we examine the elimination of lower energy peaks from the 2D spectra of a zinc porphyrin monomer upon blue-shifting the laser spectrum. The filtering of Liouville pathways is revealed through the disappearance of peaks from the amplitude spectra for a coupled vibrational mode.

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Section: Introductionmentioning

confidence: 99%

Spectral Filtering as a Tool for Two-Dimensional Spectroscopy: A Theoretical Model

et al. 2018

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“…Nonetheless their potential in routine analytical diagnosis is not yet well established and this is especially true for the non-linear techniques [1,2]. The effort to disentangle specific structural information from complex spectra of complex molecular systems is still a challenge [3]. Many studies are presently reported on short medium and even large molecular systems [3,4].…”

Section: Introductionmentioning

confidence: 99%

“…The effort to disentangle specific structural information from complex spectra of complex molecular systems is still a challenge [3]. Many studies are presently reported on short medium and even large molecular systems [3,4]. The aim is to disentangle homogeneous pieces of information out of broad inhomogeneous signals.…”

Section: Introductionmentioning

confidence: 99%

Linear and Non-Linear Middle Infrared Spectra of Penicillin G in the CO Stretching Mode Region

Ragnoni¹,

Catalini²,

Becucci

et al. 2021

Symmetry

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In this work we report the linear and non-linear IR spectral response characterization of the CO bonds of PenicillinG sodium salt in D2O and in DMSO−d6 solutions. In order to better characterize the spectral IR features in the CO stretching region, broadband middle infrared pump-probe spectra are recorded. The role of hydrogen bonds in determining the inhomogeneous broadening and in tuning anharmonicity of the different types of oscillators is exploited. Narrow band pump experiments, at the three central frequencies of β−lactam, amide and carboxylate CO stretching modes, identify the couplings between the different types of CO oscillators opening the possibility to gather structural dynamic information. Our results show that the strongest coupling is between the β−lactam and the carboxylate CO vibrational modes.

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“…With recent advancements in lasers and optics, MDS experiments are becoming routine. Applications of MDS in semiconductor photophysics [CTK + 15], medicine [FGG + 09], and other domains [PLMZ18] are currently being developed. Ultimately, MDS may become a key research tool akin to multidimensional nuclear magnetic resonance spectroscopy.…”

Section: Introductionmentioning

confidence: 99%

WrightSim: Using PyCUDA to Simulate Multidimensional Spectra

Sunden¹,

Thompson²,

Wright³

2018

Proceedings of the Python in Science Conference

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Abstract-Nonlinear multidimensional spectroscopy (MDS) is a powerful experimental technique used to interrogate complex chemical systems. MDS promises to reveal energetics, dynamics, and coupling features of and between the many quantum-mechanical states that these systems contain. In practice, simulation is typically required to connect measured MDS spectra with these microscopic physical phenomena. We present an open-source Python package, WrightSim, designed to simulate MDS. Numerical integration is used to evolve the system as it interacts with several electric fields in the course of a multidimensional experiment. This numerical approach allows WrightSim to fully account for finite pulse effects that are commonly ignored. WrightSim is made up of modules that can be exchanged to accommodate many different experimental setups. Simulations are defined through a Python interface that is designed to be intuitive for experimentalists and theorists alike. We report several algorithmic improvements that make WrightSim faster than previous implementations. We demonstrated the effect of parallelizing the simulation, both with CPU multiprocessing and GPU (CUDA) multithreading. Taken together, algorithmic improvements and parallelization have made WrightSim multiple orders of magnitude faster than previous implementations. WrightSim represents a large step towards the goal of a fast, accurate, and easy to use general purpose simulation package for multidimensional spectroscopy. To our knowledge, WrightSim is the first openly licensed software package for these kinds of simulations. Potential further improvements are discussed.

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Two-Dimensional Spectroscopy Is Being Used to Address Core Scientific Questions in Biology and Materials Science

Cited by 77 publications

References 127 publications

Spectral Filtering as a Tool for Two-Dimensional Spectroscopy: A Theoretical Model

Spectral Filtering as a Tool for Two-Dimensional Spectroscopy: A Theoretical Model

Linear and Non-Linear Middle Infrared Spectra of Penicillin G in the CO Stretching Mode Region

WrightSim: Using PyCUDA to Simulate Multidimensional Spectra

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