Coherent Two-Dimensional Optical Spectroscopy

Cho, Minhaeng

doi:10.1021/cr078377b

Cited by 768 publications

(735 citation statements)

References 534 publications

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“…This displays the third-order optical signal collected in an experiment exploiting four infrared or visible laser pulses with variable delays times between them. 1 To probe the vibrational or electronic dynamics, the delay time between the first and the second pulse pair is particularly important; this is usually referred to as the waiting time. The signal measured is complex valued, and multiple ways of plotting it have been devised.…”

Section: Resultsmentioning

confidence: 99%

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Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an α-Helix

2010

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A simulation study of the coupled dynamics of amide I and amide II vibrations in an R-helix dissolved in water shows that two-dimensional (2D) infrared spectroscopy may be used to disentangle the energy transport along the helix through each of these modes from the energy relaxation between them. Time scales for both types of processes are obtained. Using polarization-dependent 2D spectroscopy is an important ingredient in the method we propose. The method may also be applied to other two-band systems, both in the infrared (collective vibrations) and the visible (excitons) parts of the spectrum.

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Section: Resultsmentioning

confidence: 99%

“…In particular, twodimensional infrared (2DIR) and visible (2Dvis) spectroscopy 1 are rapidly gaining popularity to probe energy transport and relaxation in complex molecular systems. These spectroscopies have been developed during the past decade as analogues of two-dimensional NMR (2DNMR) experiments.…”

Section: Introductionmentioning

confidence: 99%

Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an α-Helix

2010

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“…1,2,9 The efforts to date can be subdivided into empirical models aimed at predicting the amide I band of proteins, or more recent approaches that utilize small molecule ab initio data in a parametrized fashion to construct a Hamiltonian for the system. These so called building block approaches have proven comparatively successful for simulation of polypeptides with regular secondary structures, 7 but have been found less successful for simulation of real proteins such as ubiquitin. 10 As a crucial element of these approaches, the concept of the "floating oscillator model" was established.…”

Section: Introductionmentioning

confidence: 99%

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

2012

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A new simulation protocol for the prediction of the infrared absorption of the amide I vibration of proteins was developed. The method incorporates known effects on the intrinsic frequencies (backbone conformation, inter-peptide and peptide-solvent hydrogen bonding) and couplings (nearest neighbor coupling, transition dipole coupling) of amide I oscillators in a parametrized manner. Model parameters for the simulation of amide I spectra were determined through fitting and optimization of simulated spectra to experimentally measured infrared spectra of 44 proteins that represent maximum structural variation in terms of different folds and secondary structure contents. Prediction of protein spectra using the optimized parameters resulted in good agreement with experimental spectra and in a considerable improvement compared to a description involving only transition dipole coupling.

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“…For example, nuclear magnetic resonance (NMR [1,2]) is extensively used for atomistic structure determination in solution and probing folding or unfolding dynamics on microseconds and longer time scales [3,4]. Other techniques, such as small angle X-ray scatering [5,6], circular dichroism [7], fluorescence [8], Raman [9], Fourier transform infrared (FTIR) and two dimensional infrared (2DIR) [10][11][12][13] spectroscopy are excellent complementary tools that provide insights on local and global structure and dynamics.…”

Section: Introductionmentioning

confidence: 99%

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

Roy

Lessing

Meisl

et al. 2011

The Journal of Chemical Physics

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We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D 2 O and compare with experimental observations.

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Coherent Two-Dimensional Optical Spectroscopy

Cited by 768 publications

References 534 publications

Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an α-Helix

Two-Dimensional Spectroscopy of Extended Molecular Systems: Applications to Energy Transport and Relaxation in an α-Helix

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

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