Interference, dephasing, and vibrational coupling effects between coherence pathways in doubly vibrationally enhanced nonlinear spectroscopies

Besemann, Daniel M.; Condon, Nicholas J.; Murdoch, Keith M.; Zhao, Wei; Meyer, Kent A.; Wright, John

doi:10.1016/s0301-0104(01)00227-0

Cited by 17 publications

(27 citation statements)

References 42 publications

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“…Enhanced Four-Wave Mixing spectroscopy (20)(21)(22)(23)(24)(25)] requires the overlap of two picosecond infrared (IR) beams and a picosecond visible beam on the sample. A nonlinear visible signal generated by the induced polarizations is detected.…”

Section: Evv 2dir Spectroscopy [Also Known As Doubly-vibrationallymentioning

confidence: 99%

Protein identification and quantification by two-dimensional infrared spectroscopy: Implications for an all-optical proteomic platform

Fournier¹,

Gardner

Kedra

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Twodimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to <1 min per protein by using the same technology. Finally, we show that absolute quantification of protein levels is relatively straightforward to achieve and discuss the potential of an all-optical high-throughput proteomic platform based on two-dimensional infrared spectroscopic measurements.2DIR ͉ amino acid ͉ bioinformatics ͉ vibrational T he potential of proteomic tools ranges from biomarker discovery and clinical diagnostics to the provision of data for systems biology and fundamental biological research (1-6). This broad range of applications is one of the drivers for the development of protein analysis tools with greater capability. Optical spectroscopies appear to have significant potential for protein analysis (7-9), but conventional approaches suffer from overcongested spectra, which makes feature assignment and quantification highly problematic. Multidimensional coherent infrared spectroscopic techniques, commonly referred to as twodimensional infrared (2DIR) spectroscopies, might be expected to be able to relieve the congestion of infrared spectra sufficiently to allow such assignment and quantification to take place. Indeed, we recently demonstrated how picosecond electronvibration-vibration (EVV) four-wave mixing experiments can decongest 2DIR spectra to an even greater extent (10, 11), and showed how such an EVV approach can be applied to the analysis of peptides (12). In this article we take the approach further to show that it can be used to differentiate and identify proteins and to measure absolute protein quantities. We also demonstrate that the sensitivity and throughput of our EVV 2DIR apparatus is sufficient for this method to be considered for use as a real proteomic tool.Although our previous work showed that it is possible to quantify relative amino acid levels for short peptides (12), there is always the possibility that primary, secondary, or tertiary structural effects would prevent such measurements on proteins.In this article we demonstrate that these structural sensitivities are not limiting factors either for differentiation/identification or for absolute quantification of protein levels.The key proposition of this article is that protein identification can be performed by using spectroscopically determined amino acid content, relative to an internal reference. Amino acid composition analysis is an approach that has been used to determine protein relatedness (13) and protein structural classes (14, 15). Although it is known that c...

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Section: Evv 2dir Spectroscopy [Also Known As Doubly-vibrationallymentioning

confidence: 99%

Protein identification and quantification by two-dimensional infrared spectroscopy: Implications for an all-optical proteomic platform

Fournier¹,

Gardner

Kedra

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…The effects of solvent are both static, causing variations in the average dielectric environment about the solute molecules, and dynamic, producing time‐dependent fluctuations in the energy levels of the system. Historically, simulation has played an important role in understanding the dynamics of condensed‐phase systems,1–4 and in the last two decades, time‐domain nonlinear spectroscopy has provided great insight into solvent dynamics 5–13. However, the methods that provide direct theoretical links between computation and experiment are still under development.…”

Section: Introductionmentioning

confidence: 99%

Hybrid molecular dynamics‐quantum mechanics simulations of solute spectral properties in the condensed phase: Evaluation of simulation parameters

2007

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We have explored the impact of a number of basic simulation parameters on the results of a recently developed hybrid molecular dynamics-quantum mechanics (MD-QM) method (Mercer et al., J Phys Chem B 1999, 103, 7720). The method utilizes MD simulations to explore the ground-state configuration space of the system and QM evaluation of those structures to yield the time-dependent electronic transition energy, which is transformed into the optical line-broadening function using the second-order cumulant expansion. Both linear and nonlinear optical spectra can then be generated for comparison to experiment. The dependence of the resulting spectra on the length of the MD trajectory, the QM sampling rate, and the QM model chemistry have all been examined. In particular, for the system of oxazine-4 in methanol studied here, at least 20 ps of MD trajectory are needed for qualitative convergence of linear spectral properties, and >100 ps is needed for quantitative convergence. Surprisingly, little difference is found between the 3-21G and 6-31G(d) basis sets, and the CIS and TD-B3LYP methods yield remarkably similar spectra. The semiempirical INDO/s method yields the most accurate results, reproducing the experimental Stokes shift to within 5% and the FWHM to within 20%. Nonlinear 3-pulse photon echo peak shift (3PEPS) decays have also been simulated. Decays are generally poorly reproduced, though the initial peak shift which depends on the overall coupling of motions to the solute transition energy is within 15% of experiment for all model chemistries other than those using the STO-3G basis.

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“…Thus, at least one of the transitions must involve a combination band. 23 In our examples, the ω 1 frequency is resonant with a combination band, g → , which is a mixture of the v and fundamentals. The ω 2 excitation is resonant with the g → fundamental.…”

Section: Dove Methodsmentioning

confidence: 89%

“…1,22,23 For the dominant DOVE-IR peak in CH3CN, we estimate a magnitude of 4.3 × 10 −14 cm 3 /erg. This value is close to the experimental value of 3.4 × 10 −14 cm 3 /erg.…”

Section: Relationships Between Multidimensional and One Dimensional Mmentioning

confidence: 87%

“…1,22,23 For example, the DOVE-IR and DOVE-Raman processes can be described as two amplitude level infrared transitions and a single amplitude level Raman transition. The magnitude of the DOVE-IR χ (3) value is therefore directly related to the magnitude of the infrared absorption coefficients for the two infrared transitions and the magnitude of χ (3) for the Raman transition.…”

Section: Relationships Between Multidimensional and One Dimensional Mmentioning

confidence: 99%

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Experimental Determinations of Coherent Multidimensional Vibrational Spectroscopy

Besemann¹,

Condon²,

Meyer³

et al. 2003

Bulletin of the Korean Chemical Society

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Coherent multidimensional vibrational spectroscopy is a new technique for establishing correlations between features in vibrational spectra that are caused by intra-and intermolecular interactions. These interactions cause cross-peaks between vibrational transitions that reflect the coupling. In this paper, we use Doubly Vibrationally Enhanced Infrared Spectroscopy (DOVE-IR) and DOVE-Raman processes to obtain coherent two dimensional vibrational spectra. The spectra are fitted to obtain the dephasing rates and third order susceptibilities (χ (3) ) for the nonlinear processes. We show that the DOVE χ (3) values are directly related to the molar absorptivities and Raman χ (3) . We then use these relationships to obtain estimates for the χ (3) of the stimulated photon echo and χ (5) of the six wave mixing spectroscopies, respectively. We also predict the ratio of the cascaded four wave mixing signal to the six wave mixing signal.

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Interference, dephasing, and vibrational coupling effects between coherence pathways in doubly vibrationally enhanced nonlinear spectroscopies

Cited by 17 publications

References 42 publications

Protein identification and quantification by two-dimensional infrared spectroscopy: Implications for an all-optical proteomic platform

Protein identification and quantification by two-dimensional infrared spectroscopy: Implications for an all-optical proteomic platform

Hybrid molecular dynamics‐quantum mechanics simulations of solute spectral properties in the condensed phase: Evaluation of simulation parameters

Experimental Determinations of Coherent Multidimensional Vibrational Spectroscopy

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