Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution

Schrenková, Věra; Kkadan, Mohammed Siddhique Para; Kessler, Jiří; Kapitán, Josef; Bouř, Petr

doi:10.1039/d2cp05756e

Cited by 9 publications

(8 citation statements)

References 70 publications

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“…The spectral decompositions indicate inaccuracies in the force field, but they are themselves affected by the DFT error and other approximations, and about 10–20 % uncertainty in the conformer populations thus obtained can be expected [8d,23,25] . An error about 10 % can also be estimated for GSH 3− from the conformer populations obtained from various numbers of averaged clusters (Figure S7, other forms provided similar dependencies).…”

Section: Resultsmentioning

confidence: 82%

“…The dependencies of the free energy on the ψ 2 and χ 3 torsion angles obtained by the spectral fit and MD are plotted in Figure 7, top, the resultant fitted spectra are plotted at the bottom. Note that the fitted energy surfaces, although they should converge to the true dependencies, [24] are for a limited coverage of the ( ψ 2 , χ 3 ) plane by the MD snapshots just arbitrary functions mediating the fit [25] . Yet some relations to the MD results are apparent, e. g., for GSH + the fit suggests that the most favorite position is close to conformer 5 ( ψ 2 , χ 3 )∼(140°,75°) while conformers 3 and 6 with χ 3 ∼180° are not present in the sample, etc.…”

Section: Resultsmentioning

confidence: 99%

“…To relate the spectra to the conformation of GSH backbone decomposition algorithm based on arbitrary potential energy surfaces was used [24,25] . Briefly, the experimental spectra S e were thought of as weighted sums of the calculated ones S c , shown in Equation (3):

\vcenter{\openup.5em\halign{$\displaystyle{#}$\cr S_e \approx \sum\limits_{i = 1}^N {p_i S_{c,i} } .\hfill\cr}}

…”

Section: Methodsmentioning

confidence: 99%

“…functions mediating the fit. [25] Yet some relations to the MD results are apparent, e. g., for GSH + the fit suggests that the most favorite position is close to conformer 5 (ψ 2 ,χ 3 ) ~(140°,75°) while conformers 3 and 6 with χ 3 ~180°are not present in the sample, etc. The spectral decompositions indicate inaccuracies in the force field, but they are themselves affected by the DFT error and other approximations, and about 10-20 % uncertainty in the conformer populations thus obtained can be expected.…”

Section: Chempluschemmentioning

confidence: 96%

“…To relate the spectra to the conformation of GSH backbone decomposition algorithm based on arbitrary potential energy surfaces was used. [24,25] Briefly, the experimental spectra S e were thought of as weighted sums of the calculated ones S c , shown in Equation (3):…”

Section: Spectral Decomposition and Fittingmentioning

confidence: 99%

See 4 more Smart Citations

Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics

Das¹,

Gangopadhyay

Hudecová

et al. 2023

ChemPlusChem

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Glutathione (GSH) is a common antioxidant and its biological activity depends on the conformation and protonation state. We used molecular dynamics, Raman and Raman optical activity (ROA) spectroscopies to investigate GSH structural changes in a broad pH range. Factor analysis of the spectra provided protonation constants (2.05, 3.45, 8.62, 9.41) in good agreement with previously published values. Following the analysis, spectra of differently protonated forms were obtained by extrapolation. The complete deprotonation of the thiol group above pH 11 was clearly visible in the spectra; however, many spectral features did not change much with pH. Experimental spectra at various pH values were decomposed into the simulated ones, which allowed us to study the conformer populations and quality of molecular dynamics (MD). According to this combined ROA/MD analysis conformation of the GSH backbone is affected by the pH changes only in a limited way. The combination of ROA with the computations thus has the potential to improve the MD force field and obtain more accurate populations of the conformer species. The methodology can be used for any molecule, but for a more detailed insight better computational techniques are needed in the future.

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Section: Resultsmentioning

confidence: 82%

Section: Resultsmentioning

confidence: 99%

\vcenter{\openup.5em\halign{$\displaystyle{#}$\cr S_e \approx \sum\limits_{i = 1}^N {p_i S_{c,i} } .\hfill\cr}}

…”

Section: Methodsmentioning

confidence: 99%

Section: Chempluschemmentioning

confidence: 96%

Section: Spectral Decomposition and Fittingmentioning

confidence: 99%

See 3 more Smart Citations

Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics

Das¹,

Gangopadhyay

Hudecová

et al. 2023

ChemPlusChem

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(Resonance) Raman optical activity among chiroptical spectroscopies: Quo vadis?

Halat,

Pajor,

Baranski

et al. 2024

J Raman Spectroscopy

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Although the potential of Raman Optical Activity (ROA) spectroscopy in the field of organic and inorganic materials research has been well demonstrated, its practical application is still limited. This work shows historical background, current state of the art and challenges of ROA spectroscopy facing scientists today. Expectations and development prospects for the coming years are also discussed. Efforts have already been made to improve but also to properly interpret the ROA signal when the ROA technique is combined with other spectroscopies (i.e., ROA/Electronic Circular Dichroism and ROA/Circularly Polarized Luminescence). The paper shows how to intensify the ROA effect to shorten the spectrum accumulation time, control possible artefacts and support the analysis of ROA spectra with actual and new theoretical approaches. However, the challenge is to increase the interest in this technique among the academic community, develop reliable protocols and adapt them for practical use. National and international research networks can significantly contribute to the growth of methodologies and standardization in areas in which the ROA has so far been little used. This paper presents a perspective vision for the future progress of ROA alongside other chiroptical methods.

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A Novel Incident Circular Polarized Light Raman Optical Activity (ICP‐ROA) Spectrometer With Advanced Polarization Control

Hofmann,

Martin,

Fischer

2024

J Raman Spectroscopy

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The design and setup of a novel and simple backscatter Raman optical activity (ROA) spectrometer with incident light circular polarization (ICP) is presented, constructed from commercially available components. Incident light polarization is controlled using a combination of waveplates, compensating for unwanted birefringence and beam offsets. Realignment of the spectra in post‐processing reduced artifacts caused by spatial offsets. Spurious signals from achiral solvents like toluene and water are almost completely removed. The setup was validated by measuring references samples, including α‐pinene, carvone, and glucose in aqueous solution. The spectra show very good agreement with previously published results.

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Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution

Abstract: Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between spectral shape and...

Cited by 9 publications

References 70 publications

Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics

Monitoring Conformation and Protonation States of Glutathione by Raman Optical Activity and Molecular Dynamics

(Resonance) Raman optical activity among chiroptical spectroscopies: Quo vadis?

A Novel Incident Circular Polarized Light Raman Optical Activity (ICP‐ROA) Spectrometer With Advanced Polarization Control

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