Comparison of calculated and experimental FTIR spectra of specifically labeled ubiquinones

Lamichhane, Hari Prasad; Wang, Ruili; Hastings, Gary

doi:10.1016/j.vibspec.2010.12.008

Cited by 12 publications

(29 citation statements)

References 17 publications

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“…In our calculations we used UQ models with only a single isoprene unit. As outlined previously [21], the calculated vibrational properties of UQ 1 (or UQ 1 − ) are very similar to that found for UQ (with 1). Also shown in Figure 1 are relevant internal coordinates of UQ 1 − .…”

Section: 1supporting

confidence: 78%

“…e methoxy methyl CH bending vibrations (coordinates C8 and C9) are also of considerable relevance in this paper, as they strongly couple to the C⋯O vibrations (see below). is was not found to occur for neutral UQ [21].…”

Section: 1mentioning

confidence: 82%

“…Such a scaling of the calculated frequencies is undertaken only to facilitate a comparison between calculated and experimental spectra. We are primarily interested in vibrational frequency changes that occur upon isotope labeling, and these frequency differences are accurately calculated without scaling [14,21]. Figure 1 shows a geometry-optimized UQ 1 − model with the atom numbering scheme displayed.…”

Section: 1mentioning

confidence: 99%

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Calculated Vibrational Properties of Ubisemiquinones

Lamichhane

Hastings

2013

Computational Biology Journal

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Density functional theory has been used to calculate harmonic normal mode vibrational frequencies for unlabeled and isotopelabeled ubisemiquinones in both the gas phase and in several solvents. It is shown that four methoxy group conformations are likely to be present in solution at room temperature. Boltzmann weighted infrared and Raman spectra for the four conformers were calculated, and composite spectra that are the sum of the Boltzmann weighted spectra were produced. ese composite spectra were compared to experimental FTIR and resonance Raman spectra, and it is shown that the calculated band frequencies, relative band intensities, and 13 C and 18 O isotope-induced band shis are in excellent agreement with experiment. e calculations show that the C=O and C=C modes of ubisemiquinone strongly mix with methoxy methyl CH bending vibrations, and that the degree of mixing is altered upon isotope labeling, resulting in complicated changes in mode frequencies, intensities, and composition upon isotope labeling. Upon consideration of the calculated potential energy distributions of the normal modes of ubisemiquinone, and how they change upon isotope labeling, an explanation of some puzzling features in previously published Raman spectra is provided.

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Section: 1supporting

confidence: 78%

Section: 1mentioning

confidence: 82%

Section: 1mentioning

confidence: 99%

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Calculated Vibrational Properties of Ubisemiquinones

Lamichhane

Hastings

2013

Computational Biology Journal

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“…However, due to the interaction with neighbors the composite spectrum of molecules in vivo is very complex. Isotope labeling is one of the methods of separating contribution of a particular group of vibration in the composite spectrum [1][2][3][4][5]. Frequency of vibration is generally decreases upon isotope labeling of some atom which takes part in the vibration when it is replaced with a heavier isotope.…”

Section: Introductionmentioning

confidence: 99%

“…Ubiquinones (UQ n : 2,3-dimethoxy-5-methyl-6-polyprenyl-1,4-benzoquinone) which play an important role in biological electron and proton transfer processes that occur in both respiration and photosynthesis [6] have intense IR spectral bands in the frequency region between 1700 to 1550 cm -1 in the neutral state in solvent and in the purple bacteria reaction centers [1,4,5,[7][8][9][10][11][12][13][14][15]. These IR bands are originated from the stretching vibration of C=O and C=C bonds of ubiquinone.…”

Section: Introductionmentioning

confidence: 99%

Intensity Revival of Weak Symmetric Infrared Band is Possible in Ubiquinone Molecules through the Asymmetric Site-specific Isotope Labeling

Lamichhane¹

2015

Himalayan Physics

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Computational Characterization of Perezone, Isoperezone and their Sulfur‐Derivatives: Anti‐inflammatory Activity.

et al. 2019

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Using DFT and in silico methods a theoretical study, to verify the spectroscopically characterization, this in addition to determine the anti‐inflammatory activity of a set of eight sulfur derivatives of perezone and isoperezone was performed. In this sense, conformational studies for the target sulfurs were carried out, in order to obtain the corresponding minimum energy structures. Also, the vibrational frequencies analysis, the magnitude of 1H NMR and 13C NMR spectra for perezone, isoperezone, and its sulfur‐derivatives, obtained by the DFT/B3LYP/6‐311++G(d,p) method correlated satisfactorily with the experimental data. Moreover, the calculation of physicochemical properties, and the prediction of the anti‐inflammatory activity, employing both PASS predictor and docking studies towards COX‐2 for the target compounds, showed that Benzy perezone is a good candidate as a therapeutic agent; finally, the anti‐inflammatory activity of Benzy perezone was evaluated in vivo, showing a similar naproxen activity.

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Comparison of calculated and experimental FTIR spectra of specifically labeled ubiquinones

Cited by 12 publications

References 17 publications

Calculated Vibrational Properties of Ubisemiquinones

Calculated Vibrational Properties of Ubisemiquinones

Intensity Revival of Weak Symmetric Infrared Band is Possible in Ubiquinone Molecules through the Asymmetric Site-specific Isotope Labeling

Computational Characterization of Perezone, Isoperezone and their Sulfur‐Derivatives: Anti‐inflammatory Activity.

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