Spectroscopic study of fast conformational dynamics in perdeuteriated cyclopentene and its monohydrogenated [3-1H1] and [4-1H1] derivatives

Cavagnat, D.; Banisaeid-Vahedie, S.; Lespade, L.; Rodin, S.

doi:10.1039/ft9928801845

Cited by 9 publications

(21 citation statements)

References 47 publications

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“…This suggests that the simple analysis used in NMR is not directly applicable to the vibrational case. But despite this difficulty, some authors nonetheless use an analysis analogous to that for exchange in NMR to deduce approximate values for rate constants at the temperature at which vibrational band coalescence is observed [e.g., Cavagnat et al (1992) and Turner et al (1995)], and we shall do the same here. Thus from the uncertainty relation, the lifetime broadening is given by δE ≈ h/2πτ, where τ is the lifetime, so that two spectral bands characteristic of two interconverting states and separated in frequency by δν will coalesce when τ is of the order of 1/2πδν.…”

Section: Resultsmentioning

confidence: 99%

Residual Structure in Unfolded Proteins Revealed by Raman Optical Activity

1996

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Because of its ability to probe directly the chiral elements of the peptide backbone, together with the very short time scale of the scattering process, vibrational Raman optical activity (ROA) can provide new information on structure in non-native states of proteins. Here we report ROA studies of hen egg white lysozyme and bovine ribonuclease A in unfolded denatured states, prepared by reducing all the disulfide bonds. ROA spectra of unfolded lysozyme at 45, 20, and 2 degrees C, and of unfolded ribonuclease A at 35 and 20 degrees C, are presented and discussed. At 45 and 20 degrees C, unfolded lysozyme appears to contain very little extended secondary structure, but at 2 degrees C there could be roughly 20% of the native amount of alpha-helix present but little beta-sheet. Unfolded ribonuclease A, on the other hand, appears to contain roughly 50% of its native-like secondary structure, including both alpha-helix and beta-sheet, at 20 degrees C; similar secondary structure persists at 35 degrees C, but the amount is reduced. The most striking result is the observation of three sharp ROA bands in the extended amide III region, originating in coupled C alpha-H and N-H deformations, which might monitor directly the dominant intrinsic propensities for residues to adopt particular phi, psi angles, averaged over the different amino acids in the mobile heteropolypeptide. Specifically, positive bands at approximately 1300 and 1314 cm-1 appear to monitor propensities for alpha-helix and beta-structure, respectively, and a negative band at approximately 1237 cm-1 appears to monitor that for the poly(L-proline) II helix. These signals are generated by individual residues clustering in the most favorable regions of the Ramachandran plot and are present even in the absence of signals from the corresponding extended secondary structures. At 45 degrees C, the 1300 and 1314 cm-1 ROA bands of unfolded lysozyme coalesce into a single sharp band from which an analysis similar to that used for exchange effects in NMR suggests a rate of approximately 2.6 x 10(12) s-1 for interconversion between the individual residue conformations at this temperature.

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Section: Resultsmentioning

confidence: 99%

Residual Structure in Unfolded Proteins Revealed by Raman Optical Activity

1996

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“…For comparison, we report the results of an analogous study on cyclopentene, by the same group. 40 In the latter case, a slightly greater dependence on the position in the ring, is noticed rather than from the conformation, while for cyclohexene it is the other way around. If one assumes that the vibrational optical activity observed in the NIR is generated by the interaction of the ensemble of ring CHstretchings, one can perceive that the absolute configuration and the distance from the C=C bond may influence the geometry of the normal modes of the ensemble, since a noticeable dependence of the 's in the ensemble is experimentally observed: this may be parallel to the correlation pointed out in point (2) of the introduction between VCD signals and configuration/distance from the C=C.…”

Section: Determination Of the Spectroscopic Parameters For (R)-limonementioning

confidence: 92%

Theoretical and experimental studies for the interpretation of vibrational circular dichroism spectra in the CH-stretching overtone region

2000

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Two theoretical models for the interpretation of the existing data of CH‐stretching overtones' vibrational circular dichroism data are presented. The first model is based on the quantum mechanical Van Vleck contact transformation theory and is applied to the full vibrational problem, the second is based on classical trajectories calculations, by which we treat a simplified three‐degrees of freedom Hamiltonian. The latter allows one to derive a qualitative but efficacious picture of the behavior of coupled anharmonic oscillators. In this framework, we analyze the Poincaré Surfaces of Section, and calculate the Fourier Cross Spectra of coupled CH‐stretchings. Values for the harmonic frequencies and anharmonicities are derived from absorption spectra in the near infrared on partially deuterated compounds. The effect of large amplitude, low‐frequency puckering or twisting modes on the ensemble of coupled CH‐stretching is taken into account. Chirality 12:180–190, 2000. © 2000 Wiley‐Liss, Inc.

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“…Cyclopentene constitutes a prototype of non rigid molecules interconverting via a puckering motion between two equivalent non planar ring structures. A great number of experimental investigations − has evidenced that the puckering potential has a double minimum with a barrier to planarity of some 230 cm -1 and that the equilibrium angle between the two dihedral planes of the puckering ring is situated in the range of 22° to 26°. Some mathematical − analyses have modeled the potential function by a polynomial form V ( X ) = V 2 X 2 + V 4 X , X being the puckering coordinate (Figure ).…”

Section: Introductionmentioning

confidence: 99%

“…The coupling between the ring-puckering motion and the higher energy vibrations has been pointed out in numerous studies. ,,− The CH stretching has received particular attention with the measurement of the CH stretching overtone spectra of the fully hydrogenated cyclopentene 20,21 and through the studies of different selectively deuterated compounds. − These latter studies have shown that the overtone spectra can be correctly reproduced by treating the coupling between the ring-puckering motion and the other vibrations in the adiabatic approximation and considering the rapid intramolecular vibrational redistribution (IVR) between the CH stretching and the angle deformation vibrations through Fermi resonance couplings. A model Hamiltonian has been written in internal curvilinear coordinates.…”

Section: Introductionmentioning

confidence: 99%

A New Way for IVR Induced by Fast Internal Motion As Revealed by a Jet-Cooled Spectrum of Cyclopentene

2002

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The CH stretching spectra of cyclopentene at 25 K in a molecular beam and at room temperature in a gas cell are measured and compared. These spectra are modeled with an Hamiltonian written in curvilinear coordinates and taking into account, in the adiabatic approximation, the coupling of the CH stretching vibrations with the puckering motion and the angle deformations by Fermi resonance. The curves of the vibrational energy calculated as a function of the puckering coordinate exhibit several crossings. From these crossing points, the vibrational energy can follow different ways. The probability of following one or the other way is discussed and determined from the fit of the two spectra. The presence of some stretching vibrations with an unexpected asymmetrical variation is experimentally evidenced. A correct reproduction of the experimental spectra is obtained.

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Spectroscopic study of fast conformational dynamics in perdeuteriated cyclopentene and its monohydrogenated [3-1H1] and [4-1H1] derivatives

Cited by 9 publications

References 47 publications

Residual Structure in Unfolded Proteins Revealed by Raman Optical Activity

Residual Structure in Unfolded Proteins Revealed by Raman Optical Activity

Theoretical and experimental studies for the interpretation of vibrational circular dichroism spectra in the CH-stretching overtone region

A New Way for IVR Induced by Fast Internal Motion As Revealed by a Jet-Cooled Spectrum of Cyclopentene

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