Ab initio vibrational analysis of hydrogen-bonded trans- and cis-N-methylacetamide

Mirkin, Noemi G.; Krimm, Samuel

doi:10.1021/ja00026a005

Cited by 137 publications

(124 citation statements)

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“…Figure 7 shows well that the predicted wavenumbers differ by only about 10 cm 1 from the measured data. 47,48 Taking into account the scaling procedure for the calculated frequencies and the uncertainty of measured data, this result is satisfactory.…”

Section: Comentioning

confidence: 69%

Correlations between structural, NMR and IR spectroscopic properties ofN-methylacetamide

Huelsekopf

Ludwig

2001

Magn. Reson. Chem.

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Bond lengths, quadrupole coupling constants, chemical shifts and vibrational frequencies are important probes of hydrogen bonding. This was previously demonstrated for liquid N-methylacetamide (NMA) showing that cooperativity and non-additive contributions of hydrogen bonds play a significant role. The spectroscopic properties were calculated by standard ab initio methods in combination with a quantum cluster equilibrium (QCE) model and compared with measured data from NMR and IR spectroscopy. We have now extended the QCE model to larger molecular clusters and obtained better agreement between calculated and measured liquid-phase properties over large temperature ranges. The obtained linear correlations between spectroscopic properties and bond lengths and between different spectroscopic properties allow predictions for the gas-and the solid-phase values. The results can be used as a prediction tool for larger biomolecular structures where some experimental methods cannot be used or are not accurate enough.

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Section: Comentioning

confidence: 69%

Correlations between structural, NMR and IR spectroscopic properties ofN-methylacetamide

Huelsekopf

Ludwig

2001

Magn. Reson. Chem.

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“…[39][40][41] These calculations do not yet lead to a consensus about the C=O bond order when molecules of solvent are included. [42][43][44][45] We had observed that for peptides similar to 1-3 the barrier to isomerization (ΔG ‡ ) correlates with the frequency of the amide I vibrational mode (υ), 26,46 as predicted from the traditional view. To search for an inductive effect on the rate of cis-trans prolyl peptide bond isomerization (eq 1), we measured these rates for 1 and 3 in dioxane 47 and 1 and 2 in water 48 by using inversion transfer NMR spectroscopy.…”

Section: Inductive Effect On the Amide I Vibrational Modementioning

confidence: 95%

Inductive Effects on the Energetics of Prolyl Peptide Bond Isomerization: Implications for Collagen Folding and Stability

1996

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The hydroxylation of proline residues in collagen enhances the stability of the collagen triple helix. Previous X-ray diffraction analyses had demonstrated that the presence of an electronwithdrawing substituent on the pyrrolidine ring of proline residues has significant structural consequences [Panasik, N., Jr.; Eberhardt, E. S.; Edison, A. S.; Powell, D. R.; Raines, R. T. Int. J. Pept. Protein Res. 1994, 44, 262-269]. Here, NMR and FTIR spectroscopy were used to ascertain kinetic and thermodynamic properties ofThe pK a 's of the nitrogen atom in the parent amino acids decrease in the order: proline (10.8) > 4(R)-hydroxy-L-proline (9.68) > 4(R)-fluoro-L-proline (9.23). In water or dioxane, amide I vibrational modes decrease in the order: 1 > 2 > 3. At 37 °C in dioxane, the rate constants for amide bond isomerization are greater for 3 than 1. Each of these results is consistent with the traditional picture of amide resonance coupled with an inductive effect that results in a higher bond order in the amide C=O bond and a lower bond order in the amide C-N bond. Further, at 37 °C in water or dioxane equilibrium concentrations of the trans isomer increase in the order: 1 < 2 < 3. Inductive effects may therefore have a significant impact on the folding and stability of collagen, which has a preponderance of hydroxyproline residues, all with peptide bonds in the trans conformation.

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“…These effects are here assumed to yield independent and additive shifts of the amide I frequency from the gas phase value ω NMA = 1723 cm −1 of unperturbed, uncoupled NMA, [47][48][49] which has been extensively studied as a model compound of a peptide unit. 31,[50][51][52][53][54][55][56][57] The intrinsic frequency of the amide I oscillator in residue i can thus be described as…”

Section: Amide I Band Calculationmentioning

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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Ab initio vibrational analysis of hydrogen-bonded trans- and cis-N-methylacetamide

Cited by 137 publications

References 1 publication

Correlations between structural, NMR and IR spectroscopic properties ofN-methylacetamide

Correlations between structural, NMR and IR spectroscopic properties ofN-methylacetamide

Inductive Effects on the Energetics of Prolyl Peptide Bond Isomerization: Implications for Collagen Folding and Stability

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

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