Solution-phase Raman studies of alanyl dipeptides and various isotopomers: a reevaluation of the amide III vibrational assignment

Oboodi, M. Reza; Alva, Carlos; Diem, Max

doi:10.1021/j150647a036

Cited by 56 publications

(49 citation statements)

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“…Bands in this region are usually assigned to α-helical structure [13, 14]. Generally, caution is required in associating characteristic frequency ranges with conformation for the Amide III mode given that the NH in-plane bend internal coordinate contributes to a number of modes in the 1,200–1,400 cm −1 region [15] and secondary-structure-dependent coupling occurs between the Amide III and the C α –H bending vibration [16, 17]. This complexity, in addition to the inherent heterogeneity of corneocytes and variable lipid content of the samples examined herein, precludes an in-depth analysis of the Amide III contour in the current context.…”

Section: Resultsmentioning

confidence: 99%

Vibrational microscopy and imaging of skin: from single cells to intact tissue

et al. 2006

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Vibrational microscopy and imaging offer several advantages for a variety of dermatological applications, ranging from studies of isolated single cells (corneocytes) to characterization of endogenous components in intact tissue. Two applications are described to illustrate the power of these techniques for skin research. First, the feasibility of tracking structural alterations in the components of individual corneocytes is demonstrated. Two solvents, DMSO and chloroform/methanol, commonly used in dermatological research, are shown to induce large reversible alterations (α-helix to β-sheet) in the secondary structure of keratin in isolated corneocytes. Second, factor analysis of image planes acquired with confocal Raman microscopy to a depth of 70 μm in intact pigskin, demonstrates the delineation of specific skin regions. Two particular components that are difficult to identify by other means were observed in the epidermis. One small region was formed from a conformationally ordered lipid phase containing cholesterol. In addition, the presence of nucleated cells in the tissue (most likely keratinocytes) was revealed by the spectral signatures of the phosphodiester and cytosine moieties of cellular DNA.

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Section: Resultsmentioning

confidence: 99%

Vibrational microscopy and imaging of skin: from single cells to intact tissue

et al. 2006

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“…These coordinates are defined in Table II and used in assigning the theoretical modes, frequencies, and intensities to specific assignments and/or internal coordinates. In Tables III and IV we present the assignment of the calculated vibrational frequencies for the various isotopmers for which Oboodi et al reported the Raman spectra in the amide III region [13]. This is the work that motivated us to investigate the accuracy of our force field based on the isotopic data available for LALA in aqueous solution.…”

Section: Potential Energy Distributions Based On Internal Coordinatesmentioning

confidence: 99%

“…Hence, to model this molecule (and other zwitterionic species) one should treat the aqueous environment. Early theoretical work on this model system by Diem and coworkers using empirical force fields, which did not include explicit treatment of the aqueous environment, has called into question some of the early assumptions about the nature of the amide modes (derived from an analysis of the vibrational spectra of NMA) [13]. Here, we will look into those questions as well as interpret the VA and VCD spectra of our structure with the goal of gaining not only new understanding into the nature of the "amide" and "peptide" modes but also to answer the question, what is the structure of LALA in aqueous solution, that is, is there only one unique structure (as assumed for larger peptides and proteins) or do we have a distribution of various structures based on their relative Gibbs free energies?…”

mentioning

confidence: 99%

Vibrational analysis of various isotopomers of L‐Alanyl‐L‐Alanine in aqueous solution: Vibrational absorption, vibrational circular dichroism, Raman, and Raman optical activity spectra

Jalkanen

Nieminen

Knapp-Mohammady

et al. 2003

Int J of Quantum Chemistry

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ABSTRACT:In a recent work (Knapp-Mohammady, M.; Jalkanen, K. J.; Nardi, F.; Wade, R. C.; Suhai, S. Chem Phys 1999, 240, 63-77) the structures of the zwitterionic species of l-alanyl-l-alanine (LALA) in aqueous solution using a combination of molecular mechanics (MM) and density functional theory (DFT) have been reported. Subsequently, the vibrational absorption (VA) and vibrational circular dichroism (VCD) and the Raman and Raman Optical Activity (ROA) spectra have been reported. In this work an analysis of the aqueous solution VA, VCD, Raman, and ROA spectra for various isotopomers of LALA are reported. DFT Becke3LYP/6-31G* theory has been used to determine the geometry, Hessian, atomic polar tensors (APT), and atomic axial tensors (AAT), and the electric dipole-electric dipole polarizability derivatives (EDEDPD), which are required for us to simulate the VA, VCD, and Raman spectra. The electric dipole-magnetic dipole polarizability derivatives (EDMDPD) and the electric dipole-electric quadrapole polarizability derivatives (EDEQPD) have been calculated at the RHF/6-31G* level of theory. The VA, VCD, Raman, and ROA spectral simulations for the various isotopomers are compared with the experimentally measured spectra. With the DFT, explicit water molecules, and a continuum solvent model we are better able to reproduce the vibrational absorption and Raman spectra than previously reported. The AAT have been implemented at the DFT level, although not within the continuum treatment. The VCD sign pattern could be reproduced with the DFT atomic axial tensors calculated for the LALA plus explicit water molecules. The continuum treatment of the solvent for the calculation of these tensors appears to be a secondary effect. The ROA spectra are not well reproduced due to the failure to take into account electron correlation via DFT and the continuum treatment of the solvent for the EDMDPD and EDEQPD. We look forward to reporting ROA simulations utilizing more accurate tensors in the near future.

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“…A sample of methinedeuterated L-alanyl-C,-d ,-L-alanine-C,-d, was kindly provided by Professor Max Diem of Hunter College. 23 The amino and amide hydrogens were exchanged for deuterium by dissolving the peptides in D,O and exchanging on a rotary evaporator a t least three times prior to preparation of D,O solutions. Low and high pD samples were prepared by adding approximately twofold mole excess quantities of 1M HCl or NaOH, respectively, before the deu-terium exchange.…”

Section: Samples Of L-and Dmentioning

confidence: 99%

Vibrational CD studies of the solution conformation of simple alanyl peptides as a function of pH

1989

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The CH-stretching vibrational CD (VCD) spectra of glycyl-L-alanine, L-alanylglycine, and L-alanyl-L-alanine have been studied at neutral, high, and low pH in D2O solution. The intense positive VCD band attributed to the C alpha H stretch of the alanyl residue in glycyl-L-alanine at neutral pH is absent in L-alanylglycine. In contrast to the VCD spectra of L-alanine, the positive methine-stretching VCD band in glycyl-L-alanine and L-alanyl-L-alanine is still present at pH 2. Based on the ring current mechanism, the VCD spectra are consistent with the presence of a five-membered CO...HN intramolecular hydrogen-bonded ring between the C-terminal carboxylate and peptide NH groups at neutral and high pH; and a seven-membered COH...O = C hydrogen-bonded ring between the C-terminal carboxyl OH and peptide C = O groups at low pH. In the N-terminal alanyl residue, the peptide C = O group is hydrogen bonded to the NH trans to the methine bond. The CH-stretching VCD spectra of L-alanyl-L-alanyl-L-alanine at neutral pH are consistent with two intramolecularly hydrogen-bonded conformations for the central alanyl residue.

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Solution-phase Raman studies of alanyl dipeptides and various isotopomers: a reevaluation of the amide III vibrational assignment

Cited by 56 publications

References 0 publications

Vibrational microscopy and imaging of skin: from single cells to intact tissue

Vibrational microscopy and imaging of skin: from single cells to intact tissue

Vibrational analysis of various isotopomers of L‐Alanyl‐L‐Alanine in aqueous solution: Vibrational absorption, vibrational circular dichroism, Raman, and Raman optical activity spectra

Vibrational CD studies of the solution conformation of simple alanyl peptides as a function of pH

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