IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III

comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)

Andrew P. Mendham, Trevor J. Dines, M. J. Snowden, Robert Withnall, Babur Z. Chowdhry

    Research output: Contribution to journalArticle

    15 Citations (Scopus)

    Abstract

    B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of similar to 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring. Copyright (C) 2009 John Wiley & Sons, Ltd.

    Original languageEnglish
    Pages (from-to)1508-1520
    Number of pages13
    JournalJournal of Raman Spectroscopy
    Volume40
    Issue number11
    DOIs
    Publication statusPublished - Nov 2009

    Keywords

    • cyclic di-amino acid peptides (CDAP)
    • X-ray crystallography
    • ab initio calculations
    • vibrational spectra
    • CRYSTAL-STRUCTURE
    • VIBRATIONAL ANALYSIS
    • DIKETOPIPERAZINE
    • CONFORMATION
    • DIPEPTIDE
    • IDENTIFICATION
    • POLYPEPTIDES
    • PROTEINS
    • DENSITY

    Cite this

    Mendham, Andrew P. ; Dines, Trevor J. ; Snowden, M. J. ; Withnall, Robert ; Chowdhry, Babur Z. / IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III : comparison of solid state and solution structures of cyclo(L-Ser-L-Ser). In: Journal of Raman Spectroscopy. 2009 ; Vol. 40, No. 11. pp. 1508-1520.
    @article{57720f2b070145348723580b6d61ef4e,
    title = "IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)",
    abstract = "B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of similar to 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring. Copyright (C) 2009 John Wiley & Sons, Ltd.",
    keywords = "cyclic di-amino acid peptides (CDAP), X-ray crystallography, ab initio calculations, vibrational spectra, CRYSTAL-STRUCTURE, VIBRATIONAL ANALYSIS, DIKETOPIPERAZINE, CONFORMATION, DIPEPTIDE, IDENTIFICATION, POLYPEPTIDES, PROTEINS, DENSITY",
    author = "Mendham, {Andrew P.} and Dines, {Trevor J.} and Snowden, {M. J.} and Robert Withnall and Chowdhry, {Babur Z.}",
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    IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III : comparison of solid state and solution structures of cyclo(L-Ser-L-Ser). / Mendham, Andrew P.; Dines, Trevor J.; Snowden, M. J.; Withnall, Robert; Chowdhry, Babur Z.

    In: Journal of Raman Spectroscopy, Vol. 40, No. 11, 11.2009, p. 1508-1520.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III

    T2 - comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)

    AU - Mendham, Andrew P.

    AU - Dines, Trevor J.

    AU - Snowden, M. J.

    AU - Withnall, Robert

    AU - Chowdhry, Babur Z.

    PY - 2009/11

    Y1 - 2009/11

    N2 - B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of similar to 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring. Copyright (C) 2009 John Wiley & Sons, Ltd.

    AB - B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of similar to 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring. Copyright (C) 2009 John Wiley & Sons, Ltd.

    KW - cyclic di-amino acid peptides (CDAP)

    KW - X-ray crystallography

    KW - ab initio calculations

    KW - vibrational spectra

    KW - CRYSTAL-STRUCTURE

    KW - VIBRATIONAL ANALYSIS

    KW - DIKETOPIPERAZINE

    KW - CONFORMATION

    KW - DIPEPTIDE

    KW - IDENTIFICATION

    KW - POLYPEPTIDES

    KW - PROTEINS

    KW - DENSITY

    U2 - 10.1002/jrs.2306

    DO - 10.1002/jrs.2306

    M3 - Article

    VL - 40

    SP - 1508

    EP - 1520

    JO - Journal of Raman Spectroscopy

    JF - Journal of Raman Spectroscopy

    SN - 0377-0486

    IS - 11

    ER -