Quantum chemical study of cyclic dipeptides

Zhu, Yanyan; Tang, Mingsheng; Shi, Xiaoyu; Zhao, Yufen

doi:10.1002/qua.20985

Cited by 45 publications

(25 citation statements)

References 25 publications

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“…They concluded that the energetically favourable conformers adopt a boat configuration in solution, with respect to the DKP ring. Zhu et al 19 calculated the structures of all of the cyclic peptides consisting of the same two amino acids, including cPhePhe, and found that they adopted the boat conformation. We recently summarised other previous studies of cyclic dipeptides.…”

Section: Introductionmentioning

confidence: 99%

Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly

Arachchilage

Wang

Feyer

et al. 2012

The Journal of Chemical Physics

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We have investigated the electronic structure of three cyclic dipeptides: cyclo(Histidyl-Glycyl) (cHisGly), cyclo(Tyrosyl-Prolyl) (cTyrPro), and cyclo(Phenylalanyl-Phenylalanyl) (cPhePhe) in the vapor phase, by means of photoemission spectroscopy and theoretical modeling. The last compound was evaporated from the solid linear dipeptide, but cyclised, losing water to form cPhePhe in the gas phase. The results are compared with our previous studies of three other cyclopeptides. Experimental valence and core level spectra have been interpreted in the light of calculations to identify the basic chemical properties associated with the central diketopiperazine ring, and with the additional functional groups. The valence spectra are generally characterized by a restricted set of outer valence orbitals separated by a gap from most other valence orbitals. The theoretically simulated core and valence spectra of all three cyclic dipeptides agree reasonably well with the experimental spectra. The central ring and the side chains act as independent chromophores whose spectra do not influence one another, except for prolyl dipeptides, where the pyrrole ring is fused with the central ring. In this case, significant changes in the valence and core level spectra were observed, and explained by stronger hybridization of the valence orbitals.

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Section: Introductionmentioning

confidence: 99%

Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly

Arachchilage

Wang

Feyer

et al. 2012

The Journal of Chemical Physics

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“…[24] Surprisingly, despite the large amount of experimental spectroscopic data reported for cyclo(Gly-Gly), [18 -21] relatively little work has been reported on the vibrational spectra of other cyclic peptide molecules that contain the cis-peptide group. The current study is part of a long-term program to investigate the relationship between vibrational spectroscopic characteristics and molecular structure of CDAPs.…”

Section: Introductionmentioning

confidence: 99%

Vibrational spectroscopy and DFT calculations of di‐amino acid cyclic peptides. Part I: cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) in the solid state and in aqueous solution

Mendham

Dines

Snowden

et al. 2009

J Raman Spectroscopy

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Investigations of the vibrational spectra of cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid-state and aqueous protonated samples, as well as their corresponding N-deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3-LYP/cc-pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas-phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di-amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C 2 and C 1 symmetries for the six-membered rings of cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L-AlaGly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis-peptide linkage are shown to be significantly different from those of the trans-peptides. For example, deuterium shifts have shown that the cis-amide I vibrations found in cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Ala-Gly) have larger N-H contributions compared to their trans-amide counterparts. Compared to trans-amide II vibrations, cis-amide II vibrations show a considerable decrease in N-H character.

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“…A boat conformation was, consistently, shown to be the most stable gas-phase conformation. [20] The foregoing study primarily focused on a comparison of the boat and chair conformers of CDAPs; experimental data and normal coordinate analyses were not reported.…”

Section: Geometry Optimizationsmentioning

confidence: 99%

“…[10] X-ray crystallography, [11 -15] NMR, [16,17] CD [18] and gas-phase microwave [19] spectroscopic techniques have hitherto been used in investigating the structure and conformation of a number of symmetrically substituted CDAPs. Theoretical spectroscopic investigations [20] have also played a part in structural analysis. [21] Despite the foregoing comments, detailed experimental vibrational spectroscopic experiments on CDAPs have, to date, been less common except for, e.g., the studies on the parent DKP (i.e.…”

Section: Introductionmentioning

confidence: 99%

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

Dines

Snowden

et al. 2009

J Raman Spectroscopy

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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-seryl 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-seryl 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. : 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 ∼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 α atoms, and is also indicative of a relatively unstrained DKP ring. 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

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Quantum chemical study of cyclic dipeptides

Cited by 45 publications

References 25 publications

Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly

Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly

Vibrational spectroscopy and DFT calculations of di‐amino acid cyclic peptides. Part I: cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) in the solid state and in aqueous solution

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)

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