Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring

AbstractThe potential energy surface (PES) of tyrosyl-glycyl-glycine (YGG) tripeptide in solution was explored using EDMC (Electrostatically Driven Monte Carlo) and in the gas-phase by means of ab initio quantum chemical calculations. The theoretical computational analysis revealed that this tripeptide possesses a significant molecular flexibility. A C7 backbone conformation was the most energetically preferred for the central Gly residue, using both methodologies. Some new stable conformers that have not been previously reported were identified in the gas phase as well. This study points out the interplay of backbone and side-chain contributions in determining the relative stabilities of energy minima. In addition, the peptide backbone of YGG was compared with other small peptides containing aromatic side-chains (Phe-Gly-Gly and Trp-Gly-Gly). The comparison with experimental X-ray results was also satisfactory.

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Effects of Side-Chain Orientation on the Backbone Conformation of the Dehydrophenylalanine Residue. Theoretical and X-ray Study

The Journal of Physical Chemistry B ◽

10.1021/jp200949t ◽

2011 ◽

Vol 115 (15) ◽

pp. 4295-4306 ◽

Cited By ~ 14

Author(s):

Aneta Buczek ◽

Dawid Siodłak ◽

Maciej Bujak ◽

Małgorzata A. Broda

Keyword(s):

Side Chain ◽

Chain Orientation ◽

X Ray ◽

Backbone Conformation ◽

Side Chain Orientation

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Peptide models XIX: Side-chain conformational energy surface and amide I vibrational frequencies of N-formyl-l-phenylalaninamide (For-Phe-NH2) in its γL or γinv or C7eq backbone conformation

Journal of Molecular Structure THEOCHEM ◽

10.1016/s0166-1280(96)04548-4 ◽

1996 ◽

Vol 369 (1-3) ◽

pp. 105-114 ◽

Cited By ~ 35

Author(s):

Ödön Farkas ◽

Michael A. McAllister ◽

J.H. Ma ◽

András Perczel ◽

Miklós Hollósi ◽

...

Keyword(s):

Energy Surface ◽

Vibrational Frequencies ◽

Conformational Energy ◽

Side Chain ◽

Backbone Conformation ◽

Peptide Models

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Binding motifs of cisplatin interaction with simple biomolecules and aminoacid targets probed by IR ion spectroscopy

Pure and Applied Chemistry ◽

10.1515/pac-2019-0110 ◽

2020 ◽

Vol 92 (1) ◽

pp. 3-13 ◽

Cited By ~ 3

Author(s):

Davide Corinti ◽

Roberto Paciotti ◽

Nazzareno Re ◽

Cecilia Coletti ◽

Barbara Chiavarino ◽

...

Keyword(s):

Biological Activity ◽

Amino Acid ◽

Gas Phase ◽

Quantum Chemical ◽

Ligand Substitution ◽

Side Chain ◽

Binding Motifs ◽

Distinctive Features ◽

Ion Spectroscopy ◽

Vibrational Action

AbstractThe primary intermediates resulting from the interaction of cisplatin, cis-(PtCl2(NH3)2], most widespread antitumor drug, with biomolecular targets are characterized. Electrospray ionization is used to deliver ions formed in solution into the gas phase where they are structurally interrogated by vibrational “action” spectroscopy in conjunction with quantum chemical calculations. The aquation products, cis-[PtX(NH3)2(H2O)]+ (X = Cl, OH), lying along the path responsible for biological activity, are shown to display distinctive features responding to ligation pattern and optimized geometry. The IR spectra of trans-[PtX(NH3)2(H2O)]+ are different, testifying that cis and trans complexes are stable, non interconverting species both in solution and in the gas phase. Ligand substitution by simple nucleophiles (L = pyridine, 4(5)-methylimidazole, thioanisole, trimethylphosphate, acetamide, dimethylacetamide, urea and thiourea) yields cis-[PtCl(NH3)2(L)]+ complexes displaying remarkable regioselectivity whenever L presents multiple candidate platination sites. The incipient formation of cisplatin-derived complexes with the recognized biological amino acid targets L-histidine (His) and L-methionine (Met) has been investigated revealing the primary platination event to be mainly directed at the Nπ atom of the imidazole side chain of His and to the thiomethyl sulfur of Met. The isomer and conformer population of the ensuing cis-[PtCl(NH3)2(Met/His)]+ complexes, sampled in the gas phase, can be ascertained by photofragmentation kinetics on isomer/conformer specific resonances.

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Structures of Energetic Acetylene Derivatives HC≡CCH2ONO2, (NO2)3CCH2C≡CCH2C(NO2)3 and Trinitroethane, (NO2)3CCH3

Zeitschrift für Naturforschung B ◽

10.5560/znb.2013-2311 ◽

2013 ◽

Vol 68 (5-6) ◽

pp. 719-731 ◽

Cited By ~ 7

Author(s):

Thomas M. Klapötke ◽

Burkhard Krumm ◽

Richard Moll ◽

Alexander Penger ◽

Stefan M. Sproll ◽

...

Keyword(s):

Electron Diffraction ◽

Gas Phase ◽

Quantum Chemical ◽

Room Temperature ◽

Molecular Structures ◽

X Ray Diffraction ◽

Polar Solvents ◽

X Ray ◽

Nmr Study ◽

Acetylene Derivatives

The molecular structures and relative ratios of the two conformers (anti and gauche) of HCCCH2ONO2 detected in the gas phase at room temperature have been determined by electron diffraction. The results are discussed on the basis of quantum chemical calculations. The molecular structures of (NO2)3CCH2C≡CCH2C(NO2)3 and (NO2)3CCH3 have been determined by X-ray diffraction. A109Ag NMR study was performed for silver trinitromethanide Ag[C(NO2)3] in various polar solvents.

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