Theoretical comparison of molecular properties of linear and cyclic glycine derived peptides and their phosphor analogues

Żero, Paweł; Pluciński, Franciszek; Mazurek, Alexander P.

doi:10.1016/j.theochem.2009.08.037

Cited by 6 publications

(4 citation statements)

References 29 publications

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“…investigated the possible molecular conformations in trans and cis nanorings and nanotubes constructed from cyclic peptides by a mathematical conformation analysis and Hartree–Fock (HF) calculations. Zero et al . performed a theoretical comparison of the molecular properties of linear and cyclic glycine peptides and their phosphor analogs.…”

Section: Introductionmentioning

confidence: 99%

Ionization of the Conformers of cis Nanotubular Cyclic Peptides in the Gas Phase: Effect of Size and Conformation on Ionization

Karachi

Farrokhpour

Abyar³

2018

J Chinese Chemical Soc

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Cyclic peptides, because of their unique spatial conformations, simplicity, and limited conformational freedom, are widely used as model molecules for larger peptides in chemistry and biochemistry. In this work, the ionization energies and photoelectron spectra of different conformers of the cyclic peptides (n = 2–15) were calculated using the symmetry‐adapted cluster‐configuration interaction (SAC‐CI) method and D95 + (d,p) basis set in the gas phase. The calculated photoelectron spectra were used to study the electronic structures of the cyclic peptides. It was observed that the first ionization energy of the cyclic peptides decreases with the ring size, reaches a minimum, and then increases. In addition, the first ionization band of the cyclic peptides was assigned to the ionization of the lone electron pairs of the nitrogen atoms, although there are π electrons of the CO bond and the lone electron pairs of oxygen atoms in the structure of the peptides.

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Section: Introductionmentioning

confidence: 99%

Ionization of the Conformers of cis Nanotubular Cyclic Peptides in the Gas Phase: Effect of Size and Conformation on Ionization

Karachi

Farrokhpour

Abyar³

2018

J Chinese Chemical Soc

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“…Cyclic compounds are continuously at the centre of research interest [1] and in recent years many classes of organic and bioorganic cyclic compounds which are constructed of amino acid units have been synthesised and reported [2]. These compounds exhibit various biological activities, such as antibacterial [3], antiviral [4] and antifungal [5].…”

Section: Introductionmentioning

confidence: 99%

“…In many cases, cyclic compounds are known to have much better biological properties in comparison to their linear equivalents [23,24]. They are more able to permeate cell membranes due to their smaller size, hydrophobicity and lack of charge [25,26]. The conformational behaviour of glycine oligomers is of special interest too because, as the only unsubstituted amino acid, glycine is an important contributor to the conformational flexibility of peptide fragments [27].…”

Section: Introductionmentioning

confidence: 99%

A DFT study on the kinetics and mechanism of cyclodiglycine thermal decomposition in the gas phase

Khavani

Izadyar

Mehranfar

2016

Progress in Reaction Kinetics and Mechanism

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Theoretical investigations using density functional theory have been performed on the kinetics and mechanism of cyclodiglycine (piperazine-2,5-dione) thermal decomposition in the gas phase. Five major possible paths have been proposed and analysed. α-Lactam, β-lactam, 4-imidazolidinone and smaller species such as HNCO, H 2 CNH, H 2 CCO, CO, H 2 and HCN can be produced through these paths. The route yielding aziridine and HNCO is the optimum channel for this reaction from the energy point of view. Finally, according to the quantum theory of atoms in molecules, electron localisation function and localised orbital locator analyses, it was confirmed that a concerted mechanism operates for the reaction and all critical bonds of the transition states have covalent character.

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“…38,39 Mazurek and co workers studied structures and properties of cyclo glycine and compared these with its phosphor analogues. 40 In addition, Jishi et al investigated formation of dimers of cyclo[(Gly-D-Ala)4] and concluded that dimer formation is favored by hydrogen bonding. 41 Hongge Zhao and co-workers used a cyclic decapeptide and the enantiomers of 1-phenyl-1-propanol as the host and guest molecules, respectively, to examine the separation ability of guest enantiomers by the cyclic peptide.…”

Section: Introductionmentioning

confidence: 99%

Selective complexation of alkaline earth metal ions with nanotubular cyclopeptides: DFT theoretical study

et al. 2015

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The interaction of alkaline earth metal cations including Be 2+ , Mg 2+ , Ca 2+ , Sr 2+ and Ba 2+ with cyclic peptides containing 3 or 4 (S) alanine molecules (CyAla3 and CyAla4) was investigated by density functional theory (DFT-CAM-B3LYP and DFT-B3LYP). A mixed basis set including 6-31+G(d) for C, H, O, Be 2+ , Mg 2+ , Ca 2+ and LANL2DZ for Sr 2+ and Ba 2+ were used for calculations. The optimized structures, binding energies, and various thermodynamic parameters of free ligands and related metal cation complexes were determined.The order of strength of interaction energies was found as Be 2+ > Mg 2+ > Ca 2+ > Sr 2+ > Ba 2+ . Vibrational frequency calculations showed that the selected cyclic peptides and their complexes with the alkaline earth metal cations were at local minima of their potential energy surfaces. In addition, it was found that the larger cavity CyAla4 ligand, can hold the alkaline metal cations better than CyAla3 molecule when the same metal cation is in the structure of complex. Moreover, analyzing the geometry of [M/CyAla3] 2+ and [M/CyAla4] 2+ complexes indicated that the aggregation with metal cation, caused substantial changes in the geometrical parameters of ligands.

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Theoretical comparison of molecular properties of linear and cyclic glycine derived peptides and their phosphor analogues

Cited by 6 publications

References 29 publications

Ionization of the Conformers of cis Nanotubular Cyclic Peptides in the Gas Phase: Effect of Size and Conformation on Ionization

Ionization of the Conformers of cis Nanotubular Cyclic Peptides in the Gas Phase: Effect of Size and Conformation on Ionization

A DFT study on the kinetics and mechanism of cyclodiglycine thermal decomposition in the gas phase

Selective complexation of alkaline earth metal ions with nanotubular cyclopeptides: DFT theoretical study

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