Interaction of metal ions with cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide – A theoretical study

Gopalan, P.; Kolandaivel, P.

doi:10.1016/j.theochem.2008.12.033

Cited by 10 publications

(2 citation statements)

References 57 publications

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“…Computational simulations of cyclic peptides and peptide nanotubes ,– constitute a valuable complement to the experimental investigations and may provide further insights into the structural properties of these compounds. In fact, in early 1974, a theoretical analysis of conformations by Santis and co-workers led them to predict the possibility of the formation of β-sheet-like tubular structures held together by both van der Waals and hydrogen bonds between CO and NH groups.…”

Section: Introductionmentioning

confidence: 99%

Interaction and Dimerization Energies in Methyl-Blocked α,γ-Peptide Nanotube Segments

et al. 2010

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The building blocks of a promising class of peptide nanotubes composed of alternating D-alpha-amino acids and (1R,3S)-3-aminocyclohexane (or cyclopentane) carboxylic acid (D-gamma-Ach or D-gamma-Acp) were explored by computational methods. Specifically, density functional theory (DFT) calculations on monomers and dimers of gamma-Ach-based and gamma-Acp-based alpha,gamma-cyclo-hexapeptides and cyclo-octapeptides were carried out to investigate the experimentally observed preference for alpha-alpha over gamma-gamma dimerization, associated with the two types of stacking patterns present in these peptide nanotubes, as well as the preference for heterodimerization versus homodimerization. Full geometry optimizations were performed at the B3LYP/6-31G(d) level, and single point calculations were subsequently carried out with the B3LYP and M05-2X functionals and the 6-31+G(d,p) basis set. The calculations predict that the interaction energies in the alpha-alpha species are quite similar to those in the gamma-gamma dimers. However, a comparison of dimerization energies (i.e., interaction energies plus deformation energies of monomers) shows that alpha-alpha dimerization is energetically favored over gamma-gamma dimerization. The calculations strongly suggest that the preference for alpha-alpha binding is governed by differences between the deformation energies in the alpha and gamma monomers, rather than by differences between the relative strengths of the alpha-alpha and gamma-gamma hydrogen-bonding patterns. Calculations based on local properties of the electron density support the previous suggestion that the H-N bonds of the alpha-amino acids are more polarized than those of the gamma-amino acids.

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Section: Introductionmentioning

confidence: 99%

Interaction and Dimerization Energies in Methyl-Blocked α,γ-Peptide Nanotube Segments

et al. 2010

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“…However, molecular modeling and experimental results suggested the preference of the interaction of backbone carbonyl groups of cyclic peptides with the metal ions inside the cavity. [75][76][77] For the present complexes, the charge-transfer is dened as the charge difference between a free metal ion and its complexated form. Table 5 also reveals that for the M/CyAla3, the negative charge on the nitrogen atoms changed from À0.671 esu in the free CyAla3 molecule to À0.609, À0.619, À0.632, À0.636, and À0.640 esu for the Be 2+ , Mg 2+ , Ca 2+ , Sr 2+ and Ba 2+ metal cations, respectively.…”

Section: Second-order Interaction Energies Energy Gaps and Charge Tra...mentioning

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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Selective Complexation of S‐block Cations with Nanotubular Silk Type Cyclopeptides: A DFT Study

Teimouri

Najari

Chermahini

et al. 2015

J Chinese Chemical Soc

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Density functional theory (DFT) was used to study the interaction of alkali metal cations (Li + , Na + and K + ) with cyclic peptides constructed from silk type macrocycles (Silk1, Silk2, Silk3, Silk4, Silk5 and Silk6). The calculated binding energies were used as a base for investigating the selectivity of the cyclic peptides in biniding to considered metals ions. The highest cation selectivity for Li + compared to the other alkali metal ions was observed. The orbital nature of different interactions between the metal cations and the cyclic peptides was analyzed using NBO analysis. The main types of driving force for host-guest interactions was investigated and it was found that the electron-donating O offers lone pair electrons to the contacting LP* of alkali metal cations.

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Interaction of metal ions with cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide – A theoretical study

Cited by 10 publications

References 57 publications

Interaction and Dimerization Energies in Methyl-Blocked α,γ-Peptide Nanotube Segments

Interaction and Dimerization Energies in Methyl-Blocked α,γ-Peptide Nanotube Segments

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

Selective Complexation of S‐block Cations with Nanotubular Silk Type Cyclopeptides: A DFT Study

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