Binding patterns of metal cations (Na+, K+, Cu2+, and Zn2+) with Trp-Trp di-peptide investigated by DFT, NBO, and MD simulation
| Autor: | Snehasis Bhunia, Animesh K. Ojha, Ajeet Singh, Aditya Kumar |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
inorganic chemicals
chemistry.chemical_classification 010405 organic chemistry Metal ions in aqueous solution Peptide 010402 general chemistry Condensed Matter Physics Ring (chemistry) 01 natural sciences Biochemistry 0104 chemical sciences Gas phase Metal Molecular dynamics Crystallography chemistry visual_art visual_art.visual_art_medium Physical and Theoretical Chemistry Relative energy Natural bond orbital |
| Zdroj: | Computational and Theoretical Chemistry. 1141:7-14 |
| ISSN: | 2210-271X |
| DOI: | 10.1016/j.comptc.2018.08.010 |
| Popis: | The binding patterns of metal cations (Na+, K+, Cu2+, and Zn2+) with tryptophan-tryptophan (Trp-Trp) di-peptide were studied at B3LYP, MP2 and wB97XD level of theories in gas phase. The calculated values of relative energy of the complexes indicate that the cation-π tetra-dentate or tri-dentate complex is most favourable compared to other ring-coordinated and ring un-coordinated complexes. Natural bond orbital (NBO) analysis has been carried out to explore the nature of metal-ligand co-ordination. On the basis of second order energy correction and orbital transition between the metal ions and di-peptide, the effective contribution from each binding centers of favourable multi-dentate binding motifs was determined. The stability of most favourable binding motifs of Na+, K+, Cu2+, and Zn2+ with the Trp-Trp has also been investigated by the molecular dynamics (MD) simulation. The MD trajectories of all favourable binding motifs are nicely substantiated with the possible structure favoured by DFT based relative energy calculations. |
| Databáze: | OpenAIRE |
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