Complexation of Na+and K+to Aromatic Amino Acids:  A Density Functional Computational Study of Cation-π Interactions

2000 ◽  
Vol 104 (34) ◽  
pp. 8067-8074 ◽  
Author(s):  
Robert C. Dunbar
Keyword(s):  
Amino Acids ◽  
Density Functional ◽  
Computational Study ◽  
Aromatic Amino Acids ◽  
Π Interactions

On the interaction between the imidazolium cation and aromatic amino acids. A computational study

2015 ◽  
Vol 13 (29) ◽  
pp. 7961-7972 ◽  
Author(s):  
Ana A. Rodríguez-Sanz ◽  
Enrique M. Cabaleiro-Lago ◽  
Jesús Rodríguez-Otero
Keyword(s):  
Amino Acids ◽  
Computational Study ◽  
Aromatic Amino Acids ◽  
Imidazolium Cation ◽  
Π Interactions

Phe, Tyr and Trp form parallel complexes with cation⋯π interactions. His complexes are the strongest, but without making contact with the aromatic cloud.

In silico study of binding affinity of nitrogenous bicyclic heterocycles: fragment-to-fragment approach

2020 ◽  
Vol 15 (2) ◽  
pp. 49-59
Author(s):  
Yevheniia Velihina ◽  
Nataliya Obernikhina ◽  
Stepan Pilyo ◽  
Maryna Kachaeva ◽  
Oleksiy Kachkovsky ◽  
...  
Keyword(s):  
Amino Acids ◽  
Binding Affinity ◽  
In Silico ◽  
Density Functional ◽  
Energy Levels ◽  
Aromatic Amino Acids ◽  
Electron System ◽  
High Energy ◽  
Proton Donor ◽  
Stabilization Energy

The binding affinity of model aromatic amino acids and heterocycles and their derivatives condensed with pyridine were investigated in silico and are presented in the framework of fragment-to-fragment approach. The presented model describes interaction between pharmacophores and biomolecules. Scrupulous data analysis shows that expansion of the π-electron system by heterocycles annelation causes the shifting up of high energy levels, while the appearance of new the dicoordinated nitrogen atom is accompanied by decreasing of the donor-acceptor properties. Density Functional Theory (DFT) wB97XD/6-31(d,p)/calculations of π-complexes of the heterocycles 1-3 with model fragments of aromatic amino acids, which were formed by π-stack interaction, show an increase in the stabilization energy of π-complexes during the moving from phenylalanine to tryptophan. DFT calculation of pharmacophore complexes with model proton-donor amino acid by the hydrogen bonding mechanism (H-B complex) shows that stabilization energy (DE) increases from monoheterocycles to their condensed derivatives. The expansion of the π-electron system by introducing phenyl radicals to the oxazole cycle as reported earlier [18] leads to a decrease in the stabilization energy of the [Pharm-BioM] complexes in comparison with the annelated oxazole by the pyridine cycle.

Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur

2015 ◽  
Vol 68 (3) ◽  
pp. 385 ◽  
Author(s):  
Hanzala B. Hussain ◽  
Katie A. Wilson ◽  
Stacey D. Wetmore
Keyword(s):  
Amino Acids ◽  
High Resolution ◽  
Protein Stability ◽  
Crystal Structures ◽  
Protein Complexes ◽  
Aromatic Amino Acids ◽  
Biological Macromolecules ◽  
Great Stability ◽  
Π Interactions ◽  
And Function

Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.

scholarly journals Cation-π Interactions Involving Aromatic Amino Acids

2007 ◽  
Vol 137 (6) ◽  
pp. 1504S-1508S ◽  
Author(s):  
Dennis A. Dougherty
Keyword(s):  
Amino Acids ◽  
Aromatic Amino Acids ◽  
Π Interactions

Can the solvent enhance the rate of chemical reactions through C–H/π interactions? insights from theory

2019 ◽  
Vol 21 (27) ◽  
pp. 14821-14831 ◽  
Author(s):  
Shailja Jain ◽  
Kumar Vanka
Keyword(s):  
Density Functional Theory ◽  
Chemical Reactions ◽  
Density Functional ◽  
Computational Study ◽  
Functional Theory ◽  
Π Interactions ◽  
Solvent Molecules

The current computational study with density functional theory (DFT) shows that the explicit presence of C–H/π and π–π interacting solvent molecules is seen to enhance the rate of chemical reactions.

Site specific interaction of aromatic amino acids with ZnO nanotubes: A density functional approach

2016 ◽  
Vol 1086 ◽  
pp. 36-44 ◽  
Author(s):  
Pari Sadat Maddahi ◽  
Nasser Shahtahmassebi ◽  
Mahmood Rezaee Roknabadi ◽  
Fatemeh Moosavi
Keyword(s):  
Amino Acids ◽  
Density Functional ◽  
Specific Interaction ◽  
Aromatic Amino Acids ◽  
Functional Approach ◽  
Site Specific ◽  
Zno Nanotubes

Computational Study on the Attack of.OH Radicals on Aromatic Amino Acids

2013 ◽  
Vol 19 (21) ◽  
pp. 6862-6873 ◽  
Author(s):  
J. I. Mujika ◽  
J. Uranga ◽  
J. M. Matxain
Keyword(s):  
Amino Acids ◽  
Computational Study ◽  
Aromatic Amino Acids
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