Keyword search (4,163 papers available)

"Orabi EA" Authored Publications:

Title Authors PubMed ID
1 Modeling CH sub 3 /sub SOH-aromatic complexes to probe cysteine sulfenic acid-aromatic interactions in proteins Orabi EA; English AM; 40994121
CHEMBIOCHEM
2 Modeling predicts facile release of nitrite but not nitric oxide from the thionitrate CH3SNO2 with relevance to nitroglycerin bioactivation Parmar V; Orabi EA; English AM; Peslherbe GH; 39738238
CERMM
3 Ammonium transporters achieve charge transfer by fragmenting their substrate Wang S; Orabi EA; Baday S; Bernèche S; Lamoureux G; 22631217
CERMM
4 New Megastigmane and Polyphenolic Components of Henna Leaves and Their Tumor-Specific Cytotoxicity on Human Oral Squamous Carcinoma Cell Lines Orabi MAA; Orabi EA; Awadh AAA; Alshahrani MM; Abdel-Wahab BA; Sakagami H; Hatano T; 38001804
CHEMBIOCHEM
5 Structural determination and anticholinesterase assay of C-glycosidic ellagitannins from Lawsonia inermis leaves: A study supported by DFT calculations and molecular docking Orabi MAA; Orabi EA; Abdel-Sattar ES; English AM; Hatano T; Elimam H; 36423882
CHEMBIOCHEM
6 Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H2O2 and H2O Orabi EA; English AM; 33356279
CHEMBIOCHEM
7 Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains Orabi EA; Davis RL; Lamoureux G; 31652004
CERMM
8 Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations Orabi EA; Peslherbe GH; 31297500
CHEMBIOCHEM
9 Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone Orabi EA; English AM; 31214677
CHEMBIOCHEM
10 Predicting structural and energetic changes in Met-aromatic motifs on methionine oxidation to the sulfoxide and sulfone Orabi EA; English AM; 30168822
CHEMBIOCHEM

 

Title:Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains
Authors:Orabi EADavis RLLamoureux G
Link:https://pubmed.ncbi.nlm.nih.gov/31652004/
DOI:10.1002/jcc.26084
Publication:Journal of computational chemistry
Keywords:Cation-πinteractionsDrude polarizable force fieldab initio calculationsalkali metal ionsbinding free energyquaternary ammonium ions
PMID:31652004 Category:J Comput Chem Date Added:2019-10-28
Dept Affiliation: CERMM
1 Department of Chemistry, Faculty of Science, Assiut University, Assiut, 71516, Egypt.
2 Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
3 Department of Chemistry and Center for Computational and Integrative Biology (CCIB), Rutgers University, Camden, New Jersey, 08102.
4 Centre for Research in Molecular Modeling (CERMM), Concordia University, Montréal, Québec, H4B 1R6, Canada.

Description:

Cation-p interactions play important roles in molecular recognition and in the stability and function of proteins. However, accurate description of the structure and energetics of cation-p interactions presents a challenge to both additive and polarizable force fields, which are rarely designed to account for the complexation of charged groups with aromatic moieties. We calibrate the Drude polarizable force field for complexes of alkali metal ions (Li+ , Na+ , K+ , Rb+ , Cs+ ), ammonium (NH4+ ), tetramethylammonium (TMA+ ), and tetraethylammonium (TEA+ ) with aromatic amino acid side chain model compounds (benzene, toluene, 4-methylphenol, 3-methylindole) using high-level ab initio quantum chemical properties of these complexes. Molecular dynamics simulations reveal that cation-p complexes of the hard and tightly coordinated Li+ and Na+ ions are not stable in water but that larger ions form stable complexes, with binding free energies ranging between -0.8 and -2.9 kcal/mol. Like in gas phase, all complexes at equilibrium adopt an "en-face" complexation mode in water. The optimized Drude polarizable model provides an accurate description of the cation-p interactions involving small ions and proteins. © 2019 Wiley Periodicals, Inc.





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