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Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia

Author(s): Esam A Orabi

A polarizable model for ammonia is optimized based on the ab initio properties of the NH3 molecule and the NH3-NH3 and NH3-H2O dimers calculated at the MP2 level. For larger (NH3)m, NH3(H2O)n, and H2O(NH3)n clusters (m = 2-7 and n = 1-4), the model yields s...

Article GUID: 26583551
Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia

Author(s): Esam A Orabi

A polarizable potential model for M(+)-NH3 interactions (M(+) = Li(+), Na(+), K(+), Rb(+), Cs(+)) is optimized based on the ab initio properties of the ion-ammonia dimers calculated at the MP2 level of theory. The optimized model reproduces the ab initio bi...

Article GUID: 26583725
Simulation of Liquid and Supercritical Hydrogen Sulfide and of Alkali Ions in the Pure and Aqueous Liquid

Author(s): Esam A Orabi

A polarizable model for hydrogen sulfide (H2S) is optimized based on the experimental properties of the monomer and of the bulk liquid. The model is characterized by rigid SH bonds but flexible HSH angle and the polarizability is based on the Drude oscillat...

Article GUID: 26588292
Cation-π and π-π Interactions in Aqueous Solution Studied Using Polarizable Potential Models

Author(s): Esam A Orabi

Polarizable potential models for the interaction of Li(+), Na(+), K(+), and NH4(+) ions with benzene are parametrized based on ab initio quantum mechanical calculations. The models reproduce the ab initio complexation energies and potential energy surfaces ...

Article GUID: 26592880
Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution

Author(s): Esam A Orabi

Cation-p interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH(3)^(+) and RN(CH(3))(3)^(+)) to various protein receptors and are l...

Article GUID: 29397727
Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility

Author(s): Esam A Orabi

S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H(2)S, MeSH) and Met (Me(2)S) models ...

Article GUID: 29533644
A Simple Additive Potential Model for Simulating Hydrogen Peroxide in Chemical and Biological Systems

Author(s): Esam A Orabi

Hydrogen peroxide (H(2)O(2)) has numerous industrial, environmental, medical, cosmetic, and biological applications. Given its importance, we provide a simple model as an alternative to experiment for studying the properties of pure liquid H(2)O(2) and its ...

Article GUID: 29630362
Title:Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility
Authors:Esam A Orabi
Link:https://pubmed.ncbi.nlm.nih.gov/29533644/
DOI:10.1021/acs.jpcb.8b00089
Category:J Phys Chem B
PMID:29533644
Dept Affiliation: CERMM
1 Centre for Research in Molecular Modeling (CERMM) and PROTEO , Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke Street West , Montréal , Québec H4B 1R6 , Canada.

Description:

S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H(2)S, MeSH) and Met (Me(2)S) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies...