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 structural and binding energies in good agreement with ab initio calculations without further adjustm ...

Article GUID: 26583551

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 binding energies of M(+)(NH3)n (n = 2-4) and M(+)(NH3)n(H2O)m (n, m = 1-3 and n + m = 4) clusters and ...

Article GUID: 26583725

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 oscillator model. Bonded parameters and atomic charges are based on the experimental properties of the gaseo ...

Article GUID: 26588292

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 of the cation-p dimers. They also reproduce the cooperative behavior of "stacked", cation-p-p trimer ...

Article GUID: 26592880

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 likely involved in the blockage of potassium channels by tetramethylammonium (TMA^(+)) and tetraethyl ...

Article GUID: 29397727

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 with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), a ...

Article GUID: 29533644

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 concentrated aqueous solutions, which are hazardous, and for understanding the biological roles of H ...

Article GUID: 29630362