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Full-Text Articles in Physical Sciences and Mathematics
Zinc Environment In Proteins: The Flexible And Reactive Core Of Hiv-1 Ncp7 And The Inhibitory Site Of Caspase-3, A. Gerard Daniel
Zinc Environment In Proteins: The Flexible And Reactive Core Of Hiv-1 Ncp7 And The Inhibitory Site Of Caspase-3, A. Gerard Daniel
Theses and Dissertations
Zinc is an essential cofactor of several proteins. The roles of zinc in these proteins are classified as catalytic, structural or regulatory. Zinc present in structural sites is considered to be a chemically inert, static structural element. On the contrary, previous studies on a C2H2 type zinc finger model compound and the C3H type HIV-1 NCp7 C-terminal zinc knuckle have shown that zinc at these sites can undergo coordination sphere expansion under the influence of a Pt based electrophile. The pentacoordination observed around zinc in these experiments raises an important question: are the structural zinc motifs found in the proteins …
Molecular Dynamics Simulations Using Advanced Sampling And Polarizable Force Fields, Tugba Kucukkal
Molecular Dynamics Simulations Using Advanced Sampling And Polarizable Force Fields, Tugba Kucukkal
All Dissertations
Molecular dynamics (MD) simulations were carried out for aqueous dipeptides, water over self-assembled monolayer (SAM) surfaces, and the nicotinic acetylcholine receptor (nAChR) ion channel. The main goal is to use advanced methods to increase the accuracy of molecular dynamics simulations while seeking solutions to problems relevant to chemistry, biophysics and materials science. In addition, activation energies of several cyclodimerization reactions were studied quantum mechanically. The simulations of the aqueous dipeptides and SAM surfaces involve modeling and detailed analysis of interfacial water, which is of interest to a range of fields from biology to materials science. For example, water has a …
Binding Energies And Solvation Of Organic Molecular Ions, Reactions Of Transition Metal Ions With, And Plasma Discharge Ionization Of Molecular Clusters, Isaac Kwame Attah
Binding Energies And Solvation Of Organic Molecular Ions, Reactions Of Transition Metal Ions With, And Plasma Discharge Ionization Of Molecular Clusters, Isaac Kwame Attah
Theses and Dissertations
In this dissertation, different approaches have been employed to address the quest of understanding the formation and growth mechanisms of carbon-containing molecular ions with relevance to astrochemistry. Ion mobility mass spectrometry and DFT computations were used to investigate how a second nitrogen in the pyrimidine ring will affect the formation of a covalent bond between the benzene radical cation and the neutral pyrimidine molecule, after it was shown that a stable covalent adduct can be formed between benzene radical cation and the neutral pyridine. Evidence for the formation of a more stable covalent adduct between the benzene radical cation and …