Aqueous solvation of protein secondary structures: Density functional theory study
Item
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Title
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Aqueous solvation of protein secondary structures: Density functional theory study
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Identifier
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d_2009_2013:b51f457407b9:11807
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identifier
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12426
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Creator
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Marianski, Mateusz,
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Contributor
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Joseph J. Dannenberg
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Date
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2013
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Language
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English
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Publisher
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City University of New York.
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Subject
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Chemistry | Biochemistry | ab initio | DFT | Dispersion | Protein | Solvation | Water
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Abstract
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In recent years, van der Waals forces have received considerable attention among the scientific community. It is hard to overestimate the significance of dispersion forces which are thought to play important roles in the energetics of biological molecules, such as DNA and peptides. However, the weakest of interactions is also the most difficult to approach by theoretical methods and has been troubling computational chemists for at least last two decades. In my thesis I will answer how well recently developed density functionals deal with the dispersion in the case study of dispersion-enhanced induction complexes, relative stability of pi-stacking and hydrogen bonded dimers, and protein secondary structures. The presented results undermine the belief that recent widely-parametrized and/or dispersion-corrected functionals outperforms older well-established functionals, like famous B3LYP.;In the second part of my thesis I will focus on the influence of aqueous solvent on protein structures. Water is present in all biological systems, where it is not only a static medium of the reaction, but also an active part of the process called life, and it requires careful treatment. I compare models of implicit and explicit solvation for beta-turns, alpha-helices, and beta-sheets. I find that solvation by small water clusters can alter the molecular properties of gas phase molecules and continuous methods are not able to model all effects.
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Type
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dissertation
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Source
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2009_2013.csv
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degree
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Ph.D.
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Program
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Chemistry
