MONTE CARLO COMPUTER SIMULATION STUDIES OF THE AQUEOUS HYDRATION OF THE NUCLEOTIDE BASES AND SUGARS.
Item
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Title
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MONTE CARLO COMPUTER SIMULATION STUDIES OF THE AQUEOUS HYDRATION OF THE NUCLEOTIDE BASES AND SUGARS.
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Identifier
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AAI8629713
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identifier
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8629713
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Creator
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MAYE, PETER V.
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Contributor
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David L. Beveridge
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Date
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1986
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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
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Abstract
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Monte Carlo computer simulation studies of the hydration of the five nucleic acid bases and derivatives of ribose and deoxyribose were performed in order to obtain knowledge of the microscopic hydration of these systems. A comparison was made of biomolecular hydration descriptions obtained with the use of three available biomolecular solute-water potential functions. Such a comparison, of primary importance in the improvement of the computer simulation of biomolecular hydration, has not previously been performed. Direct comparison of simulation produced transfer energies with experimentally obtained values for nine simulations distinctly demonstrates that the Berendsen-Van Gunsteren and Kollman sets provide excellent reproduction of transfer energetics in the molecular cases examined; the Clementi potentials, however, were found to greatly overestimate solute-water interactions. Examination of the first shell energetics of thymine and uracil using BVG and Kollman potentials suggest that an average first shell solute-water pair interaction of about one kcal/mole is reasonable for the nucleic acid bases. Molecular first shell coordination numbers are found to be essentially independent of the choice of potential functions. Functional group coordination numbers do not show definite trends with the variation of potential function and roughly correspond when rounded to the nearest integer. Finally, the simulation results provide qualitative microscopic characterization of the hydration of the five nucleic acid bases and two sugars in derivative form.
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Type
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dissertation
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Source
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PQT Legacy CUNY.xlsx
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degree
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Ph.D.
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Program
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Biochemistry