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Theoretical studies of molecular int...

Nguyen, Dat Huy.

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Theoretical studies of molecular interactions, dynamics, structure, and free energies of biological systems.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Theoretical studies of molecular interactions, dynamics, structure, and free energies of biological systems./
Author:	Nguyen, Dat Huy.
Description:	168 p.
Notes:	Source: Dissertation Abstracts International, Volume: 63-08, Section: B, page: 3734.
Contained By:	Dissertation Abstracts International63-08B.
Subject:	Chemistry, Physical. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3062254
ISBN:	0493781633

Theoretical studies of molecular interactions, dynamics, structure, and free energies of biological systems.
Nguyen, Dat Huy.

Theoretical studies of molecular interactions, dynamics, structure, and free energies of biological systems. - 168 p.

Source: Dissertation Abstracts International, Volume: 63-08, Section: B, page: 3734.

Thesis (Ph.D.)--University of California, Davis, 2002.

This dissertation focuses on three topics in computational chemistry and biophysics: (1) the mechanism of action of biological antifreezes in repressing the growth of the ice crystal; (2) the mechanism of various anti-cancer nitrogen mustard molecules (crosslinking agents) in causing 1--3 DNA crosslinks; and (3) the molecular basis for the physical underlying nature of interactions of various organic dyes upon forming complex with the RNA aptamer. In antifreeze problems, my work provided theoretical support for the hypothesis that the availability of multiple energy minima, thermally accessible states, and energy transfer among these states appeared to be common motifs for biological antifreezes in retarding the growth of the ice crystal. The main characteristics of these special features of biological antifreezes are to increase the local fluctuation in the vicinity of the ice-growing crystal, hence, to make it more difficult for water to set in onto the ice lattice. The finding fits well into the existing framework of the Kelvin relation for the thermal hysteresis, but from a different perspective. The new perspective here is the change of emphasis in the mechanism from one of irreversible binding to one of disposition of local energy transfer characteristics. In the 1--3 DNA crosslink problems, my study showed that the ability of forming crosslinking depends upon the composition of the active site of the drug, its mobility, and the length of the drug. The amount of DNA distortion required to create a crosslink varies greatly when the length of the crosslinking agent is short (between four and five atomic bonds). Finally, in Dye-RNA problems, I found that the electrostatic influences of the RNA backbone and surrounding counter-ions are dominant forces causing the split in the chemical shifts and accounting for 20% of absorption frequency changes in organic dyes. I also determined that the greater co-planar conformation that a dye adopts, the higher the binding affinity a dye will bind to the RNA aptamer. Finally, the greater co-planar conformation that the malachite green molecule adopts under the influence of the RNA aptamer is the origin of the red-shift in its maximum absorption frequency.

ISBN: 0493781633Subjects--Topical Terms:

560527
Chemistry, Physical.

Theoretical studies of molecular interactions, dynamics, structure, and free energies of biological systems.
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100 1 $a Nguyen, Dat Huy. $3 1932992
245 1 0 $a Theoretical studies of molecular interactions, dynamics, structure, and free energies of biological systems.
300 $a 168 p.
500 $a Source: Dissertation Abstracts International, Volume: 63-08, Section: B, page: 3734.
500 $a Adviser: William H. Fink.
502 $a Thesis (Ph.D.)--University of California, Davis, 2002.
520 $a This dissertation focuses on three topics in computational chemistry and biophysics: (1) the mechanism of action of biological antifreezes in repressing the growth of the ice crystal; (2) the mechanism of various anti-cancer nitrogen mustard molecules (crosslinking agents) in causing 1--3 DNA crosslinks; and (3) the molecular basis for the physical underlying nature of interactions of various organic dyes upon forming complex with the RNA aptamer. In antifreeze problems, my work provided theoretical support for the hypothesis that the availability of multiple energy minima, thermally accessible states, and energy transfer among these states appeared to be common motifs for biological antifreezes in retarding the growth of the ice crystal. The main characteristics of these special features of biological antifreezes are to increase the local fluctuation in the vicinity of the ice-growing crystal, hence, to make it more difficult for water to set in onto the ice lattice. The finding fits well into the existing framework of the Kelvin relation for the thermal hysteresis, but from a different perspective. The new perspective here is the change of emphasis in the mechanism from one of irreversible binding to one of disposition of local energy transfer characteristics. In the 1--3 DNA crosslink problems, my study showed that the ability of forming crosslinking depends upon the composition of the active site of the drug, its mobility, and the length of the drug. The amount of DNA distortion required to create a crosslink varies greatly when the length of the crosslinking agent is short (between four and five atomic bonds). Finally, in Dye-RNA problems, I found that the electrostatic influences of the RNA backbone and surrounding counter-ions are dominant forces causing the split in the chemical shifts and accounting for 20% of absorption frequency changes in organic dyes. I also determined that the greater co-planar conformation that a dye adopts, the higher the binding affinity a dye will bind to the RNA aptamer. Finally, the greater co-planar conformation that the malachite green molecule adopts under the influence of the RNA aptamer is the origin of the red-shift in its maximum absorption frequency.
590 $a School code: 0029.
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791 $a Ph.D.
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