Chemistry Commons^™

Raman Spectroscopic And Quantum Chemical Investigation Of The Effects Of Tri-Methylamine N-Oxide (Tmao) On Hydrated Urea, Hydrated Guanidinium, And Hydrogen Bonded Networks, Genevieve Verville

Honors Theses

Trimethylamine N-Oxide (TMAO), guanidinium, and urea are three important

osmolytes with their main significance to the biophysical field being in how they

uniquely interact with proteins. TMAO is known to stabilize and counteract the

destabilizing effects of both urea and guanidinium. The exact mechanisms by which

TMAO stabilizes and both guanidinium and urea destabilize folded proteins continue

to be debated in the literature. Some studies suggest that solvent interactions do not

play a large role in TMAO’s stabilizing effects and therefore advocate direct

stabilization, whereas others suggest that TMAO counteracts denaturation primarily

through an indirect effect of strong solvent interactions. …

An Investigation Into The Molecular Dynamics Of The Laser Induced Dissociation Of 2-Bromoethanol, Kirk French

Senior Honors Theses

The unimolecular dissociation of 2-bromoethanol is investigated using computational chemistry methods both to test the reliability of the theories and methods of computational chemistry and to explore the internal mechanism of the dissociation. The dissociation of the bromine ion from 2-bromoethanol was experimentally observed in a previous publication by Ratliff et. al. These experimental results were compared in this thesis to computational calculations of their research. The method of TD-B3LYP proved to be inadequate in this venture except for the lowest energies of the most stable conformer of 2-bromoethanol. However, interesting mechanisms were found such as the formation of HBr …

Breakthroughs In Obtaining Qm/Mm Free Energies, Phillip S. Hudson

USF Tampa Graduate Theses and Dissertations

The computation of free energy is pivotal to understanding the fundamental nature of chemical phenomena. That is, whether a specific molecular outcome occurs spontaneously or is inherently unfavorable. The need to do this with consistent accuracy begs for the use of quantum mechanical (QM) methods. However, techniques for directly computing free energy differences with QM or mixed QM/MM methods are untenable, as the computational expense is quite exorbitant. At present, the most feasible approach for obtaining QM/MM free energies is employing the so-called indirect cycle, which relies on accurately computing free energy differences between low (e.g., molecular mechanical, MM) and …