| Informations of biomolecular structure and the key influence of environment on their stability andtransition are important first step in understanding the physical chemistry in vivo. Especially, biomolecularsolvation is one of the most common reaction. As the simplest amino acid, glycine is often used as themodel molecule for experiments and theoretical simulations.Using the force field based fully conformational search and Quantum Mechanic, the interactionbetween glycine and water molecule by building a first hydration shell model, to simulate the total watereffect. The first hydration shell model was then compared with the continuum model systematically. Inaddition, the tree-step building approach was applied to build the initial structure of disaccharide anddetermined their low-energy conformations.There are five chapters in this thesis:Chapter I: Introduction to the background, the research content and significance of our study. Theimportant significance of the biomolecular structure in biophysical chemistry was first discussed and thenwe reviewed the experimental and theoretical contributions in determining the biomolecular structure andfocus on the experimental difficult and the shortage of current theories, based on which our solution waspromoted and the feasibility was assessed.Chapter II: The computational methods and software used in this thesis was introduced, such as theMonte Carlo, force field based molecular modeling, base set and the quantum chemical calculation theory.Chapter III: Using the MCMM conformational search analysis and high level computational chemistry, GlyH+·(H2O)n=1~8complexes have been investigated step by step to simulate the saturated first hydrationshell of the protonated glycine. The first three water molecules strongly bind to the hydrogen-bond donorsof the ammonium group and while only one water molecule binds to the hydrogen of the carboxyl group.Five water molecules can fully pack the positive ammonium group and seven water molecules can fullysaturate the first hydration shell of GA. We have confirmed that protonation and deprotonation result inexplicitly different first hydration shell. Finally, we studied the water stabilizing effect and compared ourmodel with the CPCM model in simulating the bulk water effect. Compared to the CPCM model, our firsthydration shell model predicts the low hydration energies and the small vibrational red-shift by watereffect. The main conclusions and perspectives from this work are following:1. This work and the previous study on deprotonated glycine illustrate that, the competition betweenthe different hydration sites changes with the hydration process and results in an alternative dynamichydration process. Based on such an insight we can simplify the building process for the micro-hydrationand thus save computational costs.2. The hydration processes of GB and GC illustrate that water plays an excellent role in stabilizing theunstable molecules. Water forms small hydrogen binding network (e.g., the bridging water) to promoteassociation between two groups, which is often involved in molecular recognition.3. The first hydration shell model is able to model the specific hydration and further reproduce aconsiderable tendency of bulk water effect, which is comparable to that of the CPCM model.4. A combination of our first hydration shell model and the polarized continuum model may simulateboth the specific hydration effect and bulk water effect.Chapter IV: The tree-step approach was applied to build the initial structures of phenyl β-cellobioside and bezyl β-lactoside and their low-energy conformations was determined using quantum chemistrycalculations. Our results are in good agreement with results in precious study and the experiments. Inaddition to this, two conformers was found firstly in this work. |
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