Study Of Phycocyanobilin And Glycine Using Ab Initio And Monte-Carlo Based Molecular Mechanics

Phycocyanobilin and glycine are computationally studied using ab initio and Monte-Carlo based molecular mechanics in this paper.First,there main methods in computational chemistry are introducted,including ab inito,molecular mechanics and Monte-Carlo method.Then our work on phycocyanobilin and glycine using ab initio and monte-carlo based molecular mechanics are introducted in detail.This thesis includes following three contents:1.A scan of the potential-energy surface(PES) of phycocyanobilin has been performed by Monte-Carlo Multiple Minimum(MCMM) searching method using the force field of MMFFs.The resulting most stable/populated structures obtained are then reoptimized with ab initio methods and density functional theory(DFT) using HF/6-31G and B3LYP/6-31G levels of theory,and all possible conformers of phycocyanobilin are investigated with these methods. Results indicate that the most stable structure is all-syn,all-Z conformation. Other local minima are also obtained,such as ZZZass,EZZass and ZZZssa, which are stabilized by intramolecular hydrogen bonds and favorable geometric structures minimizing steric interactions.2.Using Monte-Carlo based molecular mechanics and ab initio,the comformer of deprotonated glycine are studied firstly.Furthermore,the interactions of deprotonated glycine with water molecules(from one to eight molecules) are studied.The IR and Raman spectroscopies obtained from calculation indicate the second-shell water molecules have fewer effects to the vibration spectral of deprotonated glycine. The deprotonated glycine with first hydration shell is generated and its IR and Raman spectroscopy are analysised by comparing with that of deprotonated glycine under the CPCM model. 3.The interactions between glycine sodium salt and water molecule also are studied using Monte-Carlo based molecular mechanics and ab initio.By scanning of the potential-energy surface(PES) of glycine sodium salt,the resulted most stable/populated structures are then reoptimized with ab initio method.On this basis,the PES of interaction between the stable glycine sodium salts and water molecules(from one to there molecules) are also scaned to locate the stable structures on the PES.