| Materials chemistry and biochemistry have drawn lots of attention in recent yearsbecause of their great potential in applications.In materials chemistry field,nonlinearoptical material is a new type of material which developed during the last two decades.Now,it has been widely used in electro-optical switch,tunable laser,opticalinformation processing and other fields.In first four chapters of this dissertation,wediscussed the organic and inorganic nonlinear optical materials,and explored therelationships between the hyperpolarizabilities and the electronic structures of thesystems.In biochemistry field,biological enzymes play a key role in life activities.But the investigation on their reaction mechanisms is still a challenging in bothexperimental and theoretical fields.The work of another four chapters was thesimulations of phosphotriesterase (PTE) and yeast cytosine deaminase (yCD) inQM/MM MD level,and the results can give some useful suggestions to site-directedmutagenesis studies.The main work of this dissertation can be summarized asfollows:(1) The third-order nonlinear optical (NLO) properties of (ZnS)6～12 are investigatedunder the time dependent density functional theory (TDDFT) at the B3LYP/Lanl2DZ+6-31G* level.The static third-order susceptibilities X(3) and dynamicbehavior of third-order polarizabilitiesγin 0～2.5 eV are calculated under the sumover states (SOS) method.The results show that the X(3) of (ZnS)6～12 clusters are betterthan the other semiconducting clusters.(ZnS)7 and (ZnS)11 have a remarkableγvalueof -2.38*10-33 esu and 1.26*10-33esu at 1.6eV and 2.0eV respectively.(ZnS)6～12clusters will produce an obvious phenomenon of the third-order polarizabilities whenthey are excited at the largeγvalue area.(2) The frequency-dependent hyperpolarizabilities of chelidamic acid complexesMm(C7H3O5N)n (M=Cu,Ag) were investigated under the TDDFT combined with SOSmethod.The relationship between molecular orbitals and nonlinear optical properties has been explored.The results show that the charge transitions ofπ-π* and 3dM-π*are very important to the second-order polarizabilities,and the largest component ofdynamicβis 3.84×10-25 cm5 esu-1 at 0.74 eV for Ag2Cu2(C7H3O5N)4.The chargetransition betweenπ-π* is also highly crucial to the third-order polarizabilities,andthe largest component of dynamicγis-4.46×10-29 esu at 0.50 eV forAg2Cu2(C7H3O5N)4.The central Cu ion,as electron bridge,extends the range ofdelocalization and leads to an interesting phenomenon of spiroconjugation.(3) Extensive combined QM/MM molecular dynamics simulations have beenperformed to elucidate the enzymatic catalysis mechanism on the detoxification ofparaoxon by PTE.The parameters for the phosphorous atom in PM3 method wasre-optimized and the recent updated ZnB (Zinc,Biological) parameter for Zn ions wasused throughout this work.The rate-limiting step of this process is the distortion ofthe bound paraoxon in order to approach the bridging hydroxide.Conformationalanalyses indicate that Trp131 is the closest residue to the phosphoryl oxygen,andmutations to Arg,Gln,even Lys which can shorten the hydrogen bond distance withthe phosphoryl oxygen could potentially lead to a mutant with enhanced activity forthe detoxification of organophosphates.(4) The deaminasion process of cytosine to uracil by yCD is simulated by usingcombined QM(PM3)/MM molecular dynamics method.Calculated results show that,Glu264 plays the most important role in the atom transitions.The conformationalcharge from zinc-coordinate uracil to free uracil is the rate-limiting step of the wholereaction process.High energy consumption mainly because of the coordinationnumber changing of zinc ion needs to overcome the steric hindrance.So weconsidered to mutate Glu264 for some small residues,or to move Ile233 and His262away to make uracil easier escape from their interlayer,which could reduce theenergy barrier and increase the reactivity of yCD.
|
PDF Full Text Request