非线性光学材料和生物酶体系的理论研究
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摘要
材料化学和生物化学是近年来化学领域中最具应用前景的两个研究方向，也是计算化学探讨的热点方向。在材料化学中，非线性光学材料是近四十年才发展起来的一种新型材料。从技术领域到研究领域，它的应用都十分广泛，如制成电光开关、实现激光频率的调谐、进行光学信息处理等。本论文前四章即是针对无机和有机非线性光学材料进行计算，并讨论了非线性极化率和体系电子结构之间的关系。在生命活动中，生物酶起着至关重要的作用，和我们的生活也密切相关。但对它们酶催化反应机理的研究，无论在实验测定还是理论计算领域，仍存在着诸多挑战。本论文后四章即是采用分子动力学模拟结合QM／MM组合方法，计算了磷酸三酯水解酶和酵母菌胞嘧啶脱氨酶的反应机理，并对这两个体系的定点突变实验研究提出了有用的建议。总体来说，本论文主要的工作以及得出的结论包括：
(1)在TDDFT／an12DZ+6-31G~*水平下对(ZnS)_(6～12)半导体团簇的三阶非线性光学性质进行了计算，并用态求和(SOS)方法求得了静态三阶宏观极化率x~(3)和0～2．5 eV范围内输入光子能量对三阶微观极化率γ的动态行为。结果表明，(ZnS)_(6～12)的x~(3)值与其它半导体团簇相比略好。且(ZnS)_7和(ZnS)_(11)分别在1．6eV和2．0 eV处出现了很大的γ值，为-2．38~*10~(-33)esu和1．26~*10~(-33)esu。在此输入光子能量处激发，它们将会产生很强的三阶非线性光学效应。
(2)在TDDFT-SOS／Lan12DZ+3-21G~*水平下对白屈菜氨酸配合物Mm(C_7H_3O_5N)_n(M=Cu，Ag)的非线性光学性质进行了计算，并探讨了分子轨道与非线性光学性质的内在联系。结果表明，对二阶极化率有影响的电子转移为π-π~*和3d_M-π~*，且Ag_2Cu_2(C_7H_3O_5N)_4在0．74 eV处出现了很大的β值，为3．84×10~(-25)cm~5esu~(-1)。电子转移π-π~*对三阶极化率的增强有非常重要的作用，最大的γ值为Ag_2Cu_2(C_7H_3O_5N)_4出现在0．50 eV处的-4．46×10~(-29)esu。Cu离子作为电子桥，不仅增大了配体的电子离域范围，还导致了螺旋共轭现象的产生。
(3)在QM(PM3-SPR)／MM水平下对磷酸三酯酶催化水解paiaoxon的反应机理进行分子动力学模拟，并在QM(DFT)／MM水平下计算了一些关键态的能量与动力学的结果比较。模拟开始前，我们根据DFT的计算结果重新优化了PM3中磷原子的参数，并依照文献报道更新了Zn原子的参数。结果表明，paraoxon在接近羟基过程中的扭曲是整个反应的速率决定步骤。任何可以缩短NE1@Trp131和磷酸酯上O原子之间的氢键距离的突变，都有可能增强磷酸三酯酶分解有机磷的反应活性，例如把Trp131突变为精氨酸、谷氨酰胺、甚至是酪氨酸。对Phe132进行类似的突变也会有好的效果。
(4)通过QM(PM3)／MM结合MD的方法模拟了酵母菌胞嘧啶脱氨酶把胞嘧啶脱氨形成尿嘧啶的反应过程。计算结果表明，Glu264在整个反应过程中扮演了十分重要的中转站角色。由被Zn离子束缚的尿嘧啶到自由态尿嘧啶的过程为整个反应的速率决定步骤。高的能量消耗主要是由Zn离子从四配位变成五配位模式需要克服的空间位阻所造成的。所以，我们认为将Glu264突变为体积较小的残基，或是移走Ile233和His262使尿嘧啶更容易从它们的夹层中逃离，可以降低速率决定步骤的反应能垒，从而提高酵母菌胞嘧啶脱氨酶的脱氨活性。
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~(-33)esu at 1.6eV and 2.0eV respectively.(ZnS)_(6～12)clusters 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 complexesM_m(C_7H_3O_5N)_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 3d_M-π~*are very important to the second-order polarizabilities,and the largest component ofdynamicβis 3.84×10~(-25) cm~5 esu~(-1) at 0.74 eV for Ag_2Cu_2(C_7H_3O_5N)_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 forAg_2Cu_2(C_7H_3O_5N)_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.
(1)在TDDFT／an12DZ+6-31G~*水平下对(ZnS)_(6～12)半导体团簇的三阶非线性光学性质进行了计算，并用态求和(SOS)方法求得了静态三阶宏观极化率x~(3)和0～2．5 eV范围内输入光子能量对三阶微观极化率γ的动态行为。结果表明，(ZnS)_(6～12)的x~(3)值与其它半导体团簇相比略好。且(ZnS)_7和(ZnS)_(11)分别在1．6eV和2．0 eV处出现了很大的γ值，为-2．38~*10~(-33)esu和1．26~*10~(-33)esu。在此输入光子能量处激发，它们将会产生很强的三阶非线性光学效应。
(2)在TDDFT-SOS／Lan12DZ+3-21G~*水平下对白屈菜氨酸配合物Mm(C_7H_3O_5N)_n(M=Cu，Ag)的非线性光学性质进行了计算，并探讨了分子轨道与非线性光学性质的内在联系。结果表明，对二阶极化率有影响的电子转移为π-π~*和3d_M-π~*，且Ag_2Cu_2(C_7H_3O_5N)_4在0．74 eV处出现了很大的β值，为3．84×10~(-25)cm~5esu~(-1)。电子转移π-π~*对三阶极化率的增强有非常重要的作用，最大的γ值为Ag_2Cu_2(C_7H_3O_5N)_4出现在0．50 eV处的-4．46×10~(-29)esu。Cu离子作为电子桥，不仅增大了配体的电子离域范围，还导致了螺旋共轭现象的产生。
(3)在QM(PM3-SPR)／MM水平下对磷酸三酯酶催化水解paiaoxon的反应机理进行分子动力学模拟，并在QM(DFT)／MM水平下计算了一些关键态的能量与动力学的结果比较。模拟开始前，我们根据DFT的计算结果重新优化了PM3中磷原子的参数，并依照文献报道更新了Zn原子的参数。结果表明，paraoxon在接近羟基过程中的扭曲是整个反应的速率决定步骤。任何可以缩短NE1@Trp131和磷酸酯上O原子之间的氢键距离的突变，都有可能增强磷酸三酯酶分解有机磷的反应活性，例如把Trp131突变为精氨酸、谷氨酰胺、甚至是酪氨酸。对Phe132进行类似的突变也会有好的效果。
(4)通过QM(PM3)／MM结合MD的方法模拟了酵母菌胞嘧啶脱氨酶把胞嘧啶脱氨形成尿嘧啶的反应过程。计算结果表明，Glu264在整个反应过程中扮演了十分重要的中转站角色。由被Zn离子束缚的尿嘧啶到自由态尿嘧啶的过程为整个反应的速率决定步骤。高的能量消耗主要是由Zn离子从四配位变成五配位模式需要克服的空间位阻所造成的。所以，我们认为将Glu264突变为体积较小的残基，或是移走Ile233和His262使尿嘧啶更容易从它们的夹层中逃离，可以降低速率决定步骤的反应能垒，从而提高酵母菌胞嘧啶脱氨酶的脱氨活性。
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~(-33)esu at 1.6eV and 2.0eV respectively.(ZnS)_(6～12)clusters 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 complexesM_m(C_7H_3O_5N)_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 3d_M-π~*are very important to the second-order polarizabilities,and the largest component ofdynamicβis 3.84×10~(-25) cm~5 esu~(-1) at 0.74 eV for Ag_2Cu_2(C_7H_3O_5N)_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 forAg_2Cu_2(C_7H_3O_5N)_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.
引文
Materials Chemistry 2006,16(16),1573-1578.
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[1]Zhan,C.G.;de Souza,O.N.;Rittenhouse,R.C.;Omstein,R.L.,Determination of two structural forms of catalytic bridging ligand in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation.Journal of the American Chemical Society 1999,121(32),7279-7282.
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[4]Ko(?)a,J.;Zhan,C.G.;Rittenhouse,R.C.;Omstein,R.L.,Mobility of the active site bound paraoxon and satin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation.Journal of the American Chemical Society 2001,123(5),817-826.
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[11]Dapprich,S.;Komaromi,I.;Byun,K.S.;Morokuma,K.;Frisch,M.J.,A new ONIOM implementation in Gaussian98.Part I.The calculation of energies,gradients,vibrational frequencies and electric field derivatives.Journal of Molecular Structure.: THEOCHEM 1999,462,1-21.
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[14]Zhang,Y.K.;Liu,H.Y.;Yang,W.T.,Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface.Journal of Chemical Physics 2000,112(8),3483-3492.
[15]Cui,Q.;Guo,H.;Karplus,M.,Combining ab initio and density functional theories with semiempirical methods.Journal of Chemical Physics 2002,117(12),5617-5631.
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[1] Sklenak, S.; Yao, L. S.; Cukier, R. I.; Yan, H. G., Catalytic mechanism of yeast cytosine deaminase: An ONIOM computational study. Journal of the American Chemical Society 2004,126(45), 14879-14889.
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[11] Monard, G; Merz, K. M., Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Accounts of Chemical Research 1999, 32,904-911.
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[16] Truhlar, D. G; Gao, J. L.; Alhambra, C; Garcia-Viloca, M.; Corchado, J.; Sanchez, M. L.; Villa,J.,The incorporation of quantum effects in enzyme kinetics modeling.Accounts of Chemical Research 2002,35(6),341-349.
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[20]Monard,G.;Prat-Resina,X.;Gonzalez-Lafont,A.;Lluch,J.M.,Determination of enzymatic reaction pathways using QM/MM methods.International Journal of Quantum Chemistry 2003,93(3),229-244.
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