生物相关体系的密度泛函理论研究
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摘要
DNA分子和金属酶作为重要的生物体系，在生命活动中扮演着举足轻重的角色。近年来，相关领域的研究已经引起广泛的兴趣，并取得重要的进展。然而，在分子与原子水平上，理解这些生物学中独一无二的体系，及其在生命活动中相关生物化学过程的机制，仍然存在诸多挑战。我们选择了与DNA和金属酶相关的一些模型体系，对它们的结构特征与化学反应活性进行了理论计算研究，调查了低能电子诱导DNA分子损坏和金属酶催化过程的反应机理。
本文获得的主要结果如下：
(1)在腺嘌呤和鸟嘌呤阴离子中，N9位的脱氢是能量最低的反应通道。对于腺嘌呤，电子俘获对其碎片化过程具有显著影响；且随着N9-H键的伸长，低能电子组态将发生改变，由π~*始态转变成σ~*终态；当N9-H键延伸至1．22 (?)时，π~*-σ~*能量曲线交叉出现。而鸟嘌呤的阴离子具有偶极态束缚的特征，其碎片化过程对电子附着并不敏感。
(2)对于Watson-Crick A-T碱基对，电子附着可以影响分子间氢键的相互作用，导致A-T碱基对的几何结构发生显著变化。A-T碱基对中低能的脱氢通道对应于腺嘌呤中N9位和胸腺嘧啶中N1位上氢原子的解离。在脱氢过程中，阴离子A-T的碎片会逐渐改变它的低能电子组态，从π~*态转变到σ~*态，这种变化跟在单个碱基腺嘌呤和胸腺嘧啶的情况相似。
(3)对于嘧啶核苷体系，低能电子俘获可以修改它们的平衡几何构型、成键性质和碎片化性质。相对于中性分子，阴离子dCMP和dTMP中的C_5′-O_5′和C_1′-N_1键的断裂更容易发生。C-O键断裂的活化能要比C-N键断裂的活化能低，水溶剂的存在可以显著地降低C-N键断裂过程的活化能。
(4)应用密度泛函理论和QM／MM组合计算方法，研究了固氮酶辅酶FeMoco(μ_6-X)(X=C，N，O)的结构特征以及它们与CO和N_2的相互作用。计算结果表明，蛋白质环境对辅酶结构有显著影响。基于预测的辅酶结构特征、氧化还原势、CO和N_2的结合能与光谱性质，氧和氮原子均有可能是空隙原子。
(5)预测了CO脱氢酶活性簇不同氧化-还原态(C_(red1)，C_(red2)和C_(int))的结构特征和酶催化CO氧化成CO_2的反应机理。计算表明，C簇周围的氢键网络主要由保守残基His93，His96，Glu299，Lys563和四个水分子组成，该氢键网络在稳定中间体和调控质子转移的过程中，起着重要的作用。
(6)通过广泛的密度泛函计算，探索了硝酸根还原酶中钼配合物催化NO_3~-到NO_2~-的反应机理，预测了不同的反应通道和能量学性质。计算表明，双硫键的形成能够影响Mo~Ⅵ和Mo~Ⅳ氧化态之间的相互转化，在酶催化还原过程中起着重要的作用。
DNA molecules and metalloenzymes play an important role in the life domain.Inrecent years,the multidisciplinary research on DNA and enzyme has attractedconsiderable attention and remarkable progresses have been made.However,at theatomic scale level,understanding of these unique biological systems in biology andtheir molecular mechanisms involved in the bio-related chemical processes is stilldifficult and challenging.Here selected biological systems relative to DNA andmetalloenzymes were considered and their structural features and chemicalreactivities were investigated theoretically.On the basis of extensive calculations,wetry to understand fundamental aspects of DNA damages from the low energy electronattachment and catalytic mechanisms of metalloenzymes.
The main results in this dissertation are summarized as follows:
(1)Our calculations show that the dehydrogenation at the N9 site in the adenine andguanine transient anions is the lowest-energy channel to loss of hydrogen.For theadenine anion,as the N9-H bond stretches,the low-energy electron configurationmay change from the initialπ~* state to theσ~* state,and theπ~*-σ~* energy curvesintersect at 1.22(?).While the guanine anion has a character of dipole-bound state,and its fragmentation is not sensitive to the low energy electron attachment.
(2)For the Watson-Crick adenine-thymine(A-T)base pair,the electron attachment tothe A-T base pair and its derivatives significantly modifies the hydrogen bondinteractions and results in remarkable structural changes.The relatively low-costhydrogen eliminations correspond to the cleavage of(N9)-H(adenine)and(N1)-H(thymine)bonds.In the dehydrogenating process,the anionic A-T fragmentgradually changes its electronic configuration fromπ~* toσ~* state,like the singlebases adenine and thymine.
(3)The low-energy electron attachment to the pyrimidine nucleotides mayremarkably modify their equilibrium geometries,electron affinities,and bonddissociations.The C_5′-O_5′and C_1′-N_1 bonds of the anionic dCMP and dTMP were predicted to be relatively easy to break relative to their neutral species.The C-Obond cleavage has relatively low activation energy with respect to C-N bondbreaking,and the presence of the solvent water may significantly reduce theactivation energy in the C-N bond cleavage process.Present results provide abasis for understanding the single strand breaks in DNA induced by low-energyelectron attachment.
(4)Density functional theory and combined quantum mechanics and molecularmechanics(QM/MM)calculations have been used to explore structural features ofthe FeMo cofactor with an interstitial atom X(X = N,C,or O)and its interactionswith CO and N_2.Predicted frequencies of the metal-bound CO,QM/MM-optimized geometries,and calculated redox potentials of the FeMocofactor with different central ligands show that the oxygen atom is the candidatefor the interstitial atom.Calculations on the interactions of the FeMo cofactor withCO and N_2 reveal that there is a remarkable dependence of the binding energy onthe binding site and the interstitial atom.Generally,the Fe_2 site of the FeMocofactor has stronger interactions with CO and N_2 than Fe6,and both the Fe_2 andFe6 sites in the N-centered and O-centered clusters of the FeMo cofactor caneffectively bind N_2 while the coordination of N_2 to the Fe6 site of the C-centeredactive cluster is unfavorable energetically.Present results indicate that the proteinenvironment is important for computational characterization of the structure of theFeMo cofactor and properties of the metal-bound CO and N_2 are sensitive to theinterstitial atom.
(5)The catalytic oxidation of CO to CO_2 by carbon monoxide dehydrogenases hasbeen explored theoretically,and a large C-cluster model including the metal core[Ni-4Fe-4S]and surrounding residues and crystal water molecules was used indensity functional calculations.On the basis of computational results,theplausible enzymatic mechanism for the CO oxidation was proposed.In thecatalytic reaction,the first proton abstraction from the Fel-bound water leads to aprecursor to accommodate CO binding and the subsequently consecutive proton transfer from the metal-bound carboxylate to the amino acid residues facilitatesthe release of CO_2.The hydrogen-bond network around the C-cluster,formed byconserved residues His93,His96,Glu299,Lys563,and four water molecules inthe active domain plays an important role in the proton transfer and theintermediate stabilization.Predicted geometries of key species show goodagreement with their reported crystal structures.
(6)The oxidative half-reaction of oxygen atom transfer from nitrate to Mo~Ⅳcomplexwas investigated theoretically.Calculations show that the nitrate reduction canoccur through either a direct rupture of Mo-ONO_2~-bond or a bond formationbetween the nitrate ion and a Mo-bound sulfur ligand.Detailed mechanisms andreaction energetics were predicted.Present results indicate that the formation of adisulfide bond can mediate the oxidation-state interconversion of the metal centerfrom Mo~Ⅵto Mo~Ⅳ,which plays an important role in the nitrate reduction reaction.
本文获得的主要结果如下：
(1)在腺嘌呤和鸟嘌呤阴离子中，N9位的脱氢是能量最低的反应通道。对于腺嘌呤，电子俘获对其碎片化过程具有显著影响；且随着N9-H键的伸长，低能电子组态将发生改变，由π~*始态转变成σ~*终态；当N9-H键延伸至1．22 (?)时，π~*-σ~*能量曲线交叉出现。而鸟嘌呤的阴离子具有偶极态束缚的特征，其碎片化过程对电子附着并不敏感。
(2)对于Watson-Crick A-T碱基对，电子附着可以影响分子间氢键的相互作用，导致A-T碱基对的几何结构发生显著变化。A-T碱基对中低能的脱氢通道对应于腺嘌呤中N9位和胸腺嘧啶中N1位上氢原子的解离。在脱氢过程中，阴离子A-T的碎片会逐渐改变它的低能电子组态，从π~*态转变到σ~*态，这种变化跟在单个碱基腺嘌呤和胸腺嘧啶的情况相似。
(3)对于嘧啶核苷体系，低能电子俘获可以修改它们的平衡几何构型、成键性质和碎片化性质。相对于中性分子，阴离子dCMP和dTMP中的C_5′-O_5′和C_1′-N_1键的断裂更容易发生。C-O键断裂的活化能要比C-N键断裂的活化能低，水溶剂的存在可以显著地降低C-N键断裂过程的活化能。
(4)应用密度泛函理论和QM／MM组合计算方法，研究了固氮酶辅酶FeMoco(μ_6-X)(X=C，N，O)的结构特征以及它们与CO和N_2的相互作用。计算结果表明，蛋白质环境对辅酶结构有显著影响。基于预测的辅酶结构特征、氧化还原势、CO和N_2的结合能与光谱性质，氧和氮原子均有可能是空隙原子。
(5)预测了CO脱氢酶活性簇不同氧化-还原态(C_(red1)，C_(red2)和C_(int))的结构特征和酶催化CO氧化成CO_2的反应机理。计算表明，C簇周围的氢键网络主要由保守残基His93，His96，Glu299，Lys563和四个水分子组成，该氢键网络在稳定中间体和调控质子转移的过程中，起着重要的作用。
(6)通过广泛的密度泛函计算，探索了硝酸根还原酶中钼配合物催化NO_3~-到NO_2~-的反应机理，预测了不同的反应通道和能量学性质。计算表明，双硫键的形成能够影响Mo~Ⅵ和Mo~Ⅳ氧化态之间的相互转化，在酶催化还原过程中起着重要的作用。
DNA molecules and metalloenzymes play an important role in the life domain.Inrecent years,the multidisciplinary research on DNA and enzyme has attractedconsiderable attention and remarkable progresses have been made.However,at theatomic scale level,understanding of these unique biological systems in biology andtheir molecular mechanisms involved in the bio-related chemical processes is stilldifficult and challenging.Here selected biological systems relative to DNA andmetalloenzymes were considered and their structural features and chemicalreactivities were investigated theoretically.On the basis of extensive calculations,wetry to understand fundamental aspects of DNA damages from the low energy electronattachment and catalytic mechanisms of metalloenzymes.
The main results in this dissertation are summarized as follows:
(1)Our calculations show that the dehydrogenation at the N9 site in the adenine andguanine transient anions is the lowest-energy channel to loss of hydrogen.For theadenine anion,as the N9-H bond stretches,the low-energy electron configurationmay change from the initialπ~* state to theσ~* state,and theπ~*-σ~* energy curvesintersect at 1.22(?).While the guanine anion has a character of dipole-bound state,and its fragmentation is not sensitive to the low energy electron attachment.
(2)For the Watson-Crick adenine-thymine(A-T)base pair,the electron attachment tothe A-T base pair and its derivatives significantly modifies the hydrogen bondinteractions and results in remarkable structural changes.The relatively low-costhydrogen eliminations correspond to the cleavage of(N9)-H(adenine)and(N1)-H(thymine)bonds.In the dehydrogenating process,the anionic A-T fragmentgradually changes its electronic configuration fromπ~* toσ~* state,like the singlebases adenine and thymine.
(3)The low-energy electron attachment to the pyrimidine nucleotides mayremarkably modify their equilibrium geometries,electron affinities,and bonddissociations.The C_5′-O_5′and C_1′-N_1 bonds of the anionic dCMP and dTMP were predicted to be relatively easy to break relative to their neutral species.The C-Obond cleavage has relatively low activation energy with respect to C-N bondbreaking,and the presence of the solvent water may significantly reduce theactivation energy in the C-N bond cleavage process.Present results provide abasis for understanding the single strand breaks in DNA induced by low-energyelectron attachment.
(4)Density functional theory and combined quantum mechanics and molecularmechanics(QM/MM)calculations have been used to explore structural features ofthe FeMo cofactor with an interstitial atom X(X = N,C,or O)and its interactionswith CO and N_2.Predicted frequencies of the metal-bound CO,QM/MM-optimized geometries,and calculated redox potentials of the FeMocofactor with different central ligands show that the oxygen atom is the candidatefor the interstitial atom.Calculations on the interactions of the FeMo cofactor withCO and N_2 reveal that there is a remarkable dependence of the binding energy onthe binding site and the interstitial atom.Generally,the Fe_2 site of the FeMocofactor has stronger interactions with CO and N_2 than Fe6,and both the Fe_2 andFe6 sites in the N-centered and O-centered clusters of the FeMo cofactor caneffectively bind N_2 while the coordination of N_2 to the Fe6 site of the C-centeredactive cluster is unfavorable energetically.Present results indicate that the proteinenvironment is important for computational characterization of the structure of theFeMo cofactor and properties of the metal-bound CO and N_2 are sensitive to theinterstitial atom.
(5)The catalytic oxidation of CO to CO_2 by carbon monoxide dehydrogenases hasbeen explored theoretically,and a large C-cluster model including the metal core[Ni-4Fe-4S]and surrounding residues and crystal water molecules was used indensity functional calculations.On the basis of computational results,theplausible enzymatic mechanism for the CO oxidation was proposed.In thecatalytic reaction,the first proton abstraction from the Fel-bound water leads to aprecursor to accommodate CO binding and the subsequently consecutive proton transfer from the metal-bound carboxylate to the amino acid residues facilitatesthe release of CO_2.The hydrogen-bond network around the C-cluster,formed byconserved residues His93,His96,Glu299,Lys563,and four water molecules inthe active domain plays an important role in the proton transfer and theintermediate stabilization.Predicted geometries of key species show goodagreement with their reported crystal structures.
(6)The oxidative half-reaction of oxygen atom transfer from nitrate to Mo~Ⅳcomplexwas investigated theoretically.Calculations show that the nitrate reduction canoccur through either a direct rupture of Mo-ONO_2~-bond or a bond formationbetween the nitrate ion and a Mo-bound sulfur ligand.Detailed mechanisms andreaction energetics were predicted.Present results indicate that the formation of adisulfide bond can mediate the oxidation-state interconversion of the metal centerfrom Mo~Ⅵto Mo~Ⅳ,which plays an important role in the nitrate reduction reaction.
引文
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