量子化学计算的应用研究
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摘要
Ⅰ.基于价键理论的化学键电子密度拓扑研究
为了探寻化学成键的本质,我们对一系列电子对键采用从头算价键方法研究电子密度的拓扑性质。在价键理论框架下,电子密度及对应的Laplacian可分成共价,离子及共振成分。分析提供了一个基于密度特点的成键类型,并且揭示了除了共价键和离子键外,电子对键还存在着第三种成键类型,称为Charge-ShiftBond(CS-Bond)。如预期中一样,对于典型的共价键,在BCP处共价成分的Laplacian值为负值且负值很大。相反地,在CS键里,共价成分的Laplacian值很小或为正值,这与这些键的共价相互作用是弱的吸引或是排斥的特点相吻合。另一方面,在CS键中,共振成分的Laplacian值为负或接近于零,其绝对值随着与共价—离子混合相关连的动能的减小而增加。我们提出了一种新的关于在BCP处总的电子密度的阐述,从密度的观点来表征共价键,离子键和CS键。
Ⅱ.细胞色素P450单加氧化含硫原子底物的密度泛函理论研究
细胞色素P450是自然界中普遍存在的功能独特的氧化剂,但是它的反应活性物种至今没有定论,这对研究化学反应机理的化学家们构成了很迫切的挑战。关于硫醚在P450作用下发生硫氧化的反应机制的争论使这一难题显得更为突出。
我们采用DFT方法计算研究了CpdⅠ和Cpd 0催化下的二甲硫醚发生硫氧化的反应机制过程,结果表明CpdⅠ催化硫氧化反应是低自旋选择的,且反应能垒很低仅为7.1 kcal/mol,说明CpdⅠ在硫氧化反应中活性很高,催化的反应速率极快。而Cpd 0通过分步的O-O键均裂/O_d进攻的硫氧化反应需要跨越第一步至少17.8 kcal/mol的能垒,相对CpdⅠ而言,Cpd 0的活性显得很弱,对应的反应速率约比CpdⅠ的慢6个数量级。此外Cpd 0通过O-O键均裂产生活性自由基物种的反应还受到其它平行反应的有效竞争,所以我们认为,在原态的P450中对S-氧化起作用的活性物种是CpdⅠ,甚至在突变的P450中,Cpd 0的作用也可以忽略。
此外我们还对CpdⅠ和Cpd 0催化底物p-methylthio-N,N-dimethylaniline(p-MT-DMA)发生的区域选择氧化反应中的S-氧化反应进行了初步的DFT计算,结果表明,在CpdⅠ存在时,Cpd 0对S-氧化处于“寂静”状态。CpdⅠ不存在时,Cpd 0相对CpdⅠ而言,仍然是参与催化S-氧化的较差的氧化剂。
Ⅰ.Topology of Electron Charge Density for Chemical Bond from Valence Bond Theory
To characterize the nature of bonding we derive the topological properties of electron charge density of a variety of bonds,based on ab initio valence bond methods. The electron density and its associated Laplacian are partitioned into covalent,ionic, and resonance components in the valence bond spirit.The analysis provides a density-based signature of bonding types and reveals,along the classical covalent and ionic bonds,the existence of two-electron bonds in which most of the bonding arises from the covalent-ionic resonance energy,so-called charge-shift bonds.As expected, the covalent component of the Laplacian at the bond critical point is found to be largely negative for classical covalent bonds.By contrast,in charge-shift bonds,the covalent part of the Laplacian is small or positive,in agreement with the weakly attractive or repulsive character of the covalent interaction in these bonds.On the other hand,the resonance component of the Laplacian is always negative or nearly zero,and it increases in absolute value with the charge-shift character of the bond,in agreement with the decrease of kinetic energy associated with covalent-ionic mixing. A new interpretation of the topology of the total density at the bond critical point is proposed to characterize covalent,ionic and charge-shift bonding from the density point of view.
Ⅱ.DFT Study of the Monooxygenation Reactions of the Substrates Containing Sulfur Atom by Cytochrome P450
One of the major and a "hot" mechanistic problems in P450 chemistry is what is actually the oxidant species that carries the oxidative processes of this enzyme and what is the root cause of its immense versatility as a primary oxidant in nature:is it the high valent iron-oxo species,so-called CompoundⅠor the precursor species,so called Compound 0? We undertook the challenge posed by the experimental data and carried out theoretical calculations,designed to addresses the CompoundⅠ—Compound 0 conundrum in sulfoxidation of thiafatty acids by P450.Our results demonstrate that CompoundⅠleads to an extremely fast process,while Compound 0 will be at least six orders of magnitude slower.We suggest that most likely,thiafatty acids promote CompoundⅠformation even in the T→A mutant of P450_(BM3).In this manner we provide a clear answer to a major mechanistic puzzle and suggest some new experiments.
A preliminary DFT calculations were carried out on the sulfoxidation reaction by the enzyme cytochrome P450 by taking p-methylthio-N,N-dimethylaniline (p-MT-DMA) as substrate.The results reveal that in the presence of CpdⅠ,Cpd 0 is clearly silent for sulfoxidation.While in the absence of CpdⅠ,Cpd 0 is still an inferior oxidant compared with CpdⅠ.
为了探寻化学成键的本质,我们对一系列电子对键采用从头算价键方法研究电子密度的拓扑性质。在价键理论框架下,电子密度及对应的Laplacian可分成共价,离子及共振成分。分析提供了一个基于密度特点的成键类型,并且揭示了除了共价键和离子键外,电子对键还存在着第三种成键类型,称为Charge-ShiftBond(CS-Bond)。如预期中一样,对于典型的共价键,在BCP处共价成分的Laplacian值为负值且负值很大。相反地,在CS键里,共价成分的Laplacian值很小或为正值,这与这些键的共价相互作用是弱的吸引或是排斥的特点相吻合。另一方面,在CS键中,共振成分的Laplacian值为负或接近于零,其绝对值随着与共价—离子混合相关连的动能的减小而增加。我们提出了一种新的关于在BCP处总的电子密度的阐述,从密度的观点来表征共价键,离子键和CS键。
Ⅱ.细胞色素P450单加氧化含硫原子底物的密度泛函理论研究
细胞色素P450是自然界中普遍存在的功能独特的氧化剂,但是它的反应活性物种至今没有定论,这对研究化学反应机理的化学家们构成了很迫切的挑战。关于硫醚在P450作用下发生硫氧化的反应机制的争论使这一难题显得更为突出。
我们采用DFT方法计算研究了CpdⅠ和Cpd 0催化下的二甲硫醚发生硫氧化的反应机制过程,结果表明CpdⅠ催化硫氧化反应是低自旋选择的,且反应能垒很低仅为7.1 kcal/mol,说明CpdⅠ在硫氧化反应中活性很高,催化的反应速率极快。而Cpd 0通过分步的O-O键均裂/O_d进攻的硫氧化反应需要跨越第一步至少17.8 kcal/mol的能垒,相对CpdⅠ而言,Cpd 0的活性显得很弱,对应的反应速率约比CpdⅠ的慢6个数量级。此外Cpd 0通过O-O键均裂产生活性自由基物种的反应还受到其它平行反应的有效竞争,所以我们认为,在原态的P450中对S-氧化起作用的活性物种是CpdⅠ,甚至在突变的P450中,Cpd 0的作用也可以忽略。
此外我们还对CpdⅠ和Cpd 0催化底物p-methylthio-N,N-dimethylaniline(p-MT-DMA)发生的区域选择氧化反应中的S-氧化反应进行了初步的DFT计算,结果表明,在CpdⅠ存在时,Cpd 0对S-氧化处于“寂静”状态。CpdⅠ不存在时,Cpd 0相对CpdⅠ而言,仍然是参与催化S-氧化的较差的氧化剂。
Ⅰ.Topology of Electron Charge Density for Chemical Bond from Valence Bond Theory
To characterize the nature of bonding we derive the topological properties of electron charge density of a variety of bonds,based on ab initio valence bond methods. The electron density and its associated Laplacian are partitioned into covalent,ionic, and resonance components in the valence bond spirit.The analysis provides a density-based signature of bonding types and reveals,along the classical covalent and ionic bonds,the existence of two-electron bonds in which most of the bonding arises from the covalent-ionic resonance energy,so-called charge-shift bonds.As expected, the covalent component of the Laplacian at the bond critical point is found to be largely negative for classical covalent bonds.By contrast,in charge-shift bonds,the covalent part of the Laplacian is small or positive,in agreement with the weakly attractive or repulsive character of the covalent interaction in these bonds.On the other hand,the resonance component of the Laplacian is always negative or nearly zero,and it increases in absolute value with the charge-shift character of the bond,in agreement with the decrease of kinetic energy associated with covalent-ionic mixing. A new interpretation of the topology of the total density at the bond critical point is proposed to characterize covalent,ionic and charge-shift bonding from the density point of view.
Ⅱ.DFT Study of the Monooxygenation Reactions of the Substrates Containing Sulfur Atom by Cytochrome P450
One of the major and a "hot" mechanistic problems in P450 chemistry is what is actually the oxidant species that carries the oxidative processes of this enzyme and what is the root cause of its immense versatility as a primary oxidant in nature:is it the high valent iron-oxo species,so-called CompoundⅠor the precursor species,so called Compound 0? We undertook the challenge posed by the experimental data and carried out theoretical calculations,designed to addresses the CompoundⅠ—Compound 0 conundrum in sulfoxidation of thiafatty acids by P450.Our results demonstrate that CompoundⅠleads to an extremely fast process,while Compound 0 will be at least six orders of magnitude slower.We suggest that most likely,thiafatty acids promote CompoundⅠformation even in the T→A mutant of P450_(BM3).In this manner we provide a clear answer to a major mechanistic puzzle and suggest some new experiments.
A preliminary DFT calculations were carried out on the sulfoxidation reaction by the enzyme cytochrome P450 by taking p-methylthio-N,N-dimethylaniline (p-MT-DMA) as substrate.The results reveal that in the presence of CpdⅠ,Cpd 0 is clearly silent for sulfoxidation.While in the absence of CpdⅠ,Cpd 0 is still an inferior oxidant compared with CpdⅠ.
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