Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree–Fock (HF) and density functional theory (DFT) Hamiltonians with double‐zeta basis sets ranging from 6‐31G(d) to 6‐31++G(d,p), and the triple‐zeta basis set 6‐311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2‐nitroimidazole, (ii) hydrogen superoxide ion and 2‐nitrosoimidazole, and (iii) water and 2‐nitroimidazolide. The rate‐determining step is the formation of a short‐lived intermediate in which the imidazole C₂ carbon is covalently bonded to peroxynitrite nitrogen. Three short‐lived intermediates were found in the reaction path. These intermediates are involved in a proton‐hopping transport from C₂ carbon to the terminal oxygen of the ? O? O moiety of peroxynitrite via the nitroso (ON? ) oxygen. Both HF and DFT calculations (using the Becke3–Lee–Yang–Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro‐ and nitroso‐) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal/mol (calculated at the B3LYP/6‐31++G(d,p) level), too large for an enzymatic reaction. Exploratory calculations on imidazole nitration in solution, and on the reaction of 9‐methylguanine with peroxynitrite in the gas phase and solution, show that solvation increases the activation energy for both imidazole and guanine, and that the modest decrease (15 kcal mol^?1) in the activation energy, due to the adjacent six member ring of guanine, is counterbalanced by solvation. These results lead to the speculation that proton tunneling may be at the origin of experimentally observed high reaction rate of guanine nitration by peroxynitrite in solution. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

纤维素热解形成左旋葡聚糖机理的理论研究

采用密度泛函理论UB3LYP/6-31G(d)方法,对模型化合物纤维二糖热解反应机理进行了量子化学理论计算研究。设计了三种可能的热解反应途径,对各种反应的反应物、产物、中间体和过渡态的结构进行了能量梯度全优化,计算了不同温度下热解反应的标准热力学和动力学参数。计算结果表明,糖苷键均裂而形成两个自由基中间体IM₁a和IM₁b,吸收热量为321.26kJ/mol,中间体IM₁a经过渡态TS₁a进一步形成左旋葡聚糖P₁,反应势垒为202.72kJ/mol;与分步反应相比,纤维二糖经过渡态TS₂协同反应直接形成左旋葡聚糖P₁和吡喃葡萄糖P₂的反应势垒低于分步反应的总势垒,其反应势垒为377.54kJ/mol;H⁺的加入有利于糖苷键的断裂,断裂形成的中间体IM₃很难进一步反应形成左旋葡聚糖。     

Role of electron transfer processes in the oxidation of aryl sulfides catalyzed by nonheme iron complexes

ABSTRACT

The oxidation of a series of aryl 1-methyl-1-phenylethyl sulfides with H₂O₂ catalyzed by the two tetradentate nonheme-iron complexes [(PDP)Fe^II(SbF₆)₂] and [(BPMCN)Fe^II(OTf)₂] occurs by an electron transfer-oxygen transfer (ET/OT) mechanism as supported by the observation of products deriving from fragmentation of the corresponding radical cations in association with S-oxidation products (sulfoxides).     

Imidazole to NHC rearrangements at molybdenum centers: an experimental and theoretical study

Both manganese and rhenium complexes of the type [M(bipy)(CO)(3)(N-RIm)](+) (bipy=2,2'-bipyridine) undergo deprotonation of the central CH group of the N-alkylimidazole (N-RIm) ligand when treated with a strong base. However, the outcome of the reaction is very different for either metal. For Mn, the addition of the equimolar amount of an acid to the product of the deprotonation affords an N-heterocyclic carbene (NHC) complex, whereas for Re, once the deprotonation of the central imidazole CH group has occurred, the bipy ligand undergoes a nucleophilic attack on an ortho carbon, affording the C-C coupling product. The extension of these studies to pseudo-octahedral [Mo(η(3)-allyl)(bipy)(CO)(2)(N-RIm)](+) complexes has allowed us to isolate cationic NHC complexes (Mn(I)-type behavior), as well as their neutral imidazol-2-yl precursors. Theoretical studies of the reaction mechanisms using DFT computations were carried out on the deprotonation of [Mn(bipy)(CO)(3)(N-PhIm)](+), [Re(bipy)(CO)(3) (N-MesIm)](+), and [Mo(η(3)-C(4)H(7))(bipy)(CO)(2) (N-MesIm)](+) complexes (Mes=mesityl) at the B3LYP/6-31G(d) (LANL2DZ for Mn, Re, and Mo) level of theory. Our results explain why different products have been found experimentally for Mn, Mo, and Re complexes. For Re, the process leading to a C-C coupling product is clearly more favored than those forming an imidazol-2-yl product. In contrast, for Mn and Mo complexes, the lower stabilizing interaction between the central imidazole and ortho bipy C atoms, along with the higher lability of the ligands, make the formation of an NHC-type product kinetically more accessible, in good agreement with experimental findings.     

A theoretical study on the complete catalytic cycle of the hetero-Pauson-Khand-type [2+2+1] cycloaddition reaction of ketimines,carbon monoxide and ethylene catalyzed by iron carbonyl complexes

The [2+2+1] cycloaddition reaction of 1,4-diazabutadienes, carbon monoxide and ethylene catalyzed by iron carbonyl complexes produces pyrrolidin-2-one derivatives. Only one of the two imine moieties is activated during the catalysis. The mechanism of this cycloaddition reaction is studied by density functional theory at the B3LYP/6-311++G(d,p) level of theory. In accordance with experimental results, a [(diazabutadiene)Fe(CO)(3)] complex of square-pyramidal geometry is used as the starting compound S of the catalytic cycle. Based on experimental experience, the reaction with ethylene is considered to take place before any interaction with carbon monoxide. According to the computational results, the reaction does not proceed by ligand dissociation followed by addition of ethylene and subsequent intramolecular activation steps but by the approach of an ethylene molecule from the base of the square-pyramidal complex. This reaction yields an intermediate I(4) in which ethylene is coordinated to the iron centre and a new C-C bond between ethylene and one of the imine groups is formed. The insertion of a terminal carbon monoxide ligand into the metal-carbon bond between ethylene and iron produces the key intermediate I(7). The reaction proceeds by metal-assisted formation of a lactam P. The catalytic cycle is closed by a ligand-exchange reaction in which the diazabutadiene ligand substitutes P with reformation of S. This reaction pathway is found to be energetically favored over a reductive elimination. It leads to the experimentally observed heterocyclic product P and a reactive [Fe(CO)(3)] fragment.     

A theoretical study on fullerene-dizincocene hybrids

Using the density functional theory, we investigated the possible formation of fullerene-dizincocene hybrids, specifically C(60)*-Zn-Zn-Cp*, C(60)*-Zn-Zn-C(60)*, C(70)*-Zn-Zn-Cp*, and C(70)*-Zn-Zn-C(70)*, where C(60)*, Cp*, and C(70)* represent C(60)(CH(3))(5), C(5)(CH(3))(5), and C(70)(CH(3))(5) radicals. Our calculation shows that these hybrids have HOMO-LUMO gaps which are larger than has been experimentally identified for C(60)*-Fe-Cp. In addition, the strength of the Zn--Zn bonds is similar to that in Cp*-Zn-Zn-Cp* which was also synthesized recently. Furthermore, heterohybrids, C(60)*-Zn-Zn-Cp* and C(70)*-Zn-Zn-Cp* are expected to exist in equilibria with homohybrids, C(60)*-Zn-Zn-C(60)* and C(70)*-Zn-Zn-C(70)*, in which heterohybrids are much more favored. On the other hand, another hybrid involving Sc(3)N@C(68) as a fullerene unit is not highly probable.     

Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study

Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.     

Fe/Fe_2和NO反应的密度泛函理论研究

利用密度泛函理论(Density Functional Theory)中的B3LYP方法在6-311+G(d,p)的计算水平上研究了Fe/Fe_2与NO反应的相关微观机理.全参数优化了Fe+NO和Fe_2+NO反应体系在不同重态反应势能面上各驻点的几何结构,并用频率分析法以及内禀反应坐标(Intrinsic Reaction Coordinate)方法对过渡态进行了验证,得到了相对应的反应的微观反应路径.用两态反应分析反应机理,计算结果表明2个体系的优先选择路径均为低自旋态进入和高自旋态离开反应.通过对2个体系反应活化能的比较,Fe_2+NO体系更易进行.     

Biodegradation of Herbicides by a Plant Nonheme Iron Dioxygenase: Mechanism and Selectivity of Substrate Analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogues by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C²-hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R- and S-methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R-isomer give high rebound barriers.     

A theoretical investigation on the cycloaddition reaction between azocarbenium ions and nitriles

The 1,3‐dipolar cycloaddition reactions of the cationic 1,3‐dipolarophiles of azocarbenium ion 1 with HCN in the gas phase were examined using the density functional theory, QCISD method (Quadratic configuration interaction using single and double substitutions) and CCSD(T) (Coupled cluster calculations with single and double excitations and a perturbative estimate of triple contributions calculations) calculations. The theoretical results revealed that the reaction takes place via an initial formation of a 1:1 complex of the two reactants, mainly driven by charge interaction, followed by an asynchronous concerted cyclization forming the 3H‐[1,2,4]‐triazolium ion 3, which undergo [1,2]‐H shift to provide the 1H‐[1,2,4]‐triazolium ion 4. The effect of the solvent has been modeled by using the isodensity‐surface polarizable continuum (IPCM) model and the calculation showed that the reaction in CH₂Cl₂ solution proceeds in a similar manner as in gas phase with only a slight derivation of activation barrier. The substituent effects have also been investigated. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

S2BrH的构型及其异构化反应的理论研究

由于在合成化学、大气化学和环境保护中的重要性，过硫化物XSSX(X=H，CH3，F，Cl等)被广泛研究。本文采用量子化学的密度泛函方法(DFT)，对S2BrH可能存在的2种构型的几何结构、相对稳定性以及可能的分子内原子迁移过程进行研究，探讨分叉型异构体SSBrH存在的可能性。     

冠丙四肽与ⅠA和ⅡA重金属离子结合作用的初步理论研究

借助于密度泛函理论的B3LYP方法,以冠丙四肽为模型基础,对铷、锶、铯、钡等金属离子与该冠丙四肽的结合形式进行了几何构型优化、能量计算、Mulliken布局数分析等理论研究.结果表明,冠丙四肽的构型在与IA金属离子结合前后略有改变,结合过程中电子由冠肽移向金属离子,碱金属离子铷、铯与冠型环丙四肽的结合作用相差不大,其最...     

A theoretical study on nitration mechanism of benzene and solvent effects

Aromatic nitration is an important and canonical example of electrophilic substitution in organic chemistry. The research on nitration mechanism is also very important for synthesis of explosives since benzene molecule is a basic unit to build up into the energetic material. Besides the electrophilic substitution mechanism, there is an electron transfer mechanism[1,2]. The nitronium ion (NO+ 2), however, is a generally accepted active nitrating agent in the aromatic nitration. Therefore, the …     

A theoretical study of the bonding capabilities of the zinc-zinc double bond

The theoretical knowledge about the zinc-zinc bond has been recently expanded after the proposal of a zinc-zinc double bond in several [Zn₂(L)₄] compounds (Angew. Chem. Int. Ed. 2017 , 56, 10151-10155). Prompted by these results, we have selected the [Zn₂(CO)₄] species, isolobally related to ethylene, and theoretically investigated the possible η²-Zn₂-coordination to several first-row transition metal fragments. The [Zn₂(CO)₄] coordination to the metal fragment produces an elongation of the dizinc bond and a concomitant pyramidalization of the [Zn(CO)₂] unit. These structural parameters are indicative of π-backdonation from the metal to the coordinated dizinc moiety, as occurred with ethylene ligand. A quantum theory of atoms in molecules study of the Zn Zn bond shows a decrease of ρ_BCP, ∇²ρ_BCP ∫_Zn∩Znρ and delocalization indexes δ(Zn,Zn), relative to corresponding values in the parent [Zn₂(CO)₄] molecule. The Zn Zn and M Zn bonds in these [(η²-Zn₂(CO)₄)M(L)_n] complexes can be described as shared interactions with an important covalent component where the Zn Zn bond is preserved, albeit weakened, upon coordination.     

A theoretical study of hydrothermal stability of P-modified ZSM-5 zeolites

Density functional theory was employed to study the hydrothermal stability of P-modified ZSM-5 zeolites using cluster models. The calculations of hydrolysis energies indicated that the introduction of phos-phorus increases the hydrothermal stability of ZSM-5 zeolites. The initial paths of dealumination were studied with explicit water molecules. It was found that the framework Al—O coordination bond can be replaced by coodination bonds between water molecules and the aluminium. One to three water molecules ...     

From allylic alcohols to aldols by using iron carbonyls as catalysts: computational study on a novel tandem isomerization-aldolization reaction

The tandem isomerization-aldolization reaction between allyl alcohol and formaldehyde mediated by [Fe(CO)3] was studied with the density functional B3LYP method. Starting from the key [(enol)Fe(CO)3] complex, several reaction paths for the reaction with formaldehyde were explored. The results show that the most favorable reaction path involves first an enol/allyl alcohol ligand-exchange process followed by direct condensation of formaldehyde with the free enol. During this process, formation of the new C-C bond takes place simultaneously with a proton transfer between the enol and the aldehyde. Therefore, the role of [Fe(CO)3] is to catalyze the allyl alcohol to enol isomerization affording the free enol, which adds to the aldehyde in a carbonyl-ene type reaction. Similar results were obtained for the reaction between allyl alcohol and acetaldehyde.