Multi-state epoxidation of ethene by cytochrome P450: a quantum chemical study.

The epoxidation of ethene by a model for Compound I of cytochrome P450, studied by the use of density functional B3LYP calculations, involves two-state reactivity (TSR) with multiple electromer species, hence "multi-state epoxidation". The reaction is found to proceed in stepwise and effectively concerted manners. Several reactive states are involved; the reactant is an (oxo)iron(IV) porphyrin cation radical complex with two closely lying spin states (quartet and doublet), both of which react with ethene to form intermediate complexes with a covalent C-O bond and a carbon-centered radical (radical intermediates). The radical intermediates exist in two electromers that differ in the oxidation state of iron; Por(+)(*)Fe(III)OCH(2)CH(2)(*) and PorFe(IV)OCH(2)CH(2)(*) (Por = porphyrin). These radical intermediates exist in both the doublet- and quartet spin states. The quartet spin intermediates have substantial barriers for transformation to the quartet spin PorFe(III)-epoxide complex (2.3 kcal mol(-)(1) for PorFe(IV)OCH(2)CH(2)(*) and 7.2 kcal mol(-)(1) for Por(+)(*)Fe(III)OCH(2)CH(2)(*)). In contrast, the doublet spin radicals collapse to the corresponding PorFe(III)-epoxide complex with virtually no barriers. Consequently, the lifetimes of the radical intermediates are much longer on the quartet- than on the doublet spin surface. The loss of isomeric identity in the epoxide and rearrangements to other products arise therefore mostly, if not only, from the quartet process, while the doublet state epoxidation is effectively concerted (Scheme 7). Experimental trends are discussed in the light of the computed mechanistic scheme, and a comparison is made with closely related mechanistic schemes deduced from experiment.     

A quantum chemical survey of metalloporphyrin-nitrosyl linkage isomers: insights into the observation of multiple FeNO conformations in a recent crystallographic determination of nitrophorin 4

Using density functional theory-based geometry optimizations, we have searched for eta(1)-NO, eta(1)-ON (isonitrosyl), and eta(2)-NO (side-on bound NO) linkage isomers of a number of metalloporphyrin-NO complexes, M(Por)(NO)(L), where Por = porphinato dianion, M = Mn(II), Fe(II), Fe(III), Ru(II), Ru(III), Co(II), and Rh(II), and L = no ligand, SMe, Ph, and imidazole. The eta(1)-NO isomer had the lowest energy in all cases, and the isonitrosyl isomer was also located as a higher energy potential energy minimum in a number of cases. The eta(2)-NO isomer was only located as a minimum for Mn(II) (L = no ligand), Fe(III) (L = no ligand), and Ru(III) (L = Ph, imidazole, pyrdine), suggesting that an [MNO](6) electron count is important for stabilization of the eta(2) mode of ligation. However, in the presence of axial ligands L, the side-on isomers of [FeNO](6) complexes were not stable and opened up to an unusual geometry where the FeN(O) and NO vectors were tilted in opposite directions relative to the heme normal. Exactly such a geometry, as well as a "normal" upright geometry, has been observed in a recent crystallographic determination of nitrophorin 4 (Nature Struct. Biol. 2000, 7, 551), a salivary protein from the blood-sucking insect Rhodnius prolixus. Together, the calculated and experimental result illustrate the extreme softness of the FeNO potential energy surface toward various forms of tilting and bending deformations.     

Reactivity of Compound II: Electronic Structure Analysis of Methane Hydroxylation by Oxoiron(IV) Porphyrin Complexes

The methane hydroxylation reaction by a Compound II (Cpd II) mimic PorFe(IV)=O and its hydrosulfide-ligated derivative [Por(SH)Fe(IV)=O](-) is investigated by density functional theory (DFT) calculations on the ground triplet and excited quintet spin-state surfaces. On each spin surface both the σ- and π-channels are explored. H-abstraction is invariably the rate-determining step. In the case of PorFe(IV)=O the H-abstraction reaction can proceed either through the classic π-channel or through the nonclassical σ-channel on the triplet surface, but only through the classic σ-mechanism on the quintet surface. The barrier on the quintet σ-pathway is much lower than on the triplet channels so the quintet surface cuts through the triplet surfaces and a two state reactivity (TSR) mechanism with crossover from the triplet to the quintet surface becomes a plausible scenario for C-H bond activation by PorFe(IV)=O. In the case of the hydrosulfide-ligated complex the H-abstraction follows a π-mechanism on the triplet surface: the σ* is too high in energy to make a σ-attack of the substrate favorable. The σ- and π-channels are both feasible on the quintet surface. As the quintet surface lies above the triplet surface in the entrance channel of the oxidative process and is highly destabilized on both the σ- and π-pathways, the reaction can only proceed on the triplet surface. Insights into the electron transfer process accompanying the H-abstraction reaction are achieved through a detailed electronic structure analysis of the transition state species and the reactant complexes en route to the transition state. It is found that the electron transfer from the substrate σ(CH) into the acceptor orbital of the catalyst, the Fe-O σ* or π*, occurs through a rather complex mechanism that is initiated by a two-orbital four-electron interaction between the σ(CH) and the low-lying, oxygen-rich Fe-O σ-bonding and/or Fe-O π-bonding orbitals of the catalyst.     

Quantum mechanical/molecular mechanical study of mechanisms of heme degradation by the enzyme heme oxygenase: the strategic function of the water cluster

Heme degradation by heme oxygenase (HO) enzymes is important in maintaining iron homeostasis and prevention of oxidative stress, etc. In response to mechanistic uncertainties, we performed quantum mechanical/molecular mechanical investigations of the heme hydroxylation by HO, in the native route and with the oxygen surrogate donor H2O2. It is demonstrated that H2O2 cannot be deprotonated to yield Fe(III)OOH, and hence the surrogate reaction starts from the FeHOOH complex. The calculations show that, when starting from either Fe(III)OOH or Fe(III)HOOH, the fully concerted mechanism involving O-O bond breakage and O-C(meso) bond formation is highly disfavored. The low-energy mechanism involves a nonsynchronous, effectively concerted pathway, in which the active species undergoes first O-O bond homolysis followed by a barrier-free (small with Fe(III)HOOH) hydroxyl radical attack on the meso position of the porphyrin. During the reaction of Fe(III)HOOH, formation of the Por+*FeIV=O species, compound I, competes with heme hydroxylation, thereby reducing the efficiency of the surrogate route. All these conclusions are in accord with experimental findings (Chu, G. C.; Katakura, K.; Zhang, X.; Yoshida, T.; Ikeda-Saito, M. J. Biol. Chem. 1999, 274, 21319). The study highlights the role of the water cluster in the distal pocket in creating "function" for the enzyme; this cluster affects the O-O cleavage and the O-Cmeso formation, but more so it is responsible for the orientation of the hydroxyl radical and for the observed alpha-meso regioselectivity of hydroxylation (Ortiz de Montellano, P. R. Acc. Chem. Res. 1998, 31, 543). Differences/similarities with P450 and HRP are discussed.     

Dissociative addition of water to a main group 13 metal cluster: computational study of the reaction of gallium dimer with H2O

We have investigated the lowest triplet and singlet potential energy surfaces (PESs) for the reaction of Ga(2) dimer with water. Under thermal conditions, we predict formation of the triplet ground state addition complex Ga(2)···OH(2)((3)B(1)) involving Ga···O···Ga bridge interaction. At the coupled cluster CCSD(T)/AE (CCSD(T)/ECP) computational levels, Ga(2)···OH(2)((3)B(1)) is bound by 5.5 (5.7) kcal/mol with respect to the ground state reactants Ga(2)((3)Π(u)) + H(2)O. Identification of the addition complex is in agreement with the experimental evidence from matrix isolation infrared (IR) spectroscopy reported recently by Macrae and Downs. The located minimum energy crossing points (MECPs) between the triplet and singlet energy surfaces on the entrance channel of Ga(2) + H(2)O are not expected to be energetically accessible under the matrix conditions, consistent with the lack of occurrence of Ga(2) insertion into the O-H bond under such conditions. The computed energies and harmonic and anharmonic vibrational frequencies for the triplet and singlet Ga(2)(H)(OH) insertion isomers indicate the singlet double-bridged Ga(μ-H)(μ-OH)Ga isomer to be the most stable and support the experimental IR identification of this species. The energy barrier for elimination of H(2) from the second most stable singlet HGa(μ-OH)Ga insertion isomer found to be 13.9 (12.9) kcal/mol is also consistent with the available experimental data.     

Singlet and triplet potential energy surfaces of C3H2

The detailed singlet and triplet potential energy surfaces of C₃H₂ involving nine isomers and 13 transition structures are studied at the G3 level of theory. The rearrangement mechanisms and the electronic properties of various isomers in a broad energy range have been studied in both singlet and triplet states. Cyclopropenylidene and propargylene are found to be the most stable isomers in the singlet and triplet states, respectively. The singlet isomers are found to be more kinetically stable species as a result of high conversion barriers through which they pass. The calculations indicate that cyclopropyne in its triplet state is the least kinetically stable isomer. It is realized that the G3 method comprises both computational cost and accuracy and thus can be applied to investigation of potential energy surface of small molecules.     

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations

The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.     

An efficient proton-coupled electron-transfer process during oxidation of ferulic acid by horseradish peroxidase: coming full cycle

Quantum mechanics/molecular mechanics calculations were utilized to study the process of oxidation of a native substrate (ferulic acid) by the active species of horseradish peroxidase (Dunford, H. B. Heme Peroxidases; Wiley-VCH: New York, 1999), Compound I and Compound II, and the manner by which the enzyme returns to its resting state. The results match experimental findings and reveal additional novel features. The calculations demonstrate that both oxidation processes are initiated by a proton-coupled electron-transfer (PCET) step, in which the active species of the enzyme participate only as electron-transfer partners, while the entire proton-transfer event is being relayed from the substrate to and from the His42 residue by a water molecule (W402). The reason for the observed (Henriksen, A; Smith, A. T.; Gajhede, M. J. Biol. Chem. 1999, 274, 35005-35011) similar reactivities of Compound I and Compound II toward ferulic acid is that the reactive isomer of Compound II is the, hitherto unobserved, Por(*)(+)Fe(III)OH isomer that resembles Compound I. The PCET mechanism reveals that His42 and W402 are crucial moieties and they determine the function of the HRP enzyme and account for its ability to perform substrate oxidation (Poulos, T. L. Peroxidases and Cytochrome P450. In The Porphyrin Handbook; Kadish, K. M., Smith, K. M., Guilard, R., Eds.; Academic Press: New York, 2000; Vol. 4, pp 189). In view of the results, the possibility of manipulating substrate oxidation by magnetic fields is an intriguing possibility.     

SiNP分子结构及稳定性的理论研究

采用B3LYP/6-311G(d),QCISD和CCSD(T)方法,对单重态和三重态SiNP体系的异构化进行了研究.在QCISD/6-311G(d)水平下,得到了7个稳定的异构体,它们由4个过渡态所连接,其中三重态线型异构体SiNP(31,3Σ1),单重态环状异构体SiNP(14,1A')和单重态线型异构体SiNP(11,1Σ)都具有较大的热力学及动力学稳定性.     

Structure and Stability of Interstellar Molecule C_3S

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Structure and energetics of Fe2(CO)8 singlet and triplet electronic states

The singlet and triplet state potential energy surfaces (PES) of Fe2(CO)8 are explored by means of density functional theory (DFT) techniques. The two PES have different global mimima: the dibriged C(2v) isomer for the singlet and the unbridged D(2d) isomer for the triplet. The sign of the energy gap between singlet and triplet global minima depends on the type of adopted DFT functional: hybrid functionals predict the triplet is more stable than the singlet, but the opposite applies to generalized gradient approximated (GGA) functionals. The analysis of the computed CO stretching frequencies demonstrates that the experimental data for the unbridged form is compatible also with the unbridged triplet D(2d) isomer. Starting from these two facts, the electronic structure of unbridged D(2d) Fe2(CO)8 is discussed herein. Single-point energy computations at the coupled-cluster single and double (CCSD) level favor the D(2d) triplet state.     

Reactions of nitrogen oxides with the five-coordinate Fe(III)(porphyrin) nitrito intermediate Fe(Por)(ONO) in sublimed solids

Detailed experimental studies are described for reactions of several nitrogen oxides with iron porphyrin models for heme/NxOy systems. It is shown by FTIR and optical spectroscopy and by isotope labeling experiments that reaction of small increments of NO2 with sublimed thin layers of the iron(II) complex Fe(Por) (Por = meso-tetraphenylporphyrinato dianion, TPP, or meso-tetra-p-tolylporphyrinato dianion, TTP) leads to formation of the 5-coordinate nitrito complexes Fe(Por)(eta1-ONO) (1), which are fairly stable but very slowly decompose under vacuum giving mostly the corresponding nitrosyl complexes Fe(Por)(NO). Further reaction of 1 with new NO2 increments leads to formation of the nitrato complex Fe(Por)(eta2-O2NO) (2). The interaction of NO with 1 at low temperature involves ligand addition to give the nitrito-nitrosyl complexes Fe(Por)(eta1-ONO)(NO) (3); however, these isomerize to the nitro-nitrosyl analogs Fe(Por)(eta1-NO2)(NO) (4) upon warming. Experiments with labeled nitrogen oxides argue for an intramolecular isomerization ("flipping") mechanism rather than one involving dissociation and rebinding of NO2. The Fe(III) centers in the 6-coordinate species 3 and 4 are low spin in contrast to 1, which appears to be high-spin, although DFT computations of the porphinato models Fe(P)(nitrite) suggest that the doublet nitro species and the quartet and sextet nitrito complexes are all relatively close in energy. The nitro-nitrosyl complex 4 is stable under an NO atmosphere but decomposes under intense pumping to give a mixture of the ferrous nitrosyl complex Fe(Por)(NO) and the ferric nitrito complex Fe(Por)(eta1-ONO) indicating the competitive dissociation of NO and NO2. Hence, loss of NO from 4 is accompanied with nitro --> nitrito isomerization consistent with 1 being the more stable of the 5-coordinate NO2 complexes of iron porphyrins.     

SiCS分子结构及其稳定性的理论研究

采用DFT,QCISD及CCSD(T)方法对单重态、三重态SiCS的分子体系势能面进行理论计算,在QCISD/6-311G(d)水平上得到由3个过渡态连接的5个稳定构型.经动力学及热力学分析均是稳定的三重态线型分子SiCS(³1)、单重态线型分子SiCS(¹1)以及单重态的环状分子cSiCS(¹2).     

Photochemical and photophysical properties of three carbon-bridged fullerene dimers: C121 (I, II, III)

The photochemical and photophysical properties of the three C121 isomers (I, II, III) were investigated with MADLI-TOF-MS, UV-vis spectra, fluorescence spectra, absorption spectra of their DMA complexes, and theoretical calculations. The three isomers of C121 (I, II, III) have different stabilities under laser irradiation, but isomer I and isomer II show good stability against the heat-induced conversion between different isomers: No conversion between the isomers was found after heating the mixture of isomer I and isomer II at 353 K for 12 h in Ar atmosphere. The results of UV-vis absorption and fluorescence spectra indicate that interactions between two C60 moieties of C60=C=C60 in the ground and singlet states are not significant, C121 (I, II, III) behaves as an electron-acceptor similar to C60. These indicate that the formation of the fullerene chain structure (e.g., C60=C=C60) does not disturb the photochemical and photophysical properties of the C60 monomer itself, even that the properties were enhanced by the formation of the polymer. This is significant for the C60 polymer in photochemical or photoelectronic applications in which C60=C=C60 can be an excellent basic unit of polymers.     

Lowest singlet and triplet potential energy surfaces of S2N2

Forty four stationary points have been located on the lowest singlet and triplet potential energy surfaces of S(2)N(2). Ten minima and ten saddle points on the lowest singlet surface and eleven minima and thirteen saddle points on the lowest triplet surface were found. All saddle points were connected to minima or lower-order saddle points by following the intrinsic reaction coordinate. Renner-Teller effects in the linear isomers were studied by examining their bending curves. The S(2)N(2) polymerization mechanism was investigated by first locating the transition state corresponding to ring opening and then considering all species connected to it that are close in energy. The commonly accepted mechanism is problematic due to the number of species that would lead to dissociation to SN + SN. Other possible isomers that are consistent with the experimental evidence but do not connect to SN radicals in the dissociation limit were examined. A mechanism of polymerization to (SN)(x)() is proposed that involves excitation of the square planar singlet molecule to the triplet surface. The triplet species then undergoes a puckering, and polymerization occurs in a direction approximately perpendicular to the S(2)N(2) plane. Consideration of the predicted vibrational frequencies suggests the structure of the second isomer of S(2)N(2). This isomer has a trans-NSSN structure with a long SS bond. The energetics of trans-NSSN are consistent with the observed temperature effects in the dimerization of SN. Analysis of the bending curves of linear NSSN and NSNS indicates that trans-NSSN is the only isomer which has a small yet significant barrier to that dimerization.     

预测[C,O,S]体系的稳定异构体

采用 DFT, QCISD及CCSD(T)方法对单重态和三重态的COS分子体系势能面进行了理论计算, 在 QCISD/6-311G(d) 水平上得到4个过渡态连接的6个稳定构型. 经动力学及热力学分析发现只有一个单重态线性的分子11(O—C—S) 能够稳定存在.     

Theoretical study of [Si,O,C,O] species: Prediction of new species on triplet potential energy surface

The intermediates [Si,O,C,O] of the Si + CO₂ reaction have been studied in detail using high level ab iniitio methods. Both singlet and triplet [Si,O,C,O] species are characterized structurally and energetically. On the singlet potential energy surface (PES), the vdw‐OSi–CO isomer and in the triplet PES, the bent‐SiOCO isomer is found to be thermodynamically as well as kinetically most stable species. All possible isomerization transition states (TS) are located on both singlet and triplet potential surfaces. On the triplet surface, the stability of the trans‐OSiCO isomer is comparable with that of the bent‐SiOCO isomer. A non‐planar cis‐SiOCO isomer is located on the triplet PES, which is predicted for the first time. Heats of formation at 0 K (Δ_fH°, 0 K) for all singlet and triplet species are computed using G3B3, G3MP2, and CBS‐Q theories. The discrepancy between G3B3 and the other two methods for the heat of formation value for triplet trans‐OSiCO is discussed. The PESs for singlet as well as triplet species with their dissociation asymptotes are explored at the CCSD(T)/6‐311G(d,p)//MP2/6‐311G(d,p) level of theory. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Proton-coupled electron transfer reactions at a heme-propionate in an iron-protoporphyrin-IX model compound

A heme model system has been developed in which the heme-propionate is the only proton donating/accepting site, using protoporphyrin IX-monomethyl esters (PPIX(MME)) and N-methylimidazole (MeIm). Proton-coupled electron transfer (PCET) reactions of these model compounds have been examined in acetonitrile solvent. (PPIX(MME))Fe(III)(MeIm)(2)-propionate (Fe(III)~CO(2)) is readily reduced by the ascorbate derivative 5,6-isopropylidine ascorbate to give (PPIX(MME))Fe(II)(MeIm)(2)-propionic acid (Fe(II)~CO(2)H). An excess of the hydroxylamine TEMPOH or of hydroquinone similarly reduces Fe(III)~CO(2), and TEMPO and benzoquinone oxidize Fe(II)~CO(2)H to return to Fe(III)~CO(2). The measured equilibrium constants, and the determined pK(a) and E(1/2) values, indicate that Fe(II)~CO(2)H has an effective bond dissociation free energy (BDFE) of 67.8 ± 0.6 kcal mol(-1). In these PPIX models, electron transfer occurs at the iron center and proton transfer occurs at the remote heme propionate. According to thermochemical and other arguments, the TEMPOH reaction occurs by concerted proton-electron transfer (CPET), and a similar pathway is indicated for the ascorbate derivative. Based on these results, heme propionates should be considered as potential key components of PCET/CPET active sites in heme proteins.     

On the functional role of a water molecule in clade 3 catalases: a proposal for the mechanism by which NADPH prevents the formation of compound II

X-ray structures of the 13 different monofunctional heme catalases published to date were scrutinized in order to gain insight in the mechanism by which NADPH in Clade 3 catalases may protect the reactive ferryloxo intermediate Compound I (Cpd I; por (*+)Fe (IV)O) against deactivation to the catalytically inactive intermediate Compound II (Cpd II; porFe (IV)O). Striking similarities in the molecular network of the protein subunits encompassing the heme center and the surface-bound NADPH were found for all of the Clade 3 catalases. Unique features in this region are the presence of a water molecule (W1) adjacent to the 4-vinyl group of heme and a serine residue or a second water molecule hydrogen-bonded to both W1 and the carbonyl group of a threonine-proline linkage, with the proline in van der Waals contact with the dihydronicotinamide group of NADPH. A mechanism is proposed in which a hydroxyl anion released from W1 undergoes reversible nucleophilic addition to the terminal carbon of the 4-vinyl group of Cpd I, thereby producing a neutral porphyrin pi-radical ferryloxo (HO-por (*)Fe (IV)O) species of reduced reactivity. This structure is suggested to be the elusive Cpd II' intermediate proposed in previous studies. An accompanying proton-shifting process along the hydrogen-bonded network is believed to facilitate the NADPH-mediated reduction of Cpd I to ferricatalase and to serve as a funnel for electron transfer from NADPH to the heme center to restore the catalase Fe (III) resting state. The proposed reaction paths were fully supported as chemically reasonable and energetically feasible by means of density functional theory calculations at the (U)B3LYP/6-31G* level. A particularly attractive feature of the present mechanism is that the previously discussed formation of protein-derived radicals is avoided.