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Binuclear non-heme iron enzymes activate O2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reaction shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. This activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.

FeIII-(hydro)peroxy intermediates have been isolated in two classes of mononuclear non-heme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on FeIII-peroxy and end-on FeIII-hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of FeIII-peroxy intermediates in mononuclear non-heme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.

The Rieske dioxygenases are a major subclass of mononuclear nonheme iron enzymes that play an important role in bioremediation. Recently, a high-spin FeIII–(hydro)-peroxy intermediate (BZDOp) has been trapped in the peroxide shunt reaction of benzoate 1,2-dioxygenase. Defining the structure of this intermediate is essential to understanding the reactivity of these enzymes. Nuclear resonance vibrational spectroscopy (NRVS) is a recently developed synchrotron technique that is ideal for obtaining vibrational, and thus structural, information on Fe sites, as it gives complete information on all vibrational normal modes containing Fe displacement. In this study, we present NRVS data on BZDOp and assign its structure using these data coupled to experimentally calibrated density functional theory calculations. From this NRVS structure, we define the mechanism for the peroxide shunt reaction. The relevance of the peroxide shunt to the native FeII/O2 reaction is evaluated. For the native FeII/O2 reaction, an FeIII–superoxo intermediate is found to react directly with substrate. This process, while uphill thermodynamically, is found to be driven by the highly favorable thermodynamics of proton-coupled electron transfer with an electron provided by the Rieske [2Fe-2S] center at a later step in the reaction. These results offer important insight into the relative reactivities of FeIII–superoxo and FeIII–hydroperoxo species in nonheme Fe biochemistry.

Mononuclear non-haem iron (NHFe) enzymes catalyse a broad range of oxidative reactions, including halogenation, hydroxylation, ring closure, desaturation and aromatic ring cleavage reactions. They are involved in a number of biological processes, including phenylalanine metabolism, the production of neurotransmitters, the hypoxic response and the biosynthesis of secondary metabolites. The reactive intermediate in the catalytic cycles of these enzymes is a high-spin S = 2 Fe(IV)=O species, which has been trapped for a number of NHFe enzymes, including the halogenase SyrB2 (syringomycin biosynthesis enzyme 2). Computational studies aimed at understanding the reactivity of this Fe(IV)=O intermediate are limited in applicability owing to the paucity of experimental knowledge about its geometric and electronic structure. Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) is a sensitive and effective method that defines the dependence of the vibrational modes involving Fe on the nature of the Fe(IV)=O active site. Here we present NRVS structural characterization of the reactive Fe(IV)=O intermediate of a NHFe enzyme, namely the halogenase SyrB2 from the bacterium Pseudomonas syringae pv. syringae. This intermediate reacts via an initial hydrogen-atom abstraction step, performing subsequent halogenation of the native substrate or hydroxylation of non-native substrates. A correlation of the experimental NRVS data to electronic structure calculations indicates that the substrate directs the orientation of the Fe(IV)=O intermediate, presenting specific frontier molecular orbitals that can activate either selective halogenation or hydroxylation.

The iron–oxygen species iron(III)-peroxo, iron(III)-hydroperoxo and iron(IV)-oxo are key intermediates often detected in the catalytic cycles of dioxygen activation by haem and non-haem iron enzymes. The high-resolution crystal structure of a mononuclear non-haem side-on iron(III)-peroxo complex has now been determined, and a series of chemical reactions in which the iron(III)-peroxo complex is cleanly converted to an iron(III)-hydroperoxo complex is described. All three of these iron species have been spectroscopically characterized, and relative reactivity studies demonstrate that iron(III)-hydroperoxo species are viable oxidants in both nucleophilic and electrophilic reactions by iron-containing enzymes. This work shows how a series of biologically important iron–oxygen intermediates make use of a synthetic iron complex bearing a simple but versatile macrocyclic ligand. Oxygen-containing mononuclear iron species—iron(iii)–peroxo, iron(iii)–hydroperoxo and iron(iv)–oxo—are key intermediates in the catalytic activation of dioxygen by iron-containing metalloenzymes1,2,3,4,5,6,7. It has been difficult to generate synthetic analogues of these three active iron–oxygen species in identical host complexes, which is necessary to elucidate changes to the structure of the iron centre during catalysis and the factors that control their chemical reactivities with substrates. Here we report the high-resolution crystal structure of a mononuclear non-haem side-on iron(iii)–peroxo complex, [Fe(iii)(TMC)(OO)]+. We also report a series of chemical reactions in which this iron(iii)–peroxo complex is cleanly converted to the iron(iii)–hydroperoxo complex, [Fe(iii)(TMC)(OOH)]2+, via a short-lived intermediate on protonation. This iron(iii)–hydroperoxo complex then cleanly converts to the ferryl complex, [Fe(iv)(TMC)(O)]2+, via homolytic O–O bond cleavage of the iron(iii)–hydroperoxo species. All three of these iron species—the three most biologically relevant iron–oxygen intermediates—have been spectroscopically characterized; we note that they have been obtained using a simple macrocyclic ligand. We have performed relative reactivity studies on these three iron species which reveal that the iron(iii)–hydroperoxo complex is the most reactive of the three in the deformylation of aldehydes and that it has a similar reactivity to the iron(iv)–oxo complex in C–H bond activation of alkylaromatics. These reactivity results demonstrate that iron(iii)–hydroperoxo species are viable oxidants in both nucleophilic and electrophilic reactions by iron-containing enzymes.

We have studied single-walled carbon nanotubes (SWCNTs) doped with transition metal (TM) atoms with both exo and endo doping configurations. The electronic and geometric properties of these TM-doped SWCNTs were calculated within density functional theory. It was found that the endo-doped SWCNTs are less stable than the exo-doped counterparts due to the large geometric strain of the deformation in the endo-doped nanotubes. On the basis of partial charge analysis, the TM-doped SWCNTs have localized net charge distributions, whereas the spin densities in Sc-, Co-, and Cu-doped SWCNTs are delocalized over the entire nanotubes. The TM-doped SWCNTs are mostly metallic or narrow-gap semiconductive. With highly localized frontier molecular orbitals, the exo-doped SWCNTs are better electron donors than the corresponding endo-doped systems. As the dopant TM changes from Sc to Zn in the same row of the periodic table or from the top to the bottom in the same Pt group, the energy of the highest occupied crystal orbit...

Mononuclear non-heme iron (NHFe) enzymes catalyze a number of key biological reactions including hydroxylation, desaturation, ring closure and halogenation.[1-3] The reactive intermediate that carries out many of the C–H bond activations is an S = 2 FeIV=O species that has been observed and characterized in several enzyme systems.[3-5] Synthetic efforts have yielded FeIV=O model complexes that exhibit an S = 1 ground state[6, 7] in all but three cases: (H2O)5FeIV=O[8], (H3buea)FeIV=O[9] and (TMG3tren)FeIV=O (1).[10] 1 has an FeIV=O unit ligated by TMG3tren in a C3ν trigonal bipyramidal geometry (Figure 1A), and an S = 2 ground state replicating that of enzyme intermediates.[10, 11] 1 is reactive in oxo-atom transfer and H-atom abstraction, but in the latter it is only as reactive as the approximately-C4v S = 1 (N4Py)FeIV=O (2, Figure 1B) complex where both have the same reaction rate with 1,4-cyclohexadiene (CHD).[10] Original studies from our group showed that whereas S = 1 reaction coordinates only have a □-attack pathway, involving the β-d□* orbital, available for electrophilic reactivity, S = 2 systems are predicted to possess an additional -attack pathway involving the ⟨-dz2 orbital that is lowered in energy due to spin-polarization.[12, 13] This has recently been referred to as an exchange enhancement.[14] In this study, we utilize Nuclear Resonance Vibrational Spectroscopy (NRVS) to obtain ground-state vibrational data on 1 for comparison to 2[15] and, through correlations to DFT calculations, to understand the observed similar reactivities of 1 (S = 2) and 2 (S = 1). These studies define the steric and intrinsic electronic contributions to the reaction barriers and establish that both the S = 1 and S = 2 surfaces have significant steric contributions due to the different directionalities of substrate approach and thus similar intrinsic reactivities.

S K-edge X-ray absorption spectroscopy (XAS) is a direct experimental probe of metal ion electronic structure as the pre-edge energy reflects its oxidation state, and the energy splitting pattern of the pre-edge transitions reflects its spin state. The combination of sulfur K-edge XAS and density functional theory (DFT) calculations indicates that the electronic structures of {FeNO}(7) (S = 3/2) (S(Me2)N4(tren)Fe(NO), complex I) and {FeNO}(7) (S = 1/2) ((bme-daco)Fe(NO), complex II) are Fe(III)(S = 5/2)-NO(-)(S = 1) and Fe(III)(S = 3/2)-NO(-)(S = 1), respectively. When an axial ligand is computationally added to complex II, the electronic structure becomes Fe(II)(S = 0)-NO•(S = 1/2). These studies demonstrate how the ligand field of the Fe center defines its spin state and thus changes the electron exchange, an important factor in determining the electron distribution over {FeNO}(7) and {FeO2}(8) sites.

Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin Fe III peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4′ hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of Fe III BLM and ABLM as (BLM)Fe III ─OH and (BLM)Fe III ( η 1 ─OOH) species, respectively. The NRVS spectra of Fe III BLM and ABLM are strikingly different because in ABLM the δFe─O─O bending mode mixes with, and energetically splits, the doubly degenerate, intense O─Fe─N ax transaxial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways.

Interactions between atomic Pt and pristine or Stone−Wales-defective (5,5) single-walled boron nitride nanotubes (BNNTs) were studied using density functional theory (DFT) with truncated nanotube models. The binding energy of Pt on a pristine BNNT is about 20 kcal/mol with little dependency on the binding site. On the other hand, when the Stone−Wales (SW) defect is presented, the atomic Pt is preferentially inserted between the B−B bond in the SW defect region with a large binding energy of 58 kcal/mol. On an SW-defective BNNT, the atomic Pt, even placed away from the defect site, may eventually (thermodynamically) move toward the defect area until being trapped between the B−B bond, and the final adduct has decreased reactivity toward both electrophiles and nucleophiles compared with Pt adsorption to pristine BNNTs. Pt adsorption on pure or SW-defective BNNTs makes the hosting nanotube wide-gap semiconductive by introducing the valence states of the absorbed Pt into the band gap of the nanotube. In compa...

The geometries, chemical shifts, aromaticity, and reactivity of finite-length open-ended armchair single-walled carbon nanotubes (SWCNTs) have been studied within density functional theory. The widely used model of capping hydrogen atoms at the open ends of a SWCNT changes the chemical activity of the SWCNT and destabilizes the frontier molecular orbitals. The edge pi-orbital of the open ends enhances both pi- and sigma-aromaticity of the first belt of hexagons of carbon atoms at the open ends. The effect of the open ends on the structure and chemical reactivity of the SWCNT reaches only the first several layers of the hexagons of carbon atoms. Additions of carbene and dichlorocarbene to the nanotube reveal that the open ends have higher reactivities than the inner regions.

The structures, stabilities, and electronic properties of the single-vacancy-defected fullerenes, C60 and C70, and the single- and double-vacancy-defected single-walled carbon nanotubes (SWCNTs) were studied within density functional theory. The isomerization barriers for the single-vacancy-defected C60 on the triplet potential energy surface (PES) are lower than those on the singlet PES. The symmetric double-vacancy-defected (10,0) SWCNT is the most stable one among the models investigated. According to the analyses of frontier molecular orbitals (FMOs), nature bond orbitals, and local density of states, introduction of vacancy on the SWCNT decreases the band gap of semiconducting SWCNT, increases the band gap of conducting SWCNT, destructs the π conjugation of the FMOs, and gives rise to enhanced chemical activity. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

The adsorption of small gaseous molecules to the metal center in Pt-doped (5,5) single-walled carbon nanotubes has been explored within density functional theory. A model system consisting of a single Pt atom residing in the middle of a carbon nanotube with capping H atoms is used for our investigation. For all gases studied, the overall process of adsorption was found to be exothermic, where the affinity strongly depended on the orientation of the molecule. By examining the density of states and molecular orbitals of these nanotube−adsorbate complexes in comparison to the bare Pt-doped nanotube, we show that the electronic structure of these materials is strongly influenced by the presence of gases. Hence, we propose an application of Pt-doped single-walled carbon nanotubes as gas sensors and hope to motivate experimental work in this field.

The ozonization at the vacancy defect site of the single-walled carbon nanotube has been studied by static quantum mechanics and atom-centered density matrix propagation based ab initio molecular dynamics within a two-layered ONIOM approach. Among five different reaction pathways at the vacancy defect, the reaction involving the unsaturated active carbon atom is the most probable pathway, where ozone undergoes fast dissociation at the active carbon atom at 300 K. Complementary to the experiments, our work provides a microscopic understanding of the ozonization at the vacancy defect site of the single-walled carbon nanotube.

The class Ic ribonucleotide reductase (RNR) from Chlamydia trachomatis (Ct) utilizes a Mn/Fe heterobinuclear cofactor, rather than the Fe/Fe cofactor found in the β (R2) subunit of the class Ia enzymes, to react with O2. This reaction produces a stable Mn(IV)Fe(III) cofactor that initiates a radical, which transfers to the adjacent α (R1) subunit and reacts with the substrate. We have studied the Mn(IV)Fe(III) cofactor using nuclear resonance vibrational spectroscopy (NRVS) and absorption (Abs)/circular dichroism (CD)/magnetic CD (MCD)/variable temperature, variable field (VTVH) MCD spectroscopies to obtain detailed insight into its geometric/electronic structure and to correlate structure with reactivity; NRVS focuses on the Fe(III), whereas MCD reflects the spin-allowed transitions mostly on the Mn(IV). We have evaluated 18 systematically varied structures. Comparison of the simulated NRVS spectra to the experimental data shows that the cofactor has one carboxylate bridge, with Mn(IV) at the site proximal to Phe127. Abs/CD/MCD/VTVH MCD data exhibit 12 transitions that are assigned as d-d and oxo and OH(-) to metal charge-transfer (CT) transitions. Assignments are based on MCD/Abs intensity ratios, transition energies, polarizations, and derivative-shaped pseudo-A term CT transitions. Correlating these results with TD-DFT calculations defines the Mn(IV)Fe(III) cofactor as having a μ-oxo, μ-hydroxo core and a terminal hydroxo ligand on the Mn(IV). From DFT calculations, the Mn(IV) at site 1 is necessary to tune the redox potential to a value similar to that of the tyrosine radical in class Ia RNR, and the OH(-) terminal ligand on this Mn(IV) provides a high proton affinity that could gate radical translocation to the α (R1) subunit.

Mononuclear non-heme Fe (NHFe) enzymes play key roles in DNA repair, the biosynthesis of antibiotics, the response to hypoxia, cancer therapy, and many other biological processes. These enzymes catalyze a diverse range of oxidation reactions, including hydroxylation, halogenation, ring closure, desaturation, and electrophilic aromatic substitution (EAS). Most of these enzymes use an Fe(II) site to activate dioxygen, but traditional spectroscopic methods have not allowed researchers to insightfully probe these ferrous active sites. We have developed a methodology that provides detailed geometric and electronic structure insights into these NHFe(II) active sites. Using these data, we have defined a general mechanistic strategy that many of these enzymes use: they control O2 activation (and limit autoxidation and self-hydroxylation) by allowing Fe(II) coordination unsaturation only in the presence of cosubstrates. Depending on the type of enzyme, O2 activation either involves a 2e(-) reduced Fe(III)-OOH intermediate or a 4e(-) reduced Fe(IV)═O intermediate. Nuclear resonance vibrational spectroscopy (NRVS) has provided the geometric structure of these intermediates, and magnetic circular dichroism (MCD) has defined the frontier molecular orbitals (FMOs), the electronic structure that controls reactivity. This Account emphasizes that experimental spectroscopy is critical in evaluating the results of electronic structure calculations. Therefore these data are a key mechanistic bridge between structure and reactivity. For the Fe(III)-OOH intermediates, the anticancer drug activated bleomycin (BLM) acts as the non-heme Fe analog of compound 0 in heme (e.g., P450) chemistry. However BLM shows different reactivity: the low-spin (LS) Fe(III)-OOH can directly abstract a H atom from DNA. The LS and high-spin (HS) Fe(III)-OOHs have fundamentally different transition states. The LS transition state goes through a hydroxyl radical, but the HS transition state is activated for EAS without O-O cleavage. This activation is important in one class of NHFe enzymes that utilizes a HS Fe(III)-OOH intermediate in dioxygenation. For Fe(IV)═O intermediates, the LS form has a π-type FMO activated for attack perpendicular to the Fe-O bond. However, the HS form (present in the NHFe enzymes) has a π FMO activated perpendicular to the Fe-O bond and a σ FMO positioned along the Fe-O bond. For the NHFe enzymes, the presence of π and σ FMOs enables enzymatic control in determining the type of reactivity: EAS or H-atom extraction for one substrate with different enzymes and halogenation or hydroxylation for one enzyme with different substrates.

High-valent intermediates of binuclear nonheme iron enzymes are structurally unknown despite their importance for understanding enzyme reactivity. Nuclear resonance vibrational spectroscopy combined with density functional theory calculations has been applied to structurally well-characterized high-valent mono- and di-oxo bridged binuclear Fe model complexes. Low-frequency vibrational modes of these high-valent diiron complexes involving Fe motion have been observed and assigned. These are independent of Fe oxidation state and show a strong dependence on spin state. It is important to note that they are sensitive to the nature of the Fe 2 core bridges and provide the basis for interpreting parallel nuclear resonance vibrational spectroscopy data on the high-valent oxo intermediates in the binuclear nonheme iron enzymes.

The geometric and electronic structures and reactivity of an S = 5/2 (HS) mononuclear nonheme (TMC)Fe(III)-OOH complex are studied by spectroscopies, calculations, and kinetics and compared with the results of previous studies of S = 1/2 (LS) Fe(III)-OOH complexes to understand parallels and differences in mechanisms of O-O bond homolysis and electrophilic H-atom abstraction reactions. The homolysis reaction of the HS [(TMC)Fe(III)-OOH](2+) complex is found to involve axial ligand coordination and a crossing to the LS surface for O-O bond homolysis. Both HS and LS Fe(III)-OOH complexes are found to perform direct H-atom abstraction reactions but with very different reaction coordinates. For the LS Fe(III)-OOH, the transition state is late in O-O and early in C-H coordinates. However, for the HS Fe(III)-OOH, the transition state is early in O-O and further along in the C-H coordinate. In addition, there is a significant amount of electron transfer from the substrate to the HS Fe(III)-OOH at transition state, but that does not occur in the LS transition state. Thus, in contrast to the behavior of LS Fe(III)-OOH, the H-atom abstraction reactivity of HS Fe(III)-OOH is found to be highly dependent on both the ionization potential and the C-H bond strength of the substrate. LS Fe(III)-OOH is found to be more effective in H-atom abstraction for strong C-H bonds, while the higher reduction potential of HS Fe(III)-OOH allows it to be active in electrophilic reactions without the requirement of O-O bond cleavage. This is relevant to the Rieske dioxygenases, which are proposed to use a HS Fe(III)-OOH to catalyze cis-dihydroxylation of a wide range of aromatic compounds.

Mononuclear metal-dioxygen adducts, such as metal-superoxo and -peroxo species, are generated as key intermediates in the catalytic cycles of dioxygen activation by heme and non-heme metalloenzymes. We have shown recently that the geometric and electronic structure of the Ni-O2 core in [Ni(n-TMC)(O2)]+ (n = 12 and 14) varies depending on the ring size of the supporting TMC ligand. In this study, mononuclear Ni(II)-superoxo and Ni(III)-peroxo complexes bearing a common macrocylic 13-TMC ligand, such as [NiII(13-TMC)(O2)]+ and [NiIII(13-TMC)(O2)]+, were synthesized in the reaction of [NiII(13-TMC)(CH3CN)]2+ and H2O2 in the presence of tetramethylammonium hydroxide (TMAH) and triethylamine (TEA), respectively. The Ni(II)-superoxo and Ni(III)-peroxo complexes bearing the common 13-TMC ligand were successfully characterized by various spectroscopic methods, X-ray crystallography, and DFT calculations. Based on the combined experimental and theoretical studies, we conclude that the superoxo ligand in [NiII(13-TMC)(O2)]+ is bound in an end-on fashion to the nickel(II) center, whereas the peroxo ligand in [NiIII(13-TMC)(O2)]+ is bound in a side-on fashion to the nickel(III) center. Reactivity studies performed with the Ni(II)-superoxo and Ni(III)-peroxo complexes toward organic substrates reveal that the former possesses an electrophilic character, whereas the latter is an active oxidant in nucleophilic reaction.

After we thoroughly surveyed first-principles theoretical methods commonly employed in the studies of carbon nanotubes, we highlighted the performance of such ab inito methods on the electronic properties and reactivities of perfect, vacancy-defected, and hetroatom-doped single-walled carbon nanotubes. We have found that a rich chemistry can take place at the vacancy defect and doping sites of nanosystem: this very fact will enable experimental scientists to produce novel functionalized nanosize materials with much higher level of precise control of the manufacturing process

Fe III OOH and Fe IV O intermediates have now been documented in a number of nonheme iron active sites. In this Current Opinion we use spectroscopy combined with electronic structure calculations to define the frontier molecular orbitals (FMOs) of these species and their contributions to reactivity. For the low-spin Fe III OOH species in activated bleomycin we show that the reactivity of this nonheme iron intermediate is very different from that of the analogous Compound 0 of cytochrome P450. For Fe IV O S = 1 model species we experimentally define the electronic structure and its contribution to reactivity, and computationally evaluate how this would change for the Fe IV O S = 2 intermediates found in nonheme iron enzymes.

Bleomycin (BLM) is a glycopeptide anticancer drug that effectively carries out single- and double-stranded DNA cleavage. Activated BLM (ABLM), a low-spin ferric-hydroperoxide, BLM–Fe III –OOH, is the last intermediate detected before DNA cleavage. We have previously shown through experiments and DFT calculations that both ABLM decay and reaction with H atom donors proceed via direct H atom abstraction. However, the rate of ABLM decay had been previously found, based on indirect methods, to be independent of the presence of DNA. In this study, we use a circular dichroism (CD) feature unique to ABLM to directly monitor the kinetics of ABLM reaction with a DNA oligonucleotide. Our results show that the ABLM + DNA reaction is appreciably faster, has a different kinetic isotope effect, and has a lower Arrhenius activation energy than does ABLM decay. In the ABLM reaction with DNA, the small normal k H / k D ratio is attributed to a secondary solvent effect through DFT vibrational analysis of reactant and transition state (TS) frequencies, and the lower E a is attributed to the weaker bond involved in the abstraction reaction (C–H for DNA and N–H for the decay in the absence of DNA). The DNA dependence of the ABLM reaction indicates that DNA is involved in the TS for ABLM decay and thus reacts directly with BLM–Fe III –OOH instead of its decay product.

In this work, we applied a two-layered ONIOM (B3LYP/6-31G(d):UFF) method to study the reaction of nitric oxides with a 5-1DB defect on the sidewall of the single-walled carbon nanotube (SWCNT). We have chosen a suitable ONIOM model for the calculation of the SWCNT based on the analyses of the frontier molecular orbitals, local density of states, and natural bond orbitals. Our calculations clearly indicate that the 5-1DB defect is the chemically active center of the SWCNT. In the reaction of nitric oxides with the defected SWCNT, the 5-1DB defect site can capture a nitrogen atom from nitric oxides, yielding the N-substitutionally doped SWCNT. We have explored the reaction pathway in detail. Our work verifies the chemical reactivity of the 5-1DB defects of the SWCNTs, indicates that the 5-1DB defect is a possible site for the functionalization of the SWCNTs, and demonstrates a possible way to fabricate position controllable substitutionally doped SWCNTs with a low doping concentration under mild conditions via some simple chemical reactions.

The structures of the (5,5) single-walled carbon nanotube (SWCNT) segments with hemispheric carbon cages capped at the ends (SWCNT rod) and the Pt-doped SWCNT rods have been studied within density functional theory. Our theoretical studies find that the hemispheric cages introduce localized states on the caps. The cap-Pt-doped SWCNT rods can be utilized as sensors because of the sensitivity of the doped Pt atom. The Pt-doped SWCNT rods can also be used as catalysts, where the doped Pt atom serves as the enhanced and localized active center on the SWCNT. The adsorptions of C(2)H(4) and H(2) on the Pt atom in the Pt-doped SWCNT rods reveal different adsorption characteristics. The adsorption of C(2)H(4) on the Pt atom in all of the three Pt-doped SWCNT rods studied (cap-end-doped, cap-doped, and wall-doped) is physisorption with the strongest interaction occurring in the middle of the sidewall of the SWCNT. On the other hand, the adsorption of H(2) on the Pt atom at the sidewall of the SWCNT is chemisorption resulting in the decomposition of H(2), and the adsorption of H(2) at the hemispheric caps is physisorption.