Stereoelectronic Effects on Molecular Geometries and State-Energy Splittings of Ligated Monocopper Dioxygen Complexes

Spectroscopy of End-On Copper(II) Superoxido Complexes: A Wave Function-Based Analysis

Wave function methods are employed to analyze the ground and low-lying excited states of bipyramid trigonal copper(II) superoxido complexes, up to their characteristic ligand to metal charge transfer band. Several multireference methods have been combined to provide new insights into the interpretation of their experimental absorption spectra. We show that the intraligand transition on the dioxygen leads to a dark state. Among the results, we shall highlight the finding of doubly excited states in the region of the d-d transitions and the subtle interplay between Cu(I) and Cu(II) in the ground and excited states. Some of these findings could be obtained only with multireference methods.

Ligand Degradation Study of Unsymmetrical β-Diketiminato Copper Dioxygen Adducts: The Length Chelating Arm Effect

An investigation on the reactivity of O₂ binding to unsymmetrical β-diketiminato copper(I) complexes by spectroscopic and titration analysis was performed. The length of chelating pyridyl arms (pyridylmethyl arm vs pyridylethyl arm) leads to the formation of mono- or di-nuclear copper-dioxygen species at -80 °C. The pyridylmethyl arm adduct (L₁CuO₂) forms mononuclear copper-oxygen species and shows ligand degradation, resulting in the formation of (2E,3Z)-N-(2,6-diisopropylphenyl)-4-(((E)-pyridin-2-ylmethylene)amino)pent-3-en-2-imine, which slowly converts to its cyclization isomer 1-(2,6-diisopropylphenyl)-4,6-dimethyl-2-(pyridin-2-yl)-1,2-dihydropyrimidine after addition of NH₄OH at room temperature. On the other hand, the pyridylethyl arm adduct [(L₂Cu)₂(μ-O)₂] forms dinuclear species at -80 °C and does not show any ligand degradation product. Instead, free ligand formation was observed after the addition of NH₄OH. These experimental observations and product analysis results indicate that the chelating length of pyridyl arms governs the Cu/O₂ binding ratio and the ligand degradation behavior.

Theoretical Calculations on the Mechanism of Enantioselective Copper(I)-Catalyzed Addition of Enynes to Ketones

Computational investigations on the bisphospholanoethane (BPE)-ligated Cu-catalyzed enantioselective addition of enynes to ketones were performed with the density functional theory (DFT) method. Two BPE-mesitylcopper (CuMes) catalysts, BPE-CuMes and (S,S)-Ph-BPE–CuMes, were employed to probe the reaction mechanism with the emphasis on stereoselectivity. The calculations on the BPE-CuMes system indicate that the active metallized enyne intermediate acts as the catalyst for the catalytic cycle. The catalytic cycle involves two steps: (1) ketone addition to the alkene moiety of the metallized enyne; and (2) metallization of the enyne followed by the release of product with the recovery of the active metallized enyne intermediate. The first step accounts for the distribution of the products, and therefore is the stereo-controlling step in chiral systems. In the chiral (S,S)-Ph-BPE–CuMes system, the steric hindrance is vital for the distribution of products and responsible for the stereoselectivity of this reaction. The steric hindrance between the phenyl ring of the two substrates and groups at the chiral centers in the ligand skeleton is identified as the original of the stereoselectivity for the titled reaction.

Spin crossover dynamics studies on the thermally activated molecular oxygen binding mechanism on a model copper complex

The theoretical description of the primary dioxygen (O₂) binding and activation step in many copper or iron enzymes, suffers from the instrinsically electronic non-adiabaticity of the spin flip events of the triplet dioxygen molecule (³O₂), mediated by spin–orbit couplings.

The exocyclic amino group of adenine in PtII and PdII complexes: a critical comparison of the X-ray crystallographic structural data and gas phase calculations

A detailed computational (DFT level of theory) study regarding the nature of the exocyclic amino group, N6H₂, of the model nucleobase 9-methyladenine (9MeA) and its protonated (9MeAH⁺) and deprotonated forms (9MeA_-H), free and metal-complexed, has been conducted. The metals are Pt^II and Pd^II, bonded to nitrogen-containing co-ligands (NH₃, dien, bpy), with N1, N6, and N7 being the metal-binding sites, individually or in different combinations. The results obtained from gas phase calculations are critically compared with X-ray crystallography data, whenever possible. In the majority of cases, there is good qualitative agreement between calculated and experimentally determined C6-N6 bond lengths, but calculated values always show a trend to larger values, by 0.02-0.08 Å. Both methods indicate, with few exceptions, a high degree of double-bond character of C6-N6, consistent with an essentially sp²-hybridized N6 atom. The shortest values for C6-N6 distances in X-ray crystal structures are around 1.30 Å. Exceptions refer to cases in which DFT calculations suggest the existence of a hydrogen bond with N6H₂ acting as a H bond acceptor, hence a situation with N6 having undergone a substantial hybridization shift toward sp³. Nevertheless, even in these cases the C6-N6 bond (1.392 Å) is still halfway between a typical C-N single bond (1.48 Å) and a typical C=N double bond (1.28 Å). This scenario is, however, not borne out by X-ray crystallographic results, and is attributed to the absence of counter anions and solvent molecules in the calculated structures.

Copper-Oxygen Complexes Revisited: Structures, Spectroscopy, and Reactivity

A longstanding research goal has been to understand the nature and role of copper-oxygen intermediates within copper-containing enzymes and abiological catalysts. Synthetic chemistry has played a pivotal role in highlighting the viability of proposed intermediates and expanding the library of known copper-oxygen cores. In addition to the number of new complexes that have been synthesized since the previous reviews on this topic in this journal (Mirica, L. M.; Ottenwaelder, X.; Stack, T. D. P. Chem. Rev. 2004, 104, 1013-1046 and Lewis, E. A.; Tolman, W. B. Chem. Rev. 2004, 104, 1047-1076), the field has seen significant expansion in the (1) range of cores synthesized and characterized, (2) amount of mechanistic work performed, particularly in the area of organic substrate oxidation, and (3) use of computational methods for both the corroboration and prediction of proposed intermediates. The scope of this review has been limited to well-characterized examples of copper-oxygen species but seeks to provide a thorough picture of the spectroscopic characteristics and reactivity trends of the copper-oxygen cores discussed.

A mononuclear non-heme-iron dioxygen-carrying protein?

The ability of mononuclear non-heme iron complexes to function as molecular oxygen transporters is investigated by density functional theory. The factors governing the efficiency of the reversible binding of dioxygen at the active site of the dinuclear non-heme iron enzyme hemerythrin, including antiferromagnetic coupling and the conversion of dioxygen to hydroperoxo by a proton coupled 2-electron transfer mechanism, are revisited and considered as possible tools in mononuclear non-heme complexes. Several mononuclear non-heme model complexes, including active sites of enzymes already known to interact with dioxgenic ligands, are constructed and the molecular oxygen transportation capabilities of these complexes are examined computationally. The high-spin nature of the ground state of these complexes implies an intrinsic kinetic lability of the oxy structures, as also evident from potential energy surface calculations towards iron-dioxygen cleavage. Proton affinities as calibrated with reference compounds showed that these complexes are highly unlikely to undergo protonation to form hydroperoxo-like adducts. Mixed superoxo descriptions of the dissociated dioxygenic ligands in all complexes add to the overall conclusion that these model structures are significantly disadvantaged in any attempt to be employed for molecular oxygen transportation.

Bacterial nitric oxide reductase: a mechanism revisited by an ONIOM (DFT:MM) study

Bacterial nitric oxide reductase (cNOR) is an important binuclear iron enzyme responsible for the reduction of nitric oxide to nitrous oxide in the catalytic cycle of bacterial respiration. The reaction mechanism of cNOR as well as the key reactive intermediates of the reaction are still under debate. Here, we report a computational study based on ONIOM (DFT:MM) calculations aimed at investigating the reaction mechanism of cNOR. The results suggest that the reaction proceeds via the mono-nitrosyl mechanism which starts off by the binding of an NO molecule to the heme b3 center, N-N hyponitrite bond formation as a result of the reaction with a second NO molecule was found to proceed with an exothermic energy barrier to yield a hyponitrite adduct forming an open (incomplete) ring conformation with the non-heme FeB center (O-N-N-O-FeB). N-O bond cleavage to yield N2O was shown to be the rate-limiting step with an activation barrier of 22.6 kcal mol(-1). The dinitrosyl (trans) mechanism, previously proposed by several studies, was also examined and found unfavorable due to high activation barriers of the resulting intermediates.

Re-evaluating the Cu K pre-edge XAS transition in complexes with covalent metal-ligand interactions

Three [Me2NN]Cu(η2-L2) complexes (Me2NN = HC[C(Me)NAr]2; L2 = PhNO (2), (3), PhCH[double bond, length as m-dash]CH2 (4); Ar = 2,6-Me2-C6H3; ArF = 3,5-(CF3)2-C6H3) have been studied by Cu K-edge X-ray absorption spectroscopy, as well as single- and multi-reference computational methods (DFT, TD-DFT, CASSCF, MRCI, and OVB). The study was extended to a range of both known and theoretical compounds bearing 2p-element donors as a means of deriving a consistent view of how the pre-edge transition energy responds in systems with significant ground state covalency. The ground state electronic structures of many of the compounds under investigation were found to be strongly influenced by correlation effects, resulting in ground state descriptions with majority contributions from a configuration comprised of a Cu(ii) metal center anti-ferromagentically coupled to radical anion O2, PhNO, and ligands. In contrast, the styrene complex 4, which displays a Cu K pre-edge transition despite its formal d10 electron configuration, exhibits what can best be described as a Cu(i):(styrene)0 ground state with strong π-backbonding. The Cu K pre-edge features for these complexes increase in energy from 1 to 4, a trend that was tracked to the percent Cu(ii)-character in the ground state. The unexpected shift to higher pre-edge transition energies with decreasing charge on copper (Q Cu) contributed to an assignment of the pre-edge features for these species as arising from metal-to-ligand charge transfer instead of the traditional Cu1s → Cu3d designation.

Computational investigation of the initial two-electron, two-proton steps in the reaction mechanism of hydroxylamine oxidoreductase

Reported here is a computational study based on density functional theory that presents the first attempt to investigate the 2-electron 2-proton reaction of Fe(III)-H2NOH to Fe(III)-HNO in the catalytic cycle of hydroxylamine oxidoreductase-a multiheme-containing enzyme that catalyzes the conversion of hydroxylamine (HA) to nitrite in nitrifying bacteria. Two subsequent protonation events are proposed to initiate the process, of which the second is suggested to be concerted with a one-electron oxidation. The final one-electron oxidation is further proposed to be accompanied by a third deprotonation process, suggesting that Fe(III)-HNO may not be an isolable intermediate in the HAO catalytic cycle. Further explorations are suggested to be focused on the following steps in the catalytic cycle, the influence of the lateral substituents of the heme (and especially of the Cys and Tyr cross-links), the comparative study of hydrazine oxidation, the proton delivery network in the distal site and, possibly, on linkage isomerism.

Involvement of ferryl in the reaction between nitrite and the oxy forms of globins

The reaction between nitrite and the oxy forms of globins has complex autocatalytic kinetics with several branching steps and evolves through chain reactions mediated by reactive species (including radicals) such as hydrogen peroxide, ferryl and nitrogen dioxide, starting with a lag phase, after which it proceeds onto an autocatalytic phase. Reported here are UV-Vis spectra collected upon stopped-flow mixing of myoglobin with a supraphysiological excess of nitrite. The best fit to the experimental data follows an A → B → C reaction scheme involving the formation of a short-lived intermediate identified as ferryl. This is consistent with a mechanism where nitrite binds to oxy myoglobin to generate an undetectable ferrous-peroxynitrate intermediate, whose decay leads to nitrate and ferryl. The ferryl is then reduced to met by the excess nitrite. DFT calculations reveal an essentially barrierless reaction between nitrite and the oxy heme, with a notable outer-sphere component; the resulting metastable ferrous-peroxynitrate adduct is found to feature a very low barrier towards nitrate liberation, with ferryl as a final product-in good agreement with experiment.

Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism

Lytic polysaccharide monooxygenases (LPMOs) exhibit a mononuclear copper-containing active site and use dioxygen and a reducing agent to oxidatively cleave glycosidic linkages in polysaccharides. LPMOs represent a unique paradigm in carbohydrate turnover and exhibit synergy with hydrolytic enzymes in biomass depolymerization. To date, several features of copper binding to LPMOs have been elucidated, but the identity of the reactive oxygen species and the key steps in the oxidative mechanism have not been elucidated. Here, density functional theory calculations are used with an enzyme active site model to identify the reactive oxygen species and compare two hypothesized reaction pathways in LPMOs for hydrogen abstraction and polysaccharide hydroxylation; namely, a mechanism that employs a η(1)-superoxo intermediate, which abstracts a substrate hydrogen and a hydroperoxo species is responsible for substrate hydroxylation, and a mechanism wherein a copper-oxyl radical abstracts a hydrogen and subsequently hydroxylates the substrate via an oxygen-rebound mechanism. The results predict that oxygen binds end-on (η(1)) to copper, and that a copper-oxyl-mediated, oxygen-rebound mechanism is energetically preferred. The N-terminal histidine methylation is also examined, which is thought to modify the structure and reactivity of the enzyme. Density functional theory calculations suggest that this posttranslational modification has only a minor effect on the LPMO active site structure or reactivity for the examined steps. Overall, this study suggests the steps in the LPMO mechanism for oxidative cleavage of glycosidic bonds.

Transmission coefficients for chemical reactions with multiple states: role of quantum decoherence

Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τ(dec) now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τ(dec)). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases.

An anionic, tetragonal copper(II) superoxide complex

Insight into copper-oxygen species proposed as intermediates in oxidation catalysis is provided by the identification of a Cu(II)-superoxide complex supported by a sterically hindered, pyridinedicarboxamide ligand. A tetragonal, end-on superoxide structure is proposed based on DFT calculations and UV-vis, NMR, EPR, and resonance Raman spectroscopy. The complex yields a trans-1,2-peroxodicopper(II) species upon reaction with [(tmpa)Cu(CH(3)CN)]OTf and, unlike other known Cu(II)-superoxide complexes, acts as a base rather than an electrophilic (H-atom abstracting) reagent in reactions with phenols.

Density functional theory for transition metals and transition metal chemistry

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Adsorption of dioxygen to copper in CuHY zeolite

The adsorption of dioxygen to copper in CuHY zeolites has been studied by means of FTIR spectroscopy and model calculations at the quantum mechanical/molecular mechanics (QM/MM) level. Different Si/Al ratios, substitution patterns and adsorption sites within the cavities of the zeolite lead to a large number of different isomers to be studied. In addition, these parameters control the end-on vs. side-on adsorption of dioxygen. High-level multireference benchmark calculations for the singlet and triplet states of such adsorption complexes corroborate the use of density functional theory for the investigation of these systems. Comparison of the experimental and computed data allows for the identification of a preferred adsorption site and a small number of isomers which appear to be most relevant for the adsorption process. Redshifts of >250 cm(-1) are obtained for the vibrational frequencies of adsorbed O(2).

Probing the mechanism of O2 activation by a copper(I) biomimetic complex of a C-H hydroxylating copper monooxygenase

In this paper, we report, for the first time, a plausible full reaction pathway for the activation of O(2) by a tetraazamacrocyclic monocopper(I) complex and for the subsequent intramolecular alkylic hydroxylation to yield the alkoxide product. This theoretical insight offers remarkable support to the fundamental hypothesis in the field that a hydroperoxo complex of the type Cu(II)OOH intermediate is the key intermediate in this class of reactions. Overall, we give insight into an intramolecular alkylic C-H bond activation due to the O(2) binding to copper(I) with an end-on eta(1)-O(2) ligation. The loss of a water molecule involves the final substrate oxygenation. The complex we consider is a biomimetic of several systems of biological relevance, such as amine oxidases, peptidylglycine-alpha-hydroxylating monooxygenase, and dopamine-beta monooxygenases.

Generating Cu(II)-oxyl/Cu(III)-oxo species from Cu(I)-alpha-ketocarboxylate complexes and O2: in silico studies on ligand effects and C-H-activation reactivity

A mechanism for the oxygenation of Cu(I) complexes with alpha-ketocarboxylate ligands that is based on a combination of density functional theory and multireference second-order perturbation theory (CASSCF/CASPT2) calculations is elaborated. The reaction proceeds in a manner largely analogous to those of similar Fe(II)-alpha-ketocarboxylate systems, that is, by initial attack of a coordinated oxygen molecule on a ketocarboxylate ligand with concomitant decarboxylation. Subsequently, two reactive intermediates may be generated, a Cu-peracid structure and a [CuO](+) species, both of which are capable of oxidizing a phenyl ring component of the supporting ligand. Hydroxylation by the [CuO](+) species is predicted to proceed with a smaller activation free energy. The effects of electronic and steric variations on the oxygenation mechanisms were studied by introducing substituents at several positions of the ligand backbone and by investigating various N-donor ligands. In general, more electron donation by the N-donor ligand leads to increased stabilization of the more Cu(II)/Cu(III)-like intermediates (oxygen adducts and [CuO](+) species) relative to the more Cu(I)-like peracid intermediate. For all ligands investigated, the [CuO](+) intermediates are best described as Cu(II)-O(*-) species with triplet ground states. The reactivity of these compounds in C-H abstraction reactions decreases with more electron-donating N-donor ligands, which also increase the Cu-O bond strength, although the Cu-O bond is generally predicted to be rather weak (with a bond order of about 0.5). A comparison of several methods to obtain singlet energies for the reaction intermediates indicates that multireference second-order perturbation theory is likely more accurate for the initial oxygen adducts, but not necessarily for subsequent reaction intermediates.

The restricted active space followed by second-order perturbation theory method: theory and application to the study of CuO2 and Cu2O2 systems

A multireference second-order perturbation theory using a restricted active space self-consistent field wave function as reference (RASPT2/RASSCF) is described. This model is particularly effective for cases where a chemical system requires a balanced orbital active space that is too large to be addressed by the complete active space self-consistent field model with or without second-order perturbation theory (CASPT2 or CASSCF, respectively). Rather than permitting all possible electronic configurations of the electrons in the active space to appear in the reference wave function, certain orbitals are sequestered into two subspaces that permit a maximum number of occupations or holes, respectively, in any given configuration, thereby reducing the total number of possible configurations. Subsequent second-order perturbation theory captures additional dynamical correlation effects. Applications of the theory to the electronic structure of complexes involved in the activation of molecular oxygen by mono- and binuclear copper complexes are presented. In the mononuclear case, RASPT2 and CASPT2 provide very similar results. In the binuclear cases, however, only RASPT2 proves quantitatively useful, owing to the very large size of the necessary active space.