Experimental and Computational Insights into Carbon Dioxide Fixation by RZnOH Species

Organozinc hydroxides, RZnOH, possessing the proton‐reactive alkylzinc group and the CO₂‐reactive Zn?OH group, represent an intriguing group of organometallic precursors for the synthesis of novel zinc carbonates. Comprehensive experimental and computational investigations on 1) solution and solid‐state behavior of tBuZnOH ( 1 ) species in the presence of Lewis bases, namely, THF and 4‐methylpyridine; 2) step‐by‐step sequence of the reaction between 1 and CO₂; and 3) the effect of a donor ligand and/or an excess of tBu₂Zn as an external proton acceptor on the reaction course are reported. DFT calculations for the insertion of carbon dioxide into the dinuclear alkylzinc hydroxide 1 ₂ are fully consistent with ¹H NMR spectroscopy studies and indicate that this process is a multistep reaction, in which the insertion of CO₂ seems to be the rate‐determining step. Moreover, DFT studies show that the mechanism of the rearrangement between key intermediates, that is, the primary alkylzinc bicarbonate with a proximal position of hydrogen and the secondary alkylzinc bicarbonate with a distal position of hydrogen, most likely proceeds through internal rotation of the dinuclear bicarbonate.     

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole‐enzyme model of 10 800 atoms. Substrate fluoroacetate is anchored by a hydrogen‐bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the α‐carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C? F bond is greatly facilitated by the hydrogen‐bonding interactions between the leaving fluorine atom and the three amino acid residues of His149, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.     

Dinitrogen Activation by Fryzuk’s [Nb(P2N2)] Complex and Comparison with the Laplaza–Cummins [Mo{N(R)Ar}3] and Schrock [Mo(N3N)] Systems

The reaction profile of N₂ with Fryzuk’s [Nb(P₂N₂)] (P₂N₂=PhP(CH₂SiMe₂NSiMe₂CH₂)₂PPh) complex is explored by density functional calculations on the model [Nb(PH₃)₂(NH₂)₂] system. The effects of ligand constraints, coordination number, metal and ligand donor atom on the reaction energetics are examined and compared to the analogous reactions of N₂ with the three‐coordinate Laplaza‐Cummins [Mo{N(R)Ar}₃] and four‐coordinate Schrock [Mo(N₃N)] (N₃N=[(RNCH₂CH₂)₃N]^3?) systems. When the model system is constrained to reflect the geometry of the P₂N₂ macrocycle, the N? N bond cleavage step, via a N₂‐bridged dimer intermediate, is calculated to be endothermic by 345 kJ mol^?1. In comparison, formation of the single‐N‐bridged species is calculated to be exothermic by 119 kJ mol^?1, and consequently is the thermodynamically favoured product, in agreement with experiment. The orientation of the amide and phosphine ligands has a significant effect on the overall reaction enthalpy and also the N? N bond cleavage step. When the ligand constraints are relaxed, the overall reaction enthalpy increases by 240 kJ mol^?1, but the N₂ cleavage step remains endothermic by 35 kJ mol^?1. Changing the phosphine ligands to amine donors has a dramatic effect, increasing the overall reaction exothermicity by 190 kJ mol^?1 and that of the N? N bond cleavage step by 85 kJ mol^?1, making it a favourable process. Replacing Nb^II with Mo^III has the opposite effect, resulting in a reduction in the overall reaction exothermicity by over 160 kJ mol^?1. The reaction profile for the model [Nb(P₂N₂)] system is compared to those calculated for the model Laplaza and Cummins [Mo{N(R)Ar}₃] and Schrock [Mo(N₃N)] systems. For both [Mo(N₃N)] and [Nb(P₂N₂)], the intermediate dimer is calculated to lie lower in energy than the products, although the final N? N cleavage step is much less endothermic for [Mo(N₃N)]. In contrast, every step of the reaction is favourable and the overall exothermicity is greatest for [Mo{N(R)Ar}₃], and therefore this system is predicted to be most suitable for dinitrogen cleavage.     

Mechanism and Chemoselectivity for HOCl-Mediated Oxidation of Zinc-Bound Thiolates

Quantum mechanical calculations reveal the preferred mechanism and origins of chemoselectivity for HOCl-mediated oxidation of zinc-bound thiolates implicated in bacterial redox sensing. Distortion/interaction models show that minimizing geometric distortion at the zinc complex during the rate-limiting nucleophilic substitution step controls the mechanistic preference for OH over Cl transfer with HOCl and the chemoselectivity for HOCl over H₂O₂.     

Unraveling the Mechanism of Water Oxidation Catalyzed by Nonheme Iron Complexes

Density functional theory (DFT) is employed to: 1) propose a viable catalytic cycle consistent with our experimental results for the mechanism of chemically driven (Ce^IV) O₂ generation from water, mediated by nonheme iron complexes; and 2) to unravel the role of the ligand on the nonheme iron catalyst in the water oxidation reaction activity. To this end, the key features of the water oxidation catalytic cycle for the highly active complexes [Fe(OTf)₂(Pytacn)] (Pytacn: 1‐(2′‐pyridylmethyl)‐4,7‐dimethyl‐1,4,7‐triazacyclononane; OTf: CF₃SO₃^?) ( 1 ) and [Fe(OTf)₂(mep)] (mep: N,N′‐bis(2‐pyridylmethyl)‐N,N′‐dimethyl ethane‐1,2‐diamine) ( 2 ) as well as for the catalytically inactive [Fe(OTf)₂(tmc)] (tmc: N,N′,N′′,N′′′‐tetramethylcyclam) ( 3 ) and [Fe(NCCH₃)(^MePy₂CH‐tacn)](OTf)₂ (^MePy₂CH‐tacn: N‐(dipyridin‐2‐yl)methyl)‐N′,N′′‐dimethyl‐1,4,7‐triazacyclononane) ( 4 ) were analyzed. The DFT computed catalytic cycle establishes that the resting state under catalytic conditions is a [Fe^IV(O)(OH₂)(LN₄)]²⁺ species (in which LN₄=Pytacn or mep) and the rate‐determining step is the O?O bond‐formation event. This is nicely supported by the remarkable agreement between the experimental (ΔG^≠=17.6±1.6 kcal mol^?1) and theoretical (ΔG^≠=18.9 kcal mol^?1) activation parameters obtained for complex 1 . The O?O bond formation is performed by an iron(V) intermediate [Fe^V(O)(OH)(LN₄)]²⁺ containing a cis‐Fe^V(O)(OH) unit. Under catalytic conditions (Ce^IV, pH 0.8) the high oxidation state Fe^V is only thermodynamically accessible through a proton‐coupled electron‐transfer (PCET) process from the cis‐[Fe^IV(O)(OH₂)(LN₄)]²⁺ resting state. Formation of the [Fe^V(O)(LN₄)]³⁺ species is thermodynamically inaccessible for complexes 3 and 4 . Our results also show that the cis‐labile coordinative sites in iron complexes have a beneficial key role in the O?O bond‐formation process. This is due to the cis‐OH ligand in the cis‐Fe^V(O)(OH) intermediate that can act as internal base, accepting a proton concomitant to the O?O bond‐formation reaction. Interplay between redox potentials to achieve the high oxidation state (Fe^V?O) and the activation energy barrier for the following O?O bond formation appears to be feasible through manipulation of the coordination environment of the iron site. This control may have a crucial role in the future development of water oxidation catalysts based on iron.     

Synthesis and Coordination Chemistry of Iminophosphanes

Iminophosphanes are a new group of 1,3‐P,N‐ligands, readily obtainable from secondary phosphanes and nitrilium ions, having a tunable N‐donor site by means of varying the imine substituents. These ligands give, in high yields, monodentate gold complexes and bidentate rhodium and iridium complexes. Crystal structures are reported for both the ligands and the complexes.     

A DFT Study of the Nitric Oxide and Tyrosyl Radical Interaction: A Proposed Radical Mechanism

The present study employs a complete theoretical investigation, at the B3LYP/cc‐pVTZ level of theory, of the interactions between the tyrosyl radical and nitric oxide, exploring in detail the nitrotyrosine formation radical mechanism. Tyrosyl radicals play an essential role in catalytic reactions of numerous enzymes and biological systems have regulated appropriate mechanisms for their formation. Nitric oxide reacts with the tyrosyl radical and affords a weak intermediate complex which, through a sequence of non‐ionic water catalyzed and biologically feasible intermediate reactions, yields the iminoxyl radical. The iminoxyl radical further combines with hydroxyl radical, a species present in pathophysiological conditions, to yield nitrotyrosine.     

DFT Calculations Suggest a New Type of Self‐Protection and Self‐Inhibition Mechanism in the Mammalian Heme Enzyme Myeloperoxidase: Nucleophilic Addition of a Functional Water rather than One‐Electron Reduction

The mammalian heme enzyme myeloperoxidase (MPO) catalyzes the reaction of Cl^? to the antimicrobial‐effective molecule HOCl. During the catalytic cycle, a reactive intermediate “Compound I” (Cpd I) is generated. Cpd I has the ability to destroy the enzyme. Indeed, in the absence of any substrate, Cpd I decays with a half‐life of 100 ms to an intermediate called Compound II (Cpd II), which is typically the one‐electron reduced Cpd I. However, the nature of Cpd II, its spectroscopic properties, and the source of the additional electron are only poorly understood. On the basis of DFT and time‐dependent (TD)‐DFT quantum chemical calculations at the PBE0/6‐31G* level, we propose an extended mechanism involving a new intermediate, which allows MPO to protect itself from self‐oxidation or self‐destruction during the catalytic cycle. Because of its similarity in electronic structure to Cpd II, we named this intermediate Cpd II′. However, the suggested mechanism and our proposed functional structure of Cpd II′ are based on the hypothesis that the heme is reduced by charge separation caused by reaction with a water molecule, and not, as is normally assumed, by the transfer of an electron. In the course of this investigation, we found a second intermediate, the reduced enzyme, towards which the new mechanism is equally transferable. In analogy to Cpd II′, we named it Fe^II′. The proposed new intermediates Cpd II′ and Fe^II′ allow the experimental findings, which have been well documented in the literature for decades but not so far understood, to be explained for the first time. These encompass a) the spontaneous decay of Cpd I, b) the unusual (chlorin‐like) UV/Vis, circular dichroism (CD), and resonance Raman spectra, c) the inability of reduced MPO to bind CO, d) the fact that MPO‐Cpd II reduces SCN^? but not Cl^?, and e) the experimentally observed auto‐oxidation/auto‐reduction features of the enzyme. Our new mechanism is also transferable to cytochromes, and could well be viable for heme enzymes in general.     

Highly Efficient Chemical Process To Convert Mucic Acid into Adipic Acid and DFT Studies of the Mechanism of the Rhenium‐Catalyzed Deoxydehydration

The production of bulk chemicals and fuels from renewable bio‐based feedstocks is of significant importance for the sustainability of human society. Adipic acid, as one of the most‐demanded drop‐in chemicals from a bioresource, is used primarily for the large‐volume production of nylon‐6,6 polyamide. It is highly desirable to develop sustainable and environmentally friendly processes for the production of adipic acid from renewable feedstocks. However, currently there is no suitable bio‐adipic acid synthesis process. Demonstrated herein is the highly efficient synthetic protocol for the conversion of mucic acid into adipic acid through the oxorhenium‐complex‐catalyzed deoxydehydration (DODH) reaction and subsequent Pt/C‐catalyzed transfer hydrogenation. Quantitative yields (99 %) were achieved for the conversion of mucic acid into muconic acid and adipic acid either in separate sequences or in a one‐step process.     

Insights into the Mechanism of the Reaction between Tetrachloro‐p‐Benzoquinone and Hydrogen Peroxide and their Implications in the Catalytic Role of Water Molecules in Producing the Hydroxyl Radial

Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro‐p‐benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H₂O₂ has been systematically investigated at the B3LYP/6‐311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H₂O₂ onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O? O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate‐determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH₃ substituents on this reaction have also been studied.     

Nitrogen fixation under mild ambient conditions: part I--the initial dissociation/association step at molybdenum triamidoamine complexes

In several recent studies Schrock and collaborators demonstrated for the first time how molecular dinitrogen can be catalytically transformed under mild and ambient conditions to ammonia by a molybdenum triamidoamine complex. In this work, we investigate the geometrical and electronic structures involved in this process of dinitrogen activation with quantum chemical methods. Density functional theory (DFT) has been employed to calculate the coordination energies of ammonia and dinitrogen relevant for the dissociation/association step in which ammonia is substituted by dinitrogen. In the DFT calculations the triamidoamine chelate ligand has been modeled by a systematic hierarchy of increasingly complex substituents at the amide nitrogen atoms. The most complex ligand considered is an experimentally known ligand with an HMT = 3,5-(2,4,6-Me3C6H2)2C6H3 substituent. Several assumptions by Schrock and collaborators on key reaction steps are confirmed by our calculations. Additional information is provided on many species not yet observed experimentally. Particular attention is paid to the role of the charge of the complexes. The investigation demonstrates that dinitrogen coordination is enhanced for the negatively charged metal fragment, that is, coordination is more favorable for the anionic metal fragment than for the neutral species. Coordination of N2 is least favorable for the cationic metal fragment. Furthermore, ammonia abstraction from the cationic complex is energetically unfavorable, while NH3 abstraction is less difficult from the neutral and easily feasible from the anionic low-spin complex.     

Exploring Electronic and Steric Effects on the Insertion and Polymerization Reactivity of Phosphinesulfonato PdII Catalysts

Thirteen different symmetric and asymmetric phosphinesulfonato palladium complexes ([{( ^X 1 ‐Cl)‐μ‐M}_n], M=Na, Li, 1 =^X(P^O)PdMe) were prepared (see Figure 1). The solid‐state structures of the corresponding pyridine or lutidine complexes were determined for ^(MeO)2 1‐py , ^(iPrO)2 1‐lut , ^(MeO,Me2) 1‐lut , ^(MeO)3 1‐lut , ^CF3 1‐lut , and ^Ph 1‐lut . The reactivities of the catalysts ^X 1 , obtained after chloride abstraction with AgBF₄, toward methyl acrylate (MA) were quantified through determination of the rate constants for the first and the consecutive MA insertion and the analysis of β‐H and other decomposition products through NMR spectroscopy. Differences in the homo‐ and copolymerization of ethylene and MA regarding catalyst activity and stability over time, polymer molecular weight, and polar co‐monomer incorporation were investigated. DFT calculations were performed on the main insertion steps for both monomers to rationalize the effect of the ligand substitution patterns on the polymerization behaviors of the complexes. Full analysis of the data revealed that: 1) electron‐deficient catalysts polymerize with higher activity, but fast deactivation is also observed; 2) the double ortho‐substituted catalysts ^(MeO)2 1 and ^(MeO)3 1 allow very high degrees of MA incorporation at low MA concentrations in the copolymerization; and 3) steric shielding leads to a pronounced increase in polymer molecular weight in the copolymerization. The catalyst properties induced by a given P‐aryl (alkyl) moiety were combined effectively in catalysts with two different non‐chelating aryl moieties, such as ^{c HexO/(MeO)2} 1 , which led to copolymers with significantly increased molecular weights compared to the prototypical ^MeO 1 .     

Role of Water in the Reaction Mechanism and endo/exo Selectivity of 1,3-Dipolar Cycloadditions Elucidated by Quantum Chemistry and Machine Learning

Asymmetric 1,3-dipolar cycloadditions of azomethine ylides with activated olefins are among the most important and versatile methods for the synthesis of enantioenriched pyrroline and pyrrolidine derivatives. Despite both theoretical and practical importance, the role of water molecules in the reactivity and endo/exo selectivity remains unclear. To explore how water accelerates the reactions and improves the endo/exo selectivity of the cycloadditions of 1,3-dipole phthalazinium-2-dicyanomethanide ( 1 ) and two dipolarophiles, an ab initio-quality neural network potential that overcomes the computational bottleneck of explicitly considering water molecules was used. It is demonstrated that not only the nature of both the dipolarophile and the 1,3-dipole, but also the solvent medium, can perturb or even alter the reaction mechanism. An extreme case was found for the reaction of 1,3-dipole 1 with methyl vinyl ketone, in which the reaction mechanism changes from a concerted to a stepwise mode on going from MeCN to H₂O as solvent, with formation of a zwitterionic intermediate that is a very shallow minimum on the energy surface. Thus, high stereocontrol can still be expected despite the stepwise nature of the mechanism. The results indicate that water can induce global polarization along the reaction coordinate and highlight the role of microsolvation effects and bulk-phase effects in reproducing the experimentally observed aqueous acceleration and enhanced endo/exo selectivity.     

Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism

The methylation of Hg^II(SCH₃)₂ by corrinoid‐based methyl donors proceeds in a concerted manner through a single transition state by transfer of a methyl radical, in contrast to previously proposed reaction mechanisms. This reaction mechanism is a consequence of relativistic effects that lower the energies of the mercury 6p_1/2 and 6p_3/2 orbitals, making them energetically accessible for chemical bonding. In the absence of spin–orbit coupling, the predicted reaction mechanism is qualitatively different. This is the first example of relativity being decisive for the nature of an observed enzymatic reaction mechanism.     

Nonenzymatic Simulation of Nitrogenase Reactions and the Mechanism of Biological Nitrogen Fixation

The development of biologically relevant model systems of nitrogenase permitted the simulation of virtually all known reactions of the nitrogen reducing enzymes under nonenzymatic conditions. On the basis of these experiments, a mechanism of biological nitrogen fixation is formulated which is in accord with the available enzymological evidence. The key reactions of the substrates of nitrogenase occur at a molybdenum active site. The non-heme iron, which is bound to sulfur and protein-S^? groups, mediates the transport of electrons to the molybdenum active site but does not participate directly in the reduction of the substrates. ATP is required for the acceleration of the reduction and activation of the molybdenum site and is hydrolyzed to ADP and inorganic phosphate. Diimine and hydrazine were detected as intermediates in the reduction of molecular nitrogen under nonenzymatic conditions.     

Synthesis,Coordination Chemistry and Bonding of Strong N‐Donor Ligands Incorporating the 1H‐Pyridin‐(2E)‐Ylidene (PYE) Motif

A range of N‐donor ligands based on the 1H‐pyridin‐(2E)‐ylidene (PYE) motif have been prepared, including achiral and chiral examples. The ligands incorporate one to three PYE groups that coordinate to a metal through the exocyclic nitrogen atom of each PYE moiety, and the resulting metal complexes have been characterised by methods including single‐crystal X‐ray diffraction and NMR spectroscopy to examine metal–ligand bonding and ligand dynamics. Upon coordination of a PYE ligand to a proton or metal‐complex fragment, the solid‐state structures, NMR spectroscopy and DFT studies indicate that charge redistribution occurs within the PYE heterocyclic ring to give a contribution from a pyridinium–amido‐type resonance structure. Additional IR spectroscopy and computational studies suggest that PYE ligands are strong donor ligands. NMR spectroscopy shows that for metal complexes there is restricted motion about the exocyclic C? N bond, which projects the heterocyclic N‐substituent in the vicinity of the metal atom causing restricted motion in chelating‐ligand derivatives. Solid‐state structures and DFT calculations also show significant steric congestion and secondary metal–ligand interactions between the metal and ligand C? H bonds.