Carbon Monoxide Dehydrogenase Reduces Cyanate to Cyanide

The biocatalytic function of carbon monoxide dehydrogenase (CODH) has a high environmental relevance owing to its ability to reduce CO₂. Despite numerous studies on CODH over the past decades, its catalytic mechanism is not yet fully understood. In the present combined spectroscopic and theoretical study, we report first evidences for a cyanate (NCO⁻) to cyanide (CN⁻) reduction at the C-cluster. The adduct remains bound to the catalytic center to form the so-called CN⁻-inhibited state. Notably, this conversion does not occur in crystals of the Carboxydothermus hydrogenoformans CODH enzyme (CODHII_Ch), as indicated by the lack of the corresponding CN⁻ stretching mode. The transformation of NCO⁻, which also acts as an inhibitor of the two-electron-reduced C_red2 state of CODH, could thus mimic CO₂ turnover and open new perspectives for elucidation of the detailed catalytic mechanism of CODH.     

Computational and Experimental Study of Turbo-Organomagnesium Amide Reagents: Cubane Aggregates as Reactive Intermediates in Pummerer Coupling

The dynamic equilibria of organomagnesium reagents are known to be very complex, and the relative reactivity of their components is poorly understood. Herein, a combination of DFT calculations and kinetic experiments is employed to investigate the detailed reaction mechanism of the Pummerer coupling between sulfoxides and turbo-organomagnesium amides. Among the various aggregates studied, unprecedented heterometallic open cubane structures are demonstrated to yield favorable barriers through a concerted anion-anion coupling/ S−O cleavage step. Beyond a structural curiosity, these results introduce open cubane organometallics as key reactive intermediates in turbo-organomagnesium amide mixtures.     

Electronic Characterization of Reaction Intermediates: The Fluorenylium,Phenalenylium, and Benz[f]indenylium Cations and Their Radicals

Three vibrationally resolved absorption systems commencing at 538, 518, and 392 nm were detected in a 6 K neon matrix after mass‐selected deposition of C₁₃H₉⁺ ions (m/z=165) produced from fluorene in a hot‐cathode discharge ion source. The benz[f]indenylium (BfI⁺: 538 nm), fluorenylium (FL9⁺: 518 nm), and phenalenylium (PHL⁺: 392 nm) cations are the absorbing molecules. Two electronic systems corresponding to neutral species are apparent at 490 and 546 nm after irradiation of the matrix with λ<260 nm photons and were assigned to the FL9 and BfI radicals, respectively. The strongest peak at 518 nm is the origin of the 2 ¹B₂←X? ¹A₁ absorption of FL9⁺, and the 490 nm band is the 2 ²A₂←X? ²B₁ origin of FL9. The electronic systems commencing at 538 nm and 546 nm were assigned to the 1 ¹A₁←X? ¹A₁ and 1 ²A₂←X? ²A₂ transitions of BfI⁺ and BfI. The 392 nm band is the 1 ¹E′←X? ¹A₁′ transition of PHL⁺. The electronic spectra of C₁₃H₉⁺/C₁₃H₉ were assigned on the basis of the vertical excitation energies calculated with SAC‐CI and MS‐CASPT2 methods.     

Cationic Zinc Hydride Catalyzed Carbon Dioxide Reduction to Formate: Deciphering Elementary Reactions,Isolation of Intermediates,and Computational Investigations

Zinc has been an element of choice for carbon dioxide reduction in recent years. Zinc compounds have been showcased as catalysts for carbon dioxide hydrosilylation and hydroboration. The extent of carbon dioxide reduction can depend on various factors, including electrophilicity at the zinc center and the denticity of the ancillary ligands. In a few cases, the addition of Lewis acids to zinc hydride catalysts markedly influences carbon dioxide reduction. These factors have been investigated by exploring elementary reactions of carbon dioxide hydrosilylation and hydroboration by using cationic zinc hydrides bearing tetradentate tris[2-(dimethylamino)ethyl]amine and tridentate N,N,N′,N′′,N′′-pentamethyldiethylenetriamine in the presence of triphenylborane and tris(pentafluorophenyl)borane.     

Identification of Active Sites and Structural Characterization of Reactive Ionic Intermediates by Cryogenic Ion Trap Vibrational Spectroscopy

Cryogenic ion trap vibrational spectroscopy paired with quantum chemistry currently represents the most generally applicable approach for the structural investigation of gaseous cluster ions that are not amenable to direct absorption spectroscopy. Here, we give an overview of the most popular variants of infrared action spectroscopy and describe the advantages of using cryogenic ion traps in combination with messenger tagging and vibrational predissociation spectroscopy. We then highlight a few recent studies that apply this technique to identify highly reactive ionic intermediates and to characterize their reactive sites. We conclude by commenting on future challenges and potential developments in the field.     

Computational Study of Supramolecular Bis-porphyrin “Molecular Tweezers”

A computational study of a series of space separated bis-porphyrin “molecular tweezers” using semiempirical (AM1) and DFT (B3LYP and PBE1PBE) methods has been carried out. It was found that polynorbornane bis-porphyrin systems are significantly less rigid than previously thought. The variation of the metal–metal separation distance between the two porphyrin centers does not cause a significant energy change thus enabling these molecules to easily adjust to the optimal coordination distance required for complexation by various bidentate 4-pyridyl ligands inside the cavity of these “tweezers”. Article 54, ECCC-10, April 1-30 2005, http://www.eccc.monmouth.edu     

Computational and Variable‐Temperature Infrared Spectroscopic Studies on Carbon Monoxide Adsorption on Zeolite Ca‐A

Bridged Ca ²⁺ ???CO???Ca ²⁺ complexes are formed on dual‐cation sites, constituted by a pair of nearby Ca²⁺ cations, when CO is adsorbed on zeolite Ca‐A. Two types of such species can be formed, designated S2–S1 and S1–S1 (see picture). Ca²⁺???CO monocarbonyl species are also identified, and at a relatively high CO equilibrium pressure, dicarbonyl complexes can also form.

     

Electrocatalytic and Biosensing Properties of Aerobic Carbon Monoxide Dehydrogenase from Hydrogenophaga Pseudoflava Immobilized on Au Electrode towards Carbon Monoxide Oxidation

Herein, an enzyme‐electrode based on the oxygen‐insensitive carbon monoxide dehydrogenase (CODH) containing molybdenum (Mo) and copper (Cu), flavin adenine dinucleotide (FAD) and two different [2Fe‐2 S] clusters as cofactors from the aerobic bacterium Hydrogenophaga pseudoflava, is proposed as a platform for dissolved CO concentration monitoring. The immobilized CODHs on Au electrode retain their catalytic activity and demonstrates changes to cyclic voltammetry and amperometry signals upon interactions with various dissolved CO concentrations. Cyclic voltammetry shows that CODHs are capable of direct electron transfer without any mediator use as oxidative current which starts around ?0.268 V (vs Ag/AgCl) is observed in the presence of CO. When CO‐saturated standard solution was spiked sequentially into the gas‐tight reactor, amperometry analysis shows current increased accordingly with response time within 5 s. Our study demonstrates that this enzyme‐electrode is promising to serve as platform for developing an on‐line dissolved CO concentration monitoring tool which is essential to fill in the gap for conventional technologies which are limited to off‐line measurement.     

Trapping Reactive Intermediates by Mechanochemistry: Elusive Aryl N‐Thiocarbamoylbenzotriazoles as Bench‐Stable Reagents

Monitoring of mechanochemical thiocarbamoylation by in situ Raman spectroscopy revealed the formation of aryl N‐thiocarbamoylbenzotriazoles, reactive intermediates deemed unisolable in solution. The first‐time isolation and structural characterization of these elusive molecules demonstrates the ability of mechanochemistry to access otherwise unobtainable intermediates and offers a new range of masked isothiocyanate reagents.     

Rearrangement Reactions of Tritylcarbenes: Surprising Ring Expansion and Computational Investigation

As a rule, acetylides and sulfonyl azides do not undergo electrophilic azide transfer because 1,2,3‐triazoles are usually formed. We show now that treatment of tritylethyne with butyllithium followed by exposure to 2,4,6‐triisopropylbenzenesulfonyl azide leads to products that are easily explained through the generation of short‐lived tritylethynyl azide and its secondary product cyanotritylcarbene. Furthermore, it is demonstrated that tritylcarbenes generally do not produce triphenylethenes exclusively, as was stated in the literature. Instead, these carbenes always yielded also (diphenylmethylidene)cycloheptatrienes (heptafulvenes) as side products. This result is supported by static DFT, coupled cluster, and ab initio molecular dynamics calculations. From these investigations, the fused bicyclobutane intermediate was found to be essential for heptafulvene formation. Although the bicyclobutane is also capable of rearranging to the triphenylethene product, only the heptafulvene pathway is reasonable from the energetics. The ethene is formed straight from cyanotritylcarbene.     

Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase

D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.     

Structures of the Reactive Intermediates in Organocatalysis with Diarylprolinol Ethers

Structures of the reactive intermediates (enamines and iminium ions) of organocatalysis with diarylprolinol derivatives have been determined. To this end, diarylprolinol methyl and silyl ethers, 1 , and aldehydes, Ph? CH₂? CHO, ^tBu? CH₂? CHO, Ph? CH=CH? CHO, are condensed to the corresponding enamines, A and 3 (Scheme 2), and cinnamoylidene iminium salts, B and 4 (Scheme 3). These are isolated and fully characterized by melting/decomposition points, [α]_D, elemental analysis, IR and NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). Salts with BF₄, PF₆, SbF₆, and the weakly coordinating Al[OC(CF₃)₃]₄ anion were prepared. X‐Ray crystal structures of an enamine and of six iminium salts have been obtained and are described herein (Figs. 2 and 4–8, and Tables 2 and 7) and in a previous preliminary communication (Helv. Chim. Acta 2008 , 91, 1999). According to the NMR spectra (in CDCl₃, (D₆)DMSO, (D₆)acetone, or CD₃OD; Table 1), the major isomers 4 of the iminium salts have (E)‐configuration of the exocyclic N?C(1′) bond, but there are up to 11% of the (Z)‐isomer present in these solutions (Fig. 1). In all crystal structures, the iminium ions have (E)‐configuration, and the conformation around the exocyclic N‐C? C‐O bond is synclinal‐exo (cf. C and L ), with one of the phenyl groups over the pyrrolidine ring, and the RO group over the π‐system. One of the meta‐substituents (Me in 4b , CF₃ in 4c and 4e ) on a 3,5‐disubstituted phenyl group is also located in the space above the π‐system. DFT Calculations at various levels of theory (Tables 3–6) confirm that the experimentally determined structures (cf. Fig. 10) are by far (up to 8.3 kcal/mol) the most stable ones. Implications of the results with respect to the mechanism of organocatalysis by diarylprolinol derivatives are discussed.     

Synthesis and quadratic molecular hyperpolarizabilities of two new chiral boronates: Computational and experimental study

A monomeric boronate and an oxobridged chiral dimer were obtained by reaction of the ligand derived from 4-diethylaminosalicylaldehyde with (R)-(−)-phenylglycinol, and phenyl boronic acid or boric acid. The compounds were fully characterized by spectroscopic techniques (¹H, ¹³C, ¹¹B NMR, elemental analyses, IR and masses spectrometry); and their molecular hyperpolarizabilities were investigated by the electric field induced second harmonic (EFISH) technique and semi-empirical calculations. The experimental quadratic hyperpolarizability which is equal to 9.8 × 10⁻³⁰ cm⁵ esu⁻¹ at 1.064 μm for the monomeric derivative rises to 19.5 × 10⁻³⁰ cm⁵ esu⁻¹ in the dimeric specie.     

Relative Thermodynamic Stabilities of Isomeric Dimethyl Acetals Derived from 2-Acetyltetrahydrofuran. An Experimental and Computational Study

In the presence of an acid catalyst, the dimethyl acetal of 2-acetyltetrahydrofuran (1) is converted into a mixture of three isomeric acetals composed of the reactant and two diastereomers of 2-methoxy-2-(1-methoxyethyl)tetrahydrofuran (2). The relative thermodynamic stabilities of these acetals have now been determined by chemical equilibration. The least stable isomer is 1, in the liquid phase 4–6 kJ mol^–1 less stable than the two diastereomers. The geometry-optimized structures and relative energies of the title compounds were also studied by theoretical calculations (ab initio and DFT). Comparison of the theoretically determined relative stabilities of the diastereomers with the corresponding experimental data suggests the more volatile (and more stable) diastereomer to exist as a racemic mixture of the (R,S) and (S,R) configurations.     

Characterization of Paramagnetic Reactive Intermediates: Predicting the NMR Spectra of Iron(IV)–Oxo Complexes by DFT

The relative energies of spin states of several iron(IV)–oxo complexes and related species have been calculated with DFT methods by employing the B3LYP* functional. We show that such calculations can predict the correct ground spin state of Fe^IV complexes and can then be used to determine the ¹H NMR spectra of all spin states; the spectral features are remarkably different, hence calculated paramagnetic ¹H NMR spectra can be used to support the structure elucidation of numerous paramagnetic complexes. Applications to a number of stable and reactive iron(IV)–oxo species are described.     

Single‐Site Zeolite‐Anchored Organoiridium Carbonyl Complexes: Characterization of Structure and Reactivity by Spectroscopy and Computational Chemistry

A family of HY zeolite‐supported cationic organoiridium carbonyl complexes was formed by reaction of Ir(CO)₂(acac) (acac=acetylacetonate) to form supported Ir(CO)₂ complexes, which were treated at 298 K and 1 atm with flowing gas‐phase reactants, including C₂H₄, H₂, ¹²CO, ¹³CO, and D₂O. Mass spectrometry was used to identify effluent gases, and infrared and X‐ray absorption spectroscopies were used to characterize the supported species, with the results bolstered by DFT calculations. Because the support is crystalline and presents a nearly uniform array of bonding sites for the iridium species, these were characterized by a high degree of uniformity, which allowed a precise determination of the species involved in the replacement, for example, of one CO ligand of each Ir(CO)₂ complex with ethylene. The supported species include the following: Ir(CO)₂, Ir(CO)(C₂H₄)₂, Ir(CO)(C₂H₄), Ir(CO)(C₂H₅), and (tentatively) Ir(CO)(H). The data determine a reaction network involving all of these species.     

Rearrangement of azirine intermediates to nitriles: Theoretical study of cleavage of 3,4-dihydro-1aH-azirine[2,3-c]pyrrol-2-one to cyanoketene–formaldimine complex

A detailed investigation of the reaction path for the thermal rearrangement of 3,4-dihydro-1aH-azirine[2,3-c]pyrrol-2-one to yield a cyanoketene–formaldimine complex is carried out at the MP2/6-31G* and B3LYP/6-31G* levels of theory. The ring opening of the five-membered pyrrolinone ring and the formation of the nitrile group takes place in a concerted manner, presenting a significant strain energy release and allowing for an electronic stabilization by coarctate conjugation of the transition structure (TS). These two factors make possible a moderate energy barrier. Although the structural features B3LYP/6-31G* theoretical levels, it is found that the MP2 energy barrier (28.8) CCSD(T)/6-31G*//MP2/6-31G* value (17.1 kcal/mol). The complex electronic rearrangement can be rationalized using the theory of coarctate transition structures developed by Herges as the evolution of an azirine structure without referring to a hypothetical vinyl nitrene intermediate. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 912–922, 1998