Structural Insights into the Very Low Activity of the Homocoenzyme B12 Adenosylmethylcobalamin in Coenzyme B12-Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase

The X-ray structures of coenzyme B₁₂ (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. As judged from geometries, the Co−C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate; in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The impacts of incorporating an extra CH₂ group are different in the two enzymes: the DD active site is flexible, and AdoMeCbl binding causes large conformational changes that make DD unable to adopt the catalytic state, whereas the EAL active site is rigid, and AdoMeCbl binding does not induce significant conformational changes. Such flexibility and rigidity of the active sites might reflect the tightness of adenine binding. The structures provide good insights into the basis of the very low activity of AdoMeCbl in these enzymes.     

Kinetic Isotope Effects in Asymmetric Reactions

Kinetic isotope effects are exquisitely sensitive probes of transition structure. As such, kinetic isotope effects offer a uniquely useful probe for the symmetry‐breaking process that is inherent to stereoselective reactions. In this Concept article, we explore the role of steric and electronic effects in stereocontrol, and we relate these concepts to recent studies carried out in our laboratory. We also explore the way in which kinetic isotope effects serve as useful points of contact with computational models of transition structures. Finally, we discuss future opportunities for kinetic isotope effects to play a role in asymmetric catalyst development.     

Probing Substrate Diffusion in Interstitial MOF Chemistry with Kinetic Isotope Effects

Metal–organic frameworks (MOFs) have garnered substantial interest as platforms for site‐isolated catalysis. Efficient diffusion of small‐molecule substrates to interstitial lattice‐confined catalyst sites is critical to leveraging unique opportunities of these materials as catalysts. Understanding the rates of substrate diffusion in MOFs is challenging, and few in situ chemical tools are available to evaluate substrate diffusion during interstitial MOF chemistry. Herein, we demonstrate nitrogen atom transfer (NAT) from a lattice‐confined Ru₂ nitride to toluene to generate benzylamine. We use the comparison of the intramolecular deuterium kinetic isotope effect (KIE), determined for amination of a partially deuterated substrate, with the intermolecular KIE, determined by competitive amination of a mixture of perdeuterated and undeuterated substrates, to establish the relative rates of substrate diffusion and interstitial chemistry. We anticipate that the developed KIE‐based experiments will contribute to the development of porous materials for group‐transfer catalysis.     

Large Isotope Effects in Organometallic Chemistry

The kinetic isotope effect (KIE) is key to understanding reaction mechanisms in many areas of chemistry and chemical biology, including organometallic chemistry. This ratio of rate constants, k_H/k_D, typically falls between 1–7. However, KIEs up to 105 have been reported, and can even be so large that reactivity with deuterium is unobserved. We collect here examples of large KIEs across organometallic chemistry, in catalytic and stoichiometric reactions, along with their mechanistic interpretations. Large KIEs occur in proton transfer reactions such as protonation of organometallic complexes and clusters, protonolysis of metal–carbon bonds, and dihydrogen reactivity. C−H activation reactions with large KIEs occur with late and early transition metals, photogenerated intermediates, and abstraction by metal-oxo complexes. We categorize the mechanistic interpretations of large KIEs into the following three types: (a) proton tunneling, (b) compound effects from multiple steps, and (c) semi-classical effects on a single step. This comprehensive collection of large KIEs in organometallics provides context for future mechanistic interpretation.     

Homocoenzyme B12 and Bishomocoenzyme B12: Covalent Structural Mimics for Homolyzed,Enzyme‐Bound Coenzyme B12

Efficient electrochemical syntheses of “homocoenzyme B₁₂” ( 2 , Co_β‐(5′‐deoxy‐5′‐adenosyl‐methyl)‐cob(III )alamin) and “bishomocoenzyme B₁₂” ( 3 , Co_β‐[2‐(5′‐deoxy‐5′‐adenosyl)‐ethyl]‐cob(III )alamin) are reported here. These syntheses have provided crystalline samples of 2 and 3 in 94 and 77 % yield, respectively. In addition, in‐depth investigations of the structures of 2 and 3 in solution were carried out and a high‐resolution crystal structure of 2 was obtained. The two homologues of coenzyme B₁₂ ( 2 and 3 ) are suggested to function as covalent structural mimics of the hypothetical enzyme‐bound “activated” (that is, “stretched” or even homolytically cleaved) states of the B₁₂ cofactor. From crude molecular models, the crucial distances from the corrin‐bound cobalt center to the C5′ atom of the (homo)adenosine moieties in 2 and 3 were estimated to be about 3.0 and 4.4 Å, respectively. These values are roughly the same as those found in the two “activated” forms of coenzyme B₁₂ in the crystal structure of glutamate mutase. Indeed, in the crystal structure of 2 , the cobalt center was observed to be at a distance of 2.99 Å from the C5′ atom of the homoadenosine moiety and the latter was found to be present in the unusual syn conformation. In solution, the organometallic moieties of 2 and 3 were shown to be rather flexible and to be considerably more dynamic than the equivalent group in coenzyme B₁₂. The homoadenosine moiety of 2 was indicated to occur in both the syn and the anti conformations.     

Stabilisation of Methylene Radicals by Cob(II)alamin in Coenzyme B12 Dependent Mutases

Coenzyme B₁₂ initiates radical chemistry in two types of enzymatic reactions, the irreversible eliminases (e.g., diol dehydratases) and the reversible mutases (e.g., methylmalonyl‐CoA mutase). Whereas eliminases that use radical generators other than coenzyme B₁₂ are known, no alternative coenzyme B₁₂ independent mutases have been detected for substrates in which a methyl group is reversibly converted to a methylene radical. We predict that such mutases do not exist. However, coenzyme B₁₂ independent pathways have been detected that circumvent the need for glutamate, β‐lysine or methylmalonyl‐CoA mutases by proceeding via different intermediates. In humans the methylcitrate cycle, which is ostensibly an alternative to the coenzyme B₁₂ dependent methylmalonyl‐CoA pathway for propionate oxidation, is not used because it would interfere with the Krebs cycle and thereby compromise the high‐energy requirement of the nervous system. In the diol dehydratases the 5′‐deoxyadenosyl radical generated by homolysis of the carbon–cobalt bond of coenzyme B₁₂ moves about 10 Å away from the cobalt atom in cob(II )alamin. The substrate and product radicals are generated at a similar distance from cob(II )alamin, which acts solely as spectator of the catalysis. In glutamate and methylmalonyl‐CoA mutases the 5′‐deoxyadenosyl radical remains within 3–4 Å of the cobalt atom, with the substrate and product radicals approximately 3 Å further away. It is suggested that cob(II )alamin acts as a conductor by stabilising both the 5′‐deoxyadenosyl radical and the product‐related methylene radicals.     

Unraveling the Mechanism and Regioselectivity of the B12‐Dependent Reductive Dehalogenase PceA

PceA is a cobalamin‐dependent reductive dehalogenase that catalyzes the dechlorination of perchloroethylene to trichloroethylene and then to cis‐dichloroethylene as the sole final product. The reaction mechanism and the regioselectivity of this enzyme are investigated by using density functional calculations. Four different substrates, namely, perchloroethylene, trichloroethylene, cis‐dichloroethylene, and chlorotheylene, have been considered and were found to follow the same reaction mechanism pattern. The reaction starts with the reduction of Co^II to Co^I through a proton‐coupled electron transfer process, with the proton delivered to a Tyr246 anion. This is followed by concerted C?Cl bond heterolytic cleavage and proton transfer from Tyr246 to the substrate carbon atom, generating a Co^III?Cl intermediate. Subsequently, a one‐electron transfer leads to the formation of the Co^II?Cl product, from which the chloride and the dehalogenated product can be released from the active site. The substrate reactivity follows the trend perchloroethylene>trichloroethylene?cis‐dichloroethylene?chlorotheylene. The barriers for the latter two substrates are significantly higher compared with those for perchloroethylene and trichloroethylene, implying that PceA does not catalyze their degradation. In addition, the formation of cis‐dichloroethylene has a lower barrier by 3.8 kcal mol^?1 than the formation of trans‐dichloroethylene and 1,1‐dichloroethylene, reproducing the regioselectivity. These results agree quite well with the experimental findings, which show cis‐dichloroethylene as the sole product in the PceA‐catalyzed dechlorination of perchloethylene and trichloroethylene.     

Stereoselective Total Synthesis of Iso‐Cladospolide B and the 12 Membered‐Macrolactone (6S,12R)‐6‐Hydroxy‐12‐methyloxacyclododecane‐2,5‐dione

Total syntheses of iso‐cladospolide B ( 1 ) and the 12‐membered macrolactone (6S,12R)‐6‐hydroxy‐12‐methyloxacyclododecane‐2,5‐dione ( 2 ), a non‐natural product, were achieved from a common intermediate starting from commercially available 1,9‐nonane diol.     

Ensemble‐Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution

The existence of solvent fluctuations leads to populations of reactant‐state (RS) and transition‐state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of values for individual configurations. Average kinetic isotope effects 〈KIE〉 for NC^?+EtCl→NCEt+Cl^? in DMSO solution at 30 °C are best obtained as the ratio 〈f_RS〉/〈f_TS〉 of isotopic partition function ratios separately averaged over all RS and TS configurations. In this way the hybrid AM1/OPLS‐AA potential yields 〈KIE〉 values for all six isotopic substitutions (2° α‐²H₂, 2° β‐²H₃, α‐¹¹C/¹⁴C, leaving group ³⁷Cl, and nucleophile ¹³C and ¹⁵N) for this reaction in the correct direction as measured experimentally. These thermally‐averaged calculated KIEs may be compared meaningfully with experiment, and only one of them differs in magnitude from the experimental value by more than one standard deviation from the mean. This success contrasts with previous KIE calculations based upon traditional methods without averaging. The isotopic partition function ratios are best evaluated using all (internal) vibrational and (external) librational frequencies obtained from Hessians determined for subsets of atoms, relaxed to local minima or saddle points, within frozen solvent environments of structures sampled along molecular dynamics trajectories for RS and TS. The current method may perfectly well be implemented with other QM or QM/MM methods, and thus provides a useful tool for investigating KIEs in relation to studies of chemical reaction mechanisms in solution or catalyzed by enzymes.     

Substrate‐Dependent H/D Kinetic Isotope Effects and the Role of the Di(μ‐oxo)diiron(IV) Core in Soluble Methane Monooxygenase: A Theoretical Study

Soluble methane monooxygenase (sMMO) is an enzyme that converts alkanes to alcohols using a di(μ‐oxo)diiron(IV) intermediate Q at the active site. Very large kinetic isotope effects (KIEs) indicative of significant tunneling are observed for the hydrogen transfer (H‐transfer) of CH₄ and CH₃CN; however, a relatively small KIE is observed for CH₃NO₂. The detailed mechanism of the enzymatic H‐transfer responsible for the diverse range of KIEs is not yet fully understood. In this study, variational transition‐state theory including the multidimensional tunneling approximation is used to calculate rate constants to predict KIEs based on the quantum‐mechanically generated intrinsic reaction coordinates of the H‐transfer by the di(μ‐oxo)diiron(IV) complex. The results of our study reveal that the role of the di(μ‐oxo)diiron(IV) core and the H‐transfer mechanism are dependent on the substrate. For CH₄, substrate binding induces an electron transfer from the oxygen to one Fe^IV center, which in turn makes the μ‐O ligand more electrophilic and assists the H‐transfer by abstracting an electron from the C?H σ orbital. For CH₃CN, the reduction of Fe^IV to Fe^III occurs gradually with substrate binding and H‐transfer. The charge density and electrophilicity of the μ‐O ligand hardly change upon substrate binding; however, for CH₃NO₂, there seems to be no electron movement from μ‐O to Fe^IV during the H‐transfer. Thus, the μ‐O ligand appears to abstract a proton without an electron from the C?H σ orbital. The calculated KIEs for CH₄, CH₃CN, and CH₃NO₂ are 24.4, 49.0, and 8.27, respectively, at 293 K, in remarkably good agreement with the experimental values. This study reveals that diverse KIE values originate mainly from tunneling to the same di(μ‐oxo)diiron(IV) core for all substrates, and demonstrate that the reaction dynamics are essential for reproducing experimental results and understanding the role of the diiron core for methane oxidation in sMMO.     

Experimental and Theoretical Study of an Intramolecular CF3‐Group Shift in the Reactions of α‐Bromoenones with 1,2‐Diamines

The reactions of trifluoromethylated 2‐bromoenones and N,N′‐dialkyl‐1,2‐diamines have been studied. Depending on the structures of the starting compounds, the formation of 2‐trifluoroacetylpiperazine or 3‐trifluoromethylpiperazine‐2‐ones was observed. The mechanism of the reaction is discussed in terms of multistep processes involving sequential substitution of bromine in the starting α‐bromoenones and intramolecular cyclization of the captodative aminoenones as key intermediates to form the target heterocycles. The results of theoretical calculations are in perfect agreement with the experimental data. The unique role of the trifluoromethyl group in this reaction is demonstrated.     

Biomimetic Model of Coenzyme B12: Aquabis(ethane‐1,2‐diamine‐κN,κN′)ethylcobalt(III) – Its Kinetic and Binding Studies with Imidazoles and Amino Acids and Interactions with CT DNA

Pseudo‐first‐order reaction kinetics and binding studies of trans‐[Co(en)₂(Et)H₂O] complex with 1H‐imidazole, substituted 1H‐imidazoles, histidine, histamine, glycine and glycine ethyl ester were investigated by means of spectrophotometric techniques. Equilibrium constants were determined as a function of pH at 25°. Binding and kinetic studies were correlated to basicity and steric hindrance. From the equilibrium data, it was found that the entering nucleophile is participating in the transition state, an I_d mechanism is proposed. The effect of the incoming ligands on the complex was studied by molecular mechanics. The interaction of trans‐[Co(en)₂(Et)H₂O] with CT DNA was studied spectrophotometrically.     

Electrochemical Determination of Vitamin B12 Based on Cu2+‐Involved Fenton‐like Reaction

Poly(thionine) (PTH) film was generated on the electrochemically activated glassy carbon electrode (GCE(ea)) by using the two‐step cyclic voltammetric scan. Scanning electron microscopy, infrared spectral analysis and electrochemical measurement were employed to characterize the modified electrode surface. Hydroxyl radicals, which were produced by the Fenton‐like reaction, could induce the effective oxidization of PTH under near‐neutral condition and cause the notable enhancement of the cathodic peak current (I_pc) during the potential cycling process. Due to the binding of copper ions with the ligands liberated from V_B12 and the inferior catalytic ability of Co²⁺ for the generation of hydroxyl radicals, the addition of V_B12 into the Cu²⁺?H₂O₂ system inhibited the oxidization of PTH and resulted in the decrease of the I_pc value. The cathodic peak current change was linear with the logarithm of the V_B12 concentration in the range of 10 nmol L^?1–100 μmol L^?1 with a detection limit of 2 nmol L^?1 under optimal conditions. The developed sensor displayed excellent analytical performance including high sensitivity, good selectivity, acceptable reproducibility and satisfactory stability. The V_B12 content in the injection sample was measured and the recovery values were in the range of 92.0 %–102 %.     

Kinetic isotope effects in the active site of B. subtilis chorismate mutase

Kinetic isotope effects are determined for the enzyme‐catalyzed Claisen rearrangement of chorismate to prephenate using computational methods. The calculated kinetic isotope effects (KIEs) compare reasonably with the few available experimental values with both the theory and experiment obtaining a large KIE for the ether oxygen, indicating large polarization of the transition‐state geometry. Because there is a question of the extent that the experimental rate constants are for chemistry as the rate‐limiting step, the KIEs for all the atoms of the substrate are reported with the exception of the carboxylate groups. A substantial number of large regular and inverse isotope effects are predicted for the hydrogens on the cyclohexadienyl ring related to activation of the reactant and charge reorganization in the transition state. A large KIE is predicted for the hydrogen atom bound to the ether carbon atom because the largest valency change and charge transfer occurs at the ether bond in both the reactant and tansition state. Observation of the overall pattern of predicted KIEs would ensure that conditions are favorable for the rate‐limiting chemistry. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 287–292, 2003