Ab initio path‐integral calculations of kinetic and equilibrium isotope effects on base‐catalyzed RNA transphosphorylation models

Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self‐cleavage of RNA strands by 2′‐O‐transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2′‐O‐transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic‐structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a “gold‐standard” coupled‐cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path‐integral method, that is, automated integration‐free path‐integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis. © 2014 Wiley Periodicals, Inc.     

Switchover of the Mechanism between Electron Transfer and Hydrogen‐Atom Transfer for a Protonated Manganese(IV)–Oxo Complex by Changing Only the Reaction Temperature

Hydroxylation of mesitylene by a nonheme manganese(IV)–oxo complex, [(N4Py)Mn^IV(O)]²⁺ ( 1 ), proceeds via one‐step hydrogen‐atom transfer (HAT) with a large deuterium kinetic isotope effect (KIE) of 3.2(3) at 293 K. In contrast, the same reaction with a triflic acid‐bound manganese(IV)‐oxo complex, [(N4Py)Mn^IV(O)]²⁺‐(HOTf)₂ ( 2 ), proceeds via electron transfer (ET) with no KIE at 293 K. Interestingly, when the reaction temperature is lowered to less than 263 K in the reaction of 2 , however, the mechanism changes again from ET to HAT with a large KIE of 2.9(3). Such a switchover of the reaction mechanism from ET to HAT is shown to occur by changing only temperature in the boundary region between ET and HAT pathways when the driving force of ET from toluene derivatives to 2 is around ?0.5 eV. The present results provide a valuable and general guide to predict a switchover of the reaction mechanism from ET to the others, including HAT.     

Asymmetric Tandem 1,5‐Hydride Shift/Ring Closure for the Synthesis of Chiral Spirooxindole Tetrahydroquinolines

The direct functionalization of sp³ C?H bonds through a tandem 1,5‐hydride shift/ring closure is described. Various optically active spirooxindole tetrahydroquinoline derivatives bearing contiguous quaternary or tertiary stereogenic carbon centers were readily synthesized. A chiral scandium complex of N,N′‐dioxide promoted the reactions in good yields (up to 97 %) with excellent diastereoselectivities (>20:1) and enantioselectivities (up to 94 % ee). Kinetic isotope effect (KIE) experiments and internal redox reactions of chiral substrates were conducted, and the results provided intriguing information that helped clarify the mechanism of the reaction.     

Cationic Iridium/Chiral Bisphosphine‐Catalyzed Enantioselective Hydroacylation of Ketones

A facile and convenient synthesis of the chiral phthalide framework catalyzed by cationic iridium was developed. The method utilized cationic iridium/bisphosphine‐catalyzed asymmetric intramolecular carbonyl hydroacylation of 2‐keto benzaldehydes to furnish the corresponding optically active phthalide products in good to excellent enantioselectivities (up to 98% ee). The mechanistic studies using a deuterium‐labelled substrate suggested that the reaction involved an intramolecular carbonyl insertion mechanism to iridium hydride intermediate. In addition, we investigated the kinetic isotope effect (KIE) of intramolecular hydroacylation with deuterated substrate and determined that the C?H activation step is not included in the turnover‐limiting step.     

Tunneling Assists the 1,2‐Hydrogen Shift in N‐Heterocyclic Carbenes

At room temperature, 1,2‐hydrogen‐transfer reactions of N‐heterocyclic carbenes, like the imidazol‐2‐ylidene to give imidazole is shown to occurr almost entirely (>90 %) by quantum mechanical tunneling (QMT). At 60 K in an Ar matrix, for the 2, 3‐dihydrothiazol‐2‐ylidene→thiazole transformation, QMT is shown to increase the rate about 10⁵ times. Calculations including small‐curvature tunneling show that the barrier for intermolecular 1,2‐hydrogen‐transfer reaction is small, and QMT leads to a reduced rate of the forward reaction because of nonclassical reflections even at room temperature. A small barrier also leads to smaller kinetic isotope effects because of efficient QMT by both H and D. QMT does not always lead to faster reactions or larger KIE values, particularly when the barrier is small.     

Rh‐Catalyzed Direct Amination of Unactivated C(sp3)−H bond with Anthranils Under Mild Conditions

C?N Bond formation is of great significance due to the ubiquity of nitrogen‐containing compounds. Here, a mild and efficient Rh^III‐catalyzed C(sp³)?H aryl amination reaction is reported. Anthranil is employed as the nitrogen source with 100 % atom efficiency. This C?H amination reaction exhibits broad substrate scope without using any external oxidants. Mechanistic studies including rhodacycle intermediates, H–D exchange, kinetic isotope effect (KIE) experiments, and in situ IR are presented.     

Formation and High Reactivity of the anti‐Dioxo Form of High‐Spin μ‐Oxodioxodiiron(IV) as the Active Species That Cleaves Strong C−H Bonds

Recently, it was shown that μ‐oxo‐μ‐peroxodiiron(III) is converted to high‐spin μ‐oxodioxodiiron(IV) through O?O bond scission. Herein, the formation and high reactivity of the anti‐dioxo form of high‐spin μ‐oxodioxodiiron(IV) as the active oxidant are demonstrated on the basis of resonance Raman and electronic‐absorption spectral changes, detailed kinetic studies, DFT calculations, activation parameters, kinetic isotope effects (KIE), and catalytic oxidation of alkanes. Decay of μ‐oxodioxodiiron(IV) was greatly accelerated on addition of substrate. The reactivity order of substrates is toluene<ethylbenzene≈cumene<trans‐β‐methylstyrene. The rate constants increased proportionally to the substrate concentration at low substrate concentration. At high substrate concentration, however, the rate constants converge to the same value regardless of the kind of substrate. This is explained by a two‐step mechanism in which anti‐μ‐oxodioxodiiron(IV) is formed by syn‐to‐anti transformation of the syn‐dioxo form and reacts with substrates as the oxidant. The anti‐dioxo form is 620 times more reactive in the C?H bond cleavage of ethylbenzene than the most reactive diiron system reported so far. The KIE for the reaction with toluene/[D₈]toluene is 95 at ?30 °C, which the largest in diiron systems reported so far. The present diiron complex efficiently catalyzes the oxidation of various alkanes with H₂O₂.     

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.     

Solvent Choice and Kinetic Isotope Effects (KIEs) Dramatically Alter Regioselectivity in the Directed ortho Metalation (DoM) of 1,5‐Dichloro‐2,4‐dimethoxybenzene

The regioselective formation of the 6‐lithio derivative of 1,5‐dichloro‐2,4‐dimethoxybenzene (i.e., 12 ) by directed ortho metalation (DoM) with nBuLi in THF is described. Although literature reports suggest direct deprotonation at C6, a series of time‐course and labelling studies has revealed that deprotonation rather occurs exclusively at C3 followed by isomerization of the anion to C6. By contrast, when DoM was performed in Et₂O, deprotonation again occurred selectively at C3, but now no isomerization occurs, and electrophilic capture produces the regioisomer of that produced in THF. In these labeling studies, it has been found that deuterium has an enormous kinetic isotope effect (KIE) that suppresses not only the original DoM reaction at C3 when deuterium is present there, but also suppresses isomerization to C6 when the label is at that site. Remarkably, this “protecting‐group” role of the deuterium is unique to THF; in ether, full deprotonation of the deuterium at C3 was observed.     

Computational study and analysis of the kinetic isotope effects of the rearrangement of cis-bicyclo[4.2.0]oct-7-ene to cis,cis-cycloocta-1,3-diene

[reaction: see text] On the basis of KIE experiments, the ring opening of cis-bicyclo[4.2.0.]oct-7-ene has been suggested as an anti-Woodward-Hoffmann reaction candidate. We hereby report the results of a high-level computational study of the alternate reaction pathways which proves that the energy profiles show a clear preference for the conrotatory (W-H allowed) ring opening followed by double-bond isomerization. Computed KIE values for the aforementioned mechanism are in good agreement with the experimental values.     

Sulfinate‐Salt‐Mediated Radical Relay Cyclization of Cyclic Ethers with 2‐Alkynylbenzonitriles toward 3‐Alkylated 1‐Indenones

A new sulfinate salt‐mediated radical relay for the completion of C(sp³)?H bond indenylation of cyclic ethers with readily available 2‐alkynylbenzonitriles by combining silver/tert‐butyl peroxide (TBHP) was established, providing a wide range of 3‐alkylated 1‐indenones with generally good yields. Interestingly, the current reaction system can tolerate an S‐centered radical and a C‐centered radical in one pot, in which the S‐centered radical promotes the formation of the C‐centered radical to induce a radical cascade without disturbing the reaction process. A reaction mechanism is also proposed based on control experiments.     

Theoretical Treatment of a Cathodic Stripping Mechanism of an Insoluble Salt Coupled with a Chemical Reaction in Conditions of Square Wave Voltammetry. Application to 6‐Mercaptopurine‐9‐D‐Riboside in the Presence of Ni(II)

Cathodic stripping mechanism of an insoluble salt coupled with a homogenous chemical reaction is considered both theoretically and experimentally under conditions of square‐wave voltammetry. For the mercury electrode in aqueous solution, the electrode reaction is described as L(aq)+Hg(l)=HgL(s)+2e^?, where L(aq) is the reactive ligand that forms a sparingly soluble compound HgL(s). The electrode reaction is coupled with a homogenous, first‐order chemical reaction, A(aq)=L(aq). Theoretical predictions are confirmed by experiments with 6‐mercaptopurine‐9‐D‐riboside in the presence of nickel(II) ions.     

New Insight into the Hydrocarbon‐Pool Chemistry of the Methanol‐to‐Olefins Conversion over Zeolite H‐ZSM‐5 from GC‐MS,Solid‐State NMR Spectroscopy,and DFT Calculations

Over zeolite H‐ZSM‐5, the aromatics‐based hydrocarbon‐pool mechanism of methanol‐to‐olefins (MTO) reaction was studied by GC‐MS, solid‐state NMR spectroscopy, and theoretical calculations. Isotopic‐labeling experimental results demonstrated that polymethylbenzenes (MBs) are intimately correlated with the formation of olefin products in the initial stage. More importantly, three types of cyclopentenyl cations (1,3‐dimethylcyclopentenyl, 1,2,3‐trimethylcyclopentenyl, and 1,3,4‐trimethylcyclopentenyl cations) and a pentamethylbenzenium ion were for the first time identified by solid‐state NMR spectroscopy and DFT calculations under both co‐feeding ([¹³C₆]benzene and methanol) conditions and typical MTO working (feeding [¹³C]methanol alone) conditions. The comparable reactivity of the MBs (from xylene to tetramethylbenzene) and the carbocations (trimethylcyclopentenyl and pentamethylbenzium ions) in the MTO reaction was revealed by ¹³C‐labeling experiments, evidencing that they work together through a paring mechanism to produce propene. The paring route in a full aromatics‐based catalytic cycle was also supported by theoretical DFT calculations.     

Mechanism of the Reaction of Amines with 5‐[(Aryl‐ or Alkylamino)hydroxymethylene]‐2,2‐dimethyl‐1,3‐dioxane‐4,6‐diones in the Presence of Chlorotrimethylsilane (Me3SiCl)

Addition of chlorotrimethylsilane (Me₃SiCl) to the mixture of a carbamoyl‐substituted Meldrum's acid, i.e., a 5‐[(arylamino)hydroxymethylene]‐2,2‐dimethyl‐1,3‐dioxane‐4,6‐dione of type 1 and a secondary amine as nucleophile strongly accelerated the rate of their reaction. The reason for this phenomenon observed, during our previous research, remained, however, unclear. To elucidate the mechanism of this reaction, we assumed and verified three possible pathways for the action of Me₃SiCl (cf. Scheme 2): The acceleration of the reaction is caused i) by formation of a O‐trimethylsilylated Meldrum's acid of type 2 , ii) by the silylated amine 3 , or iii) by the presence of HCl liberated from Me₃SiCl. The performed experiments revealed that the faster course of reaction is caused by the formation of N‐trimethylsilylated amines of type 3 .     

Measuring the kinetic isotope effect at natural isotopic abundances for discriminating between the homogeneous and heterogeneous catalytic mechanisms in the Heck and Suzuki reactions

The kinetic isotope effect (KIE) at the natural abundances of bromine and carbon isotopes in the substrates of the Heck and Suzuki reactions have been investigated to determine the true nature of catalyst in these reactions. Data processing has demonstrated that statistically significant differences between KIE values for the Suzuki reaction of nonactivated bromobenzene are observed upon the replacement of the soluble catalyst precursor with the insoluble one. This finding unambiguously indicates that the reaction takes place on heterogeneous palladium species. Similar experiments on the Heck reaction have demonstrated that the KIE values are insensitive to the nature of the catalyst precursor, which is consistent with the true homogeneous mechanism of catalysis.     

Quantum chemistry studies of adenosine 2503 methylation by S‐adenosylmethionine‐dependent enzymes

Ribosome methylation is important for life processes and is mainly catalyzed by radical S‐Adenosylmethionine (SAM) enzymes. Two SAM molecules serve as the cofactor by providing the 5 ′‐deoxyadenosyl radical for substrate activation and the methyl. Recently, Booker and coworkers (Science 2011, 332, 604) proposed an alternative mechanism for a pair of radical SAM enzymes, RlmN and Cfr, which respectively methylate the C2 and C8 of adenosine 2503. Their deuterium labeling experiments reveal that methyl group does not transfer directly from SAM to adenosine, instead it passes to Cys³⁵⁵ first, then onto adenosine. In this article, this new reaction mechanism is studied using density functional theory with B3LYP hybrid functional. The reaction system is simulated using small model compounds in the gas phase, and the protein environment is approximated using polarizable continuum model. The structures of the transition states and the intermediates are identified, and their free energies are calculated. The activation barriers indicate that the proposed reaction mechanism is plausible. The formation of a disulfide bond is found to be the rate‐limiting step. © 2012 Wiley Periodicals, Inc.     

A photo‐oxidizable kinetic pathway of three‐component photoinitiator systems containing porphrin dye (Zn‐tpp), an electron donor and diphenyl iodonium salt

A series of kinetic experiments were conducted involving visible‐light activated free radical polymerizations with three‐component photoinitiators and 2‐hydroxyethyl methacrylate (HEMA). Three‐component photoinitiator systems generally include a light‐absorbing photosensitizer (PS), an electron donor and an electron acceptor. To compare kinetic efficiency, we used thermodynamic feasibility and measured kinetic data. For this study, 5,10,15,20‐tetraphenyl‐21H,23H‐porphyrin zinc (Zn‐tpp) and camphorquinone (CQ) were used as the PSs. The Rehm‐Weller equation was used to verify the thermodynamic feasibility for the photo‐induced electron transfer reaction. Using the thermodynamic feasibility, we suggest two different kinetic mechanisms, which are (i) photo‐reducible series mechanism of CQ and (ii) photo‐oxidizable series mechanism of Zn‐tpp. Kinetic data were measured by near‐IR spectroscopy and photo‐differential scanning calorimetry based on an equivalent concentration of excited state PS. We report that the photo‐oxidizable series mechanism using Zn‐tpp produced dramatically enhanced conversions and rates of polymerizations compared with those associated with the photo‐reducible series mechanism using CQ. It was concluded from the kinetic results that the photo‐oxidizable series mechanism efficiently retards back electron transfer and the recombination reaction step. In addition, the photo‐oxidizable series mechanism provides an efficient secondary reaction step that involves consumption of the dye‐based radical and regeneration of the original PS. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3131–3141, 2009     

One‐Pot Synthesis of 4‐(2,3‐Dihydro‐2‐hydroxy‐1,3‐dioxo‐1H‐inden‐2‐yl)‐Substituted 1‐Aryl‐1H‐pyrazole‐3‐carboxylates via a Tandem Three‐Component Reaction

The hitherto unreported, highly functionalized 1H‐pyrazole‐3‐carboxylates 3 have been synthesized in good yields via a one‐pot three‐component domino reaction of phenylhydrazines, dialkyl acetylenedicarboxylates, and ninhydrin under mild conditions for the first time. No co‐catalyst or activator is required for this multicomponent reaction, and the reaction is, from an experimental point of view, simple to perform (Scheme 1). The structures of compounds 3 were corroborated spectroscopically (IR, ¹H‐ and ¹³C‐NMR, and EI‐MS) and by elemental analyses. A plausible mechanism for this type of cyclization/addition reaction is proposed (Scheme 2).     

Light‐Driven Intramolecular C−N Cross‐Coupling via a Long‐Lived Photoactive Photoisomer Complex

Reported herein is a visible‐light‐driven intramolecular C?N cross‐coupling reaction under mild reaction conditions (metal‐ and photocatalyst‐free, at room temperature) via a long‐lived photoactive photoisomer complex. This strategy was used to rapidly prepare the N‐substituted polycyclic quinazolinone derivatives with a broad substrate scope (>50 examples) and further exploited to synthesize the natural products tryptanthrin, rutaecarpine, and their analogues. The success of gram‐scale synthesis and solar‐driven transformation, as well as promising tumor‐suppressing biological activity, proves the potential of this strategy for practical applications. Mechanistic investigations, including control experiments, DFT calculations, UV‐vis spectroscopy, EPR, and X‐ray single‐crystal structure of the key intermediate, provides insight into the mechanism.     

Gold‐Catalyzed Fluorination–Hydration: Synthesis of α‐Fluorobenzofuranones from 2‐Alkynylphenol Derivatives

The Au^I‐catalyzed fluorination–hydration of 2‐alkynylphenol derivatives in the presence of Selectfluor [1‐chloromethyl‐4‐fluoro‐1,4‐diazoniabicyclo‐[2.2.2]octane bis(tetrafluoroborate)] has been developed. This method provides straightforward access to α‐fluorobenzofuranones with the construction of C?O, C=O, and C?F bonds in a single step on the basis of an Au^I/Au^III redox catalytic cycle. Several control experiments, including the asymmetric variant of this reaction, were also conducted to gain insight into the reaction mechanism.