Electrophilic Assistance Research Articles

Detailing the elementary stages in the oxirane ring opening reactions with carboxylic acids catalyzed by tertiary amines

AbstractThe study of the reaction systems “R3N – proton‐donor reagent (NuH) – epichlorohydrin” using a complex of various kinetic methods of investigation allowed the reaction pathway and the catalysis mechanism of the oxirane ring opening by proton‐donor reagents in the presence of R3N to be detailed. It was confirmed that the catalytic activity of R3N consists in their quaternization by oxirane under the obligatory condition of its electrophilic assistance with the NuH reagent. The quaternization process of tertiary amines was studied using 1H NMR and UV spectroscopy, quantum chemical modeling, and correlation analysis. It was shown that the transition states of the quaternization stage are dissociative, and their degree of looseness depends on the electrophilic activation of the oxirane ring.

Computational simulation of mechanism and isotope effects on acetal heterolysis as a model for glycoside hydrolysis

Abstract DFT calculations for the equilibrium isotope effect for deuterium substitution at the anomeric centre Cα in 2-(p-nitrophenoxy)tetrahydropyran with continuum solvation show significant variation in the range of relative permittivity 2 ≤ ε ≤ 10. One-dimensional scans of potential energy (with implicit solvation by water) or of free energy (from QM/MM potentials of mean force with explicit aqueous solvation with a hybrid AM1/OPLS method) for heterolysis of the bond between Cα and the nucleofuge do not show a transition state. A two-dimensional free-energy surface that considers also the distance between Cα and a nucleophilic water indicates a pre-association DN*ANint ‡ mechanism with a transition state involving nucleophilic attack upon an ion-pair intermediate, and this is supported by good agreement between the mean values of the calculated and experimental α-D KIEs. However, the magnitudes of the standard deviations about the mean values for the making and breaking C–O bonds suggest that the transition state is rather plastic, with Cα–Onu≈2 ± 0.4 Å and Cα–Olg≈3 ± 0.5 Å. Not only is nucleophilic solvent assistance necessary, but there is also evidence for electrophilic assistance through specific hydrogen bonding to the nucleofuge.

Electrophilic Assistance to the Cleavage of an RNA Model Phopshodiester via Specific and General Base-Catalyzed Mechanisms

Kinetics of transesterification of the RNA model substrate 2-hydroxypropyl 4-nitrophenyl phosphate promoted by Mg(2+) and Ca(2+), the most common biological metals acting as cofactors for nuclease enzymes and ribozymes, as well as by Co(NH(3))(6)(3+), Co(en)(3)(3+), Li(+), and Na(+) cations, often employed as mechanistic probes, was studied in 80% v/v (50 mol %) aqueous DMSO, a medium that allows one to discriminate easily specific base (OH(-)-catalyzed) and general base (buffer-catalyzed) reaction paths. All cations assist the specific base reaction, but only Mg(2+) and Na(+) assist the general base reaction. For Mg(2+)-assisted reactions, the solvent deuterium isotope effects are 1.23 and 0.25 for general base and specific base mechanisms, respectively. Rate constants for Mg(2+)-assisted general base reactions measured with different bases fit the Brønsted correlation with a slope of 0.38, significantly lower than the slope for the unassisted general base reaction (0.77). Transition state binding constants for catalysts in the specific base reaction (K(‡)(OH)) both in aqueous DMSO and pure water correlate with their binding constants to 4-nitrophenyl phosphate dianion (K(NPP)) used as a minimalist transition state model. It was found that K(‡)(OH) ≈ K(NPP) for "protic" catalysts (Co(NH(3))(6)(3+), Co(en)(3)(3+), guanidinium), but K(‡)(OH) ≫ K(NPP) for Mg(2+) and Ca(2+) acting as Lewis acids. It appears from results of this study that Mg(2+) is unique in its ability to assist efficiently the general base-catalyzed transesterification often occurring in active sites of nuclease enzymes and ribozymes.

Unraveling Gold(I)‐Specific Action Towards Peptidic Disulfide Cleavage: A DFT Investigation

Ground-state disulfide dissociation is a target of prime importance in structural biochemistry. A main difficulty consists in avoiding competition with carbon–sulfur and backbone scission pathways. In tandem mass spectrometry, such selectivity is afforded using transition elements or coinage-metal ions as catalyst. Yet, the underlying gas-phase mechanistic details remain poorly understood. Gold(I)-assisted disulfide cleavage is investigated by means of DFT calculations, to elucidate the highly selective and specific catalytic action of this transition-metal cation, a most promising one in tandem mass spectrometry. The preferential cleavage of sulfur–sulfur versus carbon–sulfur linkages on dimethyldisulfide, taken as a prototypical aliphatic compound, is rationalized on the basis of molecular orbital arguments. Secondly, it is revealed that the disulfide dissociation profile is dramatically impacted by a peptidic environment. Calculations on L,L-cystine derivatives show two main factors: the topological frustration for an embedded -CH(2)-S-S-CH(2)- motif induces a 5 kcal mol(-1) penalty, whereas electrophilic assistance via complexation of nitrogen and oxygen atoms lowers activation barriers by a factor of 3. S-S weakening is both thermodynamically and kinetically driven by the versatile coordination mode of gold(I). The influence of amine-terminus group protonation is finally sketched: it gives rise to an intermediate reactivity. This study sheds lights on the key action of the peptidic environment in tuning the dissociation profile in the presence of this transition-metal monocation.

ChemInform Abstract: Substitution of the Acetoxy Groups of Dialkoxymethylacetates by Organometallic Reagents: A Route to Allyl-, Propargyl-, Homoallyl-, Homopropargyl- and α-Stannylacetals.

Abstract The substitution of the acetoxy groups of dialkoxymethylacetates by organometallic reagents has been examined in a search for new methods of preparing functional acetals. The efficiency of the substitution of the acetoxy group is highly dependent on the nature of the organometallic reagents: soft nucleophiles with strong electrophilic assistance by the counterion are the best reagents. Allyl-, propargyl-, homoallyl-, homopropargyl- and α-stannylacetals have been made by this route, in which dialkoxymethylacetates often function as useful substitutes for dialkylphenylorthoformates.

ChemInform Abstract: Ring Opening Reactions of 2-Trialkylsilylaziridines.

2-Trialkylsilylaziridines do not readily undergo nucleophilic ring opening without electrophilic assistance. In the presence of strong acids protonation at the nitrogen is followed by nucleophilic attack α to the silicon. With non-nucleophilic counterions, the protonated aziridine can be obtained. N-Alkylation gives the aziridinium salt, which also undergoes α-cleavage. However, the presence of a 3-phenyl substituent gives a stable aziridinium salt that undergoes nucleophilic attack β to the silicon. Reaction of 2-trialkylsilylaziridines with trialkylsilyl halides usually leads to α-cleavage, however, desilylation to give the enamine is also observed. Fluorodesilylation of the 2-trialkylsilylaziridine is not straightforward and only occurred readily when a 2-ethoxycarbonyl group was present. Fluorodesilylation followed by attack on a carbonyl was only observed when very dry samples of fluoride ions were employed.

Dinuclear Zn(II) catalysts as biomimics of RNA and DNA phosphoryl transfer enzymes: changing the medium from water to alcohol provides enzyme‐like rate enhancements

AbstractPhosphodiesters are notoriously hydrolytically inert compounds that are demonstrated to have large accelerations of P‐OR cleavage promoted by transition and lanthanide metal ions in methanol and ethanol media. This review commentary describes recent findings of how a simple mononuclear and a dinuclear Zn(II) complex promote the cleavage of a series of RNA models and DNA models in alcohol media. The discussion centers on the analysis of the mechanisms of cleavage, energetics of the catalytic process, on recent findings of electrophilic assistance of leaving group departure, and the observation of a rapid hydrolytic reaction of a DNA model promoted by the dinuclear Zn(II) complex in ethanol containing less than 2% water. Copyright © 2009 John Wiley & Sons, Ltd.

The Molecular Structure of Epoxide Hydrolase B from Mycobacterium tuberculosis and Its Complex with a Urea-Based Inhibitor

Mycobacterium tuberculosis ( Mtb), the intracellular pathogen that infects macrophages primarily, is the causative agent of the infectious disease tuberculosis in humans. The Mtb genome encodes at least six epoxide hydrolases (EHs A to F). EHs convert epoxides to trans-dihydrodiols and have roles in drug metabolism as well as in the processing of signaling molecules. Herein, we report the crystal structures of unbound Mtb EHB and Mtb EHB bound to a potent, low-nanomolar (IC 50 ≈ 19 nM) urea-based inhibitor at 2.1 and 2.4 Å resolution, respectively. The enzyme is a homodimer; each monomer adopts the classical α/β hydrolase fold that composes the catalytic domain; there is a cap domain that regulates access to the active site. The catalytic triad, comprising Asp104, His333 and Asp302, protrudes from the catalytic domain into the substrate binding cavity between the two domains. The urea portion of the inhibitor is bound in the catalytic cavity, mimicking, in part, the substrate binding; the two urea nitrogen atoms donate hydrogen bonds to the nucleophilic carboxylate of Asp104, and the carbonyl oxygen of the urea moiety receives hydrogen bonds from the phenolic oxygen atoms of Tyr164 and Tyr272. The phenolic oxygen groups of these two residues provide electrophilic assistance during the epoxide hydrolytic cleavage. Upon inhibitor binding, the binding-site residues undergo subtle structural rearrangement. In particular, the side chain of Ile137 exhibits a rotation of around 120° about its C α–C β bond in order to accommodate the inhibitor. These findings have not only shed light on the enzyme mechanism but also have opened a path for the development of potent inhibitors with good pharmacokinetic profiles against all Mtb EHs of the α/β type.

Role of invariant tyrosines in a crustacean mu-class glutathione S-transferase from shrimp Litopenaeus vannamei: Site-directed mutagenesis of Y7 and Y116

Y6 and Y115 are key amino acids involved in enzyme–substrate interactions in mu-class glutathione S-transferase (GST). They provide electrophilic assistance and stabilize substrates through their hydroxyl groups. Two site-directed mutants (Y7F and Y116F) and the wild-type shrimp GSTs were expressed in Escherichia coli, and the steady-state kinetic parameters were determined using CDNB as the second substrate. The mutants were modeled based on a crystal structure of a mu-class GST to obtain further insights about the changes at the active site. The Y116F mutant had an increase in k cat contrary to Y7F compared to the wild type. Molecular modeling showed that the shrimp GST has a H108 residue that may contribute to compensate and lead to a less deleterious change when conserved tyrosine residues are mutated. This work indicates that shrimp GST is a useful model to understand the catalysis mechanisms in this critical enzyme.

Steric effects on the mechanism of reaction of nucleophilic substitution of β‐substituted alkoxyvinyl trifluoromethyl ketones with four secondary amines

AbstractThe kinetics of the reaction of β‐substituted β‐alkoxyvinyl trifluoromethyl ketones R1O‐CR2CH‐COCF3 (1a–e) [(1a), R1C2H5, R2H; (1b), R1R2CH3; (1c), R1C2H5, R2C6H5; (1d), R1C2H5, R2V−pNO2C6H4; (1e), R1C2H5, R2C(CH3)3] with four aliphatic amines (2a–d) [(2a), (C2H5)2NH; (2b), (i‐C3H7)2NH; (2c), (CH2)5NH; (2d), O(CH2CH2)2NH] was studied in two aprotic solvents, hexane and acetonitrile. The least reactive stereoisomeric form of (1a–d) was the most populated (E‐s‐Z‐o‐Z) form, whereas in (1e), the more reactive form (Z‐s‐Z‐o‐Z) dominated. The reactions studied proceeded via common transition state formation whose decomposition occurred by ‘uncatalyzed’ and/or ‘catalyzed’ route. Shielding of the reaction centre by bulky β‐substituents lowered abruptly both k′ (‘uncatalyzed’ rate constant) and k″ (‘catalyzed’ rate constant) of this reaction. Bulky amines reduced k″ to a greater extent than k′ as a result of an additional steric retardation to the approach of the bulky amine to its ammonium ion in the transition state. An increase in the electron‐withdrawing ability of the β‐substituent increased ‘uncatalyzed’ k′ due to the acceleration of the initial nucleophile attack (k1) and ‘uncatalyzed’ decomposition of transition state (k2) via promoting electrophilic assistance (through transition state 8). The amine basicity determined the route of the reaction: the higher amine basicity, the higher k3/k2 ratio (a measure of the ‘catalyzed’ route contribution as compared to the ‘uncatalyzed’ process) was. ‘Uncatalyzed’ route predominated for all reactions; however in polar acetonitrile the contribution of the ‘catalyzed’ route was significant for amines with high pKa and small bulk. Copyright © 2007 John Wiley & Sons, Ltd.

Competing kinetic pathways in the bromine addition to allylic ethers in 1,2‐dichloroethane: Opposite temperature effects

AbstractThe kinetics of the electrophilic bromination of three allylic ethers in a nonprotic solvent, 1,2‐dichloroethane, has been investigated. Two of them followed a prevalent second‐order pathway, while the third one exhibited a classical, clean third order. The second‐order pathway in the first two olefins is attributed to electrophilic assistance of the ethereal oxygen to the attacking bromine molecule. In the molecular bromination of 2,4‐cis‐dimethyl‐8‐oxabicyclo[3.2.1]‐6‐octen‐3‐cis‐ol, opposite temperature dependences were found for the two different kinetic pathways. An exoergonic process for the second‐order reaction was explained by the lesser stability of the bromiranium–bromide ionic intermediate, compared to the bromiranium–tribromide in the third‐order profile. © 2007 Wiley Periodicals, Inc. 39: 197–203, 2007

Preparation of 10‐Trifluoromethyl Artemether and Artesunate. Influence of Hexafluoropropan‐2‐ol on Substitution Reaction.

AbstractFor Abstract see ChemInform Abstract in Full Text.

The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum.

The molecular structure of the pepstatin-insensitive carboxyl peptidase from Scytalidium lignicolum, formerly known as scytalidopepsin B, was solved by multiple isomorphous replacement phasing methods and refined to an R factor of 0.230 (R(free) = 0.246) at 2.1-A resolution. In addition to the structure of the unbound peptidase, the structure of a product complex of cleaved angiotensin II bound in the active site of the enzyme was also determined. We propose the name scytalidocarboxyl peptidase B (SCP-B) for this enzyme. On the basis of conserved, catalytic residues identified at the active site, we suggest the name Eqolisin for the enzyme family. The previously uninvestigated SCP-B fold is that of a beta-sandwich; each sheet has seven antiparallel strands. A tripeptide product, Ala-Ile-His, bound in the active site of SCP-B has allowed for identification of the catalytic residues and the residues in subsites S1, S2, and S3, which are important for substrate binding. The most likely hydrolytic mechanism involves nucleophilic attack of a general base (Glu-136)-activated water (OH(-)) on the si-face of the scissile peptide carbonylcarbon atom to form a tetrahedral intermediate. Electrophilic assistance and oxyanion stabilization is provided by the side-chain amide of Gln-53. Protonation of the leaving-group nitrogen is accomplished by the general acid function of the protonated carboxyl group of Glu-136.

Preparation of 10-Trifluoromethyl Artemether and Artesunate. Influence of Hexafluoropropan-2-ol on Substitution Reaction

To prepare 10-trifluoromethyl analogues of important antimalarials such as artemether and artesunate, the substitution reaction of the 10-trifluoromethyl hemiketal 6 and bromide 4 derived from artemisinin was investigated. While 6 appeared to be unreactive under various conditions, bromide 4 could easily undergo substitution with methanol under electrophilic assistance or noncatalyzed conditions. Optimization of the reaction revealed the role of CH(2)Cl(2) as solvent to avoid the competitive elimination process and the crucial influence of hexafluoro-2-propanol (HFIP) in increasing the rate and the stereoselectivity of the substitution reaction (de >98%). The efficiency of this reaction was exemplified with various alcohols and carboxylates (yield up to 89%).

The Crystal Structure of 1-D-myo-Inosityl 2-Acetamido-2-deoxy-α-D-glucopyranoside Deacetylase (MshB) from Mycobacterium tuberculosis Reveals a Zinc Hydrolase with a Lactate Dehydrogenase Fold

Mycothiol (1-D-myo-inosityl 2-(N-acetyl-L-cysteinyl)amido-2-deoxy-alpha-D-glucopyranoside, MSH or AcCys-GlcN-inositol (Ins)) is the major reducing agent in actinomycetes, including Mycobacterium tuberculosis. The biosynthesis of MSH involves a deacetylase that removes the acetyl group from the precursor GlcNAc-Ins to yield GlcN-Ins. The deacetylase (MshB) corresponds to Rv1170 of M. tuberculosis with a molecular mass of 33,400 Da. MshB is a Zn2+ metalloprotein, and the deacetylase activity is completely dependent on the presence of a divalent metal cation. We have determined the x-ray crystallographic structure of MshB, which reveals a protein that folds in a manner resembling lactate dehydrogenase in the N-terminal domain and a C-terminal domain consisting of two beta-sheets and two alpha-helices. The zinc binding site is in the N-terminal domain occupying a position equivalent to that of the NAD+ co-factor of lactate dehydrogenase. The Zn2+ is 5 coordinate with 3 residues from MshB (His-13, Asp-16, His-147) and two water molecules. One water would be displaced upon binding of substrate (GlcNAc-Ins); the other is proposed as the nucleophilic water assisted by the general base carboxylate of Asp-15. In addition to the Zn2+ providing electrophilic assistance in the hydrolysis, His-144 imidazole could form a hydrogen bond to the oxyanion of the tetrahedral intermediate. The extensive sequence identity of MshB, the deacetylase, with mycothiol S-conjugate amidase, an amide hydrolase that mediates detoxification of mycothiol S-conjugate xenobiotics, has allowed us to construct a faithful model of the catalytic domain of mycothiol S-conjugate amidase based on the structure of MshB.

The synergistic effect of dicyandiamide and resorcinol in the curing of epoxy resins

AbstractThe synergistic effect of dicyandiamide (Dicy) and phenolic substances was studied, with resorcinol as a model compound. It was found that when Dicy and resorcinol are used jointly, the curing temperature of epoxy resin can be significantly lowered. FTIR and DSC data were used to illustrate the mechanism of the synergism. The addition of the phenolic hydroxyl group to epoxide was facilitated by Dicy, which favors the formation of phenoxy anions. The reaction of Dicy with epoxide was facilitated by resorcinol, which can exert “electrophilic assistance” for the addition of the amino group to epoxide. The presence of resorcinol also favors the addition of the hydroxyl group to the cyano group. The thermal and mechanical properties of the epoxy resins cured with Dicy/resorcinol or Dicy/phloroglucinol were studied. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 1869–1874, 2003

Formation and Decomposition of the Methylplatinum(IV) Complex in the Mechanically Activated K2PtCl4 Powder–MeI Vapor System

Mechanical treatment of the K2PtCl4 solid salt in a vibrating mill results in Pt–Cl bond heterolysis to form coordinatively unsaturated Pt(II) complexes. At room temperature, the freshly treated K2PtCl4 salt absorbs methyl bromide and evolves methyl chloride to the gas phase. The reaction mechanism involves the following sequence of steps: the oxidative addition of methyl iodide to Pt(II) with the intermediate formation of Pt(IV) methyl complexes and the decomposition of the latter due to intramolecular reductive elimination with methyl chloride formation. The first step of the reaction of MeI with the preactivated surface of the K2PtCl4 salt is assisted by active sites, which are regenerated in each act of the chemical transformation of MeI into MeCl involving in the chain substitution of halogen in methyl iodide. The coordinatively unsaturated surface platinum complexes can act as such active sites. Due to their effective positive charge, they can provide electrophilic assistance to nucleophilic substitution. Chain termination is probably due to the coordination of the complex with a coordination vacancy and an interstitial chloride ion to the inactive K2PtCl4 complex.

Methyl iodide reactions on the surface of mechanically pre-activated platinum(II) salt in the heterogeneous system: K 2PtCl 4 powder–MeI vapor

Mechanically pre-activated K 2PtCl 4 salt consumes methyl iodide producing methyl chloride at room temperature. The reaction mechanism includes the following steps sequence: oxidative addition of methyl iodide to platinum(II) complexes with intermediate formation of methyl platinum(IV) complexes and further decomposition of the latter in the course of innersphere reductive elimination yielding methyl chloride. The first step of the reaction proceeds owing to the assistance of active centers regenerated in the course of each event of MeI into MeCl transformation taking part in the chain halogen substitution process. It could be assumed that the role of active centers is played by coordinatively unsaturated platinum(II) complexes located on the surface. These species bearing a positive efficient charge can render electrophilic assistance for the nucleophilic substitution. The chain termination can be caused by recombination of coordinatively unsaturated platinum(II) complexes and interstitial chloride ions forming an inactive K 2PtCl 4 complex.

Catalysis of acyl group transfer by a double-displacement mechanism: the cleavage of aryl esters catalyzed by calixcrown-Ba2+ complexes

The scope of the barium salt of p-tert-butylcalix[4]arene-crown-5 as a transacylation catalyst has been defined by evaluating its efficiency in the methanolysis of a series of aryl acetates at 25.0 degrees C in MeCN/MeOH 9:1 (v/v) under slightly basic conditions. In this system a phenolic hydroxyl is the acyl-receiving and -releasing unit in a double-displacement mechanism. The complexed barium ion acts both as a nucleophile carrier and a built-in Lewis acid in providing electrophilic assistance to the ester carbonyl both in the acylation and deacylation step (nucleophilic-electrophilic catalysis). Turnover capability is ensured by the acylated intermediate reacting with the solvent more rapidly than the original ester, but a serious drawback derives from the incursion of back-acylation of the liberated phenol. A gradual shift from rate-determining deacylation (p-nitrophenyl acetate) to rate-determining acylation (phenyl acetate) is observed along the investigated series. It is shown that the scope of the catalyst is restricted to acetate esters whose reactivity lies in the range approximately defined by the phenyl acetate-p-nitrophenyl acetate pair, with a maximum efficiency for p-chlorophenyl acetate. Moreover, the catalyst effectively promotes ester interchange between phenols, showing that its activity is not limited to solvolysis reactions. The very high sensitivity of the rate of acylation of the catalyst to leaving group basicity has been interpreted as due to rate-determining decomposition of the tetrahedral intermediate, which is believed to arise from the presumably low basicity of the metal ion stabilized nucleophile. The turnover frequency was in the range of 3.8 x 10(-4) min(-1) for phenyl acetate to 7.4 x 10(-3) min(-1) for p-nitrophenyl acetate ([ArOAc]0=4.0 mM]). A first attempt to enhance the rate of acylation of the catalyst through intramolecular general acid catalysis is also described.

Ring opening reactions of 2-trialkylsilylaziridines

2-Trialkylsilylaziridines do not readily undergo nucleophilic ring opening without electrophilic assistance. In the presence of strong acids protonation at the nitrogen is followed by nucleophilic attack α to the silicon. With non-nucleophilic counterions, the protonated aziridine can be obtained. N-Alkylation gives the aziridinium salt, which also undergoes α-cleavage. However, the presence of a 3-phenyl substituent gives a stable aziridinium salt that undergoes nucleophilic attack β to the silicon. Reaction of 2-trialkylsilylaziridines with trialkylsilyl halides usually leads to α-cleavage, however, desilylation to give the enamine is also observed. Fluorodesilylation of the 2-trialkylsilylaziridine is not straightforward and only occurred readily when a 2-ethoxycarbonyl group was present. Fluorodesilylation followed by attack on a carbonyl was only observed when very dry samples of fluoride ions were employed.