Going Full Circle with Organocatalysis and Biocatalysis: The Latent Potential of Cofactor Mimics in Asymmetric Synthesis.

Many enzymes work in tandem with small molecule cofactors, which have inspired organocatalyst designs. Chemical modification of cofactor scaffolds has increased organocatalytic reactivity and reaction scope. This synopsis presents a selection of recent advances in the use of cofactors (native and mimics) in organocatalysis and biocatalysis. We aim to highlight the benefits of combining fundamental knowledge gained in both bio- and organo-catalysis for asymmetric biocatalysis.

The Role of the Fused Ring in Bicyclic Triazolium Organocatalysts: Kinetic, X-ray, and DFT Insights.

Bicyclic triazolium scaffolds are widely employed in N-heterocyclic carbene (NHC) organocatalysis. While the incorporation of a fused ring was initially for synthetic utility in accessing chiral, modular triazolyl scaffolds, recent results highlight the potential for impact upon reaction outcome with the underpinning origins unclear. The common first step to all triazolium-catalyzed transformations is C(3)-H deprotonation to form the triazolylidene NHC. Herein, we report an analysis of the impact of size of the fused (5-, 6-, and 7-membered, n = 1, 2, and 3, respectively) ring on the C(3) proton transfer reactions of a series of bicyclic triazolium salts. Rate constants for the deuteroxide-catalyzed C(3)-H/D-exchange of triazolium salts, kDO, were significantly influenced by the size of the adjacent fused ring, with the kinetic acidity trend, or protofugalities, following the order kDO (n = 1) > kDO (n = 2) ≈ kDO (n = 3). Detailed analyses of X-ray diffraction (XRD) data for 20 triazolium salts (including 16 new structures) and of computational data for the corresponding triazolylidene NHCs provide insight on structural effects of alteration of fused ring size. In particular, changes in internal triazolyl NCN angle and positioning of the most proximal CH2 with variation in fused ring size are proposed to influence the experimental protofugality order.

Rate and equilibrium constants for the addition of triazolium salt derived N-heterocyclic carbenes to heteroaromatic aldehydes.

Heteroaromatic aldehydes are often used preferentially or exclusively in a range of NHC-catalysed processes that proceed through the generation of a reactive diaminoenol or Breslow Intermediate (BI), with the reason for their unique reactivity currently underexplored. This manuscript reports measurement of rate and equilibrium constants for the reaction between N-aryl triazolium NHCs and heteroaromatic aldehydes, providing insight into the effect of the NHC and heteroaromatic aldehyde structure up to formation of the BI. Variation in NHC catalyst and heteroaromatic aldehyde structure markedly affect the observed kinetic parameters of adduct formation, decay to starting materials and onward reaction to BI. In particular, large effects are observed with both 3-halogen (Br, F) and 3-methyl substituted pyridine-2-carboxaldehyde derivatives which substantially favour formation of the tetrahedral intermediate relative to benzaldehyde derivatives. Key observations indicate that increased steric hindrance leads to a reduction in both k 2 and k -1 for large (2,6-disubstituted)-N-Ar groups within the triazolium scaffold, and sterically demanding aldehyde substituents in the 3-position, but not in the 6-position of the pyridine-2-carboxaldehyde derivatives. As part of this study, the isolation and characterisation of twenty tetrahedral adducts formed upon addition of N-aryl triazolium derived NHCs into heteroaromatic aldehydes are described. These adducts are key intermediates in NHC-catalysed umpolung addition of heteroaromatic aldehydes and are BI precursors.

Kinetic and structure-activity studies of the triazolium ion-catalysed benzoin condensation.

Steady-state kinetic and structure-activity studies of a series of six triazolium-ion pre-catalysts 2a-2f were investigated for the benzoin condensation. These data provide quantitative insight into the role of triazolium N-aryl substitution under synthetically relevant catalytic conditions in a polar solvent environment. Kinetic behaviour was significantly different to that previously reported for a related thiazolium-ion pre-catalyst 1, with the observed levelling of initial rate constants to νmax at high aldehyde concentrations for all triazolium catalysts. Values for νmax for 2a-2f increase with electron withdrawing N-aryl substituents, in agreement with reported optimal synthetic outcomes under catalytic conditions, and vary by 75-fold across the series. The levelling of rate constants supports a change in rate-limiting step and evidence supports the assignment of the Breslow-intermediate forming step to the plateau region. Correlation of νmax reaction data yielded a positive Hammett ρ-value (ρ = +1.66) supporting the build up of electron density adjacent to the triazolium N-Ar in the rate-limiting step favoured by electron withdrawing N-aryl substituents. At lower concentrations of aldehyde, both Breslow-intermediate and benzoin formation are partially rate-limiting.

N-Terminal speciation for native chemical ligation.

Native chemical ligation (NCL) enables the chemical synthesis of peptides via reactions between N-terminal thiolates and C-terminal thioesters under mild, aqueous conditions at pH 7-8. Here we demonstrate quantitatively how thiol speciation at N-terminal cysteines and analogues varies significantly depending upon structure at typical pH values used in NCL.

Unusually high α-proton acidity of prolyl residues in cyclic peptides.

The acidity of the α-proton in peptides has an essential role in numerous biochemical reactions and underpins their stereochemical integrity, which is critical to their biological function. We report a detailed kinetic and computational study of the acidity of the α-proton in two cyclic peptide systems: diketopiperazine (DKP) and triketopiperazine (TKP). The kinetic acidity (protofugality) of the α-protons were determined though hydrogen deuterium exchange studies in aqueous solutions. The acidities of the α-proton in prolyl residues were increased by 3-89 fold relative to other amino acid residues (prolyl > glycyl ≫ alanyl > tyrosyl). Experimental and computational evidence for the stereoelectronic origins of this enhanced prolyl reactivity is presented. TKPs were 106-fold more reactive than their DKP analogues towards deprotonation, which we attribute to the advanced development of aromaticity in the earlier transition state for proton transfer in these cases. A Brønsted linear free energy analysis of the reaction data was conducted to provide estimates of α-proton pK as.

Author Correction: The identification of carbon dioxide mediated protein post-translational modifications.

The original version of this Article omitted the following from the Acknowledgements: 'This work was support by EPSRC grant EP/K504336/1 and Leverhulme Trust grant RPG-2016-017.' This has been corrected in both the PDF and HTML versions of the Article.

The identification of carbon dioxide mediated protein post-translational modifications.

Carbon dioxide is vital to the chemistry of life processes including metabolism, cellular homoeostasis, and pathogenesis. CO2 is generally unreactive but can combine with neutral amines to form carbamates on proteins under physiological conditions. The most widely known examples of this are CO2 regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase and haemoglobin. However, the systematic identification of CO2-binding sites on proteins formed through carbamylation has not been possible due to the ready reversibility of carbamate formation. Here we demonstrate a methodology to identify protein carbamates using triethyloxonium tetrafluoroborate to covalently trap CO2, allowing for downstream proteomic analysis. This report describes the systematic identification of carbamates in a physiologically relevant environment. We demonstrate the identification of carbamylated proteins and the general principle that CO2 can impact protein biochemistry through carbamate formation. The ability to identify protein carbamates will significantly advance our understanding of cellular CO2 interactions.

New Blatter-type radicals from a bench-stable carbene.

Stable benzotriazinyl radicals (Blatter's radicals) recently attracted considerable interest as building blocks for functional materials. The existing strategies to derivatize Blatter's radicals are limited, however, and synthetic routes are complex. Here, we report that an inexpensive, commercially available, analytical reagent Nitron undergoes a previously unrecognized transformation in wet acetonitrile in the presence of air to yield a new Blatter-type radical with an amide group replacing a phenyl at the C(3)-position. This one-pot reaction of Nitron provides access to a range of previously inaccessible triazinyl radicals with excellent benchtop stabilities. Mechanistic investigation suggests that the reaction starts with a hydrolytic cleavage of the triazole ring followed by oxidative cyclization. Several derivatives of Nitron were prepared and converted into Blatter-type radicals to test the synthetic value of the new reaction. These results significantly expand the scope of using functionalized benzotriazinyls as stable radical building blocks.

The synthesis, conformation and hydrolytic stability of an N,S-bridging thiophosphoramidate analogue of thymidylyl-3',5'-thymidine.

A 3'-N,5'-S-bridging thiophosphoramidate analogue of thymidylyl-3',5'-thymidine was synthesised under aqueous conditions. (1)H NMR conformational measurements show that the 3'-N-substituted deoxyribose ring is biased towards the 'north', RNA-like conformation. Rate constants for hydrolysis of the analogue were measured at 90 °C in the pH range 1.3-10.9. The pH-log kobs profile displays a pH-independent region between approximately pH 7 and 10 (t1/2 ∼13 days). Under acidic conditions, kobs displays a first order dependence on [H3O(+)].

Rate and equilibrium constants for the addition of N-heterocyclic carbenes into benzaldehydes: a remarkable 2-substituent effect.

Rate and equilibrium constants for the reaction between N-aryl triazolium N-heterocyclic carbene (NHC) precatalysts and substituted benzaldehyde derivatives to form 3-(hydroxybenzyl)azolium adducts under both catalytic and stoichiometric conditions have been measured. Kinetic analysis and reaction profile fitting of both the forward and reverse reactions, plus onwards reaction to the Breslow intermediate, demonstrate the remarkable effect of the benzaldehyde 2-substituent in these reactions and provide insight into the chemoselectivity of cross-benzoin reactions.

Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge.

Recent experimental work (J. Org. Chem., 2012, 77, 5829) demonstrated pronounced differences in measured thio-effects for the hydrolysis of (thio)phosphodichloridates by water and hydroxide nucleophiles. In the present work, we have performed detailed quantum chemical calculations of these reactions, with the aim of rationalizing the molecular bases for this discrimination. The calculations highlight the interplay between nucleophile charge and transition state solvation in SN2(P) mechanisms as the basis of these differences, rather than a change in mechanism.

Rate and Equilibrium Constants for the Addition of N-Heterocyclic Carbenes into Benzaldehydes: A Remarkable 2-Substituent Effect.

Rate and equilibrium constants for the reaction between N-aryl triazolium N-heterocyclic carbene (NHC) precatalysts and substituted benzaldehyde derivatives to form 3-(hydroxybenzyl)azolium adducts under both catalytic and stoichiometric conditions have been measured. Kinetic analysis and reaction profile fitting of both the forward and reverse reactions, plus onwards reaction to the Breslow intermediate, demonstrate the remarkable effect of the benzaldehyde 2-substituent in these reactions and provide insight into the chemoselectivity of cross-benzoin reactions.

Enzyme architecture: the effect of replacement and deletion mutations of loop 6 on catalysis by triosephosphate isomerase.

Two mutations of the phosphodianion gripper loop in chicken muscle triosephosphate isomerase (cTIM) were examined: (1) the loop deletion mutant (LDM) formed by removal of residues 170-173 [Pompliano, D. L., et al. (1990) Biochemistry 29, 3186-3194] and (2) the loop 6 replacement mutant (L6RM), in which the N-terminal hinge sequence of TIM from eukaryotes, 166-PXW-168 (X = L or V), is replaced by the sequence from archaea, 166-PPE-168. The X-ray crystal structure of the L6RM shows a large displacement of the side chain of E168 from that for W168 in wild-type cTIM. Solution nuclear magnetic resonance data show that the L6RM results in significant chemical shift changes in loop 6 and surrounding regions, and that the binding of glycerol 3-phosphate (G3P) results in chemical shift changes for nuclei at the active site of the L6RM that are smaller than those of wild-type cTIM. Interactions with loop 6 of the L6RM stabilize the enediolate intermediate toward the elimination reaction catalyzed by the LDM. The LDM and L6RM result in 800000- and 23000-fold decreases, respectively, in kcat/Km for isomerization of GAP. Saturation of the LDM, but not the L6RM, by substrate and inhibitor phosphoglycolate is detected by steady-state kinetic analyses. We propose, on the basis of a comparison of X-ray crystal structures for wild-type TIM and the L6RM, that ligands bind weakly to the L6RM because a large fraction of the ligand binding energy is utilized to overcome destabilizing electrostatic interactions between the side chains of E168 and E129 that are predicted to develop in the loop-closed enzyme. Similar normalized yields of DHAP, d-DHAP, and d-GAP are formed in LDM- and L6RM-catalyzed reactions of GAP in D2O. The smaller normalized 12-13% yield of DHAP and d-DHAP observed for the mutant cTIM-catalyzed reactions compared with the 79% yield of these products for wild-type cTIM suggests that these mutations impair the transfer of a proton from O-2 to O-1 at the initial enediolate phosphate intermediate. No products are detected for the LDM-catalyzed isomerization reactions in D2O of [1-(13)C]GA and HPi, but the L6RM-catalyzed reaction in the presence of 0.020 M dianion gives a 2% yield of the isomerization product [2-(13)C,2-(2)H]GA.

Proton transfer reactions of triazol-3-ylidenes: kinetic acidities and carbon acid pKa values for twenty triazolium salts in aqueous solution.

Second-order rate constants have been determined for deuteroxide ion-catalyzed exchange of the C(3)-proton for deuterium, k(DO) (M(-1) s(-1)), of a series of 20 triazolium salts in aqueous solution at 25 °C and ionic strength I = 1.0 (KCl). Evidence is presented that the rate constant for the reverse protonation of the triazol-3-ylidenes by solvent water is close to that for dielectric relaxation of solvent (10(11) s(-1)). These data enabled the calculation of carbon acid pK(a) values in the range 16.5-18.5 for the 20 triazolium salts. pD rate profiles for deuterium exchange of the triazolium salts reveal that protonation at nitrogen to give dicationic triazolium species occurs under acidic conditions, with estimates of pK(a)(N1) = -0.2 to 0.5.

Hydrolysis studies of phosphodichloridate and thiophosphodichloridate ions.

We report the pH-k(obs) profiles for the hydrolyses of phosphodichloridate and thiophosphodichloridate ions in aqueous solutions. Both species show broad pH-k(obs) plateaus that extend to high pHs.

peri-Dimethylamino substituent effects on proton transfer at carbon in α-naphthylacetate esters: a model for mandelate racemase.

The rate constants for exchange of hydrogen for deuterium at the α-CH(2) positions of 8-(N,N-dimethylaminonaphthalen-1-yl)acetic acid tert-butyl ester 1 and naphthalen-1-ylacetic acid tert-butyl ester 2 have been determined in potassium deuteroxide solutions in 1 : 1 D(2)O : CD(3)CN, in order to quantify the effect of the neighbouring peri-dimethylamino substituent on α-deprotonation. Intramolecular general base catalysis by the (weakly basic) neighbouring group was not detected. Second-order rate constants, k(DO), for the deuterium exchange reactions of esters 1 and 2 have been determined as 1.35 × 10(-4) M(-1) s(-1) and 3.95 × 10(-3) M(-1) s(-1), respectively. The unexpected 29-fold decrease in the k(DO) value upon the introduction of a peri-dimethylamino group is attributed to an unfavourable steric and/or electronic substituent effect on intermolecular deprotonation by deuteroxide ion. From the experimental k(DO) values, carbon acid pK(a) values of 26.8 and 23.1 have been calculated for esters 1 and 2.

pKas of the conjugate acids of N-heterocyclic carbenes in water.

pK(a) values of 19.8-28.2 are reported for the conjugate acids of a large series of NHCs in water. The effects of ring size, N-substituent and C(4)-C(5) saturation on pK(a) are discussed.