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Understanding the mechanisms of enzymatic catalysis requires a detailed understanding of the complex interplay of structure and dynamics of large systems that is a challenge for both experimental and computational approaches. More importantly, the computational demands of QM/MM simulations mean that the dynamics of the reaction can only be considered on a timescale of nanoseconds even though the conformational changes needed to reach the catalytically active state happen on a much slower timescale. Here we demonstrate an alternative approach that uses transition state force fields (TSFFs) derived by the quantum-guided molecular mechanics (Q2MM) method that provides a consistent treatment of the entire system at the classical molecular mechanics level and allows simulations at the microsecond timescale. Application of this approach to the second hydride transfer transition state of HMG-CoA reductase from Pseudomonas mevalonii (PmHMGR) identified three remote residues, R396, E399 and L407, (15–27 Å away from the active site) that have a remote dynamic effect on enzyme activity. The predictions were subsequently validated experimentally via site-directed mutagenesis. These results show that microsecond timescale MD simulations of transition states are possible and can predict rather than just rationalize remote allosteric residues., Transition state force fields enable MD simulations at the transition state of HMGCoA reductase that sample the transition state ensemble on the μs timescale to identify remote residues that affect the reaction rate.

Quantum-Guided Molecular Mechanics (Q2MM) can be used to derive transition state force fields (TSFFs) that allow the fast and accurate predictions of stereoselectivity for a wide range of catalytic enantioselective reactions. The basic ideas behind the derivation of TSFFs using Q2MM are discussed and the steps involved in obtaining a TSFF using the Q2MM code, publically available at github.com/q2mm, are shown. The applicability for a range of reactions, including several non-standard applications of Q2MM, is demonstrated. Future developments of the method are also discussed.

In two consecutive equilibria the compound (Cp*)2Zr(OMe)2 undergoes insertion of CO2 to form the mono- and bis-hemicarbonates. Both equilibria are exothermic but entropically disfavoured. Magnetisation transfer experiments gave kinetic data for the first equilibrium showing that the rate of insertion is overall second order with a rate constant of 3.20 ± 0.12 M(-1) s(-1), which is substantially higher than those reported for other early transition metal alkoxides, which are currently the best homogeneous catalysts for dimethyl carbonate formation from methanol and CO2. Activation parameters for the insertion reaction point to a highly ordered transition state and we interpret that as there being a substantial interaction between the CO2 and the metal during the C-O bond formation. This is supported by DFT calculations showing the lateral attack by CO2 to have the lowest energy transition state.

The ‘Trost Standard Ligand’ (2) is a chiral diphosphine ligand that distinguishes itself by the high selectivity it induces in the Pd-catalysed reactions of allylic substrates that generate slim cyclic or small linear intermediates. However, a range of unusual features, including memory effects, inverse dependence of selectivity and rate on catalyst concentration, high sensitivity to counter-ion, particularly chloride, and decreasing enantioselectivities at lower temperatures, are often encountered, thus requiring considerable optimisation of reaction conditions to attain optimum selectivity. These features can be accounted for by a model involving a dynamic multi-catalyst ensemble. To gain evidence for this model, the manner in which diphosphine 2 interacts with Pd–allyl cations, and in particular the higher-order systems it generates, has been investigated by use of NMR, isotopic labelling, polarimetry, UV, neutron scattering, X-ray crystallography and molecular modeling. Ligand 2 coordinates to Pd–allyl cations to generate a mononuclear P,P-chelate. This is found to readily form non-chelate oligomers, present in a range of forms, including rings, for which high homochiral selectivity in oligomerisation is demonstrated by the technique of pseudoenantiomers. All of these species are in relatively rapid equilibrium, with half-lives for interconversion in the range 2–6 s. Higher-order aggregation is also detected, and thus at even moderate concentrations (>50 mM) large rod-like aggregates are formed.

The synthesis of the components of the dynamic supramolecular hydrogen-bonded catalytic system 2 + 3 is described. The catalytic performance and substrate- and enantioselectivity of Mn(salen) catalyst 2 were investigated in the presence and absence of the Zn(porphyrin) receptor unit 3. The effects of pyridine and pyridine N-oxide donor ligands were also studied. Some aspects on the mechanism of the Jacobsen-Katsuki epoxidation, based on literature observations, are introduced as a means to analyse the behaviour of 2 and its modulation by the formation of macrocycle 1 with 3. A complete association model of the metal-free system 4 + 5 refutes the earlier assumption that macrocycle 1 is the predominant form of catalyst 2 under the standard epoxidation reaction conditions with 2 + 3. Evidence are provided that receptor-binding substrates and nonbinding substrates, respectively, are epoxidised by two different catalytic species, or two distinct distributions of species in competitive epoxidations using catalytic system 2 + 3. The two species are assigned to the endo and exo faces of the Mn(salen) catalyst in macrocycle 1, and to equivalently folded oligomeric structures with monomers 2 and 3 in adjacent positions.

A vinylsilane-ketiminium ion cyclization involving iminium species derived from amines 6 and 7 was investigated experimentally as a possible approach to some biologically interesting 1-azaspirocycles. However, even under conditions of microwave irradiation at high temperatures no such cyclization was observed whereas (in line with previous results) the corresponding vinylsilane-aldiminium ion cyclizations were more successful. Aldiminium species substituted α to nitrogen displayed no diastereoselectivity in the cyclization of precursors derived from 6 while high trans diastereoselectivity could be obtained for iminium species derived from 7. Quantum-mechanical investigations of the general reaction mechanism underlined the lack of reactivity of ketiminium species and also convincingly explained the observed diastereoselectivities of aldiminium species. The calculations further revealed that (Z)-vinylsilanes cyclize via a silicon-stabilized β-carbocation, and that any formal aza-Cope rearrangement of the starting material to an allylsilane-iminium species does not take place in a concerted fashion. However, the calculations show that the aza-Cope rearrangement precedes cyclization for the corresponding (E)-vinylsilanes, the overall reaction being energetically slightly less favoured than cyclization of the (Z)-isomers.

In the presence of a chiral lithium N,P amide, alkylation of benzaldehyde results in an enantioselective formation of 1-phenyl-pentanol. This stereoselective addition reaction has herein been studied using dispersion-corrected density functional theory. For five different chiral ligands originating from amino acids the resulting enantioselectivity has been computationally determined and compared with experimentally available enantiomeric ratios (e.r.). In all cases the experimentally preferred enantiomer could be reproduced by the computational model. The selectivity trend among the ligands was found strongly sensitive to the amount of dispersion correction included. The origin of selectivity in the alkylation reaction is found to be composed of many combined interactions. For the most selective ligand 2A the most important factors found, which are favouring the (R)-TS, are a CH-π interaction between benzaldehyde-dimethyl ether (DME), stronger Li-solvation, and Li-π interactions with the phenyl ring in the backbone of the chiral lithium N,P amide. In addition, solvation by the bulk solvent and the size of the substituent on the nitrogen are also found important factors for the enantioselectivity.

The three conformationally restricted cyclopropyl glutamate analogues (3, 4, 5) were synthesised and their affinity for ionotropic and activity at metabotropic glutamate receptors were probed. Compound 4 turned out to be a highly selective agonist at the metabotropic glutamate receptor mGluR2 with at least two orders of magnitude selectivity in potency compared to the very homologous mGluR3 as well as mGluR1, 4, 5, 7. We also tried to synthesise the two epimers of 6, but the two compounds underwent fast epimerisation in H2O. Furthermore, two cyclopropyl arginine analogues (7, 8) were synthesised and characterised pharmacologically at GPRC6A.

Reaction of 1-methylpyrazole with n-BuLi in THF followed by reaction with monodeuteromethanol (CH3OD) under kinetically controlled conditions leads to functionalisation at the methyl group, whereas reaction under thermodynamically controlled conditions leads to functionalisation at the pyrazole 5-position. The observed regioselectivity can be correctly predicted, at least qualitatively, using density functional B3LYP/6-31+G(d,p) calculations only when solvation effects (IEFPCM) are taken into account. The 1H,6Li HOESY and NOESY NMR spectra of the thermodynamic product 5-lithio-1-methylpyrazole (5-Li) in [D8]THF are consistent with an oligomeric structure.

Proposed mechanisms for the osmium-catalysed dihydroxylation are examined and kinetic rate laws derived in terms of various mechanistic rate constants. In light of the reported kinetic behaviour of these systems, particularly with asymmetric nitrogen base ligands, several constraints can be placed on the two major competing hypotheses. The chemical consequences of these constraints make stepwise formation of the two C–O bonds via an osmaoxetane the more plausible mechanistic model.