Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling.

Small molecule receptor-binding is dominated by weak, non-covalent interactions such as van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand-receptor interactions is a challenge to computational means in terms of accuracy and efficacy since the ligand may bind in a number of thermally accessible conformations. The conformational rotamer ensemble sampling tool (CREST) uses an iterative scheme to efficiently sample the conformational space and calculates energies using the semi-empirical 'Geometry, Frequency, Noncovalent, eXtended Tight Binding' (GFN2-xTB) method. This combined approach is applied to blind predictions of the modes and free energies of binding for a set of 10 drug molecule ligands to the cucurbit[n]urils CB[8] receptor from the recent 'Statistical Assessment of the Modeling of Proteins and Ligands' (SAMPL) challenge including morphine, hydromorphine, cocaine, fentanyl, and ketamine. For each system, the conformational space was sufficiently sampled for the free ligand and the ligand-receptor complexes using the quantum chemical Hamiltonian. A multitude of structures makes up the final conformer-rotamer ensemble, for which then free energies of binding are calculated. For those large and complex molecules, the results are in good agreement with experimental values with a mean error of 3 kcal/mol. The GFN2-xTB energies of binding are validated by advanced density functional theory calculations and found to be in good agreement. The efficacy of the automated QM sampling workflow allows the extension towards other complex molecular interaction scenarios.

Computational investigation of the control of the thermodynamics and microkinetics of the reductive amination reaction by solvent coordination and a co-catalyst.

Amines are among the most important and frequently used chemical compounds due to their biological activity and a wide range of applications in industry. Reductive amination reactions are an efficient and facile route to synthesize long chain amines from sustainable sources by using a different available aldehydes and ketones, and a large variety of amines including primary, secondary and tertiary forms. The pathway of the reaction process is critically dependent on reaction parameters such as the pH of the reaction medium, choice of solvent (explicitly coordinating solvent) and process conditions. These parameters are affecting the reaction performance and the selectivity but are still not fully rationalized. Here, we investigate the microkinetics and thermodynamics of the individual steps of the reductive amination reaction by exploring the systems' parameters. Explicit water coordination to the aldehyde leads to a stepwise rather than concerted nucleophilic addition with a lower activation barrier by 6-10 kcal mol-1. At low pH, the pathway is changed by a direct protonation of the amine substrate. This protonation does not strongly affect the kinetics of the reaction, but the thermodynamic equilibria. The presence of an acid as a co-catalyst leads to the formation of an iminium intermediate and this drives the reaction forward. Thus, the presence of an acid as a co-catalyst clearly renders this pathway the thermodynamically preferred one. Consequently, altering the reaction parameters does not only influence the reaction kinetics, but also the thermodynamic profile of the pathways in all cases. Further understanding of the reaction dynamics is essential to develop a microkinetic model of the reaction to then control and engineer the process in order to rationally design routes to tailor-made products.

Ag-catalyzed azide alkyne cycloaddition: a DFT approach.

In this study, the mechanism of AgAAC reaction has been studied by quantum mechanical calculations to gain insights into this promising reaction and the first successful application of a Ag catalyst alone in AAC. Elucidating the reaction mechanism will enable more control over the synthesis and help to obtain tailor made products in good yields without copper. The feasibility of the experimentally proposed reaction mechanism was investigated by modelling the profound intermediates and the transition state structures connecting them. The DFT calculations with the wB97XD functional with MWB28 effective core potential and 6-31+G* basis set combination herein show that once the silver acetylide structure forms, triazole synthesis via the experimentally proposed cycloaddition is a facile reaction in terms of energetics. The number of metal atoms involved in a click reaction is one of the main questions considered in mechanistic studies. In AgAAC reaction, comparison of mononuclear and binuclear paths shows that the barrier for binuclear cases is lower than that of mononuclear cases.