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Methods which accurately predict protein – ligand binding strengths are critical for drug discovery. In the last two decades, advances in chemical modelling have enabled steadily accelerating progress in the discovery and optimization of structure-based drug design. Most computational methods currently used in this context are based on molecular mechanics force fields that often have deficiencies in describing the quantum mechanical (QM) aspects of molecular binding. In this study, we show the competitiveness of our QM-based Molecules-in-Molecules (MIM) fragmentation method for characterizing binding energy trends for seven different datasets of protein – ligand complexes. By using molecular fragmentation, the MIM method allows for accelerated QM calculations. We demonstrate that for classes of structurally similar ligands bound to a common receptor, MIM provides excellent correlation to experiment, surpassing the more popular Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) methods. The MIM method offers a relatively simple, well-defined protocol by which binding trends can be ascertained at the QM level and is suggested as a promising option for lead optimization in structure-based drug design. 

Electrochemical dehalogenation of polyhalogenated compounds is an inefficient process as the working electrode is passivated by the deposition of short-chain polymers that form during the early stages of electrolysis. Herein, we report the use of 1, 1, 1, 3, 3, 3-hexaflouroisopropanol (HFIP) as an efficient reagent to control C–H formation over the radical association. Debromination of 1,6-dibromohexane was examined in the presence of Ni(II) salen and HFIP as the electrocatalyst and hydrogen atom source, respectively. Electrolysis of 10 mM 1,6-dibromohexane and 2 mM Ni(II) salen in the absence of HFIP yields 50% unreacted 1,6-dibromohexane and ∼40% unaccounted for starting material, whereas electrolysis with 50 mM HFIP affords 65%n-hexane. The mechanism of hydrogen atom incorporation was examined via deuterium incorporation coupled with high-resolution mass spectrometry, and density functional theory (DFT) calculations. Deuterium incorporation analysis revealed that the hydrogen atom originated from the secondary carbon of HFIP. DFT calculations showed that the deprotonation of hydroxyl moiety of HFIP, prior to the hydrogen atom transfer, is a key step for C–H formation. The scope of electrochemical dehalogenation was examined by electrolysis of 10 halogenated compounds. Our results indicate that through the use of HFIP, the formation of short-chain polymers is no longer observed, and monomer formation is the dominant product.

 

The redox potential is a powerful thermodynamic and kinetic tool used to predict numerous chemical and biochemical mechanisms. However, despite the improving predictive power of density functional theory (DFT), chemically accurate theoretical redox potentials are often difficult to achieve with DFT. For example, calculated redox potentials are sensitive to density functional choice and often fall short of the desired accuracy. Thus, ranges of errors for computed redox potentials between different density functionals can become quite large. The current study presents a cost-effective protocol that utilizes effective error cancellation schemes in order to accurately predict the redox potentials of a wide range of organic molecules. This computational protocol, called CBH-Redox, is an extension of the connectivity-based hierarchy (CBH) method, and produces thermochemical data with near-G4 accuracy. Herein, we test the CBH-Redox protocol against both experimental and G4 reference values and compare these results to DFT alone. Considering 46 C, O, N, F, Cl, and S atom-containing molecules, when using the CBH-Redox correction scheme, the MAEs for all eight density functionals tested are within the 0.09 V target accuracy versus both experiment and G4. Moreover, CBH-Redox achieves an impressive accuracy, with a MAE of 0.05 V or below when compared to G4 for six of the eight density functionals tested. In addition, when the CBH correction is applied, the error range across all functionals tested decreases from 0.12 V to about 0.05 V versus G4, and from 0.13 V to 0.04 V versus experiment. 

Cyclic voltammetry and controlled-potential (bulk) electrolysis have been employed to investigate the direct electrochemical reduction of acetochlor (1) at carbon and silver cathodes in dimethylformamide. Voltammograms of1exhibit a single irreversible cathodic peak at both cathode materials. Catalytic properties of silver towards carbon–halogen bond cleavage are evidenced by a positive shift in the reduction of acetochlor as compared to the more inert glassy carbon electrode. Voltammograms in the presence of 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), and comparisons of calculated relative interaction energies between acetochlor, possible intermediates, and deschloroacetochlor in the presence of different proton donors, suggest strong hydrogen-bonding interactions between HFIP and a carbanion intermediate. Addition of HFIP to electrolysis conditions promotes complete reduction at both cathode materials, with formation of deschloroacetochlor in high yields. In deuterium labelling studies, the use of DMF-d₇led to no evidence for deuterium atom incorporation. However, when HFIP-OD or D₂O were employed as a proton source, substantial amounts of deuterated deschloroacetochlor were observed. A mechanism for the reduction of acetochlor is proposed, in which radical intermediates do not play a significant role in reduction, rather a carbanion intermediate pathway is followed.