The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck–Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrödinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.     

High‐Level Incorporation of Silver in Gold Nanoclusters: Fluorescence Redshift upon Interaction with Hydrogen Peroxide and Fluorescence Enhancement with Herbicide

High‐level incorporation of Ag in Au nanoclusters (NCs) is conveniently achieved by controlling the concentration of Ag⁺ in the synthesis of bovine serum albumin (BSA)‐protected Au NCs, and the resulting structure is determined to be bimetallic Ag₂₈Au₁₀‐BSA NCs through a series of characterizations including energy‐dispersive X‐ray spectroscopy, mass spectroscopy, and X‐ray photoelectron spectroscopy, together with density functional theory simulations. Interestingly, the Ag₂₈Au₁₀ NCs exhibit a significant fluorescence redshift rather than quenching upon interaction with hydrogen peroxide, providing a new approach to the detection of hydrogen peroxide through direct comparison of their fluorescence peaks. Furthermore, the Ag₂₈Au₁₀ NCs are also used for the sensitive and selective detection of herbicide through fluorescence enhancement. The detection limit for herbicide (0.1 nm ) is far below the health value established by the U.S. Environmental Protection Agency; such sensitive detection was not achieved by using AuAg NCs with low‐level incorporation of Ag or by using the individual metal NCs.     

Salt effect on molecular orientation at air/liquid methanol interface

The salt effects on molecular orientation at air/liquid methanol interface were investigated by the polarization-dependent sum frequency generation vibrational spectroscopy(SFG-VS). We clarified that the average tilting angle of the methyl group to be u = 308 58 at the air/pure methanol surface assuming a d-function orientational distribution. Upon the addition of 3 mol/L Na I, the methyl group tilts further away from the surface normal with a new u = 418 38. This orientational change does not explain the enhancement of the SFG-VS intensities when adding Na I, implying the number density of the methanol molecules with a net polar ordering in the surface region also changed with the Na I concentrations. These spectroscopic findings shed new light on the salt effects on the surfaces structures of the polar organic solutions. It was also shown that the accurate determination of the bulk refractive indices and Raman depolarization ratios for different salt concentrations is crucial to quantitatively interpret the SFG-VS data.     

Asymmetric intramolecular Friedel–Crafts reaction catalyzed by a spiropyrrolidine organocatalyst: Enantioselective construction of indolizine and azepine frameworks

The asymmetric intramolecular Friedel–Crafts type Michael reaction of α,β-unsaturated aldehyde with pyrrole, catalyzed by a spiropyrrolidine (SP)-type organocatalyst, has been accomplished, which allows the construction of a series of azepine and indolizine frameworks with high to excellent enantioselectivities (up to 98% ee). Moreover, the substrate scope could be extended to generate a quaternary center in indolizine frameworks (up to 96% ee).     

The efficient in‐situ reduction and cyclization reaction of aromatic aldehyde, 1,3‐cyclopentanedione (tetronic acid), and nitro‐compound under SnCl2·2H2O‐THF medium

An efficient in‐situ reduction and cyclization reaction for the synthesis of pyrazolo[4,3‐f]quinoline, pyrazolo[3,4‐f]quinoline, and pyrazolo[3,2‐f]quinoline derivatives directly form 5‐nitroindazole, 6‐nitroindazole and 5‐nitroindole in the presence of SnCl₂·2H₂O was reported. Compared to traditional synthetic methods, this approach has the advantages of stable reagents, easy obtaining raw material, and high yields. In this research, SnCl₂·2H₂O is the efficient reducing agent for the in‐situ reduction and cyclization reaction of nitro‐compound. In addition, this process provided an alternative approach for the synthesis of target compounds.     

Electrochemical Tri- and Difluoromethylation-Triggered Cyclization Accompanied by the Oxidative Cleavage of Indole Derivatives

Considering their unique roles in organic synthesis, and pharmaceutical and agrochemical applications, the development of fluoroalkylation, cyclization, and indole oxidative cleavage are important topics. Herein, an unprecedented electrochemical tri- and difluoromethylation/cyclization/indole oxidative cleavage process occurring in an undivided cell is presented. The protocol employs a readily prepared Langlois reagent as the fluoroalkyl source, affording a series of tri- or difluoromethylated 2-(2-acetylphenyl)isoquinoline-1,3-diones in good yields with excellent stereoselectivity. It is worth noting that this new methodology merges the fluoroalkylation/cyclization of N-substituted acrylamide alkenes with the oxidative cleavage of an indole C(2)=C(3) bond under external oxidant-free conditions.     

A Convenient and Effective Synthesis of Tris-Bridged Tricationic Azolophanes

Two new macrobicyclic imidazolium and benzimidazolium phanes were synthesized by direct quaternization of the corresponding tripodal azacycles with tribromide under high dilution condition in excellent yields. The cyclophanes were identified by ¹H-NMR, ¹³C-NMR, FAB-MS, IR, elemental analysis and X-ray diffraction analysis.