A halogen bond is a highly directional, non-covalent interaction between a halogen atom and another electronegative atom. It arises due to the formation of a small region of positive electrostatic potential opposite the covalent bond to the halogen, called the “sigma hole.” Empirical force fields in which the electrostatic interactions are represented by atom-centered point charges cannot capture this effect because halogen atoms usually carry a negative charge and therefore interact unfavorably with other electronegative atoms. A strategy to overcome this problem is to attach a positively charged virtual particle to the halogen. In this work, we extend the additive CHARMM General Force Field (CGenFF) to include such interactions in model systems of phenyl-X, with X being Cl, Br or I including di- and trihalogenated species. The charges, Lennard-Jones parameters, and halogen-virtual particle distances were optimized to reproduce the orientation dependence of quantum mechanical interaction energies with water, acetone, and N-methylacetamide as well as experimental pure liquid properties and relative hydration free energies with respect to benzene. The resulting parameters were validated in molecular dynamics simulations on small-molecule crystals and on solvated protein-ligand complexes containing halogenated compounds. The inclusion of positive virtual sites leads to better agreement across experimental observables, including preservation of ligand binding poses as a direct result of the improved representation of halogen bonding.

We report the identification of three structurally diverse compounds – compound 4, GC376, and MAC-5576 – as inhibitors of the SARS-CoV-2 3CL protease. Structures of each of these compounds in complex with the protease revealed strategies for further development, as well as general principles for designing SARS-CoV-2 3CL protease inhibitors. These compounds may therefore serve as leads for the basis of building effective SARS-CoV-2 3CL protease inhibitors.

We describe a mammalian cell-based assay to identify coronavirus 3CL protease (3CLpro) inhibitors. This assay is based on rescuing protease-mediated cytotoxicity and does not require live virus. By enabling the facile testing of compounds across a range of 15 distantly related coronavirus 3CLpro enzymes, we identify compounds with broad 3CLpro inhibitory activity. We also adapt the assay for use in compound screening and in doing so uncover additional SARS-CoV-2 3CLpro inhibitors. We observe strong concordance between data emerging from this assay and those obtained from live virus testing. The reported approach democratizes the testing of 3CLpro inhibitors by developing a simplified method for identifying coronavirus 3CLpro inhibitors that can be used by the majority of laboratories, rather than the few with extensive biosafety infrastructure. We identify two lead compounds, GC376 and compound 4, with broad activity against all 3CL proteases tested including 3CLpro enzymes from understudied zoonotic coronaviruses. Importance Multiple coronavirus pandemics have occurred over the last two decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We develop and validate a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter-free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identify compounds with broad activity against 3CL proteases and uncover structural insights that contribute to their broad activity. Furthermore, we demonstrate this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.

Three selenophene-incorporated quaterchalcogenophenebased donor−acceptor copolymers PFBT2Th2Se, PFBT2Se2Th, and PFBT4Se are designed and synthesized. To systematically fine-tune the molecular properties and investigate the chalcogen effect, PFBT2Th2Se and PFBT2Se2Th hybridize two thiophenes and two selenophenes as the donor with different isomeric main-chain placement while thiophene-free PFBT4Se uses quaterselenophene as the donor. On account of the selenophene's advantageous features such as higher quinoidal population and higher molecular polarizability, the three polymers show good light-harvesting ability, strong intermolecular interactions, high crystallinity, and high charge mobilities. Bulk-heterojunction solar cells incorporating these selenophenecontaining polymers have exhibited promising photovoltaic performance with impressive current densities over 20 mA/cm 2 . The device with the PFBT2Se2Th:PC 71 BM blend showed a PCE of 9.02% with a J sc of 21.02 mA/cm 2 . In addition, the device using quaterselenophene-based PFBT4Se:PC 71 BM blend exhibited a PCE of 8.92% with a superior J sc of 22.63 mA/cm 2 which represents one of the highest current densities from polymer:fullerene-based solar cells reported in the literature.

This paper is concerned with the synthesis and reactions of enantiopure 1,8,9,16-tetraethynyltetraphenylene (3). We obtained 3 in 34% yield through four steps starting from 1,8,9,16-tetrahydroxytetraphenylene (2a) via a functional group interconversion strategy. On the basis of this chiral "helical" building block, three rigid helical macrocycles 14, 15, and 22 were designed. Complexes 14 and 15 were constructed via coordination-driven self-assembly with platinum(II) complexes 8 and 9b, while 22 cannot be obtained successfully. Then macrocycle 28 was designed on the structural basis of 22 to which octyl chains were introduced, in the hope of improving the solubility of the complex. Macrocycle 28 was finally formed and was characterized by NMR spectroscopy, elemental analysis, and electrospray mass spectrometry. For the enantiopure 15 and 28, circular dichroism (CD) spectra also exhibited chiral properties. Complexes 27 and 28 both exhibited an intense emission band at 621 nm in acetonitrile at 298 K upon excitation at λ > 420 nm.