Greener approach: Ionic liquid [Et3NH][HSO4]-catalyzed multicomponent synthesis of 4-arylidene-2-phenyl-5(4H)oxazolones under solvent-free condition

We have developed simple, greener, safer multicomponent synthesis series of 4-arylidene-2-phenyl-5(4H) oxazolones 4(a-r) catalyzed by Bronsted acid ionic liquid as triethylammonium hydrogen sulfate [Et₃NH][HSO₄] and catalytic amount of acetic anhydride and sodium acetate with excellent yields (90–99%). The protocol offers economical, environmentally benign, solvent-free conditions, and recycle–reuse of the catalyst and easily available starting as benzoyl chloride 1, amino acid 2 and a variety of aldehydes 3. The cyclization followed by condensation of benzoyl chloride, amino acid, and a variety of aldehydes catalyzed by ILs [Et₃NH][HSO₄] and catalytic amount of acetic anhydride and sodium acetate. The final products were confirmed by their characterization data such as FTIR, ¹H-NMR, ¹³C-NMR, Mass, high-resolution mass spectra and were compared with its reported method.     

Synthesis of 2,3,6-trisubstituted pyridines by transition-metal free cyclization of 1,3-diynes with amino acids

Amino acids are firstly employed in transition-metal free heterocyclization reaction of 1,3-diynes in the presence of K₃PO₄ and DMSO at 120 °C. This method produces 2,3,6-trisubstituted pyridines with up to 86% yield. The –CO₂H group on the amino acids is crucial for this heterocyclization reaction. The mechanism of such a heterocyclization reaction is discussed, as well.     

Tinker‐OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU‐based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker‐OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200‐fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host–guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc.     

Adaptive‐numerical‐bias metadynamics

A metadynamics scheme is presented in which the free energy surface is filled with progressively adding adaptive biasing potentials, obtained from the accumulated probability distribution of the collective variables. Instead of adding Gaussians with assigned height and width in conventional metadynamics method, here we add a more realistic adaptive biasing potential to the Hamiltonian of the system. The shape of the adaptive biasing potential is adjusted on the fly by sampling over the visited states. As the top of the barrier is approached, the biasing potentials become wider. This decreases the problem of trapping the system in the niches, introduced by the addition of Gaussians of fixed height in metadynamics. Our results for the free energy profiles of three test systems show that this method is more accurate and converges more quickly than the conventional metadynamics, and is quite comparable (in accuracy and convergence rate) with the well‐tempered metadynamics method. © 2017 Wiley Periodicals, Inc.     

Computational analysis for the determination of deleterious nsSNPs in human MTHFD1 gene

Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol. Out of 327 nsSNPs form human MTHFD1 gene, total 45 SNPs were predicted as functionally most significant SNPs, among which 17 were highly conserved and functional, 17 were highly conserved and structural residues. Among 45 most significant SNPs, 15 were predicted to be involved in post translational modifications. The p.Gly165Arg may interfere in homodimer interface formation. The p.Asn439Lys and p.Asp445Asn may interfere in binding interactions of MTHFD1 protein with cesium cation and potassium. The two SNPs (p.Asp562Gly and p.Gly637Cys) might interfere in interactions of MTHFD1 with ligand.     

Virtual screening of B-Raf kinase inhibitors: A combination of pharmacophore modelling,molecular docking, 3D-QSAR model and binding free energy calculation studies

B-Raf kinase has been identified as an important target in recent cancer treatment. In order to discover structurally diverse and novel B-Raf inhibitors (BRIs), a virtual screening of BRIs against ZINC database was performed by using a combination of pharmacophore modelling, molecular docking, 3D-QSAR model and binding free energy (ΔG_bind) calculation studies in this work. After the virtual screening, six promising hit compounds were obtained, which were then tested for inhibitory activities of A375 cell lines. In the result, five hit compounds show good biological activities (IC₅₀ < 50 μM). The present method of virtual screening can be applied to find structurally diverse inhibitors, and the obtained five structurally diverse compounds are expected to develop novel BRIs.     

Initiator-Loaded Gold Nanocages as a Light-Induced Free-Radical Generator for Cancer Therapy

Tumor hypoxia greatly suppresses the therapeutic efficacy of photodynamic therapy (PDT), mainly because the generation of toxic reactive oxygen species (ROS) in PDT is highly oxygen-dependent. In contrast to ROS, the generation of oxygen-irrelevant free radicals is oxygen-independent. A new therapeutic strategy based on the light-induced generation of free radicals for cancer therapy is reported. Initiator-loaded gold nanocages (AuNCs) as the free-radical generator were synthesized. Under near-infrared light (NIR) irradiation, the plasmonic heating effect of AuNCs can induce the decomposition of the initiator to generate alkyl radicals (R^.), which can elevate oxidative-stress (OS) and cause DNA damages in cancer cells, and finally lead to apoptotic cell death under different oxygen tensions. As a proof of concept, this research opens up a new field to use various free radicals for cancer therapy.     

Photochemical synthesis: Using light to build C–C bonds under mild conditions

A review of recent advancements in metal-free arylations via photogenerated triplet aryl cations and decatungstate anion ([W₁₀O₃₂]⁴⁻) photocatalyzed C–C bond formation is reported herein. These approaches are two examples of the great potentialities of photons as green activants in organic synthesis, allowing the functionalization of different chemical substrates under mild conditions (room temperature, aqueous solvents, absence of aggressive and unstable reactants and of expensive transition metal-based catalysts, and chance to use solar light as the energy source).     

Free boundary minimal hypersurfaces with spherical boundary

We first prove that a compact embedded minimal annulus in meeting two concentric spheres perpendicularly along the boundaries is part of a plane. We also prove that an embedded minimal hypersurface lying outside of a ball is part of either a catenoid or a hyperplane if it is perpendicular to the sphere along the boundary and has only one end that is asymptotic to either a catenoid if , or a hyperplane if .