Force-field parametrization based on radial and energy distribution functions

We propose a novel force-field-parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher-level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Systems biology and systems chemistry: new directions for drug discovery

Improvements in drug design have historically been centered around structure-based optimization of molecule specificity for a targeted protein, in an effort to reduce unintentional binding to other proteins and off-target effects. Although the "one-to-one" drug design strategy has been successful in impairing function of targets associated with a number of diseases, recent reports of drug promiscuity, which are a potential source of adverse reactions in patients, make a case to refine the drug design strategy such that it includes an awareness of multiple interactions from both ligand and protein perspectives. Polypharmacology and chemical biology studies are amassing interaction data at rapid rates, and the integration of such data into an interpretable model requires zooming our perspective out from the single ligand-target level to the larger network-wide level. We review some of the recent developments in systems-level research for drug design and discovery, and discuss the directions that some drug design efforts are heading toward.     

Cycloisomerization of 1,6-enynes: asymmetric multistep preparation of a hydrindane framework in water with polymeric catalysts

[Reaction: see text] Cycloisomerization of 1,6-enynes proceeded smoothly in water under heterogeneous conditions in the presence of a palladium complex supported on polystyrene-poly(ethylene glycol) copolymer resin to give the corresponding cyclopentanes with a high level of chemical greenness. Multistep asymmetric synthesis of a hydrindane framework was achieved via palladium-catalyzed asymmetric pi-allylic alkylation, propargylation, and cycloisomerization of 1,6-enynes, where all three steps were performed in water with recyclable polymeric catalysts.     

Yeasts and Lactic Acid Bacteria Mixed-Specie Biofilm Formation is a Promising Cell Immobilization Technology for Ethanol Fermentation

We previously found that some Saccharomyces cerevisiae and Lactobacillus plantarum remarkably formed mixed-specie biofilm in a static co-culture and deduced that this biofilm had potential as immobilized cells. We investigated the application of mixed-specie biofilm formed by S. cerevisiae BY4741 and L. plantarum HM23 for ethanol fermentation in repeated batch cultures. This mixed-specie biofilm was far abundantly formed and far resistant to washing compared with S. cerevisiae single biofilm. Adopting mixed-specie biofilm formed on cellulose beads as immobilized cells, we could produce enough ethanol from 10 or 20 % glucose during ten times repeated batch cultures for a duration of 10 days. Cell numbers of S. cerevisiae and L. plantarum during this period were stable. In mixed-specie biofilm system, though ethanol production was slightly lower compared to S. cerevisiae single-culture system due to by-production of lactate, pH was stably maintained under pH 4 without artificial control suggesting high resistance to contamination. Inoculated model contaminants, Escherichia coli and Bacillus subtilis, were excluded from the system in a short time. From the above results, it was indicated that the mixed-specie biofilm of S. cerevisiae and L. plantarum was a promising immobilized cell for ethanol fermentation for its ethanol productivity and robustness due to high resistance to contamination.     

Chiral bifunctional organocatalysts bearing a 1,3-propanediamine unit for the aza-MBH reaction

The introduction of a 1,3-propanediamine unit at the 3-position of (S)-BINOL using a methylene spacer led to the formation of a chiral bifunctional organocatalyst for the aza-Morita–Baylis–Hillman (aza-MBH) reaction. The organocatalyst 1k mediated aza-MBH transformations with high chemical yields and with up to 82% ee.     

Synthesis of chiral [5]helicenes using aromatic oxy-Cope rearrangement as a key step

Both enantiomers of (P)-(+)-2- and (M)-(−)-2-acetoxy-11,14-dimethyl[5]helicenes 8 were synthesized by asymmetric aromatic oxy-Cope rearrangement of the corresponding chiral bridged bicyclic compounds, which were obtained by enzymatic resolution. The absolute configurations of 8 were assigned by their circular dichroism spectra.     

A new strategy for construction of eight-membered carbocycles by Brook rearrangement mediated [6 + 2] annulation

[reaction: see text] A newly developed strategy for construction of eight-membered carbocycles via [6 + 2] annulation that involves the combination of beta-alkenoyl acylsilanes and a vinyllithium derivative is described. A unique feature of this annulative approach is that it enables in one operation and a stereoselective manner construction of eight-membered ring systems containing useful functionalities for further synthetic elaboration from readily available six- and two-carbon components.