Scanning tunneling microscopy of prochiral anthracene derivatives on graphite: chain length effects on monolayer morphology

The morphology of monolayers formed upon adsorption of prochiral 1,5-substituted anthracene derivatives on highly oriented pyrolytic graphite is investigated using scanning tunneling microscopy at the liquid-solid interface. The adsorption orientation of these prochiral anthracene derivatives positions one of their enantiotopic faces in contact with the graphite. The molecules adsorb in rows with contact between adjacent anthracenes. The anthracene side chains extend perpendicular to the direction of the row repeat. All molecules within a single row adsorb via the same enantiotopic face. Anthracenes with side chains containing an even number of non-hydrogenic atoms (C, S) form monolayers in which molecules in adjacent rows adsorb via opposite enantiotopic faces. Anthracenes with side chains that contain an odd number of non-hydrogenic atoms form two-dimensional chiral domains in which all rows contain molecules adsorbed via the same enantiotopic face. This chain length effect on monolayer morphology represents a generalized example of structural effects previously observed in alkanoic acid monolayers formed on HOPG. The variation of the STM current with position in the vicinity of the anthracenes indicates that the highest occupied molecular orbital is the predominant mediator of tunneling for the aromatic group.     

Multicomponent coupling approach to (+/-)-frondosin B and a ring-expanded analogue

[reaction: see text] A recently discovered multicomponent coupling reaction is used to give direct access to a late intermediate in the synthesis of frondosin B. This intermediate can also be efficiently converted to a ring-expanded analogue of frondosin B by sustained heating of the reaction mixture. An unprecedented tandem 1,7-hydrogen shift, 8pi-electrocyclization is proposed to explain the formation of this ring-expanded species.     

High-load, soluble oligomeric carbodiimide: synthesis and application in coupling reactions

A facile preparation of a high-load, soluble oligomeric alkyl cyclohexylcarbodiimide (OACC) reagent via ROM polymerization from commercially available starting materials is described. This reagent is exploited as a coupling reagent for esterification, amidation, and dehydration of carboxylic acids (aliphatic and aromatic) with an assortment of alcohols (aliphatic primary, secondary, and benzylic), thiols, phenols, and amines (aliphatic primary, secondary, benzylic, and aromatic/anilines), respectively. Following the coupling event, precipitation with an appropriate solvent (Et(2)O, MeOH, or EtOAc), followed by filtration through a SPE provides the products in good to excellent yield and purity.     

Novel Copolymers of 4-Fluorostyrene. 1. Alkyl Ring-Substituted 2-Phenyl-1,1-dicyanoethylenes

Novel copolymers of trisubstituted ethylene monomers, alkyl ring-substituted 2-phenyl-1,1-dicyanoethylenes, RC₆H₄CH = C(CN)₂ (where R is 2-methyl, 3-methyl, 4-methyl, 4-ethyl, 4-i-propyl, 4-butyl, 4-i-butyl, and 4-t-butyl) and 4-fluorostyrene were prepared at equimolar monomer feed composition by solution copolymerization in the presence of a radical initiator (ABCN) at 70°C. The composition of the copolymers was calculated from nitrogen analysis, and the structures were analyzed by IR, ¹H and ¹³C-NMR. The order of relative reactivity (1/r ₁) for the monomers is 4-ethyl (42.6) > 4-butyl (29.4) > 4-t-butyl (26.7) > 4-i-butyl (1.6) > 4-i-propyl (1.29) > 3-methyl (1.26) > 2-methyl (0.8) > 4-methyl (0.4). High T _g of the copolymers, in comparison with that of poly(4-fluorostyrene) indicates a substantial decrease in chain mobility of the copolymer due to the high dipolar character of the trisubstituted ethylene monomer unit. Decomposition of the copolymers in nitrogen occurred in two steps, first in 183–500°C range with residue (5–30% wt.), which then decomposed in the 500–800°C range.     

Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein–ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate binders from nonbinders in virtual screening and to more accurately predict the ligand binding modes prior to the more computationally expensive FEP calculations of binding affinity.     

A versatile protocol for the preparation of substituted 1- and 2-naphthyl piperazines from aminonaphthols

Aminonaphthols are easily transformed into a variety of 1- and 2-naphthyl piperazines using a sequence of diazotization, iodide substitution and Pd(0) catalyzed coupling reactions.     

Quinazolines and 1,4-benzodiazepines. XCV. Synthesis of 1,4-benzodiazepines by ring expansion of 2-chloromethylquinazolines with carbanions

1,4-Benzodiazepines bearing a carbon substituent at the 2-position were obtained by reaction of 2-chloromethylquinazoline 3-oxides with stabilized carbanions. The carbanions of alkyl acetates, N,N-disubstituted acetamides, acetonitrile, dimethylsulfone, N,N-dimethyl methanesulfonamide and 2-methylpyridine were successfully applied. The conversion of some of the 2-carbon substituted 1,4-benzodiazepines to imidazo[1,5-a][1,4]benzodiazepines and [1,2,5]oxadiazino[5,4-a][1,4]benzodiazepines is described.     

A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge

As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host–guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye–Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.     

Enantiospecific activity of tetracyclic PAF-antagonists

The syntheses of two enantiomeric tetracyclic compounds, the thieno[3,2-f][pyrrolo[2,1-c][1,2,4]triazolo[4,3-a][1,4]diazepines 10a and 10b are described. Testing of these enantiomers as inhibitors of platelet activating factor (PAF) revealed good enantiospecificity, meaning that one enantiomer is responsible for the observed biological activity.     

Rheological and Solubility Properties of Soy Protein Isolate

Soy protein isolate (SPI) powders often have poor water solubility, particularly at pH values close to neutral, which is an attribute that is an issue for its incorporation into complex nutritional systems. Therefore, the objective of this study was to improve SPI solubility while maintaining low viscosity. Thus, the intention was to examine the solubility and rheological properties of a commercial SPI powder at pH values of 2.0, 6.9, and 9.0, and determine if heat treatment at acidic or alkaline conditions might positively influence protein solubility, once re-adjusted back to pH 6.9. Adjusting the pH of SPI dispersions from pH 6.9 to 2.0 or 9.0 led to an increase in protein solubility with a concomitant increase in viscosity at 20 °C. Meanwhile, heat treatment at 90 °C significantly improved the solubility at all pH values and resulted in a decrease in viscosity in samples heated at pH 9.0. All SPI dispersions measured under low-amplitude rheological conditions showed elastic-like behaviour (i.e., G′ > G″), indicating a weak “gel-like” structure at frequencies less than 10 Hz. In summary, the physical properties of SPI can be manipulated through heat treatment under acidic or alkaline conditions when the protein subunits are dissociated, before re-adjusting to pH 6.9.