Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Based on torsion angle distributions of frequently occurring substructures, conformation preferences of druglike molecules are presented, accompanied by a review of the relevant literature. First, the relevance of the Cambridge Structural Database (CSD) for drug design is demonstrated by comparing substructures present in compounds entering clinical trials with those found in the CSD and protein-bound ligands in the Protein Data Bank (PDB). Next, we briefly highlight preferred conformations of elementary acyclic systems, followed by a discussion of sulfonamide conformations. Due to their central role in medicinal chemistry, we discuss properties of aryl ring substituents in depth, including biaryl systems and systems of two aryl rings connected by two acyclic bonds. For a subset of torsion motifs, we also compare torsion angle histograms derived from CSD structures with those derived from ligands in the PDB. Furthermore, selected properties of some six- and seven-membered ring systems are discussed. The article closes with a section on attractive sulfur-oxygen contacts.     

AlCl3-catalyzed tandem acetylation of hydroarylated [60]fullerenes

The AlCl3-catalyzed acetylation of 1,2-hydrophenylated [60]fullerenes, HC60-Ar, proceeded via a sequential manner involving the acetylation at the hydrogenated fullerene carbon, the following intramolecular cyclization with the adjacent aryl group, the facile loss of water, and the second acetylation of the generated indenylidene double bond. However, the similar reaction of the hydrobiphenylated analogue brought about the normal acetylation at the terminal aromatic ring prior to the same sequential reactions as did hydrophenylated fullerenes.     

Anti-babesial compounds from Curcuma xanthorrhiza

Anti-babesial ingredients, (12R)- and (12S)-12,13-dihydro-12,13-dihydroxyxanthorrhizols, were isolated from Curcuma xanthorrhiza. The structures were established by the extensive NMR techniques. The assignments of (1)H NMR data of (12R)-12,13-dihydro-12,13-dihydroxyxanthorrhizol was revised, and (12S)-12,13-dihydro-12,13-dihydroxyxanthorrhizol was isolated as a pure form for the first time. The IC(50) of the active compounds were compared with that of commercial drug, diminazene aceturate (Ganaseg). IC(50) values of Ganaseg, (12R)-, and (12S)-12,13-dihydro-12,13-dihydroxyxanthorrhizols were 0.6 microg mL(-1), 8.3 microg mL(-1) and 11.6 microg mL(-1), respectively.     

Dynamics of ice nucleation on water repellent surfaces

Prevention of ice accretion and adhesion on surfaces is relevant to many applications, leading to improved operation safety, increased energy efficiency, and cost reduction. Development of passive nonicing coatings is highly desirable, since current antiicing strategies are energy and cost intensive. Superhydrophobicity has been proposed as a lead passive nonicing strategy, yet the exact mechanism of delayed icing on these surfaces is not clearly understood. In this work, we present an in-depth analysis of ice formation dynamics upon water droplet impact on surfaces with different wettabilities. We experimentally demonstrate that ice nucleation under low-humidity conditions can be delayed through control of surface chemistry and texture. Combining infrared (IR) thermometry and high-speed photography, we observe that the reduction of water-surface contact area on superhydrophobic surfaces plays a dual role in delaying nucleation: first by reducing heat transfer and second by reducing the probability of heterogeneous nucleation at the water-substrate interface. This work also includes an analysis (based on classical nucleation theory) to estimate various homogeneous and heterogeneous nucleation rates in icing situations. The key finding is that ice nucleation delay on superhydrophobic surfaces is more prominent at moderate degrees of supercooling, while closer to the homogeneous nucleation temperature, bulk and air-water interface nucleation effects become equally important. The study presented here offers a comprehensive perspective on the efficacy of textured surfaces for nonicing applications.     

A High‐Barrier Molecular Balance for Studying Face‐to‐Face Arene–Arene Interactions in the Solid State and in Solution

An atropisomeric molecular balance was developed to study face‐to‐face arene–arene interactions. The balance has a large central 1,4,5,8‐naphthalene diimide surface that forms intramolecular arene–arene interactions with two pendent arms. The balance adopts distinct syn and anti isomers with varying numbers of intramolecular interactions. Thus, the strength of the arene–arene interaction could be quantitatively measured by NMR spectroscopy from the anti/syn ratios. The size of the arene arms was easily varied, which allowed examination of the relationship between arene size and strength of the interaction. A nonlinear size dependence was observed in solution with larger arene arms having a disproportionately stronger arene–arene interaction. The intramolecular arene–arene interactions were also characterized in the solid state by X‐ray crystallography. These studies were facilitated by the kinetic stability of the syn and anti isomers at room temperature due to the high isomerization barrier (ΔG=27.0 kcal mol^?1). Thus, the anti isomer could be selectively isolated and crystallized in its folded conformation. The X‐ray structures confirmed that the anti isomers formed two strong intramolecular arene–arene interactions with face‐to‐face geometries. The solid‐state structure analysis also reveals that the rigid framework may contribute to the observed nonlinear size trend. The acetate linker is slightly too long, which selectively destabilizes the balances with smaller arene arms. The larger arene arms are able to compensate for the longer linker and form effective intramolecular arene–arene interactions.     

Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge

Here, we test a method, called semi-explicit assembly (SEA), that computes the solvation free energies of molecules in water in the SAMPL4 blind test challenge. SEA was developed with the intention of being as accurate as explicit-solvent models, but much faster to compute. It is accurate because it uses pre-simulations of simple spheres in explicit solvent to obtain structural and thermodynamic quantities, and it is fast because it parses solute free energies into regionally additive quantities. SAMPL4 provided us the opportunity to make new tests of SEA. Our tests here lead us to the following conclusions: (1) The newest version, called Field-SEA, which gives improved predictions for highly charged ions, is shown here to perform as well as the earlier versions (dipolar and quadrupolar SEA) on this broad blind SAMPL4 test set. (2) We find that both the past and present SEA models give solvation free energies that are as accurate as TIP3P. (3) Using a new approach for force field parameter optimization, we developed improved hydroxyl parameters that ensure consistency with neat-solvent dielectric constants, and found that they led to improved solvation free energies for hydroxyl-containing compounds in SAMPL4. We also learned that these hydroxyl parameters are not just fixing solvent exposed oxygens in a general sense, and therefore do not improve predictions for carbonyl or carboxylic-acid groups. Other such functional groups will need their own independent optimizations for potential improvements. Overall, these tests in SAMPL4 indicate that SEA is an accurate, general and fast new approach to computing solvation free energies.     

Fatty acids. II. The synthesis and gas-liquid chromatographic behaviour of five trimethylene-interrupted C18-diunsaturated fatty acids.

Five trimethylene-interrupted methyl octadecadiynoates, C18 delta-2a,-7a; delta-3a,-8a; delta-4a,-9a; delta-5a,-10a and delta-6a,-11a, and the corresponding cis,cis-octadecadienoates were synthesized, and their gas-liquid chromatographic properties were studied on Apiezon L, diethylene glycol succinate polyester and Silac 10C stationary phases. The equivalent chain lengths of these esters have been determined, and the separation of mixtures and the prediction of gas chromatographic behaviour of these isomers are discussed.