Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster‐type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re‐docking of X‐ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.     

Comparative assessment of computational methods for the determination of solvation free energies in alcohol‐based molecules

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson–Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane‐alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM‐based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane‐alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane‐alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug‐binding in computer‐aided drug design. © 2013 Wiley Periodicals, Inc.     

Liquid-Crystal Based Formulations for Topical Drug Delivery

Monoolein, being a biocompatible and bioadhesive penetration enhancer that can form liquid crystalline (LC) phases, possesses remarkable characteristics for addressing drug delivery systems across the biological membrane. A range of formulations based on LC phases were investigated in this study, which includes lamellar, reverse hexagonal, and bicontinuous cubic phases along with an emulsion stabilized by LC phases. Caffeine was chosen as hydophilic model drug to evaluate in vitro release performance. The different monoolein based caffeine formulations were characterized by techniques such as polarized light microscopy, nuclear magnetic resonance (NMR) and small angle x-ray scattering (SAXS). The release experiments, performed through Franz diffusion cells, revealed that the presence of a liquid crystalline (LC) phase prevented burst release in all cases. In addition, taking into consideration that all ingredients are fully biocompatible, the creamy emulsion formulation stabilized by a hexagonal lipid LC phase can be proposed as a challenging preformulation for topical drug delivery.     

Three‐Dimensional Architectures Incorporating Stereoregular Donor–Acceptor Stacks

We report the synthesis of two [2]catenane‐containing struts that are composed of a tetracationic cyclophane (TC⁴⁺) encircling a 1,5‐dioxynaphthalene (DNP)‐based crown ether, which bears two terphenylene arms. The TC⁴⁺ rings comprise either 1) two bipyridinium (BIPY²⁺) units or 2) a BIPY²⁺ and a diazapyrenium (DAP²⁺) unit. These degenerate and nondegenerate catenanes were reacted in the presence of Cu(NO₃)₂?2.5 H₂O to yield Cu‐paddlewheel‐based MOF‐1050 and MOF‐1051. The solid‐state structures of these MOFs reveal that the metal clusters serve to join the heptaphenylene struts into grid‐like 2D networks. These 2D sheets are then held together by infinite donor–acceptor stacks involving the [2]catenanes to produce interpenetrated 3D architectures. As a consequence of the planar chirality associated with both the DNP and hydroquinone (HQ) units present in the crown ether, each catenane can exist as four stereoisomers. In the case of the nondegenerate (bistable) catenane, the situation is further complicated by the presence of translational isomers. Upon crystallization, however, only two of the four possible stereoisomers—namely, the enantiomeric RR and SS forms—are observed in the crystals. An additional element of co‐conformational selectivity is present in MOF‐1051 as a consequence of the substitution of one of the BIPY²⁺ units by a DAP²⁺ unit: only the translational isomer in which the DAP²⁺ unit is encircled by the crown ether is observed. The overall topologies of MOF‐1050 and MOF‐1051, and the selective formation of stereoisomers and translational isomers during the kinetically driven crystallization, provide evidence that weak noncovalent bonding interactions play a significant role in the assembly of these extended (super)structures.     

Surfactant Hydrogels for the Dispersion of Carbon‐Nanotube‐Based Catalysts

Novel hydrogel phases based on positively charged and zwitterionic surfactants, namely, N‐[p‐(n‐dodecyloxybenzyl)]‐N,N,N‐trimethylammonium bromide (pDOTABr) and p‐dodecyloxybenzyldimethylamine oxide (pDOAO), which combine pristine carbon nanotubes (CNTs), were obtained, thus leading to stable dispersions and enhanced cross‐linked networks. The composite hydrogel featuring a well‐defined nanostructured morphology and an overall positively charged surface was shown to efficiently immobilise a polyanionic and redox‐active tetraruthenium‐substituted polyoxometalate (Ru₄POM) by complementary charge interactions. The resulting hybrid gel has been characterised by electron microscopy techniques, whereas the electrostatic‐directed assembly has been monitored by means of fluorescence spectroscopy and ζ‐potential tests. This protocol offers a straightforward supramolecular strategy for the design of novel aqueous‐based electrocatalytic soft materials, thereby improving the processability of CNTs while tuning their interfacial decoration with multiple catalytic domains. Electrochemical evidence confirms that the activity of the catalyst is preserved within the gel media.     

Potent Antimalarial 1,2,4‐Trioxanes through Perhydrolysis of Epoxides

Perhydrolysis of a sterically congested multifunctional epoxide was achieved in ethereal H₂O₂ with the aid of a recently developed Mo catalyst. The resulting hydroperoxide cyclized to give a 1,2,4‐trioxane, which could be readily elaborated into qinghaosu and a range of novel analogues. Some of the compounds with two such trioxane moieties showed in vitro antimalarial activity comparable to or even better than that of artesunate or chloroquine.     

(Co)oxidation/cyclization processes upon irradiation of triphenylamine

Irradiation of triphenylamine (Ph₃N) in nitrogen-flushed solution leads to 9-phenylcarbazole and two tetrahydroderivatives (1,2,3,4- and 1,2,7,8-) via disproportionation of the corresponding 4a,4b-dihydrocarbazole. In oxygen-equilibrated solution oxidative cyclization occurs through the intermediacy of a triplet peroxy diradical, which either abstracts a hydrogen atom intramolecularly or (mainly) cleaves back to the reagents. The role of the key intermediates is supported by DFT calculations and by trapping by triarylphosphines (that are thus efficiently oxidized, while preventing the cyclization of Ph₃N). The hydroperoxide, on the other hand, causes inefficient co-oxidation of sulfides.     

Evaluation of As,Se and Zn in octopus samples in different points of sales of the distribution chain in Brazil

Three CRMs of different matrix composition were analysed, representing an environmental matrix sample (BCR–320R Channel Sediment), a botanical matrix sample (SRM 1547 Peach Leaves) and a zoological matrix sample (SRM 1566b Oyster Tissue). The element mass fractions were obtained using the KayWin program. Analytical measurement uncertainty was determined by two approaches: (1) the routine procedure applying combination of the overall uncertainty u(m) = 3.5 % and statistical uncertainty of the peak area determination and (2) the procedure applying the dedicated ERON program for calculating uncertainty. Performance of altogether 31 certified values was tested by means of calculating E _n numbers. For the remaining 52 non-certified values, comparison between uncertainties obtained by the two approaches was made. When using the first approach, the E _n number showed satisfactory performance in 28 cases; by using the second approach, the E _n number showed satisfactory performance in 27 cases. None of the unsatisfactory performances (E _n  > 1) appeared to be of systematic nature. The uncertainties obtained by applying the two approaches revealed a big extent of consistency. As the present nuclear database lacks lot of data that serve as input to the ERON program, in particular uncertainties of Q ₀ factors, estimates need to be introduced for the missing values, emphasising the urgent need to upgrade the database with missing data.     

Four related benzazepine derivatives in a reaction pathway leading to a benzazepine carboxylic acid: hydrogen‐bonded assembly in zero,one, two and three dimensions

(2R*,4S*)‐Methyl 2,3,4,5‐tetrahydro‐1,4‐epoxy‐1H‐benz[b]azepine‐2‐carboxylate, C₁₂H₁₃NO₃, (I), and its reduction product (2R*,4S*)‐methyl 4‐hydroxy‐2,3,4,5‐tetrahydro‐1H‐benz[b]azepine‐2‐carboxylate, C₁₂H₁₅NO₃, (II), both crystallize as single enantiomers in the space group P2₁2₁2₁, while the hydrolysis product (2RS,4SR)‐4‐hydroxy‐2,3,4,5‐tetrahydro‐1H‐benz[b]azepine‐2‐carboxylic acid, C₁₁H₁₃NO₃, (III), and the lactone (2RS,5SR)‐8‐(trifluoromethoxy)‐5,6‐dihydro‐1H‐2,5‐methanobenz[e][1,4]oxazocin‐3(2H)‐one, C₁₂H₁₀F₃NO₃, (IV), both crystallize as racemic mixtures in the space group P2₁/c. The molecules of compound (IV) are linked into centrosymmetric R₂²(10) dimers by N—H...O hydrogen bonds, and those of compound (I) are linked into chains by C—H...π(arene) hydrogen bonds. A combination of O—H...O and O—H...N hydrogen bonds links the molecules of compound (III) into sheets containing equal numbers of R₄⁴(14) and R₄⁴(26) rings, and a combination of C—H...π(arene) hydrogen bonds and three‐centre O—H...(N,O) hydrogen bonds links the molecules of compound (II) into a three‐dimensional framework structure. Comparisons are made with some related compounds.     

High-Reynolds-number effects on turbulent scalings in compressible channel flow

The effect of the Reynolds number in a supersonic isothermal channel flow is studied using a direct numerical simulation (DNS). The bulk Mach number based on the wall temperature is 1.5, and the bulk Reynolds number is increased up to Re_τ ≈︁ 1000. The use of van Driest velocity transformation in the presence of heated walls has been questioned due to the poor accuracy at low Reynolds number. For this reason alternative transformations of the velocity profile and turbulence statistics have been proposed, as, for instance, semi-local scalings. We show that the van Driest transformation recovers its accuracy as the Reynolds number is increased. The Reynolds stresses collapse on the incompressible ones, when properly scaled with density, and very good agreement with the incompressible stresses is found in the outer layer. (© 2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)