Vectorization of a classical trajectory code on a floating point systems,Inc. Model 164 attached processor

A triatomic classical trajectory code has been modified by extensive vectorization of the algorithms to achieve much improved performance on an FPS 164 attached processor. Extensive timings on both the FPS 164 and a VAX 11/780 with floating point accelerator are presented as a function of the number of trajectories simultaneously run. The timing tests involve a potential energy surface of the LEPS variety and trajectories with 1000 time steps. The results indicate that vectorization results in timing improvements on both the VAX and the FPS. For larger numbers of trajectories run simultaneously, up to a factor of 25 improvement in speed occurs between VAX and FPS vectorized code.     

α,ω-Diisocyanatocarbodiimides, -Polycarbodiimides,and Their Derivatives

Research in the field of low-molecular weight, oligomeric and polymeric α,ω-diisocyanatocarbodiimides and -polycarbodiimides has been fruitful, not only in connection with these compounds themselves, but also—as so often happens in chemistry—with quite different problems. Novel synthetic methods, discoveries concerning the properties of low-molecular weight carbodiimides and phosphane imide derivatives, as well as results on the fragmentation reactions of four-membered heterocyclic compounds containing oxygen, phosphorus, and nitrogen, and a better understanding of the diisocyanate polyaddition process are among the many by-products of this research. The “high- and low-temperature formation” of polycarbodiimides and the homogeneous and heterogeneous catalysis of this process are described, and the fundamental importance of four-membered ring fragmentation mechanisms resulting in the formation of phosphane imide derivatives is outlined. Interesting building blocks for the diisocyanate polyaddition and polycondensation processes can be synthesized by many derivatization reactions of oligomeric and high-molecular weight polycarbodiimides and polyuretonimines. The in situ production of polycarbodiimides via matrix reactions in flexible polyurethane foams leads to a cellular arrangement of the material due to the pronounced symmetrical growth processes. Combination-foams with increased carbonation tendencies are formed in this way. Attention is drawn to several industrial applications of α,ω-diisocyanatopolycarbodiimides, of high-molecular weight cross-linked polyuretonimines, and of polycarbodiimide foams.     

New pressure-density-temperature measurements and new rational equations for the saturated liquid and vapour densities of oxygen

The results of pressure, density, temperature (p, ?, T) measurements in the temperature range from 65 K to 300 K, for pressures up to 7.2 MPa, and for densities from 0.3 mol dm^?3 to 39 mol dm^?3, are presented for pure oxygen. Using the experimental results, new values for the densities of saturated liquid and vapour are evaluated. To check the accuracy of these results, corresponding sets reported in the literature are critically analysed to determine the most reliable p, ?, T set for oxygen. Finally, new equations for the densities of saturated liquid and vapour are developed using a statistical procedure.     

TreeDock: a tool for protein docking based on minimizing van der Waals energies

Predicting protein-protein and protein-ligand docking remains one of the challenging topics of structural biology. The main problems are (i) to reliably estimate the binding free energies of docked states, (ii) to enumerate possible docking orientations at a high resolution, and (iii) to consider mobility of the docking surfaces and structural rearrangements upon interaction. Here we present a novel algorithm, TreeDock, that addresses the enumeration problem in a rigid-body docking search. By representing molecules as multidimensional binary search trees and by exploring a sufficient number of docking orientations such that two chosen atoms, one from each molecule, are always in contact, TreeDock is able to explore all clash-free orientations at very fine resolution in a reasonable amount of time. Due to the speed of the program, many contact pairs can be examined to search partial or complete surface areas. The deterministic systematic search of TreeDock is in contrast to most other docking programs that use stochastic searches such as Monte Carlo or simulated annealing methods. At this point, we have used the Lennard-Jones potential as the only scoring function and show that this can predict the correct docked conformation for a number of protein-protein and protein-ligand complexes. The program is most powerful if some information is known about the location of binding faces from NMR chemical-shift perturbation studies, orientation information from residual dipolar coupling, or mutational screening. The approach has the potential to include docking-site mobility by performing molecular dynamics or other randomization methods of the docking site and docking families to families of structures. The performance of the algorithm is demonstrated by docking three complexes of immunoglobulin superfamily domains, CD2 to CD58, the V(alpha) domain of a T-cell receptor to its V(beta) domain, and a T-cell receptor to a pMHC complex as well as a small molecule inhibitor to a phosphatase.     

Tautomerism and stereochemistry of hypericin: Force field,NMR, and X-ray crystallographic investigations

Summary Stereochemistry and tautomerism of hypericin, pseudohypericin, and several of their partial structure models were investigated using an MM2 derived force field method. Besides the propeller type conformer, which was also found by the X-ray crystallographic study, the complicated energy hypersurface was shown to contain a novel double-butterfly conformer of similar stability. The upper limit interconversion barrier between these conformers and their enantiomers was found to be in the order of 115 kJ/mol.¹H-NMR experiments suggested a lower limit interconversion barrier of at least 80 kJ/mol. From the ten tautomers possible in principle, the 7,14-species was derived to be the most stable one by at least 48 kJ/mol.

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Tautomerie und Stereochemie von Hypericin: Untersuchungen mit Hilfe der Kraftfeld-Methodik, NMR-Spektroskopie und Röntgenstrukturanalyse

Zusammenfassung Die Stereochemie von Hypericin, Pseudohypericin und einigen seiner Partialstrukturmodelle wurde mit Hilfe einer von MM2 abgeleiteten Kraftfeldmethodik untersucht. In der komplizierten Energiehyperfläche wurde neben dem auch durch Röntgenstrukturanalyse gefundenen Propeller-Konformeren ein neues Doppelschmetterling-Konformer ähnlicher Stabilität aufgefunden. Die obere Grenze für die Interkonversionsbarrieren zwischen diesen Konformeren und ihren Enantiomeren sind in der Größenordnung von 115 kJ/mol. Aus¹H-NMR-Experimenten konnte eine untere Grenze von wenigstens 80 kJ/mol abgeleitet werden. Es wurde gefunden, daß von den zehn prinzipiell möglichen Tautomeren die 7,14-Spezies die um wenigstens 48 kJ/mol stabilste ist.

     

Ligand discrimination in the reaction of nitrones with [PtCl2(PhCN)2]. Selective formation of mono-oxadiazoline and mixed bis-oxadiazoline complexes under thermal and microwave conditions

[2+3] Cycloaddition of nitrones to the nitrile ligands in the complexes cis- or trans-[PtCl2(PhCN)2] occurs under ligand differentiation and allows for selective synthesis of complexes of the type cis- or trans-[PtCl2(oxadiazoline)(PhCN)]. Microwave irradiation enhances the reaction rates of the cycloaddition considerably and further favours the selectivity towards the mono-cycloadduct with respect to thermal conditions, because the first cycloaddition is accelerated to a higher extent than the second one. Reaction of the trans-substituted mono-oxadiazoline complexes with a nitrone different from the one used for the first cycloaddition step gives access to mixed bis-oxadiazoline compounds of the composition trans-[PtCl2(oxadiazoline-a)(oxadiazoline-b)]. The corresponding cis-configured complexes, however, do not undergo further cycloaddition. All reactions described occur without isomerisation of the stereochemistry around the platinum center, independently of whether thermal or microwave heating is applied.     

SIACON—Equipment for the on-line determination of the silicon content of coal

The paper describes an automatic equipment which allows to determine the silicon content of coal by neutron activation analysis. The technique is based on the measurement of gamma-ray intensity of the²⁸Al radionuclide, which is the result of the fast neutron reaction²⁸Si(n, p)²⁸ Al. The Activation part includes a Pu-238/Be neutron source which is located in the middle of the sample container; the measuring part includes two NaI(Tl)-scintillation counters. The total time of the anlysis of one sample amounts to a few minutes; the standard deviation of a single determination is 0.2% SiO₂.     

Palladium-catalyzed, stereoselective rearrangement of a tetracyclic allyl cyclopropane under arylation

The first example of a pi,sigma domino-Heck reaction under concomitant rearrangement of the tetracyclic allylcyclopropane endo,exo-bishomobarrelene (5) is reported; the stereoselective reaction proceeds via an intramolecular insertion of a primarily-formed carbopalladation intermediate into a strained cyclopropane C-C sigma-bond, giving 9.     

Synthesis and solid-state organization of coil-ring-coil block copolymers

Shape-persistent macrocycles based on the phenyl-ethynyl-butadienyl backbone containing two extraannular hydroxyl groups were prepared by the oxidative coupling of the appropriate phenylethynyl oligomers. Carbodiimide-directed coupling with independently synthesized polystyrene carboxylic acid oligomers led to ABA coil-ring-coil block copolymers in which the central macrocycle serves as rigid and the polystyrene oligomers as flexible elements. Depending on the size of the coil blocks, these structures aggregate in cyclohexane into supramolecular hollow cylindrical brushes in which the rigid core is surrounded by the flexible matrix. However, in the solid state it is not possible to identify a morphology in which isolated channels based on aggregated macrocycles are embedded in a matrix of polystyrene. Detailed X-ray and electron diffraction studies on samples prepared from a solution in cyclohexane under equilibrium conditions show that the material adopts a lamellar morphology in the solid state in which columns of macrocycles are aggregated into layers which are separated by polystyrene.