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.     

Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.     

Coulometric titration of penicillins and penicillamine with mercury(II)

An absolute coulometric method based on the titration of hydrolysed penicillins with coulometrically generated mercury(II) is presented. An amalgamated gold plate is used as anode and the titration is performed in a pH 4.6 acetate buffer solution. The method gives values which deviate by less than 1% from values obtained by other absolute methods. The relative standard deviation for determination of penicillin G is 0.4%. The determinations of penicillamine and mixtures of penicillamine and penicilloate are also reported.     

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.

---

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.

     

Reagents for (ir)reversible enzymatic acylations

Commonly, hydrolase-catalysed reactions are used for kinetic resolutions of alcohols, amines and acids. Only a few applications in total syntheses have been described. Most of these examples are for the synthesis of amides and peptides. Here, the synthesis of all the different types of activated acids that can be applied in hydrolase-catalysed acylations is described. The application of these activated acids for both the formation of esters and amides is discussed and the different reactions are compared with the equivalent chemical reactions.     

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.     

(6-4)-photolyase activity requires a charge shift reaction

A model compound containing a thymine oxetane moiety linked to a flavin chromophore was investigated regarding (6-4)-photolyase activity. The need for a charge shift reaction was demonstrated by a detailed pH-dependent kinetic analysis.