OVID and SUPER: Two overlap programs for drug design

Summary Two programs, OVID and SUPER, for exploring the similarity of molecules with respect to their action at a receptor are described. OVID accepts two molecules as input and optimizes the three-dimensional overlap of specified atoms in one molecule with specified atoms in the second molecule. The result is expressed as a percent of the theoretical maximum. OVID gives a quantitative measure of the extent of a guessed correspondence between two molecules based on volume overlap of selected atoms. The Achilles' heel of OVID is that the correspondence between the two molecules has to be guessed. We realized that it would be better to systematically examine all possible correspondences of two structures to minimize the chance of overlooking a superior correspondence. We created SUPER to satisfy this need. SUPER accepts two molecules as input and finds the top twenty correspondences of their surfaces and charge distributions, giving a quantitative measure of the extent of each correspondence. An instructive example of the application of OVID and SUPER to the design of leukotriene D₄ receptor antagonists is described. SUPER appears to be a practical brainstorming tool for the medicinal chemist trying to understand how molecules whose structures may not resemble one another in an obvious way can bind to the same site.     

Tetragonal low-temperature structure of LiAl

The cubic face-centered structure of LiAl (, at ) transforms into a tetragonal body-centered structure (I4₁/amd, , at ). This first-order phase transition at about during heating is probably the reason for the so-called “ anomalies” in some physical properties like specific heat, electrical resistivity and nuclear-spin lattice relaxation. This transition seems to be correlated with the composition Li:Al of the alloy and the amount of Li vacancies.     

Preparation of polyfluorinated cycloalk-1-enyl-, alk-1-enyl-, and alkyliodine tetrafluorides using XeF2 in the presence of appropriate Lewis acids as fluorooxidant

Previously unknown polyfluorocyclohexenyl, and acyclic perfluoroalkenyliodine tetrafluorides were prepared in high yields. Perfluorocyclohex-1-enyliodine tetrafluoride was obtained from pentafluoroiodobenzene using XeF₂-NbF₅ in aHF. The reaction of C₆F₅I with the weaker fluorooxidant XeF₂-BF₃ in 1,1,1,3,3-pentafluorobutane (PFB) yielded C₆F₅IF₂, perfluorocyclohexa-1,4-dienyliodine difluoride, C₆F₅IF₄, perfluorocyclohexa-1,4, and 1,3-dienyliodine tetrafluoride as intermediate products on parallel reaction routes. Both perfluoroalkenyl iodides, cis- and trans-(CF₃)₂CFCFCFI, reacted with XeF₂-BF₃ in PFB to give the corresponding perfluoroalkenyliodine tetrafluorides, cis- and trans-(CF₃)₂CFCFCFIF₄. Even perfluoroalkyl iodides can be fluorinated by this reagent as was demonstrated by the preparation of C₆F₁₃IF₄ from C₆F₁₃I. Generally, the CFCIF_n fragment (n = 0, 2, or 4) in cyclic or acyclic perfluoroalkenyliodine compounds R_FIF_n did not undergo a transformation to the corresponding perfluoroalkyliodine compound. Furthermore, no perfluoroorganoiodine hexafluorides were detected in reactions with the fluorooxidant XeF₂-aHF or BF₃ or NbF₅.     

Kinetik und Mechanismus der Diazotierung, 18. Mitt.: Kinetik und Mechanismus der Diazotierung des Anilins in chlorwasserstoffsaurem Methanol

Ohne ZusammenfassungI.H. Schmid undG. Muhr, Ber. dtsch. chem. Ges.70, 421 (1937); II.H. Schmid, Z. Elektrochem.43, 626 (1937); III.H. Schmid, Atti X. Congr. internat. Chim. Roma2, 484 (1938); IV.H. Schmid undA. Woppmann, Mh. Chem.83, 346 (1952); V. und VI.H. Schmid undR. Pfeifer, Mh. Chem.84, 829, 842 (1953); VII.H. Schmid, Mh. Chem.85, 424 (1954); zusammenfassender Ber.:H. Schmid, Chemiker-Ztg.78, 565, 683 (1954); VIII.H. Schmid, Mh. Chem.86, 668 (1955); IX.H. Schmid undA. F. Sami, Mh. Chem.86, 904 (1955); X.H. Schmid undE. Hallaba, Mh. Chem.87, 560 (1956); XI.H. Schmid undA. Woppmann, Mh. Chem.88, 411 (1957);H. Schmid, Mh. Chem.88, 161, 344 (1957); XII.H. Schmid undM. G. Fouad, Mh. Chem.88, 631 (1957);H. Schmid, Österr. Pat. 191 399, Kl. 12e₂ (Juni 1957);H. Schmid, Chemiker-Ztg.81, 603 (1957); XIII. und XIV.H. Schmid undCh. Essler, Mh. Chem.88, 1110 (1957);90, 222 (1959); XV.H. Schmid undA. Woppmann, Mh. Chem.90, 903 (1959); XVI.H. Schmid undCh. Essler, Mh. Chem.91, 484 (1960); XVII.H. Schmid undG. Muhr, Mh. Chem.91, 1198 (1960);H. Schmid, Mh. Chem.92, 174 (1961).     

Conformational analysis of self-organized monolayers with scanning tunneling microscopy at near-atomic resolution

We describe the synthesis and a novel approach to the conformational analysis of 2,2'-bipyridines (bpy) bearing aromatic rich Frechet-type dendritic wedges of the first and second generation as substituents. The evaporation of solutions of these new ligands on graphite surfaces under ambient conditions results in the formation of self-organized monolayers. Scanning tunneling microscopy (STM) investigations of the monolayers under ambient conditions (air, 298 K) gave images at submolecular and near-atomic resolution. The analysis of the STM images includes the following processes: (i) identification and reproduction of potential homoconformational domains, (ii) exclusion of improper data using quality criteria for drift and feedback artifacts, (iii) compilation of running averages and checking for averaging artifacts, (iv) analysis of three-dimensional and contour plots, (v) calculation of the HOMO properties of the free molecules, and (vi) final conformational assignment based on all accessible information. Following this procedure, two different conformations could be assigned to domains observed in the monolayers of the first-generation (G1) and second-generation (G2) dendritic compounds. Homoconformational domains are observed side-by-side. The different conformations arise from syn or anti arrangements at the ether substituents. An additional conformational effect is found upon treating the G1 domains with HCl gas, when a partial rearrangement of the bpy from trans to cis occurs, concomitant with protonation.     

The Molecular and Crystal Structure of the Glycopeptide A-40926 Aglycone

The crystal structure of a glycopeptide antibiotic A–40926 aglycone was investigated by X-ray analysis at ?120°. A-40926 crystallises in the orthorhombic space group P2₁2₁2₁ with two monomers in the asymmetric unit, a = 21.774(4), b = 28.603(7), c = 29.757(4) Å. ‘Conventional’ direct methods approach failed to solve the structure, but a novel iterative real/reciprocal space procedure was successful. Refinement against 11248 F² data led to R1 = 13.3% for 6770 F > 4σ (F). The two monomers of A-40926 have similar conformations and are bound by antiparallel H-bonds to form a ‘chain’ structure of connecting dimers. The antibiotic molecule possesses a ‘binding pocket’ for the C-terminal carboxy group of the cell-wall protein, which is consisten with suggestions based on NMR data and the recently reported crystal structure of ureido-balhimycin. In A-40926 the monomers are polymerically linked by H-bonds, quite unlike the tight dimer formation observed in ureido-balhimycin.     

An electrothermal vaporization unit with axially focusing convection upstream. Part II: Modeling of the condensation process

A model is presented that describes quantitatively the condensation of analytes in pico- and nanogram masses sampled with electrothermal vaporization (ETV). It presumes that the analyte vapor condensation of such low amounts occurs mainly heterogeneously, predominantly on growing carbon particulates originating from the graphite furnace before the analyte vapor achieves saturation via cooling. The model regards the coagulation of carbon particles and the diffusion of analyte atoms. The criterion whether or not an analyte atom sticks to a colliding particle is chosen as a function depending on its temperature and on the common GFAAS pretreatment temperatures. Heterogeneous condensation of six analytes with different volatilities, Ag, Cu, Fe, Ni, Mn, and Pb, is calculated for the ETV unit with an axially focusing convection upstream described in Part I. Modifier effects are taken into account. The results are compared to measured data.     

Quantitation in capillary electrophoresis-mass spectrometry

CE-MS has evolved into a strong alternative to LC-MS. Most of CE-MS applications deal with characterization and identification. However, quantitative aspects have gained importance in, e.g., pharmaceutical and biotechnological applications. Here we summarize and evaluate various methodological aspects in order to achieve sensitive and reproducible results. Similar to LC-MS, aspects of matrix influence on the electrospray process need to be carefully addressed when quantitative results are intended by CE-MS. Due to a more complicated coupling special emphasis needs to be put on the CE-MS interface. Generally linearity over more than three orders of magnitude can be achieved by CE-ESI-MS. Furthermore, a literature survey has been performed in order to give an overview over quantitative measurements performed by CE-MS. The precision can be doubled when changing from a structural related to an isotopically labeled internal standard. Thus a level of precision better than 5% RSD can be achieved.     

Absolutberechnung der Normalfrequenzen des Hydrogendifluoridions

Zusammenfassung Mit Hilfe eines einfachen quantenmechanischen Näherungsansatzes wird versucht, Bindungsabstände und Normalfrequenzen des Hydrogendifluoridions sowie des entsprechenden deuterierten Ions zu berechnen. Hierbei wird die Elektronenwechselwirkung der beiden Fluoridionen untereinander durch einen der Statistik entlehnten Ausdruck berücksichtigt. Die Methode liefert für die Abstände gute, für die Normalfrequenzen durchaus befriedigende Ergebnisse.

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On the basis of a quantum mechanical treatment the bond distances and the normal frequences of the hydrogen difluoride ion and its deuterated analogue are calculated. The electronic interaction of the two fluoride ions is approximated by a statistical calculation. The results are in fairly good agreement with the experimental values.

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Résumé Sur la base d'un traitement quantique simple, le calcul des distances de liaison et des fréquences normales est tenté pour l'ion de bifluorure d'hydrogène et son analogue deutéré. L'intéraction électronique des deux ions fluorures est approximée au moyen d'un calcul statistique. Les résultats sont en très bon accord avec les valeurs expérimentales.

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Der Deutschen Forschungsgemeinschaft danken wir für die Gewährung eines Stipendiums an Karl Hensen.     

Chemie der Pleuromutiline, 10. Mitt.: 1,2-Transposition der Carbonylfunktion im Cyclopentanonteil des tricyclischen Gerüstes

2-Hydroxy-19,20-dihydropleuromutilin (10) undergoes a stereospecific ketolisomerisation when treated with base under phase/transfer conditions (11, 12). The subsequent reductive elimination of the 3-acetoxygroup afforded mutilin with a 1,2-transposed ketofunction (13).