Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

Hydrogenation without a transition-metal catalyst: on the mechanism of the base-catalyzed hydrogenation of ketones

The hydrogenation of unsaturated organic substrates such as olefins and ketones is usually effected by homogeneous or heterogeneous transition-metal catalysts. On the other hand, a single case of a transition-metal-free and purely base-catalyzed hydrogenation of ketones was reported by Walling and Bollyky some 40 years ago. Unfortunately, the harsh reaction conditions (ca. 200 degrees C, >100 bar H(2), potassium tert-butoxide as base) limit the substrate spectrum of this reaction to robust, nonenolizable ketones such as benzophenone. We herein present a mechanistic study of this process as a basis for future rational improvement. The base-catalyzed hydrogenation of ketones was found to be irreversible, and it shows first-order kinetics with respect to the substrate ketone, hydrogen, and catalytic base. The rate of the reaction depends on the type of alkali ion present (Cs > Rb - K > Na > Li). Using D(2) instead of H(2) revealed a rapid base-catalyzed isotope exchange/equilibration between the gas phase and the solvent as a concomitant reaction. The degree of deuteration of the product alcohols did not indicate a significant kinetic isotope effect. It is proposed that both ketone reduction and isotope exchange proceed via similar six-membered cyclic transition states involving the H(2)(D(2))-molecule, the alkoxide base, and the ketone (solvent alcohol in the case of isotope exchange). Mechanistic analogies are pointed out which apparently exist between the base-catalyzed hydrogenation of ketones studied here and the Ru-catalyzed asymmetric ketone hydrogenation developed by Noyori. In both cases, heterolysis of the hydrogen molecule appears to be assisted by a Br?nsted-base (i.e., alkoxide), the latter being bound to the substrate ketone or the catalyst ligand, respectively, by a bridging Lewis-acidic alkali ion.     

Theory of absorption and emission of radiation in molecular collisions: Semiclassical model

A semiclassical transition amplitude is derived for electronically inelastic molecular collisions in the presence of an intense electromagnetic field. The calculation of this amplitude involves the integration of classical trajectories for nuclei moving on effective potential energy surfaces. These surfaces, which exhibit an avoided crossing due to the coupling through the dipole interaction around the resonance nuclear configuration, are analytically continued to their complex intersection points, where trajectories switch surfaces. Other parts of these surfaces are similar to the field-free adiabatic surfaces, where one is shifted by ?ω. Metastable states, formed at some collision energies, are suggested in the field which are absent in the field-free system.     

LiTiCl3: Synthesis and thermal behaviour

LiTiCl₃ is obtained as one example within an ample solid solution, Li_24–2nTi_nCl₂₄ (?4?n?10), by synpropotionation of TiCl₃ and Ti in the presence of LiCl (2:1:3 molar ratio) in sealed tantalum tubes at 750°C. It crystallizes with the inverse spinel-type structure according to (Li_0.67)^[4](Li_0.67Ti_1.33)^[4]Cl₄ with, at 25°C, a = 1048.62(4) pm, space group Fd3m. Thermal expansion is linear with α = 4.85 × 10^?5K^?1 up to about 300°C and thereafter, when the migration of Li⁺ from tetrahedral to octahedral interstices becomes increasingly important, it exhibits a relative decrease resulting, finally, in the phase transition to a NaCl-type structure that is observed for the first time at about 575°C.     

Charge reversal of three alkylamide ions: Free nitrenium ions

The methylnitrenium, ethylnitrenium and dimethylnitrenium ions are prepared by charge reversal collisional activation (CR CA) of the corresponding negative ions; their collisional activation mass spectra are shown to support the assigned structures. MINDO/3 energies are used to evaluate relative energies of [CH₄N]⁺ and [C₂H₆N]⁺ isomers, and to determine whether unstable forms rearrange spontaneously to stable ones. As in other examples, charge reversal here generates cations that do not exist in an energy well, but their transient existence is established because their fragmentation is more rapid than their rearrangement to a more stable form.     

NMR studies of conformations and dynamic processes—II : [26]Bicyclophanes with ethylene bridges

The conformations and dynamic processes in two bicyclophanes have been analysed on the basis of temperature-dependent ¹H NMR spectra. Both bicyclophanes are suggested to have a lowest-energy conformation of D₃ symmetry in which the substituents at all ethylene bridges are gauche⁺ (or gauche^?) oriented. The interconversion of the mirror image conformers of each bicyclophane equilibrates the two hydrogens in each methylene group, the barriers being ca 36 and 37 kJ mol^?1, respectively, as determined by line-shape analysis.     

Analysis of carboxylic acids by gas chromatography of acetonyl esters. Application to aromatic,dicarboxylic and higher fatty acids

Summary The gas chromatographic analysis of the acetonyl esters of aromatic, dicarboxylic and higher fatty acids is reported and discussed together with their electron impact and chemical ionisation mass spectra. An improved method for the preparation of acetonyl esters is discussed.     

Synthesis and photochemical properties of photoactivated antitumor prodrugs releasing 5-fluorouracil

A new family of antitumor prodrugs (1-3) of 5-fluorouracil (5-FU) possessing photolabile 2-nitrobenzyl chromophores have been designed and synthesized to investigate the efficiency and mechanism of photoactivated 5-FU release upon UV-irradiation at lambda(ex)= 365 nm. The photoactivated prodrug 3 derived from conjugation of 2 with a tumor-homing cyclic peptide Cys-Asn-Gly-Arg-Cys (CNGRC) was so designed as to manifest a tumor-targeting function.     

Photo-initiated base-formation in a polymer matrix

It was found that amines were formed efficiently by the photolysis of O-acyloximes followed by hydrolysis in polystyrene films and the relationship between structures of O-acyloximes and yields of amines were investigated. O-phenylacetyl acetophenone oxime (PaApO), O-pivaloyl acetophenone oxime (PApO), and O-benzoyl acetophenone oxime (BApO) as monofunctional O-acyloximes and O,O′-succinyl diacetophenone oxime (SDApO) and O,O′-glutaryl diacetophenone oxime (GDApO) as bifunctional O-acyloximes were examined. The yields of amines for PaApO and SDApO under N₂ were ca. 70%, which was the highest among O-acyloximes examined in this experiment. On the other hand, the yields for PApO, BApO, and GDApO were less than 15% and it was verified that the hydrogen abstraction by imino radicals via 6-membered cyclic intermediates resulted in the lowering of yields. Although the effect of oxygen under photolysis on the yields of amine for PaApO was negligible under 50% conversion of PaApO, the yield decreased with further increase in the conversion and was 50% at 90% conversion. © 1994 John Wiley & Sons, Inc.     

PCILO calculation of intermolecular energies: The water dimer

The PCILO (perturbative configuration interaction using localized orbitals) method for approximating the electronic structure of molecules has been used with some success for calculating intramolecular interactions in large molecules where intramolecular hydrogen bonding is involved. In this note we show that the PCILO method may be used to calculate the energy of interaction between two water molecules in selected configurations.