Representation of the molecular topology of cyclical structures by means of cycle graphs. 3. Hierarchical model of screening of chemical databases

The increase in the size and complexity of chemical databases necessitates the proposal and development of efficient methods of classification and recovery of information, which supposes proposal of a model of classification of database records and the use of a compatible model of screening for inspection of clusters and recovery of the molecules that satisfy the search criterion. The cycle graphs model based on consideration of all the cycles and chains (and equivalent cycles and chains) present in the molecular structure has been proven appropriate for classification of chemical databases, giving rise to a generation of different classification levels depending on the structural elements (cycles and chains) that are considered. In this paper we propose a screening model, compatible with the cycle graphs model, based on a hierarchy of levels of abstraction. The set of molecules that satisfies a screening model (or selection criterion) diminishes as we advance in the hierarchy of levels of the model, which allows filtering of records and, therefore, an increase in the efficiency of the screening process. In the following work of this series we describe and validate the screening tool developed.     

Stabilization of cobalt(II) chloro-complexes with the butanediammonium cation

Summary Cobalt(II) chlorocomplexes with empirical formulae (bnH₂)₂CoCl₆·2H₂O (1) and (bnH₂)₂CoCl₆ (2), where bnH ₂ ²⁺ represents the diprotonated species of putrescine (1,4-butanediamine), were prepared.The visible spectra in the solid state and measurement of the magnetic moments permit the assignation of an octahedral geometry for cobalt in (1) and a tetrahedral geometry for (2).     

Electroreduction of some pyridine carboxamides on carbon electrodes in aqueous solutions

The electroreductions of the NAD⁺ model compounds nicotinamide (I), N₁-methyl nicotinamide (II), N′-methyl nicotinamide (III) and isonicotinamide (IV) on carbon electrodes have been studied in aqueous media in the pH range 0–12 by linear-sweep cyclic voltammetry (Scheme 1, I-IV). Logarithmic analyses of the reduction peaks were performed by computing the convolution of the current with time as a function of the potential. On the basis of the experimental results it was concluded that the irreversibility of the electron transfers increased when a glassy carbon electrode was used, and this irreversibility being more marked when a plastic formed carbon electrode was employed. The reduction processes occurred with more difficulty on carbon electrodes than on mercury electrodes. Both the reduction and the reoxidation (when occurred) processes changed with respect to those observed on mercury electrodes, being irreversible electron transfers the rate-determining steps in most cases. Thus, for compounds I, II and III at pH < 2 the reductions occurred by the uptake of two electrons and two H⁺ ions, and the rate determining step was found to be the first one-electron transfer, for I and III, and the irreversible second electron transfer, preceded by the uptake of an H+ ion, for II. At pH>3 the processes consisted of electrodimerization reactions, preceded by the protonation of the heterocyclic nitrogen in cases I and III. The second electron transfer of the electroreduction of IV always appeared irreversible, in contrast with that found for mercury electrodes.     

Parametrization of a force field for studying some beta-lactams

A molecular mechanics force field for studying some beta-lactams was developed from ab initio and experimental data. The optimized parameters allowed accurate calculation of the geometries of both the compounds on which the parametrization was based and others on which the validity of the predictions was checked. © 1994 by John Wiley & Sons, Inc.     

Acidic and reductive dissolution of magnetite in aqueous sulfuric acid: Site-binding model and experimental results

The open circuit dissolution of ionic metal oxides in mineral acids is modelled assuming that the rate is controlled by the transfer of metal ions in hydrolytic equilibrium with bulk metal ions, from the metal oxide surface to the Stern plane. The site-binding model of the double layer metal oxide/electrolyte solution is used to obtain the pH dependence of surface and Stern potentials. The nature of the active sites is discussed and their surface concentration is assumed to be proportional to suface charge σ₀. Again, the site-binding model is used to detemine the pH dependence of σ₀. It is thus shown that the rate order in c_H⁺ is essentially defined by the potential dependence of the charge transfer process, for oxides with points of zero charge near neutrality that dissolve in mildly or strongly acidic solutions. The role of surface complexation is also discussed in terms of the site-binding model and the difficulties in interpreting dissolution experiments under constant external applied potential are discussed in terms of the complexity of the semiconductor oxide/electrolyte solution interfacial region in magnetite.An experimental study of the open circuit dissolution of magnetite in sulfuric acid is presented and interpreted according to the proposed model.The reductive dissolution of magnetite is modelled by extension of the Valverde-Wagner model of oxide dissolution. Experimental results are presented to demonstrate that the reductive dissolution rate of magnetite in ferrous containing solutions is controlled by the rate of electron transfer from adsorbed Fe(II) to Fe(III) surface states of magnetite.     

Toward inorganic electrides

Electrides are materials in which alkali metals (Li through Cs) ionize to form bound alkali cations and "excess" electrons. The electrons reside in large cavities or channels or both in the host lattice. We report here the first synthesis of thermally stable inorganic electrides with cation-to-electron ratios of 1:1 as in organic electrides. Although alkali metal adducts to alumino-silicate zeolites are well known, the cation-to-electron ratio is generally 3:1 or greater because these zeolites contain alkali cations prior to incorporation of the alkali metal. In this work, two pure silica zeolites, ITQ-4and ITQ-7, with pore diameters of approximately 7 A, absorb up to 40 wt % cesium from the vapor phase (even at room temperature). The other alkali metals (except Li) can also be introduced at elevated temperatures. The optical and magnetic properties of the cesium-loaded samples suggest ionization to form Cs+ and e- with substantial electron-spin pairing. The metal-loaded samples are stable to at least 100 degrees C and are able to reduce small aromatic molecules such as benzene and naphthalene to the radical anions within the pores of the zeolite.     

Complete characterization of the (D2O)2 ground state: high Ka rotation-tunneling levels

We report the observation of extensive a- and c-type rotation-tunneling (RT) spectra of (D2O)2 for Ka = 0-4. These data allow quantification of molecular constants and tunneling splittings for a number of previously unobserved RT states of (D2O)2. The vibrational ground state has thus been characterized to energies as high as those of some of the intermolecular vibrations, and we present the first test of the VRT(ASP-W) potential at these high Ka states.     

Complexes formed between nitrilotris(methylenephosphonic acid) and M(2+) transition metals: isostructural organic-inorganic hybrids

Nitrilotris(methylenephosphonic acid) (NTP, [N(CH(2)PO(3)H(2))(3)]) recently has been found to form three-dimensional porous structures with encapsulation of templates as well as layered and linear structures with template intercalation. It was, therefore, of interest to examine the type of organic-inorganic hybrids that would form with metal cations. Mn(II) was found to replace two of the six acid protons, while a third proton bonds to the nitrilo nitrogen, forming a zwitter ion. Two types of compounds were obtained. When the ratio of acid to Mn(II) was less than 10, a trihydrate, Mn[HN(CH(2)PO(3)H)(3)(H(2)O)(3)] (2) formed. Compound 2 is monoclinic P2(1)/c, with a = 9.283(2) A, b = 16.027(3) A, c = 9.7742(2) A, beta = 115.209(3) degrees, V = 1315.0(5) A(3), and Z = 4. The Mn atoms form zigzag chains bridged by two of the three phosphonate groups. The third phosphonate group is only involved in hydrogen bonding. The metal atoms are octahedrally coordinated with three of the sites occupied by water molecules. Adjacent chains are hydrogen-bonded to each other through POH and HN donors, and the additional participation of all the water hydrogens in H-bonding results in a corrugated sheet-like structure. Use of excess NTP at a ratio to metal of 10 to 1 yields an anhydrous compound Mn[HN(CH(2)PO(3)H)(3)] (1), P2(1)/n, a = 9.129(1) A, b = 8.408(1) A, c = 13.453(1) A, beta = 97.830(2) degrees, V = 1023.0(2) A(3), and Z = 4. Manganese is five coordinate forming a distorted square pyramid with oxygens from five different phosphonate groups. The sixth oxygen is 2.85 A from an adjacent Mn, preventing octahedral coordination. All the protonated atoms, three phosphonate oxygens and N, form moderately strong hydrogen bonds in a compact three-dimensional structure. The open-structured trihydrate forms a series of isostructural compounds with other divalent transition metal ions as well as with mixed-metal compositions. This is indicative that the hydrogen bonding controls the type of structure formed irrespective of the cation.     

C-Glycosylidene derivatives (exo-glycals): their synthesis by reaction of protected sugar lactones with tributylphosphonium ylids, conformational analysis and stereoselective reduction

Stabilised tributylphosphonium ylids Bu₃PCHCH(EWG), where EWG is CO₂Me, CO₂^tBu or CN, react with protected sugar lactones under mild conditions to give high yields of glycosylidene derivatives (4 and 5) with good Z/E selectivity. X-Ray crystallography shows that in the solid state the tetra-O-benzyl protected (Z)-glucosylideneacetonitrile (Z)-4c adopts a conformation intermediate between a boat and a twist-boat, whereas the isomeric galactose derivative (Z)-5c exists as a distorted chair. NMR data suggest that in solution chair-like conformations are again more favoured for galactosylidene derivatives than for their glucosylidene analogues. Solution phase NMR studies and molecular modelling show that the (E)-double bond geometry disfavours the chair-like geometry of the ring, even in the galactose series; this is consistent with the avoidance of allylic 1,3-strain. Reduction of the glycosylidene double bond to give stereoselective formation of β-C-glycoside derivatives may be achieved by using Et₃SiH-CF₃CO₂H or Et₃SiH-BF₃·Et₂O.     

Möbius aromaticity in [12]annulene: cis-trans isomerization via twist-coupled bond shifting

Density functional and coupled cluster calculations show that facile thermal configuration change in [12]annulene occurs via a twist-coupled bond-shifting mechanism. The transition state for this process is highly aromatic with M?bius topology. At the CCSD(T)/cc-pVDZ//BH&HLYP/6-311+G** level, the isomerization of tri-trans-[12]annulene 1a (CTCTCT) to its di-trans isomer 2 (CCCTCT) via such a mechanism has a barrier of 18.0 kcal/mol, in good agreement with earlier experiments. Two other aromatic M?bius bond-shifting transition states were located that result in configuration change for other [12]annulene conformers. This mechanism contrasts sharply with diradical configuration change for acyclic polyenes and with planar bond-shifting mechanisms generally assumed for annulenes. This constitutes evidence that neutral M?bius aromatic annulenes play a role in the dynamic processes of neutral [4n]annulenes.