Mass spectrometric characterization of isomeric terpenoic acids from the oxidation of α-pinene, β-pinene, d-limonene, and Δ3-carene in fine forest aerosol

In this study, we present liquid chromatographic and mass spectral data for predominant terpenoic acids formed through oxidation of α-pinene, β-pinene, d-limonene, and Δ(3)-carene that occur in fine forest aerosol from K-puszta, Hungary, a rural site with coniferous vegetation. Characterization of these secondary organic aerosol tracers in fine ambient aerosol is important because it allows one to gain information on monoterpene precursors and source processes such as oxidation and aging processes. The mass spectral data were obtained using electrospray ionization in the negative ion mode, accurate mass measurements, and linear ion trap tandem mass spectrometric experiments. Emphasis is given to the mass spectrometric differentiation of isobaric terpenoic acids, such as, e.g. the molecular weight (MW) 186 terpenoic acids, cis-pinic, cis-caric, homoterpenylic, ketolimononic, and limonic acids. Other targeted isobaric terpenoic acids are the MW 184 terpenoic acids, cis-pinonic and cis-caronic acids, and the MW 204 tricarboxylic acids, 3-methyl-1,2,3-butanetricarboxylic and 3-carboxyheptanedioic acids. Fragmentation pathways are proposed to provide a rational explanation for the observed isomeric differences and/or to support the suggested tentative structures. For the completeness of the data set, data obtained for recently reported lactone-containing terpenoic acids (i.e. terpenylic and terebic acids), related or isobaric compounds (i.e. norpinic acid, diaterpenylic acid acetate, and unknown MW 188 compounds) are also included, the rationale being that other groups working on this topic could use this data compilation as a reference.     

Lanthanide‐Based Functional Misfit‐Layered Nanotubes

The synthesis of nanotubes from layered compounds has generated substantial scientific interest. “Misfit” layered compounds (MLCs) of the general formula [(MX)_1+x]_m[TX₂]_n, where M can include Pb, Sb, rare earths; T=Cr, Nb, and X=S, Se can form layered structures, even though each sub‐system alone is not necessarily a layered or a stable compound. A simple chemical method is used to synthesize these complex nanotubes from lanthanide‐based misfit compounds. Quaternary nanotubular structures formed by partial substitution of the lanthanide atom in nanotubes by other elements are also confirmed. The driving force and mechanism of formation of these nanotubes is investigated by systematic temperature and time‐dependent studies. A stress‐inducement mechanism is proposed to explain the formation of the nanotubes. The resulting materials may find applications in fields that include thermoelectrics, light emitters, and catalysis and address fundamental physical issues in low dimensions.     

Solution-phase photochemistry of a [FeFe]hydrogenase model compound: evidence of photoinduced isomerisation

The solution-phase photochemistry of the [FeFe] hydrogenase subsite model (μ-S(CH(2))(3)S)Fe(2)(CO)(4)(PMe(3))(2) has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds.     

Modeling robust QSAR

Quantitative Structure Activity Relationship (QSAR) is a term describing a variety of approaches that are of substantial interest for chemistry. This method can be defined as indirect molecular design by the iterative sampling of the chemical compounds space to optimize a certain property and thus indirectly design the molecular structure having this property. However, modeling the interactions of chemical molecules in biological systems provides highly noisy data, which make predictions a roulette risk. In this paper we briefly review the origins for this noise, particularly in multidimensional QSAR. This was classified as the data, superimposition, molecular similarity, conformational, and molecular recognition noise. We also indicated possible robust answers that can improve modeling and predictive ability of QSAR, especially the self-organizing mapping of molecular objects, in particular, the molecular surfaces, a method that was brought into chemistry by Gasteiger and Zupan.     

Comparative molecular surface analysis (CoMSA) for virtual combinatorial library screening of styrylquinoline HIV-1 blocking agents

We used comparative molecular surface analysis to design molecules for the synthesis as part of the search for new HIV-1 integrase inhibitors. We analyzed the virtual combinatorial library (VCL) constituted from various moieties of styrylquinoline and styrylquinazoline inhibitors. Since imines can be applied in a strategy of dynamic combinatorial chemistry (DCC), we also tested similar compounds in which the -C=N- or -N=C- linker connected the heteroaromatic and aromatic moieties. We then used principal component analysis (PCA) or self-organizing maps (SOM), namely, the Kohonen neural networks to obtain a clustering plot analyzing the diversity of the VCL formed. Previously synthesized compounds of known activity, used as molecular probes, were projected onto this plot, which provided a set of promising virtual drugs. Moreover, we further modified the above mentioned VCL to include the single bond linker -C-N- or -N-C-. This allowed increasing compound stability but expanded also the diversity between the available molecular probes and virtual targets. The application of the CoMSA with SOM indicated important differences between such compounds and active molecular probes. We synthesized such compounds to verify the computational predictions.     

Conformational and crystal packing differences in (+)‐7,8‐Di‐tert‐butoxy‐1‐ phenyloctahydro‐1H‐pyrrolo(1,2‐b)‐1H‐phospholo(2,3‐d)isoxazole 1‐oxide diastereoisomers

The crystal and molecular structures of (1S,3aR,7S,8S,8aR,8bR)‐(+)‐7,8‐Di‐tert‐butoxy‐1‐ph‐ enyloctahydro‐1H‐pyrrolo(1,‐b)‐1H‐phospholo(2,‐ d)isoxazole 1‐oxide ( III , hereafter) and (1R,3aS,7S, 8S,8aS,8bS)‐(+)‐7,8‐Di‐tert‐butoxy‐1‐phenyloctahyd‐ ro‐1H‐pyrrolo(1,2‐b)‐1H‐phospholo(2,3‐d)isoxazole 1‐ oxide ( IV , hereafter) have been determined. III crystallizes in space group P2₁2₁2₁, and IV in P2₁ one. The conformational analysis of the puckered heteroatom three‐ring system shows the conformation of noticeable distorted envelope with puckering amplitude Q₂ = 0.397 Å, the intermediate conformation between twisted and envelope with Q₂ = 0.353 Å, and half‐chair conformation with Q₂ = 0.451 Å, for phospholane, oxazolidine, and pyrrolidine rings of III , respectively. Rings in molecule of IV adopt conformations of envelopes with Q₂ = 0.381 Å, Q₂ = 0.367 Å, and Q₂ = 0.363 Å, respectively, for the rings as described above. The molecules of III are assembled by intermolecular weak hydrogen bonds to the one‐dimensional chain along x‐axis. The structure of IV is built‐up of weak intermolecular hydrogen bonds to form a two‐dimensional hydrogen bond network. The differences in conformation between compounds III and IV cause changes in hydrogen bonding pattern, because in molecule IV there is no hydrogen cavern filled with three hydrogen bond donors, and one weak hydrogen bond has not enough strength to force such an arrangement as it is in III . © 2005 Wiley Periodicals, Inc. Heteroatom Chem 16:613–620, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20160     

Design of novel podand-like compounds with two short diphenylphosphine oxide pendant arms

Crystal and molecular structure of 1,3,5-benzenetris(methylenediphenylphosphine oxide) cyclohexylammonium chloride dibenzene solvate monohydrate has been determined. The overall arrangement of two diphenylphosphine oxide substituents atoms is imposed by intermolecular strong hydrogen bonds, O_(water) H···O_(oxide) and N H···O_{(oxide, water)}. Cyclohexylamine exists in almost ideal chair conformation and nitrogen atom is equatorial to the ring. The structure is build up from strong and weak intermolecular hydrogen bonds to form the three-dimensional infinite hydrogen bond network. Crystal and molecular structure of 1,4-bis[(diphenylphosphineoxide)methyl] - 2,5 - bis (ethoxymethyl) benzene has been determined. The phenyl rings are inclined at 80.91(7)° within the substituent, and they are involved in weak C_(phenyl) H···O_(oxide) hydrogen bonds. The arrangement of diphenylphosphine oxide substituents is imposed practically only by steric effects. Two intramolecular weak hydrogen bonds exist between diphenylphosphine oxide and ethoxymethyl substituents, which can provide additional stabilization to molecule, but it has no noticeable influence on overall molecule geometry. Molecules are assembled via weak intermolecular C H···O_(oxide) hydrogen bonds to the one-dimensional hydrogen-bonded chain along y axis. © 2004 Wiley Periodicals, Inc. Heteroatom Chem 15:233–240, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20008     

2,3‐Dihydro‐1,3‐benzothiazol‐2‐iminium hydrogen oxydiacetate: a combined structural and theoretical study

In the title compound, C₇H₇N₂S⁺·C₄H₅O₅⁻, the ions are connected by N—H...O hydrogen bonds. The hydrogen oxydiacetate residues are linked together by O—H...O hydrogen bonds disordered about centres of inversion into hydrogen‐bonded ribbon layers crosslinked by weak C—H...O and stacking interactions. The cation exists mainly in the 2,3‐dihydro‐1,3‐benzothiazol‐2‐iminium form, with a small participation of the 2‐aminobenzothiazolium form, based on the structural data and quantum mechanical calculations. This study provides structural insights relevant to the biochemical activity of benzothiazole molecules.