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A new PCR primer system that targets a wide range of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase ([PAH-RHD.[alpha]]) gene of both Gram-positive and Gram-negative bacteria was developed and used to study their abundance and diversity in two different soils in response to phenanthrene spiking. The results obtained from the analysis of amplicons confirmed the specificity of the newly developed primer system and revealed a soil type-dependent response of [PAH-RHD.sub.[alpha]] gene-carrying soil bacteria to phenanthrene spiking.

The structure and the bioassay-guided isolation of a peptide antibiotic that is highly active against the plant pathogen Enterobacteriaceae amylovora and pathovars of Pseudomonas syringae are described. The studies have shown that 2-amino-3-(oxirane-2,3-dicarboxamido)-propanyl-valine has inhibited the growth of the human pathogen Candida albicans efficiently.

The biosynthetic origin of the tumor-inhibitory derivative, BE-10988, is analyzed in Streptomyces sp. BA10988 by retrobiosynthetic NMR analysis by using [U-[super 13][C.sub.6]]glucose as a precursor. The transfer of the label from [ring-super 2][H.sub.5]]indole pyruvic acid has showed that plants and bacteria have evolved independent mechanisms of tryptophan modification in the biosynthesis of thiazolylindole derivatives.

The crystal structure and optical and magnetic properties of the newly synthesized 4-cyanopyridinium hydrogensquarate monohydrate are analyzed by using single-crystal X-ray diffraction and other spectroscopic methods. The unusual red color of the compound in the solid state is shown to be due to a strong bathochromic shift of the charge transfer band within the stable layers formed by the (2HSq.2[H.sub.2]O) fragments.

Objectives: The objective of this study was to ascertain the presence and correlations among eight important secondary metabolites viz. hypericin, pseudohypericin, emodin, hyperforin, rutin, hyperoside, quercetin and quercitrin in different organs of 17 in vitro cultured Hypericum species, along with H. tomentosum and H. tetrapterum hairy root cultures, and hairy root‐derived transgenic plants of H. tomentosum. Methods: Samples were extracted and analysed by LC‐MS. The LC‐MS data were subjected to chemometric evaluations for metabolite profiling and correlating the phytochemical compositions in different samples. Key findings: Hypericin, pseudohypericin and their proposed precursor emodin were detected in various levels in the leaves of eight Hypericum species. The highest content of hypericins and emodin was found in H. tetrapterum, which contains the studied secondary metabolites in all plant organs. A significant positive correlation between hypericins and emodin was observed both by principal component analysis (PCA) and multidimensional scaling (MDS), indicating the role of emodin as a possible precursor in the biosynthetic pathway of hypericins. Flavonoids were found in all tested plant organs except roots of H. pulchrum. The hairy roots lacked hypericin, pseudohypericin, emodin, hyperforin and rutin. However, the hairy root‐derived transgenic plants showed a significant increase in flavonoids. Conclusions: This study broadens knowledge about the phytochemical composition of selected in vitro cultured Hypericum species, compared to that of hairy root cultures and hairy root‐derived transgenic plants. [ABSTRACT FROM AUTHOR]

Abstract The issue of this work focuses on development of quantitative model equations connecting experimental mass spectrometric (MS) parameters, for instance, MS intensity, of analyte peaks with thermodynamic, kinetic and diffusion parameters of the corresponding ions with their 3D molecular and electronic structures. Our more recent contribution to this field has convincingly argued that equation D = 1.3194.10 − 17. A. I 2 ¯ − (I ¯) 2 (I − I ¯ ) 2 , obtained on the base on stochastic dynamics, is applicable to electrospray ionization (ESI), collision induced dissociation (CID) and matrix–assisted laser desorption/ionization (MALDI) mass spectrometric (MS) methods, respectively. It connects MS diffusion parameters of ions with the intensities of their peaks in the MS spectrum. There has been evidenced, that experimental diffusion parameters correspond quantitatively to theoretical quantum chemical diffusion coefficients, obtained on the base on Arrhenius' formalism. If next research effort continues to confirm the validity of the shown above quantitative relation to the behavior of the MS intensity of the analyte, with respect to time, this might imply that the mass spectrometry represents not only an irreplaceable method for quantification in the analytical practice, but it provides exact experimental information about the 3D structure of the analytes. According to the latter line of research, the first aspect of this study is an experimental and theoretical MS quantification of diffusion parameters and 3D structural determination of ions of L-tryptophyl– l –tryptophan (H–Trp–Trp–OH) under ESI(+)–MS conditions. Another issue details experimentally and theoretically the process of molecular cyclization of H–Trp–Trp–OH. This aspect of the chemical reactivity of the dipeptide has provided very important insights into major reaction paths, yielding to permuted oxazolone. Taking a step into a broad application of our model relationship stated above to different areas of science, we should underline that, no doubt, the paper contributes significantly to methodological development of mass spectrometric based methods for 3D structural analysis, exploiting herein a nontrivial case of MS fragment behavior of the peptide H–Trp–Trp–OH under ESI–MS conditions. Graphical abstract Image 1 Highlights • Electrospray ionization mass spectrometry. • Diffusion parameters. • Quantum chemistry. • 3D structural analysis. • Dipeptide. [ABSTRACT FROM AUTHOR]

This paper provides experimental and theoretical study of reaction of [2 + 2] cycloaddition of substituted α–unsaturated isophorone dyes, involving high resolution electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) tandem mass spectrometric (MS/MS) analysis in solution and in gas–phase (GP) of substituted 3-[2-(X-substituted-phenyl)-vinyl]-5,5-dimethyl-cyclohex-2-enone and configurationally locked polyenes (CLP). The ab initio and density functional theoretical (DFT) examining provides information about molecular geometry, thermodynamics, kinetics and ionization potentials of sixty six isomers of dimeric dyes, including corresponding cis -anti- cis and cis -syn- cis head-to-tail and head-to-head forms. The comparative collision induced dissociation (CID) or collision activated MS and theoretical analyses carried out bring light into the mechanisms of competitive dimerization within the frame of 3-[2-(X-substituted-phenyl)-vinyl]-5,5-dimethyl-cyclohex-2-enone; molecular and environmental factors governing regioselectivity of reaction. The analyses involve both qualitative and quantitative kinetics and thermodynamics of experimental MS data along with corresponding theoretical examining of CLP dimers. As far as 3-[2-(X-substituted-phenyl)-vinyl]-5,5-dimethyl-cyclohex-2-enone and CLP dyes have already found an industrial scale application as non-linear optical materials (NLO) for THz wave generation and detection as well as pharmaceutics for treatment of and preventing of neurodegenerative diseases, this study has a strong transdisciplinary impact to many research fields as well as to still not well understood, but crucial to fields of organic synthesis and catalysis, molecular level fundamentals of chemical reactivity in gas– and condense phases. Following the latter lines of contributions of the work, we might hopefully expect that the prospective highlighted in this study should inspired further research effort devoted to correlative quantitative thermodynamic and kinetic CID mass spectrometric and quantum chemical analyses, which allow to improve the reaction effectiveness depending on the complexity of the wanted CLP scaffolds. [ABSTRACT FROM AUTHOR]

Acetaminophen (APAP) is one of the most intensively studied compounds that causes hepatotoxicity in the pericentral region of the liver lobules. However, spatio-temporal information on the distribution of APAP, its metabolites and GSH adducts in the liver tissue is not yet available. Here, we addressed the question, whether APAP-GSH adducts and GSH depletion show a zonated pattern and whether the distribution of APAP and its glucuronide as well as sulfate conjugates in liver lobules are zonated. For this purpose, a matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) technique was established, where the MSI images were superimposed onto CYP2E1 immunostained tissue. A time-dependent analysis (5, 15, 30, 60, 120, 240, 480 min) after intraperitoneal administration of 300 mg/kg APAP and a dose-dependent analysis (56 up to 500 mg APAP/kg) at 30 min were performed. The results demonstrate that the MALDI MSI technique allows the assignment of compounds and their metabolites to specific lobular zones. APAP-GSH adducts and GSH depletion occurred predominantly in the CYP2E1-positive zone of the liver, although GSH also decreased in the periportal region. In contrast, the parent compound, APAP sulfate and APAP glucuronide did not show a zonated pattern and tissue concentrations showed a similar time course as the corresponding analyses were performed with blood from the portal and liver veins. In conclusion, the present study is in agreement with the concept that pericentral CYPs form NAPQI that in the same cell binds to and depletes GSH but a lower level of GSH adducts is also observed in the periportal region. The results also provide further evidence of the recently published concept of ‘aggravated loss of clearance capacity’ according to which also liver tissue that survives intoxication may transiently show decreased metabolic capacity. [ABSTRACT FROM AUTHOR]

The problematic that we consider in this paper treats the quantitative correlation model equations between experimental kinetic and thermodynamic parameters of coupled electrospray ionization (ESI) mass spectrometry (MS) or atmospheric pressure chemical ionization (APCI) mass spectrometry with collision induced dissociation mass spectrometry, accounting for the fact that the physical phenomena and mechanisms of ESI– and APCI–ion formation are completely different. There are described forty two fragment reactions of three analytes under independent ESI– and APCI–measurements. The developed new quantitative models allow us to study correlatively the reaction kinetics and thermodynamics using the methods of mass spectrometry, which complementary application with the methods of the quantum chemistry provide 3D structural information of the analytes. Both static and dynamic quantum chemical computations are carried out. The object of analyses are [2,3-dimethyl-4-(4-methyl-benzoyl)-2,3-di-p-tolyl-cyclobutyl]-p-tolyl-methanone (1) and the polycyclic aromatic hydrocarbons derivatives of dibenzoperylen (2) and tetrabenzo [ a,c,fg,op ]naphthacene (3) , respectively. As far as (1) is known to be a product of [2π+2π] cycloaddition reactions of chalcone (1,3-di-p-tolyl-propenone), however producing cyclic derivatives with different stereo selectivity, so that the study provide crucial data about the capability of mass spectrometry to provide determine the stereo selectivity of the analytes. This work also first provides quantitative treatment of the relations ‘ 3D molecular/electronic structures ’–‘ quantum chemical diffusion coefficient ’–‘ mass spectrometric diffusion coefficient ’, thus extending the capability of the mass spectrometry for determination of the exact 3D structure of the analytes using independent measurements and computations of the diffusion coefficients. The determination of the experimental diffusion parameters is carried out within the ‘ current monitoring method ’ evaluating the translation diffusion of charged analytes, while the theoretical modelling of MS ions and computations of theoretical diffusion coefficients are based on the Arrhenius type behavior of the charged species under ESI– and APCI–conditions. Although the study provide certain sound considerations for the quantitative relations between the reaction kinetic–thermodynamics and 3D structure of the analytes together with correlations between 3D molecular/electronic structures–quantum chemical diffusion coefficient–mass spectrometric diffusion coefficient, which contribute significantly to the structural analytical chemistry, the results have importance to other areas such as organic synthesis and catalysis as well. [ABSTRACT FROM AUTHOR]

Tropane alkaloids (TAs), especially hyoscyamine and scopolamine, are important precursors for anticholinergic and antispasmodic drugs. Hyoscyamine and scopolamine are currently obtained at commercial scale from hybrid crosses of Duboisia myoporoides Duboisia leichhardtii plants. In this study, we present a global investigation of the localization and organization of TA biosynthesis in a Duboisia myoporoides R. Br. wild-type line. The tissue-specific spatial distribution of TAs within D. myoporoides is presented, including quantification of the TAs littorine, 6-hydroxy hyoscyamine, hyoscyamine, scopolamine and, additionally, hyoscyamine aldehyde as well as scopolamine glucoside. Scopolamine (14.77 ± 5.03 mg g-1), and to a lesser extent hyoscyamine (3.01 ± 1.54 mg g-1) as well as 6-hydroxy hyoscyamine (4.35 ± 1.18 mg g-1), are accumulated in leaves during plant development, with the highest concentration of total TAs detected in 6-month-old plants. Littorine, an early precursor in TA biosynthesis, was present only in the roots (0.46 ± 0.07 mg g-1). During development, the spatial distribution of all investigated alkaloids changed due to secondary growth in the roots. Transcripts of pmt, tr-I and cyp80f1 genes, involved in early stages of TA biosynthesis, were found to be most abundant in the roots. In contrast, the transcript encoding hyoscyamine 6β-hydroxylase (h6h) was highest in the leaves of 3-month-old plants. This investigation presents the spatial distribution of biochemical components as well as gene expression profiles of genetic factors known to participate in TA biosynthesis in D. myoporoides. The results of this investigation may aid in future breeding or genetic enhancement strategies aimed at increasing the yields of TAs in these medicinally valuable plant species. [ABSTRACT FROM AUTHOR]

The present paper deals with quantitative kinetics and thermodynamics of collision induced dissociation (CID) reactions of piperazines under different experimental conditions together with a systematic description of effect of counter-ions on common MS fragment reactions of piperazines; and intra-molecular effect of quaternary cyclization of substituted piperazines yielding to quaternary salts. There are discussed quantitative model equations of rate constants as well as free Gibbs energies of series of m –independent CID fragment processes in GP, which have been evidenced experimentally. Both kinetic and thermodynamic parameters are also predicted by computational density functional theory (DFT) and ab initio both static and dynamic methods. The paper examines validity of Maxwell–Boltzmann distribution to non–Boltzmann CID processes in quantitatively as well. The experiments conducted within the latter framework yield to an excellent correspondence with theoretical quantum chemical modeling. The important property of presented model equations of reaction kinetics is the applicability in predicting unknown and assigning of known mass spectrometric (MS) patterns. The nature of “GP” continuum of CID–MS coupled scheme of measurements with electrospray ionization (ESI) source is discussed, performing parallel computations in gas–phase (GP) and polar continuum at different temperatures and ionic strengths. The effect of pressure is presented. The study contributes significantly to methodological and phenomenological developments of CID–MS and its analytical implementations for quantitative and structural analyses. It also demonstrates great prospective of a complementary application of experimental CID–MS and computational quantum chemistry studying chemical reactivity, among others. To a considerable extend this work underlies the place of computational quantum chemistry to the field of experimental analytical chemistry in particular highlighting the structural analysis. [ABSTRACT FROM AUTHOR]

The fundamental goal of this work in applying high resolution crystallographic X-ray measurements of single crystals as well as ab initio and density functional computational methods is to provide a correlation between the experimental electron densities and valence states of atoms with the theoretically predicted ones by methodological approaches of quantum chemistry. In order to test the reliability of the data, we chose to examine statistically the crystallographic datasets of nine metal-organics with Zn 2+ , Ag + and Cu 2+ ions. There are several premises to the argument for this choice: (i) the different nature of M–L interactions, (ii) various geometries of the chromophores and (iii) distinguishable chemical behavior of the dentate atoms in the inner coordination sphere (L = O, N, Cl). New insights about the nature of the M–L interactions are gained for the following bonding fashions: (a) bonded Ag I –X(Y) fragments (X, Y = O and/or N) in tetrahedral (T d ) and square planar AgX 2 Y 2 symmetries, (b) bonded Zn II –X(Y) cores (X, Y = O and/or N; or Cl) in T d Zn II X 2 Y 2 or Zn II X 2 chromophores, (c) Zn II –OH 2 interactions in the discrete octahedral {[Zn II (H 2 O)] 2+ } charged complex and (d) bonded Cu II –X(Y) systems (X, Y = O and/or N) in square planar AgX 2 Y 2 chromophores as comparative examples of complexes with the d 9 configurations of the metal ion. The methods of ‘atoms in molecules’ (AIM), ‘natural bond orbital analyses’ (NBO) and electrostatic potentials were employed. The analyses include employment of the bond valence (BV) methodology and non-covalent interaction (NCI) analysis. Quantum chemical prediction of multi-pole moments, orbital population and charge transfer effects (CT), bond covalence, iconicity, different bond order methodologies (BOs); electron density distribution and Laplacian of the total electron density (ED) were carried out. The energetics of the M–L bonds were treated using topological charge density analysis at the bond critical points (bcps). The foci of the presented theoretical and experimental designs allow us to answer our main research questions: Is the nature of the M–L bond with ions having an identical electronic configuration, d 10 , interacting with one and the same type dentate-ligands the same? and is there a quantitative statistically significant correlation between the theoretically predicted dissociation energetic of the complexes and their experimental topological crystallographic M–L bond energies? The presented comprehensive analyses of this problematic provide crucial new information of both fundamental and applied importance to the field of structural chemistry and the properties of metal–organic molecules. Such results seek to shed light on whether the theoretical models extracting information about the molecular electronic properties of the species in the crystalline state on the base on crystallographic measurements and the corresponding topological, electron density and orbital based methods of computational quantum chemistry are able to enable a common conceptualization about the relationship between ‘crystal structure’–‘molecular structure’–‘electronic structure’–‘M–L bonding type’. The low temperature redetermination of the crystal structure and new description of the structure of the Ag I complex of 2-hydroxy-5-sulfo-benzoic acid ( 1 ) is reported as well. [ABSTRACT FROM AUTHOR]

An essential part of molecular scaffolds of organosilver(I) catalysing reactions of C–H bond activation and C–X (X = C or O) bond formation of polysubstituted benzoic acids in polar medium represent biphenyls, 6H-benzo-[ c ]-chromene[6]-one, chromeno[5,4,3-cde]chromene-5,10-dione, and 4,10-dioxa-pyrene-5,9-diones. A second strand of catalytic activity is in promoting synthesis of substituted quanterphenyls. This paper is a an extend of the systematic examining of catalytic activity of Ag I –containing intermediates of substituted benzoic acids, gaining insights by synthesis of oligomers, studying benzene-1,2,4-tricarboxylic acid (124BA) and benzene-1,3,5-tricarboxylic acid (135BA). Arguably, the optimization of the latter reactions need further effort in order to achieve the standard characteristics allowing their effective implementation as routine routs in the field of organic synthesis. The purpose of this part of the research is mass spectrometric (MS) quantitative kinetic and thermodynamic treatment of collision induced dissociation (CID) reactions comparing experimental reaction kinetics and energetics with quantum chemical modelling of MS fragment processes. Analyses - experimental and theoretical - include deuterium labelled oligomers as the most useful technique studying MS reaction mechanisms. More specifically we treat eight substituted quaterphenyls both experimentally and theoretically along with a set of one hundred twenty 3D molecular models of MS fragment species. Importantly, the detail understanding of the molecular mechanistic aspects of the reactions causing for obtaining of high functionalized oligomers allows an efficient optimization of synthetic roads studying polyfunctional derivatives. This knowledge is the kay to understanding why the obtaining of the oligomer derivatives depends on the positional isomerism of the starting reagents as clearly evidenced in this study. In this context the study is relevant to the fields of organometallic synthesis and catalysis as well as the polymers' chemistry. [ABSTRACT FROM AUTHOR]