Divergent contribution of the MVA and MEP pathways to the formation of polyprenols and dolichols in Arabidopsis.

Isoprenoids, including dolichols (Dols) and polyprenols (Prens), are ubiquitous components of eukaryotic cells. In plant cells, there are two pathways that produce precursors utilized for isoprenoid biosynthesis: the mevalonate (MVA) pathway and the methylerythritol phosphate (MEP) pathway. In this work, the contribution of these two pathways to the biosynthesis of Prens and Dols was addressed using an in planta experimental model. Treatment of plants with pathway-specific inhibitors and analysis of the effects of various light conditions indicated distinct biosynthetic origin of Prens and Dols. Feeding with deuteriated, pathway-specific precursors revealed that Dols, present in leaves and roots, were derived from both MEP and MVA pathways and their relative contributions were modulated in response to precursor availability. In contrast, Prens, present in leaves, were almost exclusively synthesized via the MEP pathway. Furthermore, results obtained using a newly introduced here 'competitive' labeling method, designed so as to neutralize the imbalance of metabolic flow resulting from feeding with a single pathway-specific precursor, suggest that under these experimental conditions one fraction of Prens and Dols is synthesized solely from endogenous precursors (deoxyxylulose or mevalonate), while the other fraction is synthesized concomitantly from endogenous and exogenous precursors. Additionally, this report describes a novel methodology for quantitative separation of 2H and 13C distributions observed for isotopologues of metabolically labeled isoprenoids. Collectively, these in planta results show that Dol biosynthesis, which uses both pathways, is significantly modulated depending on pathway productivity, while Prens are consistently derived from the MEP pathway.

Gold-Catalyzed 1,2-Aryl Shift and Double Alkyne Benzannulation.

The tandem intramolecular hydroarylation of alkynes accompanied by a 1,2-aryl shift is described. Harnessing the unique electron-rich character of 1,4-dihydropyrrolo[3,2-b]pyrrole scaffold, we demonstrate that the hydroarylation of alkynes proceeds at the already occupied positions 2 and 5 leading to a 1,2-aryl shift. Remarkably, the reaction proceeds only in the presence of cationic gold catalyst, and it leads to heretofore unknown π-expanded, centrosymmetric pyrrolo[3,2-b]pyrroles. The utility is verified in the preparation of 13 products that bear six conjugated rings. The observed compatibility with various functional groups allows for increased tunability with regard to the photophysical properties as well as providing sites for further functionalization. Computational studies of the reaction mechanism revealed that the formation of the six-membered rings accompanied with a 1,2-aryl shift is both kinetically and thermodynamically favourable over plausible formation of products containing 7-membered rings. Steady-state UV/Visible spectroscopy reveals that upon photoexcitation, the prepared S-shaped N-doped nanographenes undergo mostly radiative relaxation leading to large fluorescence quantum yields. Their optical properties are rationalized through time-dependent density functional theory calculations. We anticipate that this chemistry will empower the creation of new materials with various functionalities.

Ion mobility mass spectrometry - an efficient tool for the analysis of conformational switch of macrocyclic receptors upon anion binding.

Interactions between anions and synthetic macrocyclic receptors belong to the extensively explored area of research due to the particularly important functions of anions in biological and environmental sciences. Structures of anion-macrocycle complexes are closely related to their function, highlighting the importance of structural analysis of the complexes. Here, we discuss the application of ion mobility mass spectrometry (IM-MS) and theoretical calculations to the structural analysis of tetralactam macrocycles (M) with varying flexibility and structural properties, and their complexes with anions [M + X]-. Collision cross section (CCS) values obtained from both direct drift tube (DT) and indirect using traveling-wave (TW) IM-MS measurements supplemented by theoretical calculations were successfully used to describe the structural properties of various macrocycle-anion complexes, proving the suitability of the IM-MS approach for sensitive, selective, and fast detection of anion complexes and characterization of their structures and conformations.

Polyprenols Are Synthesized by a Plastidial cis-Prenyltransferase and Influence Photosynthetic Performance.

Plants accumulate a family of hydrophobic polymers known as polyprenols, yet how they are synthesized, where they reside in the cell, and what role they serve is largely unknown. Using Arabidopsis thaliana as a model, we present evidence for the involvement of a plastidial cis-prenyltransferase (AtCPT7) in polyprenol synthesis. Gene inactivation and RNAi-mediated knockdown of AtCPT7 eliminated leaf polyprenols, while its overexpression increased their content. Complementation tests in the polyprenol-deficient yeast ∆rer2 mutant and enzyme assays with recombinant AtCPT7 confirmed that the enzyme synthesizes polyprenols of ∼55 carbons in length using geranylgeranyl diphosphate (GGPP) and isopentenyl diphosphate as substrates. Immunodetection and in vivo localization of AtCPT7 fluorescent protein fusions showed that AtCPT7 resides in the stroma of mesophyll chloroplasts. The enzymatic products of AtCPT7 accumulate in thylakoid membranes, and in their absence, thylakoids adopt an increasingly "fluid membrane" state. Chlorophyll fluorescence measurements from the leaves of polyprenol-deficient plants revealed impaired photosystem II operating efficiency, and their thylakoids exhibited a decreased rate of electron transport. These results establish that (1) plastidial AtCPT7 extends the length of GGPP to ∼55 carbons, which then accumulate in thylakoid membranes; and (2) these polyprenols influence photosynthetic performance through their modulation of thylakoid membrane dynamics.

APEX Strategy Represented by Diels-Alder Cycloadditions-New Opportunities for the Syntheses of Functionalised PAHs.

Diels-Alder cycloaddition of various dienophiles to the bay region of polycyclic aromatic hydrocarbons (PAHs) is a particularly effective and useful tool for the modification of the structure of PAHs and thereby their final properties. The Diels-Alder cycloaddition belongs to the single-step annulative π-extension (APEX) reactions and represents the maximum in synthetic efficiency for the constructions of π-extended PAHs including functionalised ones, nanographenes, and π-extended fused heteroarenes. Herein we report new applications of the APEX strategy for the synthesis of derivatives of 1,2-diarylbenzo[ghi]perylene, 1,2-diarylbenzo[ghi]perylenebisimide and 1,2-disubstituted-benzo[j]coronene. Namely, the so far unknown cycloaddition of 1,2-diarylacetylenes into the perylene and perylenebisimide bay regions was used. 1,2-Disubstituted-benzo[j]coronenes were obtained via cycloaddition of benzyne into 1,2-diarylbenzo[ghi]perylenes by using a new highly effective system for benzyne generation and/or high pressure conditions. Moreover, we report an unprecedented Diels-Alder cycloaddition-cycloaromatisation domino-type reaction between 1,4-(9,9-dialkylfluoren-3-yl)-1,3-butadiynes and perylene. The obtained diaryl-substituted core-extended PAHs were characterised by DFT calculation as well as electrochemical and spectroscopic measurements.

Beyond Size Complementary Factors in Anion-Tetralactam Macrocycle Complexes: From Intrinsic Gas-Phase to Solvent-Predicted Stabilities.

The gas-phase affinities of different types of anions X- (halogen anions, oxoanions, and hydrogenated anions) toward a model tetralactam-based macrocycle receptor (1), defined in terms of stability of an anion-receptor complex (1 + X-) against its disintegration, were evaluated by dissociation studies using a mass spectrometry-based methodology and supported by theoretical calculations (density functional theory-PBE0). The gas-phase complex with Cl- was found to be tailor-made for the macrocycle 1, while 1 + SA- (SA- = salicylate anion) and 1 + HSO4- were the weakest ones. Other complexes displayed a relatively low-stability dispersion (<1.2 kcal·mol-1). The 1/εr approach of the electrostatic contribution scaling method was used to predict the stability trends in a dimethyl sulfoxide solvent from the gas-phase binding energy partition using the symmetry-adapted perturbation theory. High deformation energy and differences in solvation energies were suggested to be the main sources of inconsistency in the predicted and experimental stabilities of 1 + F- and 1 + H2PO4- complexes.

Structural Characterization of Lactone-Containing MW 212 Organosulfates Originating from Isoprene Oxidation in Ambient Fine Aerosol.

Isoprene (C5H8) is the main non-methane hydrocarbon emitted into the global atmosphere. Despite intense research, atmospheric transformations of isoprene leading to secondary organic aerosol (SOA) are still not fully understood, including its multiphase chemical reactions. Herein, we report on the detailed structural characterization of atmospherically relevant isoprene-derived organosulfates (OSs) with a molecular weight (MW) of 212 (C5H8SO7), which are abundantly present in both ambient fine aerosol (PM2.5) and laboratory-generated isoprene SOA. The results obtained from smog chamber-generated isoprene SOA and aqueous-phase laboratory experiments coupled to the S(IV)-autooxidation chemistry of isoprene, 3-methyl-2(5H)-furanone, and 4-methyl-2(5H)-furanone, allowed us for the first time to fully elucidate the isomeric structures of the MW 212 OSs. By applying liquid chromatography interfaced to electrospray ionization high-resolution mass spectrometry, we firmly confirmed six positional isomers of the MW 212 OSs in PM2.5 collected from different sites in Europe and the United States. Our results also show that despite the low solubility of isoprene in water, aqueous-phase or multiphase chemistry can play an important role in the formation of OSs from isoprene. Possible formation mechanisms for the MW 212 OSs are also tentatively proposed.

How Do Aromatic Nitro Compounds React with Nucleophiles? Theoretical Description Using Aromaticity, Nucleophilicity and Electrophilicity Indices.

In this study, we present a complete description of the addition of a model nucleophile to the nitroaromatic ring in positions occupied either by hydrogen (the first step of the SNAr-H reaction) or a leaving group (SNAr-X reaction) using theoretical parameters including aromaticity (HOMA), electrophilicity and nucleophilicity indices. It was shown both experimentally and by our calculations, including kinetic isotope effect modeling, that the addition of a nucleophile to the electron-deficient aromatic ring is the rate limiting step of both SNAr-X and SNAr-H reactions when the fast transformation of σH-adduct into the products is possible due to the specific reaction conditions, so this is the most important step of the entire reaction. The results described in this paper are helpful for better understanding of the subtle factors controlling the reaction direction and rate.

Improved UHPLC-MS/MS Methods for Analysis of Isoprene-Derived Organosulfates.

Secondary organic aerosol (SOA) is an important yet not fully characterized constituent of atmospheric particulate matter. A number of different techniques and chromatographic methods are currently used for the analysis of SOA, so the comparison of results from different laboratories poses a challenge. So far, tentative structures have been suggested for many organosulfur compounds that have been identified as markers for the formation of SOA, including isoprene-derived organosulfates. Despite the effectiveness and robustness of LC-MS/MS analyses, the structural profiling of positional isomers of recently discovered organosulfates with molecular weights (MWs) of 214 and 212 from isoprene was entirely unsuccessful. Here, we developed a UHPLC combined with high-resolution tandem mass spectrometric method that significantly improves the separation efficiency and detection sensitivity of these compounds in aerosol matrices. We discovered that selection of the proper solvent for SOA extracts was a key factor in improving the separation parameters. Later, we took advantage of the enhanced sensitivity, combined with a short scan time window, to perform detailed structural mass-spectrometric studies. For the first time, we elucidate a number of isomers of the MW 214 and the MW 212 organosulfates and provide strong evidence for their molecular structures. The structure of trihydroxyketone sulfate MW 214 that we propose has not been previously reported. The methods we designed can be easily applied in other laboratories to foster an easy comparison of related qualitative and quantitative data obtained throughout the world.

Modeling of Dolichol Mass Spectra Isotopic Envelopes as a Tool to Monitor Isoprenoid Biosynthesis.

The cooperation of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, operating in parallel in plants to generate isoprenoid precursors, has been studied extensively. Elucidation of the isoprenoid metabolic pathways is indispensable for the rational design of plant and microbial systems for the production of industrially valuable terpenoids. Here, we describe a new method, based on numerical modeling of mass spectra of metabolically labeled dolichols (Dols), designed to quantitatively follow the cooperation of MVA and MEP reprogrammed upon osmotic stress (sorbitol treatment) in Arabidopsis (Arabidopsis thaliana). The contribution of the MEP pathway increased significantly (reaching 100%) exclusively for the dominating Dols, while for long-chain Dols, the relative input of the MEP and MVA pathways remained unchanged, suggesting divergent sites of synthesis for dominating and long-chain Dols. The analysis of numerically modeled Dol mass spectra is a novel method to follow modulation of the concomitant activity of isoprenoid-generating pathways in plant cells; additionally, it suggests an exchange of isoprenoid intermediates between plastids and peroxisomes.

Luminescent-Substituted Fluoranthenes-Synthesis, Structure, Electrochemistry, and Optical Properties.

Six novel fluoranthene derivatives, namely, three terminally substituted and three bis(fluoranthene) units with fluorene, bithiophene, and carbazole spacers, were obtained through [2+2+2] cycloaddition and characterized completely. Based on the conducted studies, the obtained derivatives can be classified as donor-acceptor (D-A) and acceptor-donor-acceptor (A-D-A) systems, in which the fluoranthene unit acts as an electron-withdrawing unit. The optical results revealed that novel fluoranthene derivatives absorb light in the range λ=236-417 nm, which originates from a π→π* transition within the conjugated system. The compounds exhibit fluorescence that range from deep blue to green, which mainly arises from intramolecular charge transfer (ICT) states. High Stoke shifts and high quantum yields in solution (ϕ=0.22-0.57) and in the solid state (ϕ=0.18-0.44) have been observed for fluoranthene derivatives. All the derivatives display multistep oxidation processes at low potentials. The electronic structure of the presented compounds is additionally supported by time-dependent DFT computations.

Sphingopyxis lindanitolerans sp. nov. strain WS5A3pT enriched from a pesticide disposal site.

An aerobic, Gram-stain-negative, rod-shaped, non-motile, mesophilic soil bacterium, strain WS5A3pT, was isolated from a pesticide burial site in north-west Poland. The strain grew at 12-37 °C, at pH 8-9 and with 0-2 % (w/v) NaCl. The main fatty acids detected in WS5A3pT were summed feature 3, summed feature 8 and C16 : 0. The major respiratory quinone was Q-10 and major polar lipids were phosphatidylethanolamine, sphingoglycolipid and phosphatidylglycerol. The G+C content of the genome was 65.1 mol%. Phylogenetic pairwise distance analysis of the 16S rRNA gene placed this strain within the genus Sphingopyxis, with the highest similarity to Sphingopyxis witflariensis W-50T (98.8 %), Sphingopyxis bauzanensis BZ30T and Sphingopyxis ginsengisoli Gsoil 250T (98.3 %) and Sphingopyxis granuli NBRC 100800T (98.09 %). Genomic similarity analyses using ANIb and dDDH algorithms indicated levels of similarity of 81.44, 80.84 and 81.16 % between WS5A3pT and S. witflariensis, S. bauzanensisand S. granuli, respectively for average nucleotide identity and 25.90, 25.00 and 26.10 % for digital DNA-DNA hybridization. Based on the phylogenetic and phenotypic data, strain WS5A3pT should be considered as a representative of a novel Sphingopyxis species. The name Sphingopyxis lindanitolerans sp. nov. is proposed with the type strain WS5A3pT (=DSM 106274T=PCM 2932T).

The lipid composition of Legionella dumoffii membrane modulates the interaction with Galleria mellonella apolipophorin III.

Apolipophorin III (apoLp-III), an insect homologue of human apolipoprotein E (apoE), is a widely used model protein in studies on protein-lipid interactions, and anti-Legionella activity of Galleria mellonella apoLp-III has been documented. Interestingly, exogenous choline-cultured Legionella dumoffii cells are considerably more susceptible to apoLp-III than non-supplemented bacteria. In order to explain these differences, we performed, for the first time, a detailed analysis of L. dumoffii lipids and a comparative lipidomic analysis of membranes of bacteria grown without and in the presence of exogenous choline. (31)P NMR analysis of L. dumoffii phospholipids (PLs) revealed a considerable increase in the phosphatidylcholine (PC) content in bacteria cultured on choline medium and a decrease in the phosphatidylethanolamine (PE) content in approximately the same range. The interactions of G. mellonella apoLp-III with lipid bilayer membranes prepared from PLs extracted from non- and choline-supplemented L. dumoffii cells were examined in detail by means of attenuated total reflection- and linear dichroism-Fourier transform infrared spectroscopy. Furthermore, the kinetics of apoLp-III binding to liposomes formed from L. dumoffii PLs was analysed by fluorescence correlation spectroscopy and fluorescence lifetime imaging microscopy using fluorescently labelled G. mellonella apoLp-III. Our results indicated enhanced binding of apoLp-III to and deeper penetration into lipid membranes formed from PLs extracted from the choline-supplemented bacteria, i.e. characterized by an increased PC/PE ratio. This could explain, at least in part, the higher susceptibility of choline-cultured L. dumoffii to G. mellonella apoLp-III.

Negative ion gas-phase chemistry of arenes.

Reactions of aromatic and heteroaromatic compounds involving anions are of great importance in organic synthesis. Some of these reactions have been studied in the gas phase and are occasionally mentioned in reviews devoted to gas-phase negative ion chemistry, but no reviews exist that collect all existing information about these reactions. This work is intended to fill this gap. In the first part of this review, methods for generating arene anions in the gas phase and studying their physicochemical properties and fragmentation reactions are presented. The main topics in this part are as follows: processes in which gas-phase arene anions are formed, measurements and calculations of the proton affinities of arene anions, proton exchange reactions, and fragmentation processes of substituted arene anions, especially phenide ions. The second part is devoted to gas-phase reactions of arene anions. The most important of these are reactions with electrophiles such as carbonyl compounds and α,ß-unsaturated carbonyl and related compounds (Michael acceptors). Other reactions including oxidation of arene anions and halogenophilic reactions are also presented. In the last part of the review, reactions of electrophilic arenes with nucleophiles are discussed. The best known of these is the aromatic nucleophilic substitution (SN Ar) reaction; however, other processes that lead to the substitution of a hydrogen atom in the aromatic ring are also very important. Aromatic substrates in these reactions are usually but not always nitroarenes bearing other substituents in the ring. The first step in these reactions is the formation of an anionic σ-adduct, which, depending on the substituents in the aromatic ring and the structure of the attacking nucleophile, is either an intermediate or a transition state in the reaction path. In the present review, we attempted to collect the results of both experimental and computational studies of the aforementioned reactions conducted since the very beginning of gas-phase negative ion chemistry.

NCN-Coordinating Ligands based on Pyrene Structure with Potential Application in Organic Electronics.

Five novel derivatives of pyrene, substituted at positions 1,3,6,8 with 4-(2,2-dimethylpropyloxy)pyridine (P1), 4-decyloxypyridine (P2), 4-pentylpyridine (P3), 1-decyl-1,2,3-triazole (P4), and 1-benzyl-1,2,3-triazole (P5), are obtained through a Suzuki-Miyaura cross-coupling reaction or CuI -catalyzed 1,3-dipolar cycloaddition reaction, respectively, and characterized thoroughly. TGA measurements reveal the high thermal stability of the compounds. Pyrene derivatives P1-P5 all show photoluminescence (PL) quantum yields (Φ) of approximately 75 % in solution. Solid-state photo- and electroluminescence characteristics of selected compounds as organic light-emitting diodes are tested. In the guest-host configuration, two matrixes, that is, poly(N-vinylcarbazole) (PVK) and a binary matrix consisting of PVK and 2-tert-butylphenyl-5-biphenyl-1,3,4-oxadiazole (PBD) (50:50 wt %), are applied. The diodes show red, green, or blue electroluminescence, depending on both the compound chemical structure and the actual device architecture. In addition, theoretical studies (DFT and TD-DFT) provide a deeper understanding of the experimental results.

Short-chain polyisoprenoids in the yeast Saccharomyces cerevisiae - New companions of the old guys.

Dolichols are, among others, obligatory cofactors of protein glycosylation in eukaryotic cells. It is well known that yeast cells accumulate a family of dolichols with Dol-15/16 dominating while upon certain physiological conditions a second family with Dol-21 dominating is noted. In this report we identified the presence of additional short-chain length polyprenols - all-trans Pren-7 in three yeast strains (SS328, BY4741 and L5366), Pren-7 was accompanied by traces of putative Pren-6 and -8. Moreover, in two of these strains a single polyprenol mainly-cis-Pren-11 was synthesized at the stationary phase of growth. Identity of polyprenols was confirmed by HR-HPLC/MS, NMR and metabolic labeling. Additionally, simvastatin inhibited their biosynthesis.

How Does Nucleophilic Aromatic Substitution Really Proceed in Nitroarenes? Computational Prediction and Experimental Verification.

The aim of this paper is to present a correct and complete mechanistic picture of nucleophilic substitution in nitroarenes based on the results obtained by theoretical calculations and experimental observations coming from numerous publications, reviews, and monographs. This work gives the theoretical background to the very well documented experimentally yet still ignored observations that the addition of nucleophiles to halo nitroarenes resulting in the formation of σ(H) adducts, which under proper reaction conditions can be transformed into the product of the SNArH reaction, is faster than the competing process of addition to the carbon atom bearing a nucleofugal group (usually a halogen atom) resulting in the "classic" SNAr reaction. Only when the σ(H) adduct cannot be transformed into the SNArH reaction product, SNAr reaction is observed.

Specific Noncovalent Association of Chiral Large-Ring Hexaimines: Ion Mobility Mass Spectrometry and PM7 Study.

Ion mobility mass spectrometry and PM7 semiempirical calculations are effective complementary methods to study gas phase formation of noncovalent complexes from vaselike macrocycles. The specific association of large-ring chiral hexaimines, derived from enantiomerically pure trans-1,2-diaminocyclohexane and various isophthaldehydes, is driven mostly by CH-π and π-π stacking interactions. The isotrianglimine macrocycles are prone to form two types of aggregates: tail-to-tail and head-to-head (capsule) dimers. The stability of the tail-to-tail dimers is affected by the size and electronic properties of the substituents at the C-5 position of the aromatic ring. Electron-withdrawing groups stabilize the aggregate, whereas bulky or electron-donating groups destabilize the complexes.

Experimental versus Calculated Proton Affinities for Aromatic Carboxylic Acid Anions and Related Phenide Ions.

Herein, we present the comparison of a large set of experimentally measured proton affinity (PA) values for 65 aromatic carboxylate anions with the values calculated by using selected popular DFT (B3LYP, PBE0, and M05-2X) and composite [G3(MP2), G4(MP2)] quantum chemistry methods. The root-mean-square error (RMSE) values for the chosen methods are RMSEPBE0 =1.7, RMSEB3LYP =4.6, RMSEM05-2X =6.6, RMSEG3MP2 =6.3, RMSEG4MP2 =4.5 kJ mol(-1) . In the second part of the study, 82 PA values for substituted phenide ions and a few heteroaromatic anions were calculated. Again, very good agreement between the calculated and experimental values has been observed: RMSEPBE0 =1.9, RMSEB3LYP =4.5, RMSEM05-2X =6.3, RMSEG3MP2 =4.9, RMSEG4MP2 =5.5 kJ mol(-1) . Our results show that, for medium-sized carboxylate anions, all tested methods give reliable results and, surprisingly, much more computationally demanding composite methods do not perform significantly better than the time-efficient DFT methods.

Gas-phase reactions of methyl thiocyanate with aliphatic carbanions - A mass spectrometry and computational study.

RATIONALE: Methyl thiocyanate, like other organic thiocyanates, is a molecule with many electrophilic reactive sites and it has many synthetic applications. For better understanding of the intrinsic reactivity of alkyl thiocyanates against nucleophiles it was important to study gas-phase reactions of methyl thiocyanate with carbanions differing by structure and proton affinity values. METHODS: All experiments were performed using a modified API 365 triple quadrupole mass spectrometer equipped with a TurboIonSpray electrospray ionization (ESI) source. Carbanions were generated in the ESI source by decarboxylation of the respective carboxylic acid anions. Methyl thiocyanate was delivered as a vapor with nitrogen used as a collision gas to the collision cell where the reactions take place. RESULTS: Mass spectra recorded for the gas-phase reactions of five aliphatic carbanions with methyl thiocyanate showed a variety of product ions formed via different reaction mechanisms, depending on the structure and proton affinity of the carbanion. The pathways considered are: SN 2 nucleophilic substitution, cyanophilic reaction, thiophilic reaction and proton transfer, followed in some instances by subsequent transformations. The proposed reaction pathways are supported by density functional theory (DFT) calculations. CONCLUSIONS: Our preliminary experiments showed that mass spectrometry together with quantum chemical calculations is a good tool for studying gas-phase reactions of alkyl thiocyanates with carbanions. In the gas phase all four theoretically possible products can be observed and their formation can be rationalized by the results of the modelling of the reaction energy profiles. Copyright © 2016 John Wiley & Sons, Ltd.