Alkene Loss Research Articles

Mechanistic investigation of charge-remote and charge-driven fragmentation processes in 2,5-diphenyl-3,4-ethylenedioxythiophene diamidines.

Diphenylfuran diamidines represent an important class of DNA minor groove binders of high therapeutic interest as antitumor and antibacterial agents. This study aimed to investigate fragmentation patterns in mass spectra of four diamidine derivatives with significant antitumor activity, in order to gain more insight into the structures and stability of their putative biological metabolites. Compounds were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) using low-energy collision-induced dissociation (CID). Density functional theory calculations were performed to confirm the main fragmentation paths. The most abundant ion present in mass spectra is the doubly protonated molecule, whereas singly protonated molecules are present to a lesser extent. In the simplest compound, 2,5-bis(4-amidinophenyl)-3,4-ethylenedioxythiophene, the main fragmentation path was loss of ammonia, followed by loss of HCN where possible. The fragmentation of the N-alkyl derivatives (N-isopropyl-, N-isobutyl-, N-cyclopentyl-) includes competition between loss of alkene and the corresponding amine, followed by loss of another alkene and formation of fragment ions present in the pathway of the parent compound. The primary sites of fragmentations of investigated compounds are amidine groups, while breaking the core 3,4-ethylenedioxythiophene ring system does not take place. Fragmentation of the singly protonated molecule [M+H](+) occurs primarily on the charged side of the molecule, but a charge-remote process is energetically viable. The fragmentation mechanism of the alkyl derivatives revealed that singly and doubly protonated molecules cleave to the singly and doubly protonated molecules of the parent compound. Once formed, they are gradually transformed into nitrile. Copyright © 2016 John Wiley & Sons, Ltd.

Preparation of synthetic alkane waxes and investigations on their suitability for application as dietary markers in farm animals

Synthetic alkanes can be applied as external markers to estimate faecal output, digestibility and passage kinetics and are furthermore easy to combine with plant alkanes for the estimation of feed intake. Successful application requires an accurate and uniform labelling of boluses or feedstuffs, which is in turn supported through simplified handling of the markers during preparation. In this study, it was tested whether melting of synthetic alkanes to wax is able to enhance the accuracy and uniformity of subsequent bolus labelling and further simplifies it. The preparation of alkane waxes was performed on model scale using a portion in a ratio of approximately 1:300 to a dosage, which is recommended for administration in large livestock 2 times a day. Additionally, the temperature sensitivity of a range of synthetic alkanes was studied to clarify so far non-explained losses of alkanes, which were observed frequently during the labelling of boluses and feedstuffs or the processing of samples for analysis. Using n-octacosane (C28), n-dotriacontane (C32) and n-hexatriacontane (C36) synthetic alkanes, three single-component waxes (of C28, C32 and C36, respectively), three binary waxes (C28:C32, C28:C36 and C32:C36) and one tertiary mixed wax (C28:C32:C36) were produced with 30 repetitions each. To assess the impact of melting and re-crystallization, the quantity of individual alkanes was determined by gas chromatographic analysis (GCA) in untreated crystals, crystalline mixtures (GCA1) and the finished model waxes (GCA2). Additionally, sub-samples of the waxes were heated for 30min at 100°C or freeze-dried for 48h, respectively, to simulate baking of boluses or freeze-drying as an alternative method for preparation (GCA3). The temperature sensitivity of n-tetracosane (C24) to n-octatriacontane (C38) even-chain alkanes was studied by thermogravimetric analysis (TGA) with consistently increasing temperature (20 to maximal 600°C at 10K/min, TGA1) and under isothermal conditions (180°C for 20min, TGA2), respectively. Depending on chain length and thus molecular weight of alkanes, weight reduction by emergence of soot during heating-up started between 176°C (C24) and 227°C (C38) and further increased rapidly. Throughout isothermal treatment, weight loss from alkanes was lowest with highest chain length (0.0% for C38) and vice versa (23.8% for C24). The originally weighed and via GCA measured quantities of crystalline alkanes did not differ (P>0.05), except for single C36, where the measured quantities were always higher than the weighed ones (P=0.019). The weighed and measured quantities of individual alkanes in single-component and of total alkanes in multi-component waxes were similar with a maximal relative difference of 6.6±5.5%, given as the mean ± standard deviation among the repetitions of a sample variant. The relative difference between weighed and measured quantities of individual alkanes in multi-component waxes was maximal 47.4±25.7% and was highly variable. Unexpectedly, the relative difference between weighed and measured quantities was low for C28 (5.9±5.8%) and C32 (5.7±4.3%) in their combined binary waxes. The additional treatment (baking or freeze-drying) did not alter the recovery of alkanes from the model waxes. Synthetic alkanes are thermolabile why exposure to high temperature during preparation of boluses or labelling of feedstuffs needs to be assessed critically. Reasons for that might be complex disorders of the conformation of alkane molecules particularly during the melting of alkane mixtures and the apparently incomplete separation following re-crystallization from the melt. This may lead to displacements within waxes, which cannot be foreseen or quantified, and thus to the loss of their suitability as dietary markers. Alkane recovery from binary waxes of C28 and C32 was unbiased on model scale and whether this can be confirmed on original scale needs to be validated further. For practical use, alkane waxes might nevertheless be beneficial because the handling is easier than that of alkane crystals.

Mass spectral characterization of the CWC‐related isomeric dialkyl alkylphosphonothiolates/alkylphosphonothionates under gas chromatography/mass spectrometry conditions

The isomeric dialkyl alkylphosphonothiolates and dialkyl alkylphosphonothionates are listed as scheduled chemicals of the Chemical Weapons Convention (CWC) implemented by the OPCW. The P-S and P-R bond connectivity has to be correctly identified for the verification of the CWC. The present study demonstrates successful identification of the target isomers by selective fragmentation under electron ionization (EI) or chemical ionization (CI) conditions. All the studied isomeric compounds (27 in total) were synthesized in our laboratory using established methods, then analyzed by EI and CI gas chromatography/mass spectrometry (GC/MS) using an Agilent 6890 gas chromatograph equipped with a HP-5MS capillary column and interfaced to a 5973 N mass-selective detector. The retention index (RI) values of all the compounds were calculated using Van den Dool's formula. GC/MS/MS and GC/HRMS experiments were also performed using a VG-Autospec (magnetic sector) and JEOL-AccuToF (time-of-flight) mass spectrometer, respectively. The EI mass spectra of all the compounds had an abundant molecular ion at m/z 182, except in the case of a few selected butyl-substituted compounds, where this ion was of low abundance. The EI fragmentation pathways include α-cleavage, McLafferty rearrangement, McLafferty + 1 rearrangement, O/S-alkyl radical loss, and an alkene loss with a hydrogen shift. The characteristic fragment ions and their relative abundances are significant in elucidating the alkyl group attached to the P/S/O-atoms as well as the P-S/P = S bond connectivity. The EI and CI mass spectra together with RI values enable unambiguous identification of all the studied isomeric compounds. The present study highlights the structural characterization of the isomeric phosphonothiolates and phosphonothionates based on their selective EI fragmentation. The assigned fragmentation pathway helps in the assignment of P-S and P-alkyl connectivity in phosphonothiolates and phosphonothionates, consequently the structure of the unknown compounds. The EI mass spectra (27 compounds) of isomeric compounds are immensely useful in the OPCW official proficiency tests and for off-site analysis.

Mass spectral analysis of N-oxides of nitrogen mustards, and N,N-dialkylaminoethyl-2-chlorides under electrospray ionization conditions

Chemical weapons convention (CWC) includes verification of chemical warfare agents and their precursors/degradation products in various environmental matrices. Nitrogen mustards and N,N-dialkylaminoethyl-2-chlorides, the precursors for the synthesis of nerve agents (VX type of compounds), are prone to undergo oxidation in environmental matrices or during decontamination process. Thus, screening of the oxidized products of the CWC related compounds is also an important task in the verification process. Here we report the successful characterization of the N-oxides of nitrogen mustards and N,N-dialkylaminoethyl-2-chlorides under positive ion electrospray ionization tandem mass spectrometry conditions. The collision-induced dissociation spectra of [M+H]+ ions show distinct product ions that enable unambiguous identification of studied N-oxides, including those of isomeric compounds. The proposed fragmentation pattern of these compounds is based on isotopic abundance ratio, high-resolution mass spectrometry data and product/precursor ion spectra. The CID spectra of [M+H]+ ions of the studied compounds include a specific product ion, [MH−(OH+CH2Cl)]+, and distinctive alkene losses to recognize the attached alkyl group to the nitrogen.

Photochemically Generated Transients from κ2- and κ3-Triphos Derivatives of Group 6 Metal Carbonyls and Their Reactivity with Olefins

The synthesis and characterization of (κ2-Triphos)M(CO)4 derivatives, where M = Mo, W and Triphos = MeC(CH2PPh2)3, are reported. Photolyses of these metal carbonyls in dichloromethane or CO2-saturated dichloromethane readily afford the (κ3-Triphos)M(CO)3 complexes with no evidence of significant solvent or carbon dioxide interactions with the site vacated by CO. However, in the presence of 1-hexene a transient (κ2-Triphos)M(CO)3(1-hexene) adduct was observed, which subsequently releases the olefin with formation of the stable κ3-tricarbonyl species. In the case of M = W the kinetic parameters for this process were assessed, with the rate of olefin replacement being inversely proportional to [1-hexene]. A dissociative rate constant of 25.6 ± 1.1 s–1 at 298 K was determined for olefin loss, with the selectivity for 1-hexene vs free phosphine arm addition to the unsaturated intermediate being somewhat surprisingly large at 22. The activation parameters measured were ΔH⧧ = 26.1 ± 0.4 kcal/mol and ΔS⧧ = 36 ± 3 eu, which are consistent with a dissociative substitution reaction. The kinetic parameters for this transformation were unaffected in the presence of excess quantities of CO2. Although no interaction of CO2 with the transient species resulting from CO loss in the κ2 complex was noted on the time scale of 50 ms, an intermediate described as an η2-HSiEt3 complex was observed upon addition of triethylsilane. This latter transient species underwent dissociation with κ3-complex formation about 15 times as fast as its 1-hexene analogue. X-ray structures of the κ2 complexes of Mo and W where the dangling phosphine arm has undergone oxidation are also reported.

The gas-phase reactions of metal porphyrins with diazoacetate esters

The Mn(III), Fe(III) and Co(III) complexes of tetraphenylporphyrin were allowed to react with ethyl and t-butyl diazoacetate in an ion trap mass spectrometer. The manganese system produces only adducts, but the iron and cobalt systems give addition with loss of N2 to produce carbene-like species. All the reactions are fast and approach the collision-controlled limit. Fragmentation of the iron and cobalt carbene species follow three major pathways: (a) alkene loss from the ester to give a carboxylic acid (which can subsequently decarboxylate to give CH2 complexed to the metal porphyrin), (b) homolytic cleavage of the ester OR bond with loss of CO2 and an alkyl radical to produce CH complexed to the metal porphyrin, and (c) alcohol loss to give CCO complexed to the metal porphyrin. Computational data from density functional theory (B3LYP) are consistent with the observed reactivity trends and indicate that all the carbene complexes prefer a MN insertion structure where the carbene carbon bonds to the metal and one of the porphyrin nitrogens (metalnitrogen bond is lost). The MN insertion structures are generally more than 25kcal/mol more stable than the conventional metal carbene structures, MC, at the B3LYP level and should dominate their reactivity.

Identification of unsaturated N‐acylhomoserine lactones in bacterial isolates of Rhodobacter sphaeroides by liquid chromatography coupled to electrospray ionization‐hybrid linear ion trap‐Fourier transform ion cyclotron resonance mass spectrometry

The identification of two unsaturated N-acylhomoserine lactones (AHLs) produced by Rhodobacter sphaeroides bacteria, based on liquid chromatography (LC) coupled to a hybrid quadrupole linear ion trap (LTQ)-Fourier transform ion cyclotron resonance (FTICR) mass spectrometer upon electrospray ionization (ESI), is presented. Besides the confirmation of the signaling molecule already described in the literature, i.e. (Z)-N-tetradec-7-enoyl-homoserine lactone (C(14:1)-HSL), we have discovered the occurrence, at low, yet significant levels, of another monounsaturated compound, C(12:1) -HSL, which may extend the number of small diffusible chemical signals known for R. sphaeroides. Both unsaturated AHLs were identified by high-resolution FTICR mass spectrometry in extracts of bacterial culture media and the occurrence of a C=C bond was assessed upon their conversion into bromohydrins. Collision-induced dissociation (CID) spectra were then collected on the LTQ mass analyzer. A careful comparison of tandem MS spectra of monounsaturated (i.e., C(12:1)-HSL and C(14:1)-HSL) and saturated AHLs (i.e. C(12)-HSL and C(14)-HSL) led to the emphasis of two series of product ions, exhibiting 14 Da spaced m/z ratios. Both series were referred to progressive fragmentations at the aliphatic end of the AHL acyl chains, followed by neutral losses of terminal alkenes (i.e. CH(2)=CH(CH(2))(n)H). In particular, the series located at the higher end of the explored m/z range (>200 Da), observed only for monounsaturated species, enabled the location of the C=C bond between carbons 7 and 8 of the acyl chain.

Mass spectral analysis of N‐oxides of Chemical Weapons Convention related aminoethanols under electrospray ionization conditions

N,N'-Dialkylaminoethanols are the hydrolyzed products or precursors of chemical warfare agents such as V-agents and nitrogen mustards, and they are prone to undergo oxidation in environmental matrices or during decontamination processes. Consequently, screening of the oxidized products of aminoethanols in aqueous samples is an important task in the verification of chemical weapons convention-related chemicals. Here we report the successful characterization of the N-oxides of N,N'-dialkylaminoethanols, alkyl diethanolamines, and triethanolamine using positive ion electrospray ionization mass spectrometry. The collision-induced dissociation (CID) spectra of the [M+H](+) and [M+Na](+) ions show diagnostic product ions that enable the unambiguous identification of the studied N-oxides, including those of isomeric compounds. The proposed fragmentation pathways are supported by high-resolution mass spectrometry data and product/precursor ion spectra. The CID spectra of [M+H](+) ions included [MH-CH(4)O(2)](+) as the key product ion, in addition to a distinctive alkene loss that allowed us to recognize the alkyl group attached to the nitrogen. The [M+Na](+) ions show characteristic product ions due to the loss of groups (R) attached to nitrogen either as a radical (R) or as a molecule [R+H or (R-H)] after hydrogen migration.

Evaluation of ligand effects in the modified cobalt hydroformylation of 1-octene. Crystal structures of [Co(L)(CO)3]2 (L = PA–C5, PCy3 and PCyp3)

A series of phosphine ligands with different electronic and steric properties were evaluated at fully modified conditions in cobalt catalysed hydroformylation of 1-octene. The steric demand of the ligands was based on the Tolman cone angle model covering a range of 132-175°. The electron donating ability was evaluated through the first order Se-P coupling constants as determined from the corresponding phosphine selenides covering a range of 672-752 Hz. Crystal structures of three phosphine modified cobalt dimers, [Co(CO)(3)(L)](2) (L = PA-C(5), PCy(3) and PCyp(3) with PA-C(5) = 1,3,5,7-tetramethyl-8-pentyl-2,4,6-trioxa-8-phosphatricyclo[3.3.1.1(3,7)]decane), are reported. The Phoban and Lim ligands (Phoban = mixture of 9-phosphabicyclo[3.3.1 and 4.2.1]nonane, Lim = 4,8-dimethyl-2-phosphabicyclo[3.3.1]nonane) resulted in systems about twice as active as most of the other ligands investigated, these ligands have a high Lewis basicity with (1)J(Se-P) values from 684-687 Hz. The linearity of the alcohol product in general decreased for the less electron donating ligands while no clear relationship was evident as a function of steric size. The parallel competing hydrogenation of 1-octene to octane varied from 9-15% for a cone angle range of 132-172°, but a sharp increase of up to 40% was observed for PA-C(5), PCy(3) and PCyp(3), all with cone angles > 169°. The catalytic behaviour provides evidence that is contrary to the dissociative substitution of CO by an alkene as the rate limiting step in all cases. For large symmetrical ligands, such as PA-C(5), PCy(3) and PCyp(3) the rate limiting step may move within the catalytic cycle and may now be situated at the carbonylation step where the chemoselectivity is also determined. The lack of clear correlation between the steric and electronic effect of the ligands and all catalytic parameters may serve as additional proof that the same system, especially in terms of the rate determining step, is not operative in all cases. The Phoban and Lim systems are superior with the highest reactivity and lowest alkene loss through hydrogenation. The unsymmetrical nature of the Phoban and Lim ligands may provide flexibility to adopt geometries inducing both high and low steric crowding, which may be a reason for its beneficial catalytic properties.

Mechanistic Insights from the Gas-Phase Reactivity of Phosphorus-Ylid-Supported Benzylidene Gold Complexes

The chemoselectivity as a function of ligand electronic properties was studied for the adducts of phosphorus-ylid-supported gold benzylidenes with methyl vinyl ether by gas-phase collision-induced dissociation experiments. The daughter channels were identified as cyclopropanation, metathesis, and regeneration of the starting benzylidene carbene via olefin loss. The observed product ratios provided linear Hammett plots with a negative slope for the cyclopropanation channel and similar positive ρ values for metathesis and olefin loss. These results are consistent with the presence of a gold-coordinated cyclopropane intermediate as a global minimum energy structure in the gas phase, from which the pathways to the different products proceed. Additionally, we discuss the anomalous case of the para-dimethylamino gold benzylidene species, which appears to be too stabilized to engage in the reactivity under investigation.

Energetics and Reaction Mechanisms for the Competitive Losses of H2, CH4 and C2H4 from Protonated Methylbenzenes—Implications to the Methanol-to-Hydrocarbons (MTH) Process

We report the unimolecular decomposition following collisional activation of protonated mono-, di- and trimethylbenzenes as a function of collision energy. The resulting energy-resolved mass spectra are then used for the quality control of high-level quantum chemical models of the respective potential energy surfaces. Distinction is made between direct dissociation products (CH(4) or H(2)) and indirect products (alkenes), since formation of the latter requires extensive rearrangement of the molecular skeleton. Very good consistency was found between model and experiment. The models thereby provide a solid foundation for discussing the reaction mechanisms of the industrial methanol-to-hydrocarbon process. The losses of CH(4), C(2)H(4) and C(3)H(6) from mesitylenium ions have been studied by (13)C and (2)H labelling and the alkene losses were found to occur via irreversible isomerisation pathways.

Electronic Effects in the Reactions of Olefin-Coordinated Gold Carbene Complexes

The influence of electronic effects on cyclopropanation, cross-metathesis, and olefin loss reactions was probed in the gas phase for the series of adducts formed by para-substituted benzylidene gold carbenes and cis-dimethoxyethylene. This information sheds light on rate-determining transition states associated with every process and suggests that tuning of the selectivity is possible.

Loss of benzene to generate an enolate anion by a site‐specific double‐hydrogen transfer during CID fragmentation of o‐alkyl ethers of ortho‐hydroxybenzoic acids

Collision-induced dissociation of anions derived from ortho-alkyloxybenzoic acids provides a facile way of producing gaseous enolate anions. The alkyloxyphenyl anion produced after an initial loss of CO(2) undergoes elimination of a benzene molecule by a double-hydrogen transfer mechanism, unique to the ortho isomer, to form an enolate anion. Deuterium labeling studies confirmed that the two hydrogen atoms transferred in the benzene loss originate from positions 1 and 2 of the alkyl chain. An initial transfer of a hydrogen atom from the C-1 position forms a phenyl anion and a carbonyl compound, both of which remain closely associated as an ion/neutral complex. The complex breaks either directly to give the phenyl anion by eliminating the neutral carbonyl compound, or to form an enolate anion by transferring a hydrogen atom from the C-2 position and eliminating a benzene molecule in the process. The pronounced primary kinetic isotope effect observed when a deuterium atom is transferred from the C-1 position, compared to the weak effect seen for the transfer from the C-2 position, indicates that the first transfer is the rate determining step. Quantum mechanical calculations showed that the neutral loss of benzene is a thermodynamically favorable process. Under the conditions used, only the spectra from ortho isomers showed peaks at m/z 77 for the phenyl anion and m/z 93 for the phenoxyl anion, in addition to that for the ortho-specific enolate anion. Under high collision energy, the ortho isomers also produce a peak at m/z 137 for an alkene loss. The spectra of meta and para compounds show a peak at m/z 92 for the distonic anion produced by the homolysis of the O-C bond. Moreover, a small peak at m/z 136 for a distonic anion originating from an alkyl radical loss allows the differentiation of para compounds from meta isomers.

Silica Surface Modification Reactions with Aluminum and Boron Alkyls and (Alkyl)Chlorides: Reactivities and Surface Nanostructures

The functionalization of nanoporous and nanoparticulate silica surfaces requires a molecular level understanding of the chemistry and structures which result from surface reactions. Various types of reactive groups on silica can participate, giving rise to different nanostructures. It is necessary to devise methods to alter the reactive nature of silica surfaces to control the nanoscale chemical structure. Various silica pretreatments are utilized to alter the silica surface prior to reaction with AlEt3, AlEtxCl(3-x), BEt3, BCl3, and TiCl4. Reactivities of these surface reactive reagents are compared. Aluminum compounds preferentially react with loss of alkane rather than HCl, in a thermodynamically controlled reaction as determined by ab initio computational methods. Consideration of the structures resulting from reaction of the boron and aluminum compounds above with silica surface diols has been taken into account. Particular attention has been paid to the possibility of forming a cyclic 4-membered ring structure. While this is unlikely to form from reactions with MCl3, such structures may be possible when reacting silicas with MMe3.

Gas-Phase Synthesis of the Homo and Hetero Organocuprate Anions [MeCuMe]-, [EtCuEt]-, and [MeCuR]-

The homocuprates [MeCuMe]- and [EtCuEt]- were generated in the gas phase by double decarboxylation of the copper carboxylate centers [MeCO2CuO2CMe]- and [EtCO2CuO2CEt]-, respectively. The same strategy was explored for generating the heterocuprates [MeCuR]- from [MeCO2CuO2CR]- (R = Et, Pr, iPr, tBu, allyl, benzyl, Ph). The formation of these organocuprates was examined by multistage mass spectrometry experiments, including collision-induced dissociation and ion-molecule reactions, and theoretically by density functional theory. A number of side reactions were observed to be in competition with the second stage of decarboxylation, including loss of the anionic carboxylate ligand and loss of neutral alkene via beta-hydride transfer elimination. Interpretation of decarboxylation of the heterocarboxylates [MeCO2CuO2CR]- was more complex because of the possibility of decarboxylation occurring at either of the two different carboxylate ligands and giving rise to the possible isomers [MeCuO2CR]- or [MeCO2CuR]-. Ion-molecule reactions of the products of initial decarboxylation with allyl iodide resulted in C-C coupling to produce the ionic products [ICuO2CR]- or [MeCO2CuI]-, which provided insights into the relative population of the isomers, and indicated that the site of decarboxylation was dependent on R. For example, [MeCO2CuO2CtBu]- underwent decarboxylation at MeCO2- to give [MeCuO2CtBu]-, while [MeCO2CuO2CCH2Ph]- underwent decarboxylation at PhCH2CO2- to give [MeCO2CuCH2Ph]-. Each of the heterocuprates [MeCuR]- (R = Et, Pr, iPr, allyl, benzyl, Ph) could be generated by the double decarboxylation strategy. However, when R = tBu, intermediate [MeCuO2CtBu]- only underwent loss of tBuCO2-, a consequence of the steric bulk of tBu disfavoring decarboxylation and stabilizing the competing channel of carboxylate anion loss. Detailed DFT calculations were carried out on the potential energy surfaces for the first and second decarboxylation reactions of all homo- and heterocuprates, as well as possible competing reactions. These reveal that in all cases the first decarboxylation reaction is favored over loss of the carboxylate ligand. In contrast, other reactions such as carboxylate ligand loss and beta-hydride transfer become more competitive with the second decarboxylation reaction.

Importance of the Sedimentary Matrix for Anaerobic Oil Degradation by Marine Bacterial Assemblages

ABSTRACT The microbial conversion of petroleum hydrocarbons is increasingly employed in bioremediation efforts. In marine sediments, oxygen levels are characteristically depleted, so anaerobic degradation coupled to sulfate reduction dominates. Prior studies have noted that anaerobic degradation is much reduced in the absence of sediments. In this study, a simple centrifugation protocol was used to extract sediment porewaters to obtain a sediment-free bacterial assemblage capable of anaerobic hydrocarbon degradation. In addition, the factors in sediment that were important to degradation rates were determined. Experiments were designed to differentiate among the effects of increased surface area associated with individual grains in sediments, differing levels of organic constituents in sediments and water, and disparate microbiota within the sedimentary matrix and those free living. Anaerobic alkane degradation, sulfate levels and bacterial community structure were monitored over 90 days in five treatments consisting of Bonny Light crude oil added to (1) intact sediment, (2) sediment-free supernate from centrifuged sediment, (3) supernate plus autoclaved sediment, (4) supernate plus organic-free (combusted) sediment, and (5) a control, with autoclaved supernate plus autoclaved sediment. Lack of surface area associated with sediment grains had little effect on degradation. Separation of porewaters from the sedimentary matrix resulted in loss of bacterial biomass, although this had only a temporary negative effect on degradation rates. Reduction of organic matter due to sediment removal had the largest effect, resulting initially in lower degradation rates. However, sulfate depletion in low organic treatments was also reduced so that long-term loss of alkanes was enhanced.

Investigation of the active site at the deuterated Schiff-base complex formed between the coenzyme vitamin B 6 and the primary amine

The Schiff-base complex ion formed between the vitamin B 6 molecule and the primary amine was investigated by electrospray ionization MS/MS in the gas phase. The two observed fragments at the MS/MS spectrum were different from the normal alkene loss (Onium reaction or McLafferty rearrangement) fragments of immonium ions. The R–CH–ND loss fragment from the 3H/D-deuterated Schiff-base complex ion was observed as one of two fragments in the MS/MS spectrum. The R–CH–ND loss fragment is thought to have originated from the simultaneous effect of a 3-OH functional group and a pyridine ring in the immonium ion.

Identification and characterization of supercritical fluid extracts of Rhizoma Chuanxiong by high performance liquid chromatography ion trap mass spectrometry

The main constituents, senkyunolide A, Z-ligustilide, neocnidilide, 3-butylphthalide, and ligustilide dimers, in supercritical CO2 fluid extracts of Rhizoma Chuanxiong, a popular Chinese traditional medicine, have been identified and characterized by high performance liquid chromatography tandem mass spectrometry. Separations were carried out on an Agilent (ECLIPSE XDB) C18 analytical column by gradient elution with 0.25% acetic acid and methanol (containing 0.25% acetic acid). An Agilent 1100 series LC/MSD XCT system was operated under positive ESI and auto MS/MS modes for mass spectrometric analysis. Collision-induced dissociation (CID) fragmentations of these phthalides have been investigated and elucidated. Phthalides have primarily undergone two ESI CID pathways: side-chain cleavage with losses of alkenes and ring-opening with eliminations of H2O followed by losses of CO. Direct neutral loss of CO has not been observed. Sodium adduct ions have demonstrated completely different CID pathways.

Electron ionization mass spectra of phosphorus‐containing heterocycles. I. 1,4,4a,5,6,7,8,8a‐octahydro‐2H‐3,1,2‐benzoxazaphosphinine 2‐oxides

The electron ionization mass spectra of 27 cis- and trans-annelated 1,4,4a,5,6,7,8,8a-octahydro-2H-3,1,2-benzoxazaphosphinine 2-oxides were recorded to clarify the effects of the ring heteroatom (O or N), ring annelation, the P configuration and the substituents attached to the ring or to the N and P atoms. For compounds 1-12 different alkyl radical and alkene losses and the cleavage of the P-heteroatom bonds, instead of the P-C bonds, were representative and dependent mainly on the substitution on the N and P atoms. The replacement of Ph and OPh by N(CH2CH2Cl)2 on the P atom had a dramatic influence on the fragmentation process: new fragment ions were obtained and very little M+ (1-3%) was formed. Only slight differences were found between some of the corresponding isomers, but interestingly the compounds formed clear groups on the basis of the differences in their fragmentation, depending on the ring-N and ring-P substituents.

A molecular-beam study of the collision dynamics of methane and ethane upon a graphitic monolayer on Pt(111)

Utilizing a supersonic molecular-beam scattering technique, the angular intensity distributions of alkane molecules (CH4 and C2H6) have been measured, which are scattered from a chemically inert and highly oriented monolayer graphite (MG) on Pt(111). A MG which covers the Pt(111) surface with a full monolayer is found to induce a large energy loss of alkanes during collision with the surface by phonon creation due to the large mass ratio of an alkane molecule with respect to MG. Based on the classical cube model, only applicable to the molecules without internal mode excitation, the effective masses of MG of 76 (six atoms of carbon) and Pt(111) of 585 (three atoms of platinum) are determined from rare-gas atom scattering data. Despite the difference in the degree of freedom between CH4 and rare-gas atoms, CH4 scattering is found to be well described by the simple hard-cube model as a result of the high symmetry of the CH4 structure. With the recently developed ellipsoid-washboard model, an extension of the hard-cube model to include some internal mode excitation of impinging molecules in addition to the surface corrugation, it is found that unlike CH4 the cartwheel rotation mode of C2H6 is significantly excited during collision, while the helicopter mode excitation is negligible on a flat MG surface.