Carbon-sulfur Bond Cleavage Research Articles

A capped trigonal pyramidal molybdenum hydrido complex and an unusually mild sulfur-carbon bond cleavage reaction.

DFT calculations reveal that a reported molybdenum hydride complex has an unprecedented geometry with the molybdenum in the base of trigonal pyramid defined by three thiolate ligands with a phosphine ligand on the apex and a hydride capping a PS2 face. This complex reacts with methanol to produce a sulfido complex by a new reaction: the protonation of an ipso carbon of a thiolate ligand by coordinated methanol.

Hydrolytic cleavage of both CS2 carbon-sulfur bonds by multinuclear Pd(II) complexes at room temperature.

Developing homogeneous catalysts that convert CS2 and COS pollutants into environmentally benign products is important for both fundamental catalytic research and applied environmental science. Here we report a series of air-stable dimeric Pd complexes that mediate the facile hydrolytic cleavage of both CS2 carbon-sulfur bonds at 25 °C to produce CO2 and trimeric Pd complexes. Oxidation of the trimeric complexes with HNO3 regenerates the dimeric starting complexes with the release of SO2 and NO2. Isotopic labelling confirms that the carbon and oxygen atoms of CO2 originate from CS2 and H2O, respectively, and reaction intermediates were observed by gas-phase and electrospray ionization mass spectrometry, as well as by Fourier transform infrared spectroscopy. We also propose a plausible mechanistic scenario based on the experimentally observed intermediates. The mechanism involves intramolecular attack by a nucleophilic Pd-OH moiety on the carbon atom of coordinated µ-OCS2, which on deprotonation cleaves one C-S bond and simultaneously forms a C-O bond. Coupled C-S cleavage and CO2 release to yield [(bpy)3Pd3(µ3-S)2](NO3)2 (bpy, 2,2'-bipyridine) provides the thermodynamic driving force for the reaction.

Proteomics and Metabolomics Analyses to Elucidate the Desulfurization Pathway of Chelatococcus sp.

Desulfurization of dibenzothiophene (DBT) and alkylated DBT derivatives present in transport fuel through specific cleavage of carbon-sulfur (C-S) bonds by a newly isolated bacterium Chelatococcus sp. is reported for the first time. Gas chromatography-mass spectrometry (GC-MS) analysis of the products of DBT degradation by Chelatococcus sp. showed the transient formation of 2-hydroxybiphenyl (2-HBP) which was subsequently converted to 2-methoxybiphenyl (2-MBP) by methylation at the hydroxyl group of 2-HBP. The relative ratio of 2-HBP and 2-MBP formed after 96 h of bacterial growth was determined at 4:1 suggesting partial conversion of 2-HBP or rapid degradation of 2-MBP. Nevertheless, the enzyme involved in this conversion process remains to be identified. This production of 2-MBP rather than 2-HBP from DBT desulfurization has a significant metabolic advantage for enhancing the growth and sulfur utilization from DBT by Chelatococcus sp. and it also reduces the environmental pollution by 2-HBP. Furthermore, desulfurization of DBT derivatives such as 4-M-DBT and 4, 6-DM-DBT by Chelatococcus sp. resulted in formation of 2-hydroxy-3-methyl-biphenyl and 2-hydroxy –3, 3/- dimethyl-biphenyl, respectively as end product. The GC and X-ray fluorescence studies revealed that Chelatococcus sp. after 24 h of treatment at 37°C reduced the total sulfur content of diesel fuel by 12% by per gram resting cells, without compromising the quality of fuel. The LC-MS/MS analysis of tryptic digested intracellular proteins of Chelatococcus sp. when grown in DBT demonstrated the biosynthesis of 4S pathway desulfurizing enzymes viz. monoxygenases (DszC, DszA), desulfinase (DszB), and an NADH-dependent flavin reductase (DszD). Besides, several other intracellular proteins of Chelatococcus sp. having diverse biological functions were also identified by LC-MS/MS analysis. Many of these enzymes are directly involved with desulfurization process whereas the other enzymes/proteins support growth of bacteria at an expense of DBT. These combined results suggest that Chelatococcus sp. prefers sulfur-specific extended 4S pathway for deep-desulphurization which may have an advantage for its intended future application as a promising biodesulfurizing agent.

Palladium-Catalyzed Regio- and Stereoselective Carbothiolation of Terminal Alkynes with Azolyl Sulfides.

Palladium-catalyzed carbothiolation of terminal alkynes with azolyl sulfides affords various 2-(azolyl)alkenyl sulfides with perfect regio- and stereoselectivities. The present addition reaction proceeded through a direct cleavage of carbon-sulfur bonds in azolyl sulfides. The resulting adducts that are useful intermediates in organic synthesis are further transformed to multisubstituted olefins containing azolyl moieties.

Dibenzothiophene desulfurization capability and evolutionary divergence of newly isolated bacteria.

Metabolically microorganisms are diverse, and they are capable of transforming almost every known group of chemical compounds present in coal and oil in various forms. In this milieu, one of the important microbial metabolic processes is the biodesulfurization [cleavage of carbon-sulfur (C-S) bond] of thiophenic compounds, such as dibenzothiophene (DBT), which is the most abundant form of organic sulfur present in fossil fuels. In the current study, ten newly isolated bacterial isolates, designated as species of genera Gordonia, Amycolatopsis, Microbacterium and Mycobacterium, were enriched from different samples in the presence of DBT as a sole source of organic sulfur. The HPLC analysis of the DBT grown cultures indicated the consumption of DBT and accumulation of 2-hydroxybiphenyl (2-HBP). Detection of 2-HBP, a marker metabolite of 4S (sulfoxide-sulfone-sulfinate-sulfate) pathway, suggested that the newly isolated strains harbored metabolic activity for DBT desulfurization through the cleavage of C-S bond. The maximum 2-HBP formation rate was 3.5µmol/g dry cell weight (DCW)/h. The phylogenetic analysis of the new isolates showed that they had diverse distribution within the phylogenetic tree and formed distinct clusters, suggesting that they might represent strains of already reported species or they were altogether new species. Estimates of evolutionary divergence showed high level of nucleotide divergence between the isolates within the same genus. The new isolates were able to use a range of heterocyclic sulfur compounds, thus making them suitable candidates for a robust biodesulfurization system for fossil fuels.

Studies toward the oxidative and reductive activation of C–S bonds in 2′-S-aryl-2ʹ-thiouridine derivatives

Studies directed toward the oxidative and reductive desulfurization of readily available 2′-S-aryl-2′-thiouridine derivatives were investigated with the prospect to functionalize the C2′-position of nucleosides. The oxidative desulfurization-difluorination strategy was successful on 2-(arylthio)alkanoate surrogates, while extension of the combination of oxidants and fluoride sources was not an efficient fluorination protocol when applied to 2′-S-aryl-2′-thiouridine derivatives, resulting mainly in C5-halogenation of the pyrimidine ring and C2′-monofluorination without desulfurization. Cyclic voltammetry of 2′-arylsulfonyl-2′-deoxyuridines and their 2′-fluorinated analogues showed that cleavage of the arylsulfone moiety could occur, although at relatively high cathodic potentials. While reductive-desulfonylation of 2′-arylsulfonyl-2′-deoxyuridines with organic electron donors (OEDs) gave predominantly base-induced furan type products, chemical (OED) and electrochemical reductive-desulfonylation of the α-fluorosulfone derivatives yielded the 2′-deoxy-2′-fluorouridine and 2′,3′-didehydro-2′,3′-dideoxy-2′-fluorouridine derivatives. These results provided good evidence of the generation of a C2′-anion through carbon-sulfur bond cleavage, opening new horizons for the reductive-functionalization approaches in nucleosides.

Palladium(ii)-catalyzed synthesis of dibenzothiophene derivatives via the cleavage of carbon-sulfur and carbon-hydrogen bonds.

A new process has been developed for the palladium(ii)-catalyzed synthesis of dibenzothiophene derivatives via the cleavage of C-H and C-S bonds. In contrast to the existing methods for the synthesis of this scaffold by C-H functionalization, this new catalytic C-H/C-S coupling method does not require the presence of an external stoichiometric oxidant or reactive functionalities such as C-X or S-H, allowing its application to the synthesis of elaborate π-systems. Notably, the product-forming step of this reaction lies in an oxidative addition step rather than a reductive elimination step, making this reaction mechanistically uncommon.

Carbon–sulfur bond cleavage of benzothiophene by Cp∗Co(C2H4)2

Cp∗Co(C2H4)2 was reacted with benzothiophene and C–S activation of the vinyl-sulfur bond was observed. The resulting product, [Cp∗Co]2(μ-κ2-C,S-C8H6S) was characterized by 1H NMR, 13C{1H} NMR, 13C DEPT-135 NMR, and 1H–13C 2D HSQC spectroscopies. The broad Cp∗ methyl peaks in these spectra suggested a fluxional structure.

Formation of Acyl and Dioxycarbene Ruthenium Complexes via Double C–S Bond Cleavage and CO Insertion

Abstract Ruthenium complexes containing an N,N,C,S-metalloligand or an N,N,C,O-organoligand with a sulfido carbonyl Ru cluster were obtained by the reaction of 6-(4′′-dibenzothienyl)-2,2′-bipyridine with [Ru3(CO)12]. The dibenzothienyl group undergoes double carbon–sulfur bond cleavage and CO insertion reactions to give a bridging acyl group and a metallacyclic dioxycarbene donor.

Formation of ortho-cyano-aminothiophenolate ligands with versatile binding modes via facile carbon-sulfur bond cleavage of 2-aminobenzothiazoles at mercury(II) centres.

Addition of 2-aminobenzothiazole and substituted derivatives to mercuric acetate in warm ethanol leads to the high yield formation of [Hg{SC6H3XN(C[triple bond, length as m-dash]N)}]n resulting from loss of hydrogen and sulfur-carbon bond cleavage. Addition of phosphines affords a series of complexes in which the new ortho-cyano-aminothiophenolate ligands adopt three different binding modes.

Theoretical studies on the desulfurization of benzothiophene (thianaphthene) and thienothiophene (thiophthene) by carbon–sulfur bond cleavage: binuclear iron carbonyl intermediates

The lowest energy (C8H6S)Fe2(CO)nand (C6H4S2)Fe2(CO)nstructures (n= 6, 5) derived from benzothiophene and thienothiophene, respectively, have an iron atom inserted into C–S bond of the ligand thiophene ring.

Metal‐to‐Ligand Alkyl Migration Inducing Carbon–Sulfur Bond Cleavage in Dialkyl Yttrium Complexes Supported by Thiazole‐Containing Amidopyridinate Ligands: Synthesis, Characterization, and Catalytic Activity in the Intramolecular Hydroamination Reaction

Neutral Y(III) dialkyl complexes supported by tridentate N(-) ,N,N monoanionic methylthiazole- or benzothiazole-amidopyridinate ligands have been prepared and completely characterized. Studies on their stability in solution revealed progressive rearrangement of the coordination sphere in the benzothiazole-containing system through an unprecedented metal-to-ligand alkyl migration and subsequent thiazole ring opening. Attempts to synthesize hydrido species from the dialkyl precursor led to the generation of a dimeric yttrium species stabilized by a trianionic N(-) ,N,N(-) ,S(-) ligand as the result of metal-to-ligand hydride migration with chemoselective thiazole ring opening and subsequent dimerization through intermolecular addition of the residual YH group to the imino fragment of a second equivalent of the ring-opened intermediate. DFT calculations were used to elucidate the thermodynamics and kinetics of the process, in support of the experimental evidence. Finally, all isolated yttrium complexes, especially their cationic forms prepared by activation with the Lewis acid Ph3 C(+) [B(C6 F5 )4 ](-) , were found to be good candidate catalysts for intramolecular hydroamination/cyclization reactions. Their catalytic performance with a number of primary and secondary amino alkenes was assessed.

Studies and X‐ray Determinations with 2‐(Acetonylthio)benzothiazole: Synthesis of 2‐(Benzothiazol‐2‐ylthio)‐1‐phenylethanone and 2‐(Acetonylthio)Benzothiazole by C―S Bond Cleavage of 2‐(Acetonylthio)benzothiazole in KOH

New route for the synthesis of 2‐(benzothiazol‐2‐ylthio)‐1‐phenylethanone (6) and 2‐(acetonylthio)benzothiazole (1) by using phenacyl bromide and α‐chloroacetone, respectively, through carbon–sulfur bond cleavage reactions in a basic medium has been generated. Treatment of 1 with malononitrile and elemental sulfur afforded the corresponding derivative of 2‐amino‐3‐cyanothiophene (12), whereas treatment of 1 with cyanoacetohydrazide afforded the corresponding derivative of cyanoacetylhydrazone derivative (13). The structure of the synthesis compounds has been established on the basis of elemental analyses, 1H‐NMR, 13C‐NMR, correlation spectroscopy, heteronuclear single quantum coherence, MS spectra, and X‐ray crystallographic investigations.

Biodesulfurization of Model Compounds and De-asphalted Bunker Oil by Mixed Culture

In this study, complicated model sulfur compounds in bunker oil and de-asphalted bunker oil were biodesulfurized in a batch process by microbial consortium enriched from oil sludge. Dibenzothiophene (DBT) and benzo[b]naphtho[1,2-d]thiophene (BNT1) were selected as model sulfur compounds. The results show that the mixed culture was able to grow by utilizing DBT and BNT1 as the sole sulfur source, while the cell density was higher using DBT than BNT1 as the sulfur source. GC-MS analysis of their desulfurized metabolites indicates that both DBT and BNT1 could be desulfurized through the sulfur-specific degradation pathway with the selective cleavage of carbon-sulfur bonds. When DBT and BNT1 coexisted, the biodesulfurization efficiency of BNT1 decreased significantly as the DBT concentrations increased (>0.1 mmol/L). BNT1 desulfurization efficiency also decreased along with the increase of 2-hydroxybiphenyl as the end product of DBT desulfurization. For real bunker oil, only 2.8 % of sulfur was removed without de-asphalting after 7 days of biotreatment. After de-asphalting, the biodesulfurization efficiency was significantly improved (26.2-36.5 %), which is mainly attributed to fully mixing of the oil and water due to the decreased viscosity of bunker oil.

Facile carbon–sulfur bond cleavage in diarylsulfonium ylides: a catalytic sulfur-to-silicon group transfer

An unusual cleavage of the non-ylidic carbon-sulfur bond of a sulfonium ylide is reported. The reaction can be catalysed by a variety of palladium(II) complexes under mild conditions. Preliminary results show that coordination of the ylide to the metal center results in significant structural changes.

Experimental Investigation of the Interaction of Dimethyl Sulfide/Ethyl Mercaptan with Nano-Manganese Dioxide

Nano-MnO2 was prepared by a sol–gel technology, and the structure was characterized by means of powder X-ray diffraction (XRD). The interaction of dimethyl sulfide (DMS) or ethyl mercaptan (EM) with the as-prepared MnO2 was investigated at ambient temperature with Fourier transform infrared (FT-IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and laser Raman spectroscopy (LRS). The results showed that DMS and EM undergo different interactions with the surface of MnO2. The interaction of DMS and MnO2 bring about carbon–sulfur bond cleavage and the oxidation of C. However, there might be hydrogen bonding between EM and MnO2 in addition to chemical bonding, which results in a weaker S–H bond in the EM molecule, so that EM is easily oxidized to sulfonates and sulfates. Tentative interaction mechanisms for DMS and EM on MnO2 are suggested.

Evolutionary Mechanisms of Microbial Genomes 2012

What is the driving force in the course of microbial genome evolution? What is the mechanism for distinguishing self-genome from others? These fundamental questions remain elusive although rigorous studies are underway by using comparative genomics. The special issue “Evolutionary mechanisms of microbial genomes” has been launched in 2011 and presented 11 original papers. Here, this new version in 2012 presents 10 papers (one review and nine research articles). Two papers are presented in phylogenomics. K. Oshima et al. revealed a close relationship of Aquificales to Thermotogales based on the whole-genome comparison in “Phylogenetic position of Aquificales based on the whole genome sequences of six Aquificales species.” An extensive and elaborate review of fish pathogenic bacteria has been presented by P. S. Sudheesh et al. in “Comparative pathogenomics of bacteria causing infectious diseases in fish.” Two papers are presented on subjects related to evolution of base composition in genomes. H. Nishida et al. in “Genome signature difference between Deinococcus radiodurans and Thermus thermophilus” observed distinct tetranucleotide frequencies between the genomes of D. radiodurans and T. thermophilus, potentially reflecting different evolutionary backgrounds of the two species after divergence from common ancestor. H. Nishida in “Comparative analyses of base compositions, DNA sizes, and dinucleotide frequency profiles in archaeal and bacterial chromosomes and plasmids” reported lower GC content (by up to ~10%) of plasmids compared to their host chromosomes and higher correlation of GC content and chromosome size in bacteria than in archaea. Two papers are presented about horizontal gene transfer in genome evolution. M. Jalasvuori in “Vehicles, replicators, and intercellular movement of genetic information: Evolutionary dissection of a bacterial cell” discussed a hypothesis that any given biosphere comprising prokaryotic cell vehicles and genetic replicators may naturally evolve toward possessing horizontally moving replicators of various types. V. S. Pylro et al. described horizontal gene transfer events of the gene dszC involved in the cleavage of carbon-sulfur bonds in “Detection of horizontal gene transfers from phylogenetic comparisons.” An article about DNA mutation is presented by Y. Shiwa et al. in “Whole-genome profiling of a novel mutagenesis technique using proofreading-deficient DNA polymerase δ.” They compared mutations created by the chemical mutagen ethyl methanesulfonate (EMS) and the proofreading-deficient DNA polymerase δ and found that the mutations created by the proofreading-deficient DNA polymerase δ generated more diverse amino acid substitution patterns than those by EMS. Three papers are presented on subjects related to metabolic pathway. H. Nishida in “Comparative analyses of homocitrate synthase genes of ascomycetous yeasts” described gene duplications of the homocitrate synthase which have occurred multiple times during evolution of the ascomycetous yeasts. H. Nishida and M. Nishiyama in “Evolution of lysine biosynthesis in the phylum Deinococcus-Thermus” reported that bacterial lysine biosynthesis genes of the common ancestor of the Deinococcus-Thermus phylum used the α-aminoadipate pathway instead of the diaminopimelate pathway. K. Ueda et al. in “Dispensabilities of carbonic anhydrase in Proteobacteria” analyzed the distribution of carbonic anhydrase (CA) in proteobacteria, compared CA-retaining and CA-deficient genomes, and found absence of coding sequence in some strains and frame shifts in others. In closing this introduction to the special issue, we would like to express our full appreciation to all the authors and reviewers for their enormous efforts that have made the timely completion of our assignment successful. We sincerely hope that this special issue will stimulate further the investigation of evolutionary mechanisms of microbial genomes. Hiromi Nishida Shinji Kondo Hideaki Nojiri Ken-ichi Noma Kenro Oshima

Self‐Assembled Monolayers of Single‐Molecule Magnets [Tb{Pc′(SR)8}2] on Gold

AbstractThe magnetic properties of the bis(phthalocyaninato)terbium complexes [Tb{Pc′(SR)8}2] (1) containing eight β‐positioned long‐chain alkylthio substituents SR (a: R=n‐C8H17, b: R=n‐C12H25) were studied by SQUID measurements, which revealed that both compounds are single‐molecule magnets with an effective energy barrier for spin reversal significantly higher than that found for pristine bis(phthalocyaninato)terbium [Tb(Pc)2]. Thin films on gold were fabricated from 1 a and 1 b by chemisorption from solution and were characterised by near‐edge X‐ray absorption fine structure (NEXAFS) and X‐ray photoelectron spectroscopy (XPS). In the case of 1 a, atomic force microscopy (AFM) was used in addition. The results are in accord with the formation of self‐assembled monolayers which contain the macrocyclic rings mainly in an approximately horizontal orientation. The chemisorption is primarily due to the peripheral SR substituents, giving rise to coordinatively bound thioether units, whose alkyl chains are in an almost parallel orientation with respect to the surface. In the case of 1 b, covalently attached thiolate units were also observed, indicating that the chemisorption process can lead to carbon–sulfur bond cleavage. In addition, the crystal structure of 1 a was determined.

Detection of horizontal gene transfers from phylogenetic comparisons.

Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases.

Synthesis, Structure, and Reactivity Study of Iron(II) Complexes with Bulky Bis(anilido)thioether Ligation

The synthesis, molecular structure, and ligand substitution reactivity of iron(II) complexes bearing the bulky N,N′-dimesityl-2,2′-diamidophenyl sulfide ligand have been studied. The ligand H2(mesNSN) (1) was synthesized by a Pd-mediated Buchwald–Hartwig amination method. An amine elimination reaction between 1 and [Fe(NTMS2)2]2 afforded the high-spin complex [(mesNSN)Fe(THF)] (2), displaying a distorted trigonal-monopyramidal geometry. Interaction of 2 with PMe3 and 2,5-di-tert-butylimidazol-1-ylidene (IBut) gave the ligand substitution products [(mesNSN)Fe(PMe3)] (3) and [(mesNSN)Fe(IBut)] (4), respectively. Both 3 and 4 are high spin and display molecular geometry similar to that of 2. The reaction of 2 with 3 equiv of isocyanide gave the low-spin complexes [(mesNSN)Fe(CNR)3] (R = But (5), Ph-2,6-Me2 (6)). Recrystallization of 6 has led to the isolation of the carbon–sulfur bond cleavage product [(mesNS)Fe(CNPh-2,6-Me2)3] (7). Quite unexpectedly, the interaction of 2 with 3-hexyne and deuterated benzene could induce Fe–N(amido) bond cleavage, giving [(mesHNSN)2Fe(THF)] (8) and [(mesHNSN)2Fe] (9), respectively. The formation of 7–9 suggests the lability of the [(mesNSN)Fe] fragment, which could suffer from degradation in the presence of bulky strong field ligands.