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A passing spaceship NMR challenge. Anal Bioanal Chem 2024; 416:1997-1998. [PMID: 38504060 DOI: 10.1007/s00216-024-05210-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 03/21/2024]
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2
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Solution to the wing-giving challenge. Anal Bioanal Chem 2023; 415:5857-5858. [PMID: 37798485 DOI: 10.1007/s00216-023-04897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2023] [Indexed: 10/07/2023]
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3
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CYPArm2 is a CYP450 monooxygenase with protoilludene 13-hydroxylase activity involved in the biosynthesis of armillyl orsellinate-type sesquiterpenoids. Chembiochem 2023:e202300179. [PMID: 37171879 DOI: 10.1002/cbic.202300179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/14/2023]
Abstract
The melleolides are a family of structurally and functionally diverse sesquiterpenoids with potential applications as fungicides, antimicrobials and cancer therapeutics. The initial and terminal steps of the biosynthesis pathway in Armillaria spp. have been characterized, but the intermediate steps are unclear. Biosynthetic gene clusters in A. mellea and A. gallica were shown to encode a terpene cyclase, a polyketide synthase, and four CYP450 monooxygenases. We have characterized CYPArm3, which is responsible for the hydroxylation of Δ-6-protoilludene, but the functions of the other CYP450s remain to be determined. Here we describe CYPArm2, which accepts Δ-6-protoilludene and 8α-hydroxy-6-protoilludene as substrates. To investigate the products in more detail, we generated recombinant Saccharomyces cerevisiae strains overexpressing CYPArm2 in combination with the previously characterized protoilludene synthase and 8α-hydroxylase. Using this total biosynthesis approach, sufficient quantities of product were obtained for NMR spectroscopy. This allowed the identification of 8α,13-dihydroxy-protoilludene, confirming that CYPArm2 is a protoilludene 13-hydroxylase.
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Wing-giving challenge. Anal Bioanal Chem 2023; 415:1583-1585. [PMID: 36881151 DOI: 10.1007/s00216-023-04561-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 03/08/2023]
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5
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Solution to the mutarotation challenge. Anal Bioanal Chem 2022; 414:7003. [PMID: 35902395 DOI: 10.1007/s00216-022-04225-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 11/01/2022]
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6
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The mutarotation challenge. Anal Bioanal Chem 2022; 414:2789-2792. [PMID: 35307780 DOI: 10.1007/s00216-022-03935-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 11/26/2022]
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7
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Isolation of a gene cluster from Armillaria gallica for the synthesis of armillyl orsellinate-type sesquiterpenoids. Appl Microbiol Biotechnol 2021; 105:211-224. [PMID: 33191459 PMCID: PMC7778616 DOI: 10.1007/s00253-020-11006-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/29/2020] [Accepted: 11/04/2020] [Indexed: 11/27/2022]
Abstract
Melleolides and armillyl orsellinates are protoilludene-type aryl esters that are synthesized exclusively by parasitic fungi of the globally distributed genus Armillaria (Agaricomycetes, Physalacriaceae). Several of these compounds show potent antimicrobial and cytotoxic activities, making them promising leads for the development of new antibiotics or drugs for the treatment of cancer. We recently cloned and characterized the Armillaria gallica gene Pro1 encoding protoilludene synthase, a sesquiterpene cyclase catalyzing the pathway-committing step to all protoilludene-type aryl esters. Fungal enzymes representing secondary metabolic pathways are sometimes encoded by gene clusters, so we hypothesized that the missing steps in the pathway to melleolides and armillyl orsellinates might be identified by cloning the genes surrounding Pro1. Here we report the isolation of an A. gallica gene cluster encoding protoilludene synthase and four cytochrome P450 monooxygenases. Heterologous expression and functional analysis resulted in the identification of protoilludene-8α-hydroxylase, which catalyzes the first committed step in the armillyl orsellinate pathway. This confirms that ∆-6-protoilludene is a precursor for the synthesis of both melleolides and armillyl orsellinates, but the two pathways already branch at the level of the first oxygenation step. Our results provide insight into the synthesis of these valuable natural products and pave the way for their production by metabolic engineering. KEY POINTS: • Protoilludene-type aryl esters are bioactive metabolites produced by Armillaria spp. • The pathway-committing step to these compounds is catalyzed by protoilludene synthase. • We characterized CYP-type enzymes in the cluster and identified novel intermediates.
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Sequence analysis and specificity of distinct types of menaquinone methyltransferases indicate the widespread potential of methylmenaquinone production in bacteria and archaea. Environ Microbiol 2020; 23:1407-1421. [PMID: 33264482 DOI: 10.1111/1462-2920.15344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
Menaquinone (MK) serves as an essential membranous redox mediator in various electron transport chains of aerobic and anaerobic respiration. In addition, the composition of the quinone/quinol pool has been widely used as a biomarker in microbial taxonomy. The HemN-like class C radical SAM methyltransferases (RSMTs) MqnK, MenK and MenK2 have recently been shown to facilitate specific menaquinone methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesize 8-methylmenaquinone, 7-methylmenaquinone and 7,8-dimethylmenaquinone. However, the vast majority of protein sequences from the MqnK/MenK/MenK2 family belong to organisms, whose capacity to produce methylated menaquinones has not been investigated biochemically. Here, representative putative menK and menK2 genes from Collinsella tanakaei and Ferrimonas marina were individually expressed in Escherichia coli (wild-type or ubiE deletion mutant) and the corresponding cells were found to produce methylated derivatives of the endogenous MK and 2-demethylmenaquinone. Cluster and phylogenetic analyses of 828 (methyl)menaquinone methyltransferase sequences revealed signature motifs that allowed to discriminate enzymes of the MqnK/MenK/MenK2 family from other radical SAM enzymes and to identify C-7-specific menaquinone methyltransferases of the MenK2 subfamily. This study will help to predict the methylation status of the quinone/quinol pool of a microbial species (or even a microbial community) from its (meta)genome and contribute to the future design of microbial quinone/quinol pools in a Synthetic Biology approach.
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Decoding the Papain Inhibitor from Streptomyces mobaraensis as Being Hydroxylated Chymostatin Derivatives: Purification, Structure Analysis, and Putative Biosynthetic Pathway. JOURNAL OF NATURAL PRODUCTS 2020; 83:2983-2995. [PMID: 32998509 DOI: 10.1021/acs.jnatprod.0c00201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Streptomyces mobaraensis produces the papain inhibitor SPI consisting of a 12 kDa protein and small active compounds (SPIac). Purification of the papain inhibitory compounds resulted in four diverse chymostatin derivatives that were characterized by NMR and MS analysis. Chymostatins are hydrophobic tetrapeptide aldehydes from streptomycetes, e.g., S. lavendulae and S. hygroscopicus, that reverse chymosin-mediated angiotensin activation and inhibit other serine and cysteine proteases. Chymotrypsin and papain were both inhibited by the SPIac compounds in the low nanomolar range. SPIac differs from the characterized chymostatins by the exchange of phenylalanine for tyrosine. The crystal structure of one of these chymostatin variants confirmed its molecular structure and revealed a S-configured hemithioacetal bond with the catalytic Cys25 thiolate as well as close interactions with hydrophobic S1 and S2 subsite amino acids. A model for chymostatin biosynthesis is provided based on the discovery of clustered genes encoding several putative nonribosomal peptide synthetases; among them, there is the unusual CstF enzyme that accommodates two canonical amino acid activation domains as well as three peptide carrier protein domains.
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Sustainable Peptide Synthesis Enabled by a Transient Protecting Group. Angew Chem Int Ed Engl 2020; 59:12984-12990. [PMID: 32324944 PMCID: PMC7496111 DOI: 10.1002/anie.202003676] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Indexed: 01/22/2023]
Abstract
The growing interest in synthetic peptides has prompted the development of viable methods for their sustainable production. Currently, large amounts of toxic solvents are required for peptide assembly from protected building blocks, and switching to water as a reaction medium remains a major hurdle in peptide chemistry. We report an aqueous solid‐phase peptide synthesis strategy that is based on a water‐compatible 2,7‐disulfo‐9‐fluorenylmethoxycarbonyl (Smoc) protecting group. This approach enables peptide assembly under aqueous conditions, real‐time monitoring of building block coupling, and efficient postsynthetic purification. The procedure for the synthesis of all natural and several non‐natural Smoc‐protected amino acids is described, as well as the assembly of 22 peptide sequences and the fundamental issues of SPPS, including the protecting group strategy, coupling and cleavage efficiency, stability under aqueous conditions, and crucial side reactions.
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Direct glucosone-based synthesis and HILIC-ESI-MS/MS characterization of N-terminal fructosylated valine and valylhistidine for validation of enzymatic HbA 1c assays in the diagnosis of diabetes mellitus. Anal Bioanal Chem 2019; 411:7967-7979. [PMID: 31754770 PMCID: PMC6920237 DOI: 10.1007/s00216-019-02186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/14/2019] [Accepted: 10/02/2019] [Indexed: 11/12/2022]
Abstract
Naturally occurring fructosamines are of high clinical significance due to their potential use in diabetes mellitus monitoring (quantification of fructosylated hemoglobin, HbA1c) or for the investigation of their reactivity in consecutive reactions and harmfulness towards the organism. Here we report the specific synthesis of the fructosylated dipeptide L-valyl-L-histidine (Fru-Val-His) and fructosylated L-valine (Fru-Val). Both are basic tools for the development and validation of enzymatic HbA1c assays. The two fructosamine derivatives were synthesized via a protected glucosone intermediate which was coupled to the primary amine of Val or Val-His, performing a reductive amination reaction. Overall yields starting from fructose were 36% and 34% for Fru-Val and Fru-Val-His, respectively. Both compounds were achieved in purities > 90%. A HILIC-ESI-MS/MS method was developed for routine analysis of the synthesized fructosamines, including starting materials and intermediates. The presented method provides a well-defined and efficient synthesis protocol with purification steps and characterization of the desired products. The functionality of the fructosylated dipeptide has been thoroughly tested in an enzymatic HbA1c assay, showing its concentration-dependent oxidative degradation by fructosyl-peptide oxidases (FPOX). Graphical abstract.
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Halomethanesulfonic Acids-A New Class of Polar Disinfection Byproducts: Standard Synthesis, Occurrence, and Indirect Assessment of Mitigation Options. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8994-9002. [PMID: 31298842 DOI: 10.1021/acs.est.9b03016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Halomethanesulfonic acids (HMSAs) are recently discovered polar disinfection byproducts without commercially available reference materials. To allow for their accurate quantification, we successfully synthesized standards for the four presumably most prevalent HMSA congeners: chloromethanesulfonic acid, bromomethanesulfonic acid, dichloromethanesulfonic acid, and bromochloromethanesulfonic acid. After structure confirmation and quantification with high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, we integrated them into a multilayer solid phase extraction and hydrophilic interaction liquid chromatography-tandem mass spectrometry method dedicated to the analysis of polar water contaminants. With this method we monitored HMSAs in drinking water production plants from four European countries and tap water samples taken in six countries. HMSAs were detected in the low μg/L range after the chlorination step during drinking water production, all tap waters samples, and two surface waters used for drinking water production. Concentrations in tap water samples ranged from 0.07 μg/L to 11.5 μg/L while the HMSA concentrations in surface waters were in the range of 100 ng/L. We utilized the HMSA formation potential to indirectly assess the behavior of hitherto unknown HMSA precursors, consequently identifying ozonation, filtration through activated carbon, and reverse osmosis as efficient removal tools for HMSA precursors, thus limiting their formation during subsequent water disinfection.
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Wheat beer challenge. Anal Bioanal Chem 2019; 411:3699-3703. [DOI: 10.1007/s00216-019-01854-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Life as a fortress – structure, function, and adaptive values of morphological and chemical defense in the oribatid mite Euphthiracarus reticulatus (Actinotrichida). BMC ZOOL 2018. [DOI: 10.1186/s40850-018-0031-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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The synthesis of brominated heteroleptic tris -cyclometallated Ir(III)-complexes as photoactive building blocks on polyaryl backbones. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.02.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Solution to through the looking-glass challenge. Anal Bioanal Chem 2018; 410:2453. [DOI: 10.1007/s00216-017-0818-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Mechanistic study on –C–O– and –C–C– hydrogenolysis over Cu catalysts: identification of reaction pathways and key intermediates. Catal Sci Technol 2018. [DOI: 10.1039/c7cy02426f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sugar alcohols are found to adsorb over Cu catalysts via two vicinal OH-groups, forming a chelate complex with selective –C–O– bond cleavage of adjacent free OH-groups. Different side reactions via unsaturated intermediates on the catalyst surface yield C1 to C5 polyols.
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Solution to NMR hide-and-seek challenge. Anal Bioanal Chem 2017; 409:2499-2500. [DOI: 10.1007/s00216-016-0177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Solution to doubling spectroscopy challenge. Anal Bioanal Chem 2016; 408:1723-4. [DOI: 10.1007/s00216-015-9267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Characterization and analysis of structural isomers of dimethyl methoxypyrazines in cork stoppers and ladybugs (Harmonia axyridis and Coccinella septempunctata). Anal Bioanal Chem 2014; 406:6429-39. [PMID: 25120181 DOI: 10.1007/s00216-014-8049-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 11/25/2022]
Abstract
The three constitutional isomers of dimethyl-substituted methoxypyrazines: 3,5-dimethyl-2-methoxypyrazine 1; 2,5-dimethyl-3-methoxypyrazine 2; and 2,3-dimethyl-5-methoxypyrazine 3 are potent flavor compounds with similar mass spectrometric, gas chromatographic, and nuclear magnetic resonance spectroscopic behavior. Therefore, unambiguous analytical determination is critical, particularly in complex matrices. The unequivocal identification of 1-3 could be achieved by homo- and heteronuclear NMR correlation experiments. The observed mass fragmentation for 1-3 is proposed and discussed, benefitting from synthesized partially deuterated 1 and 2. On common polar and apolar stationary phases used in gas chromatography (GC) 1 and 2 show similar behavior whereas 3 can be separated. In our focus on off-flavor analysis with respect to wine aroma, 1 has been described as a "moldy" off-flavor compound in cork and 2 as a constituent in Harmonia axyridis contributing to the so-called "ladybug taint," whereas 3 has not yet been described as a constituent of wine aroma. A successful separation of 1 and 2 could be achieved on octakis-(2,3-di-O-pentyl-6-O-methyl)-γ-cyclodextrin as stationary phase in GC. Applying heart-cut multidimensional GC analysis with tandem mass spectrometric detection we could confirm the presence of 1 as a "moldy" off-flavor compound in cork. However, in the case of Harmonia axyridis, a previous identification of 2 has to be reconsidered. In our experiments we identified the constitutional isomer 1, which was also found in Coccinella septempunctata, another species discussed with respect to the "ladybug taint." The analysis of such structurally related compounds is a demonstrative example for the importance of a chromatographic separation, as mass spectrometric data by itself could not guarantee the unequivocal identification.
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N-Benzoylthiocarbamoyl Amino Acid Ethyl Esters as Chelate Ligands for Transition Metal Ions. ACTA ACUST UNITED AC 2014. [DOI: 10.1515/znb-1998-0909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The reactions of benzoyl isothiocyanate with amino acid ethyl esters (N-butyl glycine ethyl ester, (S)-(-)-proline ethyl ester) give N-benzoylthiocarbamoyl amino acid ethyl esters. Apart from the expected N-benzoylthiocarbamoyl (S)-(-)-proline ethyl ester the racemic N-benzoyl thiocarbamoyl (R)/(S)-proline ethyl ester is formed because of base catalyzed racemization of the educt (S)-(-)-proline ethyl ester during the reaction of (S)-(-)-proline ethyl ester hydrochloride with triethylamine. The structures of both compounds were established by X-ray crystal structure analysis and specific optical rotation measurements. The ligands yield neutral 2:1 chelates with NiII, CuII, PdII and PtII. The carboxylic oxygen atoms are not involved in the chelation. The ligands and the resultant complexes show configurational E/Z isomerism. In the case of the chelates of the racemic N-benzoylthiocarbamoyl (R)/(S)-proline ethyl ester, additional R/S isomerism is observed as shown by NMR spectroscopy.
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Solution to angels’ share challenge. Anal Bioanal Chem 2014; 406:1817-8. [DOI: 10.1007/s00216-013-7581-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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25
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2D-NMR and EPR study of the activation of π-allyl group within the coordination sphere of the imine–amide complex of nickel(II) by the coordination of PMe. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2012.05.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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New insights into the synthesis and characterization of 2-methoxy-3-alkylpyrazines and their deuterated isotopologues. J Labelled Comp Radiopharm 2011. [DOI: 10.1002/jlcr.1888] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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"Triazole bridge": disulfide-bond replacement by ruthenium-catalyzed formation of 1,5-disubstituted 1,2,3-triazoles. Angew Chem Int Ed Engl 2011; 50:5207-11. [PMID: 21544910 DOI: 10.1002/anie.201008142] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/21/2011] [Indexed: 12/20/2022]
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“Triazolbrücke”: ein Disulfidbrückenersatz durch Ruthenium- katalysierte Bildung von 1,5-disubstituierten 1,2,3-Triazolen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008142] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Spectroscopy challenge 13. Anal Bioanal Chem 2008; 392:767-70. [DOI: 10.1007/s00216-008-2355-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Solution to spectroscopy challenge 12. Anal Bioanal Chem 2008; 390:1219-20. [DOI: 10.1007/s00216-007-1801-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Spectroscopy challenge 12. Anal Bioanal Chem 2007; 389:1297-9. [PMID: 17909763 DOI: 10.1007/s00216-007-1565-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Solution to spectroscopy challenge 11. Anal Bioanal Chem 2006; 387:135-6. [PMID: 17146623 DOI: 10.1007/s00216-006-0931-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Spectroscopy Challenge 11. Anal Bioanal Chem 2006; 386:1-3. [PMID: 16909216 DOI: 10.1007/s00216-006-0650-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Spectroscopy Challenge 10. Anal Bioanal Chem 2005; 383:723-7. [PMID: 16261322 DOI: 10.1007/s00216-005-0075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Solution to Spectroscopy Challenge 8. Anal Bioanal Chem 2005; 381:1001-2. [PMID: 15742181 DOI: 10.1007/s00216-005-3111-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Indexed: 10/25/2022]
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40
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Cyclisierungsreaktionen β,γ-ungesättigter Kohlensäurederivate. XI [1] Untersuchungen zur Stereochemie der Cyclofunktionalisierung β,γ-ungesättigter Carbamidsäureester. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/prac.19863280302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Präparative HPLC-Trennung diastereomerer Methoxybutanderivate unter Anwendung verschiedener Detektionsprinzipien. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/prac.19873290120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Spectroscopy Challenge 8. Anal Bioanal Chem 2004; 380:729-33. [PMID: 15517204 DOI: 10.1007/s00216-004-2819-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Using neural networks for (13)c NMR chemical shift prediction-comparison with traditional methods. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 157:242-252. [PMID: 12323143 DOI: 10.1006/jmre.2002.2599] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Interpretation of (13)C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network (J. Chem. Inf. Comput. Sci. 2000, 40, 1169-1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of approximately 42,500 carbons. Thus, this neural network allows fast and accurate (13)C NMR chemical shift prediction without the necessity of access to molecule or fragment databases. For an unbiased test dataset containing 100 organic structures the accuracy of the improved neural network was compared to that of a prediction method based on the HOSE code (hierarchically ordered spherical description of environment) using SPECINFO. The results show the neural network predictions to be of quality (std. dev. = 2.7 ppm) comparable to that of the HOSE code prediction (std. dev. = 2.6 ppm). Further we compare the neural network predictions to those of a wide variety of other (13)C chemical shift prediction tools including incremental methods (CHEMDRAW, SPECTOOL), quantum chemical calculation (GAUSSIAN, COSMOS), and HOSE code fragment-based prediction (SPECINFO, ACD/CNMR, PREDICTIT NMR) for the 47 (13)C-NMR shifts of Taxol, a natural product including many structural features of organic substances. The smallest standard deviations were achieved here with the neural network (1.3 ppm) and SPECINFO (1.0 ppm).
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Optical and Thermal Outer-Sphere Electron Self-Exchange Reaction of the Hexacyanoferrate(II/III) Couple: Comparative Analysis of Band-Shape and Activation Parameters and Large Solvent Kinetic Isotope Effect. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100011a028] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Validation of structural proposals by substructure analysis and 13C NMR chemical shift prediction. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2002; 42:241-8. [PMID: 11911693 DOI: 10.1021/ci010294n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 2D NMR-guided computer program COCON can be extremely valuable for the constitutional analysis of unknown compounds, if its results are evaluated by neural network-assisted 13C NMR chemical shift and substructure analyses. As instructive examples, data sets of four differently complex marine natural products were thoroughly investigated. As a significant step towards a true automated structure elucidation, it is shown that the primary COCON output can be safely diminished to less than 1% of its original size without losing the correct structural proposal.
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Fast determination of 13C NMR chemical shifts using artificial neural networks. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2000; 40:1169-76. [PMID: 11045810 DOI: 10.1021/ci000021c] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nine different artificial neural networks were trained with the spherically encoded chemical environments of more than 500000 carbon atoms to predict their 13C NMR chemical shifts. Based on these results the PC-program "C_shift" was developed which allows the calculation of the 13C NMR spectra of any proposed molecular structure consisting of the covalently bonded elements C, H, N, O, P, S and the halogens. Results were obtained with a mean deviation as low as 1.8 ppm; this accuracy is equivalent to a determination on the basis of a large database but, in a time as short as known from increment calculations, was demonstrated exemplary using the natural agent epothilone A. The artificial neural networks allow simultaneously a precise and fast prediction of a large number of 13C NMR spectra, as needed for high throughput NMR and screening of a substance or spectra libraries.
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Qualitative and quantitative determination of oxygenates in gasolines using 1H nuclear magnetic resonance spectroscopy. Anal Chim Acta 1999. [DOI: 10.1016/s0003-2670(99)00250-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Conformational analysis of thia crown ether derivatives by NMR spectroscopy and molecular mechanics calculations. MONATSHEFTE FUR CHEMIE 1996. [DOI: 10.1007/bf00844689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Photocatalytic Oxygenation of Selected Cycloalkenes in Aqueous Solutions Induced by Water-Soluble Metal Porphyrin Complexes. ACTA ACUST UNITED AC 1995. [DOI: 10.1002/cber.19951280305] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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