1
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Crull EB, Buevich AV, Martin GE, Mahar R, Qu B, Senanayake CH, Molinski TF, Williamson RT. DFT investigation of coupling constant anomalies in substituted β-lactams. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:573-582. [PMID: 38511664 DOI: 10.1002/mrc.5444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
β-lactams are a chemically diverse group of molecules with a wide range of biological activities. Having recently observed curious trends in 2JHH coupling values in studies on this structural class, we sought to obtain a more comprehensive understanding of these diagnostic NMR parameters, specifically interrogating 1JCH, 2JCH, and 2JHH, to differentiate 3- and 4-monosubstituted β-lactams. Further investigation using computational chemistry methods was employed to explore the geometric and electronic origins for the observed and calculated differences between the two substitution patterns.
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Affiliation(s)
- Emily B Crull
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co, Inc, Rahway, New Jersey, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, West Orange, New Jersey, USA
| | - Rohit Mahar
- TCG GreenChem, Inc, Ewing, New Jersey, USA
- Current address: Department of Chemistry, Hemvati Nandan Garhwal University, (A Central University), Srinagar, Uttarakhand, India
| | - Bo Qu
- TCG GreenChem, Inc, Ewing, New Jersey, USA
| | | | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
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2
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Hargett AA, Azurmendi HF, Crawford CJ, Wear MP, Oscarson S, Casadevall A, Freedberg DI. The structure of a C. neoformans polysaccharide motif recognized by protective antibodies: A combined NMR and MD study. Proc Natl Acad Sci U S A 2024; 121:e2315733121. [PMID: 38330012 PMCID: PMC10873606 DOI: 10.1073/pnas.2315733121] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/02/2023] [Indexed: 02/10/2024] Open
Abstract
Cryptococcus neoformans is a fungal pathogen responsible for cryptococcosis and cryptococcal meningitis. The C. neoformans' capsular polysaccharide and its shed exopolysaccharide function both as key virulence factors and to protect the fungal cell from phagocytosis. Currently, a glycoconjugate of these polysaccharides is being explored as a vaccine to protect against C. neoformans infection. In this study, NOE and J-coupling values from NMR experiments were consistent with a converged structure of the synthetic decasaccharide, GXM10-Ac3, calculated from MD simulations. GXM10-Ac3 was designed as an extension of glucuronoxylomannan (GXM) polysaccharide motif (M2) which is common in the clinically predominant serotype A strains and is recognized by protective forms of GXM-specific monoclonal antibodies. The M2 motif is a hexasaccharide with a three-residue α-mannan backbone, modified by β-(1→2)-xyloses (Xyl) on the first two mannoses (Man) and a β-(1→2)-glucuronic acid (GlcA) on the third Man. Combined NMR and MD analyses reveal that GXM10-Ac3 adopts an extended structure, with Xyl/GlcA branches alternating sides along the α-mannan backbone. O-acetyl esters also alternate sides and are grouped in pairs. MD analysis of a twelve M2-repeating unit polymer supports the notion that the GXM10-Ac3 structure is uniformly represented throughout the polysaccharide. This derived GXM model displays high flexibility while maintaining a structural identity, yielding insights to further explore intermolecular interactions between polysaccharides, interactions with anti-GXM mAbs, and the cryptococcal polysaccharide architecture.
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Affiliation(s)
- Audra A. Hargett
- Laboratory of Bacterial Polysaccharides, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993
| | - Hugo F. Azurmendi
- Laboratory of Bacterial Polysaccharides, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993
| | - Conor J. Crawford
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD21205
- Centre for Synthesis and Chemical Biology, University College Dublin, Dublin 4, Ireland
| | - Maggie P. Wear
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD21205
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Dublin 4, Ireland
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD21205
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993
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3
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Hargett AA, Azurmendi HF, Crawford CJ, Wear MP, Oscarson S, Casadevall A, Freedberg DI. The structure of a C. neoformans polysaccharide motif recognized by protective antibodies: A combined NMR and MD study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556507. [PMID: 37732210 PMCID: PMC10508755 DOI: 10.1101/2023.09.06.556507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Cryptococcus neoformans is a fungal pathogen responsible for cryptococcosis and cryptococcal meningitis. The C. neoformans capsular polysaccharide and shed exopolysaccharide functions both as a key virulence factor and to protect the fungal cell from phagocytosis. Currently, a glycoconjugate of these polysaccharides is being explored as a vaccine to protect against C. neoformans infection. In this combined NMR and MD study, experimentally determined NOEs and J-couplings support a structure of the synthetic decasaccharide, GXM10-Ac3, obtained by MD. GXM10-Ac3 was designed as an extension of glucuronoxylomannan (GXM) polysaccharide motif (M2) which is common in the clinically predominant serotype A strains and is recognized by protective forms of GXM-specific monoclonal antibodies. The M2 motif is characterized by a 6-residue α-mannan backbone repeating unit, consisting of a triad of α-(1→3)-mannoses, modified by β-(1→2)-xyloses on the first two mannoses and a β-(1→2)-glucuronic acid on the third mannose. The combined NMR and MD analyses reveal that GXM10-Ac3 adopts an extended structure, with xylose/glucuronic acid branches alternating sides along the α-mannan backbone. O-acetyl esters also alternate sides and are grouped in pairs. MD analysis of a twelve M2-repeating unit polymer supports the notion that the GXM10-Ac3 structure is uniformly represented throughout the polysaccharide. This experimentally consistent GXM model displays high flexibility while maintaining a structural identity, yielding new insights to further explore intermolecular interactions between polysaccharides, interactions with anti-GXM mAbs, and the cryptococcal polysaccharide architecture.
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Affiliation(s)
- Audra A. Hargett
- Laboratory of Bacterial Polysaccharides, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Hugo F. Azurmendi
- Laboratory of Bacterial Polysaccharides, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Conor J. Crawford
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
- Current address: Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Maggie P. Wear
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Darόn I. Freedberg
- Laboratory of Bacterial Polysaccharides, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
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4
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Mishra SK, Suryaprakash N. Pure shift edited NMR methodologies for the extraction of Homo- and heteronuclear couplings with ultra-high resolution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 136-137:1-60. [PMID: 37716754 DOI: 10.1016/j.pnmrs.2023.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 09/18/2023]
Abstract
The scalar couplings that result in the splitting of the signals in the NMR spectrum arise due to the interaction of the nuclear spins, whereby the spin polarization is transmitted through chemical bonds. The interaction strengths depend inter alia on the number of consecutive chemical bonds intervening between the two interacting spins and on the molecular conformation. The pairwise interaction of many spins in a molecule resulting in a complex spectrum poses a severe challenge to analyse the spectrum and hence the determination of magnitudes and signs of homo- and heteronuclear couplings. The problem is more severe in the analysis of 1H spectra than the spectra of most of the other nuclei due to the often very small chemical shift dispersion. As a consequence, the straightforward analysis and the accurate extraction of the coupling constants from the 1H spectrum of a complex spin system continues to remain a challenge, and often may be a formidable task. Over the years, the several pure shift-based one-dimensional and two-dimensional methodologies have been developed by workers in the field, which provide broadband homonuclear decoupling of proton spectra, removing the complexity but at the cost of the very informative scalar couplings. To circumvent this problem, several one-dimensional and two-dimensional NMR experiments have been developed for the determination of homonuclear and heteronuclear couplings (nJHX, where n = 1,2,3) while retaining the high resolution obtained by implementing pure shift strategies. This review attempts to summarize the extensive work reported by a large number of researchers over the years for the accurate determination of homo- and heteronuclear scalar couplings.
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Affiliation(s)
- Sandeep Kumar Mishra
- Department of Physics and NMR Research Centre, Indian Institute of Science Education and Research, Pune 411008, India.
| | - N Suryaprakash
- NMR Research Centre and Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
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5
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Bogdanova YA, Zaitseva ER, Smirnov AY, Baleeva NS, Gavrikov AS, Myasnyanko IN, Goncharuk SA, Kot EF, Mineev KS, Mishin AS, Baranov MS. NanoLuc Luciferase as a Fluorogen-Activating Protein for GFP Chromophore Based Fluorogens. Int J Mol Sci 2023; 24:ijms24097958. [PMID: 37175667 PMCID: PMC10178166 DOI: 10.3390/ijms24097958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In this work, we showed that the well-known NanoLuc luciferase can act as a fluorogen activating protein for various arylidene-imidazolones structurally similar to the Kaede protein chromophore. We showed that such compounds can be used as fluorescent sensors for this protein and can also be used in pairs with it in fluorescent microscopy as a genetically encoded tag.
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Affiliation(s)
- Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Erik F Kot
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
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6
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Cha JW, Kim MS, Park JS. A Single-Scan Ultraselective Heteronuclear Polarization Transfer Method for Unambiguous Complex Structure Assignment. Angew Chem Int Ed Engl 2023:e202304196. [PMID: 37186340 DOI: 10.1002/anie.202304196] [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: 03/23/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023]
Abstract
Complex nuclear magnetic resonance (NMR) signals of organic compounds containing multiple analogous substructures or mixtures pose a significant challenge to structural identification, thus resulting in frequent misassignment of structures. The GEMSTONE method, a single-scan technique that selectively excites a specific proton signal among the crowded NMR signals, was recently proposed as a solution. However, its extension to the polarization transfer method for heteronuclear spin systems was unsuccessful. Here, we present an extension method that addresses the altered heteronuclear polarization transfer efficiency and enables the acquisition of ultraselective 13C and 1H-13C correlation NMR subspectra with hertz-level signal selectivity in both dimensions. We demonstrate the effectiveness of this technique in the structural analysis of a chromopeptide pharmaceutical and a diastereomeric mixture fungicide.
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Affiliation(s)
- Jin Wook Cha
- KIST Gangneung Institute of Natural Products, Natural Product Informatics Research Center, 679 Saimdang-ro, 25451, Gangneung, KOREA, REPUBLIC OF
| | - Min-Seon Kim
- Korea Institute of Science and Technology, Natural Product Informatics Research Center, KOREA, REPUBLIC OF
| | - Jin-Soo Park
- Korea Institute of Science and Technology, Natural Product Informatics Research Center, KOREA, REPUBLIC OF
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7
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Kramarova EP, Borisevich SS, Khamitov EM, Korlyukov AA, Dorovatovskii PV, Shagina AD, Mineev KS, Tarasenko DV, Novikov RA, Lagunin AA, Boldyrev I, Ezdoglian AA, Karpechenko NY, Shmigol TA, Baukov YI, Negrebetsky VV. Pyridine Carboxamides Based on Sulfobetaines: Design, Reactivity, and Biological Activity. Molecules 2022; 27:7542. [PMID: 36364369 PMCID: PMC9658115 DOI: 10.3390/molecules27217542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 03/09/2024] Open
Abstract
The synthesis of the products of the 1,3-propanesultone ring opening during its interaction with amides of pyridinecarboxylic acids has been carried out. The dependence of the yield of the reaction products on the position (ortho-, meta-, para-) of the substituent in the heteroaromatic fragment and temperature condition was revealed. In contrast to the meta- and para-substituted substrates, the reaction involving ortho-derivatives at the boiling point of methanol unexpectedly led to the formation of a salt. On the basis of spectroscopic, X-Ray, and quantum-chemical calculation data, a model of the transition-state, as well as a mechanism for this alkylation reaction of pyridine carboxamides with sultone were proposed in order to explain the higher yields obtained with the nicotinamide and its N-methyl analog compared to ortho or meta parents. Based on the analysis of ESP maps, the positions of the binding sites of reagents with a potential complexing agent in space were determined. The in silico evaluation of possible biological activity showed that the synthetized compounds revealed some promising pharmacological effects and low acute toxicity.
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Affiliation(s)
- Eugene P. Kramarova
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Sophia S. Borisevich
- Laboratory of Physical Chemistry, Ufa Institute of Chemistry, Ufa Federal Research Center, Russian Academy of Sciences, 450071 Ufa, Russia
| | - Edward M. Khamitov
- Laboratory of Physical Chemistry, Ufa Institute of Chemistry, Ufa Federal Research Center, Russian Academy of Sciences, 450071 Ufa, Russia
| | - Alexander A. Korlyukov
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | | | - Anastasia D. Shagina
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitri V. Tarasenko
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Roman A. Novikov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey A. Lagunin
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Ivan Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Aiarpi A. Ezdoglian
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Natalia Yu. Karpechenko
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Tatiana A. Shmigol
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Yuri I. Baukov
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
| | - Vadim V. Negrebetsky
- Department of Medical Chemistry and Toxicology, Pirogov National Research Medical University, Ministry of Health of Russia, 117997 Moscow, Russia
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8
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Roth FA, Schmidts V, Rettig J, Thiele CM. Model free analysis of experimental residual dipolar couplings in small organic compounds. Phys Chem Chem Phys 2021; 24:281-286. [PMID: 34881759 DOI: 10.1039/d1cp02324a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Residual dipolar couplings (RDCs) contain information on the relative arrangement and dynamics of internuclear spin vectors in chemical compounds. Classically, RDC data is analyzed by fitting to structure models, while model-free approaches (MFA) directly relate RDCs to the corresponding internuclear vectors. The recently introduced software TITANIA implements the MFA and extracts structure and dynamics parameters directly from RDCs to facilitate de novo structure refinement for small organic compounds. Encouraged by our previous results on simulated data, we herein focus on the prerequisites and challenges faced when using purely experimental data for this approach. These concern mainly the fact that not all couplings are accessible in all media, leading to voids in the RDC matrix and the concomitant effects on the structure refinement. It is shown that RDC data sets obtained experimentally from currently available alignment media and measurement methods are of sufficient quality to allow relative configuration determination even when the relative configuration of the analyte is completely unknown.
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Affiliation(s)
- Felix A Roth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Jan Rettig
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany.
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9
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Roth FA, Schmidts V, Thiele CM. TITANIA: Model-Free Interpretation of Residual Dipolar Couplings in the Context of Organic Compounds. J Org Chem 2021; 86:15387-15402. [PMID: 34677977 DOI: 10.1021/acs.joc.1c01926] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) become increasingly important as additional NMR parameters in the structure elucidation of organic compounds but are usually used in fitting procedures to discriminate between (computed) structures that are in accordance with RDCs and others that can be ruled out. Thus, the determination of configurations requires prior structural information. The direct use of RDCs as restraints to construct structures based on RDCs has only recently begun also in organic compounds. No protocol has been published though that uses the vector and dynamics information available in multialignment data sets directly for the joint determination of conformation and configuration of organic compounds. This is proposed in the current study. We show that by employing these data, even a flat or random start structure converges into the correctly configured structure when employing multiple alignment data sets in our iterative procedure. The requirements in terms of the number of RDCs and alignment media necessary are discussed in detail.
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Affiliation(s)
- Felix A Roth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technical University of Darmstadt, Alarich-Weiss-Str. 16, 64287 Darmstadt, Germany
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10
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Amirtham S, Prince N, Venkateswarulu M, Chandra Mondal I, Raman S, Raj R, Rajendran E, Jebaraj B, Vaithiyalingam A, Rajasegaran R, Mukadam FA, Bhaskar A, Ghosh S, Conrad J, Beifuss U, Subramani S. Elusive Toxin in Cleistanthus collinus Causing Vasoconstriction and Myocardial Depression: Detailed NMR Analyses and Biological Studies of Cleistanthoside A. ACS OMEGA 2021; 6:24553-24561. [PMID: 34604637 PMCID: PMC8482457 DOI: 10.1021/acsomega.1c03138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Cleistanthus collinus leaf extracts are consumed for suicidal purposes in southern India. The boiled decoction is known to be more toxic than the fresh leaf juice. Although several compounds have been isolated and their toxicity tested, controversy remains as to which compounds are responsible for the high level of toxicity of C. collinus. We report herein that cleistanthoside A is the major toxin in the boiled aqueous extract of fresh leaves and causes death in rats in small doses. The toxicity of the boiled extract prepared in the manner described can be attributed entirely to cleistanthoside A. Cleistanthin A could also be isolated from the boiled extract, albeit in trace amounts. As hypotension not responding to vasoconstrictors is the cause of death in patients who have consumed the boiled extract, effects of cleistanthoside A on the determinants of blood pressure, namely, force of cardiac contraction and vascular resistance, were tested in isolated organ experiments. Cleistanthoside A has a direct vasoconstrictor effect; however, it inhibits ventricular contractility. Therefore, the notion that the shock in C. collinus poisoning is of vascular origin must be considered carefully, and the possibility of cardiogenic shock must be studied. We present the crystal structure of cleistanthin A and show the potency of fast NMR methods (NOAH4-BSCN-NUS) in the full spectral assignment of cleistanthoside A as a real-world sample of a natural product. We also compare the results of the NOAH4-BSCN-NUS NMR experiments with conventional NMR methods.
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Affiliation(s)
- Soosai
Manickam Amirtham
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Neetu Prince
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Mangili Venkateswarulu
- School
of Basic Sciences, Indian Institute of Technology, Mandi, 175005 Himachal Pradesh, India
| | - Iswar Chandra Mondal
- School
of Basic Sciences, Indian Institute of Technology, Mandi, 175005 Himachal Pradesh, India
| | - Swetha Raman
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Renu Raj
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Elanchezhian Rajendran
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Benjamin Jebaraj
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Abirami Vaithiyalingam
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Rajalakshmi Rajasegaran
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Farhan Adam Mukadam
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Anand Bhaskar
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
| | - Subrata Ghosh
- School
of Basic Sciences, Indian Institute of Technology, Mandi, 175005 Himachal Pradesh, India
| | - Jürgen Conrad
- Institut
für Chemie, Universität Hohenheim, Garbenstrasse 30, Stuttgart D-70599, Germany
| | - Uwe Beifuss
- Institut
für Chemie, Universität Hohenheim, Garbenstrasse 30, Stuttgart D-70599, Germany
| | - Sathya Subramani
- Department
of Physiology, Christian Medical College, Thorapadi post, Vellore, 632002 Tamilnadu, India
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11
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Charlier C, Cox N, Prud'homme S, Geffard A, Nuzillard JM, Luy B, Lippens G. Virtual decoupling to break the simplification versus resolution trade-off in nuclear magnetic resonance of complex metabolic mixtures. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:619-627. [PMID: 37905230 PMCID: PMC10539796 DOI: 10.5194/mr-2-619-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/19/2021] [Indexed: 11/01/2023]
Abstract
The heteronuclear single quantum correlation (HSQC) experiment developed by Bodenhausen and Ruben (1980) in the early days of modern nuclear magnetic resonance (NMR) is without a doubt one of the most widely used experiments, with applications in almost every aspect of NMR including metabolomics. Acquiring this experiment, however, always implies a trade-off: simplification versus resolution. Here, we present a method that artificially lifts this barrier and demonstrate its application towards metabolite identification in a complex mixture. Based on the measurement of clean in-phase and clean anti-phase (CLIP/CLAP) HSQC spectra (Enthart et al., 2008), we construct a virtually decoupled HSQC (vd-HSQC) spectrum that maintains the highest possible resolution in the proton dimension. Combining this vd-HSQC spectrum with a J -resolved spectrum (Pell and Keeler, 2007) provides useful information for the one-dimensional proton spectrum assignment and for the identification of metabolites in Dreissena polymorpha (Prud'homme et al., 2020).
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Affiliation(s)
- Cyril Charlier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse,
CNRS, INRAE, INSA, Toulouse, France
| | - Neil Cox
- Toulouse Biotechnology Institute (TBI), Université de Toulouse,
CNRS, INRAE, INSA, Toulouse, France
| | - Sophie Martine Prud'homme
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO
(Stress Environnementaux et Biosurveillance des milieux aquatiques), Moulin
de la Housse, Reims, France
- present address: Université de Lorraine, CNRS, LIEC, 57000, Metz, France
| | - Alain Geffard
- Université de Reims Champagne-Ardenne (URCA), UMR-I 02 SEBIO
(Stress Environnementaux et Biosurveillance des milieux aquatiques), Moulin
de la Housse, Reims, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| | - Burkhard Luy
- Institute for Biological Interfaces 4 – Magnetic Resonance,
Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1,
76344 Eggenstein-Leopoldshafen, Germany
| | - Guy Lippens
- Toulouse Biotechnology Institute (TBI), Université de Toulouse,
CNRS, INRAE, INSA, Toulouse, France
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12
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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13
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Rekowski SP, Kroener BK, Kathuria D, Wani AA, Chourasiya SS, Conrad J, Bharatam PV, Frey W, Beifuss U. A novel copper-catalyzed, hydrazine-free synthesis of N-1 unsubstituted 1H-indazoles using stable guanylhydrazone salts as substrates. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Novakovic M, Battistel MD, Azurmendi HF, Concilio MG, Freedberg DI, Frydman L. The Incorporation of Labile Protons into Multidimensional NMR Analyses: Glycan Structures Revisited. J Am Chem Soc 2021; 143:8935-8948. [PMID: 34085814 PMCID: PMC8297728 DOI: 10.1021/jacs.1c04512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Glycan structures
are often stabilized by a repertoire of hydrogen-bonded
donor/acceptor groups, revealing longer-lived structures that could
represent biologically relevant conformations. NMR provides unique
data on these hydrogen-bonded networks from multidimensional experiments
detecting cross-peaks resulting from through-bond (TOCSY) or through-space
(NOESY) interactions. However, fast OH/H2O exchange, and
the spectral proximity among these NMR resonances, hamper the use
of glycans’ labile protons in such analyses; consequently,
studies are often restricted to aprotic solvents or supercooled aqueous
solutions. These nonphysiological conditions may lead to unrepresentative
structures or to probing a small subset of accessible conformations
that may miss “active” glycan conformations. Looped,
projected spectroscopy (L-PROSY) has been recently shown to substantially
enhance protein NOESY and TOCSY cross-peaks, for 1Hs that
undergo fast exchange with water. This study shows that even larger
enhancements can be obtained for rapidly exchanging OHs in saccharides,
leading to the retrieval of previously undetectable 2D TOCSY/NOESY
cross-peaks with nonlabile protons. After demonstrating ≥300%
signal enhancements on model monosaccharides, these experiments were
applied at 1 GHz to elucidate the structural network adopted by a
sialic acid homotetramer, used as a model for α,2–8 linked
polysaccharides. High-field L-PROSY NMR enabled these studies at higher
temperatures and provided insight previously unavailable from lower-field
NMR investigations on supercooled samples, involving mostly nonlabile
nuclei. Using L-PROSY’s NOEs and other restraints, a revised
structural model for the homotetramer was obtained combining rigid
motifs and flexible segments, that is well represented by conformations
derived from 40 μs molecular dynamics simulations.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Maria-Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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15
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Wiedemann C, Fushman D, Bordusa F. 15N NMR studies provide insights into physico-chemical properties of room-temperature ionic liquids. Phys Chem Chem Phys 2021; 23:12395-12407. [PMID: 34027941 PMCID: PMC8195554 DOI: 10.1039/d1cp01492g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ionic liquids (ILs) have gained a lot of attention as alternative solvents in many fields of science in the last two decades. It is known that the type of anion has a significant influence on the macroscopic properties of the IL. To gain insights into the molecular mechanisms responsible for these effects it is important to characterize these systems at the microscopic level. Such information can be obtained from nuclear spin-relaxation studies which for compounds with natural isotope abundance are typically performed using direct 1H or 13C measurements. Here we used direct 15N measurements to characterize spin relaxation of non-protonated nitrogens in imidazolium-based ILs which are liquid at ambient temperature. We report heteronuclear 1H-15N scalar coupling constants (nJHN) and 15N relaxation parameters for non-protonated nitrogens in ten 1-ethyl-3-methylimidazolium ([C2C1IM]+)-based ILs containing a broad range of anions. The 15N relaxation rates and steady-state heteronuclear 15N-{1H} NOEs were measured using direct 15N detection at 293.2 K and two magnetic field strengths, 9.4 T and 16.4 T. The experimental data were analyzed to determine hydrodynamic characteristics of ILs and to assess the contributions to 15N relaxation from 15N chemical shift anisotropy and from 1H-15N dipolar interactions with non-bonded protons. We found that the rotational correlation times of the [C2C1IM]+ cation determined from 15N relaxation measurements at room temperature correlate linearly with the macroscopic viscosity of the ILs. Depending on the selected anion, the 15N relaxation characteristics of [C2C1IM]+ differ considerably reflecting the influence of the anion on the physicochemical properties of the IL.
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Affiliation(s)
- Christoph Wiedemann
- Martin Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle/S., Germany.
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, USA
| | - Frank Bordusa
- Martin Luther University Halle-Wittenberg, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Kurt-Mothes-Str. 3a, 06120 Halle/S., Germany.
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16
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Balogh G, Gyöngyösi T, Timári I, Herczeg M, Borbás A, Sadiq SK, Fehér K, Kövér KE. Conformational Analysis of Heparin-Analogue Pentasaccharides by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:2926-2936. [PMID: 34029080 DOI: 10.1021/acs.jcim.1c00200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Elucidation and improvement of the blood coagulant properties of heparin are the focus of intense research. In this study, we performed conformational analysis using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations on the heparin pentasaccharide analogue idraparinux, its disulfonatomethyl analogue, which features a slightly improved blood coagulation property, and a trisulfonatomethyl analogue, in which the activity has been totally abolished. As the ring conformation of the G subunit has been suggested as a major determinant of the biological properties, we analyzed the sugar ring conformations and dynamics of the interglycosidic linkages. We found that the conformation of the G ring is dominated by the 2SO skewed boat next to the 1C4 chair in all three derivatives. Both the thermodynamics and the kinetics of the conformational states were found to be highly similar in the three derivatives. Molecular kinetic analysis showed that the 2SO skewed boat state of the G ring is equally favorable in the three analogues, resulting in similar 2SO populations. Also, the transition kinetics from the 1C4 chair to the 2SO skewed boat was found to be comparable in the derivatives, which indicates a similar energy barrier between the two states of the G subunit. We also identified a slower conformational transition between the dominant 4C1 chair and the boat conformations on the E subunit. Both G and E ring flips are also accompanied by changes along the interglycosidic linkages, which take place highly synchronously with the ring flips. These findings indicate that conformational plasticity of the G ring and the dominance of the 2SO skewed boat populations do not necessarily warrant the biological activity of the derivatives and hence the impact of other factors also needs to be considered.
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Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Tamás Gyöngyösi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - István Timári
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,Research Group for Oligosaccharide Chemistry of Hungarian Academy of Sciences, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - S Kashif Sadiq
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Krisztina Fehér
- MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
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17
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Cox N, Millard P, Charlier C, Lippens G. Improved NMR Detection of Phospho-Metabolites in a Complex Mixture. Anal Chem 2021; 93:4818-4824. [PMID: 33711235 DOI: 10.1021/acs.analchem.0c04056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphorylated metabolites are omnipresent in cells, but their analytical characterization faces several technical hurdles. Here, we detail an improved NMR workflow aimed at assigning the high-resolution subspectrum of the phospho-metabolites in a complex mixture. Combining a pure absorption J-resolved spectrum (Pell, A. J.; J. Magn. Reson. 2007, 189 (2), 293-299) with alternate on- and off-switching of the 31P coupling interaction during the t1 evolution with a pure in-phase (PIP) HSQMBC experiment (Castañar, L.; Angew. Chem., Int. Ed. 2014, 53 (32), 8379-8382) without or with total correlation spectroscopy (TOCSY) transfer during the insensitive nuclei enhancement by polarization transfer (INEPT) gives access to selective identification of the individual subspectra of the phosphorylated metabolites. Returning to the initial J-res spectra, we can extract with optimal resolution the full trace for the individual phospho-metabolites, which can then be transposed on the high-resolution quantitative one dimensional spectrum.
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Affiliation(s)
- Neil Cox
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Cyril Charlier
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Guy Lippens
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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18
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Bigler P, Furrer J. Simplifying LR-HSQC spectra using a triple-quantum filter: The LR-HTQC experiment. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:52-60. [PMID: 33411358 DOI: 10.1002/mrc.5078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/14/2020] [Accepted: 07/19/2020] [Indexed: 06/12/2023]
Abstract
Long-range heteronuclear single quantum correlation (LR-HSQC) experiments may be applied for detecting long-range correlations but suffer from two disadvantages, common to all heteronuclear long-range correlation experiments: (i) The information density in LR-HSQC spectra may be too high to be used directly without "filtering out" shorter range correlations, and (ii) often, substantial differences in intensity among cross peaks exist, potentially hampering the visualization of weak, often crucial cross peaks. In this contribution, we propose a modified LR-HSQC experiment, the LR-HTQC experiment (Long-Range Heteronuclear Triple Quantum Correlation) that partially solves the problems aforementioned. We show theoretically and experimentally that the LR-HTQC experiment removes the intense cross peaks of CH spin pairs, substantially reduces the medium intensity of cross peaks originating from CHH' spin systems, whereas the typically weak intensity of cross peaks of CHH'H″ and C(H)n, n > 3 spin systems is less affected. Consequently, the LR-HTQC experiment affords simplified long-range heteronuclear shift correlation spectra and scales down large intensity differences among different types of cross peaks, although a certain general reduction of signal intensities has to be accepted.
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Affiliation(s)
- Peter Bigler
- Departement für Chemie und Biochemie, Universität Bern, Bern, Switzerland
| | - Julien Furrer
- Departement für Chemie und Biochemie, Universität Bern, Bern, Switzerland
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19
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Kim CK, Wang D, Wilson BAP, Saurí J, Voeller D, Lipkowitz S, O’Keefe BR, Gustafson KR. Suberitamides A-C, Aryl Alkaloids from a Pseudosuberites sp. Marine Sponge that Inhibit Cbl-b Ubiquitin Ligase Activity. Mar Drugs 2020; 18:E536. [PMID: 33126420 PMCID: PMC7693676 DOI: 10.3390/md18110536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022] Open
Abstract
Three new aryl alkaloids named suberitamides A-C (1-3), were isolated from an extract of the marine sponge Pseudosuberites sp. collected along the coast of North Carolina. Their planar structures were established by extensive nuclear magnetic resonance (NMR) and mass spectrometry (MS) analysis. To assign the challenging relative configuration of the saturated five-membered ring in suberitamide A (1), a simple and efficient NMR protocol was applied that is based on the analysis of 2- and 3-bond 1H-13C spin-spin coupling constants using a PIP (pure in-phase) HSQMBC (heteronuclear single quantum multiple bond correlation) IPAP (in-phase and anti-phase) experiment. Suberitamides A (1) and B (2) inhibited Cbl-b, an E3 ubiquitin ligase that is an important modulator of immune cell function, with IC50 values of approximately 11 μM.
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Affiliation(s)
- Chang-Kwon Kim
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA; (C.-K.K.); (D.W.); (B.A.P.W.); (B.R.O.)
| | - Dongdong Wang
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA; (C.-K.K.); (D.W.); (B.A.P.W.); (B.R.O.)
| | - Brice A. P. Wilson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA; (C.-K.K.); (D.W.); (B.A.P.W.); (B.R.O.)
| | - Josep Saurí
- Structure Elucidation Group, Analytical Research and Development, Merck & Co., Inc., Boston, MS 02115, USA;
| | - Donna Voeller
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1578, USA; (D.V.); (S.L.)
| | - Stanley Lipkowitz
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1578, USA; (D.V.); (S.L.)
| | - Barry R. O’Keefe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA; (C.-K.K.); (D.W.); (B.A.P.W.); (B.R.O.)
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, MD 21701-1201, USA
| | - Kirk R. Gustafson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA; (C.-K.K.); (D.W.); (B.A.P.W.); (B.R.O.)
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20
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Dal Poggetto G, Soares JV, Tormena CF. Selective Nuclear Magnetic Resonance Experiments for Sign-Sensitive Determination of Heteronuclear Couplings: Expanding the Analysis of Crude Reaction Mixtures. Anal Chem 2020; 92:14047-14053. [PMID: 32924438 PMCID: PMC7660590 DOI: 10.1021/acs.analchem.0c02976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
State-of-the-art nuclear magnetic resonance (NMR) selective experiments are capable of directly analyzing crude reaction mixtures. A new experiment named HD-HAPPY-FESTA yields ultrahigh-resolution total correlation subspectra, which are suitable for sign-sensitive determination of heteronuclear couplings, as demonstrated here by measuring the sign and magnitude for proton-fluorine couplings (JHF) from major and minor isomer products of a two-step reaction without any purification. Proton-fluorine couplings ranging from 51.5 to -2.6 Hz could be measured using HD-HAPPY-FESTA, with the smallest measured magnitude of 0.8 Hz. Experimental JHF values were used to identify the two fluoroketone intermediates and the four fluoroalcohol products. Results were rationalized and compared with the density functional theory (DFT) calculations. Experimental data were further compared with the couplings reported in the literature, where pure samples were analyzed.
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Affiliation(s)
- Guilherme Dal Poggetto
- Institute of Chemistry, University of Campinas (UNICAMP), PO BOX 6154, Campinas, São Paulo CEP 13083-970, Brazil
| | - João Vitor Soares
- Institute of Chemistry, University of Campinas (UNICAMP), PO BOX 6154, Campinas, São Paulo CEP 13083-970, Brazil
| | - Cláudio F Tormena
- Institute of Chemistry, University of Campinas (UNICAMP), PO BOX 6154, Campinas, São Paulo CEP 13083-970, Brazil
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21
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Li W, Battistel MD, Reeves H, Oh L, Yu H, Chen X, Wang LP, Freedberg DI. A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acid-containing GM3 ganglioside glycan and its 9-N-acetyl mimic. Glycobiology 2020; 30:787-801. [PMID: 32350512 PMCID: PMC8179627 DOI: 10.1093/glycob/cwaa040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 01/30/2023] Open
Abstract
O-Acetylation of carbohydrates such as sialic acids is common in nature, but its role is not clearly understood due to the lability of O-acetyl groups. We demonstrated previously that 9-acetamido-9-deoxy-N-acetylneuraminic acid (Neu5Ac9NAc) is a chemically and biologically stable mimic of the 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac2) of the corresponding sialoglycans. Here, a systematic nuclear magnetic resonance (NMR) spectroscopic and molecular dynamics (MD) simulation study was undertaken for Neu5,9Ac2-containing GM3 ganglioside glycan (GM3-glycan) and its Neu5Ac9NAc analog. GM3-glycan with Neu5Ac as the non-O-acetyl form of Neu5,9Ac2 was used as a control. Complete 1H and 13C NMR chemical shift assignments, three-bond 1H-13C trans-glycosidic coupling constants (3JCH), accurate 1H-1H coupling constants (3JHH), nuclear Overhauser effects and hydrogen bonding detection were carried out. Results show that structural modification (O- or N-acetylation) on the C-9 of Neu5Ac in GM3 glycan does not cause significant conformational changes on either its glycosidic dihedral angles or its secondary structure. All structural differences are confined to the Neu5Ac glycerol chain, and minor temperature-dependent changes are seen in the aglycone portion. We also used Density Functional Theory (DFT) quantum mechanical calculations to improve currently used 3JHH Karplus relations. Furthermore, OH chemical shifts were assigned at -10°C and no evidence of an intramolecular hydrogen bond was observed. The results provide additional evidence regarding structural similarities between sialosides containing 9-N-acetylated and 9-O-acetylated Neu5Ac and support the opportunity of using 9-N-acetylated Neu5Ac as a stable mimic to study the biochemical role of 9-O-acetylated Neu5Ac.
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Affiliation(s)
- Wanqing Li
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA
| | - Hannah Reeves
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Lisa Oh
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA
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22
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Synthesis of 5-(aminomethylidene)imidazol-4-ones by using N,N-dialkylformamide acetals. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02779-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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23
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Battistel MD, Freedberg DI. Dispersing the crowd: Adopting 13C direct detection for glycans. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106792. [PMID: 32759046 DOI: 10.1016/j.jmr.2020.106792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/08/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
As a direct consequence of technological advancements, the interest in direct detection of low-gamma/low-sensitivity heteronuclei for NMR experiments has been revived. Until recently, experimental development of 13C/15N detected experiments has been focused on protein NMR. In the present report, we extend the use of 13C-detected experiments to structural studies of glycans in natural abundance. The narrow 1H and wider 13C signal dispersion make glycans ideal candidates for heteronuclear detection. We show that 13C-detected HSQC offers a ten-fold increase in 13C dimension resolution compared to the analogous 1H-detected HSQC, when the experiments are acquired for the same amount of time. The enhanced resolution comes at the expense of 2 to 3-fold loss in SNR; however, the observed signal loss is a fraction of the theoretical 8-fold difference expected between experiments. Further, we show that by combining a 1H constant time element (CT), SMILE data reconstruction and 13C-direct detection, complete resonance assignments of highly degenerate glycan signals are possible. Finally, we demonstrate the potential of our strategy to aid in the assignment of complex glycans, by using a novel 13C-detected version of the CT-HSQC-TOCSY experiment performed on sialyl Lewis X pentasaccharide model system.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States.
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24
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Koos MRM, Navarro‐Vázquez A, Anklin C, Gil RR. Computer‐Assisted 3D Structure Elucidation (CASE‐3D): The Structural Value of
2
J
CH
in Addition to
3
J
CH
Coupling Constants. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
| | | | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
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25
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Koos MRM, Navarro‐Vázquez A, Anklin C, Gil RR. Computer‐Assisted 3D Structure Elucidation (CASE‐3D): The Structural Value of
2
J
CH
in Addition to
3
J
CH
Coupling Constants. Angew Chem Int Ed Engl 2020; 59:3938-3941. [DOI: 10.1002/anie.201915103] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Martin R. M. Koos
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
| | | | | | - Roberto R. Gil
- Department of Chemistry Carnegie Mellon University Pittsburgh PA USA
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26
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Howe PWA. Is perfection ever attainable? Strong coupling effects in the Perfect Echo. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:77-83. [PMID: 31348542 DOI: 10.1002/mrc.4927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
The Perfect Echo sequence, originally proposed in the late 1980s, has recently been popularised with many applications in the field of small-molecule proton NMR spectroscopy. The Perfect Echo refocuses all homonuclear J-couplings for AX spin systems and refocuses magnetization in-phase for more complex weakly coupled spin systems, albeit with some intensity reduction. In contrast to suggestions in previous publications, spectra acquired in our laboratory showed that the Perfect Echo caused intensity distortions in strongly coupled systems where the chemical shift difference between the coupled spins was not large compared to the J-coupling. This paper reports experimental observations and theoretical analysis of strongly coupled spins to confirm the distortions are real and that they originate principally from transfer of magnetization caused by the final inversion pulse of the Perfect Echo. The intensity changes are not large, but because of them, identifications of coupling partners based on resonance intensities ("roofing") can no longer be relied on when the Perfect Echo is used. However, theory and experiment confirm that adding an orthogonal excitation pulse at the end of the Perfect Echo greatly reduces the distortions.
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27
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Affiliation(s)
- Darón I. Freedberg
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
| | - Jeahoo Kwon
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
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28
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Parella T. Towards perfect NMR: Spin-echo versus perfect-echo building blocks. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:13-29. [PMID: 29927497 DOI: 10.1002/mrc.4776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/10/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
The development of new tools to improve the quality of nuclear magnetic resonance (NMR) spectra is a challenging task. The concept of "perfect NMR" includes the design of robust pulse sequences that allow an investigator to obtain undistorted pure in-phase signals, with pure absorption lineshapes that are free of phase anomalies derived from undesired J modulations. Here, alternative NMR building blocks to the spin-echo that are based on a general double SE module, known as a perfect-echo, are reviewed. Several implementations to minimize/remove unwanted dispersive contributions in homonuclear and heteronuclear NMR experiments are described and illustrated with some examples of broad interest for small molecules.
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Affiliation(s)
- Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
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29
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Tarazona G, Fernández R, Cruz PG, Pérez M, Rodríguez J, Jiménez C, Cuevas C. Combining JBCA and Marfey's methodology to determine the absolute configuration of threonines: the case of gunungamide A, a new cyclic depsipeptide containing chloropyrrole from the sponge Discodermia sp. Org Chem Front 2019. [DOI: 10.1039/c8qo00961a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
JBCA and Marfey's allowed us to distinguish threonines diasteroisomers.
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Affiliation(s)
- Guillermo Tarazona
- Natural Products Department
- PharmaMar S.A
- Pol. Ind. La Mina Norte
- 28770 Colmenar Viejo (Madrid)
- Spain
| | - Rogelio Fernández
- Natural Products Department
- PharmaMar S.A
- Pol. Ind. La Mina Norte
- 28770 Colmenar Viejo (Madrid)
- Spain
| | - Patricia G. Cruz
- Natural Products Department
- PharmaMar S.A
- Pol. Ind. La Mina Norte
- 28770 Colmenar Viejo (Madrid)
- Spain
| | - Marta Pérez
- Natural Products Department
- PharmaMar S.A
- Pol. Ind. La Mina Norte
- 28770 Colmenar Viejo (Madrid)
- Spain
| | - Jaime Rodríguez
- Departamento de Química. Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Universidade da Coruña. A Coruña E-15071
- Spain
| | - Carlos Jiménez
- Departamento de Química. Facultade de Ciencias e Centro de Investigacións Científicas Avanzadas (CICA) Universidade da Coruña. A Coruña E-15071
- Spain
| | - Carmen Cuevas
- Natural Products Department
- PharmaMar S.A
- Pol. Ind. La Mina Norte
- 28770 Colmenar Viejo (Madrid)
- Spain
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30
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Lin Y, Zeng Q, Lin L, Chen Z, Barker PB. High-resolution methods for the measurement of scalar coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:135-159. [PMID: 30527134 DOI: 10.1016/j.pnmrs.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/14/2018] [Accepted: 08/14/2018] [Indexed: 06/09/2023]
Abstract
Scalar couplings provide important information regarding molecular structure and dynamics. The measurement of scalar coupling constants constitutes a topic of interest and significance in NMR spectroscopy. However, the measurement of J values is often not straightforward because of complex signal splitting patterns and signal overlap. Many methods have been proposed for the measurement of scalar coupling constants, both for homonuclear and heteronuclear cases. Different approaches to the measurement of scalar coupling constants are reviewed here with several applications presented. The accurate measurement of scalar coupling constants can greatly facilitate molecular structure elucidation and the study of molecule dynamics.
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Affiliation(s)
- Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China.
| | - Qing Zeng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Liangjie Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Peter B Barker
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD 21205, USA
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31
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Dumez JN. Spatial encoding and spatial selection methods in high-resolution NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:101-134. [PMID: 30527133 DOI: 10.1016/j.pnmrs.2018.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 06/09/2023]
Abstract
A family of high-resolution NMR methods share the common concept of acquiring in parallel different sub-experiments in different spatial regions of the NMR tube. These spatial encoding and spatial selection methods were for the most part introduced independently from each other and serve different purposes, but they share common ingredients, often derived from magnetic resonance imaging, and they all benefit from a greatly improved time-efficiency. This review article provides a description of several spatial encoding and spatial selection methods, including single-scan multidimensional experiments (ultrafast 2D NMR, DOSY, Z spectroscopy, inversion recovery and Laplace NMR), pure shift and selective refocusing experiments (including Zangger-Sterk decoupling, G-SERF and PSYCHE), a Z filter, and fast-pulsing slice-selective experiments. Some key elements for spatial parallelisation are introduced and when possible a common framework is used for the analysis of each method. Sensitivity considerations are discussed, and a selection of applications is analysed to illustrate which questions can be answered thanks to spatial encoding and spatial selection methods, and discuss the perspectives for future developments and applications.
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Affiliation(s)
- Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France.
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32
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Bigler P, Furrer J. Why is HMBC superior to LR-HSQC? Influence of homonuclear couplings J HH' on the intensity of long-range correlations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:1101-1116. [PMID: 29907970 DOI: 10.1002/mrc.4762] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/16/2018] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
Long-range heteronuclear single quantum correlation (LR-HSQC) experiments may be applied as an alternative to heteronuclear multiple-bond correlation (HMBC) experiments for detecting long-range correlations but has never enjoyed popularity for that purpose. To the best of our knowledge, the exact reasons have not yet been fully established. For both experiments, it is widely accepted that the evolution of proton-proton homonuclear couplings JHH' during the polarization transfer delays Δ leads to significant losses, and that the intensity of the observable coherence is zero when JHH' matches the condition Δ = 0.5/JHH' . Here, we analyze the influence of JHH' on the intensity of long-range correlations in HMBC and LR-HSQC spectra. We show that for both experiments long-range correlations will not be canceled because of homonuclear couplings JHH' . Our theoretical and experimental results definitely establish and validate the superiority of HMBC-based experiments among the family of heteronuclear long-range correlation experiments: (a) the overall cross peak's intensity is higher, and (b) in LR-HSQC experiments, the intensity of the long-range cross peaks is additionally influenced in an unwanted way by the magnitude and number of passive homonuclear proton-proton couplings JHH' .
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Affiliation(s)
- Peter Bigler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Julien Furrer
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
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33
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Timári I, Kövér KE. Broadband homonuclear decoupled HSQMBC methods. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:910-917. [PMID: 29240977 DOI: 10.1002/mrc.4700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/03/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
Long-range heteronuclear coupling constants convey invaluable information for stereochemical and conformational analysis of molecules from synthetic and natural origin. Here, we report a real-time Zangger-Sterk CPMG-HSQMBC method for the precise and direct measurement of multiple-bond heteronuclear couplings. It is demonstrated that the real-time acquisition strategy combined with multiple slice selective excitation can provide substantial improvement in sensitivity (or reduction of experimental time) as compared to other variants of broadband homonuclear decoupled HSQMBC methods published previously. Scope and limitations of the different strategies applied for decoupling are reviewed. Moreover, practical guidelines for the choice of the most appropriate method are also presented. Applications are given on a metal complex incorporating P-heterocycles and two diglycosyl-selenides for the extraction of n J(1 H, 31 P) and n J(1 H, 77 Se), respectively.
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Affiliation(s)
- István Timári
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, 43210, Columbus, OH, USA
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
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34
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Marcó N, Gil RR, Parella T. Isotropic/Anisotropic NMR Editing by Resolution-Enhanced NMR Spectroscopy. Chemphyschem 2018; 19:1024-1029. [PMID: 29384256 DOI: 10.1002/cphc.201800094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Indexed: 11/11/2022]
Abstract
Modern resolution-enhanced NMR techniques can monitor the in situ discrimination of co-existing isotropic and anisotropic contributions of small molecules dissolved in weakly aligning PMMA/CDCl3 media. The simultaneous sign-sensitive determination of accurate Δδiso-aniso (1 H), Δδiso-aniso (13 C) and/or isotropic 1 JCH and anisotropic 1 TCH coupling constants (and consequently 1 H-13 C residual dipolar couplings and 1 H/13 C residual chemical shift anisotropies) can be performed from spectral-aliased heteronuclear single-quantum correlation spectra.
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Affiliation(s)
- Núria Marcó
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, 15213, PA, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
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35
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Uhrner F, Lederle F, Namyslo JC, Gjikaj M, Schmidt A, Hübner EG. Reaction of N-heterocyclic carbaldehydes with furanones – An investigation of reactivity and regioselectivity. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Marcó N, Gil RR, Parella T. Structural discrimination from in situ measurement of 1 D CH and 2 D HH residual dipolar coupling constants. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:540-545. [PMID: 28043096 DOI: 10.1002/mrc.4575] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 06/06/2023]
Abstract
A fast residual dipolar coupling constant-assisted strategy involving the simultaneous determination of scalar and total coupling constants from a single 1 JCH /2 JHH -resolved NMR spectrum is reported. It is shown that the concerted use of the directly measured 1 DCH (for all CHn multiplicities) and 2 DHH residual dipolar couplings allows an on-the-fly assignment of diastereotopic CH2 protons, as well as of an efficient discrimination between diastereoisomeric structures of strychnine which contains six stereocenters. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Núria Marcó
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
| | - Roberto R Gil
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear and Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
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37
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Marcó N, Souza AA, Nolis P, Gil RR, Parella T. Perfect 1J CH-resolved HSQC: Efficient measurement of one-bond proton-carbon coupling constants along the indirect dimension. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 276:37-42. [PMID: 28092787 DOI: 10.1016/j.jmr.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/30/2016] [Accepted: 01/01/2017] [Indexed: 06/06/2023]
Abstract
A versatile 1JCH-resolved HSQC pulse scheme for the speedy, accurate and automated determination of one-bond proton-carbon coupling constants is reported. The implementation of a perfectBIRD element allows a straightforward measurement from the clean doublets obtained along the highly resolved F1 dimension, even for each individual 1JCHa and 1JCHb in diastereotopic HaCHb methylene groups. Real-time homodecoupling during acquisition and other alternatives to minimize accidental signal overlapping in overcrowded spectra are also discussed.
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Affiliation(s)
- N Marcó
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
| | - A A Souza
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain; Departamento de Química, Universidade Federal do Piauí, 64049-550 Teresina, PI, Brazil
| | - P Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain
| | - R R Gil
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - T Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Catalonia, Spain.
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38
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Kline M, Pierce D, Cheatham S. Assignment of oxime and hydrazone configuration using 1 H- 15 N and 13 C- 15 N coupling measurements at natural abundance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:154-156. [PMID: 27706849 DOI: 10.1002/mrc.4536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/27/2016] [Accepted: 10/02/2016] [Indexed: 06/06/2023]
Abstract
Measurement of 1 H-15 N and 13 C-15 N coupling constants at natural abundance is demonstrated to be a reliable and generic method to determine the configuration of oximes, hydrazines, and related systems. Data on 1 H-15 N and 13 C-15 N coupling constants on a variety of systems obtained at natural abundance confirm the geometric dependence of the measured 1 H-15 N and 13 C-15 N coupling constants. In addition, we summarize a simple "decision-tree" for determining configuration based on practical considerations of sample quantity, solubility, and complexity. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Mike Kline
- DuPont Crop Protection, Stine Haskell Research Center, P.O. Box 30, Newark, DE, 19714, USA
| | - Dawn Pierce
- DuPont Crop Protection, Stine Haskell Research Center, P.O. Box 30, Newark, DE, 19714, USA
| | - Steve Cheatham
- DuPont Crop Protection, Stine Haskell Research Center, P.O. Box 30, Newark, DE, 19714, USA
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39
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Marcó N, Souza AA, Nolis P, Cobas C, Gil RR, Parella T. 1JCH NMR Profile: Identification of Key Structural Features and Functionalities by Visual Observation and Direct Measurement of One-Bond Proton-Carbon Coupling Constants. J Org Chem 2017; 82:2040-2044. [DOI: 10.1021/acs.joc.6b02873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Núria Marcó
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
| | - Alexandre A. Souza
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
- Departamento
de Química, Universidade Federal do Piauí, Teresina, PI 64049-550, Brazil
| | - Pau Nolis
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
| | - Carlos Cobas
- Mestrelab Research, Santiago de Compostela, E-15706 A Coruña, Spain
| | - Roberto R. Gil
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Teodor Parella
- Servei
de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona) Catalonia, Spain
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40
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Dickson CL, Blundell CD, Butts CP, Felton A, Jeffreys A, Takacs Z. Accurate measurement of long range proton–carbon scalar coupling constants. Analyst 2017; 142:621-633. [DOI: 10.1039/c6an02298g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The accuracy and ease-of-use of various experimental NMR methods for measuringnJCHvalues is assessed.
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Affiliation(s)
| | | | | | - Alice Felton
- University of Bristol
- School of Chemistry
- Bristol
- UK
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41
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Schmidts V. Perspectives in the application of residual dipolar couplings in the structure elucidation of weakly aligned small molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:54-60. [PMID: 27743456 DOI: 10.1002/mrc.4543] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 05/28/2023]
Abstract
This perspective article aims to review the general methodology in the application of residual dipolar couplings (RDCs) in the structure elucidation of small molecules and give the author's view on challenges for future applications. Recent improvements in the availability of alignment media, new pulse sequences for the measurement of couplings and improvements in the analysis software have garnered widespread interest in the technique. However, further generalization is needed in order to make RDC analysis into a truly "routine" method. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
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42
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Fredi A, Nolis P, Cobas C, Parella T. Access to experimentally infeasible spectra by pure-shift NMR covariance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 270:161-168. [PMID: 27494746 DOI: 10.1016/j.jmr.2016.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/14/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments.
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Affiliation(s)
- André Fredi
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Carlos Cobas
- Mestrelab Research, Santiago de Compostela, E-15706 A Coruña, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain.
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Fredi A, Nolis P, Cobas C, Martin GE, Parella T. Exploring the use of Generalized Indirect Covariance to reconstruct pure shift NMR spectra: Current Pros and Cons. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 266:16-22. [PMID: 27003379 DOI: 10.1016/j.jmr.2016.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/05/2016] [Accepted: 03/07/2016] [Indexed: 06/05/2023]
Abstract
The current Pros and Cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported for the target molecule strychnine.
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Affiliation(s)
- André Fredi
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Pau Nolis
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain
| | - Carlos Cobas
- Mestrelab Research, Santiago de Compostela, E-15706 A Coruña, Spain
| | - Gary E Martin
- NMR Structure Elucidation, Process & Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, United States
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Catalonia, Spain.
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Saurí J, Marcó N, Williamson RT, Martin GE, Parella T. Extending long-range heteronuclear NMR connectivities by HSQMBC-COSY and HSQMBC-TOCSY experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 258:25-32. [PMID: 26160012 DOI: 10.1016/j.jmr.2015.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 06/04/2023]
Abstract
The detection of long-range heteronuclear correlations presenting J(CH) coupling values smaller than 1-2Hz is a challenge in the structural analysis of small molecules and natural products. HSQMBC-COSY and HSQMBC-TOCSY pulse schemes are evaluated as complementary NMR methods to standard HMBC/HSQMBC experiments. Incorporation of an additional J(HH) transfer step in the basic HSQMBC pulse scheme can favor the sensitive observation of traditionally missing or very weak correlations and, in addition, facilitates the detection of a significant number of still longer-range connectivities to both protonated and non-protonated carbons under optimum sensitivity conditions. A comparative (1)H-(13)C study is performed using strychnine as a model compound and several examples are also provided including (1)H-(15)N applications.
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Affiliation(s)
- Josep Saurí
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain; NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
| | - Núria Marcó
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - R Thomas Williamson
- NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
| | - Gary E Martin
- NMR Structure Elucidation, Process and Analytical Chemistry, Merck & Co. Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain.
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Timári I, Szilágyi L, Kövér KE. PSYCHE CPMG–HSQMBC: An NMR Spectroscopic Method for Precise and Simple Measurement of Long‐Range Heteronuclear Coupling Constants. Chemistry 2015; 21:13939-42. [DOI: 10.1002/chem.201502641] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 11/08/2022]
Affiliation(s)
- István Timári
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H‐4032 Debrecen (Hungary)
| | - László Szilágyi
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H‐4032 Debrecen (Hungary)
| | - Katalin E. Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H‐4032 Debrecen (Hungary)
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46
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1D NMR Homodecoupled1H Spectra with Scalar Coupling Constants from 2D NemoZS-DIAG Experiments. Angew Chem Int Ed Engl 2015; 54:6016-8. [DOI: 10.1002/anie.201500831] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 02/24/2015] [Indexed: 11/07/2022]
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47
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Cotte A, Jeannerat D. 1D NMR Homodecoupled1H Spectra with Scalar Coupling Constants from 2D NemoZS-DIAG Experiments. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Ndukwe IE, Butts CP. Pure-shift IMPRESS EXSIDE – Easy measurement of 1H–13C scalar coupling constants with increased sensitivity and resolution. RSC Adv 2015. [DOI: 10.1039/c5ra24926k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Measuring long-range 1H–13C scalar coupling constants, nJCH, is made easier through improved sensitivity and resolution of the SelEXSIDE NMR experiment by incorporation of ‘pure-shift’ homonuclear decoupling and IMPRESS-Hadamard encoding.
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Affiliation(s)
- I. E. Ndukwe
- School of Chemistry
- University of Bristol
- Bristol
- UK
| | - C. P. Butts
- School of Chemistry
- University of Bristol
- Bristol
- UK
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