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The Value of Universally Available Raw NMR Data for Transparency, Reproducibility, and Integrity in Natural Product Research

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The Value of Universally Available Raw NMR Data for Transparency, Reproducibility, and Integrity in Natural Product Research Dominican Scholar Natural Sciences and Mathematics | Department of Natural Sciences and Faculty Scholarship Mathematics 1-1-2019 The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research. James B. McAlpine Center for Natural Product Technologies, University of Illinois at Chicago Shao-Nong Chen Center for Natural Product Technologies, University of Illinois at Chicago Survey: Let us know how this paper benefits you. Andrei Kutateladze Department of Chemistry and Biochemistry, University of Denver Recommended Citation John B. MacMillan McAlpine, James B.; Chen, Shao-Nong; Kutateladze, Andrei; MacMillan, John B.; Appendino, Department of Chemistry and Biochemistry, University of California, Santa Cruz Giovanni; Barison, Andersson; Beniddir, Mehdi A.; Biavatti, Maique W.; Bluml, Stefan; GioBoufridi,vanni AppendinoAsmaa; Butler, Mark S.; Capon, Robert J.; Choi, Young H.; Coppage, David; Crews, DiparPhillip;timent Crimmins,o di Scienz Michaele Chimiche, T.; Csete, Alimentari, Marie; Farmaceutiche Dewapriya, eP Fradeep;armacologiche, Egan, JosephUniversita` M.; del Garson, Piemonte OrientaleMary J.; Genta-Jouve, Grégory; Gerwick, William H; Gross, Harald; Harper, Mary Kay; Hermanto, Precilia; Hook, James M.; Hunter, Luke; Jeannerat, Damien; Ji, Nai-Yun; Johnson, Tyler A.; Kingston, David G. I.; Koshino, Hiroyuki; Lee, Hsiau-Wei; Lewin, Guy; Li, Jie; SeeLinington, next page Roger for additional G; Liu, Miaomiao; authors McPhail, Kerry L; Molinski, Tadeusz F; Moore, Bradley S; Nam, Joo-Won; Neupane, Ram P; Niemitz, Matthias; Nuzillard, Jean-Marc; Oberlies, Nicholas H; Ocampos, Fernanda M M; Pan, Guohui; Quinn, Ronald J; Reddy, D Sai; Renault, Jean- Hugues;https://doi.or Rivera-Chávez,g/10.1039/c7np00064b José; Robien, W olfgang; Saunders, Carla M; Schmidt, Thomas J; Seger, Christoph; Shen, Ben; Steinbeck, Christoph; Stuppner, Hermann; Sturm, Sonja; Taglialatela-Scafati, Orazio; Tantillo, Dean J; Verpoorte, Robert; Wang, Bin-Gui; Williams, Craig M; Williams, Philip G; Wist, Julien; Yue, Jian-Min; Zhang, Chen; Xu, Zhengren; Simmler, Charlotte; Lankin, David C; Bisson, Jonathan; and Pauli, Guido F, "The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research." (2019). Natural Sciences and Mathematics | Faculty Scholarship. 7. https://doi.org/10.1039/c7np00064b This Article is brought to you for free and open access by the Department of Natural Sciences and Mathematics at Dominican Scholar. It has been accepted for inclusion in Natural Sciences and Mathematics | Faculty Scholarship by an authorized administrator of Dominican Scholar. For more information, please contact [email protected]. Authors James B. McAlpine, Shao-Nong Chen, Andrei Kutateladze, John B. MacMillan, Giovanni Appendino, Andersson Barison, Mehdi A. Beniddir, Maique W. Biavatti, Stefan Bluml, Asmaa Boufridi, Mark S. Butler, Robert J. Capon, Young H. Choi, David Coppage, Phillip Crews, Michael T. Crimmins, Marie Csete, Pradeep Dewapriya, Joseph M. Egan, Mary J. Garson, Grégory Genta-Jouve, William H Gerwick, Harald Gross, Mary Kay Harper, Precilia Hermanto, James M. Hook, Luke Hunter, Damien Jeannerat, Nai-Yun Ji, Tyler A. Johnson, David G. I. Kingston, Hiroyuki Koshino, Hsiau-Wei Lee, Guy Lewin, Jie Li, Roger G Linington, Miaomiao Liu, Kerry L McPhail, Tadeusz F Molinski, Bradley S Moore, Joo-Won Nam, Ram P Neupane, Matthias Niemitz, Jean-Marc Nuzillard, Nicholas H Oberlies, Fernanda M M Ocampos, Guohui Pan, Ronald J Quinn, D Sai Reddy, Jean-Hugues Renault, José Rivera-Chávez, Wolfgang Robien, Carla M Saunders, Thomas J Schmidt, Christoph Seger, Ben Shen, Christoph Steinbeck, Hermann Stuppner, Sonja Sturm, Orazio Taglialatela-Scafati, Dean J Tantillo, Robert Verpoorte, Bin-Gui Wang, Craig M Williams, Philip G Williams, Julien Wist, Jian-Min Yue, Chen Zhang, Zhengren Xu, Charlotte Simmler, David C Lankin, Jonathan Bisson, and Guido F Pauli This article is available at Dominican Scholar: https://scholar.dominican.edu/natural-sciences-and- mathematics-faculty-scholarship/7 Natural Product Reports View Article Online REVIEW View Journal | View Issue The value of universally available raw NMR data for transparency, reproducibility, and integrity in Cite this: Nat. Prod. Rep.,2019,36,35 natural product research† James B. McAlpine, *a Shao-Nong Chen, a Andrei Kutateladze, b John B. MacMillan, c Giovanni Appendino, d Andersson Barison, e Mehdi A. Beniddir, f Maique W. Biavatti, g Stefan Bluml, h Asmaa Boufridi, i Mark S. Butler, j Robert J. Capon, j Young H. Choi, k David Coppage,c Phillip Crews, c Michael T. Crimmins, l Marie Csete, m Pradeep Dewapriya, j n o p Joseph M. Egan, Mary J. Garson, Gregory´ Genta-Jouve, William H. Gerwick, qr Harald Gross, s Mary Kay Harper,t Precilia Hermanto,u James M. Hook, u Luke Hunter, u Damien Jeannerat, v Nai-Yun Ji, w Tyler A. Johnson,c David G. I. Kingston, x Hiroyuki Koshino, y Hsiau-Wei Lee,c Guy Lewin,f Jie Li, r Roger G. Linington, n Miaomiao Liu,i Kerry L. McPhail, z Creative Commons Attribution 3.0 Unported Licence. Tadeusz F. Molinski, aa Bradley S. Moore, qr Joo-Won Nam, ab Ram P. Neupane,ac Matthias Niemitz, ad Jean-Marc Nuzillard, ae Nicholas H. Oberlies, af Fernanda M. M. Ocampos, e Guohui Pan, ag i b ae ah Ronald J. Quinn, D. Sai Reddy, Jean-Hugues Renault, Jose´ Rivera-Chavez,´ Wolfgang Robien, ai Carla M. Saunders, aj Thomas J. Schmidt, ak Christoph Seger, al Ben Shen, ag Christoph Steinbeck, am Hermann Stuppner, al Sonja Sturm,al Orazio Taglialatela-Scafati, an Dean J. Tantillo, aj Robert Verpoorte, k Bin-Gui Wang, wao o ac ap aq This article is licensed under a Craig M. Williams, Philip G. Williams, Julien Wist, Jian-Min Yue, Chen Zhang,ar Zhengren Xu, ag Charlotte Simmler, a David C. Lankin, a Jonathan Bisson a and Guido F. Pauli *a Open Access Article. Published on 13 July 2018. Downloaded 2/22/2019 8:02:28 PM. Covering: up to 2018 With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is Received 18th December 2017 intended to enhance the transparency of experimental protocols, augment the reproducibility of DOI: 10.1039/c7np00064b reported outcomes, including biological studies, become a regular component of responsible research, rsc.li/npr and thereby enrich the integrity of NP research and related fields. aCenter for Natural Product Technologies (CENAPT), Program for Collaborative cDepartment of Chemistry and Biochemistry, University of California, Santa Cruz, CA, Research in the Pharmaceutical Sciences (PCRPS), Department of Medicinal 95064, USA Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at dDipartimento di Scienze Chimiche, Alimentari, Farmaceutiche e Farmacologiche, Chicago, 833 S. Wood St., Chicago, IL, 60612, USA. E-mail: [email protected], Universita` del Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy [email protected] eNMR Center, Federal University of Parana,´ Curitiba, Brazil b Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, fEquipe´ “Pharmacognosie-Chimie des Substances Naturelles” BioCIS, Univ. Paris-Sud, USA CNRS, Universit´e Paris-Saclay, 5 rue J.-B. Cl´ement, 92290 Chatenay-Malabry,ˆ France This journal is © The Royal Society of Chemistry 2019 Nat. Prod. Rep.,2019,36,35–107 | 35 View Article Online Natural Product Reports Review 3.5 The structure of aldingenin B 1 Introduction 3.6 Clearing the literature of blatantly incorrect natural 1.1 Preamble product structures 1.2 Dimensionality and completeness 3.7 Bredt's rule as a check on structure correctness 1.3 Human and machine processing of NMR data 3.8 Correct analysis of coupling constants 1.4 Molecular transparency 3.9 Sulfones vs. sulnates 1.5 Molecular topography 3.10 Methylene signal assignments in the structural revision 2 Introduction to the organization of this review of aromin to montanacin D 2.1 Rationale 1 – structure revisions 3.11 The case of aglalactone 2.2 Rationale 2 – impurity detection and quantication 3.12 Diastereoisomers and rotamers 2.3 Rationale 3 – dereplication 3.13 Data ambiguity 2.4 Rationale 4 – enabling new methodology 3.14 The importance of details 2.5 Rationale 5 – other nuclei 3.15 Structural instability leads to dynamic complexity 2.6 Rationale 6 – data repositories 3.16 Acetogenins-the difficulty of congurational 2.7 Rationale 7 – clinical applications determination 3 Structure revision 3.17 Second order coupling patterns with rst order look vs. 3.1 Incorrect ring closures: furan vs. pyrone ring systems “multiplets” 3.2 Incorrect ring closures: the lipopeptide arthrofactin 4 Impurity detection and quantication 3.3 Incorrect ring closures: the case of aquatolide 4.1 Purication of thiotetronates 3.4 The case of coibamide A gDepartment of Pharmaceutical Sciences, Federal University of Santa Catarina, abCollege of Pharmacy, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk, Florianopolis,´
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