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Shin J, Porubsky V, Carothers J, Sauro HM. Standards, dissemination, and best practices in systems biology. Curr Opin Biotechnol 2023; 81:102922. [PMID: 37004298 PMCID: PMC10435326 DOI: 10.1016/j.copbio.2023.102922] [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: 12/16/2021] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 04/03/2023]
Abstract
The reproducibility of scientific research is crucial to the success of the scientific method. Here, we review the current best practices when publishing mechanistic models in systems biology. We recommend, where possible, to use software engineering strategies such as testing, verification, validation, documentation, versioning, iterative development, and continuous integration. In addition, adhering to the Findable, Accessible, Interoperable, and Reusable modeling principles allows other scientists to collaborate and build off of each other's work. Existing standards such as Systems Biology Markup Language, CellML, or Simulation Experiment Description Markup Language can greatly improve the likelihood that a published model is reproducible, especially if such models are deposited in well-established model repositories. Where models are published in executable programming languages, the source code and their data should be published as open-source in public code repositories together with any documentation and testing code. For complex models, we recommend container-based solutions where any software dependencies and the run-time context can be easily replicated.
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Affiliation(s)
- Janis Shin
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Veronica Porubsky
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - James Carothers
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
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2
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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3
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Salem MSH, Takizawa S. New anionic cobalt(III) complexes enable enantioselective synthesis of spiro-fused oxazoline and iodoacetal derivatives. Front Chem 2022; 10:1034291. [PMID: 36311431 PMCID: PMC9606352 DOI: 10.3389/fchem.2022.1034291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
Anionic salicylimine-based cobalt (III) complexes featuring chiral ligands derived from isoleucine amino acids were used as efficient bifunctional phase-transfer catalysts for electrophilic iodination of enol ethers. The Brønsted acids of these complexes enabled the enantioselective asymmetric iodocyclization of enol ethers, furnishing spiro-fused oxazoline derivatives in high yields with up to 90:10 er. In addition, chiral cobalt (III) complexes catalyze the asymmetric intermolecular iodoacetalization of enol ethers with various alcohols to afford 3-iodoacetal derivatives in high yields with up to 92:8 er.
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Affiliation(s)
- Mohamed S. H. Salem
- SANKEN, Osaka University, Ibaraki, Japan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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4
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Wang J, Pang X, Chen C, Gao C, Zhou X, Liu Y, Luo X. Chemistry, Biosynthesis, and Biological Activity of Halogenated Compounds Produced by Marine Microorganisms. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jiamin Wang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaoyan Pang
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
| | - Chunmei Chen
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Chenghai Gao
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio‐resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology Chinese Academy of Sciences Guangzhou 510301 China
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458 China
- University of Chinese Academy of Sciences 19 Yuquan Road Beijing 100049 China
| | - Xiaowei Luo
- Institute of Marine Drugs Guangxi University of Chinese Medicine Nanning 530200 China
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5
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O'Donnell TJ, Luo Y, Yoshida WY, Suzuki S, Sun R, Williams PG. Spirovetivane- and Eudesmane-Type Sesquiterpenoids Isolated from the Culture Media of Two Cyanobacterial Strains. JOURNAL OF NATURAL PRODUCTS 2022; 85:415-425. [PMID: 35142496 DOI: 10.1021/acs.jnatprod.1c01014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As part of a study examining polar metabolites produced by cyanobacterial strains, we examined media extracts of a Calothrix sp. (strain R-3-1) and a Scytonema sp. (strain U-3-3). The cell mass of each was separated from the media, and HP20 resin was added for adsorption of secreted metabolites, a relatively unexplored area of cyanobacterial chemistry. HPLC-UV-LCMS-guided isolation led to the discovery of seven sesquiterpenoid compounds with five new, one known, and one previously isolated as the methyl ester. Through a complement of 1D and 2D NMR spectroscopic techniques, the planar structures and relative configurations of the seven compounds were elucidated. Spironostoic acid (1), 11,12-didehydrospironostoic acid (2), and 12-hydroxy-2-oxo-11-epi-hinesol (4) are spirovetivane-type compounds from R-3-1, while stigolone (5), 11R,12-dihydroxystigolone (6), and 11S,12-dihydroxystigolone (7) are three eudesmane-type compounds from U-3-3. Circular dichroism was utilized to decipher the absolute configurations of new compounds 1, 2, 4, 5, 6, and 7. Due to the structural variety observed among the spirovetivane- and eudesmane-type compounds in the literature and often a lack of clarity in how determinations were made, computational spectra and model compounds were used to support the interpretation of ECD and NMR spectra. A straightforward process to determine the configuration of these systems is presented.
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Affiliation(s)
- Timothy J O'Donnell
- Department of Chemistry, University of Hawai'i at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Yuheng Luo
- Department of Chemistry, University of Hawai'i at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Wesley Y Yoshida
- Department of Chemistry, University of Hawai'i at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Sayuri Suzuki
- Center for Biomedical Research, The Queen's Medical Center, Honolulu, Hawaii 96813, United States
| | - Rui Sun
- Department of Chemistry, University of Hawai'i at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawai'i at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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7
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Marcarino MO, Cicetti S, Zanardi MM, Sarotti AM. A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide. Nat Prod Rep 2021; 39:58-76. [PMID: 34212963 DOI: 10.1039/d1np00030f] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.
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Affiliation(s)
- Maribel O Marcarino
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - Soledad Cicetti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - María M Zanardi
- Instituto de Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina.
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
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Porubsky V, Smith L, Sauro HM. Publishing reproducible dynamic kinetic models. Brief Bioinform 2021; 22:bbaa152. [PMID: 32793969 PMCID: PMC8138891 DOI: 10.1093/bib/bbaa152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/19/2020] [Accepted: 06/17/2020] [Indexed: 11/14/2022] Open
Abstract
Publishing repeatable and reproducible computational models is a crucial aspect of the scientific method in computational biology and one that is often forgotten in the rush to publish. The pressures of academic life and the lack of any reward system at institutions, granting agencies and journals means that publishing reproducible science is often either non-existent or, at best, presented in the form of an incomplete description. In the article, we will focus on repeatability and reproducibility in the systems biology field where a great many published models cannot be reproduced and in many cases even repeated. This review describes the current landscape of software tooling, model repositories, model standards and best practices for publishing repeatable and reproducible kinetic models. The review also discusses possible future remedies including working more closely with journals to help reviewers and editors ensure that published kinetic models are at minimum, repeatable. Contact: hsauro@uw.edu.
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Affiliation(s)
- Veronica Porubsky
- Department of Bioengineering, University of Washington, Seattle, 98105,USA
| | - Lucian Smith
- Department of Bioengineering, University of Washington, Seattle, 98105,USA
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, 98105,USA
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9
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Nazarski RB. Summary of DFT calculations coupled with current statistical and/or artificial neural network (ANN) methods to assist experimental NMR data in identifying diastereomeric structures. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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10
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Access to multi-functionalized oxazolines via silver-catalyzed heteroannulation of enamides with sulfoxonium ylides. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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11
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Iwanaga T, Wang HH, Hamilton SH, Grimm V, Koralewski TE, Salado A, Elsawah S, Razavi S, Yang J, Glynn P, Badham J, Voinov A, Chen M, Grant WE, Peterson TR, Frank K, Shenk G, Barton CM, Jakeman AJ, Little JC. Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach. ENVIRONMENTAL MODELLING & SOFTWARE : WITH ENVIRONMENT DATA NEWS 2021; 135:104885. [PMID: 33041631 PMCID: PMC7537632 DOI: 10.1016/j.envsoft.2020.104885] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 05/05/2023]
Abstract
System-of-systems approaches for integrated assessments have become prevalent in recent years. Such approaches integrate a variety of models from different disciplines and modeling paradigms to represent a socio-environmental (or social-ecological) system aiming to holistically inform policy and decision-making processes. Central to the system-of-systems approaches is the representation of systems in a multi-tier framework with nested scales. Current modeling paradigms, however, have disciplinary-specific lineage, leading to inconsistencies in the conceptualization and integration of socio-environmental systems. In this paper, a multidisciplinary team of researchers, from engineering, natural and social sciences, have come together to detail socio-technical practices and challenges that arise in the consideration of scale throughout the socio-environmental modeling process. We identify key paths forward, focused on explicit consideration of scale and uncertainty, strengthening interdisciplinary communication, and improvement of the documentation process. We call for a grand vision (and commensurate funding) for holistic system-of-systems research that engages researchers, stakeholders, and policy makers in a multi-tiered process for the co-creation of knowledge and solutions to major socio-environmental problems.
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Affiliation(s)
- Takuya Iwanaga
- Institute for Water Futures and Fenner School of Environment and Society, The Australian National University, Canberra, Australia
| | - Hsiao-Hsuan Wang
- Ecological Systems Laboratory, Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Serena H Hamilton
- Institute for Water Futures and Fenner School of Environment and Society, The Australian National University, Canberra, Australia
- CSIRO Land & Water, Canberra, Australia
| | - Volker Grimm
- Helmholtz Centre for Environmental Research - UFZ, Department of Ecological Modelling, Leipzig, Germany
- University of Potsdam, Plant Ecology and Nature Conservation, Potsdam, Germany
| | - Tomasz E Koralewski
- Ecological Systems Laboratory, Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Alejandro Salado
- Grado Department of Industrial and Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Sondoss Elsawah
- Institute for Water Futures and Fenner School of Environment and Society, The Australian National University, Canberra, Australia
- School of Electrical Engineering and Information Technology, University of New South Wales, Australian Defence Force Academy, Canberra, ACT, Australia
| | - Saman Razavi
- Global Institute for Water Security, School of Environment and Sustainability, Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jing Yang
- National Institute of Water and Atmospheric Research, New Zealand
| | - Pierre Glynn
- U.S. Department of the Interior, U.S. Geological Survey, Reston, VA, USA
| | - Jennifer Badham
- Centre for Research in Social Simulation, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - Alexey Voinov
- Center on Persuasive Systems for Wise Adaptive Living (PERSWADE), Faculty of Engineering & IT, University of Technology, Sydney, Australia
- Faculty of Engineering Technology, University of Twente, Netherlands
| | - Min Chen
- Key Laboratory of Virtual Geographic Environment (Ministry of Education of PRC), Nanjing Normal University, Nanjing, 210023, China
| | - William E Grant
- Ecological Systems Laboratory, Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Tarla Rai Peterson
- Environmental Science and Engineering Program, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Karin Frank
- Helmholtz Centre for Environmental Research - UFZ, Department of Ecological Modelling, Leipzig, Germany
| | - Gary Shenk
- U.S Geological Survey, Chesapeake Bay Program, Annapolis, MD, 21403, USA
| | - C Michael Barton
- Center for Social Dynamics & Complexity, School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Anthony J Jakeman
- Institute for Water Futures and Fenner School of Environment and Society, The Australian National University, Canberra, Australia
| | - John C Little
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
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12
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Carroll AR, Copp BR, Davis RA, Keyzers RA, Prinsep MR. Marine natural products. Nat Prod Rep 2021; 38:362-413. [PMID: 33570537 DOI: 10.1039/d0np00089b] [Citation(s) in RCA: 198] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review covers the literature published in 2019 for marine natural products (MNPs), with 719 citations (701 for the period January to December 2019) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1490 in 440 papers for 2019), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. Methods used to study marine fungi and their chemical diversity have also been discussed.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. and Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia and School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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13
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Lucas TCD, Pollington TM, Davis EL, Hollingsworth TD. Responsible modelling: Unit testing for infectious disease epidemiology. Epidemics 2020; 33:100425. [PMID: 33307443 PMCID: PMC7690327 DOI: 10.1016/j.epidem.2020.100425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/21/2020] [Accepted: 11/21/2020] [Indexed: 11/30/2022] Open
Abstract
Infectious disease epidemiology is increasingly reliant on large-scale computation and inference. Models have guided health policy for epidemics including COVID-19 and Ebola and endemic diseases including malaria and tuberculosis. Yet a coding bug may bias results, yielding incorrect conclusions and actions causing avoidable harm. We are ethically obliged to make our code as free of error as possible. Unit testing is a coding method to avoid such bugs, but it is rarely used in epidemiology. We demonstrate how unit testing can handle the particular quirks of infectious disease models and aim to increase the uptake of this methodology in our field.
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Affiliation(s)
- Tim C D Lucas
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK. Centre for Environment and Health, School of Public Health, Imperial College, UK.
| | - Timothy M Pollington
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK. MathSys CDT, University of Warwick, UK
| | - Emma L Davis
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
| | - T Déirdre Hollingsworth
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
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14
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Kato S, Mizukami D, Sugai T, Tsuda M, Fuwa H. Total synthesis and complete configurational assignment of amphirionin-2. Chem Sci 2020; 12:872-879. [PMID: 34163854 PMCID: PMC8179035 DOI: 10.1039/d0sc06021f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Amphirionin-2 is a linear polyketide metabolite that exhibits potent and selective cytotoxic activity against certain human cancer cell lines. We disclose herein the first total synthesis of amphirionin-2 and determination of its absolute configuration. Our synthesis featured an extensive use of cobalt-catalyzed Mukaiyama-type cyclization of γ-hydroxy olefins for stereoselective formation of all the tetrahydrofuran rings found in the natural product, and a late-stage Stille-type coupling for convergent assembly of the entire carbon backbone. Four candidate diastereomers of amphirionin-2 were synthesized in a unified, convergent manner, and their spectroscopic/chromatographic properties were compared with those of the authentic material. The present study culminated in the reassignment of the C5/C7 relative configuration, assignment of the C12/C18 relative configuration, and determination of the absolute configuration of amphirionin-2.
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Affiliation(s)
- Shota Kato
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Daichi Mizukami
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Tomoya Sugai
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
| | - Masashi Tsuda
- Center for Advanced Marine Core Research and Department of Agriculture and Marine Science, Kochi University Nankoku Kochi 783-8502 Japan
| | - Haruhiko Fuwa
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University 1-13-27 Kasuga, Bunkyo-ku Tokyo 112-8551 Japan
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15
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Structure elucidation of small organic molecules by contemporary computational chemistry methods. Arch Pharm Res 2020; 43:1114-1127. [DOI: 10.1007/s12272-020-01277-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
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16
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Li Y, Naman CB, Alexander KL, Guan H, Gerwick WH. The Chemistry, Biochemistry and Pharmacology of Marine Natural Products from Leptolyngbya, a Chemically Endowed Genus of Cyanobacteria. Mar Drugs 2020; 18:E508. [PMID: 33036172 PMCID: PMC7600079 DOI: 10.3390/md18100508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 12/23/2022] Open
Abstract
Leptolyngbya, a well-known genus of cyanobacteria, is found in various ecological habitats including marine, fresh water, swamps, and rice fields. Species of this genus are associated with many ecological phenomena such as nitrogen fixation, primary productivity through photosynthesis and algal blooms. As a result, there have been a number of investigations of the ecology, natural product chemistry, and biological characteristics of members of this genus. In general, the secondary metabolites of cyanobacteria are considered to be rich sources for drug discovery and development. In this review, the secondary metabolites reported in marine Leptolyngbya with their associated biological activities or interesting biosynthetic pathways are reviewed, and new insights and perspectives on their metabolic capacities are gained.
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Affiliation(s)
- Yueying Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China;
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA; (C.B.N.); (K.L.A.)
| | - C. Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA; (C.B.N.); (K.L.A.)
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Kelsey L. Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA; (C.B.N.); (K.L.A.)
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China;
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA; (C.B.N.); (K.L.A.)
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
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Marcarino MO, Zanardi MM, Cicetti S, Sarotti AM. NMR Calculations with Quantum Methods: Development of New Tools for Structural Elucidation and Beyond. Acc Chem Res 2020; 53:1922-1932. [PMID: 32794691 DOI: 10.1021/acs.accounts.0c00365] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structural elucidation is an important and challenging stage in the discovery of new organic molecules. Single-crystal X-ray analysis provides the most unquestionable results, though in practice the availability of suitable crystals limits its broad use. On the other hand, NMR spectroscopy has become the leading and universal technique to accomplish the task. Despite continuous advances in the field, the misinterpretation of NMR data is commonplace, evidenced by the large number of erroneous structures being published in top journals. Quantum calculations of NMR chemical shifts and scalar coupling constants emerged as ideal complements to facilitate the elucidation process when experimental NMR data is inconclusive. Since seminal reports demonstrated that affordable DFT methods provide NMR predictions accurate enough to differentiate among closely related isomers, the discipline has experienced substantial growth. The impact has been felt in different areas, and nowadays the results of such calculations are routinely seen in high impact literature.This Account describes our investigations in the field of quantum NMR calculations, focusing on the development of tools for structural elucidation and practical applications. We pioneered the use of artificial intelligence methods in the development of novel strategies of structural validation. Our first generation of trained artificial neural networks (ANNs) showed excellent ability to identify mistakes at the atom connectivity level, whereas the use of multidimensional pattern recognition pushed the performance to the stereochemical limit. In a conceptually different approach, we developed DP4+, an updated version of the DP4 probability used to determine the most likely structure among two or more candidates when one set of experimental data is available. Increasing the level of theory in NMR calculations and including unscaled data in the formalism improved the performance of the method, further validated to settle the configuration of challenging motifs such as spiroepoxides or Mosher's derivatives. One of the limitations of DP4+ is related to the relatively large computational cost involved in obtaining DFT-optimized geometries, which led to the development of a fast variant including the valuable information provided by coupling constants (J-DP4 method).These tools were explored to suggest the most probable structure of controversial natural or unnatural products originally misassigned, with some predictions further validated by synthesis (as in the case of pseudorubriflordilactone B). The possibility of predicting the structure of a natural product without requiring authentic sample was investigated in collaboration with Prof. Pilli (UNICAMP, Brazil) in the computer-guided total synthesis and stereochemical revisions of several natural products. Despite these advances, there remain considerable challenges, such as the case of configurational assessment of polar systems featuring multiple intramolecular hydrogen bonding interactions because of the poor energy predictions provided by most DFT methods. In our latest work, we tackle this problem by averaging the results provided by randomly generated ensembles, paving the way for a new paradigm in quantum NMR-assisted structural elucidation.
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Affiliation(s)
- Maribel O. Marcarino
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Marı́a M. Zanardi
- Instituto de Ingenierı́a Ambiental, Quı́mica y Biotecnologı́a Aplicada (INGEBIO), Facultad de Quı́mica e Ingenierı́a del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Soledad Cicetti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Willoughby PH, Jansma MJ, Hoye TR. Addendum: A guide to small-molecule structure assignment through computation of (¹H and ¹³C) NMR chemical shifts. Nat Protoc 2020; 15:2277. [PMID: 31949288 DOI: 10.1038/s41596-020-0293-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
| | - Matthew J Jansma
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Thomas R Hoye
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA.
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Maslovskaya LA, Savchenko AI, Krenske EH, Chow S, Holt T, Gordon VA, Reddell PW, Pierce CJ, Parsons PG, Boyle GM, Kutateladze AG, Williams CM. EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods. Chemistry 2020; 26:11862-11867. [PMID: 32864777 DOI: 10.1002/chem.202001884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.
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Affiliation(s)
- Lidia A Maslovskaya
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Andrei I Savchenko
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Sharon Chow
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208, USA
| | - Victoria A Gordon
- EcoBiotics Limited, PO Box 1, Yungaburra, 4884, Queensland, Australia
| | - Paul W Reddell
- EcoBiotics Limited, PO Box 1, Yungaburra, 4884, Queensland, Australia
| | - Carly J Pierce
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Peter G Parsons
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208, USA
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
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20
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Abstract
A major challenge for metabolomic analysis is to obtain an unambiguous identification of the metabolites detected in a sample. Among metabolomics techniques, NMR spectroscopy is a sophisticated, powerful, and generally applicable spectroscopic tool that can be used to ascertain the correct structure of newly isolated biogenic molecules. However, accurate structure prediction using computational NMR techniques depends on how much of the relevant conformational space of a particular compound is considered. It is intrinsically challenging to calculate NMR chemical shifts using high-level DFT when the conformational space of a metabolite is extensive. In this work, we developed NMR chemical shift calculation protocols using a machine learning model in conjunction with standard DFT methods. The pipeline encompasses the following steps: (1) conformation generation using a force field (FF)-based method, (2) filtering the FF generated conformations using the ASE-ANI machine learning model, (3) clustering of the optimized conformations based on structural similarity to identify chemically unique conformations, (4) DFT structural optimization of the unique conformations, and (5) DFT NMR chemical shift calculation. This protocol can calculate the NMR chemical shifts of a set of molecules using any available combination of DFT theory, solvent model, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Our protocol reduces the overall computational time by 2 orders of magnitude over methods that optimize the conformations using fully ab initio methods, while still producing good agreement with experimental observations. The complete protocol is designed in such a manner that makes the computation of chemical shifts tractable for a large number of conformationally flexible metabolites.
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Affiliation(s)
- Susanta Das
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA
| | - Arthur S. Edison
- Departments of Genetics and Biochemistry, Institute of Bioinformatics and Complex Carbohydrate Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, USA
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Fu Y, Schneider J. Towards Knowledge Maintenance in Scientific Digital Libraries with the Keystone Framework. PROCEEDINGS OF THE ... ACM/IEEE JOINT CONFERENCE ON DIGITAL LIBRARIES. ACM/IEEE JOINT CONFERENCE ON DIGITAL LIBRARIES 2020; 2020:217-226. [PMID: 34305485 PMCID: PMC8300994 DOI: 10.1145/3383583.3398514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Scientific digital libraries speed dissemination of scientific publications, but also the propagation of invalid or unreliable knowledge. Although many papers with known validity problems are highly cited, no auditing process is currently available to determine whether a citing paper's findings fundamentally depend on invalid or unreliable knowledge. To address this, we introduce a new framework, the keystone framework, designed to identify when and how citing unreliable findings impacts a paper, using argumentation theory and citation context analysis. Through two pilot case studies, we demonstrate how the keystone framework can be applied to knowledge maintenance tasks for digital libraries, including addressing citations of a non-reproducible paper and identifying statements most needing validation in a high-impact paper. We identify roles for librarians, database maintainers, knowledgebase curators, and research software engineers in applying the framework to scientific digital libraries.
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Affiliation(s)
- Yuanxi Fu
- School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, IL USA
| | - Jodi Schneider
- School of Information Sciences, University of Illinois at Urbana-Champaign, Champaign, IL USA
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Marcarino MO, Zanardi MM, Sarotti AM. The Risks of Automation: A Study on DFT Energy Miscalculations and Its Consequences in NMR-based Structural Elucidation. Org Lett 2020; 22:3561-3565. [DOI: 10.1021/acs.orglett.0c01001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Maribel O. Marcarino
- Instituto de Quı́mica Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, República Argentina
| | - María M. Zanardi
- Facultad de Quı́mica e Ingenierı́a del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Quı́mica Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, República Argentina
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23
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Gygli G, Pleiss J. Simulation Foundry: Automated and F.A.I.R. Molecular Modeling. J Chem Inf Model 2020; 60:1922-1927. [DOI: 10.1021/acs.jcim.0c00018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gudrun Gygli
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Juergen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Liu Y, Holt TA, Kutateladze A, Newhouse TR. Stereochemical revision of xylogranatin F by GIAO and DU8+ NMR calculations. Chirality 2020; 32:515-523. [PMID: 32125044 DOI: 10.1002/chir.23189] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 02/06/2023]
Abstract
This manuscript describes predicted NMR shifts for the limonoid natural product xylogranatin F. The 1 H and 13 C NMR shifts of four diastereomers were evaluated by GIAO and hybrid DFT/parametric DU8+ methods. The results of the 1 H and 13 C NMR calculations for both the GIAO method and the DU8+ calculations suggest the revised structure that was recently reassigned by chemical synthesis. Furthermore, we show that while DU8+ provides superior accuracy with less computation time, GIAO points to the correct structure with more distinguishable data in this case study.
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Affiliation(s)
- Yannan Liu
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Tina A Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Andrei Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
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Zanardi MM, Marcarino MO, Sarotti AM. Redefining the Impact of Boltzmann Analysis in the Stereochemical Assignment of Polar and Flexible Molecules by NMR Calculations. Org Lett 2019; 22:52-56. [DOI: 10.1021/acs.orglett.9b03866] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- María M. Zanardi
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Maribel O. Marcarino
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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