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Bizzo HR, Brilhante NS, Nolvachai Y, Marriott PJ. Use and abuse of retention indices in gas chromatography. J Chromatogr A 2023; 1708:464376. [PMID: 37717451 DOI: 10.1016/j.chroma.2023.464376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
The value of the concept of retention indices (RI) to the practice of gas chromatography (GC) is highlighted, where the RI of a compound is one component of the strategy to identify the compound. The widespread reliance on GC and then on mass spectrometry for 'identification', may result in inadequate confirmation of molecular identity. However, RI do provide a useful tentative indication of the possible molecule(s). Thus, the RI value is a useful first measure of the molecule identity, and shown here to be valuable provided limitations are recognised. An author has a responsibility to correctly calculate the index and then use the values for (tentative) identification. Tables of reference RI values are useful in this respect, but finding an 'exact match' RI value does not confirm the identity. Hence, it is necessary to understand how the RI value may be incorrectly used in this respect. The reviewer of written research is charged with ensuring the index values are applied in a rigorous manner. Selected case studies from our own work, support the care that must be exercised when reporting RI values. In terms of advanced GC operations, mention is made of multidimensional gas chromatography and comprehensive two-dimensional gas chromatography to acquire RI values on both the first and second columns in the two-column separation experiment.
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Affiliation(s)
- Humberto R Bizzo
- Embrapa Agroindústria de Alimentos - Avenida das Américas, 29501, Rio de Janeiro, RJ 23020-470, Brazil; Universidade Federal do Rio de Janeiro - Avenida Athos da Silveira Ramos, 149, Rio de Janeiro, RJ 21945-970, Brazil
| | - Nathália S Brilhante
- Universidade Federal do Rio de Janeiro - Avenida Athos da Silveira Ramos, 149, Rio de Janeiro, RJ 21945-970, Brazil
| | - Yada Nolvachai
- CASS Food Research Centre, School of Exercise and Nutritional Sciences, Faculty of Health, Deakin University, Burwood 3125, Victoria, Australia
| | - Philip J Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
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2
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Syntrivanis LD, Némethová I, Schmid D, Levi S, Prescimone A, Bissegger F, Major DT, Tiefenbacher K. Four-Step Access to the Sesquiterpene Natural Product Presilphiperfolan-1β-ol and Unnatural Derivatives via Supramolecular Catalysis. J Am Chem Soc 2020; 142:5894-5900. [DOI: 10.1021/jacs.0c01464] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Ivana Némethová
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Dario Schmid
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shani Levi
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alessandro Prescimone
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Fabian Bissegger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Dan T. Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 24, 4058 Basel, Switzerland
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3
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de Albuquerque ACF, Ribeiro DJ, de Amorim MB. Structural determination of complex natural products by quantum mechanical calculations of (13)C NMR chemical shifts: development of a parameterized protocol for terpenes. J Mol Model 2016; 22:183. [PMID: 27424297 DOI: 10.1007/s00894-016-3045-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 06/20/2016] [Indexed: 11/30/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most important tools for determining the structures of organic molecules. Despite the advances made in this technique, revisions of erroneously established structures for natural products are still commonly published in the literature. In this context, the prediction of chemical shifts through ab initio and density functional theory (DFT) calculations has become a very powerful tool for assisting with the structural determination of complex organic molecules. In this work, we present the development of a protocol for (13)C chemical shift calculations of terpenes, a class of natural products that are widely distributed among plant species and are very important due to their biological and pharmacological activities. This protocol consists of GIAO-DFT calculations of chemical shifts and the application of a parameterized scaling factor in order to ensure accurate structural determination of this class of natural products. The application of this protocol to a set of five terpenes yielded accurate calculated chemical shifts, showing that this is a very attractive tool for the calculation of complex organic structures such as terpenes.
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Affiliation(s)
| | - Daniel Joras Ribeiro
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Mauro Barbosa de Amorim
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.
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4
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Batista Jr. JM, Blanch EW, Bolzani VDS. Recent advances in the use of vibrational chiroptical spectroscopic methods for stereochemical characterization of natural products. Nat Prod Rep 2015; 32:1280-302. [DOI: 10.1039/c5np00027k] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A comprehensive look into application of vibrational optical activity methods for conformational and configurational assignments in natural product molecules over the last 15 years is provided.
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Affiliation(s)
- João M. Batista Jr.
- Department of Chemistry
- Federal University of São Carlos – UFSCar
- São Carlos
- Brazil
| | - Ewan W. Blanch
- School of Applied Sciences
- RMIT University
- Melbourne
- Australia
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5
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Heravi MM, Vavsari VF. Recent applications of intramolecular Diels–Alder reaction in total synthesis of natural products. RSC Adv 2015. [DOI: 10.1039/c5ra08306k] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Diels–Alder (D–A) reaction is undoubtedly the most powerful [4 + 2] cycloaddition reaction in organic synthesis.
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6
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Hong AY, Stoltz BM. Biosynthesis and chemical synthesis of presilphiperfolanol natural products. Angew Chem Int Ed Engl 2014; 53:5248-60. [PMID: 24771653 PMCID: PMC4334158 DOI: 10.1002/anie.201309494] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Indexed: 11/09/2022]
Abstract
Presilphiperfolanols constitute a family of biosynthetically important sesquiterpenes which can rearrange to diverse sesquiterpenoid skeletons. While the origin of these natural products can be traced to simple linear terpene precursors, the details of the enzymatic cyclization mechanism that forms the stereochemically dense tricyclic skeleton has required extensive biochemical, computational, and synthetic investigation. Parallel efforts to prepare the unique and intriguing structures of these compounds by total synthesis have also inspired novel strategies, thus resulting in four synthetic approaches and two completed syntheses. While the biosynthesis and chemical synthesis studies performed to date have provided much insight into the role and properties of these molecules, emerging questions regarding the biosynthesis of newer members of the family and subtle details of rearrangement mechanisms have yet to be explored.
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Affiliation(s)
- Allen Y. Hong
- Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, MC 101-20, Pasadena, CA 91125 (USA)
| | - Brian M. Stoltz
- Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, MC 101-20, Pasadena, CA 91125 (USA)
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7
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Hong AY, Stoltz BM. Biosynthese und chemische Synthese von Presilphiperfolanolen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309494] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Batista JM, da Silva Bolzani V. Determination of the Absolute Configuration of Natural Product Molecules Using Vibrational Circular Dichroism. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63294-4.00013-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Kobayashi T, Shiroi H, Abe H, Ito H. Synthetic Study of Presilphiperfolan-8-ol: Construction of the Tricyclo[5.3.1.04,11]undecane Framework Utilizing Intramolecular Aldol Condensation and McMurry Coupling. CHEM LETT 2013. [DOI: 10.1246/cl.130394] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Hidenori Shiroi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Hideki Abe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Hisanaka Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
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Hong AY, Stoltz BM. Enantioselective total synthesis of the reported structures of (-)-9-epi-presilphiperfolan-1-ol and (-)-presilphiperfolan-1-ol: structural confirmation and reassignment and biosynthetic insights. Angew Chem Int Ed Engl 2012; 51:9674-8. [PMID: 22915502 PMCID: PMC3517068 DOI: 10.1002/anie.201205276] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Allen Y. Hong
- Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd, MC 101-20 Pasadena, CA 91125 (USA)
| | - Brian M. Stoltz
- Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering Division of Chemistry and Chemical Engineering California Institute of Technology 1200 E. California Blvd, MC 101-20 Pasadena, CA 91125 (USA)
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11
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Hong AY, Stoltz BM. Enantioselective Total Synthesis of the Reported Structures of (−)-9-epi-Presilphiperfolan-1-ol and (−)-Presilphiperfolan-1-ol: Structural Confirmation and Reassignment and Biosynthetic Insights. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205276] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Dyson BS, Burton JW, Sohn TI, Kim B, Bae H, Kim D. Total Synthesis and Structure Confirmation of Elatenyne: Success of Computational Methods for NMR Prediction with Highly Flexible Diastereomers. J Am Chem Soc 2012; 134:11781-90. [DOI: 10.1021/ja304554e] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Bryony S. Dyson
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Jonathan W. Burton
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Te-ik Sohn
- The Research Institute of Pharmaceutical
Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Byungsook Kim
- The Research Institute of Pharmaceutical
Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Hoon Bae
- The Research Institute of Pharmaceutical
Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Deukjoon Kim
- The Research Institute of Pharmaceutical
Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
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13
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Muñoz MA, Urzúa A, Echeverría J, Modak B, Joseph-Nathan P. Solid State Structure and Absolute Configuration of Filifolinol Acetate. Nat Prod Commun 2011. [DOI: 10.1177/1934578x1100600604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Careful reevaluation of the 1H and 13C NMR spectroscopic data of filifolinol acetate (4) led to the reassignment of the C-10 and C-11 signals, as well as the gem-dimethyl signals. Single crystal X-ray analysis provided an independent structural confirmation of 4, and comparison of the experimental vibrational circular dichroism spectrum with calculations performed using density functional theory provided the absolute configuration of this 3H-spiro-1-benzofuran-2,1′-cyclohexane and related molecules.
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Affiliation(s)
- Marcelo A. Muñoz
- Instituto de Ciéncias Químicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Alejandro Urzúa
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Javier Echeverría
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Brenda Modak
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México, D. F., 07000 México
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14
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Smith SG, Goodman JM. Assigning stereochemistry to single diastereoisomers by GIAO NMR calculation: the DP4 probability. J Am Chem Soc 2011; 132:12946-59. [PMID: 20795713 DOI: 10.1021/ja105035r] [Citation(s) in RCA: 604] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
GIAO NMR shift calculation has been applied to the challenging task of reliably assigning stereochemistry with quantifiable confidence when only one set of experimental data are available. We have compared several approaches for assigning a probability to each candidate structure and have tested the ability of these methods to distinguish up to 64 possible diastereoisomers of 117 different molecules, using NMR shifts obtained in rapid and computationally inexpensive single-point calculations on molecular mechanics geometries without time-consuming ab initio geometry optimization. We show that a probability analysis based on the errors in each (13)C or (1)H shift is significantly more successful at making correct assignments with high confidence than are probabilities based on the correlation coefficient and mean absolute error parameters. Our new probability measure, which we have termed DP4, complements the probabilities obtained from our previously developed CP3 parameter, which applies to the case of assigning a pair of diastereoisomers when one has both experimental data sets. We illustrate the application of DP4 to assigning the stereochemistry or structure of 21 natural products that were originally misassigned in the literature or that required extensive synthesis of diastereoisomers to establish their stereochemistry.
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Affiliation(s)
- Steven G Smith
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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15
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16
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Costa FLP, de Albuquerque ACF, dos Santos FM, de Amorim MB. GIAO-HDFT scaling factor for 13
C NMR chemical shifts calculation. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1749] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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