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Cohen RD, Wood JS, Lam YH, Buevich AV, Sherer EC, Reibarkh M, Williamson RT, Martin GE. DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking. Molecules 2023; 28:molecules28062449. [PMID: 36985422 PMCID: PMC10051451 DOI: 10.3390/molecules28062449] [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: 01/25/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Density functional theory (DFT) benchmark studies of 1H and 13C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured 1H and 13C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for 1H and 13C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Maximum deviations were less than 0.5 and 6.5 ppm for 1H and 13C, respectively.
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Affiliation(s)
- Ryan D Cohen
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Jared S Wood
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
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2
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Semenov VA, Krivdin LB. Computational NMR of natural products. RUSSIAN CHEMICAL REVIEWS 2022. [DOI: 10.1070/rcr5027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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4
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Sánchez‐Andrada P, Marín‐Luna M, Alkorta I, Elguero J, Percho G, Santa María D, Claramunt RM. Conformational analysis of 2,5‐diaryl‐4‐methyl‐2,
4‐dihydro‐3
H
‐1,2,4‐triazol‐3‐ones: Multinuclear
NMR
and
DFT
calculations. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pilar Sánchez‐Andrada
- Departamento de Química Orgánica, Facultad de Química Universidad de Murcia, Regional Campus of International Excellence “Campus Mare Nostrum” Murcia Spain
| | - Marta Marín‐Luna
- Departamento de Química Orgánica, Facultad de Química Universidad de Murcia, Regional Campus of International Excellence “Campus Mare Nostrum” Murcia Spain
| | | | | | - Gema Percho
- Departamento de Química Orgánica y Bio‐Orgánica, Facultad de Ciencias UNED Madrid Spain
| | - Dolores Santa María
- Departamento de Química Orgánica y Bio‐Orgánica, Facultad de Ciencias UNED Madrid Spain
| | - Rosa M. Claramunt
- Departamento de Química Orgánica y Bio‐Orgánica, Facultad de Ciencias UNED Madrid Spain
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5
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DFT Calculations of 1H- and 13C-NMR Chemical Shifts of Geometric Isomers of Conjugated Linoleic Acid (18:2 ω-7) and Model Compounds in Solution. Molecules 2020; 25:molecules25163660. [PMID: 32796664 PMCID: PMC7463970 DOI: 10.3390/molecules25163660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
A density functional theory (DFT) study of the 1H- and 13C-NMR chemical shifts of the geometric isomers of 18:2 ω-7 conjugated linoleic acid (CLA) and nine model compounds is presented, using five functionals and two basis sets. The results are compared with available experimental data from solution high resolution nuclear magnetic resonance (NMR). The experimental 1H chemical shifts exhibit highly diagnostic resonances due to the olefinic protons of the conjugated double bonds. The "inside" olefinic protons of the conjugated double bonds are deshielded than those of the "outside" protons. Furthermore, in the cis/trans isomers, the signals of the cis bonds are more deshielded than those of the trans bonds. These regularities of the experimental 1H chemical shifts of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest energy DFT optimized single conformer, for all functionals and basis sets used. The other low energy conformers have negligible effects on the computational 1H-NMR chemical shifts. We conclude that proton NMR chemical shifts are more discriminating than carbon, and DFT calculations can provide a valuable tool for (i) the accurate prediction of 1H-NMR chemical shifts even with less demanding functionals and basis sets; (ii) the unequivocal identification of geometric isomerism of CLAs that occur in nature, and (iii) to derive high resolution structures in solution.
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Liu Y, Su L, Fang Q, Tabudravu J, Yang X, Rickaby K, Trembleau L, Kyeremeh K, Deng Z, Deng H, Yu Y. Enzymatic Reconstitution and Biosynthetic Investigation of the Bacterial Carbazole Neocarazostatin A. J Org Chem 2019; 84:16323-16328. [PMID: 31729221 DOI: 10.1021/acs.joc.9b02688] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tricyclic carbazole is an important scaffold in many naturally occurring metabolites, as well as valuable building blocks. Here we report the reconstitution of the ring A formation of the bacterial neocarazostatin A carbazole metabolite. We provide evidence of the involvement of two unusual aromatic polyketide proteins. This finding suggests how new enzymatic activities can be recruited to specific pathways to expand biosynthetic capacities. Finally, we leveraged our bioinformatics survey to identify the untapped capacity of carbazole biosynthesis.
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Affiliation(s)
- Yating Liu
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences , Wuhan University , 185 East Lake Road , Wuhan 430071 , People's Republic of China
| | - Li Su
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences , Wuhan University , 185 East Lake Road , Wuhan 430071 , People's Republic of China
| | - Qing Fang
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen , Scotland AB24 3UE , United Kingdom
| | - Jioji Tabudravu
- School of Forensic & Applied Sciences, Faculty of Science & Technology , University of Central Lancashire , Preston , Lancashire , England PR1 2HE , United Kingdom
| | - Xiaohui Yang
- School of Chemistry , Xiamen University , Xiamen 361005 , People's Republic of China
| | - Kirstie Rickaby
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen , Scotland AB24 3UE , United Kingdom
| | - Laurent Trembleau
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen , Scotland AB24 3UE , United Kingdom
| | - Kwaku Kyeremeh
- Department of Chemistry , University of Ghana , P.O. Box LG56, Legon-Accra , Ghana
| | - Zixin Deng
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences , Wuhan University , 185 East Lake Road , Wuhan 430071 , People's Republic of China
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen , Scotland AB24 3UE , United Kingdom
| | - Yi Yu
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences , Wuhan University , 185 East Lake Road , Wuhan 430071 , People's Republic of China
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7
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Tantillo DJ. Questions in natural products synthesis research that can (and cannot) be answered using computational chemistry. Chem Soc Rev 2018; 47:7845-7850. [PMID: 29900461 PMCID: PMC6205925 DOI: 10.1039/c8cs00298c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Questions of relevance to those working in the field of natural products synthesis that can be answered, at least in part, using computational chemistry approaches are described. Illustrative examples are provided, as are descriptions of limitations.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California - Davis, Davis, CA 95616, USA.
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8
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Iron MA. Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions using Density Functional Theory-The Advantage of Long-Range Corrected Functionals. J Chem Theory Comput 2017; 13:5798-5819. [PMID: 29016125 DOI: 10.1021/acs.jctc.7b00772] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The various factors influencing the accuracy of 13C NMR calculations using density functional theory (DFT), including the basis set, exchange-correlation (XC) functional, and isotropic shielding calculation method, are evaluated. A wide selection of XC functionals (over 70) were considered, and it was found that long-range corrected functionals offer a significant improvement over the other classes of functionals. Based on a thorough study, it is recommended that for calculating NMR chemical shifts (δ) one should use the CSGT method, the COSMO solvation model, and the LC-TPSSTPSS exchange-correlation functional in conjunction with the cc-pVTZ basis set. A selection of problems in natural product identification are considered in light of the newly recommended level of theory.
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Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 7610001, Israel
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9
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Gaudêncio SP, Pereira F. Dereplication: racing to speed up the natural products discovery process. Nat Prod Rep 2015; 32:779-810. [PMID: 25850681 DOI: 10.1039/c4np00134f] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 1993-2014 (July)To alleviate the dereplication holdup, which is a major bottleneck in natural products discovery, scientists have been conducting their research efforts to add tools to their "bag of tricks" aiming to achieve faster, more accurate and efficient ways to accelerate the pace of the drug discovery process. Consequently dereplication has become a hot topic presenting a huge publication boom since 2012, blending multidisciplinary fields in new ways that provide important conceptual and/or methodological advances, opening up pioneering research prospects in this field.
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Affiliation(s)
- Susana P Gaudêncio
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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10
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Mak JYW, Pouwer RH, Williams CM. Naturstoffe mit Anti-Bredt- und Brückenkopf-Doppelbindung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400932] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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11
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Mak JYW, Pouwer RH, Williams CM. Natural products with anti-Bredt and bridgehead double bonds. Angew Chem Int Ed Engl 2014; 53:13664-88. [PMID: 25399486 DOI: 10.1002/anie.201400932] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/25/2014] [Indexed: 11/11/2022]
Abstract
Well over a hundred years ago, Professor Julius Bredt embarked on a career pursuing and critiquing bridged bicyclic systems that contained ring strain induced by the presence of a bridgehead olefin. These endeavors founded what we now know as Bredt's rule (Bredtsche Regel). Physical, theoretical, and synthetic organic chemists have intensely studied this premise, pushing the boundaries of such systems to arrive at a better understood physical phenomenon. Mother nature has also seen fit to construct molecules containing bridgehead double bonds that encompass Bredt's rule. For the first time, this topic is reviewed in a natural product context.
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Affiliation(s)
- Jeffrey Y W Mak
- Institute for Molecular Bioscience, The University of Queensland, Brisbane (Australia)
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12
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Plainchont B, de Paulo Emerenciano V, Nuzillard JM. Recent advances in the structure elucidation of small organic molecules by the LSD software. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:447-53. [PMID: 23749440 DOI: 10.1002/mrc.3965] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/08/2013] [Accepted: 04/15/2013] [Indexed: 05/22/2023]
Abstract
The LSD software proposes the structures of small organic molecules that fit with structural constraints from 1D and 2D NMR spectroscopy. Its initial design introduced limits that needed to be eliminated to extend its scope and help its users choose the most likely structure among those proposed. The LSD software code has been improved, so that it recognizes a wider set of atom types to build molecules. More flexibility has been given in the interpretation of 2D NMR data, including the automatic detection of very long-range correlations. A program named pyLSD was written to deal with problems in which atom types are ambiguously defined. It also provides a (13)C NMR chemical shift-based solution ranking algorithm. PyLSD was able to propose the correct structure of hexacyclinol, a natural product whose structure determination has been highly controversal. The solution was ranked first within a list of ten structures that were produced by pyLSD from the literature NMR data. The structure of an aporphin natural product was determined by pyLSD, taking advantage of the possibility of handling electrically charged atoms. The structure generation of the insect antifeedant azadirachtin by LSD was reinvestigated by pyLSD, considering that three (13)C resonances did not lead to univocal hybridization states.
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Affiliation(s)
- Bertrand Plainchont
- Institut de Chimie Moléculaire de Reims, CNRS UMR 7312, Université de Reims-Champagne-Ardenne, BP 1039, 51687 REIMS Cedex 2, France
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Abstract
Over the past 28 years there have been several thousand publications describing the use of 2D NMR to identify and characterize natural products. During this time period, the amount of sample needed for this purpose has decreased from the 20-50 mg range to under 1 mg. This has been due to both improvements in NMR hardware and methodology. This review will focus on mainly methodology improvements, particularly in pulse sequences, acquisition and processing methods which are particularly relevant to natural product research, with lesser discussion of hardware improvements.
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Elyashberg M, Blinov K, Molodtsov S, Williams AJ. Structure revision of asperjinone using computer-assisted structure elucidation methods. JOURNAL OF NATURAL PRODUCTS 2013; 76:113-116. [PMID: 23289877 DOI: 10.1021/np300218g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The elucidated structure of asperjinone (1), a natural product isolated from thermophilic Aspergillus terreus, was revised using the expert system Structure Elucidator. The reliability of the revised structure (2) was confirmed using 180 structures containing the (3,3-dimethyloxiran-2-yl)methyl fragment (3) as a basis for comparison and whose chemical shifts contradict the suggested structure (1).
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Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development, Moscow Department, 6 Akademik Bakulev Street, Moscow 117513, Russian Federation
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15
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Lodewyk MW, Siebert MR, Tantillo DJ. Computational prediction of 1H and 13C chemical shifts: a useful tool for natural product, mechanistic, and synthetic organic chemistry. Chem Rev 2011; 112:1839-62. [PMID: 22091891 DOI: 10.1021/cr200106v] [Citation(s) in RCA: 897] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michael W Lodewyk
- Department of Chemistry, University of California-Davis, Davis, California 95616, USA
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16
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Lodewyk MW, Tantillo DJ. Prediction of the structure of nobilisitine a using computed NMR chemical shifts. JOURNAL OF NATURAL PRODUCTS 2011; 74:1339-1343. [PMID: 21469691 DOI: 10.1021/np2000446] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
1H and 13C NMR computed chemical shifts are determined for eight diastereomers of the originally proposed structure of nobilisitine A, which has recently been shown to be incorrect. On the basis of comparison of the computed chemical shifts with those reported experimentally, we predict that the true structure of nobilisitine A is likely the diastereomer shown here or its enantiomer.
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Affiliation(s)
- Michael W Lodewyk
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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17
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Elyashberg M, Williams AJ, Blinov K. Structural revisions of natural products by Computer-Assisted Structure Elucidation (CASE) systems. Nat Prod Rep 2010; 27:1296-328. [DOI: 10.1039/c002332a] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Elyashberg M, Blinov K, Williams A. A systematic approach for the generation and verification of structural hypotheses. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:371-389. [PMID: 19197914 DOI: 10.1002/mrc.2397] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
During the process of molecular structure elucidation the selection of the most probable structural hypothesis may be based on chemical shift prediction. The prediction is carried out using either empirical or quantum-mechanical (QM) methods. When QM methods are used, NMR prediction commonly utilizes the GIAO option of the DFT approximation. In this approach the structural hypotheses are expected to be investigated by scientist. In this article we hope to show that the most rational manner by which to create structural hypotheses is actually by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data and specifically using 2D NMR data. When an expert system is used the best structure(s) can be distinguished using chemical shift prediction, which is best performed either by an incremental or neural net algorithm. The time-consuming QM calculations can then be applied, if necessary, to one or more of the 'best' structures to confirm the suggested solution.
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Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development, Moscow Department, 6 Akademik Bakulev Street, Moscow 117513, Russian Federation
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19
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Elyashberg M, Blinov K, Molodtsov S, Smurnyy Y, Williams AJ, Churanova T. Computer-assisted methods for molecular structure elucidation: realizing a spectroscopist's dream. J Cheminform 2009; 1:3. [PMID: 20142986 PMCID: PMC2816863 DOI: 10.1186/1758-2946-1-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 03/17/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be described using, as an example, the expert system Structure Elucidator. RESULTS The developers of CASE systems have been forced to overcome many obstacles hindering the development of a software application capable of drastically reducing the time and effort required to determine the structures of newly isolated organic compounds. Large complex molecules of up to 100 or more skeletal atoms with topological peculiarity can be quickly identified using the expert system Structure Elucidator based on spectral data. Logical analysis of 2D NMR data frequently allows for the detection of the presence of COSY and HMBC correlations of "nonstandard" length. Fuzzy structure generation provides a possibility to obtain the correct solution even in those cases when an unknown number of nonstandard correlations of unknown length are present in the spectra. The relative stereochemistry of big rigid molecules containing many stereocenters can be determined using the StrucEluc system and NOESY/ROESY 2D NMR data for this purpose. CONCLUSION The StrucEluc system continues to be developed in order to expand the general applicability, provide improved workflows, usability of the system and increased reliability of the results. It is expected that expert systems similar to that described in this paper will receive increasing acceptance in the next decade and will ultimately be integrated directly to analytical instruments for the purpose of organic analysis. Work in this direction is in progress. In spite of the fact that many difficulties have already been overcome to deliver on the spectroscopist's dream of "fully automated structure elucidation" there is still work to do. Nevertheless, as the efficiency of expert systems is enhanced the solution of increasingly complex structural problems will be achievable.
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Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development, Moscow Department, 6 Akademik Bakulev Street, Moscow 117513, Russian Federation
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20
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Saielli G, Bagno A. Can Two Molecules Have the Same NMR Spectrum? Hexacyclinol Revisited. Org Lett 2009; 11:1409-12. [DOI: 10.1021/ol900164a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giacomo Saielli
- Istituto CNR per la Tecnologia delle Membrane, Sezione di Padova, and Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova (Italy)
| | - Alessandro Bagno
- Istituto CNR per la Tecnologia delle Membrane, Sezione di Padova, and Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova (Italy)
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21
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Shaw JT. Naturally diverse: highlights in versatile synthetic methods enabling target- and diversity-oriented synthesis. Nat Prod Rep 2009; 26:11-26. [DOI: 10.1039/b814468k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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