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Epimeric Mixture Analysis and Absolute Configuration Determination Using an Integrated Spectroscopic and Computational Approach-A Case Study of Two Epimers of 6-Hydroxyhippeastidine. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010214. [PMID: 36615407 PMCID: PMC9822407 DOI: 10.3390/molecules28010214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/26/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Structural elucidation has always been challenging, and misassignment remains a stringent issue in the field of natural products. The growing interest in discovering unknown, complex natural structures accompanies the increasing awareness concerning misassignments in the community. The combination of various spectroscopic methods with molecular modeling has gained popularity in recent years. In this work, we demonstrated, for the first time, its power to fully elucidate the 2-dimensional and 3-dimensional structures of two epimers in an epimeric mixture of 6-hydroxyhippeastidine. DFT calculation of chemical shifts was first performed to assist the assignment of planar structures. Furthermore, relative and absolute configurations were established by three different ways of computer-assisted structure elucidation (CASE) coupled with ORD/ECD/VCD spectroscopies. In addition, the significant added value of OR/ORD computations to relative and absolute configuration determination was also revealed. Remarkably, the differentiation of two enantiomeric scaffolds (crinine and haemanthamine) was accomplished via OR/ORD calculations with cross-validation by ECD and VCD.
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2
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Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
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Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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3
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Li J, Tan YF, Liu S, Wu XQ, Wang J, Xu KP, Tan GS, Zou ZX, Wang WX. Reassignment of the structures of pestalopyrones A-D. PHYTOCHEMISTRY 2022; 200:113205. [PMID: 35436477 DOI: 10.1016/j.phytochem.2022.113205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/10/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Pestalopyrones A-D are four unusual tricyclic pyrone derivatives with flexible chiral structures, isolated from the endophytic fungus Pestalotiopsis neglecta S3. The full elucidation of their structures was a challenging task, and remained unsolved in the original article. Herein, the relative configurations of pestalopyrones A and pestalopyrones B were unambiguously assigned by detailed analyses on spectroscopic data and GIAO 13C NMR calculation method with sorted training sets (STS). The planar structures of pestalopyrones C and pestalopyrones D were revised by reinterpretation of their reported spectroscopic data, and then their relative configurations were deduced by STS GIAO 13C NMR calculation and NOE analysis. The absolute configurations of all the mentioned compounds were determined by the comparison of their experimental and calculated ECD curves.
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Affiliation(s)
- Jing Li
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Yu-Fen Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Xiao-Qian Wu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Jing Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Kang-Ping Xu
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Gui-Shan Tan
- Department of Pharmacy, Xiangya Hospital, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, PR China
| | - Zhen-Xing Zou
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, PR China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410008, PR China.
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4
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Hwang TL, Yang N, Cheng G, Chen Y, Cui S. Application of 1D 15 N and band-selective 2D 1 H- 15 N CLIP-HSQMBC to detect 35/37 Cl isotope effect on nitrogen for unequivocal structure elucidation of the N-Cl moiety in molecules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:157-164. [PMID: 34376016 DOI: 10.1002/mrc.5204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 08/04/2021] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
Abstract
An impurity, designated MS204, was isolated from a scale-up production of an intermediate toward the synthesis of an active pharmaceutical ingredient. Structural elucidation of this chloro-containing impurity was performed based on the analysis of the MS and NMR data. Band-selective 2D 1 H-15 N CLIP-HSQMBC experiment was developed to unequivocally identify the ionic N-Cl moiety in the molecule by discovering the two isotope-shifted nitrogen peaks as 3 to 1 ratio separated by about 1 Δ15 N(37/35 Cl) = 19.6 ppb (1.19 Hz) due to the Cl isotope effect. 1D 15 N and 2D 1 H-15 N CLIP-HSQMBC experiments were applied to commercially available compounds to further confirm the techniques by detecting the isotope shift of nitrogen peaks for the N-Cl moiety in molecules.
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Affiliation(s)
| | - Ning Yang
- Attribute Sciences, Amgen Inc., Thousand Oaks, CA, USA
| | - Guilong Cheng
- Attribute Sciences, Amgen Inc., Thousand Oaks, CA, USA
- Department of Analytical Development and QC, Foghorn Therapeutics, Cambridge, MA, USA
| | - Ying Chen
- Drug Substance Technologies, Amgen Inc., Thousand Oaks, CA, USA
- Chemical Development, CMC, Neurocrine Biosciences, San Diego, CA, USA
| | - Sheng Cui
- Drug Substance Technologies, Amgen Inc., Thousand Oaks, CA, USA
- CMC, New Amsterdam Pharma, Miami, FL, USA
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5
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6
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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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7
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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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8
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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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Costa FLP, de Albuquerque ACF, Fiorot RG, Lião LM, Martorano LH, Mota GVS, Valverde AL, Carneiro JWM, dos Santos Junior FM. Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights. Org Chem Front 2021. [DOI: 10.1039/d1qo00034a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.
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Affiliation(s)
| | - Ana C. F. de Albuquerque
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Rodolfo G. Fiorot
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Luciano M. Lião
- Instituto de Química
- Universidade Federal de Goiás
- 74690-900 Goiânia-GO
- Brazil
| | - Lucas H. Martorano
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Gunar V. S. Mota
- Faculdade de Ciências Naturais/Instituto de Ciências Exatas e Naturais
- Universidade Federal do Pará
- Belém-PA
- Brazil
| | - Alessandra L. Valverde
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - José W. M. Carneiro
- Departamento de Química Inorgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
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10
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Li J, Liu JK, Wang WX. GIAO 13C NMR Calculation with Sorted Training Sets Improves Accuracy and Reliability for Structural Assignation. J Org Chem 2020; 85:11350-11358. [DOI: 10.1021/acs.joc.0c01451] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jing Li
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410083, PR China
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, Hubei 430074, PR China
| | - Wen-Xuan Wang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410083, PR China
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