1
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Hansen PE. The Synergy between Nuclear Magnetic Resonance and Density Functional Theory Calculations. Molecules 2024; 29:336. [PMID: 38257249 PMCID: PMC10821511 DOI: 10.3390/molecules29020336] [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: 12/23/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
This paper deals with the synergy between Nuclear Magnetic Resonance (NMR) spectroscopic investigations and DFT calculations, mainly of NMR parameters. Both the liquid and the solid states are discussed here. This text is a mix of published results supplemented with new findings. This paper deals with examples in which useful results could not have been obtained without combining NMR measurements and DFT calculations. Examples of such cases are tautomeric systems in which NMR data are calculated for the tautomers; hydrogen-bonded systems in which better XH bond lengths can be determined; cage compounds for which assignment cannot be made based on NMR data alone; revison of already published structures; ionic compounds for which reference data are not available; assignment of solid-state spectra and crystal forms; and the creation of libraries for biological molecules. In addition to these literature cases, a revision of a cage structure and substituent effects on pyrroles is also discussed.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark
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2
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Palafox MA, Belskaya NP, Kostova IP. Study of the Molecular Architectures of 2-(4-Chlorophenyl)-5-(pyrrolidin-1-yl)-2 H-1,2,3-triazole-4-carboxylic Acid Using Their Vibrational Spectra, Quantum Chemical Calculations and Molecular Docking with MMP-2 Receptor. Pharmaceutics 2023; 15:2686. [PMID: 38140027 PMCID: PMC10747663 DOI: 10.3390/pharmaceutics15122686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
1,2,3-triazole skeleton is a valuable building block for the discovery of new promising anticancer agents. In the present work, the molecular structure of the synthesized anticancer drug 2-(4-chlorophenyl)-5-(pyrrolidin-1-yl)-2H-1,2,3-triazole-4-carboxylic acid (1b) and its anionic form (2b) was characterized by means of the B3LYP, M06-2X and MP2 quantum chemical methods, optimizing their monomer, cyclic dimer and stacking forms using the Gaussian16 program package. The molecular structure was found to be slightly out of plane. The good agreement between the IR and Raman bands experimentally observed in the solid state with those calculated theoretically confirms the synthesized structures. All of the bands were accurately assigned according to functional calculations (DFT) in the monomer and dimer forms, together with the polynomic scaling equation procedure (PSE). Therefore, the effect of the substituents on the triazole ring and the effect of the chlorine atom on the molecular structure and on the vibrational spectra were evaluated through comparison with its non-substituted form. Through molecular docking calculations, it was evaluated as to how molecule 1b interacts with few amino acids of the MMP-2 metalloproteinase receptor, using Sybyl-X 2.0 software. Thus, the relevance of triazole scaffolds in established hydrogen bond-type interactions was demonstrated.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Nataliya P. Belskaya
- Department of Technology for Organic Synthesis, Ural Federal University, 19 Mira Str., 620012 Yekaterinburg, Russia;
| | - Irena P. Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
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3
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Safronov NE, Kostova IP, Palafox MA, Belskaya NP. Combined NMR Spectroscopy and Quantum-Chemical Calculations in Fluorescent 1,2,3-Triazole-4-carboxylic Acids Fine Structures Analysis. Int J Mol Sci 2023; 24:ijms24108947. [PMID: 37240293 DOI: 10.3390/ijms24108947] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
The peculiarities of the optical properties of 2-aryl-1,2,3-triazole acids and their sodium salts were investigated in different solvents (1,4-dioxane, dimethyl sulfoxide DMSO, methanol MeOH) and in mixtures with water. The results were discussed in terms of the molecular structure formed by inter- and intramolecular noncovalent interactions (NCIs) and their ability to ionize in anions. Theoretical calculations using the Time-Dependent Density Functional Theory (TDDFT) were carried out in different solvents to support the results. In polar and nonpolar solvents (DMSO, 1,4-dioxane), fluorescence was provided by strong neutral associates. Protic MeOH can weaken the acid molecules' association, forming other fluorescent species. The fluorescent species in water exhibited similar optical characteristics to those of triazole salts; therefore, their anionic character can be assumed. Experimental 1H and 13C-NMR spectra were compared to their corresponding calculated spectra using the Gauge-Independent Atomic Orbital (GIAO) method and several relationships were established. All these findings showed that the obtained photophysical properties of the 2-aryl-1,2,3-triazole acids noticeably depend on the environment and, therefore, are good candidates as sensors for the identification of analytes with labile protons.
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Affiliation(s)
- Nikita E Safronov
- Department of Technology for Organic Synthesis, Ural Federal University, 19 Mira Str., Yekaterinburg 620002, Russia
| | - Irena P Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University-Sofia, 2 Dunav Str., 1000 Sofia, Bulgaria
| | - Mauricio Alcolea Palafox
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Nataliya P Belskaya
- Department of Technology for Organic Synthesis, Ural Federal University, 19 Mira Str., Yekaterinburg 620002, Russia
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4
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Kojasoy V, Tantillo DJ. Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I. J Phys Chem A 2023; 127:2081-2090. [PMID: 36855831 DOI: 10.1021/acs.jpca.2c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
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5
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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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6
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Theoretical study of keto-enol tautomerism in 7-epi-clusianone by quantum chemical calculations of NMR chemical shifts. J Mol Model 2022; 28:239. [PMID: 35908141 DOI: 10.1007/s00894-022-05234-4] [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: 03/07/2022] [Accepted: 07/14/2022] [Indexed: 10/16/2022]
Abstract
Plants from the Garcinia genus have been used worldwide due to their therapeutic properties. Among the various metabolites isolated from this genus, 7-epi-clusianone, a tetraprenylated benzophenone, stands out for its wide range of identified biological activities. This benzophenone can exist in five tautomeric forms, although the benzene-d6 and chloroform-d3 solution nuclear magnetic resonance (NMR) spectra revealed only two tautomeric forms (B and C) in equilibrium, with concentration ratio depending on the solvent in which the spectrum was obtained. Calculated energy values suggested that tautomeric forms B and E would be prevalent in benzene-d6 solution, in contrast to the experimental data. Considering this conflicting result, we employed the statistical DP4 + method based on 13C and 1H NMR chemical shift calculations, in the gas phase and in benzene-d6 solution, to confirm that the B and C tautomeric forms of 7-epi-clusianone are the most prevalent in the experimental conditions.
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7
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New Techniques of Structure Elucidation for Sesquiterpenes. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2021; 114:253-311. [PMID: 33792862 DOI: 10.1007/978-3-030-59444-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The most significant new techniques that have been used in the twenty-first century for the structure elucidation of sesquiterpenes and some derivatives are reviewed in this chapter. A distinctive feature of these methodologies is the combination of accurate experimental measurements with theoretical data obtained by molecular modeling calculations that allow to visualize, understand, and quantify many structural characteristics. This has been the case for NMR spectroscopy, which has expanded its potential for solving complex structural problems by means of comparison with quantum mechanical molecular models. Ab initio and density functional theory calculations of chemical shifts, coupling constants, and residual chemical shift anisotropies have played important roles in the solution of many structures of sesquiterpenes. The assignments of their absolute configurations by evaluation of calculated and experimental chiroptical properties as electronic and vibrational circular dichroism are also reviewed. This chapter also includes the use of X-ray diffraction analysis with emphasis on calculations of the Flack and Hooft parameters, which are applicable to all molecules that crystallize in non-centrosymmetric space groups. The accurate molecular models of sesquiterpenes, validated by concordance with their experimental properties, are nowadays essential for the interpretation of the effects of these natural products on biological systems.
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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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9
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Martorano LH, Valverde AL, Ribeiro CMR, de Albuquerque ACF, Carneiro JWDM, Fiorot RG, M. dos Santos Junior F. Unraveling the helianane family: a complementary quantum mechanical study. NEW J CHEM 2020. [DOI: 10.1039/d0nj01396j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comprehensive work suggesting the amendment of helianane to the open ring curcudiol by means of computational spectroscopy and thermodynamic reasons.
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Affiliation(s)
- Lucas H. Martorano
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Alessandra L. Valverde
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Carlos Magno R. Ribeiro
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | | | - José Walkimar de M. Carneiro
- Department of Inorganic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Rodolfo G. Fiorot
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
| | - Fernando M. dos Santos Junior
- Department of Organic Chemistry
- Chemistry Institute
- Fluminense Federal University (UFF)
- Outeiro de São João Batista
- Niterói
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10
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Transformed Root Culture: From Genetic Transformation to NMR-Based Metabolomics. Methods Mol Biol 2018. [PMID: 29981142 DOI: 10.1007/978-1-4939-8594-4_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Hairy root (HR) culture is considered as "green factory" for mass production of bioactive molecules with pharmaceutical relevance. As such, HR culture has an immense potential as a valuable platform to elucidate biosynthetic pathways and physiological processes, generate recombinant therapeutic proteins, assist molecular breeding, and enhance phytoremediation efforts. However, some plant species appear recalcitrant to the classical Agrobacterium rhizogenes transformation techniques. Sonication-assisted Agrobacterium-mediated transformation (SAArT) is a highly effective method to deliver bacteria to target plant tissues that includes exposure of the explants to short periods of ultrasound in the presence of the bacteria.Nuclear magnetic resonance (NMR)-based metabolomics is one of the most powerful and suitable platforms for identifying and obtaining structural information on a wide range of compounds with a high analytical precision. In terms of plant science, NMR metabolomics is used to determine the phytochemical variations of medicinal plants or commercial cultivars in certain environments and conditions, including biotic stress and plant biotic interaction, structural determination of natural products, quality control of herbal drugs or dietary supplements, and comparison of metabolite differences between plants and their respective in vitro cultures.In this chapter, we attempt to summarize our knowledge and expertise in induction of hairy roots from rare and recalcitrant plant species by SAArT technique and further methodology for extraction of secondary metabolites of moderate to high polarity and their identification by using NMR-based metabolomics.
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11
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Saunders C, Khaled MB, Weaver JD, Tantillo DJ. Prediction of 19F NMR Chemical Shifts for Fluorinated Aromatic Compounds. J Org Chem 2018; 83:3220-3225. [PMID: 29470063 DOI: 10.1021/acs.joc.8b00104] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Scaling factors are reported for use in predicting 19F NMR chemical shifts for fluorinated (hetero)aromatic compounds with relatively low levels of theory. Our recommended scaling factors were developed using a curated data set of 52 compounds, with 100 individual 19F shifts spanning a range of 153 ppm. With a maximum deviation of 6.5 ppm between experimental and computed shifts, or 4% of the range tested, these scaling factors allow for the assignment of chemical shifts to specific fluorines in multifluorinated aromatics. The utility of this approach is highlighted by several structural reassignments.
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Affiliation(s)
- Carla Saunders
- Department of Chemistry , University of California-Davis , Davis , California 95616 , United States
| | - Mohammad B Khaled
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Jimmie D Weaver
- Department of Chemistry , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Dean J Tantillo
- Department of Chemistry , University of California-Davis , Davis , California 95616 , United States
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Abstract
Natural products (NPs) have been used as traditional medicines since antiquity. With more than 1060 estimated compounds with molecular weights less than 500 Da representing chemical space, NPs occupy a very small percentage; however, they are significantly overrepresented in biologically relevant chemical space. The classical approach concentrates on identifying one or more NPs with biological activity from a source organism. There is much more to be learned from NPs than we can discover this narrow view. In this review, we discuss ways to harness the global properties of NPs.
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Affiliation(s)
- Asmaa Boufridi
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia; ,
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13
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Saunders CM, Tantillo DJ. Application of Computational Chemical Shift Prediction Techniques to the Cereoanhydride Structure Problem-Carboxylate Complications. Mar Drugs 2017; 15:md15060171. [PMID: 28604638 PMCID: PMC5484121 DOI: 10.3390/md15060171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/02/2017] [Accepted: 06/08/2017] [Indexed: 11/16/2022] Open
Abstract
Despite the vast array of techniques available to modern-day chemists, structural misassignments still occur. These misassignments are often only realized upon attempted synthesis, when the spectra of synthesized products do not match previously reported spectra. This was the case with marine natural product cereoanhydride. The originally proposed 7-membered ring anhydride (1) was shown to be incorrect, although a likely precursor to the correct structure (2) in both its laboratory synthesis and biosynthesis. Herein, in addition to showing how NMR computations could have been used to arrive at the correct structure, we show that the conversion of 1 to 2 is indeed energetically viable, and we highlight complications in predicting NMR chemical shifts for molecules with acidic protons.
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Affiliation(s)
- Carla M Saunders
- Department of Chemistry, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, USA.
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