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Marcarino MO, Cicetti S, Zanardi MM, Sarotti AM. A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide. Nat Prod Rep 2021; 39:58-76. [PMID: 34212963 DOI: 10.1039/d1np00030f] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.
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Affiliation(s)
- Maribel O Marcarino
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - Soledad Cicetti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
| | - María M Zanardi
- Instituto de Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina.
| | - Ariel M Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina.
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2
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Ozcelik A, Pereira-Cameselle R, Poklar Ulrih N, Petrovic AG, Alonso-Gómez JL. Chiroptical Sensing: A Conceptual Introduction. SENSORS (BASEL, SWITZERLAND) 2020; 20:E974. [PMID: 32059394 PMCID: PMC7071115 DOI: 10.3390/s20040974] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022]
Abstract
Chiroptical responses have been an essential tool over the last decades for chemical structural elucidation due to their exceptional sensitivity to geometry and intermolecular interactions. In recent times, there has been an increasing interest in the search for more efficient sensing by the rational design of tailored chiroptical systems. In this review article, advances made in chiroptical systems towards their implementation in sensing applications are summarized. Strategies to generate chiroptical responses are illustrated. Theoretical approaches to assist in the design of these systems are discussed. The development of efficient chiroptical reporters in different states of matter, essential for the implementation in sensing devises, is reviewed. In the last part, remarkable examples of chiroptical sensing applications are highlighted.
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Affiliation(s)
- Ani Ozcelik
- Department of Organic Chemistry, University of Vigo, 36310 Vigo, Spain; (A.O.); (R.P.-C.)
| | | | - Natasa Poklar Ulrih
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Kongresni trg 12, 1000 Ljubljana, Slovenia;
| | - Ana G. Petrovic
- Department of Biological & Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA
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3
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Zanardi MM, Biglione FA, Sortino MA, Sarotti AM. General Quantum-Based NMR Method for the Assignment of Absolute Configuration by Single or Double Derivatization: Scope and Limitations. J Org Chem 2018; 83:11839-11849. [DOI: 10.1021/acs.joc.8b01749] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- María M. Zanardi
- Área Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Franco A. Biglione
- Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, Rosario 2000, Argentina
| | - Maximiliano A. Sortino
- Área Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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4
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Liu L, Bao L, Wang L, Ma K, Han J, Yang Y, Liu R, Ren J, Yin W, Wang W, Liu H. Asperorydines A–M: Prenylated Tryptophan-Derived Alkaloids with Neurotrophic Effects from Aspergillus oryzae. J Org Chem 2018; 83:812-822. [DOI: 10.1021/acs.joc.7b02802] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Liu
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
| | - Li Bao
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
| | - Long Wang
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
| | - Ke Ma
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
| | - Junjie Han
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
| | - Yanlong Yang
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
| | - Ruixing Liu
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
| | - Jinwei Ren
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
| | - Wenbing Yin
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
| | - Wenzhao Wang
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
| | - Hongwei Liu
- State
Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China
- Savaid
Medical School, University of Chinese Academy of Sciences, Beijing, 100049, People’s Republic of China
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5
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Sherer EC, Lee CH, Shpungin J, Cuff JF, Da C, Ball R, Bach R, Crespo A, Gong X, Welch CJ. Systematic approach to conformational sampling for assigning absolute configuration using vibrational circular dichroism. J Med Chem 2014; 57:477-94. [PMID: 24383452 DOI: 10.1021/jm401600u] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Systematic methods that speed-up the assignment of absolute configuration using vibrational circular dichrosim (VCD) and simplify its usage will advance this technique into a robust platform technology. Applying VCD to pharmaceutically relevant compounds has been handled in an ad hoc fashion, relying on fragment analysis and technical shortcuts to reduce the computational time required. We leverage a large computational infrastructure to provide adequate conformational exploration which enables an accurate assignment of absolute configuration. We describe a systematic approach for rapid calculation of VCD/IR spectra and comparison with corresponding measured spectra and apply this approach to assign the correct stereochemistry of nine test cases. We suggest moving away from the fragment approach when making VCD assignments. In addition to enabling faster and more reliable VCD assignments of absolute configuration, the ability to rapidly explore conformational space and sample conformations of complex molecules will have applicability in other areas of drug discovery.
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Affiliation(s)
- Edward C Sherer
- Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, New Jersey 07065, United States
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6
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Scafato P, Caprioli F, Pisani L, Padula D, Santoro F, Mazzeo G, Abbate S, Lebon F, Longhi G. Combined use of three forms of chiroptical spectroscopies in the study of the absolute configuration and conformational properties of 3-phenylcyclopentanone, 3-phenylcyclohexanone, and 3-phenylcycloheptanone. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.10.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Tantillo DJ. Walking in the woods with quantum chemistry--applications of quantum chemical calculations in natural products research. Nat Prod Rep 2013; 30:1079-86. [PMID: 23793561 DOI: 10.1039/c3np70028c] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This Highlight describes applications of quantum chemical calculations to problems in natural products chemistry, including the elucidation of natural product structures (distinguishing between constitutional isomers, distinguishing between diastereomers, and assigning absolute configuration) and determination of reasonable mechanisms for their formation.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis, 1 Shields Avenue, Davis, CA, USA.
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8
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Ding ZG, Zhao JY, Li MG, Huang R, Li QM, Cui XL, Zhu HJ, Wen ML. Griseusins F and G, spiro-naphthoquinones from a tin mine tailings-derived alkalophilic Nocardiopsis species. JOURNAL OF NATURAL PRODUCTS 2012; 75:1994-1998. [PMID: 23095059 DOI: 10.1021/np3004936] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Griseusins F (1) and G (2), two 2a-hydro-8a-(2-oxopropyl)-substituted spiro-naphthoquinones with a previously undescribed C23 polyketide skeleton, were isolated from a Yunnan tin mine tailings-derived alkalophilic actinomycete, Nocardiopsis sp. YIM DT266. Their complete structure assignments with the absolute stereochemistry were elucidated by spectroscopic data, X-ray crystal diffraction, calculation of optical rotation, and CD spectroscopic analysis. Compounds 1 and 2 exhibited strong cytotoxicity (IC50 0.37-0.82 μM) and antibacterial activity (MIC 0.80-1.65 μg/mL) against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) in vitro.
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Affiliation(s)
- Zhang-Gui Ding
- Key Laboratory for Microbial Resources, Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University , Kunming, 650091, People's Republic of China
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9
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Molinski TF, Morinaka BI. INTEGRATED APPROACHES TO THE CONFIGURATIONAL ASSIGNMENT OF MARINE NATURAL PRODUCTS. Tetrahedron 2012; 68:9307-9343. [PMID: 23814320 PMCID: PMC3694619 DOI: 10.1016/j.tet.2011.12.070] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Tadeusz F. Molinski
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive MC0358, La Jolla, CA, 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive MC0358, La Jolla, CA, 92093
| | - Brandon I. Morinaka
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive MC0358, La Jolla, CA, 92093
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10
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Polavarapu PL, Donahue EA, Hammer KC, Raghavan V, Shanmugam G, Ibnusaud I, Nair DS, Gopinath C, Habel D. Chiroptical spectroscopy of natural products: avoiding the aggregation effects of chiral carboxylic acids. JOURNAL OF NATURAL PRODUCTS 2012; 75:1441-1450. [PMID: 22877358 DOI: 10.1021/np300341z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Determination of the absolute configurations and predominant conformations of chiral natural products, occurring as carboxylic acids, using chiroptical spectroscopic methods becomes challenging due to the formation of solute aggregates (in the form of dimers, etc.) and/or solute-solvent complexes resulting from intermolecular hydrogen bonding with solvent. A hypothesis that such aggregation effects can be avoided by using corresponding sodium salts or acid anhydrides for chiroptical spectroscopic measurements has been tested. For this purpose, vibrational circular dichroism, electronic circular dichroism, and optical rotatory dispersion spectra for disodium salts of two natural products, hibiscus acid and garcinia acid, and the anhydride of acetylated garcinia acid have been measured. These experimental spectra are analyzed in combination with quantum chemical calculations of corresponding spectra. The spectral analysis for sodium salts and anhydride turned out to be simpler, suggesting that the conversion of carboxylic acids to corresponding salts or anhydride can be advantageous for the application of chiroptical spectroscopy.
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11
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Commandeur M, Commandeur C, Cossy J. Synthesis of a platform to access bistramides and their analogues. Org Lett 2011; 13:6018-21. [PMID: 22003969 DOI: 10.1021/ol202483u] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The platform C14-C40, which can be used to prepare bistramide C and 39-oxobistramide K, was synthesized in 19 steps with an overall yield of 6.2%. Furthermore, the chemoselective reduction of the ketone at C-39 was performed giving an easy access to bistramides A, B, D, K, and L. Finally, the versatility of the synthesis of the C14-C40 fragment can allow the preparation of a large variety of stereoisomers to produce bistramide analogues.
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Affiliation(s)
- Malgorzata Commandeur
- Laboratoire de Chimie Organique Associé au CNRS, ESPCI ParisTech, 10, rue Vauquelin, 75231 Paris Cedex 05, France
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12
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Ding ZG, Li MG, Ren J, Zhao JY, Huang R, Wang QZ, Cui XL, Zhu HJ, Wen ML. Phenazinolins A–E: novel diphenazines from a tin mine tailings-derived Streptomyces species. Org Biomol Chem 2011; 9:2771-6. [DOI: 10.1039/c1ob05044c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Bauder C. Asymmetric Synthesis of the C1-C13 Fragment of the Marine Metabolite Bistramide K. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000881] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Wrona IE, Lowe JT, Turbyville TJ, Johnson TR, Beignet J, Beutler JA, Panek JS. Synthesis of a 35-member stereoisomer library of bistramide A: evaluation of effects on actin state, cell cycle and tumor cell growth. J Org Chem 2010; 74:1897-916. [PMID: 19191575 DOI: 10.1021/jo802269q] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Synthesis and preliminary biological evaluation of a 35-member library of bistramide A stereoisomers are reported. All eight stereoisomers of the C1-C13 tetrahydropyran fragment of the molecule were prepared utilizing crotylsilane reagents 9 and 10 in our [4+2]-annulation methodology. In addition, the four isomers of the C14-C18 gamma-amino acid unit were accessed via a Lewis acid mediated crotylation reaction with use of both enantiomers of organosilane 11. The spiroketal subunit of bistramide A was modified at the C39-alcohol to give another point of stereochemical diversification. The fragments were coupled by using a standard peptide coupling protocol to provide 35 stereoisomers of the natural product. These stereochemical analogues were screened for their effects on cellular actin and cytotoxicity against cancer cell lines (UO-31 renal and SF-295 CNS). The results of these assays identified one analogue, 1.21, with enhanced potency relative to the natural product, bistramide A.
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Affiliation(s)
- Iwona E Wrona
- Department of Chemistry and Center for Chemical Methodology and Library Development, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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15
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Ding ZG, Li MG, Zhao JY, Ren J, Huang R, Xie MJ, Cui XL, Zhu HJ, Wen ML. Naphthospironone A: An Unprecedented and Highly Functionalized Polycyclic Metabolite from an Alkaline Mine Waste Extremophile. Chemistry 2010; 16:3902-5. [DOI: 10.1002/chem.200903198] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Autschbach J, Nitsch-Velasquez L, Rudolph M. Time-dependent density functional response theory for electronic chiroptical properties of chiral molecules. Top Curr Chem (Cham) 2010; 298:1-98. [PMID: 21321799 DOI: 10.1007/128_2010_72] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Methodology to calculate electronic chiroptical properties from time-dependent density functional theory (TDDFT) is outlined. Applications of TDDFT to computations of electronic circular dichroism, optical rotation, and optical rotatory dispersion are reviewed. Emphasis is put on publications from 2005 to 2010, but much of the older literature is also cited and discussed. The determination of the absolute configuration of chiral molecules by combined measurements and computations is an important application of TDDFT chiroptical methods and discussed in some detail. Raman optical activity (ROA) spectra are obtained from normal-mode derivatives of the optical rotation tensor and other linear response tensors. A few selected (ROA) benchmarks are reviewed.
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Affiliation(s)
- Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, New York, NY, USA.
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17
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Mukhopadhyay P, Wipf P, Beratan DN. Optical signatures of molecular dissymmetry: combining theory with experiments to address stereochemical puzzles. Acc Chem Res 2009; 42:809-19. [PMID: 19378940 DOI: 10.1021/ar8002859] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Modern chemistry emerged from the quest to describe the three-dimensional structure of molecules: van't Hoff's tetravalent carbon placed symmetry and dissymmetry at the heart of chemistry. In this Account, we explore how modern theory, synthesis, and spectroscopy can be used in concert to elucidate the symmetry and dissymmetry of molecules and their assemblies. Chiroptical spectroscopy, including optical rotatory dispersion (ORD), electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA), measures the response of dissymmetric structures to electromagnetic radiation. This response can in turn reveal the arrangement of atoms in space, but deciphering the molecular information encoded in chiroptical spectra requires an effective theoretical approach. Although important correlations between ECD and molecular stereochemistry have existed for some time, a battery of accurate new theoretical methods that link a much wider range of chiroptical spectroscopies to structure have emerged over the past decade. The promise of this field is considerable: theory and spectroscopy can assist in assigning the relative and absolute configurations of complex products, revealing the structure of noncovalent aggregates, defining metrics for molecular diversity based on polarization response, and designing chirally imprinted nanomaterials. The physical organic chemistry of chirality is fascinating in its own right: defining atomic and group contributions to optical rotation (OR) is now possible. Although the common expectation is that chiroptical response is determined solely by a chiral solute's electronic structure in a given environment, chiral imprinting effects on the surrounding medium and molecular assembly can, in fact, dominate the chiroptical signatures. The theoretical interpretation of chiroptical markers is challenging because the optical properties are subtle, resulting from the strong electric dipole and the weaker electric quadrupole and magnetic dipole perturbations by the electromagnetic field. Moreover, OR arises from a combination of nearly canceling contributions to the electronic response. Indeed, the challenge posed by the chiroptical properties delayed the advent of even qualitatively accurate descriptions for some chiroptical signatures until the past decade when, for example, prediction of the observed sign of experimental OR became accessible to theory. The computation of chiroptical signatures, in close coordination with synthesis and spectroscopy, provides a powerful framework to diagnose and interpret the dissymmetry of chemical structures and molecular assemblies. Chiroptical theory now produces new schemes to elucidate structure, to describe the specific molecular sources of chiroptical signatures, and to assist in our understanding of how dissymmetry is templated and propagated in the condensed phase.
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Affiliation(s)
- Parag Mukhopadhyay
- Departments of Chemistry and Biochemistry, Duke University, Durham, North Carolina 27708
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - David N. Beratan
- Departments of Chemistry and Biochemistry, Duke University, Durham, North Carolina 27708
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Sashidhara KV, White KN, Crews P. A selective account of effective paradigms and significant outcomes in the discovery of inspirational marine natural products. JOURNAL OF NATURAL PRODUCTS 2009; 72:588-603. [PMID: 19209899 PMCID: PMC2837139 DOI: 10.1021/np800817y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Marine natural products continue to be a source of significant molecular structures that serve as a stimulus to seed further significant research. This account reviews some of the major advances in the study of marine biomolecules made at UC Santa Cruz over more than three decades. The continuing challenge of discovery and characterization of what we term "inspirational molecular structures" will be presented in a comprehensive fashion. Examples of privileged molecular structures and their impact on biomedicinal research will be an important theme. The three major groups of organisms explored include seaweeds, sponges, and marine-derived fungi, and the study of their active principles has greatly benefited from synergistic collaborations with both academic and biopharmaceutical groups. The concluding sections of this chronicle will touch on prospects for future outcomes involving new sources and strategies.
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Affiliation(s)
- Koneni V. Sashidhara
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Kimberly N. White
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
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19
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Mazzeo G, Giorgio E, Rosini C, Fabris F, Fregonese E, Toniolo U, De Lucchi O. Synthesis, chiroptical properties, and their theoretical simulation of some highly rotating benzotricamphor derivatives. Chirality 2009; 21 Suppl 1:E86-97. [DOI: 10.1002/chir.20780] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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Tartaglia S, Padula D, Scafato P, Chiummiento L, Rosini C. A Chemical/Computational Approach to the Determination of Absolute Configuration of Flexible and Transparent Molecules: Aliphatic Diols As a Case Study. J Org Chem 2008; 73:4865-73. [DOI: 10.1021/jo800516f] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sabina Tartaglia
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Daniele Padula
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Patrizia Scafato
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Lucia Chiummiento
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Carlo Rosini
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
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21
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Zuber G, Wipf P, Beratan DN. Exploring the Optical Activity Tensor by Anisotropic Rayleigh Optical Activity Scattering. Chemphyschem 2008; 9:265-71. [DOI: 10.1002/cphc.200700660] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Giorgio E, Tanaka K, Verotta L, Nakanishi K, Berova N, Rosini C. Determination of the absolute configurations of flexible molecules: synthesis and theoretical simulation of electronic circular dichroism/optical rotation of some pyrrolo[2,3-b]indoline alkaloids--a case study. Chirality 2007; 19:434-45. [PMID: 17393468 DOI: 10.1002/chir.20395] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The paper describes the synthesis and chiroptical properties of (-)-1,2,3,3a,8,8a,-hexahydro-1,3a-dimethyl-pyrrolo[2,3-b]indole, (-)-1, one of the monomeric units of many flexible polypyrroloindoline alkaloids and (-)-chimonanthine, (-)-2. The aim of this investigation is to show that, under certain circumstances, namely, with molecules for which the sign and order of magnitude of [alpha](D) are determined by the lowest-energy valence-shell transitions (referred to as class (a) molecules), a small basis set calculation of chiroptical properties provides reliable results, and that such a treatment can be employed for absolute configurational assignment of larger oligomers, for which the increased flexibility renders the analysis as formidable task. Actually, as the aforementioned two molecules belong to class (a) systems, a TDDFT/B3LYP/6-31G* calculation of the ECD and ORD spectra gives rise to a more than satisfactory simulation of these data, assuming the reported absolute configurations. In other words, the use of the TDDFT/B3LYP method with the small 6-31G* basis set enables one to treat large and flexible molecules such as (-)-2 (52 atoms and 6 conformers) by usage of a simple PC in about 2 weeks. This protocol demonstrates that an ab initio prediction of ECD/ORD spectra results in reliable assignments of absolute configuration of even relatively large natural products, thus economizing computation time.
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Affiliation(s)
- Egidio Giorgio
- Dipartimento di Chimica, Università della Basilicata, 85100 Potenza, Italy
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23
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Abstract
This review covers the literature published in 2005 for marine natural products, with 704 citations (493 for the period January to December 2005) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, coelenterates, bryozoans, molluscs, tunicates and echinoderms. The emphasis is on new compounds (812 for 2005), together with their relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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24
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Abstract
An asymmetric synthesis of the marine metabolite bistramide A is reported. The synthesis relies on the utility of three different organosilane reagents to construct all principle fragments and 8 of the 11 stereogenic centers of the natural product. [structure: see text].
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Affiliation(s)
- Jason T Lowe
- Department of Chemistry and Center for Chemical Methodology and Library Development, Metcalf Center for Science and Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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25
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Abstract
The enantioselective synthesis of bistramide A has been achieved with a longest linear sequence of 18 steps. The synthetic strategy involves the use of a distereoselective glycolate alkylation, an aldol addition of a chlorotitanium enolate of N-acylthiazolidinthione, and a Sharpless asymmetric epoxidation to synthesize the three key fragments.
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Affiliation(s)
- Michael T Crimmins
- Department of Chemistry, Venable and Kenan Laboratories of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.
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26
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Bauder C, Biard JF, Solladié G. Synthesis of derivatives of potent antitumor bistramides D and A leading to the first crystal structure of natural bistramide D. Org Biomol Chem 2006; 4:1860-2. [PMID: 16688329 DOI: 10.1039/b603767d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report a crystalline derivative of bistramide D synthesized from natural bistramide A, and its structure was determined by X-ray analysis.
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Affiliation(s)
- Claude Bauder
- Institut de Chimie LC 03, associé au CNRS-Université Louis Pasteur, 1 rue Blaise Pascal, 67000 Strasbourg, France.
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