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Osadchuk I, Luts HE, Zahharova A, Tamm T, Borovkov V. Controlling Chirogenic Effects in Porphyrin Based Supramolecular Systems: Theoretical Analysis Versus Experimental Observations. Chemphyschem 2024; 25:e202400104. [PMID: 38693766 DOI: 10.1002/cphc.202400104] [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: 01/31/2024] [Revised: 03/18/2024] [Indexed: 05/03/2024]
Abstract
Electronic circular dichroism (ECD) spectroscopy is a widely employed method for studying chiral analysis, requiring the presence of a chromophore close to a chiral centre. Porphyrinoids are found to be one of the best chromophoric systems serving for this purpose and enabling the application of ECD spectroscopy for chirality determination across diverse classes of organic compounds. Consequently, it is crucial to understand the induction mechanisms of ECD in the porphyrin-based complexes. The present study explores systematically the influence of secondary chromophores, bonded to an achiral zinc porphyrin or to chiral guest molecules, on the B-region of ECD spectra using the time-dependent density functional theory (TD-DFT) calculations. The study analyses the impact of change in both the conformation of achiral porphyrin (host) and change in position and conformation of chiral organic molecule (guest) on the B-band of ECD spectra (energy, intensity, sign of Cotton effect). Finally, conclusions made on model complexes are applied to published experimental data, contributing to a deeper understanding of various factors influencing ECD spectra in chiral systems. In addition, a computer program aimed to help rationalise ECD spectra by visualizing corresponding orbital energies, rotatory strengths, electric and magnetic transition moments, and angles between them, is presented.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Hanna-Eliisa Luts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Aleksandra Zahharova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Toomas Tamm
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Victor Borovkov
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
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2
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Puente AR, Polavarapu PL. Influence of microsolvation on vibrational circular dichroism spectra in dimethyl sulfoxide solvent: A Bottom-Up approach using Quantum cluster growth. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123231. [PMID: 37562213 DOI: 10.1016/j.saa.2023.123231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/09/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Chiroptical spectroscopic measurements serve as routine methods to assign the absolute configuration of chiral compounds and interpret their conformational behavior in solution. One common challenge is the use of strongly hydrogen-bonding solvents, which can significantly bias the conformational ensemble and affect the vibrational circular dichroism (VCD) active bands in solution. One such solvent is dimethyl sulfoxide (DMSO)-an excellent solvent for stubborn compounds-that must be explicitly considered in VCD analysis. Explicit consideration of solvent remains a critical challenge in chiroptical spectroscopy due to the need to explore solute-solvent conformational space and the computational expense in modeling these clusters. Interested in the recent development of the Quantum Cluster Growth (QCG) program by the Grimme lab, we set out to model and interpret previously reported VCD spectra for several molecules using their efficient program. Our purposes are two-fold: (1) to investigate the applicability of the QCG program to the problem of reproducing VCD spectra in DMSO solvent and (2) to identify limitations in using this approach. We find that we can conveniently model and analyze the VCD spectra of investigated molecules in DMSO. However, the final set of conformers used for VCD calculations are functional dependent and different sets of conformers can provide satisfactory quantitative agreement between experimental and predicted VCD spectra. We hope that this study provides guidance for future chiroptical studies in the challenging DMSO solvent.
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Affiliation(s)
- Andrew R Puente
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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3
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Groß J, Kühlborn J, Pusch S, Weber C, Andernach L, Renzer G, Eckhardt P, Brauer J, Opatz T. Comparison of different density functional theory methods for the calculation of vibrational circular dichroism spectra. Chirality 2023; 35:753-765. [PMID: 37227055 DOI: 10.1002/chir.23580] [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: 01/30/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023]
Abstract
The determination of the absolute configuration (AC) of an organic molecule is still a challenging task for which the combination of spectroscopic with quantum-mechanical methods has become a promising approach. In this study, we investigated the accuracy of DFT methods (480 overall combinations of 15 functionals, 16 basis sets, and 2 solvation models) to calculate the VCD spectra of six chiral organic molecules in order to benchmark their capability to facilitate the determination of the AC.
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Affiliation(s)
- Jonathan Groß
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jonas Kühlborn
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Pusch
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Carina Weber
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Lars Andernach
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Galit Renzer
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Paul Eckhardt
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jan Brauer
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg University, Mainz, Germany
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4
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Osadchuk I, Luts HE, Norvaiša K, Borovkov V, Senge MO. Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis. Chemistry 2023; 29:e202301408. [PMID: 37227167 DOI: 10.1002/chem.202301408] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 05/26/2023]
Abstract
The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.
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Affiliation(s)
- Irina Osadchuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Hanna-Eliisa Luts
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Karolis Norvaiša
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
| | - Victor Borovkov
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Mathias O Senge
- School of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, D02R590, Dublin, Ireland
- Institute for Advanced Study (TUM-IAS), Technical University of Munich, Lichtenberg Str. 2a, 85748, Garching, Germany
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5
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Khodov IA, Belov KV, Krestyaninov MA, Dyshin AA, Kiselev MG. Investigation of the Spatial Structure of Flufenamic Acid in Supercritical Carbon Dioxide Media via 2D NOESY. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16041524. [PMID: 36837153 PMCID: PMC9961892 DOI: 10.3390/ma16041524] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 02/09/2023] [Indexed: 05/13/2023]
Abstract
The search for new forms of already known drug compounds is an urgent problem of high relevance as more potent drugs with fewer side effects are needed. The trifluoromethyl group in flufenamic acid renders its chemical structure differently from other fenamates. This modification is responsible for a large number of conformational polymorphs. Therefore, flufenamic acid is a promising structural modification of well-known drug molecules. An effective approach in this field is micronization, employing "green" supercritical fluid technologies. This research raises some key questions to be answered on how to control polymorphic forms during the micronization of drug compounds. The results presented in this work demonstrate the ability of two-dimensional nuclear Overhauser effect spectroscopy to determine conformational preferences of small molecular weight drug compounds in solutions and fluids, which can be used to predict the polymorphic form during the micronization. Quantitative analysis was carried out to identify the conformational preferences of flufenamic acid molecules in dimethyl sulfoxide-d6 medium at 25 °C and 0.1 MPa, and in mixed solvent medium containing supercritical carbon dioxide at 45 °C and 9 MPa. The data presented allows predictions of the flufenamic acid conformational preferences of poorly soluble drug compounds to obtain new micronized forms.
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6
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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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7
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Belov KV, Batista de Carvalho LAE, Dyshin AA, Efimov SV, Khodov IA. The Role of Hidden Conformers in Determination of Conformational Preferences of Mefenamic Acid by NOESY Spectroscopy. Pharmaceutics 2022; 14:2276. [PMID: 36365095 PMCID: PMC9696638 DOI: 10.3390/pharmaceutics14112276] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 12/25/2023] Open
Abstract
Mefenamic acid has been used as a non-steroidal anti-inflammatory drug for a long time. However, its practical use is quite limited due to a number of side effects on the intestinal organs. Conformational polymorphism provides mefenamic acid with unique properties regarding possible modifications obtained during the micronization process, which can improve pharmacokinetics and minimize side effects. Micronization can be performed by decompression of supercritical fluids; methods such as rapid expansion of the supercritical solution have proven their efficiency. However, this group of methods is poorly applicable for compounds with low solubility, and the modification of the method using a pharmaceutically suitable co-solvent may be useful. In our case, addition of only 2 mol% dimethyl sulfoxide increased the solubility remarkably. Information on the conformational state may be critically important for carrying out micronization. In this work, structural analysis and estimate of conformational preferences of mefenamic acid in dimethyl sulfoxide-d6 (at 25 °C and 0.1 MPa) and in a mixed solvent supercritical carbon dioxide + dimethyl sulfoxide-d6 (45 °C, 9 MPa) were performed based on nuclear Overhauser effect spectroscopy. Results show changes in the conformation fractions depending on the medium used. The importance of allowing for hidden conformers in estimating the conformational state was demonstrated in the analysis. Obtained results may be useful for improving micronization parameters.
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Affiliation(s)
- Konstantin V. Belov
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | | | - Alexey A. Dyshin
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - Sergey V. Efimov
- Institute of Physics, Kazan Federal University, 420008 Kazan, Russia
| | - Ilya A. Khodov
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
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8
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Bravin C, Mazzeo G, Abbate S, Licini G, Longhi G, Zonta C. Helicity control of a perfluorinated carbon chain within a chiral supramolecular cage monitored by VCD. Chem Commun (Camb) 2022; 58:2152-2155. [PMID: 35059695 DOI: 10.1039/d1cc06861j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Confinement within supramolecular systems is the leading technology to finely tune guest functional properties. In this communication we report the synthesis of a chiral supramolecular cage able to bias the helicity of a perfluorinated carbon chain hosted within the cage. We monitor the phenomenon of chiral induction by Vibrational Circular Dichroism (VCD) experiments complemented by DFT calculations over the possible conformers.
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Affiliation(s)
- Carlo Bravin
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova, PD, Italy.
| | - Giuseppe Mazzeo
- Department of Molecular and Translational Medicine, Università di Brescia, Viale Europa 11, 25123 Brescia, BS, Italy.
| | - Sergio Abbate
- Department of Molecular and Translational Medicine, Università di Brescia, Viale Europa 11, 25123 Brescia, BS, Italy.
| | - Giulia Licini
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova, PD, Italy.
| | - Giovanna Longhi
- Department of Molecular and Translational Medicine, Università di Brescia, Viale Europa 11, 25123 Brescia, BS, Italy.
| | - Cristiano Zonta
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova, PD, Italy.
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9
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Baydoun O, Buffeteau T, Brotin T. Enantiopure cryptophane derivatives: Synthesis and chiroptical properties. Chirality 2021; 33:562-596. [PMID: 34464474 DOI: 10.1002/chir.23347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 01/30/2023]
Abstract
This review addresses the synthesis of enantiopure cryptophane and the study of their chiroptical properties. Cryptophane derivatives represent an important class of macrocyclic compounds that can bind a large range of species in solution under different conditions. The overwhelming majority of these host molecules is chiral, and their chiroptical properties have been thoroughly investigated. The first part of this review is dedicated to the optical resolution and the synthesis of enantiopure cryptophane derivatives. In a second part, the study of the chiroptical properties of these molecular hosts by different techniques such as electronic and vibrational circular dichroism and Raman optical activity is detailed. These techniques allow the determination of the absolute configuration of cryptophane derivatives and provide useful information about their conformation in different conditions.
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Affiliation(s)
- Orsola Baydoun
- Laboratoire de Chimie, Ens de Lyon, CNRS UMR 5182, Lyon, France
| | - Thierry Buffeteau
- Institut des Sciences Moléculaires, CNRS UMR 5255, Bordeaux University, Talence, France
| | - Thierry Brotin
- Laboratoire de Chimie, Ens de Lyon, CNRS UMR 5182, Lyon, France
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10
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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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11
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Ozcelik A, Pereira-Cameselle R, Alonso-Gómez JL. From Allenes to Spirobifluorenes: On the Way to Device-compatible Chiroptical Systems. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999201013164534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The last decade has seen a huge growth in the construction of chiral systems to
expand the scope of chiroptical applications. Dependence of chiroptical response on molecular
conformation typically leads to low chiroptical intensities of chiral systems that feature
several conformations in solution. In this respect, allenes were employed for the preparation
of open and cyclic oligomers as well as molecular cages, presenting remarkable chiroptical
responses in solution. Their molecular chirality was also transferred to metal surfaces, yet
photoisomerization of allenes limited their further exploration. In search of a more robust
chiral axis, theoretical and experimental studies confirmed that spirobifluorenes could give
rise to stable systems with tailored optical and chiroptical properties. Additionally, incorporating
a conformational lock into spirobifluorene cyclic architectures served as an efficient
strategy towards the generation of distinct helical molecular orbitals. This review article outlines our results on developing
device-compatible chiroptical systems through axially chiral allenes and spirobifluorenes. The contribution
from other research groups is presented briefly.
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Affiliation(s)
- Ani Ozcelik
- Department of Organic Chemistry, Faculty of Chemistry, University of Vigo, Vigo, Spain
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12
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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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13
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Farkas V, Nagy A, Menyhárd DK, Perczel A. Assignment of Vibrational Circular Dichroism Cross-Referenced Electronic Circular Dichroism Spectra of Flexible Foldamer Building Blocks: Towards Assigning Pure Chiroptical Properties of Foldamers. Chemistry 2019; 25:14890-14900. [PMID: 31464009 PMCID: PMC6899845 DOI: 10.1002/chem.201903023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/15/2019] [Indexed: 01/09/2023]
Abstract
Assignment of the most established electronic circular dichroism (ECD) spectra of polypeptides and foldamers is either “evidence based” or relies on the 3D structures of longer oligomers of limited internal dynamics, which are derived from NMR spectroscopy (or X‐ray) data. Critics warn that the use of NMR spectroscopy and ECD side by side has severe limitations for flexible molecules because explicit knowledge of conformational ensembles is a challenge. Herein, an old–new method of comparing ab initio computed and measured vibrational circular dichroism (VCD) data is presented to validate both the structures (conf(i)) and their relative weights (c(i)) that make up the conformational ensemble. Based on the array of {conf(i), c(i)}, the pure ECD spectra, g(i)conf(i), can be ab initio calculated. The reconstructed spectrum Σc(i)g(i)conf(i) can thus help to assign any experimental ECD counterparts. Herein, such a protocol is successfully applied to flexible foldamer building blocks of sugar β‐amino acid diamides. The epimeric pair of the model system was selected because these molecules were conformationally tunable by simple chemical modification, and thus, the robustness of the current approach could be probed. The initial hydrogen bond (NH⋅⋅⋅O) eliminated by N‐methylation reorients the amide plain, which influences the chiroptical properties of the foldamer building block; this structural change is successfully monitored by changes to the VCD and ECD transitions, which are now assigned to pure conformers. The current method seems to be general and effective without requiring extensive CPU and spectroscopic resources.
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Affiliation(s)
- Viktor Farkas
- MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Adrienn Nagy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
| | - András Perczel
- MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary.,Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány P. stny. 1/A, Budapest, 1117, Hungary
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14
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Gendron F, Moore Ii B, Cador O, Pointillart F, Autschbach J, Le Guennic B. Ab Initio Study of Circular Dichroism and Circularly Polarized Luminescence of Spin-Allowed and Spin-Forbidden Transitions: From Organic Ketones to Lanthanide Complexes. J Chem Theory Comput 2019; 15:4140-4155. [PMID: 31125219 DOI: 10.1021/acs.jctc.9b00286] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complete and restricted active space self-consistent field (CAS-/RAS-SCF) wave function methods are applied for the calculation of circular dichroism (CD) and circularly polarized luminescence (CPL) of a series of molecules comprising four organic ketones, the chiral cobalt(III) complex [Co(en)3]3+, and the europium(III) complex [Eu(DPA)3]3-. The ab initio results are in good agreement with the experimental data and previous results obtained with Kohn-Sham density functional theory in the case of the spin-allowed transitions. CD and CPL properties are calculated ab initio for the spin-forbidden transitions of both a transition metal and a lanthanide complex.
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Affiliation(s)
- Frédéric Gendron
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Barry Moore Ii
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Olivier Cador
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Fabrice Pointillart
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Jochen Autschbach
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Boris Le Guennic
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
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15
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Nugroho AE, Morita H. Computationally-assisted discovery and structure elucidation of natural products. J Nat Med 2019; 73:687-695. [PMID: 31093833 PMCID: PMC6713678 DOI: 10.1007/s11418-019-01321-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
Computer hardware development coupled with the development of quantum chemistry, new computational models and algorithms, and user-friendly interfaces have lowered the barriers to the use of computation in the discovery and structure elucidation of natural products. Consequently, the use of computational chemistry software as a tool to discover and determine the structure of natural products has become more common in recent years. In this review, we provide several examples of recent studies that used computer technology to facilitate the discovery and structure determination of various natural products.
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Affiliation(s)
- Alfarius Eko Nugroho
- Faculty of Pharmaceutical Sciences, Hoshi University, Ebara 2-4-41 Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Hiroshi Morita
- Faculty of Pharmaceutical Sciences, Hoshi University, Ebara 2-4-41 Shinagawa-ku, Tokyo, 142-8501, Japan.
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16
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Johnson J, Nair DS, Pillai SM, Johnson D, Kallingathodi Z, Ibnusaud I, Polavarapu PL. Dissymmetry Factor Spectral Analysis Can Provide Useful Diastereomer Discrimination: Chiral Molecular Structure of an Analogue of (-)-Crispine A. ACS OMEGA 2019; 4:6154-6164. [PMID: 31459760 PMCID: PMC6648312 DOI: 10.1021/acsomega.8b03678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/20/2019] [Indexed: 06/10/2023]
Abstract
(1R,10bR)-1'-((R)-1,2-Dihydroxyethyl)-1-hydroxy-8,9-dimethoxy1,5,6,10b-tetrahydropyrrolo [2,1-a]isoquinolin-3(2H)-one, an analogue of (-)-crispine A, with three stereogenic centers is synthesized and its absolute configuration (AC) established using the combined information derived from the synthetic scheme and single crystal X-ray diffraction data. The experimental chiroptical spectra (namely, optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD)) and the corresponding quantum chemical (QC) predicted spectra for all diastereomers are used to evaluate the AC. The AC of the synthesized compound could be correctly established using any one of the three chiroptical spectroscopic methods (ORD, ECD, or VCD) when the relative configuration is constrained to be that derived from X-ray data or when the ACs of two of the chiral centers are constrained to be those derived from the synthetic scheme. In the absence of this outside information, the QC predicted ORD, ECD, and VCD for incorrect diastereomers are also found to satisfactorily reproduce the corresponding experimental spectra. Nevertheless, incorrect diastereomers could be eliminated when combined electronic dissymmetry factor (EDF) and vibrational dissymmetry factor (VDF) spectral analyses are included, leaving the correct diastereomer as the sole choice. Thus, the combined EDF and VDF spectral analysis is seen to be a helpful diastereomer discrimination tool.
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Affiliation(s)
- Jordan
L. Johnson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Divya Sadasivan Nair
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Sarath Muraleedharan Pillai
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Didimos Johnson
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Zabeera Kallingathodi
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Ibrahim Ibnusaud
- Institute
for Intensive Research in Basic Sciences, Mahatma Gandhi University, P.D. Hills P. O., Kottayam, Kerala 686560, India
| | - Prasad L. Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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17
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Johnson J, Polavarapu PL. Chiral Molecular Structures of Substituted Indans: Ring Puckering, Rotatable Substituents, and Vibrational Circular Dichroism. ACS OMEGA 2019; 4:4963-4976. [PMID: 31459680 PMCID: PMC6648482 DOI: 10.1021/acsomega.8b03628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/21/2019] [Indexed: 05/06/2023]
Abstract
The chiral molecular structures of four different substituted indans, namely, (S)-1-methylindan, (R)-1-methylindan-1-d, (R)-1-aminoindan, and (S)-1-indanol, were investigated using experimental vibrational absorption and vibrational circular dichroism spectra and corresponding spectra predicted using quantum chemical (QC) calculations. All of these molecules possess two ring puckering conformations, with ring puckering leading to the pseudoequatorial substituent being approximately four times more abundant over that leading to the pseudoaxial substituent. The amino group in 1-aminoindan has three conformations arising from the rotation of NH2 group, for each ring puckering conformation, resulting in a total of six conformations. Whereas 1-indanol in the nonhydrogen-bonding solvent CCl4 also has six conformations similar to those of 1-aminoindan, 1-indanol in the hydrogen-bonding solvent DMSO-d 6 adopts numerous conformations, of which 30 conformers are considered to have at least ∼1% or more population. In DMSO solution, ring puckering leading to pseudoequatorial substituent accounts for 77% population and 23% for pseudoaxial substituent. The QC spectra predicted for the geometry optimized conformers are found to be in excellent quantitative agreement with corresponding experimental spectra in all of the molecules considered. The procedures suggested in this work are hoped to provide successful pathways for future chiral molecular structural analyses.
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18
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Rode JE, Górecki M, Witkowski S, Frelek J. Solvation of 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol revealed by circular dichroism: a case of chromane helicity rule breaking. Phys Chem Chem Phys 2018; 20:22525-22536. [PMID: 30140796 DOI: 10.1039/c8cp02491j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The primary goal of this work is to clarify why 2-(hydroxymethyl)-2,5,7,8-tetramethyl-chroman-6-ol {(S)-TMChM} deviates from the chromane helicity rule under solvent change. The rule, applicable to determining the absolute configuration of molecules containing the chromane chromophore, binds the sign of the 1Lb Cotton effect (CE) with the helicity of the dihydropyran ring. In case of TMChM, however, this CE exhibits extreme solvent dependence: it is negative in non-coordinating solvents and positive in coordinating ones, irrespective of the helicity of the heterocyclic ring. TD-DFT calculations using PCM and hybrid solvation models were performed to explain origin of this phenomenon. It turned out that the 1Lb CE sign directly depends on the position of the phenolic OH group at carbon atom C6 (OHC6). In the absence of interactions with solvents (as in CCl4 or nC6H14) or when a solvent plays proton donor role (as in CHCl3), the OHC6 lies in the phenyl plane and the 1Lb CE sign follows the P/M helicity rule. In contrast, in proton acceptor solvents, like DMSO, CH3OH or CH3CN, the OHC6 group is deflected from the phenyl plane, and the 1Lb CE sign of individual (S)-TMChM conformers depends on the sector in which the OHC6 is located. Thus, in solution, the 1Lb CE sign is an average over different orientations of the OHC6 group and can be positive (as in DMSO and CH3OH) or negative (as in CH3CN) which means that it does not follow the chromane helicity rule. The impact of OHC6 on the 1Lb CE sign and thus the conclusions for the stereochemistry of chromans are demonstrated here for the first time. Additionally, a comparison of experimental and simulated ECD spectra, supported by VCD data, allowed to determine the geometry of intermolecular clusters formed in different solvents.
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Affiliation(s)
- Joanna E Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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19
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Johnson JL, Raghavan V, Cimmino A, Moeini A, Petrovic AG, Santoro E, Superchi S, Berova N, Evidente A, Polavarapu PL. Absolute configurations of chiral molecules with multiple stereogenic centers without prior knowledge of the relative configurations: A case study of inuloxin C. Chirality 2018; 30:1206-1214. [DOI: 10.1002/chir.23013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/13/2018] [Accepted: 08/10/2018] [Indexed: 12/20/2022]
Affiliation(s)
| | - Vijay Raghavan
- Department of Chemistry Vanderbilt University Nashville TN USA
| | - Alessio Cimmino
- Department of Chemical Science University of Naples Federico II Naples Italy
| | - Arash Moeini
- Department of Chemical Science University of Naples Federico II Naples Italy
| | - Ana G. Petrovic
- Department of Chemistry Columbia University New York NY USA
- Department of Life Sciences New York Institute of Technology New York NY USA
| | - Ernesto Santoro
- Department of Science University of Basilicata Potenza Italy
| | | | - Nina Berova
- Department of Chemistry Columbia University New York NY USA
| | - Antonio Evidente
- Department of Chemical Science University of Naples Federico II Naples Italy
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20
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Risso V, Farran D, Javierre G, Naubron JV, Giorgi M, Piras P, Jean M, Vanthuyne N, Fruttero R, Lorcy D, Roussel C. Atropisomerism in a 10-Membered Ring with Multiple Chirality Axes: (3 Z,9 Z)-1,2,5,8-Dithiadiazecine-6,7(5 H,8 H)-dione Series. J Org Chem 2018; 83:7566-7573. [PMID: 29884018 DOI: 10.1021/acs.joc.8b01009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, chirality in (3 Z,9 Z)-1,2,5,8-dithiadiazecine-6,7(5 H,8 H)-dione series was recognized. Enantiomers of the 4,9-dimethyl-5,8-diphenyl analogue were isolated at room temperature, and their thermal stability was determined. X-ray crystallography confirmed the occurrence of a pair of enantiomers in the crystal. Absolute configurations were assigned by comparing experimental and calculated vibrational/electronic circular dichroism spectra of isolated enantiomers. A distorted tesseract (four-dimensional hypercube) was used to visualize the calculated enantiomerization process, which requires the rotation around four chirality axes. Conformers of higher energy as well as several concurrent pathways of similar energies were revealed.
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Affiliation(s)
- Vesna Risso
- Aix-Marseille Univ., CNRS, Centrale Marseille , iSm2, Marseille , France
| | - Daniel Farran
- Aix-Marseille Univ., CNRS, Centrale Marseille , iSm2, Marseille , France
| | - Guilhem Javierre
- Aix-Marseille Univ., CNRS, Centrale Marseille , iSm2, Marseille , France
| | - Jean-Valère Naubron
- Spectropole , Aix-Marseille Université , CNRS FR 1739, Marseille 13397 Cedex 20 , France
| | - Michel Giorgi
- Spectropole , Aix-Marseille Université , CNRS FR 1739, Marseille 13397 Cedex 20 , France
| | - Patrick Piras
- Aix-Marseille Univ., CNRS, Centrale Marseille , iSm2, Marseille , France
| | - Marion Jean
- Aix-Marseille Univ., CNRS, Centrale Marseille , iSm2, Marseille , France
| | - Nicolas Vanthuyne
- Aix-Marseille Univ., CNRS, Centrale Marseille , iSm2, Marseille , France
| | - Roberta Fruttero
- Department of Drug Sciences and Technology , University of Torino , 8-10124 Torino , Italy
| | | | - Christian Roussel
- Aix-Marseille Univ., CNRS, Centrale Marseille , iSm2, Marseille , France
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21
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Perera AS, Cheramy J, Merten C, Thomas J, Xu Y. IR, Raman, and Vibrational Optical Activity Spectra of Methyl Glycidate in Chloroform and Water: The Clusters-in-a-liquid
Solvation Model. Chemphyschem 2018; 19:2234-2242. [DOI: 10.1002/cphc.201800309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joseph Cheramy
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada T6G 2G2
| | - Christian Merten
- Ruhr-University Bochum; Faculty of Chemistry and Biochemistry; 44801 Bochum Germany
| | - Javix Thomas
- Department of Chemical and Material Engineering; University of Alberta; Edmonton Alberta Canada T6G 1H
| | - Yunjie Xu
- Department of Chemistry; University of Alberta; Edmonton Alberta Canada T6G 2G2
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22
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Rode JE, Dobrowolski JC, Lyczko K, Wasiewicz A, Kaczorek D, Kawęcki R, Zając G, Baranska M. Chiral Thiophene Sulfonamide—A Challenge for VOA Calculations. J Phys Chem A 2017; 121:6713-6726. [DOI: 10.1021/acs.jpca.6b11015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Joanna E. Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Aleksandra Wasiewicz
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Dorota Kaczorek
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Grzegorz Zając
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
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23
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Srebro-Hooper M, Autschbach J. Calculating Natural Optical Activity of Molecules from First Principles. Annu Rev Phys Chem 2017; 68:399-420. [DOI: 10.1146/annurev-physchem-052516-044827] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260
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24
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Buffeteau T, Pitrat D, Daugey N, Calin N, Jean M, Vanthuyne N, Ducasse L, Wien F, Brotin T. Chiroptical properties of cryptophane-111. Phys Chem Chem Phys 2017; 19:18303-18310. [DOI: 10.1039/c7cp02045g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How the presence or not of solvent molecules inside the cavity of enantiopure cryptophanes affects their chiroptical properties.
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Affiliation(s)
- Thierry Buffeteau
- Bordeaux University
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- 33405 Talence
- France
| | - Delphine Pitrat
- Lyon 1 University
- Ecole Normale Supérieure de Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
| | - Nicolas Daugey
- Bordeaux University
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- 33405 Talence
- France
| | - Nathalie Calin
- Lyon 1 University
- Ecole Normale Supérieure de Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
| | - Marion Jean
- Aix-Marseille University
- CNRS
- Centrale Marseille
- iSm2
- Marseille
| | | | - Laurent Ducasse
- Bordeaux University
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- 33405 Talence
- France
| | - Frank Wien
- Synchrotron SOLEIL
- L'Orme des Merisiers
- 91192 Gif sur Yvette
- France
| | - Thierry Brotin
- Lyon 1 University
- Ecole Normale Supérieure de Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
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25
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Padula D, Cerezo J, Pescitelli G, Santoro F. The shape of the electronic circular dichroism spectrum of (2,6-dimethylphenyl)(phenyl)methanol: interplay between conformational equilibria and vibronic effects. Phys Chem Chem Phys 2017; 19:32349-32360. [DOI: 10.1039/c7cp06369e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Analysis of the interplay between conformational equilibria, solvent effects and vibronic contributions in the ECD spectra.
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Affiliation(s)
- Daniele Padula
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Javier Cerezo
- Departamento de Química Física
- Universidad de Murcia
- 30100 Murcia
- Spain
| | - Gennaro Pescitelli
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche – CNR
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- Pisa
- Italy
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26
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Pitrat D, Daugey N, Jean M, Vanthuyne N, Wien F, Ducasse L, Calin N, Buffeteau T, Brotin T. Unusual Chiroptical Properties of the Cryptophane-222 Skeleton. J Phys Chem B 2016; 120:12650-12659. [DOI: 10.1021/acs.jpcb.6b09771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Delphine Pitrat
- Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Lyon 1 University, 69364 Lyon, France
| | - Nicolas Daugey
- Institut des Sciences Moléculaires, CNRS UMR 5255, Bordeaux University, 33405 Talence, France
| | - Marion Jean
- Centrale Marseille, CNRS, iSm2, Aix-Marseille University, 13397 Marseille, France
| | - Nicolas Vanthuyne
- Centrale Marseille, CNRS, iSm2, Aix-Marseille University, 13397 Marseille, France
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme
des Merisiers, 91192 Gif sur Yvette, France
| | - Laurent Ducasse
- Institut des Sciences Moléculaires, CNRS UMR 5255, Bordeaux University, 33405 Talence, France
| | - Nathalie Calin
- Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Lyon 1 University, 69364 Lyon, France
| | - Thierry Buffeteau
- Institut des Sciences Moléculaires, CNRS UMR 5255, Bordeaux University, 33405 Talence, France
| | - Thierry Brotin
- Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Laboratoire de Chimie, Lyon 1 University, 69364 Lyon, France
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27
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Trapp O, Zawatzky K. Synthesis of Cryptochiral (R,R)-2,3-Dideuterooxirane as Stereochemical Reference Compound and Chemical Correlation with D-(+)-Glyceraldehyde. Isr J Chem 2016. [DOI: 10.1002/ijch.201600111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Oliver Trapp
- Ludwig-Maximilians-Universität München; Department Chemie; Butenandtstr. 5-13 81377 München Germany
- Max-Planck-Institut für Astronomie; Königstuhl 17 69117 Heidelberg Germany
| | - Kerstin Zawatzky
- Merck Research Laboratories; Department of Process & Analytical Chemistry; Rahway, New Jersey USA
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28
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Oliveira BG. The interaction strength of intermolecular systems formed by NaH⋯2(HF) and NaH⋯4(HF): Hydrogen bonds, dihydrogen bonds and halogen–hydride bonds. CR CHIM 2016. [DOI: 10.1016/j.crci.2016.03.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Jiménez-Romero C, Rode JE, Rodríguez AD. Reassignment of the absolute configuration of plakinidone from the sponge consortium Plakortis halichondrioides-Xestospongia deweerdtae using a combination of synthesis and a chiroptical approach. TETRAHEDRON, ASYMMETRY 2016; 27:410-419. [PMID: 28190935 PMCID: PMC5295471 DOI: 10.1016/j.tetasy.2016.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recent work by Wu et al. in connection with the first synthesis of the marine natural product plakinidone revealed that the most salient feature of its purported structure, a six-membered perlactone moiety, was in fact a five-membered lactone, i.e. a 3-methyl-4-hydroxy-2(5H)-furanone or tetronic acid ring. With the planar structure of plakinidone confidently revised, we undertook a new investigation to unambiguously establish its absolute configuration. Upon preparing two stable derivatives 1 and 5 from a sample of naturally occurring plakinidone extracted from the sponge association Plakortis halichondriodes-Xetospongia deweerdtae, the absolute configuration was assigned by synthesis and vibrational and electronic circular dichroism (VCD and ECD) measurements in combination with density functional theory calculations at the B3LYP/aug-cc-pVDZ/PCM(CH3CN) level of theory. Our combined efforts and the agreement between the experimental and calculated VCD/ECD spectra of 1 revealed that the absolute configuration of plakinidone was in fact (11S,17R) and not the formerly reported (11S,17S) diastereomer assigned by Wu et al.. Therefore, we propose that natural plakinidone is accurately represented by structure 12.
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Affiliation(s)
- Carlos Jiménez-Romero
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, Puerto Rico 00926
| | - Joanna E. Rode
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Abimael D. Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, Puerto Rico 00926
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30
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Zhang Y, Poopari MR, Cai X, Savin A, Dezhahang Z, Cheramy J, Xu Y. IR and Vibrational Circular Dichroism Spectroscopy of Matrine- and Artemisinin-Type Herbal Products: Stereochemical Characterization and Solvent Effects. JOURNAL OF NATURAL PRODUCTS 2016; 79:1012-1023. [PMID: 27070079 DOI: 10.1021/acs.jnatprod.5b01082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Five Chinese herbal medicines--matrine, oxymatrine, sophoridine, artemisinin, and dihydroartemisinin--were investigated using vibrational circular dichroism (VCD) experiments and density functional theory calculations to extract their stereochemical information. The three matrine-type alkaloids are available from the dry roots of Sophora flavescens and have long been used in various traditional Chinese herbal medicines to combat diseases such as cancer and cardiac arrhythmia. Artemisinin and the related dihydroartemisinin, discovered in 1979 by Professor Youyou Tu, a 2015 Nobel laureate in medicine, are effective drugs for the treatment of malaria. The VCD measurements were carried out in CDCl3 and DMSO-d6, two solvents with different dielectric constants and hydrogen-bonding characteristics. A "clusters-in-a-liquid" approach was used to model both explicit and implicit solvent effects. The studies show that effectively accounting for solvent effects is critical to using IR and VCD spectroscopy to provide unique spectroscopic features to differentiate the potential stereoisomers of these Chinese herbal medicines.
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Affiliation(s)
- Yuefei Zhang
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada , T6G 2G2
| | - M Reza Poopari
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada , T6G 2G2
| | - Xiaoli Cai
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada , T6G 2G2
| | - Aliaksandr Savin
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada , T6G 2G2
| | - Zahra Dezhahang
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada , T6G 2G2
| | - Joseph Cheramy
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada , T6G 2G2
| | - Yunjie Xu
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada , T6G 2G2
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31
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Rossi D, Nasti R, Marra A, Meneghini S, Mazzeo G, Longhi G, Memo M, Cosimelli B, Greco G, Novellino E, Da Settimo F, Martini C, Taliani S, Abbate S, Collina S. Enantiomeric 4-Acylamino-6-alkyloxy-2 Alkylthiopyrimidines As Potential A3Adenosine Receptor Antagonists: HPLC Chiral Resolution and Absolute Configuration Assignment by a Full Set of Chiroptical Spectroscopy. Chirality 2016; 28:434-40. [DOI: 10.1002/chir.22599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/19/2016] [Accepted: 03/01/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Daniela Rossi
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
| | - Rita Nasti
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
| | - Annamaria Marra
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
| | - Silvia Meneghini
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Maurizio Memo
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Barbara Cosimelli
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Napoli Italy
| | - Giovanni Greco
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Napoli Italy
| | - Ettore Novellino
- Dipartimento di Farmacia; Università di Napoli “Federico II”; Napoli Italy
| | | | | | | | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale; Università di Brescia; Brescia Italy
| | - Simona Collina
- Dipartimento di Scienze del Farmaco; Università di Pavia; Pavia Italy
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32
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Pescitelli G, Bruhn T. Good Computational Practice in the Assignment of Absolute Configurations by TDDFT Calculations of ECD Spectra. Chirality 2016; 28:466-74. [PMID: 27098594 DOI: 10.1002/chir.22600] [Citation(s) in RCA: 353] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/03/2016] [Accepted: 03/05/2016] [Indexed: 01/10/2023]
Abstract
Quantum-mechanical calculations of chiroptical properties have rapidly become the most popular method for assigning absolute configurations (AC) of organic compounds, including natural products. Black-box time-dependent Density Functional Theory (TDDFT) calculations of electronic circular dichroism (ECD) spectra are nowadays readily accessible to nonexperts. However, an uncritical attitude may easily deliver a wrong answer. We present to the Chirality Forum a discussion on what can be called good computational practice in running TDDFT ECD calculations, highlighting the most crucial points with several examples from the recent literature. Chirality 28:466-474, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy
| | - Torsten Bruhn
- Institut für Organische Chemie, Universität Würzburg Am Hubland, Würzburg, Germany
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33
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Perera AS, Thomas J, Poopari MR, Xu Y. The Clusters-in-a-Liquid Approach for Solvation: New Insights from the Conformer Specific Gas Phase Spectroscopy and Vibrational Optical Activity Spectroscopy. Front Chem 2016; 4:9. [PMID: 26942177 PMCID: PMC4766311 DOI: 10.3389/fchem.2016.00009] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/08/2016] [Indexed: 11/30/2022] Open
Abstract
Vibrational optical activity spectroscopies, namely vibrational circular dichroism (VCD) and Raman optical activity (ROA), have been emerged in the past decade as powerful spectroscopic tools for stereochemical information of a wide range of chiral compounds in solution directly. More recently, their applications in unveiling solvent effects, especially those associated with water solvent, have been explored. In this review article, we first select a few examples to demonstrate the unique sensitivity of VCD spectral signatures to both bulk solvent effects and explicit hydrogen-bonding interactions in solution. Second, we discuss the induced solvent chirality, or chiral transfer, VCD spectral features observed in the water bending band region in detail. From these chirality transfer spectral data, the related conformer specific gas phase spectroscopic studies of small chiral hydration clusters, and the associated matrix isolation VCD experiments of hydrogen-bonded complexes in cold rare gas matrices, a general picture of solvation in aqueous solution emerges. In such an aqueous solution, some small chiral hydration clusters, rather than the chiral solutes themselves, are the dominant species and are the ones that contribute mainly to the experimentally observed VCD features. We then review a series of VCD studies of amino acids and their derivatives in aqueous solution under different pHs to emphasize the importance of the inclusion of the bulk solvent effects. These experimental data and the associated theoretical analyses are the foundation for the proposed "clusters-in-a-liquid" approach to account for solvent effects effectively. We present several approaches to identify and build such representative chiral hydration clusters. Recent studies which applied molecular dynamics simulations and the subsequent snapshot averaging approach to generate the ROA, VCD, electronic CD, and optical rotatory dispersion spectra are also reviewed. Challenges associated with the molecular dynamics snapshot approach are discussed and the successes of the seemingly random "ad hoc explicit solvation" reported before are also explained. To further test and improve the "clusters-in-a-liquid" model in practice, future work in terms of conformer specific gas phase spectroscopy of sequential solvation of a chiral solute, matrix isolation VCD measurements of small chiral hydration clusters, and more sophisticated models for the bulk solvent effects would be highly valuable.
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Affiliation(s)
| | | | | | - Yunjie Xu
- Department of Chemistry, University of AlbertaEdmonton, AB, Canada
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34
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Cimmino A, Mathieu V, Masi M, Baroncelli R, Boari A, Pescitelli G, Ferderin M, Lisy R, Evidente M, Tuzi A, Zonno MC, Kornienko A, Kiss R, Evidente A. Higginsianins A and B, Two Diterpenoid α-Pyrones Produced by Colletotrichum higginsianum, with in Vitro Cytostatic Activity. JOURNAL OF NATURAL PRODUCTS 2016; 79:116-25. [PMID: 26697898 PMCID: PMC4944208 DOI: 10.1021/acs.jnatprod.5b00779] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Two new diterpenoid α-pyrones, named higginsianins A (1) and B (2), were isolated from the mycelium of the fungus Colletotrichum higginsianum grown in liquid culture. They were characterized as 3-[5a,9b-dimethyl-7-methylene-2-(2-methylpropenyl)dodecahydronaphtho[2,1-b]furan-6-ylmethyl]-4-hydroxy-5,6-dimethylpyran-2-one and 4-hydroxy-3-[6-hydroxy-5,8a-dimethyl-2-methylene-5-(4-methylpent-3-enyl)decahydronaphthalen-1-ylmethyl]-5,6-dimethylpyran-2-one, respectively, by using NMR, HRESIMS, and chemical methods. The structure and relative configuration of higginsianin A (1) were confirmed by X-ray diffractometric analysis, while its absolute configuration was assigned by electronic circular dichroism (ECD) experiments and calculations using a solid-state ECD/TDDFT method. The relative and absolute configuration of higginsianin B (2), which did not afford crystals suitable for X-ray analysis, were determined by NMR analysis and by ECD in comparison with higginsianin A. 1 and 2 were the C-8 epimers of subglutinol A and diterpenoid BR-050, respectively. The evaluation of 1 and 2 for antiproliferative activity against a panel of six cancer cell lines revealed that the IC50 values, obtained with cells reported to be sensitive to pro-apoptotic stimuli, are by more than 1 order of magnitude lower than their apoptosis-resistant counterparts (1 vs >80 μM). Finally, three hemisynthetic derivatives of 1 were prepared and evaluated for antiproliferative activity. Two of these possessed IC50 values and differential sensitivity profiles similar to those of 1.
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Affiliation(s)
- Alessio Cimmino
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Veronique Mathieu
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marco Masi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Riccardo Baroncelli
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University of Western Brittany, Avenue du Technopole, Plouzané, 29280 Brest, France
| | - Angela Boari
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70125 Bari, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Universita di Pisa, Via Moruzzi 3, 56124 Pisa, Italy
| | - Marlène Ferderin
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Romana Lisy
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marco Evidente
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Angela Tuzi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
| | - Maria Chiara Zonno
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70125 Bari, Italy
| | - Alexander Kornienko
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, United States
| | - Robert Kiss
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Antonio Evidente
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Via Cintia 4, 80126, Napoli, Italy
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35
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Gorunova ON, Novitskiy IM, Grishin YK, Gloriozov IP, Roznyatovsky VA, Khrustalev VN, Kochetkov KA, Dunina VV. Determination of the Absolute Configuration of CN-Palladacycles by 31P{1H} NMR Spectroscopy Using (1R,2S,5R)-Menthyloxydiphenylphosphine as the Chiral Derivatizing Agent: Efficient Chirality Transfer in Phosphinite Adducts. Organometallics 2016. [DOI: 10.1021/acs.organomet.5b00706] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Olga N. Gorunova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Street 28, 119991 Moscow, Russian Federation
| | - Ivan M. Novitskiy
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Lenin Hills, 119991, Moscow, Russian Federation
| | - Yuri K. Grishin
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Lenin Hills, 119991, Moscow, Russian Federation
| | - Igor P. Gloriozov
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Lenin Hills, 119991, Moscow, Russian Federation
| | - Vitaly A. Roznyatovsky
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Lenin Hills, 119991, Moscow, Russian Federation
| | - Victor N. Khrustalev
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Street 28, 119991 Moscow, Russian Federation
- Inorganic Chemistry Department, Peoples’ Friendship University of Russia, Miklukho-Maklay Street 6, 117198 Moscow, Russian Federation
| | - Konstantin A. Kochetkov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova Street 28, 119991 Moscow, Russian Federation
| | - Valery V. Dunina
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Lenin Hills, 119991, Moscow, Russian Federation
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36
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Berardozzi R, Badetti E, Carmo dos Santos NA, Wurst K, Licini G, Pescitelli G, Zonta C, Di Bari L. Co(ii)-induced giant vibrational CD provides a new design of methods for rapid and sensitive chirality recognition. Chem Commun (Camb) 2016; 52:8428-31. [DOI: 10.1039/c6cc04167a] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enhanced VCD signals correlate easily with the absolute configuration of the α-aminoacid used in our new self assembly and paving the way to easy and sensitive VCD methods.
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Affiliation(s)
- Roberto Berardozzi
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Elena Badetti
- Dipartimento di Scienze Chimiche
- Università di Padova
- I-35131 Padova
- Italy
| | | | - Klaus Wurst
- Institute of General
- Inorganic and Theoretical Chemistry University of Innsbruck
- A-6020 Innsbruck
- Austria
| | - Giulia Licini
- Dipartimento di Scienze Chimiche
- Università di Padova
- I-35131 Padova
- Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Cristiano Zonta
- Dipartimento di Scienze Chimiche
- Università di Padova
- I-35131 Padova
- Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
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37
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Reinscheid F, Reinscheid U. Stereochemical analysis of menthol and menthylamine isomers using calculated and experimental optical rotation data. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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38
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Affiliation(s)
- Veronica L. Murphy
- Department of Chemistry and
Molecular Design Institute, New York University, 100 Washington Square East, Silver
Center, Room 1001, New York, New York 10003, United States
| | - Adam Reyes
- Department of Chemistry and
Molecular Design Institute, New York University, 100 Washington Square East, Silver
Center, Room 1001, New York, New York 10003, United States
| | - Bart Kahr
- Department of Chemistry and
Molecular Design Institute, New York University, 100 Washington Square East, Silver
Center, Room 1001, New York, New York 10003, United States
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39
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Lavoie S, Gauthier C, Mshvildadze V, Legault J, Roger B, Pichette A. DFT Calculations and ROESY NMR Data for the Diastereochemical Characterization of Cytotoxic Tetraterpenoids from the Oleoresin of Abies balsamea. JOURNAL OF NATURAL PRODUCTS 2015; 78:2896-2907. [PMID: 26592897 DOI: 10.1021/acs.jnatprod.5b00492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Eight non-carotenoid tetraterpenoids, abibalsamins C-J (3-10), were isolated from the oleoresin of Abies balsamea. Their chemical structures were determined based on analysis of 1D/2D NMR and MS data. The assignment of their relative configurations was accomplished using homonuclear coupling constants in tandem with ROESY data. However, the presence of two stereogenic centers on a flexible side chain complicated the characterization. In silico models and ROESY data were analyzed in order to assign relative configurations of the isolated tetraterpenoids. Abibalsamins B and H-J showed moderate cytotoxicity against human A549 lung carcinoma cells, with IC50 values ranging between 6.7 and 10 μM.
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Affiliation(s)
- Serge Lavoie
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi , 555 Boulevard de l'Université, Chicoutimi, Québec, Canada , G7H 2B1
| | - Charles Gauthier
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi , 555 Boulevard de l'Université, Chicoutimi, Québec, Canada , G7H 2B1
- Institut de Chimie IC2MP, CNRS-UMR 7285, Équipe Synthèse Organique, Université de Poitiers , 4 Rue Michel Brunet, 86073 Poitiers Cedex 9, France
| | - Vakhtang Mshvildadze
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi , 555 Boulevard de l'Université, Chicoutimi, Québec, Canada , G7H 2B1
| | - Jean Legault
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi , 555 Boulevard de l'Université, Chicoutimi, Québec, Canada , G7H 2B1
| | - Benoit Roger
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi , 555 Boulevard de l'Université, Chicoutimi, Québec, Canada , G7H 2B1
| | - André Pichette
- Chaire de Recherche sur les Agents Anticancéreux d'Origine Naturelle, Laboratoire LASEVE, Département des Sciences Fondamentales, Université du Québec à Chicoutimi , 555 Boulevard de l'Université, Chicoutimi, Québec, Canada , G7H 2B1
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40
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Jose KVJ, Beckett D, Raghavachari K. Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach. J Chem Theory Comput 2015; 11:4238-47. [DOI: 10.1021/acs.jctc.5b00647] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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41
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Sato H, Yajima T, Yamagishi A. Chiroptical Studies on Supramolecular Chirality of Molecular Aggregates. Chirality 2015; 27:659-66. [DOI: 10.1002/chir.22482] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Hisako Sato
- Graduated of Science and Engineering; Ehime University; Matsuyama Japan
| | - Tomoko Yajima
- Department of Chemistry; Ochanomizu University; Tokyo Japan
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42
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Affiliation(s)
- Veronica L. Murphy
- Department
of Chemistry and
Molecular Design Institute, New York University, 100 Washington Square East, Silver
Center, Room 1001, New York, New York 10003, United States
| | - Bart Kahr
- Department
of Chemistry and
Molecular Design Institute, New York University, 100 Washington Square East, Silver
Center, Room 1001, New York, New York 10003, United States
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43
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Tedesco D, Bertucci C. Induced circular dichroism as a tool to investigate the binding of drugs to carrier proteins: Classic approaches and new trends. J Pharm Biomed Anal 2015; 113:34-42. [PMID: 25769668 DOI: 10.1016/j.jpba.2015.02.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 10/24/2022]
Abstract
Induced circular dichroism (ICD) is a spectroscopic phenomenon that provides versatile and useful methods for characterizing the structural and dynamic properties of the binding of drugs to target proteins. The understanding of biorecognition processes at the molecular level is essential to discover and validate new pharmacological targets, and to design and develop new potent and selective drugs. The present article reviews the main applications of ICD to drug binding studies on serum carrier proteins, going from the classic approaches for the derivation of drug binding parameters and the identification of binding sites, to an overview of the emerging trends for the characterization of binding modes by means of quantum chemical (QC) techniques. The advantages and limits of the ICD methods for the determination of binding parameters are critically reviewed; the capability to investigate the binding interactions of drugs and metabolites to their target proteins is also underlined, as well as the possibility of characterizing the binding sites to obtain a complete picture of the binding mechanism and dynamics. The new applications of ICD methods to identify stereoselective binding modes of drug/protein complexes are then reviewed with relevant examples. The combined application of experimental ICD spectroscopy and QC calculations is shown to identify qualitatively the bound conformations of ligands to target proteins even in the absence of a detailed structure of the binding sites, either obtained from experimental X-ray crystallography and NMR measurements or from computational models of the complex.
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Affiliation(s)
- Daniele Tedesco
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Carlo Bertucci
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy.
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44
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Poopari MR, Dezhahang Z, Shen K, Wang L, Lowary TL, Xu Y. Absolute Configuration and Conformation of Two Fráter–Seebach Alkylation Reaction Products by Film VCD and ECD Spectroscopic Analyses. J Org Chem 2014; 80:428-37. [DOI: 10.1021/jo502438a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mohammad Reza Poopari
- Department of Chemistry, University of Alberta, 11227 Saskatchewan
Drive, Edmonton, Alberta T6G
2G2, Canada
| | - Zahra Dezhahang
- Department of Chemistry, University of Alberta, 11227 Saskatchewan
Drive, Edmonton, Alberta T6G
2G2, Canada
| | - Ke Shen
- Department of Chemistry, University of Alberta, 11227 Saskatchewan
Drive, Edmonton, Alberta T6G
2G2, Canada
| | - Lei Wang
- Department of Chemistry, University of Alberta, 11227 Saskatchewan
Drive, Edmonton, Alberta T6G
2G2, Canada
| | - Todd L. Lowary
- Department of Chemistry, University of Alberta, 11227 Saskatchewan
Drive, Edmonton, Alberta T6G
2G2, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, 11227 Saskatchewan
Drive, Edmonton, Alberta T6G
2G2, Canada
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45
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Tedesco D, Zanasi R, Kirchner B, Bertucci C. Short-range solvation effects on chiroptical properties: a time-dependent density functional theory and ab initio molecular dynamics computational case study on austdiol. J Phys Chem A 2014; 118:11751-7. [PMID: 25479132 DOI: 10.1021/jp511428v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The description of solvation effects on the chiroptical properties of chiral molecules is still a difficult challenge in the field of computational spectroscopy; this issue is critical in stereochemical characterization, since a reliable assessment of absolute configuration requires high accuracy. The present case study reports the huge effect of solvation on the chiroptical properties of austdiol, a fungal metabolite of known stereochemistry. Standard protocols based on time-dependent density functional theory calculations failed to reproduce its experimental chiroptical properties in methanol. When short-range solvation effects are explicitly considered by means of ab initio molecular dynamics, the correlation between calculated and experimental data is greatly improved because of a better description of the chiral environment around the ketone chromophore, showing that the modeling of subtle solvent-induced perturbations may require the most accurate computational methods.
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Affiliation(s)
- Daniele Tedesco
- Department of Pharmacy and Biotechnology, University of Bologna , Via Belmeloro 6, I-40126 Bologna, Italy
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46
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Jorge FE, Jorge SS, Suave RN. Electronic circular dichroism of chiral alkenes: B3LYP and CAM-B3LYP calculations. Chirality 2014; 27:23-31. [PMID: 25283773 DOI: 10.1002/chir.22384] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 08/02/2014] [Indexed: 11/07/2022]
Abstract
Time-dependent density functional theory (TDDFT) calculations of electronic circular dichroism (ECD) are widely used to determine absolute configurations (ACs) of chiral molecules. Two very popular DFT exchange-correlation functionals, one hybrid (B3LYP) and one long-range corrected (CAM-B3LYP), along with a hierarchical sequence of basis sets were investigated, and the ECD spectra predicted for eight alkenes and compared to gas-phase experimental spectra. Little variation in predicted ECD spectra was found with the basis set size enlargement, but the sensitivity to the functional is greater. Good agreement was obtained only with the CAM-B3LYP functional, leading to the conclusion that TDDFT calculations of ECD spectra can routinely provide reliable ACs if and only if an appropriate functional is used. For camphene, twistene, syn-(E)-bisfenchylidene, and phyllocladene, solvent effects were estimated.
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Affiliation(s)
- Francisco E Jorge
- Departamento de Física, Universidade Federal do Espírito Santo, Vitória, Brazil
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47
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Derewacz D, McNees CR, Scalmani G, Covington CL, Shanmugam G, Marnett LJ, Polavarapu PL, Bachmann BO. Structure and Stereochemical Determination of Hypogeamicins from a Cave-Derived Actinomycete. JOURNAL OF NATURAL PRODUCTS 2014; 77:1759-63. [PMID: 25046128 PMCID: PMC4334282 DOI: 10.1021/np400742p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 05/07/2023]
Abstract
Culture extracts from the cave-derived actinomycete Nonomuraea specus were investigated, resulting in the discovery of a new S-bridged pyronaphthoquinone dimer and its monomeric progenitors designated hypogeamicins A-D (1-4). The structures were elucidated using NMR spectroscopy, and the relative stereochemistries of the pyrans were inferred using NOE and comparison to previously reported compounds. Absolute stereochemistry was determined using quantum chemical calculations of specific rotation and vibrational and electronic circular dichroism spectra, after an extensive conformational search and including solute-solvent polarization effects, and comparing with the corresponding experimental data for the monomeric congeners. Interestingly, the dimeric hypogeamicin A (1) was found to be cytotoxic to the colon cancer derived cell line TCT-1 at low micromolar ranges, but not bacteria, whereas the monomeric precursors possessed antibiotic activity but no significant TCT-1 cytotoxicity.
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Affiliation(s)
- Dagmara
K. Derewacz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - C. Ruth McNees
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | | | - Cody L. Covington
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ganesh Shanmugam
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lawrence J. Marnett
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Prasad L. Polavarapu
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brian O. Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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48
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Dezhahang Z, Poopari MR, Hernández FE, Diaz C, Xu Y. Diastereomeric preference of a triply axial chiral binaphthyl based molecule: a concentration dependent study by chiroptical spectroscopies. Phys Chem Chem Phys 2014; 16:12959-67. [DOI: 10.1039/c4cp01704h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Polavarapu PL, Covington CL. Comparison of experimental and calculated chiroptical spectra for chiral molecular structure determination. Chirality 2014; 26:539-52. [PMID: 24644231 DOI: 10.1002/chir.22316] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/26/2014] [Accepted: 02/07/2014] [Indexed: 01/30/2023]
Abstract
For three different chiroptical spectroscopic methods, namely, vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and Raman optical activity (ROA), the measures of similarity of the experimental spectra to the corresponding spectra predicted using quantum chemical theories are summarized. In determining the absolute configuration and/or predominant conformations of chiral molecules, these similarity measures provide numerical estimates of agreement between experimental observations and theoretical predictions. Selected applications illustrating the similarity measures for absorption, circular dichroism, and corresponding dissymmetry factor (DF) spectra, in the case of VCD and ECD, and for Raman, ROA, and circular intensity differential (CID) spectra in the case of ROA, are presented. The analysis of similarity in DF or CID spectra is considered to be much more discerning and accurate than that in absorption (or Raman) and circular dichroism (or ROA) spectra, undertaken individually.
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50
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Zawatzky K, Herwig P, Grieser M, Heber O, Jordon-Thaden B, Krantz C, Novotný O, Repnow R, Schurig V, Schwalm D, Vager Z, Wolf A, Kreckel H, Trapp O. Coulomb Explosion Imaged Cryptochiral (R,R)-2,3-Dideuterooxirane: Unambiguous Access to the Absolute Configuration of (+)-Glyceraldehyde. Chemistry 2014; 20:5555-8. [DOI: 10.1002/chem.201400296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Indexed: 11/05/2022]
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