1
|
Jung Y, Mitsuhashi T, Kageyama K, Kikuchi T, Sato S, Fujita M. Conformational Analysis of (+)-Germacrene D-4-ol Using the Crystalline Sponge Method to Elucidate the Origin of its Instability. Chemistry 2024; 30:e202400512. [PMID: 38742865 DOI: 10.1002/chem.202400512] [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: 02/04/2024] [Revised: 04/04/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
Unsaturated cyclic terpenes often exhibit instability due to the proximation of C=C bonds in the cyclic skeleton, leading to nonenzymatic degradation. In this study, the crystalline sponge (CS) method was employed for the X-ray conformational analysis of a minute amount of oily and cyclic terpene compound, (+)-germacrene D-4-ol, which was produced by a terpene synthase OILTS under in vitro conditions. The CS method revealed a reactive conformation of the cyclic terpene with proximal double bonds. Under weakly acidic in vivo conditions, OILTS gave four pseudo-natural products or artifacts. The CS method also elucidated the structures of these degraded compounds, proposing a degradation mechanism triggered by the transannular reactions.
Collapse
Affiliation(s)
- Youngcheol Jung
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Takaaki Mitsuhashi
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Ko Kageyama
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubaracho, Akishima, Tokyo, 196-8666, Japan
| | - Sota Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
- Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
- Tokyo College, Institutes for Advanced Study, The University of Tokyo, Mitsui Link Lab Kashiwanoha 1, FS CREATION, 6-6-2 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| |
Collapse
|
2
|
Ou G, Zhang Y, Wang Q, Tan Y, Zhou Q, Zeng F. Host-Guest Cocrystallization of Phenanthrene[2]arene Macrocycles Facilitating Structure Determination of Liquid Organic Molecules. Molecules 2024; 29:2523. [PMID: 38893399 PMCID: PMC11173633 DOI: 10.3390/molecules29112523] [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: 04/25/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Single-crystal X-ray diffraction analysis has emerged as the most reliable method for determining the structures of organic molecules. However, numerous analytes, such as liquid organic molecules, pose challenges in crystallization, making their structures directly elusive via X-ray crystallography methods. Herein, we introduced the rapid cocrystallization of a macrocycle named phenanthrene[2]arene (PTA, host) with 15 liquid organic molecules (guests). The guest liquid organic molecules were successively cocrystallized with the aid of the PTA host. Moreover, the chemical structures of the liquid organic molecules could be determined through single-crystal X-ray diffraction analysis. PTA exhibited high adaptivity and was capable of encapsulating liquid organic molecules without forming covalent bonds or strong directional interactions. The results revealed that the adaptive crystals of PTA exhibited excellent cocrystallization capacity. Weak noncovalent interactions between the host and guest molecules were crucial for organizing the guests in an ordered pattern.
Collapse
Affiliation(s)
- Guangchuan Ou
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, China; (Q.W.); (Y.T.); (Q.Z.)
| | - Yanfeng Zhang
- Agricultural Comprehensive Service Center, Yongzhou 425000, China;
| | - Qiong Wang
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, China; (Q.W.); (Y.T.); (Q.Z.)
| | - Yingzhi Tan
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, China; (Q.W.); (Y.T.); (Q.Z.)
| | - Qiang Zhou
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, China; (Q.W.); (Y.T.); (Q.Z.)
| | - Fei Zeng
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, China; (Q.W.); (Y.T.); (Q.Z.)
| |
Collapse
|
3
|
Zigon N, Solano F, Auban-Senzier P, Grolleau S, Devic T, Zolotarev PN, Proserpio DM, Barszcz B, Olejniczak I, Avarvari N. A redox active rod coordination polymer from tetrakis(4-carboxylic acid biphenyl)tetrathiafulvalene. Dalton Trans 2024; 53:4805-4813. [PMID: 38372362 DOI: 10.1039/d3dt04280d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
An enlarged version of the ubiquitous tetrathiafulvalene-tetrabenzoic acid is described, with 4,4'-biphenyl moieties as spacers between the coordination moieties and the electroactive core. The obtained rectangular ligand has a 14 × 22 Å2 size and is combined with Zn(II) under solvothermal conditions to yield a coordination polymer endowed with large cavities of ca. 15 × 11 Å2/10 × 10 Å2. The topology of the material is discussed in detail using the Points of Extension and Metals (PE&M) or the Straight-rod (STR) representation, and the sqc1121 or tfo topological type of the structure is observed, respectively. Its stability towards solvent removal and electrical properties are discussed. The material does not present any permanent porosity upon desolvation according to nitrogen sorption measurements at 77 K. Nevertheless, a significant increase in conductivity is observed on compressed pellets of the material upon post-synthetic oxidation with iodine. Raman spectroscopy combined with density functional theory (DFT) calculations has been used to characterize the oxidation state of tetrakis(4-carboxylic acid biphenyl)tetrathiafulvalene for coordination polymers.
Collapse
Affiliation(s)
- Nicolas Zigon
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France.
| | - Federica Solano
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France.
| | - Pascale Auban-Senzier
- Université Paris-Saclay, CNRS, UMR 8502, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Stéphane Grolleau
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, F-44000 Nantes, France
| | - Thomas Devic
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, F-44000 Nantes, France
| | - Pavel N Zolotarev
- Università degli studi di Milano, Dipartimento di Chimica, Via Golgi 19, 20133 Milano, Italy
| | - Davide M Proserpio
- Università degli studi di Milano, Dipartimento di Chimica, Via Golgi 19, 20133 Milano, Italy
| | - Bolesław Barszcz
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznań, Poland
| | - Iwona Olejniczak
- Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego 17, 60-179 Poznań, Poland
| | - Narcis Avarvari
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France.
| |
Collapse
|
4
|
Carroll RC, Harrowven DC, Pearce JE, Coles SJ. A systematic study of the interplay between guest molecule structure and intermolecular interactions in crystalline sponges. IUCRJ 2023; 10:497-508. [PMID: 37409807 PMCID: PMC10324488 DOI: 10.1107/s2052252523005146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
Utilization of the crystalline sponge {[(ZnI2)3(tpt)2·x(solvent)]n} method has enabled characterization of a novel family of synthetic organic oils. The systematic structural differences and diversity of functional groups offered by 13 related molecular adsorbates provide a detailed quantitative understanding of the relationship between the guest structure, its conformation, and the type of intermolecular interactions adopted with neighbouring guests and the host framework. This analysis is extended to assess the connection of these factors to the resulting quality indicators for a particular molecular structure elucidation.
Collapse
Affiliation(s)
- Robert C. Carroll
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
| | - David C. Harrowven
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
| | - James E. Pearce
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
| | - Simon J. Coles
- School of Chemistry, University of Southampton, University Road, Southampton, Hampshire SO17 1BJ, United Kingdom
| |
Collapse
|
5
|
Metherall JP, Carroll RC, Coles SJ, Hall MJ, Probert MR. Advanced crystallisation methods for small organic molecules. Chem Soc Rev 2023; 52:1995-2010. [PMID: 36857636 DOI: 10.1039/d2cs00697a] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Molecular materials based on small organic molecules often require advanced structural analysis, beyond the capability of spectroscopic techniques, to fully characterise them. In such cases, diffraction methods such as single crystal X-ray diffraction (SCXRD), are one of the most powerful tools available to researchers, providing molecular and structural elucidation at atomic level resolution, including absolute stereochemistry. However SCXRD, and related diffraction methods, are heavily dependent on the availability of suitable, high-quality crystals, thus crystallisation often becomes the major bottleneck in preparing samples. Following a summary of classical methods for the crystallisation of small organic molecules, this review will focus on a number of recently developed advanced methods for crystalline material sample preparation for SCXRD. This review will cover two main areas of modern small organic molecule crystallisation, namely the inclusion of molecules within host complexes (e.g., "crystalline sponge" and tetraaryladamantane based inclusion chaperones) and the use of high-throughput crystallisation, employing "under-oil" approaches (e.g., microbatch under-oil and ENaCt). Representative examples have been included for each technique, together with a discussion of their relative advantages and limitations to aid the reader in selecting the most appropriate technique to overcome a specific analytical challenge.
Collapse
Affiliation(s)
- J P Metherall
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
| | - R C Carroll
- University of Southampton, School of Chemistry, Southampton, SO17 1BJ, UK
| | - S J Coles
- University of Southampton, School of Chemistry, Southampton, SO17 1BJ, UK
| | - M J Hall
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
| | - M R Probert
- Newcastle University, Chemistry - School of Natural Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK.
| |
Collapse
|
6
|
Highly Luminescent Crystalline Sponge: Sensing Properties and Direct X-ray Visualization of the Substrates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228055. [PMID: 36432154 PMCID: PMC9692560 DOI: 10.3390/molecules27228055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022]
Abstract
A phenomenon of crystalline sponge is represented by guest-dependent structural fluidity of the host polymeric lattice in highly crystalline sorbents, such as metal-organic frameworks, driven by multiple weak intermolecular interactions. Such induced fitting in MOFs is a valuable property in selective adsorption, guest determination by single-crystal XRD and in-situ structural analysis under external stimuli. In this work, a porous three-dimensional metal-organic framework [Eu2(DMF)4(ttdc)3]·4.45DMF (1DMF; DMF = N,N-dimethylformamide, ttdc2- = trans-thienothiophenedicarboxylate anion) was applied as a crystalline sponge bearing luminescent functionality to couple its sensing properties with direct structural determination of the adsorbed molecules. As a result, the paper discusses crystal structures and luminescent properties for the successfully obtained new adducts with the crystallographic formulae [Eu2(DMSO)4(ttdc)3]·2.5DMSO·2.2H2O (1DMSO; DMSO = dimethylsulfoxide), [Eu2(DMF)4(ttdc)3]·3phet (1phet; phet = phenylethanal) and [Eu2(DMF)3.5(cin)0.5(ttdc)3]·1.64cin (1cin; cin = trans-cinnamaldehyde). As a result of inclusion of DMSO into 1, a slight increase in the quantum yield and excited state phosphorescence lifetime was observed, while the adsorption of phet leads to a considerable (up to three times) decrease in the corresponding values. The incorporation of cinnamal results in a full quenching of QY, from 20% down to zero, and a more than order of magnitude diminishing of the excited state lifetime compared to the initial 1DMF. The effective sensing of cinnamal was explained from the structural point of view by its direct coordination to the Eu3+ emitter, as well as by multiple weak intermolecular interactions with ttdc antenna ligand, both capable of enhancing the non-radiative energy dissipation.
Collapse
|
7
|
Meurer F, von Essen C, Kühn C, Puschmann H, Bodensteiner M. The benefits of Cu Kβ radiation for the single-crystal X-ray structure determination of crystalline sponges. IUCRJ 2022; 9:349-354. [PMID: 35546798 PMCID: PMC9067116 DOI: 10.1107/s2052252522002147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/23/2022] [Indexed: 06/15/2023]
Abstract
The crystalline sponge method facilitates the X-ray structure determination of samples that do not crystallize or are too sparsely available to afford viable crystallization. By including these materials in a metal-organic framework, the structure of the guest molecules can be determined. Some of the inherent difficulties of this method are discussed and the use of Cu Kβ radiation is presented as a simple and effective means to improve the quality of the diffraction data that can be obtained from a sponge crystal.
Collapse
Affiliation(s)
- Florian Meurer
- University of Regensburg, Universitätsstrasse 31, Regensburg, 93053 Bayern, Germany
| | - Carolina von Essen
- Merck Innovation Center, Merck KGaA, Frankfurter Strasse 250, Darmstadt, 64293 Hessen, Germany
| | - Clemens Kühn
- Merck Innovation Center, Merck KGaA, Frankfurter Strasse 250, Darmstadt, 64293 Hessen, Germany
| | - Horst Puschmann
- OlexSys Ltd, Chemistry Department, Durham University, Durham DH1 3LE, United Kingdom
| | - Michael Bodensteiner
- University of Regensburg, Universitätsstrasse 31, Regensburg, 93053 Bayern, Germany
| |
Collapse
|
8
|
Negro C, Escamilla P, Bruno R, Ferrando‐Soria J, Armentano D, Pardo E. Metal-Organic Frameworks as Unique Platforms to Gain Insight of σ-Hole Interactions for the Removal of Organic Dyes from Aquatic Ecosystems. Chemistry 2022; 28:e202200034. [PMID: 35188315 PMCID: PMC9314587 DOI: 10.1002/chem.202200034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 11/08/2022]
Abstract
The combination of high crystallinity and rich host-guest chemistry in metal-organic frameworks (MOFs), have situated them in an advantageous position, with respect to traditional porous materials, to gain insight on specific weak noncovalent supramolecular interactions. In particular, sulfur σ-hole interactions are known to play a key role in the biological activity of living beings as well as on relevant molecular recognitions processes. However, so far, they have been barely explored. Here, we describe both how the combination of the intrinsic features of MOFs, especially the possibility of using single-crystal X-ray crystallography (SCXRD), can be an extremely valuable tool to gain insight on sulfur σ-hole interactions, and how their rational exploitation can be enormously useful in the efficient removal of harmful organic molecules from aquatic ecosystems. Thus, we have used a MOF, prepared from the amino acid L-methionine and possessing channels decorated with -CH2 CH2 SCH3 thioalkyl chains, to remove a family of organic dyes at very low concentrations (10 ppm) from water. This MOF is able to efficiently capture the four dyes in a very fast manner, reaching within five minutes nearly the maximum removal. Remarkably, the crystal structure of the different organic dyes within MOFs channels could be determined by SCXRD. This has enabled us to directly visualize the important role sulfur σ-hole interactions play on the removal of organic dyes from aqueous solutions, representing one of the first studies on the rational exploitation of σ-hole interactions for water remediation.
Collapse
Affiliation(s)
- Cristina Negro
- Instituto de Ciencia Molecular (ICMOL)Universitat de ValènciaPaterna46980, ValènciaSpain
| | - Paula Escamilla
- Instituto de Ciencia Molecular (ICMOL)Universitat de ValènciaPaterna46980, ValènciaSpain
| | - Rosaria Bruno
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria87030Rende, CosenzaItaly
| | - Jesus Ferrando‐Soria
- Instituto de Ciencia Molecular (ICMOL)Universitat de ValènciaPaterna46980, ValènciaSpain
| | - Donatella Armentano
- Dipartimento di Chimica e Tecnologie ChimicheUniversità della Calabria87030Rende, CosenzaItaly
| | - Emilio Pardo
- Instituto de Ciencia Molecular (ICMOL)Universitat de ValènciaPaterna46980, ValènciaSpain
| |
Collapse
|
9
|
Ou GC, Chen HY, Wang Q, Zhou Q, Zeng F. Structure and absolute configuration of liquid molecules based on adamantane derivative cocrystallization. RSC Adv 2022; 12:6459-6462. [PMID: 35424635 PMCID: PMC8981717 DOI: 10.1039/d1ra09284g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/31/2022] [Indexed: 12/03/2022] Open
Abstract
Liquid molecules are difficult to crystallize, and their structures and absolute configurations cannot be directly determined by X-ray crystallography. We herein report the rapid cocrystallization of tetraaryladamantanes with liquid molecules. The structure of the liquid small molecules can be obtained by determining the crystal structure of the cocrystallized compound. The absolute configuration of chiral molecules can also be assigned, which cannot be accomplished by other methods such as nuclear magnetic resonance. In this paper, liquid compounds such as phenylethanol and phenylpropanol derivatives were selected. 1,3,5,7-Tetrakis(2,4-diethoxyphenyl)adamantane (TEO) powder was heated and dissolved in liquid molecules and allowed to stand overnight to undergo cocrystallization. The results show that the single-crystal structures and the absolute configurations of 16 liquid molecules were determined by cocrystallization, and the homochiral natures of chiral compounds were confirmed by solid circular dichroism spectral measurements.
Collapse
Affiliation(s)
- Guang-Chuan Ou
- College of Chemistry and Bioengineering/Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan University of Science and Engineering Yongzhou Hunan 425199 P.R. China
| | - Hai-Yang Chen
- Medical College, Guangxi University Nanning Guangxi 530004 P.R. China
| | - Qiong Wang
- College of Chemistry and Bioengineering/Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan University of Science and Engineering Yongzhou Hunan 425199 P.R. China
| | - Qiang Zhou
- College of Chemistry and Bioengineering/Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan University of Science and Engineering Yongzhou Hunan 425199 P.R. China
| | - Fei Zeng
- College of Chemistry and Bioengineering/Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan University of Science and Engineering Yongzhou Hunan 425199 P.R. China
| |
Collapse
|
10
|
Chen P, Liu Y, Zhang C, Huang F, Liu L, Sun J. Crystalline Sponge Method by Three-Dimensional Electron Diffraction. Front Mol Biosci 2022; 8:821927. [PMID: 35198600 PMCID: PMC8859408 DOI: 10.3389/fmolb.2021.821927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
Abstract
The crystalline sponge method has shown to be a novel strategy for the structure determination of noncrystalline, oily, or trace amount of a compound. A target compound was absorbed and oriented orderly in the pregrown porous crystal for x-ray diffraction analysis. However, the diffusion in the micron-sized crystals is rather difficult. Lots of trial-and-error experiments are needed to optimize the guest-soaking process and to improve data quality. Nanocrystals are better in diffusion, yet it could not conduct a single crystal x-ray diffraction (SCXRD) analysis. Three-dimensional electron diffraction (3D-ED) is a powerful diffraction tool for the structure determination of small crystals. In this work, we successfully carried out the crystalline sponge method by 3D-ED technique using {(ZnI2)3-[2,4,6-tris(4-pyridyl)-1,3,5-triazine]2·x(guest)}n (1-Guest) porous complex nanocrystals. On account of the better diffuse ability of nanocrystals, the time needed for solvent exchange and guest soaking protocols are shortened 50-fold faster versus the original protocol. The crystal structure of the crystalline sponge incorporated with three different guests was fully resolved using a merged dataset. The structure model was identical to previously reported ones using x-ray, showing that the accuracy of the 3D-ED was comparable with SCXRD. The refinement results can also give the precise occupancy of the guest molecule soaked in the porous crystal. This work not only provides a new data collection strategy for crystalline sponge method but also demonstrates the potential of 3D-ED techniques to study host-guest interaction by solving the fine structure of porous material.
Collapse
Affiliation(s)
- Pohua Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yang Liu
- ReadCrystal Technology Co., Jiangsu, China
| | | | - Fei Huang
- ReadCrystal Technology Co., Jiangsu, China
| | | | - Junliang Sun
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| |
Collapse
|
11
|
Zigon N, Duplan V, Wada N, Fujita M. Crystalline Sponge Method: X‐ray Structure Analysis of Small Molecules by Post‐Orientation within Porous Crystals—Principle and Proof‐of‐Concept Studies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Vincent Duplan
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Naoki Wada
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Division of Advanced Molecular Science Institute for Molecular Science (IMS) 5-1 Higashiyama Myodaiji Okazaki Aichi 444-8787 Japan
| |
Collapse
|
12
|
Taniguchi Y, Kikuchi T, Sato S, Fujita M. Comprehensive Structural Analysis of the Bitter Components in Beer by the HPLC-Assisted Crystalline Sponge Method. Chemistry 2021; 28:e202103339. [PMID: 34755407 DOI: 10.1002/chem.202103339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/10/2022]
Abstract
Trans-iso-α-acid is one of the main contributors to the bitter taste of fresh beer and is known to transform into various derivatives during beer aging. However, structural characterization of the derivatives has been a challenging task because of the formation of too many components. Herein, we report that most of the transformation products of trans-iso-α-acid, isolated in this study in only small quantities by HPLC, can be structurally analyzed with the crystalline sponge method. Thirteen compounds, including eight that were previously unreported, have been successfully isolated and analyzed with complete assignment of their absolute configuration. This provides an improved understanding of the chemical transformations that occur during beer aging.
Collapse
Affiliation(s)
- Yoshimasa Taniguchi
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company, Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo, 196-8666, Japan
| | - Sota Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Integrated Molecular Structure Analysis Laboratory Social Cooperation Program, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Integrated Molecular Structure Analysis Laboratory Social Cooperation Program, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Division of Advanced Molecular Science, Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| |
Collapse
|
13
|
Xu H, Schotte C, Cox RJ, Dickschat JS. Stereochemical characterisation of the non-canonical α-humulene synthase from Acremonium strictum. Org Biomol Chem 2021; 19:8482-8486. [PMID: 34533184 DOI: 10.1039/d1ob01769a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The non-canonical fungal α-humulene synthase was investigated through isotopic labelling experiments for its stereochemical course regarding inversion or retention at C-1, the face selectivity at C-11, and the stereoselectivity of the final deprotonation. A new and convenient desymmetrisation strategy was developed to enable a full stereochemical analysis of the catalysed steps to the achiral α-humulene product from stereoselectively labelled farnesyl diphosphate.
Collapse
Affiliation(s)
- Houchao Xu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany.
| | - Carsten Schotte
- Institute of Organic Chemistry, University of Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Russell J Cox
- Institute of Organic Chemistry, University of Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany.
| |
Collapse
|
14
|
Taniguchi Y, Miwa M, Kitada N. Crystalline sponge X-ray analysis coupled with supercritical fluid chromatography: a novel analytical platform for the rapid separation, isolation, and characterization of analytes. Analyst 2021; 146:5230-5235. [PMID: 34373868 DOI: 10.1039/d1an00948f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystalline sponge (CS) based X-ray diffraction (XRD) analysis allows for the observation of the structure of an analyte, including its absolute configuration. Herein we report a powerful analytical platform for the separation, isolation, and structural elucidation of a target analyte in a seamless way by coupling supercritical fluid chromatography (SFC) with CS-based XRD analysis (SFC-CSXRD). The efficacy of this methodology is demonstrated by the rapid characterization of regio- and stereoisomers using three types of CSs with differing tolerances to the solvents used in SFC and guest-soaking.
Collapse
Affiliation(s)
- Yoshimasa Taniguchi
- Kirin Central Research Institute, Research & Development Division, Kirin Holdings Company Ltd., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | | | | |
Collapse
|
15
|
Zigon N, Duplan V, Wada N, Fujita M. Crystalline Sponge Method: X-ray Structure Analysis of Small Molecules by Post-Orientation within Porous Crystals-Principle and Proof-of-Concept Studies. Angew Chem Int Ed Engl 2021; 60:25204-25222. [PMID: 34109717 DOI: 10.1002/anie.202106265] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Indexed: 01/05/2023]
Abstract
This Review discusses, along with the historical background, the principles as well as proof-of-concept studies of the crystalline sponge (CS) method, a new single-crystal X-ray diffraction (SCXRD) method for the analysis of the structures of small molecules without sample crystallization. The method uses single-crystalline porous coordination networks (crystalline sponges) that can absorb small guest molecules within their pores. The absorbed guest molecules are ordered in the pores through molecular recognition and become observable by conventional SCXRD analysis. The complex {[(ZnI2 )3 (tpt)2 ]⋅x(solvent)}n (tpt=tris(4-pyridyl)-1,3,5-triazine) was first proposed as a crystalline sponge and has been most generally used. Crystalline sponges developed later are also discussed here. The principle of the CS method can be described as "post-crystallization" of the absorbed guest, whose ordering is templated by the pre-latticed cavities. The method has been widely applied to synthetic chemistry as well as natural product studies, for which proof-of-concept examples will be shown here.
Collapse
Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Vincent Duplan
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Naoki Wada
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Division of Advanced Molecular Science, Institute for Molecular Science (IMS), 5-1 Higashiyama Myodaiji, Okazaki, Aichi, 444-8787, Japan
| |
Collapse
|
16
|
Bemis CY, Ungarean CN, Shved AS, Jamieson CS, Hwang T, Lee KS, Houk KN, Sarlah D. Total Synthesis and Computational Investigations of Sesquiterpene-Tropolones Ameliorate Stereochemical Inconsistencies and Resolve an Ambiguous Biosynthetic Relationship. J Am Chem Soc 2021; 143:6006-6017. [DOI: 10.1021/jacs.1c02150] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christopher Y. Bemis
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Chad N. Ungarean
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Alexander S. Shved
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Cooper S. Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Taehwan Hwang
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Ken S. Lee
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - David Sarlah
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| |
Collapse
|
17
|
Cardenal A, Ramadhar TR. Application of Crystalline Matrices for the Structural Determination of Organic Molecules. ACS CENTRAL SCIENCE 2021; 7:406-414. [PMID: 33791424 PMCID: PMC8006175 DOI: 10.1021/acscentsci.0c01492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 06/12/2023]
Abstract
While single-crystal X-ray diffraction (SC-XRD) is one of the most powerful structural determination techniques for organic molecules, the requirement of obtaining a suitable crystal for analysis limits its applicability, particularly for liquids and amorphous solids. The emergent use of preformed porous crystalline matrices that can absorb organic compounds and stabilize them via host-guest interactions for observation via SC-XRD offers a way to overcome this hindrance. A topical and current discussion of SC-XRD in organic chemistry and the use of preformed matrices for the in crystallo analysis of organic compounds, with a particular focus on the absolute structure determination of chiral molecules, is presented. Preformed crystalline matrices that are covered include metal-organic frameworks (MOFs) as used in the crystalline sponge method, metal-organic polyhedra (MOPs, coordination cages), porous organic materials (POMs)/porous organic molecular crystals (POMCs), and biological scaffolds. An outlook and perspective on the current technology and on its future directions is provided.
Collapse
Affiliation(s)
- Ashley
D. Cardenal
- Department of Chemistry, Howard University, Washington, DC 20059, United States
| | - Timothy R. Ramadhar
- Department of Chemistry, Howard University, Washington, DC 20059, United States
| |
Collapse
|
18
|
Yu MH, Liu XT, Space B, Chang Z, Bu XH. Metal-organic materials with triazine-based ligands: From structures to properties and applications. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213518] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
19
|
Krupp F, Frey W, Richert C. Absolute Configuration of Small Molecules by Co-Crystallization. Angew Chem Int Ed Engl 2020; 59:15875-15879. [PMID: 32441841 PMCID: PMC7540501 DOI: 10.1002/anie.202004992] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 12/18/2022]
Abstract
The most reliable method to determine the absolute configuration of chiral molecules is X-ray crystallography, but small molecules can be difficult to crystallize. We report rapid co-crystallization of tetraaryladamantanes with small molecules as different as n-decane to nicotine to produce crystals for X-ray analysis and the assignment of absolute configuration when the molecules are chiral. A screen of 52 diverse compounds gave inclusion in co-crystals for 88 % of all cases and a high-resolution structure in 77 % of cases. Furthermore, starting from three milligrams of analyte, a combination of NMR spectroscopy and X-ray crystallography produced a full structure in less than three days using an adamantane crystallization chaperone that encapsulates the analyte at room temperature.
Collapse
Affiliation(s)
- Felix Krupp
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Wolfgang Frey
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Clemens Richert
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| |
Collapse
|
20
|
Krupp F, Frey W, Richert C. Absolute Configuration of Small Molecules by Co‐Crystallization. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Felix Krupp
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Wolfgang Frey
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| | - Clemens Richert
- Institute of Organic Chemistry University of Stuttgart 70569 Stuttgart Germany
| |
Collapse
|
21
|
Young RJ, Huxley MT, Pardo E, Champness NR, Sumby CJ, Doonan CJ. Isolating reactive metal-based species in Metal-Organic Frameworks - viable strategies and opportunities. Chem Sci 2020; 11:4031-4050. [PMID: 34122871 PMCID: PMC8152792 DOI: 10.1039/d0sc00485e] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/19/2020] [Indexed: 02/01/2023] Open
Abstract
Structural insight into reactive species can be achieved via strategies such as matrix isolation in frozen glasses, whereby species are kinetically trapped, or by confinement within the cavities of host molecules. More recently, Metal-Organic Frameworks (MOFs) have been used as molecular scaffolds to isolate reactive metal-based species within their ordered pore networks. These studies have uncovered new reactivity, allowed observation of novel metal-based complexes and clusters, and elucidated the nature of metal-centred reactions responsible for catalysis. This perspective considers strategies by which metal species can be introduced into MOFs and highlights some of the advantages and limitations of each approach. Furthermore, the growing body of work whereby reactive species can be isolated and structurally characterised within a MOF matrix will be reviewed, including discussion of salient examples and the provision of useful guidelines for the design of new systems. Novel approaches that facilitate detailed structural analysis of reactive chemical moieties are of considerable interest as the knowledge garnered underpins our understanding of reactivity and thus guides the synthesis of materials with unprecedented functionality.
Collapse
Affiliation(s)
- Rosemary J Young
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
- School of Chemistry, The University of Nottingham Nottingham UK
| | - Michael T Huxley
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
| | - Emilio Pardo
- Institute of Molecular Science, University of Valencia Valencia Spain
| | | | - Christopher J Sumby
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
| | - Christian J Doonan
- Department of Chemistry, Centre for Advanced Nanomaterials, The University of Adelaide Adelaide Australia
| |
Collapse
|
22
|
Tominaga M, Hyodo T, Maekawa Y, Kawahata M, Yamaguchi K. One‐Step Synthesis of Cyclophanes as Crystalline Sponge and Their [2]Catenanes through S
N
Ar Reactions. Chemistry 2020; 26:5157-5161. [DOI: 10.1002/chem.201905854] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/24/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Masahide Tominaga
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
| | - Tadashi Hyodo
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
| | - Yumi Maekawa
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
| | - Masatoshi Kawahata
- Showa Pharmaceutical University 3–3165 Higashi-Tamagawagakuen, Machida Tokyo 194-8543 Japan
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa CampusTokushima Bunri University 1314-1 Shido, Sanuki Kagawa 769-2193 Japan
| |
Collapse
|
23
|
Abstract
Host-guest interactions are the key to the supramolecular chemistry and the further application of the receptors to study the structural details of the small guest molecules. Crystalline sponges as a kind of supramolecular receptor need to be investigated in terms of the binding ability with the guests. We found in this work that one guest with σ-hole donors and another with electron-donating species were separately entrapped in two distinct channels of the host framework via the crystalline sponge method. Halogen bonding and weak hydrogen bonding were detected between the host and the two guests, respectively. The ability of the crystalline sponge to absorb and sort guests of different types was unambiguously confirmed by X-ray crystallography.
Collapse
Affiliation(s)
- Liangqian Yuan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, College of Chemistry , Central China Normal University , Luoyu Road 152 , Wuhan 430079 , People's Republic of China
| | - Siyu Li
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, College of Chemistry , Central China Normal University , Luoyu Road 152 , Wuhan 430079 , People's Republic of China
| | - Fangfang Pan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, College of Chemistry , Central China Normal University , Luoyu Road 152 , Wuhan 430079 , People's Republic of China
| |
Collapse
|
24
|
Li PJ, Dräger G, Kirschning A. A General Biomimetic Hetero-Diels-Alder Approach to the Core Skeletons of Xenovulene A and the Sterhirsutins A and B. Org Lett 2019; 21:998-1001. [PMID: 30694066 DOI: 10.1021/acs.orglett.8b04003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A biomimetic, regio- and stereoselective approach to the 5,6,11-tricyclic core skeleton of xenovulene A, as well as sterhirsutins A and B, is described. The key steps are a biomimetic inverse-electron-demand hetero-Diels-Alder cycloaddition of α-humulene and a ribose-derived vinyl ketone, followed by acid-catalyzed rearrangement of the 1,3-dioxolane that neighbors the resultant cyclic enol ether.
Collapse
Affiliation(s)
- Pei-Jun Li
- Institute of Organic Chemistry and Center of Biomolecular Drug Research (BMWZ) , Leibniz Universität Hannover , Schneiderberg 1 B , 30167 Hannover , Germany
| | - Gerald Dräger
- Institute of Organic Chemistry and Center of Biomolecular Drug Research (BMWZ) , Leibniz Universität Hannover , Schneiderberg 1 B , 30167 Hannover , Germany
| | - Andreas Kirschning
- Institute of Organic Chemistry and Center of Biomolecular Drug Research (BMWZ) , Leibniz Universität Hannover , Schneiderberg 1 B , 30167 Hannover , Germany
| |
Collapse
|
25
|
Kunde T, Schmidt BM. Microcrystal Electron Diffraction (MicroED) for Small-Molecule Structure Determination. Angew Chem Int Ed Engl 2018; 58:666-668. [PMID: 30548517 DOI: 10.1002/anie.201813215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Indexed: 01/08/2023]
Abstract
The development of new methods to analyze and determine molecular structures parallels the ability to accelerate synthetic research. For many decades, single-crystal analysis by X-ray diffraction (SXRD) has been the definitive tool for structural analysis at the atomic level; the drawback, however, is that a suitable single crystal of the analyte needs to be grown. The recent innovation of the crystalline sponge (CS) method allows the microanalysis of compounds simply soaked in a readily prepared CS crystal, thus circumventing the need to screen crystallization conditions while also using only a trace amount of the sample. In this context, electron diffraction for the structure determination of small molecules is discussed as potentially the next big development in this field.
Collapse
Affiliation(s)
- Tom Kunde
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Bernd M Schmidt
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| |
Collapse
|
26
|
Kunde T, Schmidt BM. Mikrokristalline Elektronenbeugung (MicroED) zur Strukturaufklärung niedermolekularer Verbindungen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201813215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tom Kunde
- Institut für Organische Chemie und Makromolekulare ChemieHeinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Deutschland
| | - Bernd M. Schmidt
- Institut für Organische Chemie und Makromolekulare ChemieHeinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Deutschland
| |
Collapse
|
27
|
DFT-calculated structures based on 1H NMR chemical shifts in solution vs. structures solved by single-crystal X-ray and crystalline-sponge methods: Assessing specific sources of discrepancies. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
28
|
Du Q, Peng J, Wu P, He H. Review: Metal-organic framework based crystalline sponge method for structure analysis. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
29
|
Abstract
The crystallography of supramolecular host-guest complexes is reviewed and discussed as a part of small molecule crystallography. In these complexes, the host binds the guests through weak supramolecular interactions, such as hydrogen and halogen bonding, cation-π, anion-π, C-H-π, π-π, C-H-anion interactions and the hydrophobic effect. As the guest often shows severe disorder, large thermal motion and low occupancies, the reliable crystallographic determination of the guest can be very demanding. The analysis of host-guest interactions using tools such as Hirshfeld and cavity volume surface analysis will help to look closely at the most important host-guest interactions. The jewel in the crown of utilizing host-guest interactions in the solid-state is the recently developed Crystalline Sponge Method (CSM) by Makoto Fujita. This method, when successful, gives an accurate and unambiguous 3-D structure of the structurally unknown guest molecule from only micro- or nanogram amounts of the guest molecule. In the case of an optically pure enantiomer, its absolute configuration can be determined.
Collapse
Affiliation(s)
- Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, Nanoscience Center, Survontie 9 B, Jyvaskyla, 40014, Finland.
| |
Collapse
|
30
|
Gee WJ. The growing importance of crystalline molecular flasks and the crystalline sponge method. Dalton Trans 2018; 46:15979-15986. [PMID: 29106430 DOI: 10.1039/c7dt03136j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article showcases recent advancements made using crystalline molecular flasks and the widening list of prospective applications for the crystalline sponge method. This expansion has coincided with an increasing number of materials termed crystalline sponges, and a report of a predictive means of identifying candidates from crystallographic databases. The crystalline sponge method's primary application has been determination of absolute configuration, and this has evolved from the analysis of carefully chosen planar aromatic guests to more diverse identification of natural products, biological metabolites, and analysis of volatile chemical components. However with time-resolved X-ray crystallography providing arguably the most informative atomic scale insights of dynamic chemical processes, this application of the crystalline sponge method may soon eclipse structural determination in terms of importance.
Collapse
Affiliation(s)
- William J Gee
- School of Physical Sciences, University of Kent, Canterbury, Kent CT2 7NH, UK.
| |
Collapse
|
31
|
de Poel W, Tinnemans PT, Duchateau ALL, Honing M, Rutjes FPJT, Vlieg E, de Gelder R. Racemic and Enantiopure Camphene and Pinene Studied by the Crystalline Sponge Method. CRYSTAL GROWTH & DESIGN 2018; 18:126-132. [PMID: 29317854 PMCID: PMC5754839 DOI: 10.1021/acs.cgd.7b00942] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/28/2017] [Indexed: 05/31/2023]
Abstract
The use of an achiral metal-organic framework for structure determination of chiral compounds is demonstrated for camphene and pinene. The structure of enantiopure β-pinene can be resolved using the crystalline sponge method. However, α-pinene cannot be resolved using enantiopure material alone because no ordering of guest molecules takes place in that case. Interestingly, enantiomeric pairs order inside the channels of the host framework when impure (+)-camphene is offered to the host, which is also the case when a racemic mixture of α-pinene is used. A mixture of (+)-α-pinene and (-)-β-pinene also leads to ordered incorporation in the host, showing the influence of the presence of an inversion center in the host framework. We further show that powder X-ray diffraction provides a direct view on incorporation of ordered guest molecules. This technique, therefore, provides a way to determine the optimal and/or minimal soaking time. In contrast, color change of the crystal only demonstrates guest uptake, not ordering. Moreover, we show that color change can also be caused by guest-induced host degradation.
Collapse
Affiliation(s)
- Wester de Poel
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Paul T. Tinnemans
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | | | - Maarten Honing
- DSM,
Resolve, Urmonderbaan
22, Geleen, 6160 MD, The Netherlands
| | - Floris P. J. T. Rutjes
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Elias Vlieg
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - René de Gelder
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
32
|
Sakurai F, Khutia A, Kikuchi T, Fujita M. X‐ray Structure Analysis of N‐Containing Nucleophilic Compounds by the Crystalline Sponge Method. Chemistry 2017; 23:15035-15040. [DOI: 10.1002/chem.201704176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Fumie Sakurai
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
| | - Anupam Khutia
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubara-cho Tokyo Akishima-shi 196–8628 Japan
| | - Makoto Fujita
- Department of Applied Chemistry School of Engineering The University of Tokyo 7-3-1 Hongo Tokyo Bunkyo-ku 113–8656 Japan
| |
Collapse
|
33
|
Yan K, Dubey R, Arai T, Inokuma Y, Fujita M. Chiral Crystalline Sponges for the Absolute Structure Determination of Chiral Guests. J Am Chem Soc 2017; 139:11341-11344. [DOI: 10.1021/jacs.7b06607] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- KaKing Yan
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ritesh Dubey
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tatsuhiko Arai
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuhide Inokuma
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, and ACCEL (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
34
|
Sairenji S, Kikuchi T, Abozeid MA, Takizawa S, Sasai H, Ando Y, Ohmatsu K, Ooi T, Fujita M. Determination of the absolute configuration of compounds bearing chiral quaternary carbon centers using the crystalline sponge method. Chem Sci 2017; 8:5132-5136. [PMID: 28970900 PMCID: PMC5615217 DOI: 10.1039/c7sc01524k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022] Open
Abstract
Determination of the absolute configuration of chiral tetra-substituted carbon centers is one of the most taxing steps in the enantioselective construction of this structural motif in asymmetric synthesis. Here, we demonstrate that the crystalline sponge method provides an effective way to crystallographically determine the absolute configuration of organic compounds bearing chiral quaternary carbons (including tetra-substituted ones) that are synthesized by recently developed enantioselective catalytic reactions.
Collapse
Affiliation(s)
- Shiho Sairenji
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
- JST ACCEL , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Takashi Kikuchi
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
- JST ACCEL , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Mohamed Ahmed Abozeid
- The Institute of Scientific and Industrial Research (ISIR) , Osaka University , Mihogaoka , Ibaraki-shi , Osaka 567-0047 , Japan
| | - Shinobu Takizawa
- The Institute of Scientific and Industrial Research (ISIR) , Osaka University , Mihogaoka , Ibaraki-shi , Osaka 567-0047 , Japan
| | - Hiroaki Sasai
- The Institute of Scientific and Industrial Research (ISIR) , Osaka University , Mihogaoka , Ibaraki-shi , Osaka 567-0047 , Japan
| | - Yuichiro Ando
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Nagoya 464-8602 , Japan
| | - Kohsuke Ohmatsu
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Nagoya 464-8602 , Japan
| | - Takashi Ooi
- Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Nagoya 464-8602 , Japan
| | - Makoto Fujita
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
- JST ACCEL , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| |
Collapse
|
35
|
Zigon N, Kikuchi T, Ariyoshi J, Inokuma Y, Fujita M. Structural Elucidation of Trace Amounts of Volatile Compounds Using the Crystalline Sponge Method. Chem Asian J 2017; 12:1057-1061. [DOI: 10.1002/asia.201700515] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Nicolas Zigon
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Takashi Kikuchi
- Rigaku Corporation; 3-9-12 Matsubara-cho, Akishima-shi Tokyo 196-8666 Japan
| | - Junko Ariyoshi
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Yasuhide Inokuma
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Present address: Division of Applied Chemistry; Faculty of Engineering; Hokkaido University; Kita 13 Nishi 8 Kita-ku Sapporo Hokkaido 060-8628 Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| |
Collapse
|
36
|
Abstract
The development in the strategies for elucidating the structures of natural products from 1916 to 2016 are reviewed revealing the transition from chemical to spectroscopic methods and using examples drawn from the chemistry of terpenoids and steroids.
Collapse
|
37
|
Ohtsu H, Bennett TD, Kojima T, Keen DA, Niwa Y, Kawano M. Amorphous–amorphous transition in a porous coordination polymer. Chem Commun (Camb) 2017; 53:7060-7063. [DOI: 10.1039/c7cc03333h] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amorphous state plays a key role in porous coordination polymer and metal–organic framework phase transitions.
Collapse
Affiliation(s)
- Hiroyoshi Ohtsu
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo
- Japan
| | - Thomas D. Bennett
- Department of Materials Science and Metallurgy
- University of Cambridge
- Cambridge CB3 0FS
- UK
| | - Tatsuhiro Kojima
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - David A. Keen
- ISIS Facility
- Rutherford Appleton Laboratory
- Oxfordshire OX11 0QX
- UK
- Department of Physics
| | - Yasuhiro Niwa
- Photon Factory
- Institute of Materials Structure Science
- High Energy Accelerator Research Organization (KEK)
- Tsukuba
- Japan
| | - Masaki Kawano
- Department of Chemistry
- School of Science
- Tokyo Institute of Technology
- Tokyo
- Japan
| |
Collapse
|
38
|
Sairenji S, Lee S, Fujita M. Absolute Configuration Determination by the Crystalline Sponge Method. J SYN ORG CHEM JPN 2017. [DOI: 10.5059/yukigoseikyokaishi.75.538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo
| |
Collapse
|
39
|
Inokuma Y, Matsumura K, Yoshioka S, Fujita M. Finding a New Crystalline Sponge from a Crystallographic Database. Chem Asian J 2016; 12:208-211. [DOI: 10.1002/asia.201601551] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Yasuhide Inokuma
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- JST PRESTO; 4-8-1 Honcho Kawaguchi Saitama 332-0012 Japan
- Current address: Division of Applied Chemistry; Faculty of Engineering; Hokkaido University; Kita 13, Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Kazuki Matsumura
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shota Yoshioka
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Current address: Division of Applied Chemistry; Faculty of Engineering; Hokkaido University; Kita 13, Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Makoto Fujita
- Department of Applied Chemistry; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| |
Collapse
|
40
|
Waldhart GW, Mankad NP, Santarsiero BD. Improvements to the Practical Usability of the "Crystalline Sponge" Method for Organic Structure Determination. Org Lett 2016; 18:6112-6115. [PMID: 27934356 PMCID: PMC5502779 DOI: 10.1021/acs.orglett.6b03119] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A microwell droplet approach provided high-quality samples in ≥90% yield of the "crystalline sponge", which was exhibited previously as a revolutionary organic structure determination method. The new protocol, from crystal growth to guest soaking, was conducted in 1-7 days (depending on the guest) and was robust toward user errors, marking improvements over existing protocols. Unit cell determination was used as a practical crystal screening metric. These advances improve the practicality of the crystalline sponge technique for characterizing unknown organic molecules.
Collapse
Affiliation(s)
- Greyson W. Waldhart
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Neal P. Mankad
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Bernard D. Santarsiero
- Center for Natural Product Technologies and Department of Medicinal Chemistry & Pharmacognosy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, Illinois 60607, United States
| |
Collapse
|
41
|
Lee S, Hoshino M, Fujita M, Urban S. Cycloelatanene A and B: absolute configuration determination and structural revision by the crystalline sponge method. Chem Sci 2016; 8:1547-1550. [PMID: 28572911 PMCID: PMC5452270 DOI: 10.1039/c6sc04288k] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 10/26/2016] [Indexed: 01/30/2023] Open
Abstract
The crystalline sponge method revealed the absolute configuration of cycloelatanene A and B.
Cycloelatanene A and B are marine natural products first reported a few years ago. Their relative structures had been elucidated by an extensive NMR study and found to be epimers. However, their absolute configurations had not been established because they were isolated in only minute quantities as oily compounds. In this study, the complete structures of cycloelatanene A and B, including absolute configurations, were determined by the crystalline sponge method. The structure analysis confirmed the unique tricyclic structure involving a spiro[5.5]undecene skeleton. One stereogenic centre at C4 was revised as a result of this analysis. Since it only took 1–2 weeks to complete the experiments using the crystalline sponge method (guest-soaking followed by crystallographic analysis), this method is now highly recommended as a first port of call to achieve complete natural product structure elucidation.
Collapse
Affiliation(s)
- Shoukou Lee
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , Hongo, Bunkyo-ku , Tokyo , 113-8656 , Japan .
| | - Manabu Hoshino
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , Hongo, Bunkyo-ku , Tokyo , 113-8656 , Japan .
| | - Makoto Fujita
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , Hongo, Bunkyo-ku , Tokyo , 113-8656 , Japan .
| | - Sylvia Urban
- School of Science (Discipline of Applied Chemistry and Environmental Science) , RMIT University , GPO Box 2476 , Melbourne 3001 , Victoria , Australia .
| |
Collapse
|
42
|
High-resolution X-ray structure of methyl salicylate, a time-honored oily medicinal drug, solved by crystalline sponge method. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
43
|
Kikuchi H, Nishimura T, Kwon E, Kawai J, Oshima Y. Development of a Terpenoid Alkaloid-like Compound Library Based on the Humulene Skeleton. Chemistry 2016; 22:15819-15825. [DOI: 10.1002/chem.201603224] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Haruhisa Kikuchi
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Takehiro Nishimura
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Eunsang Kwon
- Research and Analytical Center for Giant Molecules, Graduate School of Science; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Junya Kawai
- Mushroom Research Laboratory; Hokuto Corporation; Nagano 381-0008 Japan
| | - Yoshiteru Oshima
- Graduate School of Pharmaceutical Sciences; Tohoku University; 6-3, Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| |
Collapse
|
44
|
Yoshioka S, Inokuma Y, Duplan V, Dubey R, Fujita M. X-ray Structure Analysis of Ozonides by the Crystalline Sponge Method. J Am Chem Soc 2016; 138:10140-2. [DOI: 10.1021/jacs.6b05817] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shota Yoshioka
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuhide Inokuma
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Vincent Duplan
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ritesh Dubey
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makoto Fujita
- Department of Applied Chemistry,
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
45
|
Lam HC, Spence JTJ, George JH. Biomimetic Total Synthesis of Hyperjapones A–E and Hyperjaponols A and C. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiu C. Lam
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| | | | - Jonathan H. George
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| |
Collapse
|
46
|
Lam HC, Spence JTJ, George JH. Biomimetic Total Synthesis of Hyperjapones A-E and Hyperjaponols A and C. Angew Chem Int Ed Engl 2016; 55:10368-71. [PMID: 27461748 DOI: 10.1002/anie.201606091] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Indexed: 11/08/2022]
Abstract
Hyperjapones A-E and hyperjaponols A-C are complex natural products of mixed aromatic polyketide and terpene biosynthetic origin that have recently been isolated from Hypericum japonicum. We have synthesized hyperjapones A-E using a biomimetic, oxidative hetero-Diels-Alder reaction to couple together dearomatized acylphloroglucinol and cyclic terpene natural products. Hyperjapone A is proposed to be the biosynthetic precursor of hyperjaponol C through a sequence of: 1) epoxidation; 2) acid-catalyzed epoxide ring-opening; and 3) a concerted, asynchronous alkene cyclization and 1,2-alkyl shift of a tertiary carbocation. Chemical mimicry of this proposed biosynthetic sequence allowed a concise total synthesis of hyperjaponol C to be completed in which six carbon-carbon bonds, six stereocenters, and three rings were constructed in just four steps.
Collapse
Affiliation(s)
- Hiu C Lam
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Justin T J Spence
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jonathan H George
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia.
| |
Collapse
|
47
|
Coletta M, McLellan R, Murphy P, Leube BT, Sanz S, Clowes R, Gagnon KJ, Teat SJ, Cooper AI, Paterson MJ, Brechin EK, Dalgarno SJ. Bis-Calix[4]arenes: From Ligand Design to the Directed Assembly of a Metal-Organic Trigonal Antiprism. Chemistry 2016; 22:8791-5. [PMID: 27166930 DOI: 10.1002/chem.201600762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 11/05/2022]
Abstract
Calix[4]arenes (C[4]s) are versatile platforms for the construction of polymetallic clusters containing paramagnetic metal ions. Synthetic modification at the C[4] methylene bridge allows for the design of bis-C[4]s that, depending on the linker employed, can be used to either dictate which clusters can be formed or direct the assembly of a new metal-organic polyhedron (MOP). The assembly resulting from the latter approach displays thermal stability and uptake of N2 or H2 gas, confirming that this is a viable route to the synthesis of new, functional supramolecular architectures.
Collapse
Affiliation(s)
- Marco Coletta
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Ross McLellan
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Paul Murphy
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Bernhard T Leube
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Sergio Sanz
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Rob Clowes
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Kevin J Gagnon
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 947240, USA
| | - Simon J Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 947240, USA
| | - Andrew I Cooper
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Martin J Paterson
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Euan K Brechin
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Scott J Dalgarno
- Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK.
| |
Collapse
|
48
|
Inokuma Y, Ukegawa T, Hoshino M, Fujita M. Structure determination of microbial metabolites by the crystalline sponge method. Chem Sci 2016; 7:3910-3913. [PMID: 30155035 PMCID: PMC6013795 DOI: 10.1039/c6sc00594b] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 02/23/2016] [Indexed: 11/21/2022] Open
Abstract
The structures of metabolites produced in microgram quantities by enzymatic reductions with baker's yeast were analyzed using the crystalline sponge method. The X-ray data provided reliable structures for trace metabolites including their relative and absolute stereochemistries that are not fully addressed by conventional NMR and LC-MS analyses. Technically, combining two or more chromatographic purification techniques is essential because, unlike abundant synthetic compounds, extracted metabolites contain many low level UV-silent impurities. The crystalline sponge method coupled with HPLC purification (LC-SCD) would thus be a useful method for metabolic analysis and drug discovery.
Collapse
Affiliation(s)
- Yasuhide Inokuma
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
- JST PRESTO , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Tomoya Ukegawa
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
| | - Manabu Hoshino
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
- JST ACCEL , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Makoto Fujita
- Department of Applied Chemistry , School of Engineering , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan .
- JST ACCEL , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| |
Collapse
|
49
|
Sanna E, Escudero-Adán EC, López C, Ballester P, Rotger C, Costa A. Macrocyclic Tetraimines: Synthesis and Reversible Uptake of Diethyl Phthalate by a Porous Macrocycle. J Org Chem 2016; 81:5173-80. [DOI: 10.1021/acs.joc.6b00768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena Sanna
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
| | - Eduardo C. Escudero-Adán
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avda. Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Carlos López
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
| | - Pablo Ballester
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avda. Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain
| | - Carmen Rotger
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
| | - Antonio Costa
- Department
of Chemistry, Universitat de les Illes Balears, 07122 Palma, Spain
| |
Collapse
|
50
|
Kutchukian PS, Dropinski JF, Dykstra KD, Li B, DiRocco DA, Streckfuss EC, Campeau LC, Cernak T, Vachal P, Davies IW, Krska SW, Dreher SD. Chemistry informer libraries: a chemoinformatics enabled approach to evaluate and advance synthetic methods. Chem Sci 2016; 7:2604-2613. [PMID: 28660032 PMCID: PMC5477042 DOI: 10.1039/c5sc04751j] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022] Open
Abstract
Major new advances in synthetic chemistry methods are typically reported using simple, non-standardized reaction substrates, and reaction failures are rarely documented. This makes the evaluation and choice of a synthetic method difficult. We report a standardized complex molecule diagnostic approach using collections of relevant drug-like molecules which we call chemistry informer libraries. With this approach, all chemistry results, successes and failures, can be documented to compare and evolve synthetic methods. To aid in the visualization of chemistry results in drug-like physicochemical space we have used an informatics methodology termed principal component analysis. We have validated this method using palladium- and copper-catalyzed reactions, including Suzuki-Miyaura, cyanation and Buchwald-Hartwig amination.
Collapse
Affiliation(s)
- Peter S Kutchukian
- Department of Structural Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Boston , MA 02115 , USA
| | - James F Dropinski
- Department of Process and Analytical Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Kevin D Dykstra
- Department of Discovery Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Bing Li
- Department of Discovery Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Daniel A DiRocco
- Department of Process and Analytical Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Eric C Streckfuss
- Department of Discovery Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Louis-Charles Campeau
- Department of Process and Analytical Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Tim Cernak
- Department of Discovery Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Petr Vachal
- Department of Discovery Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Ian W Davies
- Department of Process and Analytical Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Shane W Krska
- Department of Discovery Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| | - Spencer D Dreher
- Department of Process and Analytical Chemistry , Merck Research Laboratories , Merck and Co., Inc. , Rahway , NJ 07065 , USA .
| |
Collapse
|