1
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Ratto A, Honek JF. Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry. Curr Med Chem 2024; 31:1172-1213. [PMID: 36915986 DOI: 10.2174/0929867330666230313141452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 03/15/2023]
Abstract
The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.
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Affiliation(s)
- Amanda Ratto
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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2
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Gallarati S, van Gerwen P, Laplaza R, Vela S, Fabrizio A, Corminboeuf C. OSCAR: an extensive repository of chemically and functionally diverse organocatalysts. Chem Sci 2022; 13:13782-13794. [PMID: 36544722 PMCID: PMC9710326 DOI: 10.1039/d2sc04251g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022] Open
Abstract
The automated construction of datasets has become increasingly relevant in computational chemistry. While transition-metal catalysis has greatly benefitted from bottom-up or top-down strategies for the curation of organometallic complexes libraries, the field of organocatalysis is mostly dominated by case-by-case studies, with a lack of transferable data-driven tools that facilitate both the exploration of a wider range of catalyst space and the optimization of reaction properties. For these reasons, we introduce OSCAR, a repository of 4000 experimentally derived organocatalysts along with their corresponding building blocks and combinatorially enriched structures. We outline the fragment-based approach used for database generation and showcase the chemical diversity, in terms of functions and molecular properties, covered in OSCAR. The structures and corresponding stereoelectronic properties are publicly available (https://archive.materialscloud.org/record/2022.106) and constitute the starting point to build generative and predictive models for organocatalyst performance.
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Affiliation(s)
- Simone Gallarati
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Puck van Gerwen
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland,National Center for Competence in Research – Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Ruben Laplaza
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland,National Center for Competence in Research – Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Sergi Vela
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Alberto Fabrizio
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland,National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland,National Center for Competence in Research – Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland,National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL)1015 LausanneSwitzerland
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3
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York E, McNaughton DA, Roseblade A, Cranfield CG, Gale PA, Rawling T. Structure-Activity Relationship and Mechanistic Studies of Bisaryl Urea Anticancer Agents Indicate Mitochondrial Uncoupling by a Fatty Acid-Activated Mechanism. ACS Chem Biol 2022; 17:2065-2073. [PMID: 35854216 DOI: 10.1021/acschembio.1c00807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Targeting the cancer cell mitochondrion is a promising approach for developing novel anticancer agents. The experimental anticancer agent N,N'-bis(3,5-dichlorophenyl)urea (SR4) induces apoptotic cell death in several cancer cell lines by uncoupling mitochondrial oxidative phosphorylation (OxPhos) using a protein-free mechanism. However, the precise mechanism by which SR4 depolarizes mitochondria is unclear because SR4 lacks an acidic functional group typically found in protein-independent uncouplers. Recently, it was shown that structurally related thioureas can facilitate proton transport across lipid bilayers by a fatty acid-activated mechanism, in which the fatty acid acts as the site of protonation/deprotonation and the thiourea acts as an anion transporter that shuttles deprotonated fatty acids across the phospholipid bilayer to enable proton leak. In this paper, we show that SR4-mediated proton transport is enhanced by the presence of free fatty acids in the lipid bilayer, indicating that SR4 uncouples mitochondria through the fatty acid-activated mechanism. This mechanistic insight was used to develop a library of substituted bisaryl ureas for structure-activity relationship studies and subsequent cell testing. It was found that lipophilic electron-withdrawing groups on bisaryl ureas enhanced electrogenic proton transport via the fatty acid-activated mechanism and had the capacity to depolarize mitochondria and reduce the viability of MDA-MB-231 breast cancer cells. The most active compound in the series reduced cell viability with greater potency than SR4 and was more effective at inhibiting adenosine triphosphate production.
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Affiliation(s)
- Edward York
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | | | - Ariane Roseblade
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Charles G Cranfield
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Philip A Gale
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute (SydneyNano), The University of Sydney, Sydney, NSW 2006, Australia
| | - Tristan Rawling
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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4
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Gallarati S, Laplaza R, Corminboeuf C. Harvesting the fragment-based nature of bifunctional organocatalysts to enhance their activity. Org Chem Front 2022. [DOI: 10.1039/d2qo00550f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enhancing the activity of bifunctional organocatalysts: a fragment-based approach coupled with activity maps helps identifying better-performing catalytic motifs.
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Affiliation(s)
- Simone Gallarati
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ruben Laplaza
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research – Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research – Catalysis (NCCR-Catalysis), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Computational Design and Discovery of Novel Materials (MARVEL), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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5
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Liu M, Wang B, Li P, Liu X, Li Y. Sequentially bridging anionic addition and ring-opening polymerization by cooperative organocatalysis: Well-defined block copolymers from methacrylates and cyclic esters. Polym Chem 2022. [DOI: 10.1039/d2py00339b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organocatalytic sequential block copolymerization of dissimilar monomers with distinct chemical characteristics is great challenging, usually involving the integration of different polymerization mechanism. In this contribution, we reported the synthesis of...
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6
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Sandler I, Sharma S, Chan B, Ho J. Accurate Quantum Chemical Prediction of Gas-Phase Anion Binding Affinities and Their Structure-Binding Relationships. J Phys Chem A 2021; 125:9838-9851. [PMID: 34739245 DOI: 10.1021/acs.jpca.1c06648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper systematically examines the performance of contemporary wavefunction and density functional theory methods to identify robust and cost-efficient methods for predicting gas-phase anion binding energies. This includes the local coupled cluster LNO-CCSD(T) and DLPNO-CCSD(T), as well as double-hybrid DSD-PBEP86-D3(BJ) and various hybrid functionals M06-2X, B3LYP-D3(BJ), ωB97M-V, and ωB97X-V. The focus is on dual-hydrogen-bonding anion receptors that are commonly found in supramolecular chemistry and organocatalysis, namely, (thio)ureas, deltamides, (thio)squaramides, and croconamides as well as the yet-to-be-explored rhodizonamides. Of the methods examined, M06-2X emerged as the overall best performing method as the other functionals including DSD-PBEP86-D3(BJ) and the local coupled cluster DLPNO-CCSD(T) method displayed systematic errors that increase with the degree of carbonylation of the receptors. Hybrid ONIOM models that employed semiempirical methods (PM7, GFN1-xTB, and GFN2-xTB) and "threefold"-corrected small-basis set potentials (HF-3c, B97-3c, and PBEh-3c) were explored, and the best models resulted in 50- to 500-fold reduction in CPU time compared to W1-local. These calculations provide important insight into the structure-binding relationships where there is a direct correlation between Brønsted acidity and anion binding affinity, though the strength of the correlation also depends on other factors such as hydrogen-bonding geometry and the geometrical distortion that the receptor needs to undergo to bind the anion.
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Affiliation(s)
- Isolde Sandler
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Shaleen Sharma
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bukyo-Machi 1-14, Nagasaki 852-8521, Japan
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
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7
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Filiti J, Hearn K, Rudebeck E, Ngo HT, Pham-Tran NN, Pfeffer F. Comparing the anion binding of 4-amido- with 4-amino-1,8-naphthalimides. Org Biomol Chem 2021; 19:9260-9265. [PMID: 34657949 DOI: 10.1039/d1ob01664d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and evaluation of a new anion receptor based on the 4-amido-1,8-naphthalimide scaffold is described. The findings indicate that the amide N-H is an enhanced H-bond donor but is otherwise restricted in its ability to participate in the binding of simple anions.
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Affiliation(s)
- Jacob Filiti
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Geelong, 3216, Australia.
| | - Kyle Hearn
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Geelong, 3216, Australia.
| | - Elley Rudebeck
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Geelong, 3216, Australia.
| | - Huynh Thien Ngo
- Center for Functional Sensors & Actuators (CFSN), Research Center for Functional Materials, National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan
| | - Nguyen-Nguyen Pham-Tran
- Faculty of Chemistry, University of Science, Vietnam National University, Ho Chi Minh City, 721337, Vietnam
| | - Frederick Pfeffer
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Geelong, 3216, Australia.
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8
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García‐Urricelqui A, Cózar A, Campano TE, Mielgo A, Palomo C. syn
‐Selective Michael Reaction of α‐Branched Aryl Acetaldehydes with Nitroolefins Promoted by Squaric Amino Acid Derived Bifunctional Brønsted Bases. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ane García‐Urricelqui
- Departamento de Química Orgánica I Universidad del País Vasco UPV/EHU Manuel Lardizábal 3 20018 San Sebastián Spain
| | - Abel Cózar
- Departamento de Química Orgánica I Universidad del País Vasco UPV/EHU Manuel Lardizábal 3 20018 San Sebastián Spain
- IKERBASQUE Basque Foundation for Science 48009 Blbao Spain
| | - Teresa E. Campano
- Departamento de Química Orgánica I Universidad del País Vasco UPV/EHU Manuel Lardizábal 3 20018 San Sebastián Spain
| | - Antonia Mielgo
- Departamento de Química Orgánica I Universidad del País Vasco UPV/EHU Manuel Lardizábal 3 20018 San Sebastián Spain
| | - Claudio Palomo
- Departamento de Química Orgánica I Universidad del País Vasco UPV/EHU Manuel Lardizábal 3 20018 San Sebastián Spain
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9
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Lane JDE, Berry SN, Lewis W, Ho J, Jolliffe KA. Diaminomethylenemalononitriles and Diaminomethyleneindanediones as Dual Hydrogen Bond Donors for Anion Recognition. J Org Chem 2021; 86:4957-4964. [PMID: 33755453 DOI: 10.1021/acs.joc.0c02801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diaminomethylenemalononitriles (DMMs) and diaminomethyleneindanediones (DMIs) are dual H-bond donors that have previously been used as organocatalysts, but their anion binding ability has not been investigated. We report the synthesis of both alkyl- and aryl-substituted DMMs and DMIs, together with a comparison of their anion binding ability with that of the analogous thioureas. The DMMs display affinity for monovalent anions, with similar anion binding affinities observed to that of the thioureas in acetonitrile, albeit with differing trends for the N,N'-dialkyl versus N,N'-diaryl compounds. In contrast, the DMIs do not bind to monovalent anions under similar conditions as a result of conformational locking through the formation of intramolecular H-bonds. This can be overcome upon addition of sulfate ions, and binding of sulfate is enhanced in a more competitive solvent (DMSO).
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Affiliation(s)
- Jakob D E Lane
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Stuart N Berry
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - William Lewis
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Sydney Analytical, The University of Sydney, Sydney, NSW 2006, Australia
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Katrina A Jolliffe
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia
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10
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Sandler I, Chen J, Taylor M, Sharma S, Ho J. Accuracy of DLPNO-CCSD(T): Effect of Basis Set and System Size. J Phys Chem A 2021; 125:1553-1563. [PMID: 33560853 DOI: 10.1021/acs.jpca.0c11270] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The DLPNO-CCSD(T) method is designed to study large molecular systems at significantly reduced cost relative to its canonical counterpart. However, the error in this approach is also size-extensive and relies on cancellation of errors for the calculation of relative energies. This work provides a direct comparison of canonical CCSD(T) and TightPNO DLPNO-CCSD(T) calculations of reaction energies and barriers of a broad range of chemical reactions. The dataset includes acidities, anion binding affinities, enolization, Diels-Alder, nucleophilic substitution, and atom transfer reactions and complements existing theoretical datasets in terms of system size as well as new reaction types (e.g., anion binding affinities and chlorine atom transfer reactions). The performance of DLPNO-CCSD(T) was further examined with respect to systematic variation of basis set and system size and amounts of nonbonded interaction present in the system. The errors in the DLPNO-CCSD(T) were found to be relatively insensitive to the choice of basis set for small systems but increase monotonically with system size. Additionally, calculations of barriers appear to be more challenging than reaction energies with errors exceeding 5 kJ mol-1 for many Diels-Alder reactions. Further tests on three realistic organic reactions reveal the impact of the DLPNO approximation in calculating absolute and relative barriers that are important for predictions such as stereoselectivity.
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Affiliation(s)
- Isolde Sandler
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Junbo Chen
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mackenzie Taylor
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shaleen Sharma
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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11
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Gui H, Meng Z, Xiao Z, Yang Z, Wei Y, Shi M. Stereo‐ and Regioselective Construction of Spirooxindoles Having Continuous Spiral Rings via Asymmetric [3+2] Cyclization of 3‐Isothiocyanato Oxindoles with Thioaurone Derivatives. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001146] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hou‐Ze Gui
- State Key Laboratory of Organometallic Chemistry Center for Excellence in Molecular Synthesis University of Chinese Academy of Sciences 345 Lingling Road 200032 Shanghai China
| | - Zhe Meng
- State Key Laboratory of Organometallic Chemistry Center for Excellence in Molecular Synthesis University of Chinese Academy of Sciences 345 Lingling Road 200032 Shanghai China
| | - Zhan‐Shuai Xiao
- State Key Laboratory of Organometallic Chemistry Center for Excellence in Molecular Synthesis University of Chinese Academy of Sciences 345 Lingling Road 200032 Shanghai China
| | - Ze‐Ren Yang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals School of Chemistry & Molecular Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
| | - Yin Wei
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals School of Chemistry & Molecular Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
| | - Min Shi
- State Key Laboratory of Organometallic Chemistry Center for Excellence in Molecular Synthesis University of Chinese Academy of Sciences 345 Lingling Road 200032 Shanghai China
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals School of Chemistry & Molecular Engineering East China University of Science and Technology 130 Meilong Road 200237 Shanghai China
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12
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Kondoh A, Ishikawa S, Terada M. Enantioselective hydrophosphinylation of 1-alkenylphosphine oxides catalyzed by chiral strong Brønsted base. Org Biomol Chem 2020; 18:7814-7817. [PMID: 32969444 DOI: 10.1039/d0ob01778g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A catalytic enantioselective addition of diarylphosphine oxides to 1-alkenyl(diaryl)phosphine oxides was achieved by using a chiral ureate as a chiral strong Brønsted base catalyst. The reaction followed by the reduction of phosphine oxide moieties provided chiral 1,2-diphosphinoalkanes, which are a family of useful chiral ligands for asymmetric transition metal catalysis.
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Affiliation(s)
- Azusa Kondoh
- Research and Analytical Center for Giant Molecules, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
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13
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Agnew-Francis KA, Williams CM. Squaramides as Bioisosteres in Contemporary Drug Design. Chem Rev 2020; 120:11616-11650. [DOI: 10.1021/acs.chemrev.0c00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kylie A. Agnew-Francis
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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14
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Yang Q, Li Y, Yang J, Liu Y, Zhang L, Luo S, Cheng J. Holistic Prediction of the p
K
a
in Diverse Solvents Based on a Machine‐Learning Approach. Angew Chem Int Ed Engl 2020; 59:19282-19291. [DOI: 10.1002/anie.202008528] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/13/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Qi Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yao Li
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Dong Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yidi Liu
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Long Zhang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Sanzhong Luo
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Pei Cheng
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
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15
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Yang Q, Li Y, Yang J, Liu Y, Zhang L, Luo S, Cheng J. Holistic Prediction of the p
K
a
in Diverse Solvents Based on a Machine‐Learning Approach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008528] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qi Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yao Li
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Dong Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yidi Liu
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Long Zhang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Sanzhong Luo
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Pei Cheng
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
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16
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Sandler I, Larik FA, Mallo N, Beves JE, Ho J. Anion Binding Affinity: Acidity versus Conformational Effects. J Org Chem 2020; 85:8074-8084. [PMID: 32407087 DOI: 10.1021/acs.joc.0c00888] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
High-level quantum chemical calculations were used to elucidate the gas- and solution-phase conformational equilibria for a series of symmetrically substituted (thio)ureas, (thio)squaramides, and croconamides. Gas-phase calculations predict that the thermodynamic conformer of many of these anion receptors is not the dual-hydrogen-bond-facilitating anti-anti conformer as is commonly assumed. For N,N'-diaryl thiosquaramides and croconamides, the syn-syn conformer is typically the predominant conformer. Solution-phase calculations show that the anti-anti conformer is increasingly stabilized as the polarity of the solvent increases. However, the syn-syn conformer remains the lowest energy conformation for croconamides. These predictions are used to explain the acidity versus chloride binding affinity correlations recently reported for some of these compounds. The chloride binding constants for thioureas and croconamides are significantly lower than expected on the basis of their pKa values, and this may be due in part to the need for these receptors to reorganize into the anti-anti conformer. Experimental NMR nuclear Overhauser effect (NOE) measurements of an asymmetrically substituted squaramide and its thio analogue are consistent with the syn-syn conformation being predominant at 298 K. The conformational equilibria should therefore be an important consideration for the design and development of future anion receptors and organocatalysts.
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Affiliation(s)
- Isolde Sandler
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Fayaz Ali Larik
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Neil Mallo
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jonathon E Beves
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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17
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Ong WSY, Smaldone RA, Dodani SC. A neutral porous organic polymer host for the recognition of anionic dyes in water. Chem Sci 2020; 11:7716-7721. [PMID: 34094147 PMCID: PMC8159435 DOI: 10.1039/d0sc02941f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/19/2020] [Indexed: 11/21/2022] Open
Abstract
Neutral hosts for the recognition of anionic guests in water remain underdeveloped due to the inherent thermodynamic barrier for desolvation. To address this challenge, we have repurposed crosslinked porous organic polymers (POPs) as hosts. This polymer architecture affords a hydrophobic environment with a densely packed array of urea hydrogen bond donors to cooperatively promote anion desolvation and recognition in water. Using the principles of supramolecular design, we demonstrate through adsorption assays that the resulting Urea-POP-1 can recognize structurally different dyes containing phosphonate, sulfonate, and carboxylate anions in water. Moreover, when compared to Methyl-POP-1, a control POP lacking hydrogen bond donors, we find that the driving force for desolvation and adsorption of each dye is achieved through hydrophobic interactions with the POP backbone and, more importantly, cooperative hydrogen bonding interactions with the urea sidechains. This starting point sets the stage to exploit the modularity of our design to build a family of neutral polymer hosts with tunable pore sizes and anion preferences for fundamental investigations and targeted applications.
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Affiliation(s)
- Whitney S Y Ong
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA
| | - Ronald A Smaldone
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas 800 West Campbell Road Richardson TX 75080 USA
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18
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Yoshimitsu T, Kuboyama Y, Nishiguchi S, Nakajima M, Sugiura M. O-Monoacyltartaric Acid/(Thio)urea Cooperative Organocatalysis for Enantioselective Conjugate Addition of Boronic Acid. Org Lett 2020; 22:3780-3784. [PMID: 32330049 DOI: 10.1021/acs.orglett.0c00981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(Thio)urea cocatalyst accelerates O-monoacyltartaric acid (MAT)-catalyzed enantioselective conjugate addition of boronic acid to unsaturated ketone. Kinetic studies of this reaction revealed first-order dependence of each substrate and catalyst and second-order dependence of (thio)urea, leading to reduction of the catalyst loading and development of more active and enantioselective MAT monoaryl ester catalyst.
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Affiliation(s)
- Takuto Yoshimitsu
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yukinobu Kuboyama
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Sari Nishiguchi
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Makoto Nakajima
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Masaharu Sugiura
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
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19
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Kondoh A, Ishikawa S, Terada M. Development of Chiral Ureates as Chiral Strong Brønsted Base Catalysts. J Am Chem Soc 2020; 142:3724-3728. [DOI: 10.1021/jacs.9b13922] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Azusa Kondoh
- Research and Analytical Center for Giant Molecules, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Sho Ishikawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Masahiro Terada
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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20
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Fan L, Xu T, Feng J, Ji Z, Li L, Shi X, Tian C, Qin Y. Tripodal Squaramide Derivative as a Neutral Chloride Ionophore for Whole Blood and Sweat Chloride Measurement. ELECTROANAL 2020. [DOI: 10.1002/elan.201900693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lingling Fan
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
| | - Tingting Xu
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
| | - Junjun Feng
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
| | - Zihan Ji
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
| | - Le Li
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
| | - Xinhao Shi
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
| | - Chunxiu Tian
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
| | - Yu Qin
- Eaglenos, Inc.5th Floor, Building 8 No 11 Yaogu Avenue, Nanjing Jiangbei New Area Nanjing China 210063
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21
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Nagy S, Fehér Z, Dargó G, Barabás J, Garádi Z, Mátravölgyi B, Kisszékelyi P, Dargó G, Huszthy P, Höltzl T, Balogh GT, Kupai J. Comparison of Cinchona Catalysts Containing Ethyl or Vinyl or Ethynyl Group at Their Quinuclidine Ring. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E3034. [PMID: 31540532 PMCID: PMC6766286 DOI: 10.3390/ma12183034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/1970] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 11/17/2022]
Abstract
Numerous cinchona organocatalysts with different substituents at their quinuclidine unit have been described and tested, but the effect of those saturation has not been examined before. This work presents the synthesis of four widely used cinchona-based organocatalyst classes (hydroxy, amino, squaramide, and thiourea) with different saturation on the quinuclidine unit (ethyl, vinyl, ethynyl) started from quinine, the most easily available cinchona derivative. Big differences were found in basicity of the quinuclidine unit by measuring the pKa values of twelve catalysts in six solvents. The effect of differences was examined by testing the catalysts in Michael addition reaction of pentane-2,4-dione to trans-β-nitrostyrene. The 1.6-1.7 pKa deviation in basicity of the quinuclidine unit did not result in significant differences in yields and enantiomeric excesses. Quantum chemical calculations confirmed that the ethyl, ethynyl, and vinyl substituents affect the acid-base properties of the cinchona-thiourea catalysts only slightly, and the most active neutral thione forms are the most stable tautomers in all cases. Due to the fact that cinchonas with differently saturated quinuclidine substituents have similar catalytic activity in asymmetric Michael addition application of quinine-based catalysts is recommended. Its vinyl group allows further modifications, for instance, recycling the catalyst by immobilization.
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Affiliation(s)
- Sándor Nagy
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Zsuzsanna Fehér
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Gergő Dargó
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
- Chemical Department, Chemical Works of Gedeon Richter Plc., P.O. Box 27, H-1103 Budapest, Hungary.
| | - Júlia Barabás
- Department of Inorganic & Analytical Chemistry, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Zsófia Garádi
- Department of Inorganic & Analytical Chemistry, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Béla Mátravölgyi
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Péter Kisszékelyi
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Gyula Dargó
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Péter Huszthy
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
| | - Tibor Höltzl
- Department of Inorganic & Analytical Chemistry, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
- Furukawa Electric Institute of Technology, Késmárk utca 28/A, H-1158 Budapest, Hungary.
| | - György Tibor Balogh
- Chemical Department, Chemical Works of Gedeon Richter Plc., P.O. Box 27, H-1103 Budapest, Hungary.
- Department of Chemical & Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary.
| | - József Kupai
- Department of Organic Chemistry & Technology, Budapest University of Technology & Economics, Szent Gellért tér 4, H-1111 Budapest, Hungary.
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22
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Balaji PV, Brewitz L, Kumagai N, Shibasaki M. Achiral Trisubstituted Thioureas as Secondary Ligands to Cu
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Catalysts: Direct Catalytic Asymmetric Addition of α‐Fluoronitriles to Imines. Angew Chem Int Ed Engl 2019; 58:2644-2648. [DOI: 10.1002/anie.201812673] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Indexed: 12/27/2022]
Affiliation(s)
| | - Lennart Brewitz
- Institute of Microbial Chemistry(BIKAKEN) 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Naoya Kumagai
- Institute of Microbial Chemistry(BIKAKEN) 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry(BIKAKEN) 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
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23
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Balaji PV, Brewitz L, Kumagai N, Shibasaki M. Achiral Trisubstituted Thioureas as Secondary Ligands to Cu
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Catalysts: Direct Catalytic Asymmetric Addition of α‐Fluoronitriles to Imines. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812673] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Lennart Brewitz
- Institute of Microbial Chemistry (BIKAKEN) 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Naoya Kumagai
- Institute of Microbial Chemistry (BIKAKEN) 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN) 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
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24
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Zhang CJ, Hu LF, Wu HL, Cao XH, Zhang XH. Dual Organocatalysts for Highly Active and Selective Synthesis of Linear Poly(γ-butyrolactone)s with High Molecular Weights. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01757] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Cheng-Jian Zhang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou Shi, Zhejiang Sheng 310027, China
| | - Lan-Fang Hu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou Shi, Zhejiang Sheng 310027, China
| | - Hai-Lin Wu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou Shi, Zhejiang Sheng 310027, China
| | - Xiao-Han Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou Shi, Zhejiang Sheng 310027, China
| | - Xing-Hong Zhang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou Shi, Zhejiang Sheng 310027, China
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25
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Wang Z, Zheng Y, Zheng Y, Xue XS, Ji P. A Systematic Theoretical Study on the Acidities for Cations of Ionic Liquids in Dimethyl Sulfoxide. J Phys Chem A 2018; 122:5750-5755. [DOI: 10.1021/acs.jpca.8b02265] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhen Wang
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
- State Key Laboratory on Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yongjun Zheng
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Yong Zheng
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Xiao-Song Xue
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
- State Key Laboratory on Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pengju Ji
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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26
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Lin B, Waymouth RM. Organic Ring-Opening Polymerization Catalysts: Reactivity Control by Balancing Acidity. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00540] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Binhong Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Robert M. Waymouth
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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27
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Spooner MJ, Gale PA. A tripodal tris-selenourea anion transporter matches the activity of its thio- analogue but shows distinct selectivity. Supramol Chem 2018. [DOI: 10.1080/10610278.2018.1431394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Philip A. Gale
- School of Chemistry, The University of Sydney, Sydney, Australia
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28
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Zwicker VE, Yuen KKY, Smith DG, Ho J, Qin L, Turner P, Jolliffe KA. Deltamides and Croconamides: Expanding the Range of Dual H‐bond Donors for Selective Anion Recognition. Chemistry 2017; 24:1140-1150. [DOI: 10.1002/chem.201704388] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - David G. Smith
- School of Chemistry The University of Sydney NSW 2006 Australia
| | - Junming Ho
- School of Chemistry University of New South Wales NSW 2052 Australia
| | - Lei Qin
- School of Chemistry The University of Sydney NSW 2006 Australia
| | - Peter Turner
- School of Chemistry The University of Sydney NSW 2006 Australia
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