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Jakubec M, Císařová I, Karban J, Sýkora J. The Effect of Deoxyfluorination on Intermolecular Interactions in the Crystal Structures of 1,6-Anhydro-2,3-epimino-hexopyranoses. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27010278. [PMID: 35011510 PMCID: PMC8746508 DOI: 10.3390/molecules27010278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022]
Abstract
The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-Fax and C4-Feq epimines presented here.
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Affiliation(s)
- Martin Jakubec
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, v. v. i., Rozvojová 135, 165 02 Prague, Czech Republic; (M.J.); (J.K.)
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague, Czech Republic;
| | - Jindřich Karban
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, v. v. i., Rozvojová 135, 165 02 Prague, Czech Republic; (M.J.); (J.K.)
| | - Jan Sýkora
- Institute of Chemical Process Fundamentals of the Czech Academy of Sciences, v. v. i., Rozvojová 135, 165 02 Prague, Czech Republic; (M.J.); (J.K.)
- Correspondence:
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2
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Richardson P. Applications of fluorine to the construction of bioisosteric elements for the purposes of novel drug discovery. Expert Opin Drug Discov 2021; 16:1261-1286. [PMID: 34074189 DOI: 10.1080/17460441.2021.1933427] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction There continues to be an exponential rise in the number of small molecule drugs that contain either a fluorine atom or a fluorinated fragment. While the unique properties of fluorine enable the precise modulation of a molecule's physicochemical properties, strategic bioisosteric replacement of fragments with fluorinated moieties represents an area of significant growth.Areas covered This review discusses the strategic employment of fluorine substitution in the design and development of bioisosteres in medicinal chemistry. In addition, the classic exploitation of trifluoroethylamine group as an amide bioisostere is discussed. In each of the case studies presented, emphasis is placed on the context-dependent influence of the fluorinated fragment on the overall properties/binding of the compound of interest.Expert opinion Whereas utilization of bioisosteric replacements to modify molecular structures is commonplace within drug discovery, the overarching lesson to be learned is that the chances of success with this strategy significantly increase as the knowledge of the structure/environment of the biological target grows. Coupled to this, breakthroughs and learnings achieved using bioisosteres within a specific program are context-based, and though may be helpful in guiding future intuition, will not necessarily be directly translated to future programs. Another important point is to bear in mind what implications a structural change based on a bioisosteric replacement will have on the candidate molecule. Finally, the development of new methods and reagents for the controlled regioselective introduction of fluorine and fluorinated moieties into biologically relevant compounds particularly in drug discovery remains a contemporary challenge in organic chemistry.
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3
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Linclau B, Ardá A, Reichardt NC, Sollogoub M, Unione L, Vincent SP, Jiménez-Barbero J. Fluorinated carbohydrates as chemical probes for molecular recognition studies. Current status and perspectives. Chem Soc Rev 2021; 49:3863-3888. [PMID: 32520059 DOI: 10.1039/c9cs00099b] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review provides an extensive summary of the effects of carbohydrate fluorination with regard to changes in physical, chemical and biological properties with respect to regular saccharides. The specific structural, conformational, stability, reactivity and interaction features of fluorinated sugars are described, as well as their applications as probes and in chemical biology.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO171BJ, UK
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain.
| | | | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Luca Unione
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Stéphane P Vincent
- Department of Chemistry, Laboratory of Bio-organic Chemistry, University of Namur (UNamur), B-5000 Namur, Belgium
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain. and Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain and Department of Organic Chemistry II, Faculty of Science and Technology, UPV/EHU, 48940 Leioa, Spain
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4
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Remete AM, Kiss L. Synthesis of Fluorine-Containing Molecular Entities Through Fluoride Ring Opening of Oxiranes and Aziridines. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900981] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Attila Márió Remete
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6720 Szeged Hungary
- Interdisciplinary Excellence Centre; Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6720 Szeged Hungary
| | - Loránd Kiss
- Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6720 Szeged Hungary
- Interdisciplinary Excellence Centre; Institute of Pharmaceutical Chemistry; University of Szeged; Eötvös u. 6 6720 Szeged Hungary
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5
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Lu X, Huang C, Lowinger MB, Yang F, Xu W, Brown CD, Hesk D, Koynov A, Schenck L, Su Y. Molecular Interactions in Posaconazole Amorphous Solid Dispersions from Two-Dimensional Solid-State NMR Spectroscopy. Mol Pharm 2019; 16:2579-2589. [DOI: 10.1021/acs.molpharmaceut.9b00174] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xingyu Lu
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chengbin Huang
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
- School of Pharmacy, University of Wisconsin−Madison, Madison, Wisconsin 53705, United States
| | - Michael B. Lowinger
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Fengyuan Yang
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
- Ashland Inc., Wilmington, Delaware 19808, United States
| | - Wei Xu
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chad D. Brown
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - David Hesk
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Athanas Koynov
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Luke Schenck
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Merck Research Laboratories (MRLs), Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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6
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Constantinides CP, Lawson DB, Berezin AA, Zissimou GA, Manoli M, Leitus GM, Koutentis PA. Ferromagnetic interactions in a 1D Heisenberg linear chain of 1-phenyl-3,7-bis(trifluoromethyl)-1,4-dihydro-1,2,4-benzotriazin-4-yls. CrystEngComm 2019. [DOI: 10.1039/c9ce00739c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
1-Phenyl-3,7-bis(trifluoromethyl)-1,4-dihydro-1,2,4-benzotriazin-4-yl (2), was characterized by single crystal X-ray diffractometry and variable temperature SQUID magnetometry to investigate its structure-magnetism correlation.
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Affiliation(s)
| | - Daniel B. Lawson
- Department of Natural Sciences
- University of Michigan – Dearborn
- Dearborn
- USA
| | | | | | - Maria Manoli
- Department of Chemistry
- University of Cyprus
- 1678 Nicosia
- Cyprus
| | - Gregory M. Leitus
- Department of Organic Chemistry
- Weizmann Institute of Science
- 76100 Rehovot
- Israel
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7
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Levina EO, Chernyshov IY, Voronin AP, Alekseiko LN, Stash AI, Vener MV. Solving the enigma of weak fluorine contacts in the solid state: a periodic DFT study of fluorinated organic crystals. RSC Adv 2019; 9:12520-12537. [PMID: 35515880 PMCID: PMC9063672 DOI: 10.1039/c9ra02116g] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/15/2019] [Indexed: 01/22/2023] Open
Abstract
The nature and strength of weak interactions with organic fluorine in the solid state are revealed by periodic density functional theory (periodic DFT) calculations coupled with experimental data on the structure and sublimation thermodynamics of crystalline organofluorine compounds. To minimize other intermolecular interactions, several sets of crystals of perfluorinated and partially fluorinated organic molecules are considered. This allows us to establish the theoretical levels providing an adequate description of the metric and electron-density parameters of the C–F⋯F–C interactions and the sublimation enthalpy of crystalline perfluorinated compounds. A detailed comparison of the C–F⋯F–C and C–H⋯F–C interactions is performed using the relaxed molecular geometry in the studied crystals. The change in the crystalline packing of aromatic compounds during their partial fluorination points to the structure-directing role of C–H⋯F–C interactions due to the dominant electrostatic contribution to these contacts. C–H⋯F–C and C–H⋯O interactions are found to be identical in nature and comparable in energy. The factors that determine the contribution of these interactions to the crystal packing are revealed. The reliability of the results is confirmed by considering the superposition of the electrostatic potential and electron density gradient fields in the area of the investigated intermolecular interactions. The nature and strength of weak C–H⋯F–C and C–F⋯F–C interactions and their role in organofluorine molecular crystals were studied using periodic DFT coupled with CSD data mining and experimental sublimation enthalpies.![]()
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Affiliation(s)
- Elena O. Levina
- Moscow Institute of Physics and Technology
- Russia
- Research Centre of Biotechnology
- Russian Academy of Sciences
- Moscow
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8
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Hebeisen P, Weiss U, Alker A, Kuhn B, Müller K, Wang F, Surya Prakash GK. Molecular Structure and Crystal Packing of Monofluoromethoxyarenes. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Paul Hebeisen
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Urs Weiss
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - André Alker
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Bernd Kuhn
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Klaus Müller
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Fang Wang
- Loker Hydrocarbon Research Institute; Department of Chemistry; University of Southern California; 1661 Los Angeles CA 90089- USA
| | - G. K. Surya Prakash
- Loker Hydrocarbon Research Institute; Department of Chemistry; University of Southern California; 1661 Los Angeles CA 90089- USA
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9
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Dhingra S, Barman DJ, Yadav HR, Eyyathiyil J, Bhowmik P, Kaur P, Adhikari D, Roy Choudhury A. Structural and computational understanding of weak interactions in “bridge-flipped” isomeric tetrafluoro-bis-benzylideneanilines. CrystEngComm 2018. [DOI: 10.1039/c7ce01872j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural and computational insights into inter-molecular interactions in isomeric bridge-flipped tetrafluoro-bis-benzylideneanilines.
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Affiliation(s)
- Shallu Dhingra
- Department of Chemistry and Centre of Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
| | | | - Hare Ram Yadav
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Mohali
- Mohali
- India
| | - Jusaina Eyyathiyil
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| | - Prasanta Bhowmik
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Mohali
- Mohali
- India
| | - Parmeet Kaur
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Mohali
- Mohali
- India
| | - Debashis Adhikari
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Mohali
- Mohali
- India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Mohali
- Mohali
- India
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10
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Quiquempoix L, Bogdan E, Wells NJ, Le Questel JY, Graton J, Linclau B. A Study of Intramolecular Hydrogen Bonding in Levoglucosan Derivatives. Molecules 2017; 22:E518. [PMID: 28338623 PMCID: PMC6154293 DOI: 10.3390/molecules22040518] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/09/2017] [Accepted: 03/21/2017] [Indexed: 11/17/2022] Open
Abstract
Organofluorine is a weak hydrogen-bond (HB) acceptor. Bernet et al. have demonstrated its capability to perturb OH···O intramolecular hydrogen bonds (IMHBs), using conformationally rigid carbohydrate scaffolds including levoglucosan derivatives. These investigations are supplemented here by experimental and theoretical studies involving six new levoglucosan derivatives, and complement the findings of Bernet et al. However, it is shown that conformational analysis is instrumental in interpreting the experimental data, due to the occurrence of non-intramolecular hydrogen-bonded populations which, although minor, cannot be neglected and appears surprisingly significant. The DFT conformational analysis, together with the computation of NMR parameters (coupling constants and chemical shifts) and wavefunction analyses (AIM, NBO), provides a full picture. Thus, for all compounds, the most stabilized structures show the OH groups in a conformation allowing IMHB with O5 and O6, when possible. Furthermore, the combined approach points out the occurrence of various IMHBs and the effect of the chemical modulations on their features. Thus, two-center or three-center IMHB interactions are observed in these compounds, depending on the presence or absence of additional HB acceptors, such as methoxy or fluorine.
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Affiliation(s)
- Lucas Quiquempoix
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Elena Bogdan
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière-BP 92208, 44322 Nantes CEDEX 3, France.
| | - Neil J Wells
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière-BP 92208, 44322 Nantes CEDEX 3, France.
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2 rue de la Houssinière-BP 92208, 44322 Nantes CEDEX 3, France.
| | - Bruno Linclau
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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11
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12
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Ray C, Bañuelos J, Arbeloa T, Maroto BL, Moreno F, Agarrabeitia AR, Ortiz MJ, López-Arbeloa I, de la Moya S. Push–pull flexibly-bridged bis(haloBODIPYs): solvent and spacer switchable red emission. Dalton Trans 2016; 45:11839-48. [DOI: 10.1039/c6dt01849a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Uncommon flexibly-bridged bis(BODIPYs) displaying switchable red emission are described.
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Affiliation(s)
- César Ray
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid
- Spain
| | - Jorge Bañuelos
- Departamento de Química Física
- Universidad del País Vasco-EHU
- Bilbao
- Spain
| | - Teresa Arbeloa
- Departamento de Química Física
- Universidad del País Vasco-EHU
- Bilbao
- Spain
| | - Beatriz L. Maroto
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid
- Spain
| | - Florencio Moreno
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid
- Spain
| | - Antonia R. Agarrabeitia
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid
- Spain
| | - María J. Ortiz
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid
- Spain
| | | | - Santiago de la Moya
- Departamento de Química Orgánica I
- Facultad de CC. Químicas
- Universidad Complutense de Madrid
- Madrid
- Spain
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13
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Limitations and extensions of the lock-and-key principle: differences between gas state, solution and solid state structures. Int J Mol Sci 2015; 16:6694-717. [PMID: 25815592 PMCID: PMC4424984 DOI: 10.3390/ijms16046694] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 03/16/2015] [Indexed: 12/30/2022] Open
Abstract
The lock-and-key concept is discussed with respect to necessary extensions. Formation of supramolecular complexes depends not only, and often not even primarily on an optimal geometric fit between host and guest. Induced fit and allosteric interactions have long been known as important modifications. Different binding mechanisms, the medium used and pH effects can exert a major influence on the affinity. Stereoelectronic effects due to lone pair orientation can lead to variation of binding constants by orders of magnitude. Hydrophobic interactions due to high-energy water inside cavities modify the mechanical lock-and-key picture. That optimal affinities are observed if the cavity is only partially filled by the ligand can be in conflict with the lock-and-key principle. In crystals other forces than those between host and guest often dominate, leading to differences between solid state and solution structures. This is exemplified in particular with calixarene complexes, which by X-ray analysis more often than other hosts show guest molecules outside their cavity. In view of this the particular problems with the identification of weak interactions in crystals is discussed.
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14
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Sajid M, Kehr G, Wiegand T, Eckert H, Schwickert C, Pöttgen R, Cardenas AJP, Warren TH, Fröhlich R, Daniliuc CG, Erker G. Noninteracting, Vicinal Frustrated P/B-Lewis Pair at the Norbornane Framework: Synthesis, Characterization, and Reactions. J Am Chem Soc 2013; 135:8882-95. [DOI: 10.1021/ja400338e] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Muhammad Sajid
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstr.
40, 48149 Münster, Germany
| | - Gerald Kehr
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstr.
40, 48149 Münster, Germany
| | - Thomas Wiegand
- Institut für Physikalische
Chemie and Graduate School of Chemistry, Westfälische Wilhelms-Universität, Corrensstr. 28/30, 48149
Münster, Germany
| | - Hellmut Eckert
- Institut für Physikalische
Chemie and Graduate School of Chemistry, Westfälische Wilhelms-Universität, Corrensstr. 28/30, 48149
Münster, Germany
| | - Christian Schwickert
- Institut
für Anorganische
und Analytische Chemie, Westfälische Wilhelms-Universität, Corrensstr. 28/30, 48149 Münster, Germany
| | - Rainer Pöttgen
- Institut
für Anorganische
und Analytische Chemie, Westfälische Wilhelms-Universität, Corrensstr. 28/30, 48149 Münster, Germany
| | - Allan Jay P. Cardenas
- Department of Chemistry, Georgetown University, P.O. Box 571227, Washington,
D.C. 20057-1227, United States
| | - Timothy H. Warren
- Department of Chemistry, Georgetown University, P.O. Box 571227, Washington,
D.C. 20057-1227, United States
| | - Roland Fröhlich
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstr.
40, 48149 Münster, Germany
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstr.
40, 48149 Münster, Germany
| | - Gerhard Erker
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität, Corrensstr.
40, 48149 Münster, Germany
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15
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Dramatic effect of furanose C2' substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom. J Am Chem Soc 2013; 135:5344-7. [PMID: 23521511 DOI: 10.1021/ja401954t] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human telomeric DNA quadruplexes can adopt different conformations in solution. We have found that arabinose, 2'F-arabinose, and ribose substitutions stabilize the propeller parallel G-quadruplex form over competing conformers, allowing NMR structural determination of this particularly significant nucleic acid structure. 2'F-arabinose substitution provides the greatest stabilization as a result of electrostatic (F-CH---O4') and pseudo-hydrogen-bond (F---H8) stabilizing interactions. In contrast, 2'F-rG substitution provokes a dramatic destabilization of the quadruplex structure due to unfavorable electrostatic repulsion between the phosphate and the 2'-F.
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16
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Affiliation(s)
- Robert E. Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky
40508, United States
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17
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Martín-Pintado N, Yahyaee-Anzahaee M, Campos-Olivas R, Noronha AM, Wilds CJ, Damha MJ, González C. The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion. Nucleic Acids Res 2012; 40:9329-39. [PMID: 22798499 PMCID: PMC3467067 DOI: 10.1093/nar/gks672] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We report here the first structure of double helical arabino nucleic acid (ANA), the C2′-stereoisomer of RNA, and the 2′-fluoro-ANA analogue (2′F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of arabino nucleotides, flanked by two 2′-deoxy-2′F-ANA wings was studied. Our data show that this chimeric oligonucleotide can adopt two different structures of comparable thermal stabilities. One structure is a monomeric hairpin in which the stem is formed by base paired 2′F-ANA nucleotides and the loop by unpaired ANA nucleotides. The second structure is a bimolecular duplex, with all the nucleotides (2′F-ANA and ANA) forming Watson–Crick base pairs. The duplex structure is canonical B-form, with all arabinoses adopting a pure C2′-endo conformation. In the ANA:ANA segment, steric interactions involving the 2′-OH substituent provoke slight changes in the glycosidic angles and, therefore, in the ANA:ANA base pair geometry. These distortions are not present in the 2′F-ANA:2′F-ANA regions of the duplex, where the –OH substituent is replaced by a smaller fluorine atom. 2′F-ANA nucleotides adopt the C2′-endo sugar pucker and fit very well into the geometry of B-form duplex, allowing for favourable 2′F···H8 interactions. This interaction shares many features of pseudo-hydrogen bonds previously observed in 2′F-ANA:RNA hybrids and in single 2′F-ANA nucleotides.
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Affiliation(s)
- Nerea Martín-Pintado
- Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, 28006 Madrid, Spain
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Schneider HJ. Hydrogen bonds with fluorine. Studies in solution, in gas phase and by computations, conflicting conclusions from crystallographic analyses. Chem Sci 2012. [DOI: 10.1039/c2sc00764a] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Linclau B, Golten S, Light M. The Crystal Structure of 4,6-Di-O-Benzyl-2,3-Dideoxy-2,2,3,3-Tetrafluorogalactose. J Carbohydr Chem 2011. [DOI: 10.1080/07328303.2011.618895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Bruno Linclau
- a School of Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK
| | - Samuel Golten
- a School of Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK
| | - Mark Light
- a School of Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK
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Karban J, Císařová I, Strašák T, Šťastná LČ, Sýkora J. Skeletal rearrangements resulting from reactions of 1,6:2,3- and 1,6:3,4-dianhydro-β-D-hexopyranoses with diethylaminosulphur trifluoride. Org Biomol Chem 2011; 10:394-403. [PMID: 22083416 DOI: 10.1039/c1ob06336g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A complete series of eight 1,6:2,3- and 1,6:3,4-dianhydro-β-D-hexopyranoses were subjected to fluorination with DAST. The 1,6:3,4-dianhydropyranoses yielded solely products of skeletal rearrangement resulting from migration of the tetrahydropyran oxygen (educts of D-altro and D-talo configuration) or of the 1,6-anhydro bridge oxygen (D-allo, D-galacto). The major products yielded by the 1,6:2,3-dianhydropyranoses were compounds arising from nucleophilic substitution, with configuration at C4 either retained (D-talo, D-gulo) or inverted (D-manno), or from C6 migration (D-allo). The minor products in the 1,6:2,3-series resulted from migration of the tetrahydropyran oxygen (D-gulo) or the oxirane oxygen (D-manno), or from nucleophilic substitution with retention of configuration (D-manno). The structure of most of the rearranged products was verified by X-ray crystallography.
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Affiliation(s)
- Jindřich Karban
- Institute of the Chemical Process Fundamentals of the ASCR, v.v.i. Rozvojová 135, 165 02, Praha 6, Czech Republic.
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Mehta G, Sen S, Thangam M. (4a R,8a S,9a R,10a S)-8a,9a-Difluoro-1,4,4a,5,8,8a,9,9a,10,10a-decahydroanthracene-4a,10a-diol hemihydrate. Acta Crystallogr C 2011; 67:o294-6. [DOI: 10.1107/s0108270111024413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 06/21/2011] [Indexed: 11/10/2022] Open
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Mehta G, Sen S, Suresha Kumara T. Can the conformational flexibility of cis-decalins be modulated through intramolecular O–H⋯O hydrogen bonding? Profiling the molecular and supramolecular attributes of designer cis-fused polycyclitols. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.03.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Linclau B, Golten S, Light M, Sebban M, Oulyadi H. The conformation of tetrafluorinated methyl galactoside anomers: crystallographic and NMR studies. Carbohydr Res 2011; 346:1129-39. [PMID: 21531398 DOI: 10.1016/j.carres.2011.04.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 03/27/2011] [Accepted: 04/03/2011] [Indexed: 10/18/2022]
Abstract
The first single-crystal X-ray diffraction study of tetrafluorinated monosaccharide derivatives is presented. Both α- and β-methyl 2,3-dideoxy-2,2,3,3-tetrafluoro-d-galactopyranoside anomers adopt the (4)C(1) conformation. The values for the C1-O1 and C1-O5 bond lengths and the O5-C1-O1-CH(3) dihedral angles are in line with what can be expected from the anomeric and exo-anomeric effects. The chair conformations are slightly distorted, presumably due to repulsion between 1,3-diaxial C-O and C-F bonds. The asymmetric unit of both compounds contains up to three independent molecules, which differ in the conformation of the hydroxymethyl group (including in one case a 'forbidden'gg rotamer). The molecular packing of the β-anomer shows a clear segregation between fluorinated and hydrophilic domains, while for the α-anomer the regions of fluorine segregation are broken by interleafing of OMe groups. There is one close OH⋯F contact, which is likely to arise from the crystal packing. NMR studies show that the two anomers also adopt a (4)C(1) conformation in solution (D(2)O, CDCl(3)).
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom.
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Mehta G, Sen S. A vicarious one-pot transformation of a fluorocyclitol to a polycyclitol: observation of a formal 4-fold axial-equatorial epimerization on a conformationally locked scaffold. J Org Chem 2010; 75:8287-90. [PMID: 21053978 DOI: 10.1021/jo101660x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A conformationally locked fluoropentol undergoes an interesting transformation to (trans,anti,trans,anti,trans)-perhydro-2,3,4a,6,7,8a-naphthalenehexol essentially under conditions of base-induced transesterification. The proposed rationale for the observed metamorphosis involves a nucleophilic displacement of fluoride, and subsequent stereo- and regioselective anti-Fürst-Plattner-type ring-opening of the epoxide thus formed.
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Affiliation(s)
- Goverdhan Mehta
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India.
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Mehta G, Sen S. (2R,3R,4aS,6S,7S,8aS)-4a-Fluoro-8a-hy-droxy-perhydro-naphthalene-2,3,6,7-tetrayl tetraacetate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:o3095. [PMID: 21589402 PMCID: PMC3011589 DOI: 10.1107/s1600536810044314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 10/29/2010] [Indexed: 12/02/2022]
Abstract
The title compound, C(18)H(25)FO(9), exhibits a similar unit cell and packing to the α polymorph of axial 4a,8a-dihy-droxy-per-hydro-naph-tha-lene-2,3,6,7-tetrayl tetraacetate. The carbonyl O atoms of two of the four acetate groups in the molecule are disordered over two sites with occupancy ratios of 0.59 (4):0.41 (4) and 0.57 (6):0.43 (6). Crystal packing is effected via inter-molecular O-H⋯O hydrogen bonds, which link the tetra-acetate mol-ecules into tapes along the c axis.
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Affiliation(s)
- Goverdhan Mehta
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, Karnataka, India
| | - Saikat Sen
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, Karnataka, India
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