1
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Morimoto A, Shimizu K, Suzuki N, Yagi S, Sueyoshi K, Endo T, Hisamoto H. Water detection in organic solvents using a copolymer membrane immobilised with a fluorescent intramolecular charge transfer-type dye: effects of intramolecular hydrogen bonds. Analyst 2024; 149:1939-1946. [PMID: 38381155 DOI: 10.1039/d3an02165c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Numerous fluorescent dye-based optical sensors have been developed to detect water in organic solvents. However, only a few such sensors can detect water in polar solvents such as methanol or dimethyl sulfoxide, and their detection range is generally narrow. Therefore, in this study, a copolymer membrane incorporated with a pyridinium betaine dye (denoted PB1), which exhibited intramolecular charge transfer (ICT) characteristics, was developed to realise simple water detection in organic solvents. The pyridinium betaine structure, comprising intramolecular hydrogen bonds between the oxygen in the maleimide moiety and the hydrogen in the pyridinium, was vital for achieving efficient fluorescence emission. The membrane was prepared by copolymerising PB1 with the N,N-dimethyl acrylamide/acrylamide monomer on a glass plate, and the fluorescence in water-mixed organic solvents was investigated (λabs = 490 nm, λfl = 630 nm). The fluorescence intensity of the dye-immobilised membrane decreased with increasing water content of the organic solvents. The detection ranges in tetrahydrofuran, ethanol, methanol, and dimethyl sulfoxide were approximately <40, <40, <40, and <60 vol% water, respectively. In contrast, membranes based on a quaternary pyridinium dye (without intramolecular hydrogen bonds) did not detect water in methanol and dimethyl sulfoxide, although it was more sensitive than PB1 in the narrow region of low water concentration in THF. Theoretical calculations corroborated the importance of the pyridinium betaine structure in detecting water in organic solvents, with the increase in polarity and the formation of intermolecular hydrogen bonds between PB1 and water found to induce molecular rotation and fluorescence quenching.
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Affiliation(s)
- Ami Morimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan.
| | - Kei Shimizu
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan.
| | - Naoya Suzuki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan.
| | - Shigeyuki Yagi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan.
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan.
- CREST, Japan Science and Technology Agency, Japan
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan.
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531 Japan.
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2
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Di Mino C, Seel AG, Clancy AJ, Headen TF, Földes T, Rosta E, Sella A, Skipper NT. Strong structuring arising from weak cooperative O-H···π and C-H···O hydrogen bonding in benzene-methanol solution. Nat Commun 2023; 14:5900. [PMID: 37736749 PMCID: PMC10516861 DOI: 10.1038/s41467-023-41451-y] [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: 11/08/2022] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Weak hydrogen bonds, such as O-H···π and C-H···O, are thought to direct biochemical assembly, molecular recognition, and chemical selectivity but are seldom observed in solution. We have used neutron diffraction combined with H/D isotopic substitution to obtain a detailed spatial and orientational picture of the structure of benzene-methanol mixtures. Our analysis reveals that methanol fully solvates and surrounds each benzene molecule. The expected O-H···π interaction is highly localised and directional, with the methanol hydroxyl bond aligned normal to the aromatic plane and the hydrogen at a distance of 2.30 Å from the ring centroid. Simultaneously, the tendency of methanol to form chain and cyclic motifs in the bulk liquid is manifest in a highly templated solvation structure in the plane of the ring. The methanol molecules surround the benzene so that the O-H bonds are coplanar with the aromatic ring while the oxygens interact with C-H groups through simultaneous bifurcated hydrogen bonds. This demonstrates that weak hydrogen bonding can modulate existing stronger interactions to give rise to highly ordered cooperative structural motifs that persist in the liquid phase.
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Affiliation(s)
- Camilla Di Mino
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Andrew G Seel
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK.
| | - Adam J Clancy
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas F Headen
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK
| | - Támas Földes
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK
| | - Andrea Sella
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Neal T Skipper
- Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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3
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Saunders LK, Irving D, Chater PA, Diaz-Lopez M. Noncovalent bonding assessment by pair distribution function. Faraday Discuss 2023; 244:356-369. [PMID: 37158101 DOI: 10.1039/d2fd00159d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Noncovalent interactions are essential in the formation and properties of a diverse range of materials. However, reliably identifying noncovalent interactions remains challenging using conventional methods such as X-ray diffraction, especially in nanocrystalline, poorly crystalline or amorphous materials which lack long-range lattice periodicity. Here, we demonstrate the accurate determination of deviations in the local structure and tilting of aromatic rings during the temperature-induced first order structural transition in the 1 : 1 adduct of 4,4'-bipyridinium squarate (BIPY:SQA) from the low temperature form HAZFAP01 to high temperature HAZFAP07 by X-ray pair distribution function. This work demonstrates how pair distribution function analyses can improve our understanding of local structural deviations resulting from noncovalent bonds and guide the development of novel functional materials.
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Affiliation(s)
- Lucy K Saunders
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Daniel Irving
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Philip A Chater
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Maria Diaz-Lopez
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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4
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Caruso T, De Luca O, Melfi N, Policicchio A, Pisarra M, Godbert N, Aiello I, Giorno E, Pacilè D, Moras P, Martín F, Rudolf P, Agostino RG, Papagno M. Nearly-freestanding supramolecular assembly with tunable structural properties. Sci Rep 2023; 13:2068. [PMID: 36740719 PMCID: PMC9899781 DOI: 10.1038/s41598-023-28865-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/25/2023] [Indexed: 02/07/2023] Open
Abstract
The synthesis and design of two-dimensional supramolecular assemblies with specific functionalities is one of the principal goals of the emerging field of molecule-based electronics, which is relevant for many technological applications. Although a large number of molecular assemblies have been already investigated, engineering uniform and highly ordered two-dimensional molecular assemblies is still a challenge. Here we report on a novel approach to prepare wide highly crystalline molecular assemblies with tunable structural properties. We make use of the high-reactivity of the carboxylic acid functional moiety and of the predictable structural features of non-polar alkane chains to synthesize 2D supramolecular assemblies of 4-(decyloxy)benzoic acid (4DBA;C[Formula: see text]H[Formula: see text]O[Formula: see text]) on a Au(111) surface. By means of scanning tunneling microscopy, density functional theory calculations and photoemission spectroscopy, we demonstrate that these molecules form a self-limited highly ordered and defect-free two-dimensional single-layer film of micrometer-size, which exhibits a nearly-freestanding character. We prove that by changing the length of the alkoxy chain it is possible to modify in a controlled way the molecular density of the "floating" overlayer without affecting the molecular assembly. This system is especially suitable for engineering molecular assemblies because it represents one of the few 2D molecular arrays with specific functionality where the structural properties can be tuned in a controlled way, while preserving the molecular pattern.
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Affiliation(s)
- Tommaso Caruso
- grid.7778.f0000 0004 1937 0319Dipartimento di Fisica, Università della Calabria, 87036 Rende (Cs), Italy ,grid.7778.f0000 0004 1937 0319Laboratorio di Spettroscopia Avanzata dei Materiali, STAR IR, Via Tito Flavio, Università della Calabria, 87036 Rende (CS), Italy
| | - Oreste De Luca
- grid.7778.f0000 0004 1937 0319Laboratorio di Spettroscopia Avanzata dei Materiali, STAR IR, Via Tito Flavio, Università della Calabria, 87036 Rende (CS), Italy ,grid.4830.f0000 0004 0407 1981Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Nicola Melfi
- grid.7778.f0000 0004 1937 0319Dipartimento di Fisica, Università della Calabria, 87036 Rende (Cs), Italy
| | - Alfonso Policicchio
- grid.7778.f0000 0004 1937 0319Dipartimento di Fisica, Università della Calabria, 87036 Rende (Cs), Italy ,grid.7778.f0000 0004 1937 0319Laboratorio di Spettroscopia Avanzata dei Materiali, STAR IR, Via Tito Flavio, Università della Calabria, 87036 Rende (CS), Italy
| | - Michele Pisarra
- grid.6045.70000 0004 1757 5281INFN, Sezione LNF, Gruppo Collegato di Cosenza, Cubo 31C, 87036 Rende (CS), Italy ,grid.482876.70000 0004 1762 408XInstituto IMDEA Nanociencia, Calle Faraday 9, 28049 Madrid, Spain ,grid.5515.40000000119578126Departamento de Química, Universidad Autónoma de Madrid, Módulo 13, 28049, Madrid Spain
| | - Nicolas Godbert
- grid.7778.f0000 0004 1937 0319MAT_InLAB (Laboratorio di Materiali Molecolari Inorganici), Centro di Eccellenza CEMIF.CAL, LASCAMM CR-INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende (CS), Italy ,grid.7778.f0000 0004 1937 0319LPM-Laboratorio Preparazione Materiali, STAR-Lab, Università della Calabria, Via Tito Flavio, 28049 Rende (CS), Italy
| | - Iolinda Aiello
- grid.7778.f0000 0004 1937 0319MAT_InLAB (Laboratorio di Materiali Molecolari Inorganici), Centro di Eccellenza CEMIF.CAL, LASCAMM CR-INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende (CS), Italy ,grid.7778.f0000 0004 1937 0319LPM-Laboratorio Preparazione Materiali, STAR-Lab, Università della Calabria, Via Tito Flavio, 28049 Rende (CS), Italy ,grid.7778.f0000 0004 1937 0319CNR-Nanotec, UoS di Cosenza, Dipartimento di Fisica, Università della Calabria, 87036 Rende (CS), Italy
| | - Eugenia Giorno
- grid.7778.f0000 0004 1937 0319MAT_InLAB (Laboratorio di Materiali Molecolari Inorganici), Centro di Eccellenza CEMIF.CAL, LASCAMM CR-INSTM, Unità INSTM della Calabria, Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende (CS), Italy ,grid.7778.f0000 0004 1937 0319LPM-Laboratorio Preparazione Materiali, STAR-Lab, Università della Calabria, Via Tito Flavio, 28049 Rende (CS), Italy
| | - Daniela Pacilè
- grid.7778.f0000 0004 1937 0319Dipartimento di Fisica, Università della Calabria, 87036 Rende (Cs), Italy
| | - Paolo Moras
- grid.472712.5Istituto di Struttura della Materia-CNR (ISM-CNR), 34149 Trieste, Italy
| | - Fernando Martín
- grid.482876.70000 0004 1762 408XInstituto IMDEA Nanociencia, Calle Faraday 9, 28049 Madrid, Spain ,grid.5515.40000000119578126Departamento de Química, Universidad Autónoma de Madrid, Módulo 13, 28049, Madrid Spain ,Condensed Matter Physics Center (IFIMAC), Cantoblanco, 28049 Madrid Spain
| | - Petra Rudolf
- grid.4830.f0000 0004 0407 1981Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Raffaele Giuseppe Agostino
- grid.7778.f0000 0004 1937 0319Dipartimento di Fisica, Università della Calabria, 87036 Rende (Cs), Italy ,grid.7778.f0000 0004 1937 0319Laboratorio di Spettroscopia Avanzata dei Materiali, STAR IR, Via Tito Flavio, Università della Calabria, 87036 Rende (CS), Italy
| | - Marco Papagno
- grid.7778.f0000 0004 1937 0319Dipartimento di Fisica, Università della Calabria, 87036 Rende (Cs), Italy ,grid.7778.f0000 0004 1937 0319Laboratorio di Spettroscopia Avanzata dei Materiali, STAR IR, Via Tito Flavio, Università della Calabria, 87036 Rende (CS), Italy
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5
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Asghar S, Hameed S, Tahir MN, Naseer MM. Molecular duplexes featuring NH···N, CH···O and CH···π interactions in solid-state self-assembly of triazine-based compounds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220603. [PMID: 36397969 PMCID: PMC9626258 DOI: 10.1098/rsos.220603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Synthetic supramolecular structures constructed through the cooperative action of numerous non-covalent forces are highly desirable as models to unravel and understand the complexity of systems created in nature via self-assembly. Taking advantage of the low cost of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and the sequential nucleophilic substitution reactions with almost all types of nucleophiles, a series of six structurally related novel s-triazine derivatives 1-6 were synthesized and structurally characterized based on their physical, spectral and crystallographic data. The solid-state structures of all the six compounds showed intriguing and unique molecular duplexes featuring NH···N, CH···O and CH···π interactions. Careful analysis of different geometric parameters of the involved H-bonds indicates that they are linear, significant and are therefore responsible for guiding the three-dimensional structure of these compounds in the solid state. The prevalence of sextuple hydrogen bond array-driven molecular duplexes and the possibility of structural modifications on the s-triazine ring render these novel triazine derivatives 1-6 attractive as a platform to create heteroduplex constructs and their subsequent utility in the field of supramolecular chemistry and crystal engineering.
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Affiliation(s)
- Shazia Asghar
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Shahid Hameed
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
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6
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Vinod Mouli MSS, Kumar Mishra A. Divergent Crystallographic Architecture for Silver‐Flavin Complexes Induced via pH Variation. ChemistrySelect 2022. [DOI: 10.1002/slct.202202126] [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)
- M. S. S. Vinod Mouli
- Department of Chemistry Indian Institute of Technology Hyderabad Kandi Sangareddy 502285 Telangana
| | - Ashutosh Kumar Mishra
- Department of Chemistry Indian Institute of Technology Hyderabad Kandi Sangareddy 502285 Telangana
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7
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Preparation and characterization of five 3D crystalline adducts from caffeine and organic acids. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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wang K, Wu M, Cheng B, Li H. Synthesis, characterization, and fluorescence of a highly stable two‐dimensional zinc coordination polymer. Z Anorg Allg Chem 2022. [DOI: 10.1002/zaac.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- kuikui wang
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter CHINA
| | - Mingyan Wu
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter CHINA
| | - Bo Cheng
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter CHINA
| | - Hengbo Li
- Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter CHINA
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9
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Stereoisomer-dependent conversion of dinaphthothienothiophene precursor films. Sci Rep 2022; 12:4448. [PMID: 35292720 PMCID: PMC8924201 DOI: 10.1038/s41598-022-08505-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/08/2022] [Indexed: 11/12/2022] Open
Abstract
Soluble precursor materials of organic semiconductors are employed for fabricating solution-processable thin film devices. While the so-called precursor approach has already been tried for various organic electronic devices such as transistors and solar cells, understanding of the conversion process in the film lags far behind. Here, we report that molecular aggregation of the precursor compound significantly influences the thermal conversion reaction in the film. For this study, two stereoisomers of a dinaphthothienothiophene (DNTT) precursor that are the endo- and exo-DNTT-phenylmaleimide monoadducts are focused on. The structural change during the thermal conversion process has been investigated by a combination of infrared spectroscopy and X-ray diffraction techniques. The results show that the endo-isomer is readily converted to DNTT in the film by heating, whereas the exo-isomer exhibits no reaction at all. This reaction suppression is found to be due to the self-aggregation property of the exo-isomer accompanying the intermolecular C–H\documentclass[12pt]{minimal}
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\begin{document}$$\cdots$$\end{document}⋯O interactions. This finding shows a new direction of controlling the on-surface reaction, as well as the importance of analyzing the film structure at the initial stage of the reaction.
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10
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Crystallographic, spectroscopic, thermal and computational studies of polymeric cobalt(II)–mellitate complex with 2,2′-bipyridine. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Husband JT, Xie Y, Wilks TR, Male L, Torrent-Sucarrat M, Stavros VG, O'Reilly RK. Rigidochromism by imide functionalisation of an aminomaleimide fluorophore. Chem Sci 2021; 12:10550-10557. [PMID: 34447549 PMCID: PMC8356812 DOI: 10.1039/d1sc03307g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022] Open
Abstract
Fluorescent dyes that exhibit high solid state quantum yields and sensitivity to the mechanical properties of their local environment are useful for a wide variety of applications, but are limited in chemical diversity. We report a trityl-functionalised maleimide that displays rigidochromic behaviour, becoming highly fluorescent when immobilised in a solid matrix, while displaying negligible fluorescence in solution. Furthermore, the dye's quantum yield is shown to be sensitive to the nature of the surrounding matrix. Computational studies reveal that this behaviour arises from the precise tuning of inter- and intramolecular noncovalent interactions. This work expands the diversity of molecules exhibiting solid state environment sensitivity, and provides important fundamental insights into their design.
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Affiliation(s)
- Jonathan T Husband
- School of Chemistry, University of Birmingham, Edgbaston Birmingham B15 2TT UK
| | - Yujie Xie
- School of Chemistry, University of Birmingham, Edgbaston Birmingham B15 2TT UK
| | - Thomas R Wilks
- School of Chemistry, University of Birmingham, Edgbaston Birmingham B15 2TT UK
| | - Louise Male
- School of Chemistry, University of Birmingham, Edgbaston Birmingham B15 2TT UK
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Universidad del País Vasco (UPV/EHU), Donostia International Physics Center (DIPC) Manuel Lardizabal Ibilbidea 3 Donostia 20018 Spain
- Ikerbasque, Basque Foundation for Science Plaza Euskadi 5 48009 Bilbao Euskadi Spain
| | | | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham, Edgbaston Birmingham B15 2TT UK
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12
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Dual XH-π Interaction of Hexafluoroisopropanol with Arenes. Molecules 2021; 26:molecules26154558. [PMID: 34361719 PMCID: PMC8347120 DOI: 10.3390/molecules26154558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
The dual XH (OH and CH) hydrogen-bond-donating property of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) and the strong dual XH-π interaction with arenes were firstly disclosed by theoretical studies. Here, the high accuracy post-Hartree-Fock methods, CCSD(T)/CBS, reveal the interaction energy of HFIP/benzene complex (-7.22 kcal/mol) and the contribution of the electronic correlation energy in the total interaction energy. Strong orbital interaction between HFIP and benzene was found by using the DFT method in this work to disclose the dual XH-π intermolecular orbital interaction of HFIP with benzene-forming bonding and antibonding orbitals resulting from the orbital symmetry of HFIP. The density of states and charge decomposition analyses were used to investigate the orbital interactions. Isopropanol (IP), an analogue of HFIP, and chloroform (CHCl3) were studied to compare them with the classical OH-π, and non-classical CH-π interactions. In addition, the influence of the aggregating effect of HFIP, and the numbers of substituted methyl groups in benzene rings were also studied. The interaction energies of HFIP with the selected 24 common organic compounds were calculated to understand the role of HFIP as solvent or additive in organic transformation in a more detailed manner. A single-crystal X-ray diffraction study of hexafluoroisopropyl benzoate further disclosed and confirmed that the CH of HFIP shows the non-classical hydrogen-bond-donating behavior.
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13
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Xiao Y, Tao J, Peng X, Song Y, Lei P, Xu H, Xiao X, Tu B, Zeng Q. Two-Dimensional Molecular Network Built from Hierarchy Self-Assembly of Perylene Bisimide Derivatives. ACS APPLIED MATERIALS & INTERFACES 2021; 13:17129-17138. [PMID: 33818059 DOI: 10.1021/acsami.1c03201] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The structures of two-dimensional (2D) self-assembled molecular networks formed by a series of perylene bisimide (PBI) derivatives were investigated by scanning tunneling microscopy (STM). By introducing different functional groups to the PBI rings, we successfully built a different self-assembled molecular network on the liquid-solid interface. When the substituent is propanol, PBI is aligned in lines. When we introduced either an ester group or an amide group to the PBI compounds, they tended to form dimers and trimers. Especially, the PBI with the amide groups can form a 2D porous molecular network by hierarchy self-assembly. The 2D porous molecular network has a great potential to be the host molecule for the accommodation of a guest molecule, coronene (COR), and the structure of the 2D porous molecular network can be tuned by varying the concentration. The density functional theory calculations were also performed to disclose the mechanisms involved.
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Affiliation(s)
- Yuchuan Xiao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- School of Materials and Chemical Engineering, Ningbo University of Technology, Ningbo 315211, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayu Tao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xuan Peng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Song
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Peng Lei
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haijun Xu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xunwen Xiao
- School of Materials and Chemical Engineering, Ningbo University of Technology, Ningbo 315211, China
| | - Bin Tu
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Janczak J. Structure and phase transition in 1-(diaminomethylene)thiouron-1-ium m-nitrobenzoate monohydrate and the structure of its anhydrous deuterated analogue. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Kretić DS, Radovanović JI, Veljković DŽ. Can the sensitivity of energetic materials be tuned by using hydrogen bonds? Another look at the role of hydrogen bonding in the design of high energetic compounds. Phys Chem Chem Phys 2021; 23:7472-7479. [PMID: 33876107 DOI: 10.1039/d1cp00189b] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Strongly positive electrostatic potential in the central areas of molecules of energetic materials is one of the most important factors that determines the sensitivity of these molecules towards detonation. Quantum chemical and density functional theory calculations were used to reveal the influence of hydrogen bonding on the values of electrostatic potential above the central areas of molecules of three conventional explosives: 1,3,5-trinitrobenzene, 2,4,6-trinitrophenol, and 2,4,6-trinitrotoluene. Both the case when energetic molecules act as hydrogen atom donors and when they act as hydrogen atom acceptors were considered. Results of the calculations performed using the M06/cc-PVDZ level of theory showed that there are significant differences in the influence of hydrogen bonding on the electrostatic potential of energetic molecules acting as hydrogen atom donors and hydrogen atom acceptors. In the case when energetic molecules act as hydrogen acceptors, an increase of 10% in the strength of positive electrostatic potential was identified. In the case when energetic molecules act as hydrogen atom donors, a significant decrease (20-25%) in the strength of the positive potential on the molecular surface was calculated. These differences give an opportunity for fine-tuning the impact sensitivities of energetic compounds and provide new guidelines for the design of explosives with desirable characteristics.
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Affiliation(s)
- Danijela S Kretić
- University of Belgrade - Faculty of Chemistry, Studentski trg 12-16, Belgrade 11000, Serbia.
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16
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Ousaka N, Itakura M, Nagasaka A, Ito M, Hattori T, Taura D, Ikai T, Yashima E. Water-Mediated Reversible Control of Three-State Double-Stranded Titanium(IV) Helicates. J Am Chem Soc 2021; 143:4346-4358. [PMID: 33688731 DOI: 10.1021/jacs.0c13351] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A stimuli-responsible reversible structural transformation is of key importance in biological systems. We now report a unique water-mediated reversible transformation among three discrete double-stranded dinuclear titanium(IV) achiral meso- and chiral rac-helicates linked by a mono(μ-oxo) or a bis(μ-hydroxo) bridge between the titanium ions through hydration/dehydration or its combination with a water-mediated dynamic cleavage/re-formation of the titanium-phenoxide (Ti-OPh) bonds. The bis(μ-hydroxo) bridged titanium(IV) meso-helicate prepared from two tetraphenol strands with titanium(IV) oxide was readily dehydrated in CD3CN containing a small amount of water upon heating, accompanied by Ti-OPh bond cleavage/re-formation catalyzed by water, resulting in the formation of the mono(μ-oxo)-bridged rac-helicate, which reverted back to the original bis(μ-hydroxo)-bridged meso-helicate upon hydration in aqueous CD3CN. These reversible transformations between the meso- and rac-helicates were also promoted in the presence of a catalytic amount of an acid, which remarkably accelerated the reactions at lower temperature. Interestingly, in anhydrous CD3CN, the bis(μ-hydroxo)-bridged meso-helicate was further slowly converted to a different helicate, while its meso-helicate framework was maintained, namely the mono(μ-oxo)-bridged meso-helicate, through dehydration upon heating and its meso to meso transformation was significantly accelerated in the presence of cryptand[2.2.1], which contributes to removing Na+ ions coordinated to the helicate. Upon cooling, the backward meso to meso transformation took place via hydration. Hence, three different, discrete double-stranded chiral rac- and achiral meso-titanium(IV) helicates linked by a mono(μ-oxo) or a bis(μ-hydroxo) bridge were successfully generated in a controllable manner by a change in the water content of the reaction media.
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Affiliation(s)
- Naoki Ousaka
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.,Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Manabu Itakura
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Akira Nagasaka
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Masaki Ito
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tomonari Hattori
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Daisuke Taura
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.,Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tomoyuki Ikai
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Eiji Yashima
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.,Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
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17
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Design, structural investigations and antimicrobial activity of pyrazole nucleating copper and zinc complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114991] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Gak Simić K, Đorđević I, Lazić A, Radovanović L, Petković-Benazzouz M, Rogan J, Trišović N, Janjić G. On the supramolecular outcomes of fluorination of cyclohexane-5-spirohydantoin derivatives. CrystEngComm 2021. [DOI: 10.1039/d0ce01841d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The crystal packing of two spirohydantoins was analyzed through the contribution of dimeric motifs and different interactions. The cooperative effect was rationalized in terms of the formation of a new region, as a result of the F⋯F interaction.
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Affiliation(s)
- Kristina Gak Simić
- Innovation Centre of the Faculty of Technology and Metallurgy
- 11120 Belgrade
- Serbia
| | - Ivana Đorđević
- Institute of Chemistry, Technology and Metallurgy
- National Institute of the Republic of Serbia
- University of Belgrade
- 11001 Belgrade
- Serbia
| | - Anita Lazić
- Innovation Centre of the Faculty of Technology and Metallurgy
- 11120 Belgrade
- Serbia
| | - Lidija Radovanović
- Innovation Centre of the Faculty of Technology and Metallurgy
- 11120 Belgrade
- Serbia
| | | | - Jelena Rogan
- Faculty of Technology and Metallurgy
- University of Belgrade
- 11120 Belgrade
- Serbia
| | - Nemanja Trišović
- Faculty of Technology and Metallurgy
- University of Belgrade
- 11120 Belgrade
- Serbia
| | - Goran Janjić
- Institute of Chemistry, Technology and Metallurgy
- National Institute of the Republic of Serbia
- University of Belgrade
- 11001 Belgrade
- Serbia
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19
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Keshri SK, Nakanishi W, Takai A, Ishizuka T, Kojima T, Takeuchi M. Discrete π Stack of a Tweezer-Shaped Naphthalenediimide-Anthracene Conjugate. Chemistry 2020; 26:13288-13294. [PMID: 32583576 DOI: 10.1002/chem.202002477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 12/22/2022]
Abstract
The design and synthesis of a tweezer-shaped naphthalenediimide (NDI)-anthracene conjugate (2NDI) are reported. In the structure of the closed form (πNDI ⋅⋅⋅πNDI stack) of 2NDI, which was elucidated by single-crystal XRD, the existence of C-H⋅⋅⋅O hydrogen bonding involving the nearest carbonyl oxygen atom of an NDI unit was suggested. The tunability of πNDI ⋅⋅⋅πNDI interactions was studied by means of UV/Vis absorption, fluorescence and NMR spectroscopy and molecular modelling. This revealed that the πNDI ⋅⋅⋅πNDI interactions in 2NDI affect the absorption and emission properties depending on the temperature. Furthermore, in polar solvents, 2NDI prefers the stronger πNDI ⋅⋅⋅πNDI stack, whereas the πNDI ⋅⋅⋅πNDI interaction is diminished in nonpolar solvents. Importantly, the conformational variations of 2NDI can be reversibly switched by variation in temperature, and this suggests potential application for fluorogenic molecular switches upon temperature changes.
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Affiliation(s)
- Sudhir Kumar Keshri
- Molecular Design and Function Group, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, 305-0047, Japan
| | - Waka Nakanishi
- Molecular Design and Function Group, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, 305-0047, Japan
| | - Atsuro Takai
- Molecular Design and Function Group, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, 305-0047, Japan
| | - Tomoya Ishizuka
- Department of Chemistry, Faculty of Pure & Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, Faculty of Pure & Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan
| | - Masayuki Takeuchi
- Molecular Design and Function Group, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, 305-0047, Japan
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20
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Mohsen M, Naeem I, Awaad M, Tantawy H, Baraka A. A cadmium-imidazole coordination polymer as solid state buffering material: Synthesis, characterization and its use for photocatalytic degradation of ionic dyes. J SOLID STATE CHEM 2020. [DOI: 10.1016/j.jssc.2020.121493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Toader AM, Zarić SD, Zalaru CM, Ferbinteanu M. The Structural Details of Aspirin Molecules and Crystals. Curr Med Chem 2020; 27:99-120. [PMID: 30381068 DOI: 10.2174/0929867325666181031132823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 11/22/2022]
Abstract
We revisit, in the key of structural chemistry, one of the most known and important drugs: the aspirin. Although apparently simple, the factors determining the molecular structure and supramolecular association in crystals are not trivial. We addressed the problem from experimental and theoretical sides, considering issues from X-ray measurements and results of first-principle reconstruction of molecule and lattices by ab initio calculations. Some puzzling problems can give headaches to specialists and intrigue the general public. Thus, the reported polymorphism of aspirin is disputed, a so-called form II being alleged as a result of misinterpretation. At the same time, were presented evidences that the structure of common form I can be disrupted by domains where the regular packing is changed to the pattern of form II. The problems appear even at the level of independent molecule: the most stable conformation computed by various techniques of electronic structure differs from those encountered in crystals. Because the energy difference between the related conformational isomers (computed as most stable vs. the experimental structure) is small, about 1 kcal/mol, comprised in the error bars of used methods, the unresting question is whether the modelling is imprecise, or the supramolecular factors are mutating the conformational preferences. By a detective following of the issue, the intermolecular effects were made responsible for the conformation of the molecule in crystal. The presented problems were gathered from literature results, debates, glued with modelling and analysis redone by ourselves, in order to secure the unitary view of the considered prototypic topic.
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Affiliation(s)
| | - Snezana D Zarić
- Department of Chemistry, University of Belgrade, Belgrade, Serbia.,Department of Chemistry, Texas A&M University at Qatar, Doha, Qatar
| | - Christina M Zalaru
- Department of Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, Bucharest, Romania
| | - Marilena Ferbinteanu
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Bucharest, Bucharest, Romania
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22
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Kempe F, Riehle F, Komber H, Matsidik R, Walter M, Sommer M. Semifluorinated, kinked polyarylenes via direct arylation polycondensation. Polym Chem 2020. [DOI: 10.1039/d0py00973c] [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
The Tg of semifluorinated polyarylenes made via DAP is varied between 35–195 °C depending on side chain, but solubilities are much less side chain dependent. This is explained by interactions between alkoxyphenyl and tetrafluorobenzene units.
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Affiliation(s)
- Fabian Kempe
- Chemnitz University of Technology
- 09111 Chemnitz
- Germany
| | - Felix Riehle
- Institute for Macromolecular Chemistry
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Hartmut Komber
- Leibniz Institute of Polymer Research
- 01069 Dresden
- Germany
| | | | - Michael Walter
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT)
- University of Freiburg
- 79110 Freiburg
- Germany
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23
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Veljković IS, Veljković DŽ, Sarić GG, Stanković IM, Zarić SD. What is the preferred geometry of sulfur–disulfide interactions? CrystEngComm 2020. [DOI: 10.1039/d0ce00211a] [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
Combined crystallographic and quantum chemical studies showed that in most cases, in crystal structures, interactions between sulphur atoms and disulphide bonds are bifurcated.
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Affiliation(s)
- Ivana S. Veljković
- Institute of Chemistry, Technology and Metallurgy
- University of Belgrade
- 11000 Belgrade
- Serbia
| | | | | | - Ivana M. Stanković
- Institute of Chemistry, Technology and Metallurgy
- University of Belgrade
- 11000 Belgrade
- Serbia
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24
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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25
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Zeng T, Lu Y, Jin S, Sun L, Zhong B, Wang D, Wang J, Liu H. Noncovalent bonded 3D structures of eight anhydrous organic salts from tris(hydroxymethyl)aminomethane and organic acids. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Angnes RA, Thompson LM, Mashuta MS, Correia CRD, Hammond GB. Non‐Covalent Substrate Directed Enantioselective Heck Desymmetrization of
cis
‐Cyclohex‐4‐ene‐1,2‐diol: Synthesis of all
cis
Chiral 5‐Aryl‐cyclohex‐3‐ene‐1,2‐diols and Mechanistic Investigation. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800785] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ricardo A. Angnes
- Chemistry Department University of Louisville 40292-0001 Louisville, KY USA
- Chemistry Department University of Campinas, C.P. 6154, CEP. 13083-970 Campinas, SP Brazil
| | - Lee M. Thompson
- Chemistry Department University of Louisville 40292-0001 Louisville, KY USA
| | - Mark S. Mashuta
- Chemistry Department University of Louisville 40292-0001 Louisville, KY USA
| | - Carlos R. D. Correia
- Chemistry Department University of Campinas, C.P. 6154, CEP. 13083-970 Campinas, SP Brazil
| | - Gerald B. Hammond
- Chemistry Department University of Louisville 40292-0001 Louisville, KY USA
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27
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Rajkumar M, Muthuraja P, Dhandapani M, Chandramohan A. Supramolecular network through N H…O, O H…O and C H…O hydrogen bonding interaction and density functional theory studies of 4-methylanilinium-3-carboxy-4-hydroxybenzenesulphonate crystal. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Dong L, Jin S, Jin S, Gao X, Xie X, Lin Z, Wang Y, Xu W, Wang D. Supramolecular salts of 5,7-dimethyl-1,8-naphthyridine-2-amine and acids through classical H-Bonds and other intermolecular interactions. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.09.102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Veljković DŽ. Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size. J Mol Graph Model 2018; 80:121-125. [PMID: 29331729 DOI: 10.1016/j.jmgm.2017.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 10/18/2022]
Abstract
Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions.
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Affiliation(s)
- Dušan Ž Veljković
- Department of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
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30
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Structural Determination of Ruthenium Complexes Containing Bi-Dentate Pyrrole-Ketone Ligands. MOLECULES (BASEL, SWITZERLAND) 2018; 23:molecules23010159. [PMID: 29342833 PMCID: PMC6016999 DOI: 10.3390/molecules23010159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/06/2018] [Accepted: 01/12/2018] [Indexed: 12/28/2022]
Abstract
A series of ruthenium compounds containing a pyrrole-ketone bidentate ligand, 2-(2′-methoxybenzoyl)pyrrole (1), have been synthesized and characterized. Reacting 1 with [(η6-cymene)RuCl2]2 and RuHCl(CO)(PPh3)3 generated Ru(η6-cymene)[C4H3N-2-(CO-C6H4-2-OMe)]Cl (2) and {RuCl(CO)(PPh3)2[C4H3N-2-(COC6H4-2-OMe)]} (3), respectively, in moderate yields. Successively reacting 2 with sodium cyanate and sodium azide gave {Ru(η6-cymene)[C4H3N-2-(CO-C6H4-2-OMe)]X} (4, X=OCN; 5, X=N3) with the elimination of sodium chloride. Compounds 2–5 were all characterized by 1H and 13C-NMR spectra and their structures were also determined by X-ray single crystallography.
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31
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Zhang X, Wang H, Yuan J, Guo S. Palladacycles incorporating a carboxylate-functionalized phosphine ligand: syntheses, characterization and their catalytic applications toward Suzuki couplings in water. TRANSIT METAL CHEM 2017. [DOI: 10.1007/s11243-017-0181-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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32
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Damron JT, Kersten KM, Pandey MK, Mroue KH, Yarava JR, Nishiyama Y, Matzger AJ, Ramamoorthy A. Electrostatic Constraints Assessed by 1H MAS NMR Illuminate Differences in Crystalline Polymorphs. J Phys Chem Lett 2017; 8:4253-4257. [PMID: 28825828 PMCID: PMC6295661 DOI: 10.1021/acs.jpclett.7b01650] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Atomically resolved crystal structures not only suffer from the inherent uncertainty in accurately locating H atoms but also are incapable of fully revealing the underlying forces enabling the formation of final structures. Therefore, the development and application of novel techniques to illuminate intermolecular forces in crystalline solids are highly relevant to understand the role of hydrogen atoms in structure adoption. Novel developments in 1H NMR MAS methodology can now achieve robust measurements of 1H chemical shift anisotropy (CSA) tensors which are highly sensitive to electrostatics. Herein, we use 1H CSA tensors, measured by MAS experiments and characterized using DFT calculations, to reveal the structure-driving factors between the two polymorphic forms of acetaminophen (aka Tylenol or paracetamol) including differences in hydrogen bonding and the role of aromatic interactions. We demonstrate how the 1H CSAs can provide additional insights into the static picture provided by diffraction to elucidate rigid molecules.
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Affiliation(s)
- Joshua T. Damron
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kortney M. Kersten
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Manoj Kumar Pandey
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Kamal H. Mroue
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | | | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- JEOL RESONANCE, Inc., Musashino, Akishima, Tokyo 186-8558, Japan
| | - Adam J. Matzger
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Macromolecular Science and Engineering, University of Michigan, 2300 Hayward Avenue, Ann Arbor, Michigan 48109, United States
- Corresponding Authors: .
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Corresponding Authors: .
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33
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Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures. Biophys J 2017; 110:1967-79. [PMID: 27166805 DOI: 10.1016/j.bpj.2016.03.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 01/08/2023] Open
Abstract
Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched N-H…N H-bonds in two different sets of protein structures. Data set I consists of neutron diffraction and ultrahigh-resolution x-ray structures (0.9 Å resolution or better) and the hydrogen atom positions in these structures were determined experimentally. Data set II contains structures determined using x-ray diffraction (resolution ≤ 1.8 Å) and the positions of hydrogen atoms were generated using a computational method. We identified 114 and 14,347 potential N-H…N H-bonds from these two data sets, respectively, and 56-66% of these were of the Ni+1-Hi+1…Ni type, with Ni being the proline backbone nitrogen. To further understand the nature of such unusual contacts, we performed quantum chemical calculations on the model compound N-acetyl-L-proline-N-methylamide (Ace-Pro-NMe) with coordinates taken from the experimentally determined structures. A potential energy profile generated by varying the ψ dihedral angle in Ace-Pro-NMe indicates that the conformation with the N-H…N H-bond is the most stable. An analysis of H-bond-forming proline residues reveals that more than 30% of the proline carbonyl groups are also involved in n → π(∗) interactions with the carbonyl carbon of the preceding residue. Natural bond orbital analyses demonstrate that the strength of N-H…N H-bonds is less than half of that observed for a conventional H-bond. This study clearly establishes the H-bonding capability of proline nitrogen and its prevalence in protein structures. We found many proteins with multiple instances of H-bond-forming prolines. With more than 15% of all proline residues participating in N-H…N H-bonds, we suggest a new, to our knowledge, structural role for proline in providing stability to loops and capping regions of secondary structures in proteins.
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34
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Kawai S, Nishiuchi T, Kodama T, Spijker P, Pawlak R, Meier T, Tracey J, Kubo T, Meyer E, Foster AS. Direct quantitative measurement of the C═O⋅⋅⋅H-C bond by atomic force microscopy. SCIENCE ADVANCES 2017; 3:e1603258. [PMID: 28508080 PMCID: PMC5429039 DOI: 10.1126/sciadv.1603258] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/14/2017] [Indexed: 05/05/2023]
Abstract
The hydrogen atom-the smallest and most abundant atom-is of utmost importance in physics and chemistry. Although many analysis methods have been applied to its study, direct observation of hydrogen atoms in a single molecule remains largely unexplored. We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C═O⋅⋅⋅H-C hydrogen bonding just before the onset of Pauli repulsion. The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs and polymers, building the capabilities of AFM toward quantitative probing of local chemical reactivity.
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Affiliation(s)
- Shigeki Kawai
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Tomohiko Nishiuchi
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Takuya Kodama
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Peter Spijker
- Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, PO Box 11100, FI-00076 Aalto, Finland
| | - Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Tobias Meier
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - John Tracey
- Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, PO Box 11100, FI-00076 Aalto, Finland
| | - Takashi Kubo
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
| | - Adam S. Foster
- Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, PO Box 11100, FI-00076 Aalto, Finland
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
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35
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Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning. J Chem Theory Comput 2016; 12:2312-23. [PMID: 27057643 PMCID: PMC4864407 DOI: 10.1021/acs.jctc.6b00027] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Molecular mechanics
force fields, which are commonly used in biomolecular
modeling and computer-aided drug design, typically treat nonbonded
interactions using a limited library of empirical parameters that
are developed for small molecules. This approach does not account
for polarization in larger molecules or proteins, and the parametrization
process is labor-intensive. Using linear-scaling density functional
theory and atoms-in-molecule electron density partitioning, environment-specific
charges and Lennard-Jones parameters are derived directly from quantum
mechanical calculations for use in biomolecular modeling of organic
and biomolecular systems. The proposed methods significantly reduce
the number of empirical parameters needed to construct molecular mechanics
force fields, naturally include polarization effects in charge and
Lennard-Jones parameters, and scale well to systems comprised of thousands
of atoms, including proteins. The feasibility and benefits of this
approach are demonstrated by computing free energies of hydration,
properties of pure liquids, and the relative binding free energies
of indole and benzofuran to the L99A mutant of T4 lysozyme.
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Affiliation(s)
- Daniel J Cole
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States.,TCM Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jonah Z Vilseck
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Mike C Payne
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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36
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Andrić JM, Misini-Ignjatović MZ, Murray JS, Politzer P, Zarić SD. Hydrogen Bonding between Metal-Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies. Chemphyschem 2016; 17:2035-42. [PMID: 26989883 DOI: 10.1002/cphc.201501200] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Indexed: 12/28/2022]
Abstract
The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal-ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground-state molecules, prior to interaction, can provide considerable insight into the interactions.
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Affiliation(s)
- Jelena M Andrić
- Innovation Center of the Department of Chemistry, Studentski trg 12-16, 11000, Belgrade, Serbia
| | | | - Jane S Murray
- Department of Chemistry, University of New Orleans, New Orleans, LA, 71048, USA
| | - Peter Politzer
- Department of Chemistry, University of New Orleans, New Orleans, LA, 71048, USA
| | - Snežana D Zarić
- Department of Chemistry, Texas A & M University at Qatar, P.O. Box 23874, Doha, Qatar. .,Department of Chemistry, University of Belgrade, Studentski trg 12-16, 11000, Belgrade, Serbia.
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37
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Marchione D, McCoustra MRS. Non-covalent interaction of benzene with methanol and diethyl ether solid surfaces. Phys Chem Chem Phys 2016; 18:20790-801. [DOI: 10.1039/c6cp01787h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have investigated the interactions involved at the interface of binary, layered ices (benzene on methanol and on diethyl ether) by means of laboratory experiments and ab initio calculations on model clusters.
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38
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Nath JK, Baruah JB. Cyclic aromatic imides as a potential class of molecules for supramolecular interactions. CrystEngComm 2015. [DOI: 10.1039/c5ce01485a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Prospects of stacking interactions of imides beneficial to generation of new soft materials are projected by analysing examples of primary building blocks that provide a basis for understanding at the molecular level.
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Affiliation(s)
- Jayanta K. Nath
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati 781 039, India
| | - Jubaraj B. Baruah
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati 781 039, India
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39
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Mitoraj MP, Janjić GV, Medaković VB, Veljković DŽ, Michalak A, Zarić SD, Milčić MK. Nature of the water/aromatic parallel alignment interactions. J Comput Chem 2014; 36:171-80. [DOI: 10.1002/jcc.23783] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/05/2014] [Accepted: 10/17/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Mariusz P. Mitoraj
- Faculty of Chemistry; Department of Theoretical Chemistry; Jagiellonian University; R. Ingardena 3, 30-060 Krakow Poland
| | - Goran V. Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade; Njegoševa 12 11000 Belgrade Serbia
| | - Vesna B. Medaković
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
| | - Dušan Ž. Veljković
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
| | - Artur Michalak
- Faculty of Chemistry; Department of Theoretical Chemistry; Jagiellonian University; R. Ingardena 3, 30-060 Krakow Poland
| | - Snežana D. Zarić
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
- Department of Chemistry; Texas A & M University at Qatar; P.O. Box 23874 Doha Qatar
| | - Miloš K. Milčić
- Department of Chemistry; University of Belgrade; Studentski trg 12-16 11000 Belgrade Serbia
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40
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Janjić GV, Malkov SN, Zivković MV, Zarić SD. What are preferred water-aromatic interactions in proteins and crystal structures of small molecules? Phys Chem Chem Phys 2014; 16:23549-53. [PMID: 25271703 DOI: 10.1039/c4cp00929k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The distribution of water molecules around aromatic rings in the protein structures and crystal structures of small molecules shows quite a small number of the strongest OH-π interactions, a larger number of parallel interactions, and the largest number of the weakest CH-O interactions.
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Affiliation(s)
- Goran V Janjić
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, P.O. Box 473, Belgrade, Serbia
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41
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Vojislavljević-Vasilev DZ, Janjić GV, Medaković VB, Blagojević JP, Zarić SD. Parallel water/aromatic interactions of non-coordinated and coordinated water. Chemphyschem 2014; 15:2386-96. [PMID: 24840235 DOI: 10.1002/cphc.201402004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/19/2014] [Indexed: 11/07/2022]
Abstract
The parallel interactions of non-coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel-down orientation in which one OH bond is parallel to the aromatic ring, whereas the other OH bond points to the plane of the ring. The interactions of aqua complexes with parallel-down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is -14.89 kcal mol(-1) . The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.
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42
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Kawatkar SP, Keating TA, Olivier NB, Breen JN, Green OM, Guler SY, Hentemann MF, Loch JT, McKenzie AR, Newman JV, Otterson LG, Martínez-Botella G. Antibacterial inhibitors of Gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region. J Med Chem 2014; 57:4584-97. [PMID: 24828090 DOI: 10.1021/jm500463c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Thymidylate kinase (TMK), an essential enzyme in bacterial DNA biosynthesis, is an attractive therapeutic target for the development of novel antibacterial agents, and we continue to explore TMK inhibitors with improved potency, protein binding, and pharmacokinetic potential. A structure-guided design approach was employed to exploit a previously unexplored region in Staphylococcus aureus TMK via novel interactions. These efforts produced compound 39, with 3 nM IC50 against S. aureus TMK and 2 μg/mL MIC against methicillin-resistant S. aureus (MRSA). This compound exhibits a striking inverted chiral preference for binding relative to earlier compounds and also has improved physical properties and pharmacokinetics over previously published compounds. An example of this new series was efficacious in a murine S. aureus infection model, suggesting that compounds like 39 are options for further work toward a new Gram-positive antibiotic by maintaining a balance of microbiological potency, low clearance, and low protein binding that can result in lower efficacious doses.
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Affiliation(s)
- Sameer P Kawatkar
- Infection Innovative Medicines and ‡Discovery Sciences, AstraZeneca , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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43
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Pang J, Jiang F, Yuan D, Zheng J, Wu M, Liu G, Su K, Hong M. SO42− anion directed hexagonal-prismatic cages via cooperative C–H⋯O hydrogen bonds. Chem Sci 2014. [DOI: 10.1039/c4sc01973c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Hexagonal-prismatic cages are constructed from cubane-like Ni4(μ3-OH)4 clusters generated in situ and clip-like organic ligands.
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Affiliation(s)
- Jiandong Pang
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
| | - Feilong Jiang
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
| | - Daqiang Yuan
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
| | - Jun Zheng
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
| | - Mingyan Wu
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
| | - Guoliang Liu
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
| | - Kongzhao Su
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
| | - Maochun Hong
- Key Lab of Coal to Ethylene Glycol and Its Related Technology
- State Key Lab of Structure Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou, China
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44
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Veljković DŽ, Medaković VB, Andrić JM, Zarić SD. C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study. CrystEngComm 2014. [DOI: 10.1039/c4ce00595c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.
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Affiliation(s)
- D. Ž. Veljković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - J. M. Andrić
- Innovation Center
- Department of Chemistry
- 11000 Belgrade, Serbia
| | - S. D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A&M University at Qatar
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45
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Malenov DP, Janjić GV, Veljković DŽ, Zarić SD. Mutual influence of parallel, CH/O, OH/π and lone pair/π interactions in water/benzene/water system. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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46
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Yang H, Wong MW. Oxyanion Hole Stabilization by C–H···O Interaction in a Transition State—A Three-Point Interaction Model for Cinchona Alkaloid-Catalyzed Asymmetric Methanolysis of meso-Cyclic Anhydrides. J Am Chem Soc 2013; 135:5808-18. [DOI: 10.1021/ja4005893] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Yang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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47
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Vojislavljević DZ, Janjić GV, Ninković DB, Kapor A, Zarić SD. The influence of water molecule coordination onto the water–aromatic interaction. Strong interactions of water coordinating to a metal ion. CrystEngComm 2013. [DOI: 10.1039/c2ce25621e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Dragelj JL, Janjić GV, Veljković DŽ, Zarić SD. Crystallographic and ab initio study of pyridine CH–O interactions: linearity of the interactions and influence of pyridine classical hydrogen bonds. CrystEngComm 2013. [DOI: 10.1039/c3ce40759d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Sigalov MV, Doronina EP, Sidorkin VF. CAr–H···O Hydrogen Bonds in Substituted Isobenzofuranone Derivatives: Geometric, Topological, and NMR Characterization. J Phys Chem A 2012; 116:7718-25. [DOI: 10.1021/jp304009g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mark V. Sigalov
- Department of Chemistry, Ben-Gurion University of the Negev, 84105 Beer-Sheva,
Israel
| | - Evgeniya P. Doronina
- Irkutsk Institute of Chemistry, Siberian Division of RAS, Favorsky st.
1, 664033 Irkutsk, Russia
| | - Valery F. Sidorkin
- Irkutsk Institute of Chemistry, Siberian Division of RAS, Favorsky st.
1, 664033 Irkutsk, Russia
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50
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Seidel RW, Goddard R, Breidung J, Bamfaste P, Neff D, Oppel IM. Reversible crystal-to-crystal phase transition of a 4,4′-bipyridine-linked dinuclear copper(II) complex. Struct Chem 2012. [DOI: 10.1007/s11224-012-0044-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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