1
|
Lopresti M, Palin L, Calegari G, Milanesio M. The Peculiar H-Bonding Network of 4-Methylcatechol: A Coupled Diffraction and In Silico Study. Molecules 2024; 29:2173. [PMID: 38792035 PMCID: PMC11124409 DOI: 10.3390/molecules29102173] [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: 03/27/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
The crystal structure of 4-methylcatechol (4MEC) has, to date, never been solved, despite its very simple chemical formula C7O2H8 and the many possible applications envisaged for this molecule. In this work, this gap is filled and the structure of 4MEC is obtained by combining X-ray powder diffraction and first principle calculations to carefully locate hydrogen atoms. Two molecules are present in the asymmetric unit. Hirshfeld analysis confirmed the reliability of the solved structure, since the two molecules show rather different environments and H-bond interactions of different directionality and strength. The packing is characterised by a peculiar hydrogen bond network with hydroxyl nests formed by two adjacent octagonal frameworks. It is noteworthy that the observed short contacts suggest strong inter-molecular interactions, further confirmed by strong inter-crystalline aggregation observed by microscopic images, indicating the growth, in many crystallization attempts, of single aggregates taller than half a centimetre and, often, with spherical shapes. These peculiarities are induced by the presence of methyl group in 4MEC, since the parent compound catechol, despite its chemical similarity, shows a standard layered packing alternating hydrophobic and polar layers. Finally, the complexity and peculiarity of the packing and crystal growth features explain why a single crystal could not be obtained for a standard structural analysis.
Collapse
Affiliation(s)
- Mattia Lopresti
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy; (M.L.); (L.P.)
| | - Luca Palin
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy; (M.L.); (L.P.)
- Nova Res s.r.l., Via D. Bello 3, 28100 Novara, Italy
| | | | - Marco Milanesio
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy; (M.L.); (L.P.)
| |
Collapse
|
2
|
Dittrich B, Connor LE, Fabbiani FPA, Piechon P. Linking solid-state phenomena via energy differences in `archetype crystal structures'. IUCRJ 2024; 11:347-358. [PMID: 38629168 PMCID: PMC11067740 DOI: 10.1107/s2052252524002641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/20/2024] [Indexed: 05/04/2024]
Abstract
Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305-318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder - and disappearing disorder - occurs in an average structure. Part of the concept is that disorder, as probed by diffraction, affects entire molecules, rather than just the parts of a molecule with differing conformations, and the finding that an R·T energy difference between disorder archetypes is usually not exceeded. An illustrative example combining disorder and special positions is the crystal structure of oestradiol hemihydrate analysed here, where its space-group/subgroup relationship is required to explain its disorder of hydrogen-bonded hydrogen atoms. In addition, we show how high-Z' structures can also be analysed energetically and understood via archetypes: high-Z' structures occur when an energy gain from combining different rather than overall alike conformations in a crystal significantly exceeds R·T, and this finding is discussed in the context of earlier explanations in the literature. Twinning is not related to archetype structures since it involves macroscopic domains of the same crystal structure. Archetype crystal structures are distinguished from crystal structure prediction trial structures in that an experimental reference structure is required for them. Categorization into archetype structures also has practical relevance, leading to a new practice of disorder modelling in experimental least-squares refinement alluded to in the above-mentioned publication.
Collapse
Affiliation(s)
- B. Dittrich
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
- Mathematisch Naturwiss. Fakultät, Universität Zürich, Winterthurerstrasse 190, Zürich CH-8057, Switzerland
| | - L. E. Connor
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
| | - F. P. A. Fabbiani
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
| | - P. Piechon
- Novartis Campus, Novartis Pharma AG, Postfach, Basel CH-4002, Switzerland
| |
Collapse
|
3
|
Pacholski R, Durka K, Buchalski P. Synthesis and crystal structure of an iron triazole complex resulting from the unexpected ligand cleavage of a triazolium carbene precursor. Acta Crystallogr C Struct Chem 2024; 80:148-152. [PMID: 38607673 DOI: 10.1107/s2053229624002973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/07/2024] [Indexed: 04/13/2024] Open
Abstract
Typically reactions of N-heterocyclic carbenes with transition metals are straightforward and require a carbene salt, a base strong enough to deprotonate such a salt and a metal. Yet when carbene precursors are in the form of triazolium salts, reaction may not proceed as easily as expected. In our work, we intended to obtain a triazolylidene complex of iron(II) chloride, but due to the presence of small amounts of water in the tetrahydrofuran solvent used, bis(acetonitrile)tetrakis(1-benzyl-1H-1,2,4-triazole-κN4)iron(II) μ-oxido-bis[trichloridoferrate(III)] acetonitrile disolvate, [Fe(C9H9N3)4(CH3CN)2][Fe2Cl6O]·2CH3CN - an interesting anion with a linear geometry of the O atom - was formed instead of the iron carbene complex. Reaction proceeded via cleavage of the alkyl N-substituent of the triazolium salt. The formation of the product was confirmed by X-ray crystallography. The crystal structure and possible reaction pathways are discussed.
Collapse
Affiliation(s)
- Roman Pacholski
- Organic Chemistry Department, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Krzysztof Durka
- Organic Chemistry Department, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Piotr Buchalski
- Organic Chemistry Department, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| |
Collapse
|
4
|
Gould A, Schalk DR, Fleagle ME, Wheeler KA. Benzoyl Valine Quasiracemates: Pairing CF 3 Quasienantiomers with H to t-Butyl. CRYSTAL GROWTH & DESIGN 2024; 24:3967-3976. [PMID: 38708368 PMCID: PMC11066836 DOI: 10.1021/acs.cgd.4c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 05/07/2024]
Abstract
Understanding the interplay of structural features responsible for molecular assembly is essential for molecular crystal engineering. When assembling molecules with encoded motifs, first choice supramolecular strategies almost always include robust directional nonbonded contacts. Quasiracemic materials, considered near racemates since cocrystallization occurs with chemically unique components, lack a molecular framework or functional group restrictions, highlighting the importance of molecular shape to molecular assembly. Recently, our group reported quasiracemates derived from benzoyl leucine/phenylalanine derivatives with two points of chemical difference. In this study, we modified the chemical framework with valine and increased the scope of the work by imposing a larger variance in the side chain substituents. Pairing a CF3 component with quasienantiomers that differ iteratively from hydrogen to t-butyl offers an important view into the supramolecular landscape of these materials. Single-crystal X-ray crystallography and lattice energy assessments, coupled with conformational and crystal structure similarity searches, show an elevated degree of isomorphism for many of the targeted 17 racemates and quasiracemates. These benzoyl amino acid molecular architectures create extended hydrogen-bond patterns in the crystal that provide enhanced opportunities to study the shape space and molecular recognition profiles for a diverse family of quasienantiomeric components.
Collapse
Affiliation(s)
- Ashah
M. Gould
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, Washington 99251, United States
| | - Danielle R. Schalk
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, Washington 99251, United States
| | - Molly E. Fleagle
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, Washington 99251, United States
| | - Kraig A. Wheeler
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, Washington 99251, United States
| |
Collapse
|
5
|
Brunner H, Ikeshita M, Tsuno T. Pyramidalization of the Carboxamide sp 2-Center in Peptide Structures. J Org Chem 2024; 89:5511-5517. [PMID: 38592436 DOI: 10.1021/acs.joc.3c02973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
A CSD search in the Cambridge Crystallographic Database for the substructure N-CαH-C'(═O)-N gave 24,180 peptide structures for analysis of the pyramidalization of the sp2-hybridized carboxamide group C'(═O)NCα, which had not been investigated before. The dependence of the pyramidalization θ = O-N-C'-Cα on the rotation angle ψ = O═C'-Cα-N about bond C'-Cα resulted in a curve with three maxima, three minima, and six zero-crossings. Surprisingly, the ψ/θ analysis of the individual amino acid building blocks showed that all of them exhibited similar curves, irrespective of their different R substituents. This unusual behavior is explained by a 3-fold short-range potential set up by the three covalent bonds, emanating from Cα. The tie-up of the rotation angle ψ and the pyramidalization θ in a rigid coupling is remarkable. In the 24,180 peptide structures, subjected to X-ray crystallography, there is no dynamics. For peptides in solution, the rotation/pyramidalization curve ψ/θav determines the degree of pyramidalization θ, when the rotation angle ψ runs through a full 360° circle. Density functional theory (DFT) calculations of alaninamide supported the analysis.
Collapse
Affiliation(s)
- Henri Brunner
- Institut für Anorganische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Masahiro Ikeshita
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Narashino, Chiba 275-8575, Japan
| | - Takashi Tsuno
- Department of Applied Molecular Chemistry, College of Industrial Technology, Nihon University, Narashino, Chiba 275-8575, Japan
| |
Collapse
|
6
|
Ye Z, Wang N, Zhou J, Ouyang D. Organic crystal structure prediction via coupled generative adversarial networks and graph convolutional networks. Innovation (N Y) 2024; 5:100562. [PMID: 38379785 PMCID: PMC10878116 DOI: 10.1016/j.xinn.2023.100562] [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: 07/19/2023] [Accepted: 12/29/2023] [Indexed: 02/22/2024] Open
Abstract
Organic crystal structures exert a profound impact on the physicochemical properties and biological effects of organic compounds. Quantum mechanics (QM)-based crystal structure predictions (CSPs) have somewhat alleviated the dilemma that experimental crystal structure investigations struggle to conduct complete polymorphism studies, but the high computing cost poses a challenge to its widespread application. The present study aims to construct DeepCSP, a feasible pure machine learning framework for minute-scale rapid organic CSP. Initially, based on 177,746 data entries from the Cambridge Crystal Structure Database, a generative adversarial network was built to conditionally generate trial crystal structures under selected feature constraints for the given molecule. Simultaneously, a graph convolutional attention network was used to predict the density of stable crystal structures for the input molecule. Subsequently, the distances between the predicted density and the definition-based calculated density would be considered to be the crystal structure screening and ranking basis, and finally, the density-based crystal structure ranking would be output. Two such distinct algorithms, performing the generation and ranking functionalities, respectively, collectively constitute the DeepCSP, which has demonstrated compelling performance in marketed drug validations, achieving an accuracy rate exceeding 80% and a hit rate surpassing 85%. Inspiringly, the computing speed of the pure machine learning methodology demonstrates the potential of artificial intelligence in advancing CSP research.
Collapse
Affiliation(s)
- Zhuyifan Ye
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Nannan Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
| | - Jiantao Zhou
- State Key Laboratory of Internet of Things for Smart City, University of Macau, Macau 999078, China
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Macau 999078, China
| | - Defang Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
- Department of Public Health and Medicinal Administration, Faculty of Health Sciences, University of Macau, Macau 999078, China
| |
Collapse
|
7
|
Coady Z, Smith JN, Wilson KA, White NG. Stereoselective Single Step Cyclization to Give Belt-Functionalized Pillar[6]arenes. J Org Chem 2024; 89:1397-1406. [PMID: 38214497 DOI: 10.1021/acs.joc.3c01868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Two macrocycles were synthesized through cyclization reactions of secondary benzylic alcohols, giving pillar[6]arenes with a methyl substituent at each belt position. These macrocycles form stereoselectively with only the rtctct isomer with alternating up and down orientations of the belt methyl groups definitively identified. Isolated yields were modest (7 and 9%), but the macrocycles are prepared in a single step from either a commercially available alcohol or a very readily prepared precursor. X-ray crystal structures of the macrocycles indicate they have a capsule-like structure, which is far from the conventional pillar shape. Density functional theory calculations reveal that the energy barrier required to obtain the pillar conformation is significantly higher for these belt-functionalized macrocycles than for conventional belt-unfunctionalized pillar[6]arenes.
Collapse
Affiliation(s)
- Zeke Coady
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jordan N Smith
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Katie A Wilson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1C 5S7, Canada
| | - Nicholas G White
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| |
Collapse
|
8
|
Goodwin RJ, White NG. A Cationic Catechol Derivative Binds Anions in Competitive Aqueous Media. Chem Asian J 2024:e202301121. [PMID: 38269957 DOI: 10.1002/asia.202301121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/09/2024] [Indexed: 01/26/2024]
Abstract
A simple dihydroxy isoquinolinium molecule (3+ ) was prepared by a modification of a literature procedure. Interestingly, during optimisation of the synthesis a small amount of the natural product pseudopalmatine was isolated, and characterised for the first time by X-ray crystallography. Compound 3+ contains a catechol motif and positive charge on the same scaffold and was found to be a potent anion receptor, binding sulfate strongly in 8 : 2 d6 -acetone:D2 O and 7 : 3 d6 -acetone:D2 O (Ka >104 and 2,100 M-1 , respectively). Unsurprisingly, chloride binding was much weaker, even in the less polar solvent mixture 9 : 1 d6 -acetone:D2 O. The sulfate binding is remarkably strong for such a simple molecule, however anion binding studies were complicated by the tendency of the molecule to react with BPh4 - or BF4 - species during anion metathesis reactions. This gave two unusual zwitterions containing tetrahedral boronate centres, which were both characterised by X-ray crystallography.
Collapse
Affiliation(s)
- Rosemary J Goodwin
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Nicholas G White
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| |
Collapse
|
9
|
Chatziorfanou E, Romero AR, Chouchane L, Dömling A. Crystal Clear: Decoding Isocyanide Intermolecular Interactions through Crystallography. J Org Chem 2024; 89:957-974. [PMID: 38175810 PMCID: PMC10804414 DOI: 10.1021/acs.joc.3c02038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/13/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
The isocyanide group is the chameleon among the functional groups in organic chemistry. Unlike other multiatom functional groups, where the electrophilic and nucleophilic moieties are typically separated, isocyanides combine both functionalities in the terminal carbon. This unique feature can be rationalized using the frontier orbital concept and has significant implications for its intermolecular interactions and the reactivity of the functional group. In this study, we perform a Cambridge Crystallographic Database-supported analysis of isocyanide intramolecular interactions to investigate the intramolecular interactions of isocyanides in the solid state, excluding isocyanide-metal complexes. We discuss examples of different interaction classes, including the isocyanide as a hydrogen bond acceptor (RNC···HX), halogen bonding (RNC···X), and interactions involving the isocyanide and carbon atoms (RNC···C). The latter interaction serves as an intriguing illustration of a Bürgi-Dunitz trajectory and represents a crucial experimental detail in the well-known multicomponent reactions such as the Ugi- and Passerini-type mechanisms. Understanding the spectrum of intramolecular interactions that isocyanides can undergo holds significant implications in fields such as medicinal chemistry, materials science, and asymmetric catalysis.
Collapse
Affiliation(s)
- Eleftheria Chatziorfanou
- Innovative
Chemistry Group, Institute of Molecular and Translational Medicine,
Faculty of Medicine and Dentistry and Czech Advanced Technology and
Research Institute, Palacky University in
Olomouc, Olomouc 779 00, Czech Republic
| | - Atilio Reyes Romero
- Genetic
Intelligence Laboratory, Weill Cornell Medicine-Qatar, Qatar Foundation, P.O.
Box 24144, Doha, Qatar
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York 10021, United States
- Department
of Genetic Medicine, Weill Cornell Medicine, New York 10021, United States
| | - Lotfi Chouchane
- Genetic
Intelligence Laboratory, Weill Cornell Medicine-Qatar, Qatar Foundation, P.O.
Box 24144, Doha, Qatar
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York 10021, United States
- Department
of Genetic Medicine, Weill Cornell Medicine, New York 10021, United States
| | - Alexander Dömling
- Innovative
Chemistry Group, Institute of Molecular and Translational Medicine,
Faculty of Medicine and Dentistry and Czech Advanced Technology and
Research Institute, Palacky University in
Olomouc, Olomouc 779 00, Czech Republic
| |
Collapse
|
10
|
Chen SS, Meyer Z, Jensen B, Kraus A, Lambert A, Ess DH. ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design. J Chem Inf Model 2023; 63:7412-7422. [PMID: 37987743 DOI: 10.1021/acs.jcim.3c01310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are likely to be synthesized. Here, we provide a solution to this impediment with our ReaLigands library that contains >30,000 monodentate, bidentate (didentate), tridentate, and larger ligands cultivated by dismantling experimentally reported crystal structures. Individual ligands from mononuclear crystal structures were identified using a modified depth-first search algorithm and charge was assigned using a machine learning model based on quantum-chemical calculated features. In the library, ligands are sorted based on direct ligand-to-metal atomic connections and on denticity. Representative principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analyses were used to analyze several tridentate ligand categories, which revealed both the diversity of ligands and connections between ligand categories. We also demonstrated the utility of this library by implementing it with our building and optimization tools, which resulted in the very rapid generation of barriers for 750 bidentate ligands for Rh-hydride ethylene migratory insertion.
Collapse
Affiliation(s)
- Shu-Sen Chen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Zack Meyer
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Brendan Jensen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Alex Kraus
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Allison Lambert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| | - Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84604 United States
| |
Collapse
|
11
|
Folmsbee D, Koes DR, Hutchison GR. Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences. J Chem Inf Model 2023; 63:7401-7411. [PMID: 38000780 PMCID: PMC10716907 DOI: 10.1021/acs.jcim.3c01278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
We performed exhaustive torsion sampling on more than 3 million compounds using the GFN2-xTB method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that must be stable, synthetically accessible, and able to be crystallized. In this work, we evaluate the differences in torsional preferences of experimental crystallographic geometries and gas-phase computed conformers from a broad selection of compounds to determine whether torsional angle distributions obtained from semiempirical methods are suitable priors for conformer sampling. We find that differences in torsion preferences can be mostly attributed to a lack of available experimental crystallographic data with small deviations derived from gas-phase geometry differences. GFN2 demonstrates the ability to provide accurate and reliable torsional preferences that can provide a basis for new methods free from the limitations of experimental data collection. We provide Gaussian-based fits and sampling distributions suitable for torsion sampling and propose an alternative to the widely used "experimental torsion and knowledge distance geometry" (ETKDG) method using quantum torsion-derived distance geometry (QTDG) methods.
Collapse
Affiliation(s)
- Dakota
L. Folmsbee
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Department
of Anesthesiology & Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - David R. Koes
- Department
of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Geoffrey R. Hutchison
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemical & Petroleum Engineering, University of Pittsburgh, 3700 O’Hara Street, Pittsburgh, Pennsylvania 15261, United States
| |
Collapse
|
12
|
Dyba A, Wiącek E, Nowak M, Janczak J, Nartowski KP, Braun DE. Metronidazole Cocrystal Polymorphs with Gallic and Gentisic Acid Accessed through Slurry, Atomization Techniques, and Thermal Methods. CRYSTAL GROWTH & DESIGN 2023; 23:8241-8260. [PMID: 37937188 PMCID: PMC10626573 DOI: 10.1021/acs.cgd.3c00951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/26/2023] [Indexed: 11/09/2023]
Abstract
In this study, key features of metronidazole (MNZ) cocrystal polymorphs with gallic acid (GAL) and gentisic acid (GNT) were elucidated. Solvent-mediated phase transformation experiments in 30 solvents with varying properties were employed to control the polymorphic behavior of the MNZ cocrystal with GAL. Solvents with relative polarity (RP) values above 0.35 led to cocrystal I°, the thermodynamically stable form. Conversely, solvents with RP values below 0.35 produced cocrystal II, which was found to be only 0.3 kJ mol-1 less stable in enthalpy. The feasibility of electrospraying, including solvent properties and process conditions required, and spray drying techniques to control cocrystal polymorphism was also investigated, and these techniques were found to facilitate exclusive formation of the metastable MNZ-GAL cocrystal II. Additionally, the screening approach resulted in a new, high-temperature polymorph I of the MNZ-GNT cocrystal system, which is enantiotropically related to the already known form II°. The intermolecular energy calculations, as well as the 2D similarity between the MNZ-GAL polymorphs and the 3D similarity between MNZ-GNT polymorphs, rationalized the observed transition behaviors. Furthermore, the evaluation of virtual cocrystal screening techniques identified molecular electrostatic potential calculations as a supportive tool for coformer selection.
Collapse
Affiliation(s)
- Aleksandra
J. Dyba
- Institute
of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
- Department
of Drug Form Technology, Wroclaw Medical
University, Borowska 211A, 50-556 Wroclaw, Poland
| | - Ewa Wiącek
- Department
of Drug Form Technology, Wroclaw Medical
University, Borowska 211A, 50-556 Wroclaw, Poland
| | - Maciej Nowak
- Department
of Drug Form Technology, Wroclaw Medical
University, Borowska 211A, 50-556 Wroclaw, Poland
| | - Jan Janczak
- Institute
of Low Temperature and Structure Research, Polish Academy of Sciences, P.O. Box 1410, Okolna 2, 50-950 Wroclaw, Poland
| | - Karol P. Nartowski
- Department
of Drug Form Technology, Wroclaw Medical
University, Borowska 211A, 50-556 Wroclaw, Poland
- School
of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, U.K.
| | - Doris E. Braun
- Institute
of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| |
Collapse
|
13
|
Li X, Hu L, Lu G, Wang Y. Carbon-Bonding Metal Catalysis (CBMC): A Supramolecular Complex Directs Structural-Isomer Selection in Gold-Catalyzed Reactions. J Am Chem Soc 2023; 145:21554-21561. [PMID: 37668596 DOI: 10.1021/jacs.3c07551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Carbon is a primary element to constitute organic molecules, while metal catalysis is a basic tool in organic synthesis. The establishment of a link between the ubiquitous carbon bonding and metal catalysis is thus a fundamentally important problem. However, there is yet no experimental example to introduce the role of carbon bonding in a metal catalysis process. Herein, we merged the topics of carbon bonding and metal catalysis together and demonstrated that a supramolecular carbon-bonding metal complex can not only give rise to catalytic activity but, more remarkably, direct structural-isomer selection events in gold-catalyzed reactions. The experimental results unveil the fact that the imposing of weak carbon-bonding interactions on a gold complex can alter the carbene as well as the Lewis acid property of these catalysts. These results illustrate a non-negligible role of weak carbon-bonding interactions in the modulation of metal catalysis. As such, carbon-bonding metal catalysis is suggested to be used as a routine tool not only in the development of reactions but more frequently in analyzing reaction processes in metal catalysis.
Collapse
Affiliation(s)
- Xinxin Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Lingfei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Yao Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| |
Collapse
|
14
|
Kennedy AR, Cruickshank L, Maher P, McKinnon Z. A structural comparison of salt forms of dopamine with the structures of other phenylethylamines. Acta Crystallogr C Struct Chem 2023; 79:386-394. [PMID: 37721716 PMCID: PMC10551880 DOI: 10.1107/s2053229623007696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023] Open
Abstract
The structures of four salt forms of dopamine are reported. These are dopamine [2-(3,4-dihydroxyphenyl)ethan-1-aminium] benzoate, C8H12NO2+·C7H5O2-, I, dopamine 4-nitrobenzoate, C8H12NO2+·C7H4NO4-, II, dopamine ethanedisulfonate, 2C8H12NO2+·C2H4O6S22-, III, and dopamine 4-hydroxybenzenesulfonate monohydrate, C8H12NO2+·C6H5O4S-·H2O, IV. In all four structures, the dopamine cation adopts an extended conformation. Intermolecular interaction motifs that are common in the salt forms of tyramine can be found in related dopamine structures, but hydrogen bonding in the dopamine structures appear to be more variable and less predictable than for tyramine. Packing analysis discovered three dopamine-containing groups of structures that can be described as isostructural with regards to the cation positions. Two of these groups contain both dopamine and tyramine species, and one of these is also highly variable in other ways too, containing anhydrous and hydrated forms, different anion types and ionized and neutral phenylethylamine species. As such, the group illustrates that packing behaviour can be robust and similar even where intermolecular interactions such as hydrogen bonds are very different.
Collapse
Affiliation(s)
- Alan R. Kennedy
- Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow, G1 1XL, United Kingdom
| | - Laura Cruickshank
- Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow, G1 1XL, United Kingdom
| | - Pamela Maher
- Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow, G1 1XL, United Kingdom
| | - Zoe McKinnon
- Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow, G1 1XL, United Kingdom
| |
Collapse
|
15
|
Thompson AL, White NG. Hydrogen atoms in supramolecular chemistry: a structural perspective. Where are they, and why does it matter? Chem Soc Rev 2023; 52:6254-6269. [PMID: 37599586 DOI: 10.1039/d3cs00516j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Hydrogen bonding interactions are ubiquitous across the biochemical and chemical sciences, and are of particular interest to supramolecular chemists. They have been used to assemble hydrogen bonded polymers, cages and frameworks, and are the functional motif in many host-guest systems. Single crystal X-ray diffraction studies are often used as a key support for proposed structures, although this presents challenges as hydrogen atoms interact only weakly with X-rays. In this Tutorial Review, we discuss the information that can be gleaned about hydrogen bonding interactions through crystallographic experiments, key limitations of the data, and emerging techniques to overcome these limitations.
Collapse
Affiliation(s)
- Amber L Thompson
- Chemical Crystallography, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK.
| | - Nicholas G White
- Research School of Chemistry, The Australian National University, Canberra 2601, ACT, Australia.
| |
Collapse
|
16
|
Kaplan Ö, Truszkowska M, Kali G, Knoll P, Blanco Massani M, Braun DE, Bernkop-Schnürch A. Thiolated α-cyclodextrin: The likely smallest drug carrier providing enhanced cellular uptake and endosomal escape. Carbohydr Polym 2023; 316:121070. [PMID: 37321712 DOI: 10.1016/j.carbpol.2023.121070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023]
Abstract
This study aimed to evaluate the effect of thiolated α-cyclodextrin (α-CD-SH) on the cellular uptake of its payload. For this purpose, α-CD was thiolated using phosphorous pentasulfide. Thiolated α-CD was characterized by FT-IR and 1H NMR spectroscopy, differential scanning calorimetry (DSC), and powder X-ray diffractometry (PXRD). Cytotoxicity of α-CD-SH was evaluated on Caco-2, HEK 293, and MC3T3 cells. Dilauryl fluorescein (DLF) and coumarin-6 (Cou) serving as surrogates for a pharmaceutical payload were incorporated in α-CD-SH, and cellular uptake was analyzed by flow cytometry and confocal microscopy. Endosomal escape was investigated by confocal microscopy and hemolysis assay. Results showed no cytotoxic effect within 3 h, while dose-dependent cytotoxicity was observed within 24 h. The cellular uptake of DLF and Cou was up to 20- and 11-fold enhanced by α-CD-SH compared to native α-CD, respectively. Furthermore, α-CD-SH provided an endosomal escape. According to these results, α-CD-SH is a promising carrier to shuttle drugs into the cytoplasm of target cells.
Collapse
Affiliation(s)
- Özlem Kaplan
- Department of Genetics and Bioengineering, Rafet Kayış Faculty of Engineering, Alanya Alaaddin Keykubat University, 07400 Antalya, Turkey; Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, 34134 Istanbul, Turkey
| | - Martyna Truszkowska
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Gergely Kali
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Patrick Knoll
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Mariana Blanco Massani
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Doris Elfriede Braun
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Andreas Bernkop-Schnürch
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
| |
Collapse
|
17
|
Ellis GFR. Efficient, Formal, Material, and Final Causes in Biology and Technology. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1301. [PMID: 37761600 PMCID: PMC10529506 DOI: 10.3390/e25091301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
This paper considers how a classification of causal effects as comprising efficient, formal, material, and final causation can provide a useful understanding of how emergence takes place in biology and technology, with formal, material, and final causation all including cases of downward causation; they each occur in both synchronic and diachronic forms. Taken together, they underlie why all emergent levels in the hierarchy of emergence have causal powers (which is Noble's principle of biological relativity) and so why causal closure only occurs when the upwards and downwards interactions between all emergent levels are taken into account, contra to claims that some underlying physics level is by itself causality complete. A key feature is that stochasticity at the molecular level plays an important role in enabling agency to emerge, underlying the possibility of final causation occurring in these contexts.
Collapse
Affiliation(s)
- George F R Ellis
- Mathematics Department, The New Institute, University of Cape Town, 20354 Hamburg, Germany
| |
Collapse
|
18
|
Zheng L, Zhu B, Wu Z, Guo M, Chen J, Hong M, Liu G, Li W, Ren G, Tang Y. Pharmaceutical Cocrystal Discovery via 3D-SMINBR: A New Network Recommendation Tool Augmented by 3D Molecular Conformations. J Chem Inf Model 2023. [PMID: 37399241 DOI: 10.1021/acs.jcim.3c00066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Cocrystals have significant potential in various fields such as chemistry, material, and medicine. For instance, pharmaceutical cocrystals have the ability to address issues associated with physicochemical and biopharmaceutical properties. However, it can be challenging to find proper coformers to form cocrystals with drugs of interest. Herein, a new in silico tool called 3D substructure-molecular-interaction network-based recommendation (3D-SMINBR) has been developed to address this problem. This tool first integrated 3D molecular conformations with a weighted network-based recommendation model to prioritize potential coformers for target drugs. In cross-validation, the performance of 3D-SMINBR surpassed the 2D substructure-based predictive model SMINBR in our previous study. Additionally, the generalization capability of 3D-SMINBR was confirmed by testing on unseen cocrystal data. The practicality of this tool was further demonstrated by case studies on cocrystal screening of armillarisin A (Arm) and isoimperatorin (iIM). The obtained Arm-piperazine and iIM-salicylamide cocrystals present improved solubility and dissolution rate compared to their parent drugs. Overall, 3D-SMINBR augmented by 3D molecular conformations would be a useful network-based tool for cocrystal discovery. A free web server for 3D-SMINBR can be freely accessed at http://lmmd.ecust.edu.cn/netcorecsys/.
Collapse
Affiliation(s)
- Lulu Zheng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Laboratory of Molecular Modeling & Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Bin Zhu
- State Key Laboratory of Bioreactor Engineering, Engineering Research Centre of Pharmaceutical Process Chemistry, Ministry of Education; Laboratory of Pharmaceutical Crystal Engineering & Technology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Laboratory of Molecular Modeling & Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Mei Guo
- State Key Laboratory of Bioreactor Engineering, Engineering Research Centre of Pharmaceutical Process Chemistry, Ministry of Education; Laboratory of Pharmaceutical Crystal Engineering & Technology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jinyao Chen
- State Key Laboratory of Bioreactor Engineering, Engineering Research Centre of Pharmaceutical Process Chemistry, Ministry of Education; Laboratory of Pharmaceutical Crystal Engineering & Technology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Minghuang Hong
- State Key Laboratory of Bioreactor Engineering, Engineering Research Centre of Pharmaceutical Process Chemistry, Ministry of Education; Laboratory of Pharmaceutical Crystal Engineering & Technology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Laboratory of Molecular Modeling & Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Laboratory of Molecular Modeling & Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guobin Ren
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Laboratory of Molecular Modeling & Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, Engineering Research Centre of Pharmaceutical Process Chemistry, Ministry of Education; Laboratory of Pharmaceutical Crystal Engineering & Technology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Laboratory of Molecular Modeling & Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
19
|
Surov AO, Drozd KV, Ramazanova AG, Churakov AV, Vologzhanina AV, Kulikova ES, Perlovich GL. Polymorphism of Carbamazepine Pharmaceutical Cocrystal: Structural Analysis and Solubility Performance. Pharmaceutics 2023; 15:1747. [PMID: 37376195 DOI: 10.3390/pharmaceutics15061747] [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: 05/15/2023] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Polymorphism is a common phenomenon among single- and multicomponent molecular crystals that has a significant impact on the contemporary drug development process. A new polymorphic form of the drug carbamazepine (CBZ) cocrystal with methylparaben (MePRB) in a 1:1 molar ratio as well as the drug's channel-like cocrystal containing highly disordered coformer molecules have been obtained and characterized in this work using various analytical methods, including thermal analysis, Raman spectroscopy, and single-crystal and high-resolution synchrotron powder X-ray diffraction. Structural analysis of the solid forms revealed a close resemblance between novel form II and previously reported form I of the [CBZ + MePRB] (1:1) cocrystal in terms of hydrogen bond networks and overall packing arrangements. The channel-like cocrystal was found to belong to a distinct family of isostructural CBZ cocrystals with coformers of similar size and shape. Form I and form II of the 1:1 cocrystal appeared to be related by a monotropic relationship, with form II being proven to be the thermodynamically more stable phase. The dissolution performance of both polymorphs in aqueous media was significantly enhanced when compared with parent CBZ. However, considering the superior thermodynamic stability and consistent dissolution profile, the discovered form II of the [CBZ + MePRB] (1:1) cocrystal seems a more promising and reliable solid form for further pharmaceutical development.
Collapse
Affiliation(s)
- Artem O Surov
- G.A. Krestov Institute of Solution Chemistry RAS, Akademicheskaya Str. 1, 153045 Ivanovo, Russia
| | - Ksenia V Drozd
- G.A. Krestov Institute of Solution Chemistry RAS, Akademicheskaya Str. 1, 153045 Ivanovo, Russia
| | - Anna G Ramazanova
- G.A. Krestov Institute of Solution Chemistry RAS, Akademicheskaya Str. 1, 153045 Ivanovo, Russia
| | - Andrei V Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry RAS, Leninsky Prosp. 31, 119991 Moscow, Russia
| | - Anna V Vologzhanina
- A.N. Nesmeyanov Institute of Organoelement Compounds RAS, Vavilova Str. 28, 119334 Moscow, Russia
| | - Elizaveta S Kulikova
- National Research Center Kurchatov Institute, 1 Kurchatova pl., 123098 Moscow, Russia
| | - German L Perlovich
- G.A. Krestov Institute of Solution Chemistry RAS, Akademicheskaya Str. 1, 153045 Ivanovo, Russia
| |
Collapse
|
20
|
Germann LS, Carlino E, Taurino A, Magdysyuk OV, Voinovich D, Dinnebier RE, Bučar D, Hasa D. Modulating Thermal Properties of Polymers through Crystal Engineering. Angew Chem Int Ed Engl 2023; 62:e202212688. [PMID: 36617841 PMCID: PMC10947328 DOI: 10.1002/anie.202212688] [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: 08/28/2022] [Revised: 12/12/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023]
Abstract
Crystal engineering has exclusively focused on the development of advanced materials based on small organic molecules. We now demonstrate how the cocrystallization of a polymer yields a material with significantly enhanced thermal stability but equivalent mechanical flexibility. Isomorphous replacement of one of the cocrystal components enables the formation of solid solutions with melting points that can be readily fine-tuned over a usefully wide temperature range. The results of this study credibly extend the scope of crystal engineering and cocrystallization from small molecules to polymers.
Collapse
Affiliation(s)
- Luzia S. Germann
- Max Planck Institute for Solid State ResearchHeisenberg Straße 170569StuttgartGermany
| | - Elvio Carlino
- Istituto di Cristallografia—Consiglio Nazionale delle Ricerche (IC—CNR)Via Amendola 122/O70126BariItaly
| | - Antonietta Taurino
- Institute for Microelectronics and Microsystems, Consiglio Nazionale delle Ricerche (IMM—CNR)Via Monteroni73100LecceItaly
| | - Oxana V. Magdysyuk
- Diamond Light Source Ltd.Harwell Science and Innovation CampusDidcotOX11 0DEUK
| | - Dario Voinovich
- Department of Chemical and Pharmaceutical SciencesUniversity of TriesteVia Giorgieri 134127TriesteItaly
| | - Robert E. Dinnebier
- Max Planck Institute for Solid State ResearchHeisenberg Straße 170569StuttgartGermany
| | - Dejan‐Krešimir Bučar
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Dritan Hasa
- Department of Chemical and Pharmaceutical SciencesUniversity of TriesteVia Giorgieri 134127TriesteItaly
| |
Collapse
|
21
|
Voronin AP, Surov AO, Churakov AV, Vener MV. Supramolecular Organization in Salts of Riluzole with Dihydroxybenzoic Acids—The Key Role of the Mutual Arrangement of OH Groups. Pharmaceutics 2023; 15:pharmaceutics15030878. [PMID: 36986739 PMCID: PMC10051219 DOI: 10.3390/pharmaceutics15030878] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Intermolecular interactions, in particular hydrogen bonds, play a key role in crystal engineering. The ability to form hydrogen bonds of various types and strengths causes competition between supramolecular synthons in pharmaceutical multicomponent crystals. In this work, we investigate the influence of positional isomerism on the packing arrangements and the network of hydrogen bonds in multicomponent crystals of the drug riluzole with hydroxyl derivatives of salicylic acid. The supramolecular organization of the riluzole salt containing 2,6-dihydroxybenzoic acid differs from that of the solid forms with 2,4- and 2,5-dihydroxybenzoic acids. Because the second OH group is not at position 6 in the latter crystals, intermolecular charge-assisted hydrogen bonds are formed. According to periodic DFT calculations, the enthalpy of these H-bonds exceeds 30 kJ·mol−1. The positional isomerism appears to have little effect on the enthalpy of the primary supramolecular synthon (65–70 kJ·mol−1), but it does result in the formation of a two-dimensional network of hydrogen bonds and an increase in the overall lattice energy. According to the results of the present study, 2,6-dihydroxybenzoic acid can be treated as a promising counterion for the design of pharmaceutical multicomponent crystals.
Collapse
Affiliation(s)
| | - Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, 119991 Moscow, Russia
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, 119991 Moscow, Russia
- Correspondence:
| |
Collapse
|
22
|
Kusumoto S, Atoini Y, Masuda S, Koide Y, Kim JY, Hayami S, Kim Y, Harrowfield J, Thuéry P. Flexible Aliphatic Diammonioacetates as Zwitterionic Ligands in UO 22+ Complexes: Diverse Topologies and Interpenetrated Structures. Inorg Chem 2023; 62:3929-3946. [PMID: 36811464 DOI: 10.1021/acs.inorgchem.2c04321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
N,N,N',N'-Tetramethylethane-1,2-diammonioacetate (L1) and N,N,N',N'-tetramethylpropane-1,3-diammonioacetate (L2) are two flexible zwitterionic dicarboxylates which have been used as ligands for the uranyl ion, 12 complexes having been obtained from their coupling to diverse anions, mostly anionic polycarboxylates, or oxo, hydroxo and chlorido donors. The protonated zwitterion is a simple counterion in [H2L1][UO2(2,6-pydc)2] (1), where 2,6-pydc2- is 2,6-pyridinedicarboxylate, but it is deprotonated and coordinated in all the other complexes. [(UO2)2(L2)(2,4-pydcH)4] (2), where 2,4-pydc2- is 2,4-pyridinedicarboxylate, is a discrete, binuclear complex due to the terminal nature of the partially deprotonated anionic ligands. [(UO2)2(L1)(ipht)2]·4H2O (3) and [(UO2)2(L1)(pda)2] (4), where ipht2- and pda2- are isophthalate and 1,4-phenylenediacetate, are monoperiodic coordination polymers in which central L1 bridges connect two lateral strands. Oxalate anions (ox2-) generated in situ give [(UO2)2(L1)(ox)2] (5) a diperiodic network with the hcb topology. [(UO2)2(L2)(ipht)2]·H2O (6) differs from 3 in being a diperiodic network with the V2O5 topological type. [(UO2)2(L1)(2,5-pydc)2]·4H2O (7), where 2,5-pydc2- is 2,5-pyridinedicarboxylate, is a hcb network with a square-wave profile, while [(UO2)2(L1)(dnhpa)2] (8), where dnhpa2- is 3,5-dinitro-2-hydroxyphenoxyacetate, formed in situ from 1,2-phenylenedioxydiacetic acid, has the same topology but a strongly corrugated shape leading to interdigitation of layers. (2R,3R,4S,5S)-Tetrahydrofurantetracarboxylic acid (thftcH4) is only partially deprotonated in [(UO2)3(L1)(thftcH)2(H2O)] (9), which crystallizes as a diperiodic polymer with the fes topology. [(UO2)2Cl2(L1)3][(UO2Cl3)2(L1)] (10) is an ionic compound in which discrete, binuclear anions cross the cells of the cationic hcb network. 2,5-Thiophenediacetate (tdc2-) is peculiar in promoting self-sorting of the ligands in the ionic complex [(UO2)5(L1)7(tdc)(H2O)][(UO2)2(tdc)3]4·CH3CN·12H2O (11), which is the first example of heterointerpenetration in uranyl chemistry, involving a triperiodic, cationic framework and diperiodic, anionic hcb networks. Finally, [(UO2)7(O)3(OH)4.3Cl2.7(L2)2]Cl·7H2O (12) crystallizes as a 2-fold interpenetrated, triperiodic framework in which chlorouranate undulating monoperiodic subunits are bridged by the L2 ligands. Complexes 1, 2, 3, and 7 are emissive with photoluminescence quantum yields in the range of 8-24%, and their solid-state emission spectra show the usual dependence on number and nature of donor atoms.
Collapse
Affiliation(s)
- Sotaro Kusumoto
- Department of Material and Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Youssef Atoini
- Technical University of Munich, Campus Straubing, Schulgasse 22, 94315 Straubing, Germany
| | - Shunya Masuda
- Department of Material and Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yoshihiro Koide
- Department of Material and Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Jee Young Kim
- Department of Food and Nutrition, Kosin University, 194 Wachiro, Yongdo-Gu, Busan 49104, South Korea
| | - Shinya Hayami
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yang Kim
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Jack Harrowfield
- Université de Strasbourg, ISIS, 8 allée Gaspard Monge, 67083 Strasbourg, France
| | - Pierre Thuéry
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| |
Collapse
|
23
|
Surov AO, Ramazanova AG, Voronin AP, Drozd KV, Churakov AV, Perlovich GL. Virtual Screening, Structural Analysis, and Formation Thermodynamics of Carbamazepine Cocrystals. Pharmaceutics 2023; 15:pharmaceutics15030836. [PMID: 36986697 PMCID: PMC10052035 DOI: 10.3390/pharmaceutics15030836] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
In this study, the existing set of carbamazepine (CBZ) cocrystals was extended through the successful combination of the drug with the positional isomers of acetamidobenzoic acid. The structural and energetic features of the CBZ cocrystals with 3- and 4-acetamidobenzoic acids were elucidated via single-crystal X-ray diffraction followed by QTAIMC analysis. The ability of three fundamentally different virtual screening methods to predict the correct cocrystallization outcome for CBZ was assessed based on the new experimental results obtained in this study and data available in the literature. It was found that the hydrogen bond propensity model performed the worst in distinguishing positive and negative results of CBZ cocrystallization experiments with 87 coformers, attaining an accuracy value lower than random guessing. The method that utilizes molecular electrostatic potential maps and the machine learning approach named CCGNet exhibited comparable results in terms of prediction metrics, albeit the latter resulted in superior specificity and overall accuracy while requiring no time-consuming DFT computations. In addition, formation thermodynamic parameters for the newly obtained CBZ cocrystals with 3- and 4-acetamidobenzoic acids were evaluated using temperature dependences of the cocrystallization Gibbs energy. The cocrystallization reactions between CBZ and the selected coformers were found to be enthalpy-driven, with entropy terms being statistically different from zero. The observed difference in dissolution behavior of the cocrystals in aqueous media was thought to be caused by variations in their thermodynamic stability.
Collapse
Affiliation(s)
- Artem O Surov
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia
| | - Anna G Ramazanova
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia
| | | | - Ksenia V Drozd
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia
| | - Andrei V Churakov
- Institute of General and Inorganic Chemistry RAS, Leninsky Prosp. 31, 119991 Moscow, Russia
| | - German L Perlovich
- G.A. Krestov Institute of Solution Chemistry RAS, 153045 Ivanovo, Russia
| |
Collapse
|
24
|
David AHG, Goodwin RJ, White NG. Supramolecular chemistry of two new bis(1,2,3-triazolyl)pyridine macrocycles: metal complexation, self-assembly and anion binding. Dalton Trans 2023; 52:1902-1912. [PMID: 36722436 DOI: 10.1039/d2dt03985k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Two new macrocycles containing the bis(1,2,3-triazolyl)pyridine (btp) motif were prepared in high yields from a btp diazide precursor (1). Solution 1H NMR studies show that this diazide undergoes self-assembly with divalent transition metal ions to form ML2 complexes with pendant azide groups, apparently suitable for conversion into metal-templated catenanes; however attempts to form these catenanes were unsuccessful. Instead a new macrocycle containing two btp motifs was prepared, which forms a nanotube structure in the solid state. Reduction of the azide groups to amines followed by amide bond formation was used to convert 1 into macrocycle 8 containing btp and isophthalamide functionalities. This macrocycle binds halide and oxalate anions in acetonitrile solely through the isophthalamide motif, and binds aromatic dicarboxylates very strongly through both the isophthalamide amide donors and the btp triazole donors. The macrocycle was complexed with Pd(II) and the resulting complexes were shown to bind strongly to halide anions. The solid state structures of [Pd·8·X]BF4 (X = Cl-, Br-, I-) were investigated by X-ray crystallography, which showed that [Pd·8·Br] forms an unusual "chain of dimers" structure assembled by metal complexation, N-H⋯Br- hydrogen bonding and short Pd⋯Pd contacts.
Collapse
Affiliation(s)
- Arthur H G David
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia. .,Institut des Sciences Chimiques de Rennes, Université de Rennes 1, 35042, Rennes, France
| | - Rosemary J Goodwin
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nicholas G White
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
| |
Collapse
|
25
|
Malec LM, Brela MZ, Stadnicka KM. Ab Initio Study of H-Bond Dynamics in Three-Component Crystals Comprising (DABCOH + ) n Polycationic Chains. Chemphyschem 2023; 24:e202200517. [PMID: 36213982 DOI: 10.1002/cphc.202200517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/06/2022] [Indexed: 11/16/2022]
Abstract
In this work, the dynamic character of hydrogen-bond (H-bond) networks in two three-component crystals comprising polycationic chains was described. The first studied system was 1,4-diazabicyclo[2.2.2]octan-1-ium (DABCOH+ ) sulfamate monohydrate, known for its large negative linear compressibility. The second analyzed material was the newly obtained polar salt co-crystal: 1,4-diazabicyclo[2.2.2]octan-1-ium sulfamate urea. X-ray diffraction measurements enabled us to study the H-bond systems in both crystals using the graph set analysis. Obtained structures served as the initial models for Born-Oppenheimer molecular dynamics computations. A detailed study of intermolecular interactions and power spectra was conducted. The analysis of time and space correlations between the changes in H-bonds enabled the detection of proton transfer occurring in both systems at 300 K. Further study of those dynamic phenomena was done using the Energy Decomposition Analysis for selected trajectory fragments. Our work should improve the understanding of dielectric and ferroelectric properties of hybrid organic-inorganic materials.
Collapse
Affiliation(s)
- Leszek M Malec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Katarzyna M Stadnicka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| |
Collapse
|
26
|
Thuéry P, Harrowfield J. (R,R)-Tartrate as a polytopic ligand for UO22+: mono- and diperiodic coordination polymers including di- and tetranuclear subunits. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
|
27
|
Is the phosphorous atom a stereogenic center? Crystallographic findings in five new dithiophosphonate compounds supported with non covalent interaction index (NCI), theoretical approach and spectroscopic analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
28
|
Castillo AE, Pérez-Gutiérrez E, Ceballos P, Venkatesan P, Thamotharan S, Siegler MA, Percino MJ. Non-covalent interactions towards 2-(4-(2,2-dicyanovinyl) benzylidene)malononitrile packing polymorphism due to solvent effect. Experimental and theoretical spectroscopy approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
29
|
Thuéry P, Harrowfield J. Anionic uranyl ion complexes with pyrazinetetracarboxylate: Influence of structure-directing cations. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
30
|
Density Estimation Method for Individual Compounds from X-Ray Diffraction Analysis of their Solvated Forms. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03126-2] [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]
|
31
|
Gibaldi M, Kwon O, White A, Burner J, Woo TK. The HEALED SBU Library of Chemically Realistic Building Blocks for Construction of Hypothetical Metal-Organic Frameworks. ACS APPLIED MATERIALS & INTERFACES 2022; 14:43372-43386. [PMID: 36121788 DOI: 10.1021/acsami.2c13100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Advancements in hypothetical metal-organic framework (hMOF) databases and construction tools have resulted in a rapidly expanding chemical design space for nanoporous materials. The bulk of these hypothetical structures are constructed using structural building units (SBUs) derived from experimental MOF structures, often collected from the CoRE-MOF database. Recent investigations into the state of these deposited experimental structures' chemical accuracy identified an array of common structural errors, including omitted protons, missing counterions, and disordered structures. These structural errors propagate into the SBUs mined from experimental MOFs, culminating in inaccurate hMOF structures possessing net charges or missing atoms which were not accounted for previously. This work demonstrates how manual investigation was applied to diagnose structural errors in SBUs obtained from several popular hMOF construction tools and databases. An analysis of the prevailing errors discovered during the examination process is provided along with representative cases to aid with error detection in future studies involving SBU extraction and hMOF construction. A novel repair protocol was established and employed to generate a library of SBUs that are hand-examined and labeled with enhanced detail (HEALED). This repaired library of SBUs contains 952 inorganic SBUs and 568 organic SBUs ideally suited for the generation of hypothetical frameworks that are chemically accurate and properly charge labeled. Additionally, case studies following the effects of SBU errors on electrostatic potential-fitted charges and GCMC-simulated gas adsorption predictions are presented to highlight the significance of using chemically accurate hMOF structures exclusively in all screening efforts going forward.
Collapse
Affiliation(s)
- Marco Gibaldi
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie Private, Ottawa K1N 6N5, Canada
| | - Ohmin Kwon
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie Private, Ottawa K1N 6N5, Canada
| | - Andrew White
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie Private, Ottawa K1N 6N5, Canada
| | - Jake Burner
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie Private, Ottawa K1N 6N5, Canada
| | - Tom K Woo
- Department of Chemistry and Biomolecular Science, University of Ottawa, 10 Marie Curie Private, Ottawa K1N 6N5, Canada
| |
Collapse
|
32
|
Thomas CM, Liang W, Preston D, Doonan CJ, White NG. Post‐Synthetic Modification of a Porous Hydrocarbon Cage to Give a Discrete Co
24
Organometallic Complex**. Chemistry 2022; 28:e202200958. [PMID: 35863888 PMCID: PMC9544953 DOI: 10.1002/chem.202200958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/11/2022]
Abstract
A new alkyne‐based hydrocarbon cage was synthesized in high overall yield using alkyne‐alkyne coupling in the cage forming step. The cage is porous and displays a moderately high BET surface area (546 m2 g−1). The cage loses crystallinity on activation and thus is porous in its amorphous form, while very similar cages have been either non‐porous, or retained crystallinity on activation. Reaction of the cage with Co2(CO)8 results in exhaustive metalation of its 12 alkyne groups to give the Co24(CO)72 adduct of the cage in good yield.
Collapse
Affiliation(s)
- Chriso M. Thomas
- Research School of ChemistryThe Australian National UniversityCanberraACTAustralia
| | - Weibin Liang
- Department of Chemistry and Centre for Advanced MaterialsThe University of AdelaideSAAustralia
| | - Dan Preston
- Research School of ChemistryThe Australian National UniversityCanberraACTAustralia
| | - Christian J. Doonan
- Department of Chemistry and Centre for Advanced MaterialsThe University of AdelaideSAAustralia
| | - Nicholas G. White
- Research School of ChemistryThe Australian National UniversityCanberraACTAustralia
| |
Collapse
|
33
|
Kusumoto S, Atoini Y, Masuda S, Kim JY, Hayami S, Kim Y, Harrowfield J, Thuéry P. Zwitterionic and Anionic Polycarboxylates as Coligands in Uranyl Ion Complexes, and Their Influence on Periodicity and Topology. Inorg Chem 2022; 61:15182-15203. [PMID: 36083206 DOI: 10.1021/acs.inorgchem.2c02426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The three zwitterionic di- and tricarboxylate ligands 1,1'-[(2,3,5,6-tetramethylbenzene-1,4-diyl)bis(methylene)]bis(pyridin-1-ium-4-carboxylate) (pL1), 1,1'-[(2,3,5,6-tetramethylbenzene-1,4-diyl)bis(methylene)]bis(pyridin-1-ium-3-carboxylate) (mL1), and 1,1',1″-[(2,4,6-trimethylbenzene-1,3,5-triyl)tris(methylene)]tris(pyridin-1-ium-4-carboxylate) (L2) have been used as ligands to synthesize a series of 15 uranyl ion complexes involving various anionic coligands, in most cases polycarboxylates. [(UO2)2(pL1)2(cbtc)(H2O)2]·10H2O (1, cbtc4- = cis,trans,cis-1,2,3,4-cyclobutanetetracarboxylate) is a discrete, dinuclear ring-shaped complex with a central cbtc4- pillar. While [UO2(pL1)(NO3)2] (2), [UO2(pL1)(OAc)2] (3), and [UO2(pL1)(HCOO)2] (4) are simple chains, [(UO2)2(mL1)(1,3-pda)2] (5, 1,3-pda2- = 1,3-phenylenediacetate) is a daisy chain and [UO2(pL1)(pdda)]3·10H2O (6, pdda2- = 1,2-phenylenedioxydiacetate) is a double-stranded, ribbon-like chain. Both [UO2(pL1)(pht)]·5H2O (7, pht2- = phthalate) and [(UO2)3(mL1)(pht)2(OH)2] (8) crystallize as diperiodic networks with the sql topology, the latter involving hydroxo-bridged trinuclear nodes. [(UO2)2(pL1)(c/t-1,3-chdc)2] (9, c/t-1,3-chdc2- = cis/trans-1,3-cyclohexanedicarboxylate) and [UO2(pL1)(t-1,4-chdc)]·1.5H2O (10, t-1,4-chdc2- = trans-1,4-cyclohexanedicarboxylate) are also diperiodic, with the V2O5 and sql topologies, respectively. Both [(UO2)2(mL1)(c/t-1,4-chdc)2] (11) and [(UO2)2(pL1)(1,2-pda)2] (12, 1,2-pda2- = 1,2-phenylenediacetate) crystallize as diperiodic networks with hcb topology, and they display threefold parallel interpenetration. [HL2][(UO2)3(L2)(adc)3]Br (13, adc2- = 1,3-adamantanedicarboxylate) contains a very corrugated hcb network with two different kinds of cells, and the uncoordinated HL2+ molecule associates with the coordinated L2 to form a capsule containing the bromide anion. [(UO2)2(pL1)(kpim)2] (14, kpim2- = 4-ketopimelate) is a three-periodic framework with pL1 molecules pillaring fes diperiodic subunits, whereas [(UO2)2(L2)2(t-1,4-chdc)](NO3)1.7Br0.3·6H2O (15), the only cationic complex in the series, is a triperiodic framework with dmc topology and t-1,4-chdc2- anions pillaring fes diperiodic subunits. Solid-state emission spectra and photoluminescence quantum yields are reported for all complexes.
Collapse
Affiliation(s)
- Sotaro Kusumoto
- Department of Material & Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Youssef Atoini
- Technical University of Munich Campus Straubing, Schulgasse 22, 94315 Straubing, Germany
| | - Shunya Masuda
- Department of Material & Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Jee Young Kim
- Department of Food and Nutrition, Kosin University, 194 Wachiro, Yongdo-Gu, Busan 49104, South Korea
| | - Shinya Hayami
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yang Kim
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Jack Harrowfield
- ISIS, Université de Strasbourg, 8 allée Gaspard Monge, 67083 Strasbourg, France
| | - Pierre Thuéry
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| |
Collapse
|
34
|
Rauh D, Blankenburg C, Fischer TG, Jung N, Kuhn S, Schatzschneider U, Schulze T, Neumann S. Data format standards in analytical chemistry. PURE APPL CHEM 2022. [DOI: 10.1515/pac-2021-3101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Research data is an essential part of research and almost every publication in chemistry. The data itself can be valuable for reuse if sustainably deposited, annotated and archived. Thus, it is important to publish data following the FAIR principles, to make it findable, accessible, interoperable and reusable not only for humans but also in machine-readable form. This also improves transparency and reproducibility of research findings and fosters analytical work with scientific data to generate new insights, being only accessible with manifold and diverse datasets. Research data requires complete and informative metadata and use of open data formats to obtain interoperable data. Generic data formats like AnIML and JCAMP-DX have been used for many applications. Special formats for some analytical methods are already accepted, like mzML for mass spectrometry or nmrML and NMReDATA for NMR spectroscopy data. Other methods still lack common standards for data. Only a joint effort of chemists, instrument and software vendors, publishers and infrastructure maintainers can make sure that the analytical data will be of value in the future. In this review, we describe existing data formats in analytical chemistry and introduce guidelines for the development and use of standardized and open data formats.
Collapse
Affiliation(s)
- David Rauh
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data , Weinberg 3 , 06120 Halle , Germany
| | - Claudia Blankenburg
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data , Weinberg 3 , 06120 Halle , Germany
| | - Tillmann G. Fischer
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data , Weinberg 3 , 06120 Halle , Germany
| | - Nicole Jung
- Karlsruhe Institute of Technology, Institute for Chemical and Biological Systems (IBCS-FMS) , Hermann von Helmholtz Platz 1 , 76344 Eggenstein-Leopolshafen , Germany
| | - Stefan Kuhn
- School of Computer Science and Informatics , De Montfort University , Leicester , UK
| | - Ulrich Schatzschneider
- Institut für Anorganische Chemie , Julius-Maximilians-Universität Würzburg , Am Hubland , D-97074 Würzburg , Germany
| | - Tobias Schulze
- Department of Effect-Directed Analysis , Helmholtz Centre for Environmental Research – UFZ , Permoserstr. 15, 04318 Leipzig , Germany
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data , Weinberg 3 , 06120 Halle , Germany
| |
Collapse
|
35
|
Xiouras C, Cameli F, Quilló GL, Kavousanakis ME, Vlachos DG, Stefanidis GD. Applications of Artificial Intelligence and Machine Learning Algorithms to Crystallization. Chem Rev 2022; 122:13006-13042. [PMID: 35759465 DOI: 10.1021/acs.chemrev.2c00141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Artificial intelligence and specifically machine learning applications are nowadays used in a variety of scientific applications and cutting-edge technologies, where they have a transformative impact. Such an assembly of statistical and linear algebra methods making use of large data sets is becoming more and more integrated into chemistry and crystallization research workflows. This review aims to present, for the first time, a holistic overview of machine learning and cheminformatics applications as a novel, powerful means to accelerate the discovery of new crystal structures, predict key properties of organic crystalline materials, simulate, understand, and control the dynamics of complex crystallization process systems, as well as contribute to high throughput automation of chemical process development involving crystalline materials. We critically review the advances in these new, rapidly emerging research areas, raising awareness in issues such as the bridging of machine learning models with first-principles mechanistic models, data set size, structure, and quality, as well as the selection of appropriate descriptors. At the same time, we propose future research at the interface of applied mathematics, chemistry, and crystallography. Overall, this review aims to increase the adoption of such methods and tools by chemists and scientists across industry and academia.
Collapse
Affiliation(s)
- Christos Xiouras
- Chemical Process R&D, Crystallization Technology Unit, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Fabio Cameli
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Gustavo Lunardon Quilló
- Chemical Process R&D, Crystallization Technology Unit, Janssen R&D, Turnhoutseweg 30, 2340 Beerse, Belgium.,Chemical and BioProcess Technology and Control, Department of Chemical Engineering, Faculty of Engineering Technology, KU Leuven, Gebroeders de Smetstraat 1, 9000 Ghent, Belgium
| | - Mihail E Kavousanakis
- School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, 15780 Zografou, Greece
| | - Dionisios G Vlachos
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States
| | - Georgios D Stefanidis
- School of Chemical Engineering, National Technical University of Athens, Heroon Polytechniou 9, 15780 Zografou, Greece.,Laboratory for Chemical Technology, Ghent University; Tech Lane Ghent Science Park 125, B-9052 Ghent, Belgium
| |
Collapse
|
36
|
Bolla G, Sarma B, Nangia AK. Crystal Engineering of Pharmaceutical Cocrystals in the Discovery and Development of Improved Drugs. Chem Rev 2022; 122:11514-11603. [PMID: 35642550 DOI: 10.1021/acs.chemrev.1c00987] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The subject of crystal engineering started in the 1970s with the study of topochemical reactions in the solid state. A broad chemical definition of crystal engineering was published in 1989, and the supramolecular synthon concept was proposed in 1995 followed by heterosynthons and their potential applications for the design of pharmaceutical cocrystals in 2004. This review traces the development of supramolecular synthons as robust and recurring hydrogen bond patterns for the design and construction of supramolecular architectures, notably, pharmaceutical cocrystals beginning in the early 2000s to the present time. The ability of a cocrystal between an active pharmaceutical ingredient (API) and a pharmaceutically acceptable coformer to systematically tune the physicochemical properties of a drug (i.e., solubility, permeability, hydration, color, compaction, tableting, bioavailability) without changing its molecular structure is the hallmark of the pharmaceutical cocrystals platform, as a bridge between drug discovery and pharmaceutical development. With the design of cocrystals via heterosynthons and prototype case studies to improve drug solubility in place (2000-2015), the period between 2015 to the present time has witnessed the launch of several salt-cocrystal drugs with improved efficacy and high bioavailability. This review on the design, synthesis, and applications of pharmaceutical cocrystals to afford improved drug products and drug substances will interest researchers in crystal engineering, supramolecular chemistry, medicinal chemistry, process development, and pharmaceutical and materials sciences. The scale-up of drug cocrystals and salts using continuous manufacturing technologies provides high-value pharmaceuticals with economic and environmental benefits.
Collapse
Affiliation(s)
- Geetha Bolla
- Department of Chemistry, Ben-Gurion University of the Negev, Building 43, Room 201, Sderot Ben-Gurion 1, Be'er Sheva 8410501, Israel
| | - Bipul Sarma
- Department of Chemical Sciences, Tezpur University, Napaam, Tezpur, Assam 784028, India
| | - Ashwini K Nangia
- School of Chemistry, University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500046, India
| |
Collapse
|
37
|
Shevchenko AP, Smolkov MI, Wang J, Blatov VA. Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds. J Chem Inf Model 2022; 62:2332-2340. [PMID: 35522594 DOI: 10.1021/acs.jcim.2c00080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a universal scheme for predicting the oxidation states of metal atoms in ionic and coordination compounds with a small set of structural descriptors, which include the parameters of atomic Voronoi polyhedra. The scheme has been trained and checked with more than 35,000 crystal structures containing more than 90,000 metal atoms in the oxygen environment. The accuracy of the prediction exceeded 95%; we have detected a number of wrong oxidation states and incorrect chemical compositions in the crystallographic databases using this scheme. The scheme is easily extendable to any kind of atomic environment and can be used to search for correlations between geometrical and physical properties of crystal structures.
Collapse
Affiliation(s)
- Alexander P Shevchenko
- SCTMS, Samara State Technical University, Samara 443100, Russian Federation.,Samara Branch, P.N. Lebedev Physical Institute of the Russian Academy of Sciences, Samara 443011, Russian Federation
| | - Michail I Smolkov
- SCTMS, Samara State Technical University, Samara 443100, Russian Federation.,Povolzhskiy State University of Telecommunications and Informatics, Samara 443010, Russian Federation
| | - Junjie Wang
- State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, People's Republic of China
| | - Vladislav A Blatov
- SCTMS, Samara State Technical University, Samara 443100, Russian Federation.,State Key Laboratory of Solidification Processing, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, People's Republic of China
| |
Collapse
|
38
|
Thuéry P, Harrowfield J. Multiple aspects of chirality in coordination polymers formed by the uranyl ion with (1R,3S)-(+)-camphorate ligands. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
39
|
Wilhelm-Romero K, Quirós-Fallas MI, Vega-Baudrit JR, Guillén-Girón T, Vargas-Huertas F, Navarro-Hoyos M, Araya-Sibaja AM. Evaluation of Piperine as Natural Coformer for Eutectics Preparation of Drugs Used in the Treatment of Cardiovascular Diseases. AAPS PharmSciTech 2022; 23:127. [PMID: 35474407 DOI: 10.1208/s12249-022-02270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022] Open
Abstract
Piperine (PIP) was evaluated as a natural coformer in the preparation of multicomponent organic materials for enhancing solubility and dissolution rate of the poorly water-soluble drugs: curcumin (CUR), lovastatin (LOV), and irbesartan (IBS). A screening based on liquid assisted grinding technique was performed using 1:1 drug-PIP molar ratio mixtures, followed by differential scanning calorimetry (DSC) and powder X-ray diffraction (PXRD) analyses. Three eutectic mixtures (EMs) composed of CUR-PIP, LOV-PIP, and IBS-PIP were obtained. Therefore, binary phase and Tamman's diagrams were constructed for each system to obtain the exact eutectic composition, which was 0.41:0.59, 0.29:0.71, and 0.31:0.69 for CUR-PIP, LOV-PIP, and IBS-PIP, respectively. Further, bulk materials of each system were prepared to characterize them through DSC, PXRD fully, Fourier transform infrared spectroscopy (FT-IR), and solution-state nuclear magnetic resonance (NMR) spectroscopy. In addition, the contact angle, solubility, and dissolution rate of each system were evaluated. The preserved characteristic in the PXRD patterns and FT-IR spectra of the bulk material of each system confirmed the formation of EM mixture without molecular interaction in solid-state. The formation of EM resulted in improved aqueous solubility and dissolution rate associated with the increased wettability observed by the decrease in contact angle. In addition, solution NMR analyses of CUR-PIP, LOV-PIP, and IBS-PIP suggested no significant intermolecular interactions in solution between the components of the EM. Hence, this study concludes that PIP could be an effective coformer to improve the solubility and dissolution rate of CUR, LOV, and IBS.
Collapse
Affiliation(s)
- Krissia Wilhelm-Romero
- Laboratorio Nacional de Nanotecnología LANOTEC-CeNAT-CONARE, 1174-1200, Pavas, San José, Costa Rica
- Escuela de Química, Laboratorio BIODESS, Universidad de Costa Rica, San Pedro de Montes de Oca, 2060, San José, Costa Rica
| | - María Isabel Quirós-Fallas
- Escuela de Química, Laboratorio BIODESS, Universidad de Costa Rica, San Pedro de Montes de Oca, 2060, San José, Costa Rica
| | - José Roberto Vega-Baudrit
- Laboratorio Nacional de Nanotecnología LANOTEC-CeNAT-CONARE, 1174-1200, Pavas, San José, Costa Rica
- Laboratorio de Investigación y Tecnología de Polímeros POLIUNA, Escuela de Química, Universidad Nacional de Costa Rica, Heredia, 86-3000, Costa Rica
| | - Teodolito Guillén-Girón
- Centro de Investigación y Extensión en Materiales, Escuela de Ciencia E Ingeniería de los Materiales, Tecnológico de Costa Rica, Cartago, 159-7050, Costa Rica
| | - Felipe Vargas-Huertas
- Escuela de Química, Laboratorio BIODESS, Universidad de Costa Rica, San Pedro de Montes de Oca, 2060, San José, Costa Rica
| | - Mirtha Navarro-Hoyos
- Escuela de Química, Laboratorio BIODESS, Universidad de Costa Rica, San Pedro de Montes de Oca, 2060, San José, Costa Rica
| | - Andrea Mariela Araya-Sibaja
- Laboratorio Nacional de Nanotecnología LANOTEC-CeNAT-CONARE, 1174-1200, Pavas, San José, Costa Rica.
- Universidad Técnica Nacional, Alajuela, 159-7050, Costa Rica.
| |
Collapse
|
40
|
Te⋯N secondary-bonding interactions in tellurium crystals: Supramolecular aggregation patterns and a comparison with their lighter congeners. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
41
|
Price L, Price SL. Packing Preferences of Chalcones: A Model Conjugated Pharmaceutical Scaffold. CRYSTAL GROWTH & DESIGN 2022; 22:1801-1816. [PMID: 35571354 PMCID: PMC9097456 DOI: 10.1021/acs.cgd.1c01381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/02/2022] [Indexed: 06/15/2023]
Abstract
We sought the crystal packing preferences of the chalcone scaffold by analyzing 232 single-component crystal structures of chalcones with a small (six or fewer non-hydrogen atoms) substituent on either or both rings, including the unsubstituted molecule. This covers 216 molecules, as some are polymorphic, and 277 independent molecular conformations, as 16% of the crystal structures have more than one symmetry independent molecule. Quantum mechanical conformational profiles of the unsubstituted molecule and the almost 5000 crystal structures within 20 kJ mol-1 of the global minimum generated in a crystal structure prediction (CSP) study have been used to complement this analysis. Although π conjugation would be expected to favor a planar molecule, there are a significant number of crystal structures containing nonplanar molecules with an approximately 50° angle between the aromatic rings. The relative orientations of the molecules in the inversion-related dimers and translation-related dimers in the experimental crystal structures show the same trends as in the CSP-generated structures for the unsubstituted molecule, allowing for the substituent making the side-to-side distances larger. There is no type of dimer geometry associated with particularly favorable lattice energies for the chalcone core. Less than a third of the experimental structures show a face-to-face contact associated with π···π stacking. Analysis of the experimental crystal structures with XPac and Mercury finds various pairs of isostructural crystals, but the largest isostructural set had only 15 structures, with all substituents (mainly halogens) in the para position. The most common one-dimensional motif, found in half of the experimental crystal structures, is a translation-related side-to-side packing, which can be adopted by all the observed conformations. This close-packed motif can be adopted by chalcones with a particularly wide variety of substituents as the substituents are at the periphery. Thus, although the crystal structures of the substituted chalcones show thermodynamically plausible packings of the chalcone scaffold, there is little evidence for any crystal engineering principle of preferred chalcone scaffold packing beyond close packing of the specific molecule.
Collapse
|
42
|
Ouvry G. Recent applications of seven-membered rings in drug design. Bioorg Med Chem 2022; 57:116650. [PMID: 35123178 DOI: 10.1016/j.bmc.2022.116650] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/28/2023]
Abstract
This short review aims at highlighting recent design strategies hinged on using seven-membered rings. Analyses of the different selected examples coupled with torsion profiles derived from the CCDC suggest some of these strategies could have broad applications.
Collapse
Affiliation(s)
- Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| |
Collapse
|
43
|
Thuéry P, Harrowfield J. Contrasting Networks and Entanglements in Uranyl Ion Complexes with Adipic and trans, trans-Muconic Acids. Inorg Chem 2022; 61:2790-2803. [PMID: 35089692 DOI: 10.1021/acs.inorgchem.1c03168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Adipic (hexane-1,6-dicarboxylic, adpH2) and trans,trans-muconic (trans,trans-hexa-2,4-diene-1,6-dicarboxylic, mucH2) acids have been reacted with uranyl cations under solvo-hydrothermal conditions, yielding nine homo- or heterometallic complexes displaying in their crystal structure the effects of the different flexibility of the ligands. The complexes [PPh4]2[(UO2)2(adp)3] (1) and [Ni(bipy)3][(UO2)2(muc)3]·5H2O (2), where bipy is 2,2'-bipyridine, crystallize as diperiodic networks with the hcb topology, the layers being strongly puckered or quasiplanar, respectively. Whereas [(UO2)2(adp)3Ni(cyclam)]·2H2O (3), where cyclam is 1,4,8,11-tetraazacyclotetradecane, crystallizes as a diperiodic network, [(UO2)2(muc)3Ni(cyclam)]·2H2O (4) is a triperiodic framework in which the NiII cations are introduced as pillars within a uranyl-muc2- framework with the mog topology. [UO2(adp)(HCOO)2Cu(R,S-Me6cyclam)]·2H2O (5), where R,S-Me6cyclam is 7(R),14(S)-5,5,7,12,12,14-hexamethylcyclam, is a diperiodic assembly with the sql topology, and it crystallizes together with [H2NMe2]2[(UO2)2(adp)3] (6), a highly corrugated hcb network with a square-wave profile, which displays 3-fold parallel interpenetration. In contrast, [(UO2)3(muc)2(O)2Cu(R,S-Me6cyclam)] (7) is a diperiodic assembly containing hexanuclear, μ3-oxido-bridged secondary building units which are the nodes of a network with the hxl topology. The two related complexes [PPh3Me]2[(UO2)2(adp)3]·4H2O (8) and [PPh3Me]2[(UO2)2(muc)3]·H2O (9) crystallize as hcb networks, but their different shapes, undulated or quasiplanar, respectively, result in different entanglements, 2-fold parallel interpenetration in 8 and 2-fold inclined 2D → 3D polycatenation in 9.
Collapse
Affiliation(s)
- Pierre Thuéry
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Jack Harrowfield
- Université de Strasbourg, ISIS, 8 allée Gaspard Monge, 67083 Strasbourg, France
| |
Collapse
|
44
|
Zhao J, Zheng X. Progress on Exploring the Luminescent Properties of Organic Molecular Aggregates by Multiscale Modeling. Front Chem 2022; 9:808957. [PMID: 35096770 PMCID: PMC8790572 DOI: 10.3389/fchem.2021.808957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/03/2021] [Indexed: 11/20/2022] Open
Abstract
Luminescent molecular aggregates have attracted worldwide attention because of their potential applications in many fields. The luminescent properties of organic aggregates are complicated and highly morphology-dependent, unraveling the intrinsic mechanism behind is urgent. This review summarizes recent works on investigating the structure-property relationships of organic molecular aggregates at different environments, including crystal, cocrystal, amorphous aggregate, and doped systems by multiscale modeling protocol. We aim to explore the influence of intermolecular non-covalent interactions on molecular packing and their photophysical properties and then pave the effective way to design, synthesize, and develop advanced organic luminescent materials.
Collapse
Affiliation(s)
- Jingyi Zhao
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science of Ministry of Education, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Xiaoyan Zheng
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science of Ministry of Education, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| |
Collapse
|
45
|
Tan SL, Lo KM, Tan YS, Tiekink ERT. Structural systematics in the isomorphous binary co-crystal solvates comprising 2,2'-dithiodibenzoic acid, 4-halobenzoic acid and dimethylformamide (1:1:1), for halide = chloride, bromide and iodide. CrystEngComm 2022. [DOI: 10.1039/d2ce00094f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 1:1:1 binary co-crystal solvates formulated as 2,2'-dithiodibenzoic acid (DTBA), 4-halobenzoic acid (4-XBA) and dimethylformamide (DMF) for X = Cl (1), Br (2) and I (3) are isomorphous and the...
Collapse
|
46
|
Liu Y, Biczysko M, Moriarty NW. A radical approach to radicals. Acta Crystallogr D Struct Biol 2022; 78:43-51. [PMID: 34981760 DOI: 10.1107/s2059798321010809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
Nitroxide radicals are characterized by a long-lived spin-unpaired electronic ground state and are strongly sensitive to their chemical surroundings. Combined with electron paramagnetic resonance spectroscopy, these electronic features have led to the widespread application of nitroxide derivatives as spin labels for use in studying protein structure and dynamics. Site-directed spin labelling requires the incorporation of nitroxides into the protein structure, leading to a new protein-ligand molecular model. However, in protein crystallographic refinement nitroxides are highly unusual molecules with an atypical chemical composition. Because macromolecular crystallography is almost entirely agnostic to chemical radicals, their structural information is generally less accurate or even erroneous. In this work, proteins that contain an example of a radical compound (Chemical Component Dictionary ID MTN) from the nitroxide family were re-refined by defining its ideal structural parameters based on quantum-chemical calculations. The refinement results show that this procedure improves the MTN ligand geometries, while at the same time retaining higher agreement with experimental data.
Collapse
Affiliation(s)
- Youjia Liu
- International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
| | - Malgorzata Biczysko
- International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| |
Collapse
|
47
|
Kusumoto S, Atoini Y, Masuda S, Koide Y, Kim JY, Hayami S, Kim Y, Harrowfield J, Thuéry P. Varied role of organic carboxylate dizwitterions and anionic donors in mixed-ligand uranyl ion coordination polymers. CrystEngComm 2022. [DOI: 10.1039/d2ce01187e] [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
Two organic dizwitterions were combined with various anionic donors to generate a series of five uranyl ion complexes crystallizing as mono- or diperiodic coordination polymers, with separation into two distinct networks in one case.
Collapse
Affiliation(s)
- Sotaro Kusumoto
- Department of Material & Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Youssef Atoini
- Technical University of Munich, Campus Straubing, Schulgasse 22, 94315 Straubing, Germany
| | - Shunya Masuda
- Department of Material & Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yoshihiro Koide
- Department of Material & Life Chemistry, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Jee Young Kim
- Department of Food and Nutrition, Kosin University, 194 Wachiro, Yongdo-Gu, Busan 49104, South Korea
| | - Shinya Hayami
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yang Kim
- Department of Chemistry, Graduate School of Science and Technology, Institute of Industrial Nanomaterials (IINa), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Jack Harrowfield
- ISIS, Université de Strasbourg, 8 Allée Gaspard Monge, 67083 Strasbourg, France
| | - Pierre Thuéry
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| |
Collapse
|
48
|
Celedón S, Hamon P, Artigas V, Fuentealba M, Kahlal S, Carrillo D, Saillard JY, Hamon JR, Manzur C. Ferrocene functionalized enantiomerically pure Schiff bases and their Zn( ii) and Pd( ii) complexes: a spectroscopic, crystallographic, electrochemical and computational investigation. NEW J CHEM 2022. [DOI: 10.1039/d1nj06106b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A combination of X-ray diffraction, IR, UV-vis and NMR spectroscopy together with computational methods was used to characterize and study the properties of the title compounds.
Collapse
Affiliation(s)
- Salvador Celedón
- Laboratorio de Química Inorgánica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - Paul Hamon
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226, F-35000 Rennes, France
| | - Vania Artigas
- Laboratorio de Cristalografía, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - Mauricio Fuentealba
- Laboratorio de Cristalografía, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - Samia Kahlal
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226, F-35000 Rennes, France
| | - David Carrillo
- Laboratorio de Química Inorgánica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - Jean-Yves Saillard
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226, F-35000 Rennes, France
| | - Jean-René Hamon
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226, F-35000 Rennes, France
| | - Carolina Manzur
- Laboratorio de Química Inorgánica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso, Chile
| |
Collapse
|
49
|
Harrowfield J, Atoini Y, Thuéry P. Plumbing the uncertainties of solvothermal synthesis involving uranyl ion carboxylate complexes. CrystEngComm 2022. [DOI: 10.1039/d1ce01663f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Uranyl ion complexes with long-chain, saturated or unsaturated aliphatic dicarboxylate ligands illustrate how solvo-hydrothermal synthetic conditions sometimes result in the formation of species different from those hoped for.
Collapse
Affiliation(s)
- Jack Harrowfield
- ISIS, Université de Strasbourg, 8 allée Gaspard Monge, 67083 Strasbourg, France
| | - Youssef Atoini
- Biogenic Functional Materials Group, Technical University of Munich, Campus Straubing, Schulgasse 22, 94315 Straubing, Germany
| | - Pierre Thuéry
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| |
Collapse
|
50
|
Xue R, Liang C, Li Y, Chen X, Li F, Ren S, Chen F. Solid-state separation of hypoxanthine tautomers through a doping strategy. CrystEngComm 2022. [DOI: 10.1039/d2ce00146b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solid-state separation of hypoxanthine tautomers was realized by a doping strategy. The doping forms of hypoxanthine in HAmG, AG β and AG α are N7-hypoxanthine, and in GM and dehydrated-GM are N9-hypoxanthine.
Collapse
Affiliation(s)
- Rongrong Xue
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, Fujian, China
| | - Chengfeng Liang
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, Fujian, China
| | - Yanping Li
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, Fujian, China
| | - Xiuzhi Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, Fujian, China
| | - Fuying Li
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, Fujian, China
| | - Shizhao Ren
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, Fujian, China
| | - Fenghua Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming 365004, Fujian, China
| |
Collapse
|