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Kong Y, Zhang R, Li B, Zhao W, Wang J, Sun XW, Lv H, Liu R, Tang J, Wu B. Applying a Tripodal Hexaurea Receptor for Binding to an Antitumor Drug, Combretastatin-A4 Phosphate. MATERIALS (BASEL, SWITZERLAND) 2024; 17:2570. [PMID: 38893834 PMCID: PMC11173554 DOI: 10.3390/ma17112570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Phosphates play a crucial role in drug design, but their negative charge and high polarity make the transmembrane transport of phosphate species challenging. This leads to poor bioavailability of phosphate drugs. Combretastatin-A4 phosphate (CA4P) is such an anticancer monoester phosphate compound, but its absorption and clinical applicability are greatly limited. Therefore, developing carrier systems to effectively deliver phosphate drugs like CA4P is essential. Anion receptors have been found to facilitate the transmembrane transport of anions through hydrogen bonding. In this study, we developed a tripodal hexaurea anion receptor (L1) capable of binding anionic CA4P through hydrogen bonding, with a binding constant larger than 104 M-1 in a DMSO/water mixed solvent. L1 demonstrated superior binding ability compared to other common anions, and exhibited negligible cell cytotoxicity, making it a promising candidate for future use as a carrier for drug delivery.
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Affiliation(s)
- Yu Kong
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Rong Zhang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Boyang Li
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China;
| | - Wei Zhao
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Ji Wang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Xiao-Wen Sun
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Huihui Lv
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Rui Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Juan Tang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
| | - Biao Wu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China; (Y.K.); (R.Z.); (W.Z.); (J.W.); (X.-W.S.); (H.L.); (R.L.)
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2
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The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123690. [PMID: 35744821 PMCID: PMC9229234 DOI: 10.3390/molecules27123690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/22/2022] [Accepted: 05/29/2022] [Indexed: 11/17/2022]
Abstract
The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.
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Anzline C, Israel S, Sujatha K, Sheeba RAJR. Structure, charge density, and Hirshfeld surface analysis of proton transfer complex 2‐amino‐4‐methylpyridinium 2‐(3‐methylphenyl)‐acetate. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Samuel Israel
- Department of Physics The American college Madurai India
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4
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Rees GJ, Pitak MB, Lari A, Day SP, Yates JR, Gierth P, Barnsley K, Smith ME, Coles SJ, Hanna JV, Wallis JD. Mapping of N−C Bond Formation from a Series of Crystalline Peri‐Substituted Naphthalenes by Charge Density and Solid‐State NMR Methodologies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gregory J. Rees
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
- Department of Materials University of Oxford Parks Rd Oxford OX1 3PH UK
| | - Mateusz B. Pitak
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - Alberth Lari
- School of Science and Technology Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Stephen P. Day
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Jonathan R. Yates
- Department of Materials University of Oxford Parks Rd Oxford OX1 3PH UK
| | | | - Kristian Barnsley
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Mark E. Smith
- Vice-Chancellor's Office University of Southampton Highfield Southampton SO17 1BJ UK
| | - Simon J. Coles
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - John V. Hanna
- Department of Physics University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - John D. Wallis
- School of Science and Technology Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
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5
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Rees GJ, Pitak MB, Lari A, Day SP, Yates JR, Gierth P, Barnsley K, Smith ME, Coles SJ, Hanna JV, Wallis JD. Mapping of N-C Bond Formation from a Series of Crystalline Peri-Substituted Naphthalenes by Charge Density and Solid-State NMR Methodologies. Angew Chem Int Ed Engl 2021; 60:23878-23884. [PMID: 34464506 PMCID: PMC8596510 DOI: 10.1002/anie.202111100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/21/2022]
Abstract
A combination of charge density studies and solid state nuclear magnetic resonance (NMR) 1 JNC coupling measurements supported by periodic density functional theory (DFT) calculations is used to characterise the transition from an n-π* interaction to bond formation between a nucleophilic nitrogen atom and an electrophilic sp2 carbon atom in a series of crystalline peri-substituted naphthalenes. As the N⋅⋅⋅C distance reduces there is a sharp decrease in the Laplacian derived from increasing charge density between the two groups at ca. N⋅⋅⋅C = 1.8 Å, with the periodic DFT calculations predicting, and heteronuclear spin-echo NMR measurements confirming, the 1 JNC couplings of ≈3-6 Hz for long C-N bonds (1.60-1.65 Å), and 1 JNC couplings of <1 Hz for N⋅⋅⋅C >2.1 Å.
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Affiliation(s)
- Gregory J. Rees
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
- Department of MaterialsUniversity of OxfordParks RdOxfordOX1 3PHUK
| | - Mateusz B. Pitak
- School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Alberth Lari
- School of Science and TechnologyNottingham Trent UniversityClifton LaneNottinghamNG11 8NSUK
| | - Stephen P. Day
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | | | | | - Kristian Barnsley
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - Mark E. Smith
- Vice-Chancellor's OfficeUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - Simon J. Coles
- School of ChemistryUniversity of SouthamptonHighfieldSouthamptonSO17 1BJUK
| | - John V. Hanna
- Department of PhysicsUniversity of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - John D. Wallis
- School of Science and TechnologyNottingham Trent UniversityClifton LaneNottinghamNG11 8NSUK
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6
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Grgurić T, Cetina M, Petroselli M, Bacchiocchi C, Dzolić Z, Cametti M. Anion binding with biphenyl-bis-urea derivatives: solution and solid-state studies. NEW J CHEM 2020. [DOI: 10.1039/d0nj03670f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bis-urea derivatives 1–3, featuring a biphenyl spacer, were synthesized, characterized and investigated about their anion binding properties in DMSO solution and in the solid state.
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Affiliation(s)
| | - Mario Cetina
- University of Zagreb
- Faculty of Textile Technology
- Department of Applied Chemistry
- 10000 Zagreb
- Croatia
| | - Manuel Petroselli
- Department of Chemistry
- Materials and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- Milano
- Italy
| | - Corrado Bacchiocchi
- School of Science and Technology
- Chemistry Division
- University of Camerino
- I-62032 Camerino (MC)
- Italy
| | | | - Massimo Cametti
- Department of Chemistry
- Materials and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- Milano
- Italy
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7
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Saravanan K, Hunday G, Kumaradhas P. Binding and stability of indirubin-3-monoxime in the GSK3β enzyme: a molecular dynamics simulation and binding free energy study. J Biomol Struct Dyn 2019; 38:957-974. [DOI: 10.1080/07391102.2019.1591301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Govindasamy Hunday
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, Tamil Nadu, India
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8
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Amendola V, Boiocchi M, Fabbrizzi L, La Cognata S, Legnani L, Lo Presti E, Mangano C, Miljkovic A. Anion-induced isomerization of fluorescent semi(thio)carbazones. Org Chem Front 2018. [DOI: 10.1039/c7qo00805h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An anion-controlled flapping motion has been observed in a series of novel semi(thio)carbazone molecules.
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Affiliation(s)
- Valeria Amendola
- Dipartimento di Chimica
- Università degli Studi di Pavia
- Pavia
- Italy
| | - Massimo Boiocchi
- Centro Grandi Strumenti
- Università degli Studi di Pavia
- Pavia
- Italy
| | - Luigi Fabbrizzi
- Dipartimento di Chimica
- Università degli Studi di Pavia
- Pavia
- Italy
| | - Sonia La Cognata
- Dipartimento di Chimica
- Università degli Studi di Pavia
- Pavia
- Italy
| | - Laura Legnani
- Dipartimento di Chimica
- Università degli Studi di Pavia
- Pavia
- Italy
| | - Eliana Lo Presti
- Dipartimento di Chimica
- Università degli Studi di Pavia
- Pavia
- Italy
| | - Carlo Mangano
- Dipartimento di Chimica
- Università degli Studi di Pavia
- Pavia
- Italy
| | - Ana Miljkovic
- Dipartimento di Chimica
- Università degli Studi di Pavia
- Pavia
- Italy
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9
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Saunders LK, Nowell H, Spencer HCE, Hatcher LE, Shepherd HJ, Thomas LH, Jones CL, Teat SJ, Raithby PR, Wilson CC. Tuning charge-assisted and weak hydrogen bonds in molecular complexes of the proton sponge DMAN by acid co-former substitution. CrystEngComm 2018. [DOI: 10.1039/c8ce00443a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Varying the electronic character of the acid co-former substituent group predictably alters weak and strong intermolecular interactions.
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Affiliation(s)
- Lucy K. Saunders
- Diamond Light Source
- Harwell Science and Innovation Campus
- Didcot
- UK
| | - Harriott Nowell
- Diamond Light Source
- Harwell Science and Innovation Campus
- Didcot
- UK
| | | | | | - Helena J. Shepherd
- Department of Chemistry
- University of Bath
- Bath
- UK
- School of Physical Sciences
| | | | | | - Simon J. Teat
- Advanced Light Source
- Lawrence Berkeley National Lab
- Berkeley
- USA
| | - Paul R. Raithby
- Department of Chemistry
- University of Bath
- Bath
- UK
- Research Complex at Harwell
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10
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Zwicker VE, Yuen KKY, Smith DG, Ho J, Qin L, Turner P, Jolliffe KA. Deltamides and Croconamides: Expanding the Range of Dual H‐bond Donors for Selective Anion Recognition. Chemistry 2017; 24:1140-1150. [DOI: 10.1002/chem.201704388] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - David G. Smith
- School of Chemistry The University of Sydney NSW 2006 Australia
| | - Junming Ho
- School of Chemistry University of New South Wales NSW 2052 Australia
| | - Lei Qin
- School of Chemistry The University of Sydney NSW 2006 Australia
| | - Peter Turner
- School of Chemistry The University of Sydney NSW 2006 Australia
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11
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Hübschle CB, van Smaalen S. The electrostatic potential of dynamic charge densities. J Appl Crystallogr 2017; 50:1627-1636. [PMID: 29217990 PMCID: PMC5713142 DOI: 10.1107/s1600576717013802] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/25/2017] [Indexed: 11/10/2022] Open
Abstract
A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of dl-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at T = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å-3 isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.
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Affiliation(s)
| | - Sander van Smaalen
- Laboratory of Crystallography, University of Bayreuth, 95440 Bayreuth, Germany
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12
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Casula A, Fornasier M, Montis R, Bettoschi A, Argent SP, Blake AJ, Lippolis V, Marongiu L, Picci G, Tidey JP, Caltagirone C. Halogen-substituted ureas for anion binding: solid state and solution studies. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1377343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Arianna Casula
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
| | - Marco Fornasier
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
| | - Riccardo Montis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
- Department of Materials, Imperial College London, London, UK
| | - Alexandre Bettoschi
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
| | | | | | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
| | - Laura Marongiu
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
| | - Giacomo Picci
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
| | | | - Claudia Caltagirone
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Monserrato, Italy
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13
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Rahnamaye Aliabad HA, Chahkandi M. Comprehensive SPHYB and B3LYP-DFT Studies of Two Types of Ferrocene. Z Anorg Allg Chem 2017. [DOI: 10.1002/zaac.201600423] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Mohammad Chahkandi
- Department of Chemistry; Hakim Sabzevari University; 96179-76487 Sabzevar Iran
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14
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Quantum Chemical Investigation on the Antioxidant Activity of Neutral and Anionic Forms of Juglone: Metal Chelation and Its Effect on Radical Scavenging Activity. J CHEM-NY 2017. [DOI: 10.1155/2017/3281684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The chelation ability of divalent Mg, Ca, Fe, Co, Ni, Cu, Zn, and monovalent Cu ions by neutral and anionic forms of juglone has been investigated at DFT/B3LYP/6-31+G(d,p) level of theory in gas and aqueous phases. It is noteworthy that only the 1 : 1 stoichiometry was considered herein. The effects of these metals on the radical scavenging activity of neutral juglone were evaluated via the usual descriptors of hydrogen atom transfer. According to our results, metal chelation by the two forms of juglone was spontaneous and exothermic in both media. Based on the binding energies, Cu(II) ion showed the highest affinity for the ligands. QTAIM analyses identified the metal-ligand bonds as intermediate type interactions in all the chelates, except those of Ca and Mg. It was also found that the chelates were better radical scavengers than the ligands. In the gas phase, the scavenging activity of the compounds was found to be governed by direct hydrogen atom transfer, the Co(II) chelate being the most reactive. In the aqueous phase also, the sequential proton loss electron transfer was preferred by all the molecules, while the Cu(II) chelates were the most reactive.
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15
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Pfeifer L, Engle KM, Pidgeon GW, Sparkes HA, Thompson AL, Brown JM, Gouverneur V. Hydrogen-Bonded Homoleptic Fluoride–Diarylurea Complexes: Structure, Reactivity, and Coordinating Power. J Am Chem Soc 2016; 138:13314-13325. [DOI: 10.1021/jacs.6b07501] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lukas Pfeifer
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Keary M. Engle
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - George W. Pidgeon
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hazel A. Sparkes
- ISIS Facility,
STFC-Rutherford Appleton Laboratory, OX11
0QX Didcot, United Kingdom
| | - Amber L. Thompson
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - John M. Brown
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Véronique Gouverneur
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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16
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Huidobro‐Meezs IL, Segovia‐Poncelis M, Barquera‐Lozada JE. The Role of Bulkiness in Haptotropic Shifts of Metal–Cumulene Complexes. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Isaac L. Huidobro‐Meezs
- Physical Chemistry DepartmentChemistry InstituteUniversidad Nacional Autónoma de MéxicoCircuito exteriorCiudad UniversitariaMéxico
| | - Midori Segovia‐Poncelis
- Physical Chemistry DepartmentChemistry InstituteUniversidad Nacional Autónoma de MéxicoCircuito exteriorCiudad UniversitariaMéxico
| | - José Enrique Barquera‐Lozada
- Physical Chemistry DepartmentChemistry InstituteUniversidad Nacional Autónoma de MéxicoCircuito exteriorCiudad UniversitariaMéxico
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17
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Recognition of halides and Y-shaped oxoanions by carbonylchromium-based urea-like molecules: A theoretical analysis of hydrogen bonding modes. J Mol Graph Model 2016; 64:1-10. [PMID: 26751799 DOI: 10.1016/j.jmgm.2015.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/07/2015] [Accepted: 12/18/2015] [Indexed: 11/21/2022]
Abstract
One of the major challenges in anion recognition is to design hosts that can be used to distinguish between anions of different shapes. Urea-based molecules are widely used in anion recognition because the pair of -NH groups acts as an electron acceptor. Although these hosts can bind to both spherical anions (halides) and Y-shaped anions (oxoanions), experimental evidence to date does not provide a clear picture of what differences in the nature of the hydrogen bonding interactions could be used to distinguish between anions of different shapes. Here, we use several computational topology analyses to study the non-covalent interactions between Cr(CO)3-based organometallic urea-like hosts and halides and Y-shaped oxoanions. Our results suggest that the F(-) and AcO(-) anions are recognized experimentally due to a combination of strong interaction and large infrared (IR) shifts upon complexation, verifying the remarkable IR-reporting ability of the Cr(CO)3 moiety and its potential applications in anion recognition. The lone pairs of the oxygen atom in Y-shaped oxoanions directly interact with the -NH groups of the hosts, while all the shell electrons of the halides participate as a group in the interaction; however, the relative contributions of electrostatic and charge-transfer interactions are quite similar for the two types of anions. This insight into the nature of the anion-host interactions can be used to provide guidance for the design of hosts that differentiate between anions.
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18
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Blažek Bregović V, Basarić N, Mlinarić-Majerski K. Anion binding with urea and thiourea derivatives. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.03.011] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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19
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Kirby IL, Pitak MB, Coles SJ, Gale PA. Systematic Experimental Charge Density: Linking Structural Modifications to Electron Density Distributions. CHEM LETT 2015. [DOI: 10.1246/cl.140929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kirby IL, Pitak MB, Wilson C, Gale PA, Coles SJ. Electron density distribution studies as a tool to explore the behaviour of thiourea-based anion receptors. CrystEngComm 2015. [DOI: 10.1039/c5ce00213c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Building on previous studies of anion-receptor complexes based on a urea scaffold substituted symmetrically with electron-withdrawing nitro groups, the electron density distribution in an analogous thiourea receptor complex and the related asymmetrically substituted urea and thiourea receptors are described.
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Affiliation(s)
| | | | - Claire Wilson
- Diamond Light Source
- Diamond House
- Harwell Science and Innovation Campus
- Didcot, UK
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21
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Dittrich B, Matta CF. Contributions of charge-density research to medicinal chemistry. IUCRJ 2014; 1:457-69. [PMID: 25485126 PMCID: PMC4224464 DOI: 10.1107/s2052252514018867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/20/2014] [Indexed: 06/04/2023]
Abstract
This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3M, Canada
- Department of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H 3C3, Canada
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22
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Li QZ, Zhuo HY, Li HB, Liu ZB, Li WZ, Cheng JB. Tetrel–Hydride Interaction between XH3F (X = C, Si, Ge, Sn) and HM (M = Li, Na, BeH, MgH). J Phys Chem A 2014; 119:2217-24. [DOI: 10.1021/jp503735u] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qing-Zhong Li
- The Laboratory
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
| | - Hong-Ying Zhuo
- The Laboratory
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
| | - Hai-Bei Li
- School of Ocean, Shandong University, Weihai 264209, People’s Republic of China
| | - Zhen-Bo Liu
- The Laboratory
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
| | - Wen-Zuo Li
- The Laboratory
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
| | - Jian-Bo Cheng
- The Laboratory
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
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