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Cellupica E, Gaiassi A, Rocchio I, Rovelli G, Pomarico R, Sandrone G, Caprini G, Cordella P, Cukier C, Fossati G, Marchini M, Bebel A, Airoldi C, Palmioli A, Stevenazzi A, Steinkühler C, Vergani B. Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6. Int J Mol Sci 2024; 25:5885. [PMID: 38892072 PMCID: PMC11172862 DOI: 10.3390/ijms25115885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Histone deacetylase 6 (HDAC6) is increasingly recognized for its potential in targeted disease therapy. This study delves into the mechanistic and structural nuances of HDAC6 inhibition by difluoromethyl-1,3,4-oxadiazole (DFMO) derivatives, a class of non-hydroxamic inhibitors with remarkable selectivity and potency. Employing a combination of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) kinetic experiments, comprehensive enzymatic characterizations, and X-ray crystallography, we dissect the intricate details of the DFMO-HDAC6 interaction dynamics. More specifically, we find that the chemical structure of a DMFO and the binding mode of its difluoroacetylhydrazide derivative are crucial in determining the predominant hydrolysis mechanism. Our findings provide additional insights into two different mechanisms of DFMO hydrolysis, thus contributing to a better understanding of the HDAC6 inhibition by oxadiazoles in disease modulation and therapeutic intervention.
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Affiliation(s)
- Edoardo Cellupica
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aureliano Gaiassi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Ilaria Rocchio
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Grazia Rovelli
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Roberta Pomarico
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Giovanni Sandrone
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Gianluca Caprini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Paola Cordella
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Cyprian Cukier
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Gianluca Fossati
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Mattia Marchini
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Aleksandra Bebel
- Department of Biochemistry, Selvita S.A., 30-394 Kraków, Poland; (C.C.); (A.B.)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy; (C.A.); (A.P.)
| | - Andrea Stevenazzi
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Christian Steinkühler
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
| | - Barbara Vergani
- Research and Development, Italfarmaco Group, 20092 Milan, Italy; (E.C.); (A.G.); (I.R.); (G.R.); (R.P.); (G.S.); (G.C.); (P.C.); (G.F.); (M.M.); (A.S.); (C.S.)
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Van Lijsebetten F, Maes S, Winne JM, Du Prez FE. Thermoswitchable catalysis to inhibit and promote plastic flow in vitrimers. Chem Sci 2024; 15:7061-7071. [PMID: 38756803 PMCID: PMC11095380 DOI: 10.1039/d4sc00417e] [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: 01/18/2024] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Acid-base catalysis is a common strategy to induce covalent bond exchanges in dynamic polymer networks. Strong acids or strong bases can promote rapid network rearrangements, and are simultaneously preferred catalysts for chemical reactions where maximum efficiency at the lowest possible temperature is aimed for. However, within the context of dynamic polymer networks, the incorporation of highly active catalysts can negatively affect the longer term application potential. Network dynamicity can diminish through catalyst ageing or quenching and highly active catalysts may prematurely activate bond exchanges, leading to dimensional instability and thus low creep resistance of the polymer networks. Herein, we present several examples where we explicitly explored weak acids (carboxylic acids) as catalysts for dynamic bond exchanges, using vinylogous urethanes (VU) as a well-understood protic acid catalysed vitrimer chemistry. Surprisingly, we have found that the sought-after long-term stability offered by a weak acid does not necessarily bring lower activity at high temperature. In fact, the weak acids show a remarkable thermoswitchable catalytic behaviour, going from an inactive hydrogen bonded state to an active state where the polymer matrix is protonated, with a profound impact on the network reactivity and rheology. Carboxylic acids with different electronic or steric environments show clear reactivity trends and their fine-tuning resulted in the most thermally responsive VU vitrimers studied to date. Our findings point out that catalyst choice and design for vitrimers is only poorly informed by catalyst performance in more traditional chemical reactions (in solvent), and that a more tailored catalyst design holds great promise for the field of vitrimers.
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Affiliation(s)
- Filip Van Lijsebetten
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC) and Laboratory of Organic Synthesis, Departement of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281-S4 Ghent 9000 Belgium
| | - Stephan Maes
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC) and Laboratory of Organic Synthesis, Departement of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281-S4 Ghent 9000 Belgium
| | - Johan M Winne
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC) and Laboratory of Organic Synthesis, Departement of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281-S4 Ghent 9000 Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC) and Laboratory of Organic Synthesis, Departement of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281-S4 Ghent 9000 Belgium
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3
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Qiao T, Shi W, Zhuang H, Zhao G, Xin X, Li Y. Effects of substitution and conjugation on photophysical properties of ESIPT-based fluorophores with the core of 4-aminophthalimide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123802. [PMID: 38184881 DOI: 10.1016/j.saa.2023.123802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
4-Aminophthalimide is a highly fluorescent signaling unit with excellent photophysical properties and wide application foregrounds. Based on this, a range of theoretical investigations are conducted on the fluorescent probe (E)-5-((2-hydroxybenzylidene) amino) isoindoline-1, 3-dione (HID) with the core of 4-aminophthalimide using density functional theory (DFT) and time-containing density functional theory (TD-DFT) methods in this paper. The optimized configurations, vertical excitation and emission energies, electronic characteristics and excited-state intramolecular proton transfer (ESIPT) behaviors of the probe HID are discussed in detail. Furthermore, to enhance the luminescent properties of HID, five novel compounds have been designed based on the structure of HID by introducing amino, methoxy and naphthalene groups (-NH2, -OMe and C10H8). Our work thoroughly explores how the property and position of substituents and conjugation affect photophysical characteristics and ESIPT processes. We find that the ESIPT dynamics can be modulated by the substitution and conjugation effects. Specifically, the introduction of amino and methoxy groups at the ortho-position and the introduction of the naphthalene group promote the ESIPT behavior of HID1, whereas the introduction of amino and methoxy groups at the meta-position exhibits the contrary impact. Therefore, we boldly infer that the introduction of electron-donating groups in the ortho-position and the introduction of the conjugated group make the ESIPT process more effortless to occur, whereas the introduction of substituents with opposing natures in the meta-position makes the ESIPT process more difficult to occur. In addition, the ionization potentials (IP), electron affinities (EA) and reorganization energies (λh and λe) of molecules are calculated to assess their potential as luminescent materials. Our work not only reveals the luminescence and ESIPT mechanism of the probe HID1, but also proposes to modulate the ESIPT process through the substitution and conjugation effects. In particular, the designed molecules have better photoelectric properties as a result of their red-shifted absorption and fluorescence spectra, smaller energy gaps, larger transferred charges and greater charge transferred distances, which offers some valuable ideas for the experimental development of more efficient organic luminescent materials with ESIPT properties.
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Affiliation(s)
- Tiantian Qiao
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Wei Shi
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Hongbin Zhuang
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Guijie Zhao
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Xin Xin
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Yongqing Li
- School of Physics, Liaoning University, Shenyang 110036, PR China.
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4
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Wzgarda-Raj K, Dominikowska J, Husik N, Rybarczyk-Pirek AJ. 2,2'-Dithiobispyrazine: about the disulfide bond. Acta Crystallogr C Struct Chem 2023; 79:374-380. [PMID: 37642977 DOI: 10.1107/s2053229623007416] [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: 05/23/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
X-ray diffraction studies reveal that pyrazine-2-thiol undergoes condensation to 2,2'-dithiobispyrazine [systematic name: 2-(pyrazin-2-yldisulfanyl)pyrazine], C8H6N4S2 (I), under aerial conditions. In the molecule of I, the pyrazine rings are arranged in an almost perpendicular manner, with an absolute value of the C-S-S-C torsion angle of -91.45 (6)°. A search in the Cambridge Structural Database confirmed that such a conformation is typical for disulfide compounds. Three different rotamers of disulfide I were studied using quantum theoretical studies. The rotamer of lowest energy was observed in the crystalline state in the structure stabilized by hydrogen-bond, chalcogen-bond and stacking interactions. Further quantum chemical computations confirm that 2,2'-dithiobispyrazine can react according to the SN2 mechanism.
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Affiliation(s)
- Kinga Wzgarda-Raj
- Department of Physical Chemistry, University of Łódź, Pomorska 163/165, Łódź 91-236, Poland
| | - Justyna Dominikowska
- Department of Physical Chemistry, University of Łódź, Pomorska 163/165, Łódź 91-236, Poland
| | - Natallia Husik
- Department of Physical Chemistry, University of Łódź, Pomorska 163/165, Łódź 91-236, Poland
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5
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Pinto CB, Dos Santos LHR, Rodrigues BL. Experimental charge density and topological analysis of tetraaquabis(hydrogenmaleato)nickel(II): a comparison with Hirshfeld atom refinement. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2023; 79:281-295. [PMID: 37402161 DOI: 10.1107/s2052520623004377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/20/2023] [Indexed: 07/06/2023]
Abstract
Experimental charge density analysis is conducted on the coordination compound tetraaquabis(hydrogenmaleato)nickel(II), which exhibits a short intramolecular hydrogen bond. Through topological analysis, the nature of Ni-O bonds is concluded to be intermediate between ionic and covalent, but mainly presenting an ionic character, while the short hydrogen bond is classified as covalent in nature. The compound was also analysed after Hirshfeld atom refinement performed using NoSpherA2. A topological analysis was conducted on the molecular wavefunction and the results are compared with those obtained from experiment. In general, there is good agreement between the refinements, and the chemical bonds involving H atoms are in better agreement with what is expected from neutron data after HAR than they are after multipole refinement.
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Affiliation(s)
- Camila B Pinto
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Leonardo H R Dos Santos
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Bernardo L Rodrigues
- Department of Chemistry, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
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Modena D, Moras ML, Sandrone G, Stevenazzi A, Vergani B, Dasgupta P, Kliever A, Gulde S, Marangelo A, Schillmaier M, Luque RM, Bäuerle S, Pellegata NS, Schulz S, Steinkühler C. Identification of a Novel SSTR3 Full Agonist for the Treatment of Nonfunctioning Pituitary Adenomas. Cancers (Basel) 2023; 15:3453. [PMID: 37444563 DOI: 10.3390/cancers15133453] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Somatostatin receptor (SSTR) agonists have been extensively used for treating neuroendocrine tumors. Synthetic therapeutic agonists showing selectivity for SSTR2 (Octreotide) or for SSTR2 and SSTR5 (Pasireotide) have been approved for the treatment of patients with acromegaly and Cushing's syndrome, as their pituitary tumors highly express SSTR2 or SSTR2/SSTR5, respectively. Nonfunctioning pituitary adenomas (NFPAs), which express high levels of SSTR3 and show only modest response to currently available SSTR agonists, are often invasive and cannot be completely resected, and therefore easily recur. The aim of the present study was the evaluation of ITF2984, a somatostatin analog and full SSTR3 agonist, as a new potential treatment for NFPAs. ITF2984 shows a 10-fold improved affinity for SSTR3 compared to Octreotide or Pasireotide. Molecular modeling and NMR studies indicated that the higher affinity for SSTR3 correlates with a higher stability of a distorted β-I turn in the cyclic peptide backbone. ITF2984 induces receptor internalization and phosphorylation, and triggers G-protein signaling at pharmacologically relevant concentrations. Furthermore, ITF2984 displays antitumor activity that is dependent on SSTR3 expression levels in the MENX (homozygous mutant) NFPA rat model, which closely recapitulates human disease. Therefore, ITF2984 may represent a novel therapeutic option for patients affected by NFPA.
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Affiliation(s)
- Daniela Modena
- Preclinical R&D, Italfarmaco Group, 20092 Cinisello Balsamo, Milan, Italy
| | - Maria Luisa Moras
- Preclinical R&D, Italfarmaco Group, 20092 Cinisello Balsamo, Milan, Italy
| | - Giovanni Sandrone
- Preclinical R&D, Italfarmaco Group, 20092 Cinisello Balsamo, Milan, Italy
| | - Andrea Stevenazzi
- Preclinical R&D, Italfarmaco Group, 20092 Cinisello Balsamo, Milan, Italy
| | - Barbara Vergani
- Preclinical R&D, Italfarmaco Group, 20092 Cinisello Balsamo, Milan, Italy
| | - Pooja Dasgupta
- Institute of Pharmacology and Toxicology, Universitätsklinikum Jena, Friedrich-Schiller-Universität, 07747 Jena, Germany
| | - Andrea Kliever
- Institute of Pharmacology and Toxicology, Universitätsklinikum Jena, Friedrich-Schiller-Universität, 07747 Jena, Germany
| | - Sebastian Gulde
- Institute for Diabetes and Cancer, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Alessandro Marangelo
- Institute for Diabetes and Cancer, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Mathias Schillmaier
- Department of Nuclear Medicine, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 80333 Munich, Germany
- Department of Diagnostic and Interventional Radiology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, 80333 Munich, Germany
| | - Raul M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Stephen Bäuerle
- Department of Mathematics, Technical University Munich, 85748 Garching, Germany
| | - Natalia S Pellegata
- Institute for Diabetes and Cancer, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Program, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Stefan Schulz
- Institute of Pharmacology and Toxicology, Universitätsklinikum Jena, Friedrich-Schiller-Universität, 07747 Jena, Germany
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Wojtkowiak K, Jezierska A. Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach. Pharmaceuticals (Basel) 2023; 16:ph16040479. [PMID: 37111236 PMCID: PMC10146004 DOI: 10.3390/ph16040479] [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: 12/30/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using ωB97X functional with Grimme D3 dispersion corrections as well as a Becke-Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability.
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Affiliation(s)
- Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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El-Hendawy MM, Desoky IM, Mohamed MMA, Curran HJ. Pyridinium-Inspired Organocatalysts for Carbon Dioxide Fixation: A Density Functional Theory Inspection. J Phys Chem A 2023; 127:29-37. [PMID: 36595451 DOI: 10.1021/acs.jpca.2c05931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The current project aims to apply the virtues of minimalism to examine the catalytic ability of commercially organic compounds of small chemical structures to catalyze the coupling reaction between carbon dioxide and propylene oxide (PO) under mild conditions. The proposed catalysts are pyridinium iodide (A), 2-hydroxypyridinium iodide (B), and piperidinium iodide (C), where their structure is based on cooperative acidic and nucleophilic motifs. The quantum chemistry model, M062X-D3/def2-TZVP//M062X-D3/def2-SVPP, was used to understand the reaction mechanism and the catalytic performance. Since the coupling reaction was performed under excess PO, we proposed that PO serves as a reactant and solvent. Therefore, calculations were performed in gas and liquid phases for comparison. The findings indicated that the rate-determining step depends on the chemical structure of the catalyst and whether the phase is a gas or liquid phase. In general, modeling in the liquid phase produces potential energy surfaces of lower energy barriers. The noncovalent interactions reflect the role of hydrogen bonding in controlling the kinetic behavior of the coupling reaction. Based on the finding, catalyst A is the best candidate for transforming CO2 into cyclic carbonates.
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Affiliation(s)
- Morad M El-Hendawy
- Department of Chemistry, Faculty of Science, New Valley University, Kharga 72511, Egypt.,Combustion Chemistry Centre, School of Chemistry, Ryan Institute, MaREI, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Ibtesam M Desoky
- Department of Chemistry, Faculty of Science, New Valley University, Kharga 72511, Egypt
| | - Mahmoud M A Mohamed
- Department of Chemistry, Faculty of Science, New Valley University, Kharga 72511, Egypt
| | - Henry J Curran
- Combustion Chemistry Centre, School of Chemistry, Ryan Institute, MaREI, National University of Ireland Galway, Galway H91 TK33, Ireland
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9
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Liu Y, Li N, Du C, Wang Y, He K, Zheng H, Xue Z, Chen Q, Li X. Various hydrogen bonds make different fates of pharmaceutical contaminants on oxygen-rich nanomaterials. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120572. [PMID: 36335784 DOI: 10.1016/j.envpol.2022.120572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/18/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Various hydrogen bonds, especially charge-assisted hydrogen bond (CAHB), is considered as one of vital mechanisms affecting the environmental behavior and risk of pharmaceutical contaminants (PCs). Herein the sorption/desorption of three PCs including clofibric acid (CA), acetaminophen (ACT), and sulfamerazine (SMZ) on three Oxygen-rich (O-rich) nanoparticles (nano-silica: Nano-SiO2, nano-alumina: Nano-Al2O3, and oxidized carbon nanotubes: O-CNTs) were investigated to explore the effect of various hydrogen bonds with different strengths on environmental behaviors of PCs. The results indicated that although solvent-assisted CAHB, solvent-uninvolved CAHB, and ordinary hydrogen bond (OHB) all played a crucial role in sorption of PCs on three O-rich nanomaterials, they showed significantly different effects on the desorption behaviors of PCs from three sorbents. Compared with OHB (hysteresis index ≤0.0766), the stronger CAHB (hysteresis index ≥0.1981) between PCs and O-rich nanoparticles having comparable pKa with PCs, caused obvious desorption hysteresis of PCs, resulting in their better immobilization on O-rich nanomaterials. The FTIR characterization found that both solvent-assisted and solvent-uninvolved CAHB formation resulted in a new characteristic peak appeared in the high frequency (3660 cm-1 for Nano-SiO2, 3730 cm-1 for Nano-Al2O3, and 3780 cm-1 for O-CNTs). Also, density functional theory (DFT) calculation verified that the smaller |ΔpKa| between PCs and O-rich sorbents, the shorter bond length, and the larger bond angle resulted in the stronger hydrogen bond formed, thereby leading to the greater immobilization of PCs. These results provide in-depth understanding of the environmental behavior and risk of PCs, and light new idea for designed materials to control PCs pollution in the environment.
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Affiliation(s)
- Yifan Liu
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Nana Li
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Cong Du
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Yue Wang
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Kunyu He
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Hao Zheng
- Institute of Coastal Environmental Pollution Control, Ministry of Education Key Laboratory of Marine Environment and Ecology, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China
| | - Zhijing Xue
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Qin Chen
- Northwest Land and Resource Research Center, Shaanxi Normal University, Xi'an, 710119, China
| | - Xiaoyun Li
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China; International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-environmental Health, Xi'an, 710119, China.
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10
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Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide, Quinoline and Benzoic Acid Derivatives. Molecules 2022; 27:molecules27248847. [PMID: 36557978 PMCID: PMC9783803 DOI: 10.3390/molecules27248847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car-Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers.
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11
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Luo Z, Cao B, Song T, Xing Z, Ren J, Wang Z. Visible-Light Organophotoredox-Mediated [3 + 2] Cycloaddition of Arylcyclopropylamine with Structurally Diverse Olefins for the Construction of Cyclopentylamines and Spiro[4. n] Skeletons. J Org Chem 2022; 87:15511-15529. [PMID: 36318193 DOI: 10.1021/acs.joc.2c02061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We developed a visible-light-mediated [3 + 2] cycloaddition of arylcyclopropylamine with structurally diverse olefins using QXPT-NPh as a highly efficient organic photoredox catalyst. We first achieved the use of various alkyl-substituted alkenes in intermolecular [3 + 2] cycloadditions with cyclopropylamine. We also developed a general and efficient strategy for the construction of structurally diverse cyclopentane-based spiro[4.n] skeletons with 1,3-difunctional groups, which broadly exist in natural products and synthetic molecules. Furthermore, we proposed a hydrogen-bond mode between the arylcyclopropylamine and the photocatalyst QXPT-NPh.
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Affiliation(s)
- Zhengshan Luo
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 94# Weijin Road, Tianjin 300071, China
| | - Bowen Cao
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 94# Weijin Road, Tianjin 300071, China
| | - Tianhang Song
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 94# Weijin Road, Tianjin 300071, China
| | - Zequn Xing
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 94# Weijin Road, Tianjin 300071, China
| | - Jun Ren
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 94# Weijin Road, Tianjin 300071, China
| | - Zhongwen Wang
- State Key Laboratory of Elemento-Organic Chemistry, Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 94# Weijin Road, Tianjin 300071, China
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12
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New insights into the interaction between monomers from acrylamide-based polymeric flocculants and montmorillonite: A DFT study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Li X, Wang Q, Song L, Zhao J, Jin B. Effects of substitution and conjugation on ESIPT behavior of Schiff base derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121377. [PMID: 35617834 DOI: 10.1016/j.saa.2022.121377] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The excited-state proton transfer (ESIPT) behavior of organic fluorophores has been of great interest due to their unique photophysical properties. In this work, we have focused on the excited state kinetic behavior of four Schiff base organic molecules (i.e. CPMP, CPMMP, CPMDP, and CPMN) in acetonitrile solvents. The electron-donating of substituents and conjugation effects on the photophysical properties and ESIPT process of the Schiff base derivatives are investigated by theoretical methods. The results show that the hydrogen bonds are all enhanced in the excited states, which could provide the impetus for the ESIPT process. To further reveal the reaction process of ESIPT, we have scanned the potential energy curves of the ESIPT process and compared the potential barriers. It is found that the stronger the substituents give electrons and the conjugation effects the more favorable the excited state proton transfer (ESIPT). In the meantime, this study paves the way for the development of new Schiff base materials based on ESIPT.
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Affiliation(s)
- Xiaoxiao Li
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Qiujie Wang
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Liying Song
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Jinfeng Zhao
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Bing Jin
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China.
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14
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Hidaoui S, Hamdi N, Akouibaa M, Benali-Cherif R, Vaclav E, Dusek M, Lachkar M, Bali BE. Synthesis, crystal structure and catalytic activity of the new hybrid phosphate (C4H12N2)[Co(H2O)6](HPO4)2. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Zhang L, Li N, Chen Z, Li X, Fan A, Shao H. Investigating the substitution of intermolecular hydrogen bonds on the surface of self-assembled monolayer by scanning electrochemical microscopy. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Li X, Zhang J, Jin Y, Liu Y, Li N, Wang Y, Du C, Xue Z, Zhang N, Chen Q. Effect of pH-Dependent Homo/Heteronuclear CAHB on Adsorption and Desorption Behaviors of Ionizable Organic Compounds on Carbonaceous Materials. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12118. [PMID: 36231423 PMCID: PMC9566536 DOI: 10.3390/ijerph191912118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Herein, the adsorption/desorption behaviors of benzoic acid (BA) and phthalic acid (PA) on three functionalized carbon nanotubes (CNTs) at various pH were investigated, and the charge-assisted H-bond (CAHB) was verified by DFT and FTIR analyses to play a key role. The results indicated that the adsorption order of BA and PA on CNTs was different from Kow of that at pH 2.0, 4.0, and 7.0 caused by the CAHB interaction. The strength of homonuclear CAHB (≥78.96 kJ·mol-1) formed by BA/PA on oxidized CNTs is stronger than that of heteronuclear CAHB formed between BA/PA and amino-functionalized CNTs (≤51.66 kJ·mol-1). Compared with the heteronuclear CAHB (Hysteresis index, HI ≥ 1.47), the stronger homonuclear CAHB leads to clearly desorption hysteresis (HI ≥ 3.51). Additionally, the contribution of homonuclear CAHB (≥52.70%) was also greater than that of heteronuclear CAHB (≤45.79%) at pH 7.0. These conclusions were further confirmed by FTIR and DFT calculation, and the crucial evidence of CAHB formation in FTIR was found. The highlight of this work is the identification of the importance and difference of pH-dependent homonuclear/heteronuclear CAHB on the adsorption and desorption behaviors of ionizable organic compounds on carbonaceous materials, which can provide a deeper understanding for the removal of ionizable organic compounds by designed carbonaceous materials.
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Affiliation(s)
- Xiaoyun Li
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-Environmental Health, Xi’an 710119, China
| | - Jinlong Zhang
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
| | - Yaofeng Jin
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
| | - Yifan Liu
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
| | - Nana Li
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
| | - Yue Wang
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
| | - Cong Du
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
| | - Zhijing Xue
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi’an 710119, China
| | - Nan Zhang
- Environmental Protection Department of Mahe Town, Yuyang District, Yulin 719000, China
| | - Qin Chen
- Northwest Land and Resource Research Center, Shaanxi Normal University, Xi’an 710119, China
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17
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Li S, Cao Y, Dong H. Solvent polarity dependent excited state behaviors for 2‐(2‐hydroxyphenyl) benzothiazole‐5‐(9H‐carbazol‐9‐yl)phenol fluorophore: A theoretical study. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Songtao Li
- Hebei Key Laboratory of Physics and Energy Technology, Department of Mathematics and Physics North China Electric Power University Baoding China
| | - Yahui Cao
- Hebei Key Laboratory of Physics and Energy Technology, Department of Mathematics and Physics North China Electric Power University Baoding China
| | - Hao Dong
- Hebei Key Laboratory of Physics and Energy Technology, Department of Mathematics and Physics North China Electric Power University Baoding China
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18
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Yamasaki K, Adachi N, Ngwe Tun MM, Ikeda A, Moriya T, Kawasaki M, Yamasaki T, Kubota T, Nagashima I, Shimizu H, Tateno H, Morita K. Core fucose-specific Pholiota squarrosa lectin (PhoSL) as a potent broad-spectrum inhibitor of SARS-CoV-2 infection. FEBS J 2022; 290:412-427. [PMID: 36007953 PMCID: PMC9539343 DOI: 10.1111/febs.16599] [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: 02/23/2022] [Revised: 08/06/2022] [Accepted: 08/22/2022] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S protein) is highly N-glycosylated, and a "glycan shield" is formed to limit the access of other molecules; however, a small open area coincides with the interface to the host's receptor and also neutralising antibodies. Most of the variants of concern have mutations in this area, which could reduce the efficacy of existing antibodies. In contrast, N-glycosylation sites are relatively invariant, and some are essential for infection. Here, we observed that the S proteins of the ancestral (Wuhan) and Omicron strains bind with Pholiota squarrosa lectin (PhoSL), a 40-amino-acid chemically synthesised peptide specific to core-fucosylated N-glycans. The affinities were at a low nanomolar level, which were ~ 1000-fold stronger than those between PhoSL and the core-fucosylated N-glycans at the micromolar level. We demonstrated that PhoSL inhibited infection by both strains at similar submicromolar levels, suggesting its broad-spectrum effect on SARS-CoV-2 variants. Cryogenic electron microscopy revealed that PhoSL caused an aggregation of the S protein, which was likely due to the multivalence of both the trimeric PhoSL and S protein. This characteristic is likely relevant to the inhibitory mechanism. Structural modelling of the PhoSL-S protein complex indicated that PhoSL was in contact with the amino acids of the S protein, which explains the enhanced affinity with S protein and also indicates the significant potential for developing specific binders by the engineering of PhoSL.
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Affiliation(s)
- Kazuhiko Yamasaki
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure ScienceHigh Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
| | - Akihito Ikeda
- Structural Biology Research Center, Institute of Materials Structure ScienceHigh Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure ScienceHigh Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure ScienceHigh Energy Accelerator Research Organization (KEK)TsukubaJapan
| | - Tomoko Yamasaki
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Tomomi Kubota
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Izuru Nagashima
- Cellular and Molecular Biotechnology Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Hiroki Shimizu
- Cellular and Molecular Biotechnology Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN)Nagasaki UniversityNagasakiJapan
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19
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Jia M, Xu K, Lv J, Yang D. Theoretical study of the atomic electronegativity effects on the ESIPT of 4-methoxy-3-hydroxyflavone derivatives. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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20
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Adsorption Mechanism of High-Concentration Ammonium by Chinese Natural Zeolite with Experimental Optimization and Theoretical Computation. WATER 2022. [DOI: 10.3390/w14152413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Natural zeolite, as an abundant aluminosilicate mineral with a hierarchically porous structure, has a strong affinity to ammonium in solutions. Adsorption mechanism of high-concentration ammonium (1000~4000 mg-N/L) in an aqueous solution without pH adjustment onto Chinese natural zeolite with the dosage of 5 g/L was revealed by the strategy of experimental optimization integrated with Molecular Dynamics (MD) simulation, and found the maximum ammonium adsorption capacity was 26.94 mg/g. The adsorption kinetics and isotherm analysis showed that this adsorption process fitted better with descriptions of the pseudo-second-order kinetics and Freundlich model. The theoretical calculations and infrared-spectrum characterization results verified the existence of hydrogen bonds and chemisorption. Therefore, the adsorption mechanism by natural zeolites of high-concentration NH4+ is defined as a process under the joint influence of multiple effects, which is mainly promoted by the synergy of the ion exchange process, electrostatic attraction, and chemisorption. Meanwhile, the hydrogen bond also plays an auxiliary role in this efficient adsorption. This study presents important theoretical significance for enriching the mechanism of zeolites adsorbing NH4+ from water, and provides reference and theoretical guidance for further exploring the potential application of natural zeolites.
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21
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Andi B, Kumaran D, Kreitler DF, Soares AS, Keereetaweep J, Jakoncic J, Lazo EO, Shi W, Fuchs MR, Sweet RM, Shanklin J, Adams PD, Schmidt JG, Head MS, McSweeney S. Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci Rep 2022; 12:12197. [PMID: 35842458 PMCID: PMC9287821 DOI: 10.1038/s41598-022-15930-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 07/01/2022] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (Mpro also known as 3CLpro) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the Mpro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the Mpro as potential COVID-19 therapeutics for further testing and possibly clinical trials.
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Affiliation(s)
- Babak Andi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Dale F Kreitler
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Alexei S Soares
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | | | - Jean Jakoncic
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Edwin O Lazo
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Wuxian Shi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Martin R Fuchs
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Robert M Sweet
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Sean McSweeney
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
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22
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Zhang J, Zheng H, Li X, Li N, Liu Y, Li T, Wang Y, Xing B. Direct Spectroscopic Evidence for Charge-Assisted Hydrogen-Bond Formation between Ionizable Organic Chemicals and Carbonaceous Materials. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9356-9366. [PMID: 35729743 DOI: 10.1021/acs.est.2c00417] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct evidence for the formation of charge-assisted hydrogen bond (CAHB) between the charged groups of ionizable organic chemicals (IOCs) and carbonaceous materials with similar proton affinity remains elusive. We therefore selected three pharmaceutical contaminants (PCs) as representative IOCs to provide the direct evidence of CAHB formation between IOCs and functionalized carbon nanotubes (CNTs) and its intensity/contribution to PC sorption on CNTs by NMR, FTIR, and DFT analyses. Sorption of PCs on functionalized CNTs resulted in the FTIR characteristic peak that appeared at a higher frequency (3787 cm-1) and the 1H NMR characteristic peak that emerged at an extremely low-field region (<18.0 ppm), which can be used as the direct spectroscopic evidence for CAHB formation. Both homonuclear CAHB (HM-CAHB, e.g., [O-H···O]-) and heteronuclear CAHB (HT-CAHB, e.g., [N+-H···O-]/[O-H···N]+) exhibited a much higher sorption energy (|Eads| ≥ 56.24 kJ/mol) than ordinary hydrogen bond (OHB, |Eads| ≤ 6.136 kJ/mol), leading to a greater sorption contribution (HM-/HT-CAHB ≥ 42.3%, OHB ≤ 36.5%) and irreversibility (hysteresis index: HM-/HT-CAHB ≥ 1.69, OHB ≤ 0.43) of PCs on CNTs. This work presents the direct evidence for CAHB formation between IOCs and CNTs, which is significant for understanding and predicting the environmental fate and risk of IOCs, thus providing new insights for controlling their pollution using specifically designed carbonaceous materials.
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Affiliation(s)
- Jinlong Zhang
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-environmental Health, Xi'an 710119, China
| | - Hao Zheng
- Institute of Coastal Environmental Pollution Control, Ministry of Education Key Laboratory of Marine Environment and Ecology, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Xiaoyun Li
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Centre of Shaanxi Province for Pollutants Exposure and Eco-environmental Health, Xi'an 710119, China
| | - Nana Li
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an 710119, China
| | - Yifan Liu
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an 710119, China
| | - Tao Li
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an 710119, China
| | - Yue Wang
- Department of Environmental Science, School of Geography and Tourism, Shaanxi Normal University, Xi'an 710119, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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23
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Guan Y, Tang Z, Ju L, Zhao J. Solvent polarity‐dependent
ESIPT
behavior for 5‐(benzothiazole‐2‐yl)‐4‐hydroxyisophthalaldehyde fluorophore: A theoretical study. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yanlong Guan
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University Qingdao China
- School of Science Shenyang Aerospace University Shenyang Liaoning China
| | - Zhe Tang
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University Qingdao China
- State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian Liaoning China
| | - Liping Ju
- School of Science Shenyang Aerospace University Shenyang Liaoning China
| | - Jinfeng Zhao
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University Qingdao China
- State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian Liaoning China
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24
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Yang J, Li Y, Qiu Q, Wang R, Yan W, Yu Y, Niu L, Pei H, Wei H, Ouyang L, Ye H, Xu D, Wei Y, Chen Q, Chen L. Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond. J Med Chem 2022; 65:9159-9173. [PMID: 35762925 DOI: 10.1021/acs.jmedchem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Here, we report a novel mechanism to selectively degrade target proteins. 3-(3-Phenoxybenzyl)amino-β-carboline (PAC), a tubulin inhibitor, promotes selective degradation of αβ-tubulin heterodimers. Biochemical studies have revealed that PAC specifically denatures tubulin, making it prone to aggregation that predisposes it to ubiquitinylation and then degradation. The degradation is mediated by a single hydrogen bond formed between the pyridine nitrogen of PAC and βGlu198, which is identified as a low-barrier hydrogen bond (LBHB). In contrast, another two tubulin inhibitors that only form normal hydrogen bonds with βGlu198 exhibit no degradation effect. Thus, the LBHB accounts for the degradation. We then screened for compounds capable of forming an LBHB with βGlu198 and demonstrated that BML284, a Wnt signaling activator, also promotes tubulin heterodimer degradation through the LBHB. Our study provided a unique example of LBHB function and identified a novel approach to obtain tubulin degraders.
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Affiliation(s)
- Jianhong Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Li
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Qiu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Wei Yan
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yamei Yu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lu Niu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heying Pei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoche Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoyu Ye
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuquan Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lijuan Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
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25
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Song Y, Wang Q, Gao W, He Z, Wu Y. Effects of solvents on the excited‐state intramolecular proton transfer in 3‐HTC. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yao‐Dong Song
- School of Electronic, Electrical Engineering and Physics Fujian University of Technology Fuzhou Fujian China
| | - Qian‐Ting Wang
- Fujian Provincial Key Laboratory of Advanced Materials Processing and Application Fuzhou Fujian China
- Sanming University Sanming Fujian China
- Fujian Provincial Engineering Research Center of Die & Mold Fuzhou Fujian China
- Mould Technology Development Base of Fujian Province Fuzhou Fujian China
- Fuzhou Innovation Platform for Novel Materials and Mould Technology Fuzhou Fujian China
| | - Wei‐wei Gao
- School of Electronic, Electrical Engineering and Physics Fujian University of Technology Fuzhou Fujian China
| | - Zhixiong He
- School of Electronic, Electrical Engineering and Physics Fujian University of Technology Fuzhou Fujian China
| | - Yan Wu
- School of Electronic, Electrical Engineering and Physics Fujian University of Technology Fuzhou Fujian China
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26
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Cicolella A, C. D'Alterio M, Duran J, Simon S, Talarico G, Poater A. Combining Both Acceptorless Dehydrogenation and Borrowing Hydrogen Mechanisms in One System as Described by DFT Calculations. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alessandra Cicolella
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona C/ Maria Aurèlia Capmany, 69, Girona Catalonia 17003 Spain
- Dipartimento di Scienze Chimiche Università di Napoli Federico II Via Cintia Napoli I‐80126 Italy
| | - Massimo C. D'Alterio
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona C/ Maria Aurèlia Capmany, 69, Girona Catalonia 17003 Spain
- Dipartimento di Chimica e Biologia "A. Zambelli" Università di Salerno Via Giovanni Paolo II 132 Fisciano Salerno 84084 Italy
| | - Josep Duran
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona C/ Maria Aurèlia Capmany, 69, Girona Catalonia 17003 Spain
| | - Sílvia Simon
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona C/ Maria Aurèlia Capmany, 69, Girona Catalonia 17003 Spain
| | - Giovanni Talarico
- Dipartimento di Scienze Chimiche Università di Napoli Federico II Via Cintia Napoli I‐80126 Italy
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona C/ Maria Aurèlia Capmany, 69, Girona Catalonia 17003 Spain
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27
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Gašparič L, Poberžnik M, Kokalj A. DFT study of hydrogen bonding between metal hydroxides and organic molecules containing N, O, S, and P heteroatoms: clusters vs. surfaces. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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28
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Zhang S, Xiao T, Fadaei Tirani F, Scopelliti R, Nazeeruddin MK, Zhu D, Dyson PJ, Fei Z. The Chemistry of the Passivation Mechanism of Perovskite Films with Ionic Liquids. Inorg Chem 2022; 61:5010-5016. [PMID: 35290056 DOI: 10.1021/acs.inorgchem.1c03862] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Passivation of perovskite films by ionic liquids (ILs) improves the performance (efficiency and stability) of perovskite solar cells (PSCs). However, the role of ILs in the passivation of perovskite films is not fully understood. Here, we report the reactions of commonly used ILs with the components of perovskites. The reaction of ILs with perovskite precursors (PbI2 and methylammonium iodide or formamidinium iodide) in a 1:1:1 molar ratio affords one-dimensional (1D) salts composed of the IL cation interspersed along infinite 1D polymeric [PbI3]-n chains. If the IL is applied in excess, the resulting crystal is composed of six cations surrounding a discrete [Pb3I12]6- cluster. All the isolated salts were unambiguously characterized by single-crystal X-ray diffraction analysis, which also reveals extensive hydrogen-bonding interactions.
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Affiliation(s)
- Shunlin Zhang
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tianyu Xiao
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Farzaneh Fadaei Tirani
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Mohammad Khaja Nazeeruddin
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Dunru Zhu
- College of Chemical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Zhaofu Fei
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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29
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Meng X, Song L, Han H, Zhao J, Zheng D. A novel mechanism of intramolecular proton transfer in the excited state of 3-hydroxy-4H-benzochromone derivatives: A new explanation at the theoretical level. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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30
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Meng X, Song L, Zhao J, Han H, Zheng D. Theoretical insights into effects of solvent polarity on excited‐state N–H proton transfer behavior for a new fluorophore of 3‐tosylamino‐
N
‐cyclohexylphthalimide. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4320] [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)
- Xuan Meng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science Shandong University Qingdao China
| | - Liying Song
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science Shandong University Qingdao China
| | - Jinfeng Zhao
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science Shandong University Qingdao China
| | - Haiyun Han
- Heze Dingtao People's Hospital Heze Shandong China
| | - Daoyuan Zheng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science Shandong University Qingdao China
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31
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Meng X, Song L, Han H, Zhao J, Zheng D. Solvent polarity dependent ESIPT behavior for the novel flavonoid-based solvatofluorochromic chemosensors. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120383. [PMID: 34536893 DOI: 10.1016/j.saa.2021.120383] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/07/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
In this work, we explore the excited-state intramolecular proton transfer (ESIPT) mechanisms and relative solvent effects for three novel 3-hydroxylflavone derivatives (i.e., HOF, SHOF, and NSHOF) in acetonitrile, dichloromethane, and toluene solvents. Through calculations, we optimize the structures of HOF, SHOF, and NSHOF. Through the analysis of a series of structural parameters related to hydrogen bonding interactions, it could be found that the hydrogen bonds of the three derivatives are all enhanced in the S1 state, and more importantly, the excited-state hydrogen bonds of HOF are stronger than those of SHOF and NSHOF. In order to explore the effects of solvent polarity, we analyze the core-valence bifurcation (CVB) index, infrared (IR) vibration spectrum, and the potential energy curves. We find that for HOF, SHOF, and NSHOF, the strength of the excited-state hydrogen bonds increases as the solvent polarity decreases. The solvent polarity dependent ESIPT mechanisms pave the way for further designing novel flavonoid-based solvatofluorochromic probes in future.
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Affiliation(s)
- Xuan Meng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Liying Song
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Haiyun Han
- People's Hospital of Dingtao District, Heze, Shandong Province 274199, China
| | - Jinfeng Zhao
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China.
| | - Daoyuan Zheng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China.
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32
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Song L, Meng X, Zhao J, Han H, Zheng D. Effects of azole rings with different chalcogen atoms on ESIPT behavior for benzochalcogenazolyl-substituted hydroxyfluorenes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120296. [PMID: 34454130 DOI: 10.1016/j.saa.2021.120296] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
ESIPT behavior has attracted a lot of eyes of researchers in recent years because of its unique optical properties. Due to its large Stokes shift and double emission fluorescence, white light can be generated in the fluorophore based on the excited state intramolecular proton transfer (ESIPT) principle. The excited state proton transfer behavior of hydroxylated benzoxazole (BO-OH), benzothiazole (BS-OH) and benzoselenazole (BSe-OH) have been investigated in heptane, chloroform and DMF solvents. By comparing the infrared vibration spectra and the variation of bond parameters from the S0 to S1 states, and analyzing the frontier molecular orbitals, the influence of hydrogen bond dynamics, the solvent polarity, charge redistribution and the effects of different proton acceptors on proton transfer were observed. The only structural difference among the three substituted hydroxyfluorenes is the heteroatom in the azole ring (oxygen, sulfur and selenium, respectively). We have scanned the potential energy curve of the ESIPT process, and compared the potential barrier, it is found that the heavier chalcogen atoms are more favorable for proton transfer. At the same time, the potential application of changing heteroatoms in the azole ring by walking down the chalcogenic group in crystal luminescence color regulation is also discussed.
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Affiliation(s)
- Liying Song
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Xuan Meng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China
| | - Jinfeng Zhao
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China.
| | - Haiyun Han
- People's Hospital of Dingtao District, Heze, Shandong Province 274199, China
| | - Daoyuan Zheng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, China.
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33
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Wzgarda-Raj K, Książkiewicz O, Palusiak M. Co-crystals synthesis of 2- and 4-mercaptopyridine with thiourea and its analogue, trithiocyanuric acid. CrystEngComm 2022. [DOI: 10.1039/d2ce00592a] [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
This article describes the synthesis of four new co-crystals obtained via cross-crystallisation of 2- and 4-mercaptopyridine with thiourea and trithiocyanuric acid, and examines their crystal structures. The resulting structures are...
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34
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Wzgarda-Raj K, Rybarczyk-Pirek A, Wojtulewski S, Palusiak M. Novel melamine – salicylic salt solvates and co-crystals; an analysis of the energetic parameters of the intermolecular hydrogen bonds stabilizing the crystal structure. CrystEngComm 2022. [DOI: 10.1039/d2ce00684g] [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 novel crystal structures based on melamine and salicylic acid, with either water (I) (4:3:8 molecular ratio) or ethanol (II) (2:2:1 molecular ratio), can be treated as salt solvates. In...
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35
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Song L, Meng X, Han H, Zhao J, Zheng D. Theoretical regulation of ESIPT behavior by varying the π-expansion of proton acceptor for substituted hydroxyl fluorenes. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111376] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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36
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Domagała M, Simon S, Palusiak M. Resonance-Assisted Hydrogen Bond-Revisiting the Original Concept in the Context of Its Criticism in the Literature. Int J Mol Sci 2021; 23:ijms23010233. [PMID: 35008659 PMCID: PMC8745518 DOI: 10.3390/ijms23010233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/26/2022] Open
Abstract
In the presented research, we address the original concept of resonance-assisted hydrogen bonding (RAHB) by means of the many-body interaction approach and electron density delocalization analysis. The investigated molecular patterns of RAHBs are open chains consisting of two to six molecules in which the intermolecular hydrogen bond stabilizes the complex. Non-RAHB counterparts are considered to be reference systems. The results show the influence of the neighbour monomers on the unsaturated chains in terms of the many-body interaction energy contribution. Exploring the relation between the energy parameters and the growing number of molecules in the chain, we give an explicit extrapolation of the interaction energy and its components in the infinite chain. Electron delocalization within chain motifs has been analysed from three different points of view: three-body delocalization between C=C-C, two-body hydrogen bond delocalization indices and also between fragments (monomers). A many-body contribution to the interaction energy as well as electron density helps to establish the assistance of resonance in the strength of hydrogen bonds upon the formation of the present molecular chains. The direct relation between interaction energy and delocalization supports the original concept, and refutes some of the criticisms of the RAHB idea.
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Affiliation(s)
- Małgorzata Domagała
- Department of Physical Chemistry, Faculty of Chemistry, University of Łódź, Pomorska 163/165, 90236 Łódź, Poland;
- Correspondence: (M.D.); (S.S.)
| | - Sílvia Simon
- Institut de Química Computacional I Catàlisi, Departament de Química, Universitat de Girona, C/Ma Aurèlia Capmany, 69, 17003 Girona, Spain
- Correspondence: (M.D.); (S.S.)
| | - Marcin Palusiak
- Department of Physical Chemistry, Faculty of Chemistry, University of Łódź, Pomorska 163/165, 90236 Łódź, Poland;
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37
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Song L, Meng X, Zhao J, Han H, Zheng D. Excited-state intramolecular double proton transfer mechanism associated with solvent polarity for 9,9-dimethyl-3,6-dihydroxy-2,7-bis(4,5-dihydro-4,4-dimethyl-2-oxazolyl)fluorene compound. Mol Phys 2021. [DOI: 10.1080/00268976.2021.2007307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Liying Song
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
| | - Xuan Meng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
| | - Jinfeng Zhao
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
| | - Haiyun Han
- People's Hospital of Dingtao District, Heze, People’s Republic of China
| | - Daoyuan Zheng
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, People’s Republic of China
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38
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Zahl P, Yakutovich AV, Ventura-Macías E, Carracedo-Cosme J, Romero-Muñiz C, Pou P, Sadowski JT, Hybertsen MS, Pérez R. Hydrogen bonded trimesic acid networks on Cu(111) reveal how basic chemical properties are imprinted in HR-AFM images. NANOSCALE 2021; 13:18473-18482. [PMID: 34580697 DOI: 10.1039/d1nr04471k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High resolution non-contact atomic force microscopy measurements characterize assemblies of trimesic acid molecules on Cu(111) and the link group interactions, providing the first fingerprints utilizing CO-based probes for this widely studied paradigm for hydrogen bond driven molecular self assembly. The enhanced submolecular resolution offered by this technique uniquely reveals key aspects of the competing interactions. Accurate comparison between full-density-based modeled images and experiment allows to identify key structural elements in the assembly in terms of the electron-withdrawing character of the carboxylic groups, interactions of those groups with Cu atoms in the surface, and the valence electron density in the intermolecular region of the hydrogen bonds. This study of trimesic acid assemblies on Cu(111) combining high resolution atomic force microscopy measurements with theory and simulation forges clear connections between fundamental chemical properties of molecules and key features imprinted in force images with submolecular resolution.
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Affiliation(s)
- Percy Zahl
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Aliaksandr V Yakutovich
- Swiss Federal Laboratories for Materials Science and Technology (Empa), nanotech@surfaces laboratory, CH-8600 Dübendorf, Switzerland
| | - Emiliano Ventura-Macías
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jaime Carracedo-Cosme
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Quasar Science Resources S.L., Camino de las Ceudas 2, E-28232 Las Rozas, Madrid, Spain
| | - Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Ctra. Utrera Km. 1, E-41013, Seville, Spain
| | - Pablo Pou
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Jerzy T Sadowski
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Mark S Hybertsen
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973-5000, USA.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
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39
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Ebrahim A, Riley BT, Kumaran D, Andi B, Fuchs MR, McSweeney S, Keedy DA. The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.05.03.437411. [PMID: 33972941 PMCID: PMC8109201 DOI: 10.1101/2021.05.03.437411] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or Mpro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of Mpro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded Mpro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for Mpro, including mobile solvent interleaved between the catalytic dyad, mercurial conformational heterogeneity in a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to counter-punch COVID-19 and combat future coronavirus pandemics.
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Affiliation(s)
- Ali Ebrahim
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Blake T. Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973
| | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
- National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, United States
| | - Martin R. Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
| | - Sean McSweeney
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
- National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, United States
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- Ph.D. Programs in Biochemistry, Biology, and Chemistry, The Graduate Center – City University of New York, New York, NY 10016
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40
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Pereira F, López R, Rodríguez-Cordero A, Robles L, Suárez D, Aller A. New models involving quantum chemical parameters for assessing the chromatographic retention process. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
We performed a structural study of N-alkylated halogenopyridinium cations to examine whether choice of the N-substituent has any considerable effect on the halogen bonding capability of the cations. For that purpose, we prepared a series of N-ethyl-3-halopyridinium iodides and compared them with their N-methyl-3-halopyridinium analogues. Structural analysis revealed that N-ethylated halogenopyridinium cations form slightly shorter C−X⋯I− halogen bonds with iodide anion. We have also attempted synthesis of ditopic symmetric bis-(3-iodopyridinium) dications. Although successful in only one case, the syntheses have afforded two novel ditopic asymmetric monocations with an iodine atom bonded to the pyridine ring and another on the aliphatic N-substituent. Here, the C−I⋯I− halogen bond lengths involving pyridine iodine atom were notably shorter than those involving an aliphatic iodine atom as a halogen bond donor. This trend in halogen bond lengths is in line with the charge distribution on the Hirshfeld surfaces of the cations—the positive charge is predominantly located in the pyridine ring making the pyridine iodine atom σ-hole more positive than the one on the alkyl chan.
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Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces. Molecules 2021; 26:molecules26185642. [PMID: 34577113 PMCID: PMC8468954 DOI: 10.3390/molecules26185642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.
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Saunders LK, Pallipurath AR, Gutmann MJ, Nowell H, Zhang N, Allan DR. A quantum crystallographic approach to short hydrogen bonds. CrystEngComm 2021; 23:6180-6190. [PMID: 34588923 PMCID: PMC8436739 DOI: 10.1039/d1ce00355k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022]
Abstract
In this work we use high-resolution synchrotron X-ray diffraction for electron density mapping, in conjunction with ab initio modelling, to study short O-H⋯O and O+-H⋯O- hydrogen bonds whose behaviour is known to be tuneable by temperature. The short hydrogen bonds have donor-acceptor distances in the region of 2.45 Å and are formed in substituted urea and organic acid molecular complexes of N,N'-dimethylurea oxalic acid 2 : 1 (1), N,N-dimethylurea 2,4-dinitrobenzoate 1 : 1 (2) and N,N-dimethylurea 3,5-dinitrobenzoic acid 2 : 2 (3). From the combined analyses, these complexes are found to fall within the salt-cocrystal continuum and exhibit short hydrogen bonds that can be characterised as both strong and electrostatic (1, 3) or very strong with a significant covalent contribution (2). An additional charge assisted component is found to be important in distinguishing the relatively uncommon O-H⋯O pseudo-covalent interaction from a typical strong hydrogen bond. The electron density is found to be sensitive to the extent of static proton transfer, presenting it as a useful parameter in the study of the salt-cocrystal continuum. From complementary calculated hydrogen atom potentials, we attribute changes in proton position to the molecular environment. Calculated potentials also show zero barrier to proton migration, forming an 'energy slide' between the donor and acceptor atoms. The better fundamental understanding of the short hydrogen bond in the 'zone of fluctuation' presented in a salt-cocrystal continuum, enabled by studies like this, provide greater insight into their related properties and can have implications in the regulation of pharmaceutical materials.
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Affiliation(s)
- Lucy K Saunders
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
| | - Anuradha R Pallipurath
- School of Chemical and Process Engineering, University of Leeds Leeds LS2 9JT UK
- Research Complex at Harwell Didcot Oxfordshire OX11 0DE UK
- EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Advanced Crystallization, University of Strathclyde G1 1RD UK
| | - Matthias J Gutmann
- ISIS Pulsed Muon and Neutron Source, Rutherford Appleton Laboratory, Harwell Oxford Didcot OX11 0QX UK
| | - Harriott Nowell
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
| | - Ningjin Zhang
- Chemistry, Faculty of Natural and Environmental Sciences, Highfield Campus, University of Southampton Southampton SO17 1HE UK
| | - David R Allan
- Diamond Light Source, Harwell Science and Innovation Campus Didcot OX11 0DE UK
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Li J, Hou C, Ma X, Guo S, Zhang H, Shi L, Liao C, Zheng B, Ye L, Yang L, He X. Entropy-Enthalpy Compensations Fold Proteins in Precise Ways. Int J Mol Sci 2021; 22:9653. [PMID: 34502559 PMCID: PMC8431812 DOI: 10.3390/ijms22179653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 12/16/2022] Open
Abstract
Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.
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Affiliation(s)
- Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Hongchi Zhang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education), School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (X.M.); (S.G.); (H.Z.); (L.S.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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Jiang G, Tang Z, Han H, Ding J, Zhou P. Effects of Intermolecular Hydrogen Bonding and Solvation on Enol-Keto Tautomerism and Photophysics of Azomethine-BODIPY Dyads. J Phys Chem B 2021; 125:9296-9303. [PMID: 34376051 DOI: 10.1021/acs.jpcb.1c04776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Boron-dipyrromethene derivatives (BODIPYs) are a category of molecules with excellent photophysical properties and can be applied to various fields. This work investigates the fluorescent properties of two azomethine-BODIPY dyads in different solvents based on the time-dependent density functional theory (TD-DFT) method. The potential energy curves (PECs) show that the polar protic solvent and the enhanced π-conjugation effect can lower the proton-transfer (PT) barriers, causing the main configuration of NA-BODIPY in methanol to be the keto form, while the main configuration of NA-BODIPY in toluene and SA-BODIPY in methanol and toluene is the enol form. The keto forms of the two compounds possess the twisted intramolecular charge transfer (TICT) decay pathway in the excited state identified by the optimized twisted configurations and the appropriate barriers of the TICT process, whereas the twisted configurations of the enol forms are nonexistent. TICT successfully competes with excited-state proton transfer (ESIPT) of the keto form, which leads to the fluorescence quenching of NA-BODIPY in methanol. This work provides new ideas for the influence of enol-keto tautomerism and the competitiveness of TICT and ESIPT on the photophysical properties of BODIPYs and is expected to provide guidance for the design of new BODIPY functional molecules.
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Affiliation(s)
- Gaoshang Jiang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhe Tang
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China
| | - Haiyun Han
- Heze Dingtao People's Hospital, Heze 274199, Shandong, P. R. China
| | - Junxia Ding
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, P. R. China
| | - Panwang Zhou
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, Shandong, P. R. China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, P. R. China
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Rincón D, Doerr M, Daza MC. Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study. ACS OMEGA 2021; 6:20992-21004. [PMID: 34423207 PMCID: PMC8375099 DOI: 10.1021/acsomega.1c02559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.
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Polarization of ionic liquid and polymer and its implications for polymerized ionic liquids: An overview towards a new theory and simulation. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Akutagawa T, Takeda T, Hoshino N. Dynamics of proton, ion, molecule, and crystal lattice in functional molecular assemblies. Chem Commun (Camb) 2021; 57:8378-8401. [PMID: 34369489 DOI: 10.1039/d1cc01586a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic molecular processes, such as short- or long-range proton (H+) and ion (M+) motions, and molecular rotations in electrical conducting and magnetic molecular assemblies enable the fabrication of electron-H+ (or M+) coupling systems, while crystal lattice dynamics and molecular conformation changes in hydrogen-bonded molecular crystals have been utilised in external stimuli responsive reversible gas-induced gate opening and molecular adsorption/desorption behavior. These dynamics of the polar structural units are responsible for the dielectric measurements. The H+ dynamics are formed from ferroelectrics and H+ conductors, while the dynamic M+ motions of Li+ and Na+ involve ionic conductors and coupling to the conduction electrons. In n-type organic semiconductors, the crystal lattices are modulated by replacing M+ cations, with cations such as Li+, Na+, K+, Rb+, and Cs+. The use of polar rotator or inversion structures such as alkyl amides, m-fluoroanilinium cations, and bowl-shaped trithiasumanene π-cores enables the formation of ferroelectric molecular assemblies. The host-guest molecular systems of ESIPT fluorescent chromic molecules showed interesting molecular sensing properties using various bases, where the dynamic transformation of the crystal lattice and the molecular conformational change were coupled to each other.
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Affiliation(s)
- Tomoyuki Akutagawa
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
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Zarycz MNC, Schiel MA, Angelina E, Enriz RD. Covalence and π-electron delocalization influence on hydrogen bonds in proton transfer process of o-hydroxy aryl Schiff bases: A combined NMR and QTAIM analysis. J Chem Phys 2021; 155:054307. [PMID: 34364326 DOI: 10.1063/5.0058422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Within the framework of the density functional theory approach, we studied the relationship between the chemical nature of intramolecular hydrogen bonds (HBs) and nuclear magnetic resonance (NMR) parameters, J-couplings and 1H-chemical shifts [δ(1H)], of the atoms involved in such bonds in o-hydroxyaryl Schiff bases during the proton transfer process. For the first time, the shape of the dependence of the degree of covalence in HBs on 1J(N-H), 1J(O-H), 2hJ(O-N), and δ(1H) during the proton transfer process in o-hydroxyaryl Schiff bases was analyzed. Parameters obtained from Bader's theory of atoms in molecules were used to assess the dependence of covalent character in HBs with both the NMR properties. The influence of π-electronic delocalization on 2hJ(N-O) under the proton transfer process was investigated. 2hJ(O-N) in a Mannich base was also studied in order to compare the results with an unsaturated system. In addition, substituent effects on the phenolic ring were investigated. Our results indicate that the covalent character of HBs on both sides of the transition state undergoes a smooth exponential increase as the δ(1H) moves downfield. The degree of covalence of the N⋯H (O⋯H) bond increases linearly as 1J(N-H) (1J(O-H)) becomes more negative, even after reaching the transition state. Non-vanishing values of spin dipolar (SD) and paramagnetic spin orbital terms of 2hJ(O-N) show that π-electronic delocalization has a non-negligible effect on tautomeric equilibrium and gives evidence of the presence of the resonance assisted HB.Variation of the SD term of 2hJ(O-N) follows a similar pattern as the change in the para-delocalization aromaticity index of the chelate ring.
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Affiliation(s)
- M Natalia C Zarycz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - M Ayelén Schiel
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste; Instituto de Química Básica y Aplicada (IQUIBA-NEA). CONICET, Avda. Libertad 5460, 3400 Corrientes, Argentina
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL). CONICET, Ejército de los Andes 950, 5700 San Luis, Argentina
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50
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Yang Z, Kulik HJ. Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase. J Phys Chem B 2021; 125:7774-7784. [PMID: 34236200 DOI: 10.1021/acs.jpcb.1c05320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-Hpro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-Hpro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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