1
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Mó O, Montero-Campillo MM, Yáñez M, Alkorta I, Elguero J. Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size. J Comput Chem 2024; 45:1702-1715. [PMID: 38567760 DOI: 10.1002/jcc.27356] [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: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 06/13/2024]
Abstract
We have reported in the last years the strong effect that Be- and Mg-containing Lewis acids have on the intrinsic properties of typical bases, which become acids upon complexation. In an effort to investigate these changes when the Be and Mg derivatives form clusters of increasing size, we have examined the behavior of the (MX2)n (M = Be, Mg; X = H, F; n = 1, 2, 3) clusters when they interact with ammonia, methanimine, hydrogen cyanide and pyridine, and with their corresponding deprotonated forms. The complexes obtained at the M06-2X/aug-cc-pVTZ level were analyzed using the MBIE energy decomposition formalism, in parallel with QTAIM, ELF, NCIPLOT and AdNDP analyses of their electron density. For n = 1 the interaction enthalpy for the different families of monomers, Be (Mg) hydrides and Be (Mg) fluorides, follows the same trend as the intrinsic basicity of the base that interacts with them. This interaction is greatly reinforced after the deprotonation of the base, resulting in a significant enhancement of the intrinsic acidity of the corresponding MX2-Base complex. For (MX2)2 clusters a further reinforcement of the interaction with the base is observed, this reinforcement being again larger for the deprotonated complexes. However, the concomitant increase of their intrinsic acidity is one order of magnitude larger for hydrides than for fluorides. Unexpectedly, the cyclic conformers (MX2)3, which are more unstable than the linear ones, become the global minima after association with the base and the same is true for the deprotonated complex. Accordingly, a further increase of the intrinsic acidity of the (MX2)3-Base complexes with respect to the (MX2)2-Base ones is observed. This effect is maximum for (MgF2)3 clusters, to the point that the (MgF2)3-Base complexes become more acidic than nitric acid, the extreme case being the cluster (MgF2)3-NCH, whose acidity is higher than that of perchloric acid.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
| | - M Merced Montero-Campillo
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, IQM-CSIC, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, IQM-CSIC, Madrid, Spain
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2
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Zhu J, Tuo DH, Wang XD, Ao YF, Wang QQ, Wang DX. Anion-Carbonyl Interactions. Org Lett 2024; 26:5984-5988. [PMID: 38975861 DOI: 10.1021/acs.orglett.4c02060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Presented herein is the exploration of a novel non-covalent anion-carbonyl (X-···C═O) interaction using aromatic imides as receptors and halides as lone pair donors. Combined theoretical calculations and experimental methods including 13C NMR, IR, and crystallographic analyses were performed to provide the physical origin and experimental evidence of anion-carbonyl interactions. The EDA analysis (energy decomposition analysis) based on DFT calculation indicates that electrostatic terms are the dominant contributions for the binding energy while electron delocalization also significantly contributes alongside the electrostatic attraction. Orbital interaction (n → π*) involving the delocalization of halide lone pairs on the carbonyl antibonding orbitals was visualized with NBO (Natural Bond Orbital) analysis. 13C NMR and IR spectra demonstrated upfield chemical shifts and red-shift frequency of hosts upon the addition of halides, reflecting the effect of orbital overlap between the halide lone pairs and π* of carbonyl (n → π* contribution). The anion-carbonyl interactions were directly revealed by X-ray structural analysis of anion and benzene triimide complexes.
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Affiliation(s)
- Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - De-Hui Tuo
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Velasquez JD, Keshtkar N, Polo V, Munárriz J, Echeverría J. Unveiling the Potential of Haloalkenes as Electron Density Acceptors. CRYSTAL GROWTH & DESIGN 2024; 24:5775-5780. [PMID: 38983119 PMCID: PMC11232035 DOI: 10.1021/acs.cgd.4c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
We report herein, by means of structural and computational analyses, a comprehensive study of the capability of differently substituted haloalkenes to behave as electron density acceptors in noncovalent interactions. The nature of these interactions between haloalkenes and Lewis bases highly depends on the number and nature of the halogen atoms bound to the carbon-carbon double bond. When hydrogen bonds, which generally dominate for mono- and dihaloalkenes, cannot be formed, we observe the establishment of attractive interactions in which an sp2 carbon atom, belonging to an acyclic C=C double bond, plays the role of the Lewis acid via its π* antibonding orbital.
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Affiliation(s)
- Juan D Velasquez
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Noushin Keshtkar
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Víctor Polo
- Departmento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Julen Munárriz
- Departmento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jorge Echeverría
- Instituto de Síntesis Química y Catalisis Homogénea (ISQCH) and Departmento de Química Inorgánica, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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4
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Carré V, Godard P, Méreau R, Jacquot de Rouville HP, Jonusauskas G, McClenaghan N, Tassaing T, Vincent JM. Photogeneration of Chlorine Radical from a Self-Assembled Fluorous 4CzIPN•Chloride Complex: Application in C-H Bond Functionalization. Angew Chem Int Ed Engl 2024; 63:e202402964. [PMID: 38634355 DOI: 10.1002/anie.202402964] [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: 02/12/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
The chlorine radical is a strong HAT (Hydrogen Atom Transfer) agent that is very useful for the functionalization of C(sp3)-H bonds. Albeit highly attractive, its generation from the poorly oxidizable chloride ion mediated by an excited photoredox catalyst is a difficult task. We now report that 8Rf8-4CzIPN, an electron-deficient fluorous derivative of the benchmark 4CzIPN photoredox catalyst belonging to the donor-acceptor carbazole-cyanoarene family, is not only a better photooxidant than 4CzIPN, but also becomes an excellent host for the chloride ion. Combining these two properties ultimately makes the self-assembled 8Rf8-4CzIPN•Cl- dual catalyst highly reactive in redox-neutral Giese-type C(sp3)-H bond alkylation reactions promoted by the chlorine radical. Additionally, because of its fluorous character, the efficient separation/recovery of 8Rf8-4CzIPN could be envisioned.
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Affiliation(s)
- Victor Carré
- Institut des Sciences Moléculaires, CNRS UMR 5255, Université de Bordeaux, 351, Crs de la Libération, 33405, Talence, France
| | - Pascale Godard
- Institut des Sciences Moléculaires, CNRS UMR 5255, Université de Bordeaux, 351, Crs de la Libération, 33405, Talence, France
| | - Raphaël Méreau
- Institut des Sciences Moléculaires, CNRS UMR 5255, Université de Bordeaux, 351, Crs de la Libération, 33405, Talence, France
| | | | - Gediminas Jonusauskas
- Laboratoire Ondes et Matière d'Aquitaine, CNRS UMR 5798, Univ. Bordeaux, 351, Crs de la Libération, 33405, Talence, France
| | - Nathan McClenaghan
- Institut des Sciences Moléculaires, CNRS UMR 5255, Université de Bordeaux, 351, Crs de la Libération, 33405, Talence, France
| | - Thierry Tassaing
- Institut des Sciences Moléculaires, CNRS UMR 5255, Université de Bordeaux, 351, Crs de la Libération, 33405, Talence, France
| | - Jean-Marc Vincent
- Institut des Sciences Moléculaires, CNRS UMR 5255, Université de Bordeaux, 351, Crs de la Libération, 33405, Talence, France
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5
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Panwaria P, Das A. N···C═O n → π* Interaction: Gas-Phase Electronic and Vibrational Spectroscopy Combined with Quantum Chemistry Calculations. J Phys Chem A 2024; 128:4685-4693. [PMID: 38814588 DOI: 10.1021/acs.jpca.4c02181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Herein, we have used gas-phase electronic and vibrational spectroscopic techniques for the first time to study the N···C═O n → π* interaction in ethyl 2-(2-(dimethylamino) phenyl) acetate (NMe2-Ph-EA). We have measured the electronic spectra of NMe2-Ph-EA in the mass channels of its two distinct fragments of m/z = 15 and 192 using a resonant two-photon ionization technique as there was extensive photofragmentation of NMe2-Ph-EA. Identical electronic spectra obtained in the mass channels of both fragments confirm the dissociation of NMe2-Ph-EA in the ionic state, and hence, the electronic spectrum of the fragment represents that of NMe2-Ph-EA only. UV-UV hole-burning spectroscopy proved the presence of a single conformer of NMe2-Ph-EA in the experiment. Detailed quantum chemistry calculations reveal the existence of a N···C═O n → π* interaction in all six low-energy conformers of NMe2-Ph-EA. A comparison of the IR spectrum of NMe2-Ph-EA acquired from the gas-phase experiment with those obtained from theoretical calculations indicates that the experimentally observed conformer has a N···C═O n → π* interaction. The present finding might be further valuable in drug design and their recognition based on the N···C═O n → π* interaction.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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6
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Zhang W, Huang HH, Luo ZM, Ma F, Gonell S, Ke Z, Tan L, Wang JW. Unveiling the Activity and Mechanism Alterations by Pyrene Decoration on a Co(II) Macrocyclic Catalyst for CO 2 Reduction. CHEMSUSCHEM 2024; 17:e202301113. [PMID: 38287461 DOI: 10.1002/cssc.202301113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/04/2024] [Accepted: 01/29/2024] [Indexed: 01/31/2024]
Abstract
Mechanistic studies involving characterization of crucial intermediates are desirable for rational optimization of molecular catalysts toward CO2 reduction, while fundamental challenges are associated with such studies. Herein we present the systematic mechanistic investigations on a pyrene-appended CoII macrocyclic catalyst in comparison with its pyrene-free prototype. The comparative results also verify the reasons of the higher catalytic activity of the pyrene-tethered catalyst in noble-metal-free CO2 photoreduction with various photosensitizers, where a remarkable apparent quantum yield of 36±3 % at 425 nm can be obtained for selective CO production. Electrochemical and spectroelectrochemical studies in conjunction with DFT calculations between the two catalysts have characterized the key CO-bound intermediates and revealed their different CO-binding behavior, demonstrating that the pyrene group endows the corresponding CoII catalyst a lower catalytic potential, a higher stability, and a greater ease in CO release, all of which contribute to its better performance.
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Affiliation(s)
- Weilu Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Hai-Hua Huang
- School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhi-Mei Luo
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai, 519082, China
| | - Fan Ma
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai, 519082, China
| | - Sergio Gonell
- Institute of Advanced Materials (INAM), Universitat Jaume I, Av. Vicente Sos Baynat s/n., Castelló, 12006, Spain
| | - Zhuofeng Ke
- School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liang Tan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
| | - Jia-Wei Wang
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai, 519082, China
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7
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Yin C, Ye H, Hai Y, Zou H, You L. Aromatic-Carbonyl Interactions as an Emerging Type of Non-Covalent Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310337. [PMID: 38561959 PMCID: PMC11165483 DOI: 10.1002/advs.202310337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Aromatic-carbonyl (Ar···C═O) interactions, attractive interactions between the arene plane and the carbon atom of carbonyl, are in the infancy as one type of new supramolecular bonding forces. Here the study and functionalization of aromatic-carbonyl interactions in solution is reported. A combination of aromatic-carbonyl interactions and dynamic covalent chemistry provided a versatile avenue. The stabilizing role and mechanism of arene-aldehyde/imine interactions are elucidated through crystal structures, NMR studies, and computational evidence. The movement of imine exchange equilibria further allowed the quantification of the interplay between arene-aldehyde/imine interactions and dynamic imine chemistry, with solvent effects offering another handle and matching the electrostatic feature of the interactions. Moreover, arene-aldehyde/imine interactions enabled the reversal of kinetic and thermodynamic selectivity and sorting of dynamic covalent libraries. To show the functional utility diverse modulation of fluorescence signals is realized with arene-aldehyde/imine interactions. The results should find applications in many aspects, including molecular recognition, assemblies, catalysis, and intelligent materials.
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Affiliation(s)
- Chaowei Yin
- State Key Laboratory of Structural ChemistryFujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouFujian350002China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
| | - Hebo Ye
- State Key Laboratory of Structural ChemistryFujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouFujian350002China
| | - Yu Hai
- State Key Laboratory of Structural ChemistryFujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouFujian350002China
| | - Hanxun Zou
- State Key Laboratory of Structural ChemistryFujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouFujian350002China
| | - Lei You
- State Key Laboratory of Structural ChemistryFujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouFujian350002China
- University of Chinese Academy of SciencesChinese Academy of SciencesBeijing100049China
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8
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Moreira Costa MA, de Sousa NF, Mansur Pontes CL, Scotti MT, de Assis FF, Braga AL, Sandjo LP. Inhibitory effects against SARSCoV-2 main protease (M pro) of biflavonoids and benzophenones from the fruit of Platonia insignis. Fitoterapia 2024; 173:105784. [PMID: 38128621 DOI: 10.1016/j.fitote.2023.105784] [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: 10/05/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
The SARS-CoV-2 mutation and the limitation of the approved drug against COVID-19 are still a challenge in many country healthcare systems and need to be affronted despite the set of vaccines to prevent this viral infection. To contribute to the identification of new antiviral agents, the present study focused on natural products from an edible fruit with potential inhibitory effects against the SARS-CoV-2 main protease (Mpro). First, LC-ESIMS analysis of Platonia insignis fruits was performed and showed the presence of biflavonoids and benzophenones in the seed and pulp, respectively. Then, maceration and chromatographic purification led to the identification of two triglycerides (1 and 2) alongside chamaejasmine (3) and volkensiflavone (4) from the seed and isogarcinol (5) and cycloxanthochymol (6), from the pulp. Compounds 1-6 after evaluating their inhibitory against Mpro, displayed from no to significant activity. Compound 5 was the most potent with an IC50 value of 0.72 μM and was more active than the positive control, Ebselen (IC50 of 3.4 μM). It displayed weak and no cytotoxicity against THP-1 (CC50 of 116.2 μM) and Vero cell lines, respectively. Other active compounds showed no cytotoxicity against THP-1. and Vero cell lines. Molecular docking studies revealed interactions in the catalytic pocket between compound 5 and amino acid residues that composed the catalytic dyads (His 41 and Cyst 145).
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Affiliation(s)
- Monalisa A Moreira Costa
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Natália F de Sousa
- Department of Chemistry, Center for Exact and Natural Sciences, Universidade Federal de Paraíba, Campus I, João Pessoa, PB, Brazil
| | - Carime L Mansur Pontes
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Marcus T Scotti
- Department of Chemistry, Center for Exact and Natural Sciences, Universidade Federal de Paraíba, Campus I, João Pessoa, PB, Brazil
| | - Francisco F de Assis
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Antonio L Braga
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Louis P Sandjo
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil.
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9
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Zhou Y, Zeng Z, Fu J, Gao Y, Ma J, Zhang Z, Zu D, Han B, Lu X, Ma J, Jiang J. New Insights into the Role of Humic Acid in Permanganate Oxidation of Diclofenac: A Novel Electron Transfer Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4019-4028. [PMID: 38366980 DOI: 10.1021/acs.est.3c10703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Humic acid (HA) ubiquitously existing in aquatic environments has been reported to significantly impact permanganate (KMnO4) decontamination processes. However, the underlying mechanism of the KMnO4/HA system remained elusive. In this study, an enhancing effect of HA on the KMnO4 oxidation of diclofenac (DCF) was observed over a wide solution pH range of 5-9. Surprisingly, the mechanism of HA-induced enhancement varied with solution pH. Quenching and chemical probing experiments revealed that manganese intermediates (Mn(III)-HA and MnO2) were responsible for the enhancement under acidic conditions but not under neutral and alkaline conditions. By combining KMnO4 decomposition, galvanic oxidation process experiments, electrochemical tests, and FTIR and XPS analysis, it was interestingly found that HA could effectively mediate the electron transfer from DCF to KMnO4 in neutral and alkaline solutions, which was reported for the first time. The formation of an organic-catalyst complex (i.e., HA-DCF) with lower reduction potential than the parent DCF was proposed to be responsible for the accelerated electron transfer from DCF to KMnO4. This electron transfer likely occurred within the complex molecule formed through the interaction between HA-DCF and KMnO4 (i.e., HA-DCF-KMnO4). These results will help us gain a more comprehensive understanding of the role of HA in the KMnO4 oxidation processes.
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Affiliation(s)
- Yang Zhou
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhu Zeng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Junhao Fu
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Yuan Gao
- School of Civil and Transportation Engineering, Guangdong University of Technology, Guangzhou 510006, Guangdong, China
| | - Jinxing Ma
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhong Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Daoyuan Zu
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Bin Han
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Xixin Lu
- China MCC17 Group Co., Ltd., Ma'anshan 243000, Anhui, China
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jin Jiang
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
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10
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Hou Y, Jia A, Qin X, Yang X, Xie J, Li X, Zhao Y. New insights on the preparation of amine covalent organic polymer and its adsorption properties. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122659. [PMID: 37839682 DOI: 10.1016/j.envpol.2023.122659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023]
Abstract
Dye pollution is becoming increasingly severe. This study used the Schiff base reaction to synthesize a polyaromatic ring covalent organic polymer material with amide bonds and high electronegativity named SLEL-9 to adsorb Methylene Blue (MB) and Rhodamine B (RhB). SLEL-9 was characterized by Fourier transform infra-red spectra, X-ray photoelectron spectra, Brunauer-Emmett-Teller (BET), zeta potential analysis, and other techniques. It was found that SLEL-9 material contains C-C, CN, C-N, and CO. SLEL-9 had a zeta potential of about -45 mV under neutral conditions, which proved that the material had been synthesized successfully. The BET and Langmuir surface areas of SLEL-9 were 35.187 m2 g-1 and 56.419 m2 g-1, respectively. The adsorptions of SLEL-9 on low concentration (10 mg L-1) Methylene Blue and Rhodamine B reached equilibrium within 48 h. The results showed that SLEL-9's adsorption of dye molecules are more consistent with pseudo-second-order kinetic and Langmuir isotherm model. The adsorption experiments showed that the adsorption process is a spontaneous endothermic reaction, mainly chemisorption. The maximum adsorption capacity of SLEL-9 for MB and RhB were 132.45 mg g-1 and 101.94 mg g-1. In addition, this study investigated to determine the optimal reaction parameters. The primary mechanisms of SLEL-9 adsorption of two dyes are n→π* interaction, π-π EDA interaction and electrostatic attraction. Selective adsorb ability experiment results showed that SLEL-9 could selectively adsorb MB and RhB to a certain extent. Finally, it was found that SLEL-9 can maintain over 70% adsorption capacity after five reuses and can maintain stability after soaking in different pH water and organic solvents for 120 h. SLEL-9 proved to be a promising organic covalent polymer adsorption material for the removal of Methylene Blue and Rhodamine B in water.
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Affiliation(s)
- Yutong Hou
- Key Lab of Groundwater Resources and Environment (Ministry of Education), College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Aiyuan Jia
- Key Lab of Groundwater Resources and Environment (Ministry of Education), College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Xueming Qin
- Key Lab of Groundwater Resources and Environment (Ministry of Education), College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Xinru Yang
- Key Lab of Groundwater Resources and Environment (Ministry of Education), College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Jiayin Xie
- Key Lab of Groundwater Resources and Environment (Ministry of Education), College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Xiaoyu Li
- Key Lab of Groundwater Resources and Environment (Ministry of Education), College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Yongsheng Zhao
- Key Lab of Groundwater Resources and Environment (Ministry of Education), College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, 2519 Jiefang Road, Changchun, 130021, PR China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, College of New Energy and Environment, Jilin University, Changchun, 130021, PR China.
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11
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Li B, Zhao Y. Facile synthesis and ultrastrong adsorption of a novel polyacrylamide-modified diatomite/cerium alginate hybrid aerogel for anionic dyes from aqueous environment. Int J Biol Macromol 2023; 253:127114. [PMID: 37778584 DOI: 10.1016/j.ijbiomac.2023.127114] [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: 08/11/2023] [Revised: 09/02/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
An eco-friendly cationic polyacrylamide (CPAM)-modified diatomite/Ce(III)-crosslinked sodium alginate hybrid aerogel (CPAM-Dia/Ce-SA) was synthesized successfully and characterized by SEM-EDS, XRD, FTIR, UV-Vis and XPS. Adsorption performance, interaction mechanism and reusability of CPAM-Dia/Ce-SA used for the removal of acid blue 113 (AB 113), acid blue 80 (AB 80), acid yellow 117 (AY 117), Congo red (CR) and Direct Green 6 (DG 6) anionic dyes from aqueous media were investigated in detail. The results demonstrate that CPAM-Dia/Ce-SA aerogel is macroscopic polymer hybrid spheres with a particle size of around 1.3 mm, unique undulating mountain-like surface and porous mesostructure, and exhibits outstanding adsorption capacity for anionic dyes and good reusability. The maximum adsorption amounts of AB 113, AB 80, AY 117, CR and DG 6 by CPAM-Dia/Ce-SA were 3008, 1208, 914, 1832 and 1232 mg/g at pH 2.0, 60 min contact time and 25 °C, and corresponding removal efficiency reached individually 97.5, 96.6, 99.7, 99.9 and 98.5 % respectively and were less affected by increasing pH up to 10.0. Dye adsorption behaviour and adsorption processes with spontaneous and exothermic nature were perfectly interpreted by the Langmuir and Pseudo-second-order rate models respectively. Physicochemical and multisite-H-bonding synergies promoted the ultrastrong biosorption of anionic dyes by CPAM-Dia/Ce-SA.
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Affiliation(s)
- Beigang Li
- Chemistry & Environment Science College, Inner Mongolia Normal University, China; Inner Mongolia Key Laboratory of Environmental Chemistry, Hohhot 010022, China.
| | - Yuting Zhao
- Chemistry & Environment Science College, Inner Mongolia Normal University, China; Inner Mongolia Key Laboratory of Environmental Chemistry, Hohhot 010022, China
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12
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Meeus EJ, Igareta NV, Morita I, Ward TR, de Bruin B, Reek JNH. A Co(TAML)-based artificial metalloenzyme for asymmetric radical-type oxygen atom transfer catalysis. Chem Commun (Camb) 2023; 59:14567-14570. [PMID: 37987161 DOI: 10.1039/d3cc04723g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
We show that the incorporation of a biotinylated Co(TAML) cofactor within streptavidin enables asymmetric radical-type oxygen atom transfer catalysis with improved activity and enantioselectivity.
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Affiliation(s)
- Eva J Meeus
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam (UvA), Science Park 904, Amsterdam 1098XH, The Netherlands.
| | - Nico V Igareta
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4002, Switzerland.
| | - Iori Morita
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4002, Switzerland.
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4002, Switzerland.
| | - Bas de Bruin
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam (UvA), Science Park 904, Amsterdam 1098XH, The Netherlands.
| | - Joost N H Reek
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam (UvA), Science Park 904, Amsterdam 1098XH, The Netherlands.
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13
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You L. Dual reactivity based dynamic covalent chemistry: mechanisms and applications. Chem Commun (Camb) 2023; 59:12943-12958. [PMID: 37772969 DOI: 10.1039/d3cc04022d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Dynamic covalent chemistry (DCC) focuses on the reversible formation, breakage, and exchange of covalent bonds and assemblies, setting a bridge between irreversible organic synthesis and supramolecular chemistry and finding wide utility. In order to enhance structural and functional diversity and complexity, different types of dynamic covalent reactions (DCRs) are placed in one vessel, encompassing orthogonal DCC without crosstalk and communicating DCC with a shared reactive functional group. As a means of adding tautomers, widespread in chemistry, to interconnected DCRs and combining the features of orthogonal and communicating DCRs, a concept of dual reactivity based DCC and underlying structural and mechanistic insights are summarized. The manipulation of the distinct reactivity of structurally diverse ring-chain tautomers allows selective activation and switching of reaction pathways and corresponding DCRs (C-N, C-O, and C-S) and assemblies. The coupling with photoswitches further enables light-mediated formation and scission of multiple types of reversible covalent bonds. To showcase the capability of dual reactivity based DCC, the versatile applications in dynamic polymers and luminescent materials are presented, paving the way for future functionalization studies.
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Affiliation(s)
- Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350108, China
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14
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Briceño-Vargas FM, Quesadas-Rojas M, Mirón-López G, Cáceres-Castillo D, Carballo RM, Mena-Rejón GJ, Quijano-Quiñones RF. Molecular orbital and topological electron density study of n → π* interactions: amides and thioamides cases. RSC Adv 2023; 13:31321-31329. [PMID: 37901275 PMCID: PMC10600513 DOI: 10.1039/d3ra06038a] [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: 09/05/2023] [Accepted: 10/18/2023] [Indexed: 10/31/2023] Open
Abstract
The n → π* interactions were studied in amides and thioamides systems models, through the analysis of the electron density topology along with the Natural Bonding Orbital (NBO) approach. The effect of the dispersion terms was assessed using different DFT functionals. The NBO, independent gradient model (IGM), and the analysis of the reduced density gradient outcomes show that dispersion forces play a significant role in the strength of n → π* interactions. The IGM results indicate that δg height values for n → π* interactions do not extend beyond 0.025. All the methods used in this work predict that n → π* interaction between pairs of thioamides is stronger than those between amides. However, the electron density topology-based methods were not able to replicate the trends in the relative force of this interaction found in the experimental and NBO results.
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Affiliation(s)
- Flor María Briceño-Vargas
- Laboratory of Theoretical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | | | - Gumersindo Mirón-López
- Laboratory of Nuclear Magnetic Resonance, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - David Cáceres-Castillo
- Laboratory of Pharmaceutical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - Rubén M Carballo
- Laboratory of Pharmaceutical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - Gonzalo J Mena-Rejón
- Laboratory of Pharmaceutical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
| | - Ramiro F Quijano-Quiñones
- Laboratory of Theoretical Chemistry, Faculty of Chemistry, Autonomous University of Yucatan Merida Yucatan 97069 Mexico
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15
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Li X, Hu L, Lu G, Wang Y. Carbon-Bonding Metal Catalysis (CBMC): A Supramolecular Complex Directs Structural-Isomer Selection in Gold-Catalyzed Reactions. J Am Chem Soc 2023; 145:21554-21561. [PMID: 37668596 DOI: 10.1021/jacs.3c07551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Carbon is a primary element to constitute organic molecules, while metal catalysis is a basic tool in organic synthesis. The establishment of a link between the ubiquitous carbon bonding and metal catalysis is thus a fundamentally important problem. However, there is yet no experimental example to introduce the role of carbon bonding in a metal catalysis process. Herein, we merged the topics of carbon bonding and metal catalysis together and demonstrated that a supramolecular carbon-bonding metal complex can not only give rise to catalytic activity but, more remarkably, direct structural-isomer selection events in gold-catalyzed reactions. The experimental results unveil the fact that the imposing of weak carbon-bonding interactions on a gold complex can alter the carbene as well as the Lewis acid property of these catalysts. These results illustrate a non-negligible role of weak carbon-bonding interactions in the modulation of metal catalysis. As such, carbon-bonding metal catalysis is suggested to be used as a routine tool not only in the development of reactions but more frequently in analyzing reaction processes in metal catalysis.
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Affiliation(s)
- Xinxin Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Lingfei Hu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
| | - Yao Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, Shandong University, Jinan 250100, P. R. China
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16
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Zytkiewicz E, Shkel IA, Cheng X, Rupanya A, McClure K, Karim R, Yang S, Yang F, Record MT. Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2O, N, C and sp 3C Unified Atoms with Naphthalene sp 2C Atoms in Water. Biochemistry 2023; 62:2841-2853. [PMID: 37695675 DOI: 10.1021/acs.biochem.3c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp2 atoms of amides, aromatics, and other groups occur in protein self-assembly processes including folding, oligomerization, and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp2O with amide sp2N unified atoms (presumably C═O···H-N hydrogen bonds) and amide/aromatic sp2C (lone pair π, n-π*) are particularly favorable. Sp3C-sp3C (hydrophobic), sp3C-sp2C (hydrophobic, CH-π), sp2C-sp2C (hydrophobic, π-π), and sp3C-sp2N interactions are favorable, sp2C-sp2N interactions are neutral, while sp2O-sp2O and sp2N-sp2N self-interactions and sp2O-sp3C interactions are unfavorable. Here, from determinations of favorable effects of 14 amides on naphthalene solubility at 10, 25, and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp2O, sp2N, sp2C, and sp3C unified atoms with aromatic sp2C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp2O-aromatic sp2C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g., lone pair-π), while amide sp3C- and sp2C-aromatic sp2C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp2 atoms in protein processes.
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Affiliation(s)
- Emily Zytkiewicz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Irina A Shkel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xian Cheng
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anuchit Rupanya
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kate McClure
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rezwana Karim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sumin Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Felix Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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17
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Sun YK, Qiao JB, Xin YM, Zhou Q, Ma ZH, Shao H, Zhao YM. Total Synthesis of Metaphanine and Oxoepistephamiersine. Angew Chem Int Ed Engl 2023; 62:e202310917. [PMID: 37602680 DOI: 10.1002/anie.202310917] [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: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Herein, we report a concise and divergent synthesis of the complex hasubanan alkaloids metaphanine and oxoepistephamiersine from commercially available and inexpensive cyclohexanedione monoethylene acetal. Our synthesis features a palladium-catalyzed cascade cyclization reaction to set the tricyclic carbon framework of the desired molecules, a regioselective Baeyer-Villiger oxidation followed by a MeNH2 triggered skeletal reorganization cascade to construct the benzannulated aza[4.4.3]propellane, and a strategically late-stage regio-/diastereoselective oxidative annulation of sp3 C-H bond to form the challenging THF ring system and hemiketal moiety in a single step. In addition, a highly enantioselective alkylation of cyclohexanedione monoethylene acetal paved the way for the asymmetric synthesis of target molecular.
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Affiliation(s)
- Ya-Kui Sun
- Key Laboratory of Applied Surface and Colloid Chemistry & School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Ave, Xi'an, 710119, China
| | - Jin-Bao Qiao
- Key Laboratory of Applied Surface and Colloid Chemistry & School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Ave, Xi'an, 710119, China
| | - Yu-Meng Xin
- Key Laboratory of Applied Surface and Colloid Chemistry & School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Ave, Xi'an, 710119, China
| | - Qin Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry & School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Ave, Xi'an, 710119, China
| | - Zhi-Hua Ma
- Key Laboratory of Applied Surface and Colloid Chemistry & School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Ave, Xi'an, 710119, China
| | - Hui Shao
- Key Laboratory of Applied Surface and Colloid Chemistry & School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Ave, Xi'an, 710119, China
| | - Yu-Ming Zhao
- Key Laboratory of Applied Surface and Colloid Chemistry & School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang'an Ave, Xi'an, 710119, China
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18
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Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023; 32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.
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Affiliation(s)
- Maral Afshinpour
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Logan A. Smith
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Suvobrata Chakravarty
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
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19
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Akl MA, Mostafa AG, Abdelaal MY, Nour MAK. Surfactant supported chitosan for efficient removal of Cr(VI) and anionic food stuff dyes from aquatic solutions. Sci Rep 2023; 13:15786. [PMID: 37737297 PMCID: PMC10517148 DOI: 10.1038/s41598-023-43034-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
In order to develop a novel and cost-effective adsorbent with outstanding adsorption capacity and excellent recyclability for anionic pollutants, the chitosan-modified cetyltrimethylammonium bromide sorbent (CS@CTAB) was fabricated. Fourier-transform infrared spectroscopy, N2 adsorption-desorption isotherm, elemental analysis, Thermogravimetric analysis, X-ray diffraction, and Scanning electron microscopy have been applied to evaluate both raw and surfactant modified chitosan (CS@CTAB). Azorubine, Sunset Yellow, and hexavalent chromium were used to study the adsorption behavior of CS@CTAB under various parameters such as adsorbent dose, initial dye and metal ion concentration, contact time, and temperature. Adsorption equilibrium, kinetics models and thermodynamic parameters were investigated. The adsorption isotherm fitted well with the Langmuir isotherm model, with a maximum adsorption capacity of 492.6 mg/g, 492.6 mg/g, and 490.196 mg/g for Azorubine, Sunset Yellow, and Hexavalent Chromium, respectively. The kinetic studies showed that the pseudo-second-order model provided a better correlation between experimental data. Furthermore, the calculated thermodynamic parameters confirmed that the adsorption of Cr(VI), E110, and E122 by CS@CTAB material is a spontaneous and exothermic process. The fabricated CS@CTAB adsorbent was employed for the efficient elimination of Azorubine, Sunset Yellow, and hexavalent chromium from real water samples, synthetic mixtures, and colored soft drinks, with a percentage of recovery of ~ 96%. The plausible adsorption mechanisms of Azorubine, Sunset Yellow, and hexavalent chromium on the surface of CS@CTAB are elucidated. The adsorption anticipated to be due to electrostatic interaction and hydrogen bond formation for hexavalent chromium; while the adsorption of Azorubine and Sunset Yellow, was assumed to be due to electrostatic interaction, hydrogen bonding, and n-π interaction. Finally, the study demonstrates the efficiency of CS@CTAB for the removal of anionic species from several samples, including natural water and colored beverages.
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Affiliation(s)
- Magda A Akl
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| | - Aya G Mostafa
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Magdy Y Abdelaal
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mennat Allah K Nour
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
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20
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Wang XD, Zhu J, Wang DX. Intermolecular n→π* Interactions in Supramolecular Chemistry and Catalysis. Chempluschem 2023; 88:e202300288. [PMID: 37609956 DOI: 10.1002/cplu.202300288] [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: 06/14/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
The n→π* interactions describing attractive force between lone pairs (lps) of nucleophile and carbonyl or polarized unsaturated bonds have recently attracted growing attentions in various disciplines. So far, such non-covalent driving force are mainly concentrated to intramolecular systems. Intermolecular n→π* interactions in principle could produce fascinated supramolecular systems or facilitate organic reactions, however, they remain largely underexplored due to the very weak energy of individual interaction. This review attempts to give an overview of the challenging intermolecular n→π* interactions, much efforts emphasize the supramolecular systems, catalytic processes and spectroscopic measurements.
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Affiliation(s)
- Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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21
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Panwaria P, Das A. Modulation of n → π* Interaction in the Complexes of p-Substituted Pyridines with Aldehydes: A Theoretical Study. J Phys Chem A 2023. [PMID: 37463490 DOI: 10.1021/acs.jpca.3c03103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
n → π* interaction is analogous to the hydrogen bond in terms of the delocalization of the electron density between the two orbitals. Studies on the intermolecular complexes stabilized by the n → π* interaction are scarce in the literature. Herein, we have studied intermolecular N···C═O n → π* interactions in the complexes of p-substituted pyridines (p-R-Py) with formaldehyde (HCHO), formyl chloride (HCOCl), and acetaldehyde (CH3CHO) using quantum chemistry calculations. We have shown that the strength of the n → π* interaction can be modulated by varying the electronic substituents at the donor and acceptor sites in the complexes. Variation of the substituents at the para position of the pyridine ring from the electron-withdrawing groups (EWGs) to the electron-donating groups (EDGs) results in a systematic increase in the strength of the n → π* interaction. The strength of this interaction is also modulated by tuning the electron density toward the carbonyl bond by substituting the hydrogen atom of HCHO with the methyl and chloro groups. The modulation of this interaction due to the electronic substitutions at the n → π* donor and acceptor sites in the complexes is monitored by probing the relevant geometrical parameters, binding energies, C═O frequency redshift, NBO energies, and electron density for this interaction derived from QTAIM and NCI index analyses. Energy decomposition analysis reveals that the electrostatic interaction dominates the binding energies of these complexes, while the charge transfer interaction, which is representative of the n → π* interaction, also has a significant contribution to these.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
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22
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Zytkiewicz E, Shkel IA, Cheng X, Rupanya A, McClure K, Karim R, Yang S, Yang F, Record MT. Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally-determined Enthalpic and Entropic Contributions to Interactions of Amide sp 2 O, N, C and sp 3 C Unified Atoms with Naphthalene sp 2 C Atoms in Water. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548600. [PMID: 37503153 PMCID: PMC10370101 DOI: 10.1101/2023.07.12.548600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp 2 atoms of amides, aromatics and other groups occur in protein self-assembly processes including folding, oligomerization and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp 2 O with amide sp 2 N unified atoms (presumably C=O···H-N hydrogen bonds) and amide/aromatic sp 2 C (lone pair-π, n-π * ) are particularly favorable. Sp 3 C-sp 3 C (hydrophobic), sp 3 C-sp 2 C (hydrophobic, CH-π), sp 2 C-sp 2 C (hydrophobic, π-π) and sp 3 C-sp 2 N interactions are favorable, sp 2 C-sp 2 N interactions are neutral, while sp 2 O-sp 2 O and sp 2 N-sp 2 N self-interactions and sp 2 O-sp 3 C interactions are unfavorable. Here, from determinations of favorable effects of fourteen amides on naphthalene solubility at 10, 25 and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp 2 O, sp 2 N, sp 2 C and sp 3 C unified atoms with aromatic sp 2 C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp 2 O-aromatic sp 2 C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g. lone pair-π) while amide sp 3 C- and sp 2 C-aromatic sp 2 C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp 2 atoms in protein processes. Table of Contents Graphic
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Affiliation(s)
- Emily Zytkiewicz
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Irina A. Shkel
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Xian Cheng
- Biophysics Program, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Anuchit Rupanya
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Kate McClure
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Rezwana Karim
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Sumin Yang
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Felix Yang
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - M. Thomas Record
- Department of Biochemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
- Biophysics Program, University of Wisconsin – Madison, Madison, Wisconsin 53706
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
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23
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Shen Y, Li B, Zhang Z. Super-efficient removal and adsorption mechanism of anionic dyes from water by magnetic amino acid-functionalized diatomite/yttrium alginate hybrid beads as an eco-friendly composite. CHEMOSPHERE 2023; 336:139233. [PMID: 37336439 DOI: 10.1016/j.chemosphere.2023.139233] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/29/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
The development of eco-friendly, large-capacity and easy-to-separate adsorbent materials has always been the focus and difficulty of adsorption technology in wastewater treatment applications based on the characteristics of dye wastewater. Therefore, in this study, a green magnetic glycine(Gly)-functionalized diatomite(Dia)/yttrium alginate (Y-SA) hybrid bead composite (Dia-Gly-Y-SA@Fe3O4) was synthesized by the droplet polymerization, and characterized by various modern analytical techniques. The adsorption performance and adsorption mechanism of the composite were evaluated and elucidated by the removal of anionic dyes direct Blue 106 (DB 106), Congo red (CR) and direct red 13 (DR 13) from water. The results show that the composite is a macroparticle gelpolymer with an average particle size of about 1.5 mm, flower-like fold surface structure, abundant porosity and sensitive magnetic response, and displays ultrastrong adsorption ability for three dyes. The adsorption equilibrium of each dye can be reached quickly within 30 min, and the removal efficiency is more than 95% at pH 2.0 and decreases slightly with pH up to 9.0. The adsorption processes could be explained by the Pseudo-second-order rate equation well. All isotherm data fitted the Langmuir model well, and the maximum adsorption capacities were 1635, 2359 and 1165 mg/g for DB 106, CR and DR 13 at 298 K, respectively. The ultrastrong adsorption performance was due to the multisite interaction of physicochemical action and various hydrogen bonds between hybrid beads and dye anions. As a cost-effective magnetic macroparticle adsorbent prepared by natural ingredients, Dia-Gly-Y-SA@Fe3O4 composite exhibits much more stronger adsorption efficiency, better collectability and no secondary pollution than powder Dia, and would have a good application prospect for the purification of anionic dye wastewater with a wide pH range.
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Affiliation(s)
- Yanlong Shen
- Chemistry & Environment Science College, Inner Mongolia Normal University, China; Inner Mongolia Key Laboratory of Environmental Chemistry, Hohhot, 010022, China
| | - Beigang Li
- Chemistry & Environment Science College, Inner Mongolia Normal University, China; Inner Mongolia Key Laboratory of Environmental Chemistry, Hohhot, 010022, China.
| | - Zhibin Zhang
- Chemistry & Environment Science College, Inner Mongolia Normal University, China; Inner Mongolia Key Laboratory of Environmental Chemistry, Hohhot, 010022, China
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24
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Mecheri R, Zobeidi A, Atia S, Neghmouche Nacer S, Salih AAM, Benaissa M, Ghernaout D, Arni SA, Ghareba S, Elboughdiri N. Modeling and Optimizing the Crystal Violet Dye Adsorption on Kaolinite Mixed with Cellulose Waste Red Bean Peels: Insights into the Kinetic, Isothermal, Thermodynamic, and Mechanistic Study. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16114082. [PMID: 37297216 DOI: 10.3390/ma16114082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
In this study, a new eco-friendly kaolinite-cellulose (Kaol/Cel) composite was prepared from waste red bean peels (Phaseolus vulgaris) as a source of cellulose to serve as a promising and effective adsorbent for the removal of crystal violet (CV) dye from aqueous solutions. Its characteristics were investigated through the use of X-ray diffraction, Fourier-transform infrared spectroscopy, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and zero-point of charge (pHpzc). The Box-Behnken design was used to improve CV adsorption on the composite by testing its primary affecting factors: loading Cel into the composite matrix of Kaol (A: 0-50%), adsorbent dosage (B: 0.02-0.05 g), pH (C: 4-10), temperature (D: 30-60 °C), and duration (E: 5-60 min). The significant interactions with the greatest CV elimination efficiency (99.86%) are as follows: BC (adsorbent dose vs. pH) and BD (adsorbent dose vs. temperature) at optimum parameters (A: 25%, B: 0.05 g, C: 10, D: 45 °C, and E: 17.5 min) for which the CV's best adsorption capacity (294.12 mg/g) was recorded. The Freundlich and pseudo-second-order kinetic models were the best isotherm and kinetic models fitting our results. Furthermore, the study investigated the mechanisms responsible for eliminating CV by utilizing Kaol/Cel-25. It detected multiple types of associations, including electrostatic, n-π, dipole-dipole, hydrogen bonding interactions, and Yoshida hydrogen bonding. These findings suggest that Kaol/Cel could be a promising starting material for developing a highly efficient adsorbent that can remove cationic dyes from aqueous environments.
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Affiliation(s)
- Razika Mecheri
- Pollution & Waste Treatment Laboratory (PWTL), University of Ouargla, P.O. Box 511, Ouargla 30000, Algeria
| | - Ammar Zobeidi
- Pollution & Waste Treatment Laboratory (PWTL), University of Ouargla, P.O. Box 511, Ouargla 30000, Algeria
- Department of Chemistry, Faculty of Exact Sciences, University of El-Oued, P.O. Box 789, El-Oued 39000, Algeria
| | - Salem Atia
- Pollution & Waste Treatment Laboratory (PWTL), University of Ouargla, P.O. Box 511, Ouargla 30000, Algeria
| | - Salah Neghmouche Nacer
- Department of Chemistry, Faculty of Exact Sciences, University of El-Oued, P.O. Box 789, El-Oued 39000, Algeria
| | - Alsamani A M Salih
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
- Department of Chemical Engineering, Faculty of Engineering, Al Neelain University, Khartoum 12702, Sudan
| | - Mhamed Benaissa
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
| | - Djamel Ghernaout
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
- Chemical Engineering Department, Faculty of Engineering, University of Blida, Blida 09000, Algeria
| | - Saleh Al Arni
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
| | - Saad Ghareba
- Department of Chemical and Petroleum Engineering, University Elmergib, Al-Khums P.O. Box 40161, Libya
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, P.O. Box 2440, Ha'il 81441, Saudi Arabia
- Chemical Engineering Process Department, National School of Engineers Gabes, University of Gabes, Gabes 6029, Tunisia
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25
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Akl MA, El-Zeny AS, Hashem MA, El-Gharkawy ESRH, Mostafa AG. Flax fiber based semicarbazide biosorbent for removal of Cr(VI) and Alizarin Red S dye from wastewater. Sci Rep 2023; 13:8267. [PMID: 37217542 PMCID: PMC10203277 DOI: 10.1038/s41598-023-34523-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
In the present study, flax fiber based semicarbazide biosorbent was prepared in two successive steps. In the first step, flax fibers were oxidized using potassium periodate (KIO4) to yield diadehyde cellulose (DAC). Dialdehyde cellulose was, then, refluxed with semicarbazide.HCl to produce the semicarbazide functionalized dialdehyde cellulose (DAC@SC). The prepared DAC@SC biosorbent was characterized using Brunauer, Emmett and Teller (BET) and N2 adsorption isotherm, point of zero charge (pHPZC), elemental analysis (C:H:N), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analyses. The DAC@SC biosorbent was applied for the removal of the hexavalent chromium (Cr(VI)) ions and the alizarin red S (ARS) anionic dye (individually and in mixture). Experimental variables such as temperature, pH, and concentrations were optimized in detail. The monolayer adsorption capacities from the Langmuir isotherm model were 97.4 mg/g and 18.84 for Cr(VI) and ARS, respectively. The adsorption kinetics of DAC@SC indicated that the adsorption process fit PSO kinetic model. The obtained negative values of ΔG and ΔH indicated that the adsorption of Cr(VI) and ARS onto DAC@SC is a spontaneous and exothermic process. The DAC@SC biocomposite was successfully applied for the removal of Cr(VI) and ARS from synthetic effluents and real wastewater samples with a recovery (R, %) more than 90%. The prepared DAC@SC was regenerated using 0.1 M K2CO3 eluent. The plausible adsorption mechanism of Cr(VI) and ARS onto the surface of DAC@SC biocomposite was elucidated.
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Affiliation(s)
- Magda A Akl
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| | - Abdelrahman S El-Zeny
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mohamed A Hashem
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | | | - Aya G Mostafa
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
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26
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Deka JKR, Borah D, Das P, Sahariah B, Vishnoi P, Sarma BK. Synergistic n → π* and n N → π* Ar interactions in C-terminal modified prolines: effect on Xaa-Pro cis/ trans equilibrium. Chem Commun (Camb) 2023; 59:6080-6083. [PMID: 37128689 DOI: 10.1039/d3cc01494k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Carbonyl-carbonyl (CO⋯CO) n → π* interaction often coexists with a hydrogen bond (HB) or another n → π* interaction. Although the interplay between HB and n → π* interaction was previously studied, there is no systematic investigation that shows a synergistic relationship of n → π* with another noncovalent interaction. Herein, we have studied a set of proline-diacylhydrazine (Pro-DAH) molecules and observed that increase in the strength of the nN → π*Ar interaction on their DAH side strengthened the n → π* interaction on the Pro side, which was experimentally determined by measuring the Ktrans/cis of the Xaa-Pro amide bond. Overall, we describe a simple C-terminal modification strategy to stabilize the trans-Pro geometry that could be useful to stabilize PPII helices and collagen triple helices that require Pro to adopt the trans amide geometry.
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Affiliation(s)
- Jugal Kishore Rai Deka
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Debashree Borah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Paramesh Das
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Pratap Vishnoi
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India.
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27
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Panwaria P, Das A. Effect of Substituents on the Intramolecular n→π* Interaction in 3-[2-(Dimethylamino) phenyl] propanal: A Computational Study. J Phys Chem A 2023; 127:3339-3346. [PMID: 37036493 DOI: 10.1021/acs.jpca.2c08641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
n→π* non-covalent interaction (NCI) and hydrogen bond have similarity in terms of delocalization of the electron density between the two orbitals involved in the interaction. Hydrogen bond (X-H···Y) involves delocalization of the lone pair electrons (n) on the Y atom into the σ* orbital of the X-H bond. In contrast, the n→π* interaction deals with delocalizing the lone pair electrons (n) on the N, O, or S atom into the π* orbital of a C═O group or aromatic ring. Herein, we have shown a resemblance of this weak n→π* interaction with the relatively stronger hydrogen bond in terms of folding the side chains in flexible molecules. This work reports the study of folding of the flexible side-chain in 3-[2-(dimethylamino) phenyl] propanal (DMAPhP) through a N···C═O n→π* interaction using various computational approaches such as NBO, QTAIM, and NCI analyses. The folding of the molecule by the n→π* interaction observed in this study is found to be similar to that present in the secondary structures of peptides or proteins through hydrogen bonding interactions. Interestingly, the stabilization of the global minimum conformer of DMAPhP by the n→π* interaction demonstrates the importance of this NCI in providing conformational preferences in molecular systems. Another important finding of this study is that the theoretical redshift obtained in the C═O stretching frequency of the most stable conformer of the DMAPhP is contributed mostly by the n→π* interaction as the C═O group is not involved in hyperconjugation with any neighboring heteroatom, which is a common phenomenon in any ester or amide. We have also demonstrated here that the strength of the intramolecular n→π* interaction can be modulated by varying the electronic substituents at the para position of the donor group involved in the interaction.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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28
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Lindberg MF, Deau E, Arfwedson J, George N, George P, Alfonso P, Corrionero A, Meijer L. Comparative Efficacy and Selectivity of Pharmacological Inhibitors of DYRK and CLK Protein Kinases. J Med Chem 2023; 66:4106-4130. [PMID: 36876904 DOI: 10.1021/acs.jmedchem.2c02068] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Dual-specificity, tyrosine phosphorylation-regulated kinases (DYRKs) and cdc2-like kinases (CLKs) play a large variety of cellular functions and are involved in several diseases (cognitive disorders, diabetes, cancers, etc.). There is, thus, growing interest in pharmacological inhibitors as chemical probes and potential drug candidates. This study presents an unbiased evaluation of the kinase inhibitory activity of a library of 56 reported DYRK/CLK inhibitors on the basis of comparative, side-by-side, catalytic activity assays on a panel of 12 recombinant human kinases, enzyme kinetics (residence time and Kd), in-cell inhibition of Thr-212-Tau phosphorylation, and cytotoxicity. The 26 most active inhibitors were modeled in the crystal structure of DYRK1A. The results show a rather large diversity of potencies and selectivities among the reported inhibitors and emphasize the difficulties to avoid "off-targets" in this area of the kinome. The use of a panel of DYRKs/CLKs inhibitors is suggested to analyze the functions of these kinases in cellular processes.
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Affiliation(s)
| | - Emmanuel Deau
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Jonas Arfwedson
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Nicolas George
- Oncodesign, 25-27 avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Patricia Alfonso
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Ana Corrionero
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
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29
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Yin C, Lu H, Ye H, Feng Z, Zou H, Zhang M, You L. Double n→π* Interactions with One Electron Donor: Structural and Mechanistic Insights. Org Lett 2023; 25:1470-1475. [PMID: 36856609 DOI: 10.1021/acs.orglett.3c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Double n→π* interactions between one common electron donor of the carbonyl oxygen and two individual acceptor aldehyde/imine units are presented. The structural and mechanistic insights were revealed through a collection of experimental and computational evidence. The orientation and further energetic dependence of orbital interactions were facilely regulated by the size of cyclic urea scaffolds, the bulkiness of aldehydes/imines, and the flexibility of imine macrocycles.
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Affiliation(s)
- Chaowei Yin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanwei Lu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zelin Feng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Hanxun Zou
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Meilan Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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30
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Milašinović V, Vuković V, Krawczuk A, Molčanov K, Hennig C, Bodensteiner M. The nature of π-hole interactions between iodide anions and quinoid rings in the crystalline state. IUCRJ 2023; 10:156-163. [PMID: 36692857 PMCID: PMC9980391 DOI: 10.1107/s2052252523000052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The investigated co-crystal of 3-chloro-N-methylpyridinium iodide with tetrabromoquinone (3-Cl-N-MePy·I·Br4Q) reveals a π-hole interaction between an iodide anion and a quinoid ring involving an n → π* charge transfer. The quinoid ring has a partial negative charge (estimated to be in the range 0.08-0.11e) and a partial radical character, which is related to the black colour of the crystals (crystals of neutral tetrabromoquinone are yellow). A detailed X-ray charge density study revealed two symmetry-independent bond critical points between the iodide anions and carbon atoms of the ring. Their maximum electron density of 0.065 e Å-3 was reproduced by quantum chemical modelling. The energy of the interaction is estimated to be -11.16 kcal mol-1, which is comparable to the strength of moderate hydrogen bonding (about -10 kcal mol-1); it is dominantly electrostatic in nature, with a considerable dispersion component.
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Affiliation(s)
- Valentina Milašinović
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Vedran Vuković
- Universität Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Anna Krawczuk
- Institut für Anorganische Chemie, Universität Göttingen, Tammanstraβe 4, 37077 Göttingen, Germany
| | - Krešimir Molčanov
- Department of Physical Chemistry, Rudjer Bošković Institute, Bijenička 54, Zagreb 10000, Croatia
| | - Christoph Hennig
- The Rossendorf Beamline (BM20), European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble 38043, France
- Institute of Resource Ecology, Helmholz Zentrum Dresden Rosendorf, Bauztner Landstrasse 400, 01328 Dresden, Germany
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31
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Shkurenko A. The dominant component of strong π-hole interactions: electrostatic attraction versus charge transfer. IUCRJ 2023; 10:145-146. [PMID: 36862487 PMCID: PMC9980390 DOI: 10.1107/s2052252523001720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A long-asked question concerning the dominant component of strong π-hole interactions is addressed.
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Affiliation(s)
- Aleksander Shkurenko
- Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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32
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Zhu J, Wang XD, Ao YF, Wang QQ, Wang DX. Intermolecular n→π* Interactions Based on a Tailored Multicarbonyl-Containing Macrocycle. Chemistry 2023; 29:e202203485. [PMID: 36445795 DOI: 10.1002/chem.202203485] [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: 11/09/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Towards unexplored intermolecular n→π* interactions, presented herein are the synthesis, structure, self-assembly and function of a multicarbonyl-containing macrocycle calix[2]arene[2]barbiturate 1. X-ray single crystal diffraction reveals the presence of Cl⋅⋅⋅C=O interactions in CH2 Cl2 ⊂1 host-guest complex and multiple intermolecular C=O⋅⋅⋅C=O interactions between molecules 1 in crystalline state. The intermolecular C=O⋅⋅⋅C=O interactions as attractive driving force led to unprecedented self-assembly of nanotube with diameter around 1.4 nm and inner surface engineered by aromatic rings. SEM and TEM images of the self-assembly of 1 demonstrated temperature-dependent morphologies which allows the observation of spheres at 25 °C and rods at 0 °C, respectively. XRD analysis indicated consistent hexagonal patterns in the self-assembly and single crystal lattice, indicating the nanotubes driven by C=O⋅⋅⋅C=O interactions constitute the basic structural architectures of both aggregates. The nanoscopic tubes (pores) formed in the rodlike single crystal engendering the separation of moving dyes were preliminarily investigated by a single-crystal chromatography and crystal-packed column chromatography.
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Affiliation(s)
- Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
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33
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Hiew SH, Lu Y, Han H, Gonçalves RA, Alfarano SR, Mezzenga R, Parikh AN, Mu Y, Miserez A. Modulation of Mechanical Properties of Short Bioinspired Peptide Materials by Single Amino-Acid Mutations. J Am Chem Soc 2023; 145:3382-3393. [PMID: 36730942 DOI: 10.1021/jacs.2c09853] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The occurrence of modular peptide repeats in load-bearing (structural) proteins is common in nature, with distinctive peptide sequences that often remain conserved across different phylogenetic lineages. These highly conserved peptide sequences endow specific mechanical properties to the material, such as toughness or elasticity. Here, using bioinformatic tools and phylogenetic analysis, we have identified the GX8 peptide with the sequence GLYGGYGX (where X can be any residue) in a wide range of organisms. By simple mutation of the X residue, we demonstrate that GX8 can be self-assembled into various supramolecular structures, exhibiting vastly different physicochemical and viscoelastic properties, from liquid-like coacervate microdroplets to hydrogels to stiff solid materials. A combination of spectroscopic, electron microscopy, mechanical, and molecular dynamics studies is employed to obtain insights into molecular scale interactions driving self-assembly of GX8 peptides, underscoring that π-π stacking and hydrophobic interactions are the drivers of peptide self-assembly, whereas the X residue determines the extent of hydrogen bonding that regulates the macroscopic mechanical response. This study highlights the ability of single amino-acid polymorphism to tune the supramolecular assembly and bulk material properties of GX8 peptides, enabling us to cover a broad range of potential biomedical applications such as hydrogels for tissue engineering or coacervates for drug delivery.
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Affiliation(s)
- Shu Hui Hiew
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yang Lu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Hao Han
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Rui A Gonçalves
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Serena Rosa Alfarano
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Zürich 8092, Switzerland
| | - Atul N Parikh
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,Departments of Biomedical Engineering and Materials Science & Engineering, University of California, Davis, California 95616, United States
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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34
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Villaseñor-Granados TO, Sánchez-Ruiz SA, Rojas-Sáenz HJ, Flores-Parra A. New 1,3,5-dithiazinanes bearing β-alcohol or β-sulphonates chains at C2. Non classical S→phenyl and S→C interactions. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134388] [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]
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35
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Tominaga M, Nanbara S, Hyodo T, Kawahata M, Yamaguchi K. Orientation of carbonyl groups in inclusion crystals formed from ketones with aromatic diimide-based macrocycles. CrystEngComm 2023. [DOI: 10.1039/d2ce01641a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Inclusion crystals were formed from ketones with aromatic diimide-based macrocycles possessing adamantane units, where the oxygen atoms of guests interacted with the electron-deficient π-surfaces of the aromatic diimides through CO⋯π contacts.
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Affiliation(s)
- Masahide Tominaga
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
| | - Sakito Nanbara
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
| | - Tadashi Hyodo
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
| | | | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
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36
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Panwaria P, Juanes M, Mishra KK, Saragi R, Borish K, Usabiaga I, Camiruaga A, Fernández JA, Lesarri A, Das A. Microhydration of Phenyl Formate: Gas-Phase Laser Spectroscopy, Microwave Spectroscopy, and Quantum Chemistry Calculations. Chemphyschem 2022; 23:e202200330. [PMID: 35984348 DOI: 10.1002/cphc.202200330] [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: 05/13/2022] [Revised: 08/17/2022] [Indexed: 01/04/2023]
Abstract
Herein, we have investigated the structure of phenyl formate⋅⋅⋅water (PhOF⋅⋅⋅H2 O) dimer and various non-covalent interactions present there using gas-phase laser spectroscopy and microwave spectroscopy combined with quantum chemistry calculations. Two conformers of PhOF⋅⋅⋅H2 O (C1 and T1), built on the two cis/trans conformers of the bare molecule, have been observed in the experiment. In cis-PhOF, there is an nCO → π A r * ${{{\rm \pi }}_{{\rm A}{\rm r}}^{{\rm {^\ast}}}}$ interaction between the lone-pair orbital of the carbonyl oxygen atom and the π* orbital of the phenyl ring, which persists in the monohydrated C1 conformer of PhOF⋅⋅⋅H2 O according to the NBO and NCI analyses. On the other hand, this interaction is absent in the trans-PhOF conformer as the C=O group is away from the phenyl ring. The C1 conformer is primarily stabilized by an interplay between O-H⋅⋅⋅O=C hydrogen bond and O-H⋅⋅⋅π interactions, while the stability of the T1 conformer is primarily governed by the O-H⋅⋅⋅O=C hydrogen bond. The most important finding of the present work is that the conformational preference of the PhOF monomer is retained in its monohydrated complex.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.,Present address: Department of Chemistry, University of Kentucky, Lexington, Kentucky, 40503, USA
| | - Rizalina Saragi
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Imanol Usabiaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Ander Camiruaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias-I.U. CINQUIMA, Universidad de Valladolid, Paseo de Belén, 7, 47011, Valladolid, Spain
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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37
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Dutta J, Routray C, Pandey S, Biswal HS. Intermolecular noncovalent interactions with carbon in solution. Chem Sci 2022; 13:14327-14335. [PMID: 36545132 PMCID: PMC9749111 DOI: 10.1039/d2sc05431k] [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: 09/29/2022] [Accepted: 11/20/2022] [Indexed: 11/22/2022] Open
Abstract
One of the most familiar carbon-centered noncovalent interactions (NCIs) involving an antibonding π*-orbital situated at the Bürgi-Dunitz angle from the electron donor, mostly lone pairs of electrons, is known as n → π* interactions, and if it involves a σ* orbital in a linear fashion, then it is known as the carbon bond. These NCIs can be intra- or inter-molecular and are usually weak in strength but have a paramount effect on the structure and function of small-molecular crystals and proteins. Surprisingly, the experimental evidence of such interactions in the solution phase is scarce. It is even difficult to determine the interaction energy in the solution. Using NMR spectroscopy aided with molecular dynamics (MD) simulation and high-level quantum mechanical calculations, herein we provide the experimental evidence of intermolecular carbon-centered NCIs in solution. The challenge was to find appropriate heterodimers that could sustain room temperature thermal energy and collisions from the solvent molecules. However, after several trial model compounds, the pyridine-N-oxide:dimethyltetracyanocyclopropane (PNO-DMTCCP) complex was found to be a good candidate for the investigation. NBO analyses show that the PNO:DMTCCP complex is stabilized mainly by intermolecular n → π* interaction when a weaker carbon bond gives extra stability to the complex. From the NMR study, it is observed that the NCIs between DMTCCP and PNO are enthalpy driven with an enthalpy change of -28.12 kJ mol-1 and dimerization energy of ∼-38 kJ mol-1 is comparable to the binding energies of a conventional hydrogen-bonded dimer. This study opens up a new strategy to investigate weak intermolecular interactions such as n → π* interaction and carbon bonds in the solution phase.
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Affiliation(s)
- Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Chinmay Routray
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Shalini Pandey
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO - Bhimpur-Padanpur, Via-Jatni, District - Khurda PIN - 752050 Bhubaneswar India +91-674-2494-185, +91-674-2494-186
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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38
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Acharige UAI, Saunders GC. The Influence of the Halide in the Crystal Structures of 1-(2,3,5,6-Tetrafluoro-4-pyridyl)-3-benzylimidazolium Halides. Molecules 2022; 27:molecules27217634. [PMID: 36364461 PMCID: PMC9656857 DOI: 10.3390/molecules27217634] [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: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022] Open
Abstract
The crystal structures of 1-(2,3,5,6-tetrafluoro-4-pyridyl)-3-benzylimidazolium chloride (1) and iodide (3) have been determined by single crystal X-ray diffraction. The crystal structure of 1 is similar to that of the bromide salt (2), possessing anion···C5F5N···C6H5 motifs, whilst that of 3 contains columns of alternating iodide anions and parallel tetrafluoropyridyl rings. All three crystal structures possess C(1)−H∙∙∙X− and C(2)−H∙∙∙X− hydrogen bonding. DFT calculations reveal that the strengths of the hydrogen bonding interactions lie in the order C(1)−H···X− > C(3)−H···X− > C(2)−H···X− for the same halide (X−) and Cl− > Br− > I− for each position. It is suggested that salt 3 adopts a different structure to salts 1 and 2 because of the larger size of iodide.
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39
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Chakraborty J. An account of noncovalent interactions in homoleptic palladium(II) and platinum(II) complexes within the DFT framework: A correlation between geometries, energy components of symmetry-adapted perturbation theory and NCI descriptors. Heliyon 2022; 8:e11408. [DOI: 10.1016/j.heliyon.2022.e11408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/26/2022] [Accepted: 10/31/2022] [Indexed: 11/10/2022] Open
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40
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Xu EY, Werth J, Roos CB, Bendelsmith AJ, Sigman MS, Knowles RR. Noncovalent Stabilization of Radical Intermediates in the Enantioselective Hydroamination of Alkenes with Sulfonamides. J Am Chem Soc 2022; 144:18948-18958. [PMID: 36197450 PMCID: PMC9668373 DOI: 10.1021/jacs.2c07099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Noncovalent interactions (NCIs) are critical elements of molecular recognition in a wide variety of chemical contexts. While NCIs have been studied extensively for closed-shell molecules and ions, very little is understood about the structures and properties of NCIs involving free radical intermediates. In this report, we describe a detailed mechanistic study of the enantioselective radical hydroamination of alkenes with sulfonamides and present evidence suggesting that the basis for asymmetric induction in this process arises from attractive NCIs between a neutral sulfonamidyl radical intermediate and a chiral phosphoric acid (CPA). We describe experimental, computational, and data science-based evidence that identifies the specific radical NCIs that form the basis for the enantioselectivity. Kinetic studies support that C-N bond formation determines the enantioselectivity. Density functional theory investigations revealed the importance of both strong H-bonding between the CPA and the N-centered radical and a network of aryl-based NCIs that serve to stabilize the favored diastereomeric transition state. The contributions of these specific aryl-based NCIs to the selectivity were further confirmed through multivariate linear regression analysis by comparing the measured enantioselectivity to computed descriptors. These results highlight the power of NCIs to enable high levels of enantioselectivity in reactions involving uncharged open-shell intermediates and expand our understanding of radical-molecule interactions.
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Affiliation(s)
- Eve Y. Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey, 08544, United States
| | - Jacob Werth
- Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112, United States
| | - Casey B. Roos
- Department of Chemistry, Princeton University, Princeton, New Jersey, 08544, United States
| | - Andrew J. Bendelsmith
- Department of Chemistry, Princeton University, Princeton, New Jersey, 08544, United States
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, Salt Lake City, Utah, 84112, United States
| | - Robert R. Knowles
- Department of Chemistry, Princeton University, Princeton, New Jersey, 08544, United States
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41
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In silico Study of Conjugated Nitrogen Heterocycles Affinity in their Biological Complexes. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03107-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
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42
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Isomeric effect in structural studies of substituted nitro hydroxy-3-methoxy-benzaldehyde and nitro 2,3-dimethoxy-benzaldehyde derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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43
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Harry SA, Kazim M, Nguyen PM, Zhu A, Xiang MR, Catazaro J, Siegler M, Lectka T. The Close Interaction of a C-F Bond with an Amide Carbonyl: Crystallographic and Spectroscopic Characterization. Angew Chem Int Ed Engl 2022; 61:e202207966. [PMID: 35716396 PMCID: PMC9544880 DOI: 10.1002/anie.202207966] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/26/2022]
Abstract
The putative interaction of a C−F bond with an amide carbonyl has been an intriguing topic of interest in this century for reasons spanning basic physical organic chemistry to biochemistry. However, to date, there exist no examples of a close, well‐defined interaction in which its unique aspects can be identified and exploited. Herein, we finally present an engineered system possessing an exceptionally tight C−F‐amide interaction, allowing us to obtain spectroscopic, crystallographic, and kinetic details of a distinctive, biochemically relevant chemical system for the first time. In turn, we also explore Lewis acid coordination, C−F bond promotion of amide isomerization, enantiomerization, and ion protonation processes.
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Affiliation(s)
- Stefan Andrew Harry
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Muhammad Kazim
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Phuong Minh Nguyen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | | | - Michael Richard Xiang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Jonathan Catazaro
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Maxime Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
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44
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Flavin-enabled reductive and oxidative epoxide ring opening reactions. Nat Commun 2022; 13:4896. [PMID: 35986005 PMCID: PMC9391479 DOI: 10.1038/s41467-022-32641-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/08/2022] [Indexed: 12/23/2022] Open
Abstract
Epoxide ring opening reactions are common and important in both biological processes and synthetic applications and can be catalyzed in a non-redox manner by epoxide hydrolases or reductively by oxidoreductases. Here we report that fluostatins (FSTs), a family of atypical angucyclines with a benzofluorene core, can undergo nonenzyme-catalyzed epoxide ring opening reactions in the presence of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NADH). The 2,3-epoxide ring in FST C is shown to open reductively via a putative enol intermediate, or oxidatively via a peroxylated intermediate with molecular oxygen as the oxidant. These reactions lead to multiple products with different redox states that possess a single hydroxyl group at C-2, a 2,3-vicinal diol, a contracted five-membered A-ring, or an expanded seven-membered A-ring. Similar reactions also take place in both natural products and other organic compounds harboring an epoxide adjacent to a carbonyl group that is conjugated to an aromatic moiety. Our findings extend the repertoire of known flavin chemistry that may provide new and useful tools for organic synthesis. Epoxide ring opening reactions are important in both biological processes and synthetic applications. Here, the authors show that flavin cofactors can catalyze reductive and oxidative epoxide ring opening reactions and propose the underlying mechanisms.
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Panwaria P, Das A. Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches. Phys Chem Chem Phys 2022; 24:22371-22389. [PMID: 35822956 DOI: 10.1039/d2cp02070j] [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
Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.
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Affiliation(s)
- Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India.
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46
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Harry SA, Kazim M, Nguyen PM, Zhu A, Xiang MR, Catazaro J, Siegler M, Lectka T. The Close Interaction of a C‐F Bond with an Amide Carbonyl: Crystallographic and Spectroscopic Characterization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207966] [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)
- Stefan Andrew Harry
- Johns Hopkins University Chemistry 3400 n Charles 21212 Baltimore UNITED STATES
| | | | | | - Andrea Zhu
- Johns Hopkins University chemistry UNITED STATES
| | | | | | | | - Thomas Lectka
- Johns Hopkins University Chemistry 3400 N. Charles Street 21218-2685 Baltimore UNITED STATES
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47
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Jena S, Dutta J, Tulsiyan KD, Sahu AK, Choudhury SS, Biswal HS. Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking. Chem Soc Rev 2022; 51:4261-4286. [PMID: 35560317 DOI: 10.1039/d2cs00133k] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Shubhranshu Shekhar Choudhury
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050, Bhubaneswar, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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48
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O‧‧‧C═O interaction, its occurrence and implications for protein structure and folding. Proteins 2022; 90:1159-1169. [DOI: 10.1002/prot.26298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/07/2022]
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49
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Wang Y, Pigeon P, Li W, Yan J, Dansette PM, Othman M, McGlinchey MJ, Jaouen G. Diversity-oriented synthesis and bioactivity evaluation of N-substituted ferrocifen compounds as novel antiproliferative agents against TNBC cancer cells. Eur J Med Chem 2022; 234:114202. [DOI: 10.1016/j.ejmech.2022.114202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
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50
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Tominaga M, Kondo S, Hyodo T, Kawahata M, Yamaguchi K. Structure analysis of inclusion crystals of diimide-based macrocycles with halocarbons. CrystEngComm 2022. [DOI: 10.1039/d2ce00118g] [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
Inclusion crystals containing several halocarbons were formed by three types of diimide-based macrocycles. Iodomethane was encapsulated within the cavity of the macrocycle through halogen-related interactions.
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Affiliation(s)
- Masahide Tominaga
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
| | - Sana Kondo
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
| | - Tadashi Hyodo
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
| | | | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Sanuki, Kagawa 769-2193, Japan
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