1
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Ge K, Shao H, Raymundo-Piñero E, Taberna PL, Simon P. Cation desolvation-induced capacitance enhancement in reduced graphene oxide (rGO). Nat Commun 2024; 15:1935. [PMID: 38431624 PMCID: PMC10908864 DOI: 10.1038/s41467-024-46280-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Understanding the local electrochemical processes is of key importance for efficient energy storage applications, including electrochemical double layer capacitors. In this work, we studied the charge storage mechanism of a model material - reduced graphene oxide (rGO) - in aqueous electrolyte using the combination of cavity micro-electrode, operando electrochemical quartz crystal microbalance (EQCM) and operando electrochemical dilatometry (ECD) tools. We evidence two regions with different charge storage mechanisms, depending on the cation-carbon interaction. Notably, under high cathodic polarization (region II), we report an important capacitance increase in Zn2+ containing electrolyte with minimum volume expansion, which is associated with Zn2+ desolvation resulting from strong electrostatic Zn2+-rGO interactions. These results highlight the significant role of ion-electrode interaction strength and cation desolvation in modulating the charging mechanisms, offering potential pathways for optimized capacitive energy storage. As a broader perspective, understanding confined electrochemical systems and the coupling between chemical, electrochemical and transport processes in confinement may open tremendous opportunities for energy, catalysis or water treatment applications in the future.
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Affiliation(s)
- Kangkang Ge
- Université Paul Sabatier, CIRIMAT UMR CNRS 5085, 118 Route de Narbonne, 31062, Toulouse, France
| | - Hui Shao
- i-Lab, CAS Center for Excellence in Nanoscience, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences (CAS), Suzhou, 215123, China
| | - Encarnacion Raymundo-Piñero
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, Amiens, France
- Université Orléans, CNRS, CEMHTI UPR3079, Orléans, France
| | - Pierre-Louis Taberna
- Université Paul Sabatier, CIRIMAT UMR CNRS 5085, 118 Route de Narbonne, 31062, Toulouse, France.
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, Amiens, France.
| | - Patrice Simon
- Université Paul Sabatier, CIRIMAT UMR CNRS 5085, 118 Route de Narbonne, 31062, Toulouse, France.
- Réseau sur le Stockage Electrochimique de l'Energie (RS2E), FR CNRS 3459, Amiens, France.
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2
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Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [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: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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3
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de Souza Neto LR, Montoya BO, Brandão-Neto J, Verma A, Bowyer S, Moreira-Filho JT, Dantas RF, Neves BJ, Andrade CH, von Delft F, Owens RJ, Furnham N, Silva-Jr FP. Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni. Sci Rep 2024; 14:1582. [PMID: 38238498 PMCID: PMC10796382 DOI: 10.1038/s41598-024-52018-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Schistosomiasis is caused by parasites of the genus Schistosoma, which infect more than 200 million people. Praziquantel (PZQ) has been the main drug for controlling schistosomiasis for over four decades, but despite that it is ineffective against juvenile worms and size and taste issues with its pharmaceutical forms impose challenges for treating school-aged children. It is also important to note that PZQ resistant strains can be generated in laboratory conditions and observed in the field, hence its extensive use in mass drug administration programs raises concerns about resistance, highlighting the need to search for new schistosomicidal drugs. Schistosomes survival relies on the redox enzyme thioredoxin glutathione reductase (TGR), a validated target for the development of new anti-schistosomal drugs. Here we report a high-throughput fragment screening campaign of 768 compounds against S. mansoni TGR (SmTGR) using X-ray crystallography. We observed 49 binding events involving 35 distinct molecular fragments which were found to be distributed across 16 binding sites. Most sites are described for the first time within SmTGR, a noteworthy exception being the "doorstop pocket" near the NADPH binding site. We have compared results from hotspots and pocket druggability analysis of SmTGR with the experimental binding sites found in this work, with our results indicating only limited coincidence between experimental and computational results. Finally, we discuss that binding sites at the doorstop/NADPH binding site and in the SmTGR dimer interface, should be prioritized for developing SmTGR inhibitors as new antischistosomal drugs.
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Affiliation(s)
- Lauro Ribeiro de Souza Neto
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bogar Omar Montoya
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - José Brandão-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
| | - Anil Verma
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sebastian Bowyer
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - José Teófilo Moreira-Filho
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Rafael Ferreira Dantas
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
- CRAFT - Center for Research and Advancement of Fragments and Molecular Targets, University of São Paulo, São Paulo, Brazil
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Structural Biology, Rosalind Franklin Institute, Harwell, UK.
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Floriano Paes Silva-Jr
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
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4
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Carter-Fenk K, Liu M, Pujal L, Loipersberger M, Tsanai M, Vernon RM, Forman-Kay JD, Head-Gordon M, Heidar-Zadeh F, Head-Gordon T. The Energetic Origins of Pi-Pi Contacts in Proteins. J Am Chem Soc 2023; 145. [PMID: 37917924 PMCID: PMC10655088 DOI: 10.1021/jacs.3c09198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein's stability and structure. Pi-pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi-pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi-pi contact motifs. We find that neutral pi-pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter-Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi-pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi-pi contacts in polar media and like typical ion-pi interactions in nonpolar environments. Like-charged pairs such as arginine-arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi-pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.
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Affiliation(s)
- Kevin Carter-Fenk
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Meili Liu
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Leila Pujal
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Loipersberger
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Maria Tsanai
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert M. Vernon
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Julie D. Forman-Kay
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Martin Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Farnaz Heidar-Zadeh
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Center
for Molecular Modeling (CMM), Ghent University, 9052 Zwijnaarde, Belgium
| | - Teresa Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
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5
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Wei Y, Xin D, Tie S, Yang N, Yuan R, Zheng X. Additive-Induced Synergies of Ion Migration Inhibition and Defect Passivation toward Sensitive Perovskite X-ray Detectors. J Phys Chem Lett 2023; 14:3313-3319. [PMID: 36988394 DOI: 10.1021/acs.jpclett.3c00563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Two-dimensional (2D) Ruddlesden-Popper (RP) metal halide perovskites have emerged as a promising material for X-ray detection. However, defects and ion migration generated nonradiative recombination and high dark current could cause severe performance degradation, which hinders their application. Herein, rubrene was added to the precursor solution of BA2MA3Pb4I13 to modulate the performance of the 2D RP perovskite X-ray detectors. The cation-π interaction between rubrene and perovskite could passivate the defects and inhibit the ion migration, resulting in improved performance and stability. The detectors made with rubrene exhibited a sensitivity of 354.30 μC·Gyair-1 cm-2 and a detection limit of 112.85 nGyair s-1. This work highlights the synergistic effect of rubrene in defect passivation and ion migration inhibition, providing a facile approach toward sensitive perovskite X-ray detectors.
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Affiliation(s)
- Yazhou Wei
- Institute of Chemical Materials, China Academy of Engineering Physics, Mianyang 621900, China
| | - Deyu Xin
- Institute of Chemical Materials, China Academy of Engineering Physics, Mianyang 621900, China
| | - Shujie Tie
- Institute of Chemical Materials, China Academy of Engineering Physics, Mianyang 621900, China
| | - Ning Yang
- Institute of Chemical Materials, China Academy of Engineering Physics, Mianyang 621900, China
| | - Ruihan Yuan
- Institute of Chemical Materials, China Academy of Engineering Physics, Mianyang 621900, China
- Sichuan Research Center of New Materials, Chengdu 610200, China
| | - Xiaojia Zheng
- Institute of Chemical Materials, China Academy of Engineering Physics, Mianyang 621900, China
- Sichuan Research Center of New Materials, Chengdu 610200, China
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6
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Di W, Xue K, Cai J, Zhu Z, Li Z, Fu H, Lei H, Hu W, Tang C, Wang W, Cao Y. Single-Molecule Force Spectroscopy Reveals Cation-π Interactions in Aqueous Media Are Highly Affected by Cation Dehydration. PHYSICAL REVIEW LETTERS 2023; 130:118101. [PMID: 37001074 DOI: 10.1103/physrevlett.130.118101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/24/2023] [Indexed: 06/19/2023]
Abstract
Cation-π interactions underlie many important processes in biology and materials science. However, experimental investigations of cation-π interactions in aqueous media remain challenging. Here, we studied the cation-π binding strength and mechanism by pulling two hydrophobic polymers with distinct cation binding properties, i.e., poly-pentafluorostyrene and polystyrene, in aqueous media using single-molecule force spectroscopy and nuclear magnetic resonance measurement. We found that the interaction strengths linearly depend on the cation concentrations, following the order of Li^{+}<NH_{4}^{+}<Na^{+}<K^{+}. The binding energies are 0.03-0.23 kJ mol^{-1} M^{-1}. This order is distinct from the strength of cation-π interactions in gas phase and may be caused by the different dehydration ability of the cations. Taken together, our method provides a unique perspective to investigate cation-π interactions under physiologically relevant conditions.
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Affiliation(s)
- Weishuai Di
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Kai Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- School of Physical and Mathematical Science Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Jun Cai
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Zhenshu Zhu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Zihan Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Fu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wenbing Hu
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Wenzhou Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Institute for Brain Sciences, Nanjing University, Nanjing 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210093, China
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7
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da Silva GCQ, Simon JM, Salazar JM. When less is more: does more Na +-cations mean more adsorption sites for toluene in faujasites? Phys Chem Chem Phys 2023; 25:8028-8042. [PMID: 36876505 DOI: 10.1039/d2cp04644j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The unique properties of zeolites make them an interesting material to be used in separation processes. The possibility of tailoring some of their characteristics, like the Si/Al ratio, allows optimizing their synthesis for a given task. Concerning the adsorption of toluene by faujasites an understanding of the effect of cations is necessary to foster the elaboration of new materials, which can capture molecules with a high degree of selectivity and sensitivity. Undoubtedly, this knowledge is relevant for a wide range of applications going from the elaboration of technologies for improving the air-quality to diagnostic procedures to prevent health risks. The studies reported here using Grand Canonical Monte Carlo simulations elucidate the role of Na-cations in the adsorption of toluene by faujasites with different Si/Al ratios. They detail how the location of the cations inhibits or enhances the adsorption. The cations located at site II are shown to be those enhancing the adsorption of toluene on faujasites. Interestingly, the cations located at site III generate a hindrance at high loading. This becomes an impediment for the organization of toluene molecules inside faujasites.
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Affiliation(s)
- G C Q da Silva
- Laboratoire ICB UMR 6303, Université Bourgogne Franche-Comté, 21078 Dijon, France.
| | - J M Simon
- Laboratoire ICB UMR 6303, Université Bourgogne Franche-Comté, 21078 Dijon, France.
| | - J Marcos Salazar
- Laboratoire ICB UMR 6303, Université Bourgogne Franche-Comté, 21078 Dijon, France.
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8
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Harnessing the cation-π interactions of metalated gold monolayer-protected clusters to detect aromatic volatile organic compounds. Talanta 2023; 253:123915. [PMID: 36155323 DOI: 10.1016/j.talanta.2022.123915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/18/2022] [Accepted: 09/02/2022] [Indexed: 12/13/2022]
Abstract
The strong, non-covalent interactions between π-systems and cations have been the focus of numerous studies on biomolecule structure and catalysis. These interactions, however, have yet to be explored as a sensing mechanism for detecting trace levels of volatile organic compounds (VOCs). In this article, we provide evidence that cation-π interactions can be used to elicit sensitive and selective chemiresistor responses to aromatic VOCs. The chemiresistors are fitted with carboxylate-linked alkali metals bound to the surface of gold monolayer-protected clusters formulated on microfabricated interdigitated electrodes. Sensor responses to aromatic and non-aromatic VOCs are consistent with a model for cation-π interactions arising from association of electron-rich aromatic π-systems to metal ions with the relative strength of attraction following the order K+ > Na+ > Li+. The results point toward cation-π interactions as a promising research avenue to explore for developing aromatic VOC-selective sensors.
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9
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Dalle Vedove A, Cazzanelli G, Batiste L, Marchand JR, Spiliotopoulos D, Corsi J, D’Agostino VG, Caflisch A, Lolli G. Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. ACS Med Chem Lett 2022; 13:1434-1443. [PMID: 36105334 PMCID: PMC9465710 DOI: 10.1021/acsmedchemlett.2c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
![]()
BAZ2A is an epigenetic regulator affecting transcription
of ribosomal
RNA. It is overexpressed in aggressive and recurrent prostate cancer,
promoting cellular migration. Its bromodomain is characterized by
a shallow and difficult-to-drug pocket. Here, we describe a structure-based
fragment-growing campaign for the identification of ligands of the
BAZ2A bromodomain. By combining docking, competition binding assays,
and protein crystallography, we have extensively explored the interactions
of the ligands with the rim of the binding pocket, and in particular
ionic interactions with the side chain of Glu1820, which is unique
to BAZ2A. We present 23 high-resolution crystal structures of the
holo BAZ2A bromodomain and analyze common bromodomain/ligand motifs
and favorable intraligand interactions. Binding of some of the compounds
is enantiospecific, with affinity in the low micromolar range. The
most potent ligand has an equilibrium dissociation constant of 7 μM
and a good selectivity over the paralog BAZ2B bromodomain.
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Affiliation(s)
- Andrea Dalle Vedove
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, via Sommarive 9, 38123 Povo - Trento, Italy
| | - Giulia Cazzanelli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, via Sommarive 9, 38123 Povo - Trento, Italy
| | - Laurent Batiste
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jessica Corsi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, via Sommarive 9, 38123 Povo - Trento, Italy
| | - Vito Giuseppe D’Agostino
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, via Sommarive 9, 38123 Povo - Trento, Italy
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Graziano Lolli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, via Sommarive 9, 38123 Povo - Trento, Italy
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10
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Leferink NGH, Escorcia AM, Ouwersloot BR, Johanissen LO, Hay S, van der Kamp MW, Scrutton NS. Molecular Determinants of Carbocation Cyclisation in Bacterial Monoterpene Synthases. Chembiochem 2022; 23:e202100688. [PMID: 35005823 PMCID: PMC9303655 DOI: 10.1002/cbic.202100688] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Indexed: 11/24/2022]
Abstract
Monoterpene synthases are often promiscuous enzymes, yielding product mixtures rather than pure compounds due to the nature of the branched reaction mechanism involving reactive carbocations. Two previously identified bacterial monoterpene synthases, a linalool synthase (bLinS) and a cineole synthase (bCinS), produce nearly pure linalool and cineole from geranyl diphosphate, respectively. We used a combined experimental and computational approach to identify critical residues involved in bacterial monoterpenoid synthesis. Phe77 is essential for bCinS activity, guiding the linear carbocation intermediate towards the formation of the cyclic α-terpinyl intermediate; removal of the aromatic ring results in variants that produce acyclic products only. Computational chemistry confirmed the importance of Phe77 in carbocation stabilisation. Phe74, Phe78 and Phe179 are involved in maintaining the active site shape in bCinS without a specific role for the aromatic ring. Phe295 in bLinS, and the equivalent Ala301 in bCinS, are essential for linalool and cineole formation, respectively. Where Phe295 places steric constraints on the carbocation intermediates, Ala301 is essential for bCinS initial cyclisation and activity. Our multidisciplinary approach gives unique insights into how carefully placed amino acid residues in the active site can direct carbocations down specific paths, by placing steric constraints or offering stabilisation via cation-π interactions.
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Affiliation(s)
- Nicole G H Leferink
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Bodi R Ouwersloot
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Linus O Johanissen
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Marc W van der Kamp
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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11
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Prediction of molecular interactions and physicochemical properties relevant for vasopressin V2 receptor antagonism. J Mol Model 2022; 28:31. [PMID: 34997307 DOI: 10.1007/s00894-021-05022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
We have developed two ligand- and receptor-based computational approaches to study the physicochemical properties relevant to the biological activity of vasopressin V2 receptor (V2R) antagonist and eventually to predict the expected binding mode to V2R. The obtained quantitative structure activity relationship (QSAR) model showed a correlation of the antagonist activity with the hydration energy (EH2O), the polarizability (P), and the calculated partial charge on atom N7 (q6) of the common substructure. The first two descriptors showed a positive contribution to antagonist activity, while the third one had a negative contribution. V2R was modeled and further relaxed on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocoline (POPC) membrane by molecular dynamics simulations. The receptor antagonist complexes were guessed by molecular docking, and the stability of the most relevant structures was also evaluated by molecular dynamics simulations. As a result, amino acid residues Q96, W99, F105, K116, F178, A194, F307, and M311 were identified with the probably most relevant antagonist-receptor interactions on the studied complexes. The proposed QSAR model could explain the molecular properties relevant to the antagonist activity. The contributions to the antagonist-receptor interaction appeared also in agreement with the binding mode of the complexes obtained by molecular docking and molecular dynamics. These models will be used in further studies to look for new V2R potential antagonist molecules.
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12
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Sparrow ZM, Ernst BG, Joo PT, Lao KU, DiStasio RA. NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts. J Chem Phys 2021; 155:184303. [PMID: 34773949 DOI: 10.1063/5.0068862] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (Eint) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The Eint values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) Eint value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the Eint values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive Eint values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.
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Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Paul T Joo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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13
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Zhou X, Malakar S, Dugan T, Wang K, Sattler A, Marler DO, Emge TJ, Krogh-Jespersen K, Goldman AS. Alkane Dehydrogenation Catalyzed by a Fluorinated Phebox Iridium Complex. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Xiaoguang Zhou
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, United States
| | - Santanu Malakar
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, United States
| | - Thomas Dugan
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, United States
| | - Kun Wang
- ExxonMobil Research and Engineering, Annandale, New Jersey 08801, United States
| | - Aaron Sattler
- ExxonMobil Research and Engineering, Annandale, New Jersey 08801, United States
| | - David O. Marler
- ExxonMobil Research and Engineering, Annandale, New Jersey 08801, United States
| | - Thomas J. Emge
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, United States
| | - Karsten Krogh-Jespersen
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, United States
| | - Alan S. Goldman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, United States
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14
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Mkhadder H, Denis M, Giménez-Marqués M, Cañón-Mancisidor W, Humbert B, Deunf E, Poizot P, Devic T. A tris-oxovanadium pyrogallate complex: synthesis, structure, and magnetic and electronic properties. Dalton Trans 2021; 50:13399-13406. [PMID: 34473151 DOI: 10.1039/d1dt01990b] [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
With the aim of identifying new cation-phenolate complexes, we herein investigated the reactivity of pyrogallol (H3pgal) with vanadium salts. A trimetallic anionic complex was identified, and found to be formed under a broad set of reaction conditions. This complex, with the formula V3O3(pgal)33-, consists of three oxovanadium(IV) units connected together by three pyrogallate ligands to afford a bowl-shaped species presenting a pseudo 3-fold symmetry axis. Its crystal structure is reported, as well as its characterisation by a broad set of techniques, including powder X-ray diffraction, thermogravimetric analysis, infrared and Raman spectroscopy, and solid state UV-visible diffuse reflectance. Its redox activity both in solution and in the solid state is described, together with its magnetic behavior. Finally, the relevance of this trimetallic unit in the field of phenolic-based biocoatings and Metal Organic Framework (MOF) synthesis is briefly discussed.
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Affiliation(s)
- Hassan Mkhadder
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France.
| | - Morgane Denis
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France.
| | - Mónica Giménez-Marqués
- Instituto de Ciencia Molecular (ICMol), c/Catedrático José Beltrán, 2, 46980 Paterna, Spain
| | - Walter Cañón-Mancisidor
- Facultad de Ingeniería, Ciencia y Tecnología, Depto. Matemáticas y Ciencias de la Ingeniería, Universidad Bernardo O'Higgins, Chile.,Centro de Nanociencia y Nanotecnología CEDENNA, Chile
| | - Bernard Humbert
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France.
| | - Elise Deunf
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France.
| | - Philippe Poizot
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France.
| | - Thomas Devic
- Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France.
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15
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Helfrich F, Scheidig AJ. Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-π interaction. Acta Crystallogr D Struct Biol 2021; 77:1317-1335. [PMID: 34605434 PMCID: PMC8489232 DOI: 10.1107/s2059798321008937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines influence medically relevant processes in the opportunistic pathogen Pseudomonas aeruginosa, including virulence, biofilm formation and susceptibility to antibiotics. Although homospermidine synthase (HSS) is part of the polyamine metabolism in various strains of P. aeruginosa, neither its role nor its structure has been examined so far. The reaction mechanism of the nicotinamide adenine dinucleotide (NAD+)-dependent bacterial HSS has previously been characterized based on crystal structures of Blastochloris viridis HSS (BvHSS). This study presents the crystal structure of P. aeruginosa HSS (PaHSS) in complex with its substrate putrescine. A high structural similarity between PaHSS and BvHSS with conservation of the catalytically relevant residues is demonstrated, qualifying BvHSS as a model for mechanistic studies of PaHSS. Following this strategy, crystal structures of single-residue variants of BvHSS are presented together with activity assays of PaHSS, BvHSS and BvHSS variants. For efficient homospermidine production, acidic residues are required at the entrance to the binding pocket (`ionic slide') and near the active site (`inner amino site') to attract and bind the substrate putrescine via salt bridges. The tryptophan residue at the active site stabilizes cationic reaction components by cation-π interaction, as inferred from the interaction geometry between putrescine and the indole ring plane. Exchange of this tryptophan for other amino acids suggests a distinct catalytic requirement for an aromatic interaction partner with a highly negative electrostatic potential. These findings substantiate the structural and mechanistic knowledge on bacterial HSS, a potential target for antibiotic design.
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Affiliation(s)
- F. Helfrich
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
| | - Axel J. Scheidig
- Zoological Institute, University of Kiel, Am Botanischen Garten 1–9, 24118 Kiel, Germany
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16
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Kim G, Lee SE, Jeong S, Lee J, Park D, Chang S. Multivalent electrostatic pi-cation interaction between synaptophysin and synapsin is responsible for the coacervation. Mol Brain 2021; 14:137. [PMID: 34496937 PMCID: PMC8424992 DOI: 10.1186/s13041-021-00846-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022] Open
Abstract
We recently showed that synaptophysin (Syph) and synapsin (Syn) can induce liquid-liquid phase separation (LLPS) to cluster small synaptic-like microvesicles in living cells which are highly reminiscent of SV cluster. However, as there is no physical interaction between them, the underlying mechanism for their coacervation remains unknown. Here, we showed that the coacervation between Syph and Syn is primarily governed by multivalent pi-cation electrostatic interactions among tyrosine residues of Syph C-terminal (Ct) and positively charged Syn. We found that Syph Ct is intrinsically disordered and it alone can form liquid droplets by interactions among themselves at high concentration in a crowding environment in vitro or when assisted by additional interactions by tagging with light-sensitive CRY2PHR or subunits of a multimeric protein in living cells. Syph Ct contains 10 repeated sequences, 9 of them start with tyrosine, and mutating 9 tyrosine to serine (9YS) completely abolished the phase separating property of Syph Ct, indicating tyrosine-mediated pi-interactions are critical. We further found that 9YS mutation failed to coacervate with Syn, and since 9YS retains Syph's negative charge, the results indicate that pi-cation interactions rather than simple charge interactions are responsible for their coacervation. In addition to revealing the underlying mechanism of Syph and Syn coacervation, our results also raise the possibility that physiological regulation of pi-cation interactions between Syph and Syn during synaptic activity may contribute to the dynamics of synaptic vesicle clustering.
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Affiliation(s)
- Goeun Kim
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Sang-Eun Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
- UK Dementia Research Institute, University College London, Cruciform Building, Gower St, London, WC1E 6BT, UK
| | - Seonyoung Jeong
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Jeongkun Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Daehun Park
- Departments of Neuroscience and Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea.
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17
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Ferretti A, Prampolini G, d’Ischia M. Noncovalent interactions in catechol/ammonium-rich adhesive motifs: Reassessing the role of cation-π complexes? Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Mu L, Yang Y, Liu J, Du W, Chen J, Shi G, Fang H. Hydrated cation-π interactions of π-electrons with hydrated Li +, Na +, and K + cations. Phys Chem Chem Phys 2021; 23:14662-14670. [PMID: 34213518 DOI: 10.1039/d1cp01609a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-π interactions are essential for many chemical, biological, and material processes, and these processes usually involve an aqueous salt solution. However, there is still a lack of a full understanding of the hydrated cation-π interactions between the hydrated cations and the aromatic ring structures on the molecular level. Here, we report a molecular picture of hydrated cation-π interactions, by using the calculations of density functional theory (DFT). Specifically, the graphene sheet can distort the hydration shell of the hydrated K+ to interact with K+ directly, which is hereafter called water-cation-π interactions. In contrast, the hydration shell of the hydrated Li+ is quite stable and the graphene sheet interacts with Li+ indirectly, mediated by water molecules, which we hereafter call the cation-water-π interactions. The behavior of hydrated cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated cations adsorbed onto the graphene surface.
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Affiliation(s)
- Liuhua Mu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yizhou Yang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China.
| | - Jian Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wei Du
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jige Chen
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Guosheng Shi
- Shanghai Applied Radiation Institute and State Key Lab. Advanced Special Steel, Shanghai University, Shanghai 200444, China.
| | - Haiping Fang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China. and Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
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19
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Al Mughram MH, Catalano C, Bowry JP, Safo MK, Scarsdale JN, Kellogg GE. 3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. J Chem Inf Model 2021; 61:2937-2956. [PMID: 34101460 DOI: 10.1021/acs.jcim.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ1, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.
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Affiliation(s)
- Mohammed H Al Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - John P Bowry
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - J Neel Scarsdale
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
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20
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Kinens A, Balkaitis S, Ahmad OK, Piotrowski DW, Suna E. Acylative Dynamic Kinetic Resolution of Secondary Alcohols: Tandem Catalysis by HyperBTM and Bäckvall's Ruthenium Complex. J Org Chem 2021; 86:7189-7202. [PMID: 33974415 DOI: 10.1021/acs.joc.1c00545] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Non-enzymatic dynamic kinetic resolution (DKR) of secondary alcohols by enantioselective acylation using an isothiourea-derived HyperBTM catalyst and racemization of slowly reacting alcohol by Bäckvall's ruthenium complex is reported. The DKR approach features high enantioselectivities (up to 99:1), employs easy-to-handle crystalline 4-nitrophenyl isobutyrate as the acylating reagent, and proceeds at room temperature and under an ambient atmosphere. The stereoinduction model featuring cation-π system interactions between the acylated HyperBTM catalyst and π electrons of an alcohol aryl subunit has been elaborated by DFT calculations.
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Affiliation(s)
- Artis Kinens
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia.,Department of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Simonas Balkaitis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia.,Department of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Omar K Ahmad
- Worldwide Medicinal Chemistry, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - David W Piotrowski
- Worldwide Medicinal Chemistry, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia.,Department of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
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21
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Singh VB. Spectroscopic Signatures and the Cation-π Interaction in Conformational Preferences of the Neurotransmitter Dopamine in Aqueous Solution. ACS Chem Neurosci 2021; 12:613-625. [PMID: 33523624 DOI: 10.1021/acschemneuro.0c00597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The precise determination of the neurotransmitter dopamine's conformational preferences in aqueous solution is crucial for understanding its neurobiological function. The first principle Møller-Plesset perturbation theory (MP2) and dispersion corrected density functional theory (DFT-D3) methods, employing the basis set aug-cc-pVDZ(/pVTZ), are used to reinvestigate the nine lowest-energy (isolated) structures of protonated dopamine (DAH+) in both gas and aqueous phases. DAH+ trans isomer t1 is found higher in energy than lowest-energy gauche isomer g+1 (g + 1) by 6.4 and 5.7 kJ mol-1, at the MP2 and B3LYP-D3 levels of theory, respectively, in the aqueous environment within the polarizable continuum model (PCM). We found that the solvated cation, NH3+, retains its attractive character, which supports the previous report that agonist DAH+ can be involved in cation (NH3+)-π interaction in the active states of the D2 dopamine receptor. The dispersion corrected DFT evaluation of anharmonicity allows us to confirm the most experimental frequencies and suggest some new interpretations. The IR and Raman spectra's influential band for both gauche and the trans conformers observed at 1287/1288 cm-1 were enhanced in aqueous solution. The experimental Raman spectrum for dopamine was compared with the conformer-specific computed Raman spectrum of protonated dopamine (DAH+). The intense Raman band at 1451 cm-1 indicates the necessity of DAH+ calculated values in interpreting the Raman spectra. The most intense Raman band at 750 cm-1 arises due to the trans DAH+, t1, revealed by MP2/aug-cc-pVDZ Raman spectra, indicating trans DAH+ dominance in the bulk DAH+ of extracellular fluid.
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22
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Prampolini G, d'Ischia M, Ferretti A. The phenoxyl group-modulated interplay of cation-π and σ-type interactions in the alkali metal series. Phys Chem Chem Phys 2020; 22:27105-27120. [PMID: 33225336 DOI: 10.1039/d0cp03707a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The interaction potential energy surfaces (IPESs) of four alkaline metal cations (Na+, K+, Rb+ and Cs+) complexed with phenol and catechol were explored by accurate ab initio calculations to investigate the interplay of different noncovalent interactions and their behavior along the alkali metal series and upon -OH substitution. Selected one-dimensional interaction energy curves revealed two different minimum energy configurations for all phenol- and catechol-metal complexes, characterized either by cation-π or σ-type interactions. For each investigated complex several two-dimensional IPES maps were also computed, exploiting the computational advantages of the MP2mod approach. The size of the alkali cation was found to play a similar role in modulating both kinds of complexes, as the interaction strength always decreases along the metal series, from Na+ to Cs+. Conversely, the number of hydroxyl substituents markedly affected cation-π complexes vs. σ-type ones. As a most relevant finding, in catechol-metal complexes the strength of cation-π interactions is around half that of the σ-type ones. It is argued that the combined effect of cation dimensions and hydroxyl substitution in catechol-Na+ complexes makes σ-type configurations remarkably more stable and easily accessible than cation-π ones. Besides shedding new light on the origin of biological phenomena connected with underwater adhesion, the quantum mechanical interaction energy database provided herein may offer a useful reference for tuning accurate force fields, suitable for molecular dynamics simulations, where environmental effects might be also taken into account.
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Affiliation(s)
- Giacomo Prampolini
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
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23
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Zidar M, Rozman P, Belko-Parkel K, Ravnik M. Control of viscosity in biopharmaceutical protein formulations. J Colloid Interface Sci 2020; 580:308-317. [DOI: 10.1016/j.jcis.2020.06.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 01/21/2023]
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24
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Turupcu A, Tirado-Rives J, Jorgensen WL. Explicit Representation of Cation-π Interactions in Force Fields with 1/ r4 Nonbonded Terms. J Chem Theory Comput 2020; 16:7184-7194. [PMID: 33048555 DOI: 10.1021/acs.jctc.0c00847] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The binding energies for cation-π complexation are underestimated by traditional fixed-charge force fields owing to their lack of explicit treatment of ion-induced dipole interactions. To address this deficiency, an explicit treatment of cation-π interactions has been introduced into the OPLS-AA force field. Following prior work with atomic cations, it is found that cation-π interactions can be handled efficiently by augmenting the usual 12-6 Lennard-Jones potentials with 1/r4 terms. Results are provided for prototypical complexes as well as protein-ligand systems of relevance for drug design. Alkali cation, ammonium, guanidinium, and tetramethylammonium were chosen for the representative cations, while benzene and six heteroaromatic molecules were used as the π systems. The required nonbonded parameters were fit to reproduce structure and interaction energies for gas-phase complexes from density functional theory (DFT) calculations at the ωB97X-D/6-311++G(d,p) level. The impact of the solvent was then examined by computing potentials of mean force (pmfs) in both aqueous and tetrahydrofuran (THF) solutions using the free-energy perturbation (FEP) theory. Further testing was carried out for two cases of strong and one case of weak cation-π interactions between druglike molecules and their protein hosts, namely, the JH2 domain of JAK2 kinase and macrophage migration inhibitory factor. FEP results reveal greater binding by 1.5-4.4 kcal/mol from the addition of the explicit cation-π contributions. Thus, in the absence of such treatment of cation-π interactions, errors for computed binding or inhibition constants of 101-103 are expected.
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Affiliation(s)
- Aysegul Turupcu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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Ou X, Xue B, Lao Y, Wutthinitikornkit Y, Tian R, Zou A, Yang L, Wang W, Cao Y, Li J. Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability. SCIENCE ADVANCES 2020; 6:6/39/eabb7620. [PMID: 32978166 PMCID: PMC7518861 DOI: 10.1126/sciadv.abb7620] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/12/2020] [Indexed: 05/11/2023]
Abstract
Mussels can strongly adhere to hydrophilic minerals in sea habitats by secreting adhesive proteins. The adhesion ability of these proteins is often attributed to the presence of Dopa derived from posttranslational modification of Tyr, whereas the contribution of structural feature is overlooked. It remains largely unknown how adhesive proteins overcome the surface-bound water layer to establish underwater adhesion. Here, we use molecular dynamics simulations to probe the conformations of adhesive protein Pvfp-5β and its salt-tolerant underwater adhesion on superhydrophilic mica. Dopa and positively charged basic residues form pairs, in this intrinsically disordered protein, and these residue pairs can lead to firm surface binding. Our simulations further suggest that the unmodified Tyr shows similar functions on surface adhesion by forming pairing structure with a positively charged residue. We confirm the presence of these residue pairs and verify the strong binding ability of unmodified proteins using nuclear magnetic resonance spectroscopy and lap shear tests.
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Affiliation(s)
- Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yichong Lao
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Yanee Wutthinitikornkit
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Aodong Zou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Lingyun Yang
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai 201210, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China.
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China.
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26
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Biggins N, Ziebel ME, Gonzalez MI, Long JR. Crystallographic characterization of the metal-organic framework Fe 2(bdp) 3 upon reductive cation insertion. Chem Sci 2020; 11:9173-9180. [PMID: 34123166 PMCID: PMC8163410 DOI: 10.1039/d0sc03383a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Precisely locating extra-framework cations in anionic metal–organic framework compounds remains a long-standing, yet crucial, challenge for elucidating structure–performance relationships in functional materials. Single-crystal X-ray diffraction is one of the most powerful approaches for this task, but single crystals of frameworks often degrade when subjected to post-synthetic metalation or reduction. Here, we demonstrate the growth of sizable single crystals of the robust metal–organic framework Fe2(bdp)3 (bdp2− = benzene-1,4-dipyrazolate) and employ single-crystal-to-single-crystal chemical reductions to access the solvated framework materials A2Fe2(bdp)3·yTHF (A = Li+, Na+, K+). X-ray diffraction analysis of the sodium and potassium congeners reveals that the cations are located near the center of the triangular framework channels and are stabilized by weak cation–π interactions with the framework ligands. Freeze-drying with benzene enables isolation of activated single crystals of Na0.5Fe2(bdp)3 and Li2Fe2(bdp)3 and the first structural characterization of activated metal–organic frameworks wherein extra-framework alkali metal cations are also structurally located. Comparison of the solvated and activated sodium-containing structures reveals that the cation positions differ in the two materials, likely due to cation migration that occurs upon solvent removal to maximize stabilizing cation–π interactions. Hydrogen adsorption data indicate that these cation–framework interactions are sufficient to diminish the effective cationic charge, leading to little or no enhancement in gas uptake relative to Fe2(bdp)3. In contrast, Mg0.85Fe2(bdp)3 exhibits enhanced H2 affinity and capacity over the non-reduced parent material. This observation shows that increasing the charge density of the pore-residing cation serves to compensate for charge dampening effects resulting from cation–framework interactions and thereby promotes stronger cation–H2 interactions. Single-crystal X-ray diffraction reveals structural influences on gas adsorption properties in anionic metal–organic frameworks.![]()
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Affiliation(s)
- Naomi Biggins
- Department of Chemistry, University of California Berkeley California 94720 USA .,Materials Sciences Division, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
| | - Michael E Ziebel
- Department of Chemistry, University of California Berkeley California 94720 USA .,Materials Sciences Division, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
| | - Miguel I Gonzalez
- Department of Chemistry, University of California Berkeley California 94720 USA
| | - Jeffrey R Long
- Department of Chemistry, University of California Berkeley California 94720 USA .,Department of Chemical and Biomolecular Engineering, University of California Berkeley California 94720 USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory Berkeley California 94720 USA
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27
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Li J, Moumbock AFA, Günther S. Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation Reader Proteins. J Chem Inf Model 2020; 60:5225-5233. [DOI: 10.1021/acs.jcim.0c00765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jianyu Li
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Aurélien F. A. Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
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28
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Theoretical investigation on the non-covalent interactions of acetaminophen complex in different solvents: study of the enhancing effect of the cation–π interaction on the intramolecular hydrogen bond. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02650-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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29
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Bandyopadhyay D, Bhatnagar A, Jain S, Pratyaksh P. Selective Stabilization of Aspartic Acid Protonation State within a Given Protein Conformation Occurs via Specific "Molecular Association". J Phys Chem B 2020; 124:5350-5361. [PMID: 32484348 DOI: 10.1021/acs.jpcb.0c02629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins involved in proton-/electron-transfer processes often possess "functional" aspartates/aspartic acids (Asp) with variable protonation states. The mechanism of Asp protonation-deprotonation within proteins is unclear. Two questions were asked-the possible types of determinants responsible for Asp protonation-deprotonation and the spatial arrangements of the determinants leading to selective stabilization. The questions were analyzed using nine different solvent models, which scanned the complete protein dielectric range, and four protein models, which illustrated the spatial arrangements around Asp, termed as "molecular association". The methods employed were quantum chemical calculations and constant pH simulations. The types of the determinants identified were charge-charge interaction, H bonding, dipole-π interaction, extended electronic conjugation, dielectric effect, and solvent accessibility. All solvent-exposed Asp [buried fraction (BF) less than 0.5] were aspartates, and buried Asp were either aspartic acids or aspartates, each having a different "molecular association". The exposed aspartates were stabilized via a H-bonding network with bulk water, buried aspartates via salt bridge or, minimum, two intramolecular H bonds, and buried aspartic acids via, minimum, one intramolecular H bond. An "acid-alcohol pair" (involving Ser/Thr/Tyr) was a common determinant to any "functional" buried aspartate/aspartic acid. Higher energy "molecular associations" observed within proteins compared to those within water, presumably, indicated easy molecular restructuring and alteration of the Asp protonation states during a protein-mediated proton/electron transfer.
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Affiliation(s)
- Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad campus, Hyderabad 500078, India
| | - Akshay Bhatnagar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad campus, Hyderabad 500078, India
| | - Shobhit Jain
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad campus, Hyderabad 500078, India
| | - Prabhav Pratyaksh
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad campus, Hyderabad 500078, India
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31
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Transition-metal-free formal cross-coupling of aryl methyl sulfoxides and alcohols via nucleophilic activation of C-S bond. Nat Commun 2020; 11:2890. [PMID: 32513962 PMCID: PMC7280189 DOI: 10.1038/s41467-020-16713-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/11/2020] [Indexed: 01/06/2023] Open
Abstract
Employment of sulfoxides as electrophiles in cross-coupling reactions remains underexplored. Herein we report a transition-metal-free cross-coupling strategy utilizing aryl(heteroaryl) methyl sulfoxides and alcohols to afford alkyl aryl(heteroaryl) ethers. Two drug molecules were successfully prepared using this protocol as a key step, emphasizing its potential utility in medicinal chemistry. A DFT computational study suggests that the reaction proceeds via initial addition of the alkoxide to the sulfoxide. This adduct facilitates further intramolecular addition of the alkoxide to the aromatic ring wherein charge on the aromatic system is stabilized by the nearby potassium cation. Rate-determining fragmentation then delivers methyl sulfenate and the aryl or heteroaryl ether. This study establishes the feasibility of nucleophilic addition to an appended sulfoxide as a means to form a bond to aryl(heteroaryl) systems and this modality is expected to find use with many other electrophiles and nucleophiles leading to new cross-coupling processes. Cross-coupling processes without the use of transition metals are challenging to achieve. Here, the authors show a transition-metal-free cross-coupling utilizing aryl(heteroaryl) methyl sulfoxides and alcohols to afford alkyl aryl(heteroaryl) ethers and propose a nucleophilic addition mechanism based on experiments and theory.
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32
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Van Den Broeck E, Verbraeken B, Dedecker K, Cnudde P, Vanduyfhuys L, Verstraelen T, Van Hecke K, Jerca VV, Catak S, Hoogenboom R, Van Speybroeck V. Cation−π Interactions Accelerate the Living Cationic Ring-Opening Polymerization of Unsaturated 2-Alkyl-2-oxazolines. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Elias Van Den Broeck
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Bart Verbraeken
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
| | - Karen Dedecker
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Pieter Cnudde
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Louis Vanduyfhuys
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Kristof Van Hecke
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281-S3, B-9000 Ghent, Belgium
| | - Valentin Victor Jerca
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
- Centre for Organic Chemistry “Costin D. Nenitzescu”, Romanian Academy, 202B Spl. Independentei CP 35-108, Bucharest 060023, Romania
| | - Saron Catak
- Center for Molecular Modeling, Ghent University, Technologiepark 46, 9052 Zwijnaarde, Belgium
- Department of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium
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33
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Ferretti A, d’Ischia M, Prampolini G. Benchmarking Cation−π Interactions: Assessment of Density Functional Theory and Möller–Plesset Second-Order Perturbation Theory Calculations with Optimized Basis Sets (mp2mod) for Complexes of Benzene, Phenol, and Catechol with Na+, K+, Rb+, and Cs+. J Phys Chem A 2020; 124:3445-3459. [DOI: 10.1021/acs.jpca.0c02090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Alessandro Ferretti
- Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Marco d’Ischia
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, I-80126 Napoli, Italy
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34
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Ernst BG, Lao KU, Sullivan AG, DiStasio Jr. RA. Attracting Opposites: Promiscuous Ion−π Binding in the Nucleobases. J Phys Chem A 2020; 124:4128-4140. [DOI: 10.1021/acs.jpca.0c02766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brian G. Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Andrew G. Sullivan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Robert A. DiStasio Jr.
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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35
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Aster A, Licari G, Zinna F, Brun E, Kumpulainen T, Tajkhorshid E, Lacour J, Vauthey E. Tuning symmetry breaking charge separation in perylene bichromophores by conformational control. Chem Sci 2019; 10:10629-10639. [PMID: 34040711 PMCID: PMC8133027 DOI: 10.1039/c9sc03913a] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Understanding structure-property relationships in multichromophoric molecular architectures is a crucial step in establishing new design principles in organic electronics as well as to fully understand how nature exploits solar energy. Here, we study the excited state dynamics of three bichromophores consisting of two perylene chromophores linked to three different crown-ether backbones, using stationary and ultrafast electronic spectroscopy combined with molecular dynamics simulations. The conformational space available to the bichromophores depends on the structure and geometry of the crown-ether and can be significantly changed upon cation binding, strongly affecting the excited-state dynamics. We show that, depending on the conformational restrictions and the local environment, the nature of the excited state varies greatly, going from an excimer to a symmetry-broken charge separated state. These results can be rationalised in terms of a structure-property relationship that includes the effect of the local environment.
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Affiliation(s)
- Alexander Aster
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Giuseppe Licari
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois USA.,Department of Biochemistry, Center for Biophysics and Quantitative Biology Urbana Illinois USA
| | - Francesco Zinna
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Elodie Brun
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Tatu Kumpulainen
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois USA.,Department of Biochemistry, Center for Biophysics and Quantitative Biology Urbana Illinois USA
| | - Jérôme Lacour
- Department of Organic Chemistry, University of Geneva CH-1211 Geneva Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva CH-1211 Geneva Switzerland
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36
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Nir S, Zanuy D, Zada T, Agazani O, Aleman C, Shalev DE, Reches M. Tailoring the self-assembly of a tripeptide for the formation of antimicrobial surfaces. NANOSCALE 2019; 11:8752-8759. [PMID: 30778487 DOI: 10.1039/c8nr10043h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The accumulation of bacteria on surfaces is currently one of the greatest concerns for the management of proper healthcare systems, water and energy. Here, we describe the mechanism by which a single peptide forms two pH-dependent supramolecular particles that resist bacterial contamination. By using NMR and molecular dynamics (MD), we determined the structures of the peptide monomers and showed the forces directing the self-assembly of each structure under different conditions. These peptide assemblies change the characteristics of bare glass and confer it with the ability to prevent biofilm formation. Furthermore, they can adsorb and release active compounds as demonstrated with an anticancer drug, antibiotic and enzyme. This synergism and the detailed understanding of the processes are necessary for developing new sterile surfaces for healthcare systems, water purification devices, food packaging or any environment that suffers from biocontamination.
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Affiliation(s)
- Sivan Nir
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904. Israel.
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37
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Castro EF, Casal JJ, de Marco MJE, Battini L, Fabiani M, Fernández GA, Bruno AM, Cavallaro LV, Bollini M. Identification of potent bovine viral diarrhea virus inhibitors by a structure-based virtual screening approach. Bioorg Med Chem Lett 2019; 29:262-266. [PMID: 30501966 DOI: 10.1016/j.bmcl.2018.11.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/08/2018] [Accepted: 11/21/2018] [Indexed: 10/27/2022]
Abstract
Bovine viral diarrhea virus (BVDV) is a pestivirus whose infection in cattle is globally distributed. The use of antivirals could complement vaccination as a tool of control and reduce economic losses. The RNA-dependent RNA polymerase (RdRp) of the virus is essential for its genome replication and constitutes an attractive target for the identification of antivirals. With the aim of obtaining selective BVDV inhibitors, the crystal structure of BVDV RdRp was used to perform a virtual screening. Approximately 15,000 small molecules from commercial and in-house databases were evaluated and several structurally different compounds were tested in vitro for antiviral activity. Interestingly, of twelve evaluated compounds, five were active and displayed EC50 values in the sub and low-micromolar range. Time of drug addition experiment and measured intracellular BVDV RNA showed that compound 7 act during RNA synthesis. Molecular Dynamics and MM/PBSA calculation were done to characterize the interaction of the most active compounds with RdRp, which will allow future ligand optimization. These studies highlight the use of in silico screening to identify a new class of BVDV inhibitors.
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Affiliation(s)
- Eliana F Castro
- Cátedra de Virología, Departamento de Microbiología, Inmunología y Biotecnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan J Casal
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-CONICET, Ciudad de Buenos Aires, Argentina
| | - María J España de Marco
- Cátedra de Virología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leandro Battini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-CONICET, Ciudad de Buenos Aires, Argentina
| | - Matías Fabiani
- Cátedra de Virología, Departamento de Microbiología, Inmunología y Biotecnología, Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriela A Fernández
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-CONICET, Ciudad de Buenos Aires, Argentina
| | - Ana M Bruno
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Química Orgánica, Junín 956, C1113AAD, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía V Cavallaro
- Cátedra de Virología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, 1113, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Mariela Bollini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-CONICET, Ciudad de Buenos Aires, Argentina.
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38
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Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Leduskrasts K, Suna E. Aggregation induced emission by pyridinium–pyridinium interactions. RSC Adv 2019; 9:460-465. [PMID: 35521587 PMCID: PMC9059268 DOI: 10.1039/c8ra08771g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/18/2018] [Indexed: 12/15/2022] Open
Abstract
Non-covalent intermolecular interactions between pyridinium subunits in a crystal-state are an efficient means to accomplish aggregation induced emission and avoid aggregation caused quenching. Non-covalent intermolecular pyridinium–pyridinium and pyridinium–arene-π system interactions result in aggregation induced emission (AIE).![]()
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Affiliation(s)
| | - Edgars Suna
- Latvian Institute of Organic Synthesis
- Riga
- Latvia
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40
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Brüllingen E, Neudörfl JM, Goldfuss B. Ligand's electronegativity controls the sense of enantioselectivity in BIFOP-X palladium-catalyzed allylic alkylations. NEW J CHEM 2019. [DOI: 10.1039/c9nj02798j] [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
Palladium-catalyzed allylic alkylations of Na(CH(CO2Me)2 with 1,3-diphenylallyl acetate, employing BIFOP-X (X = H, D, Cl, CN, N3) ligands, yield the C–C coupling product (up to 91% yield, 70% ee). A NBO effect reveals a change of stereochemistry.
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Affiliation(s)
- Eric Brüllingen
- Department of Chemistry
- University of Cologne
- Organic Chemistry
- 50939 Cologne
- Germany
| | - Jörg-Martin Neudörfl
- Department of Chemistry
- University of Cologne
- Organic Chemistry
- 50939 Cologne
- Germany
| | - Bernd Goldfuss
- Department of Chemistry
- University of Cologne
- Organic Chemistry
- 50939 Cologne
- Germany
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Sharmah N, Bhattacharyya PK. Cation-mediated sandwich formation between benzene and pillar[5]arene: a DFT study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1540802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Yourdkhani S, Chojecki M, Korona T. Interaction of Non-polarizable Cations with Azaborine Isomers and Their Mono-Substituted Derivatives: Position, Induction, and Non-Classical Effects Matter. Chemphyschem 2018; 19:3092-3106. [DOI: 10.1002/cphc.201800691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Sirous Yourdkhani
- Department of Chemical Physics and Optics; Faculty of Mathematics and Physics; Charles University; Ke Karlovu 3, CZ- 12116 Prague 2 Czech Republic
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Michał Chojecki
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
| | - Tatiana Korona
- Faculty of Chemistry; University of Warsaw; ul. Pasteura 1 02-093 Warsaw Poland
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Sha SC, Tcyrulnikov S, Li M, Hu B, Fu Y, Kozlowski MC, Walsh PJ. Cation-π Interactions in the Benzylic Arylation of Toluenes with Bimetallic Catalysts. J Am Chem Soc 2018; 140:12415-12423. [PMID: 30185030 PMCID: PMC6200331 DOI: 10.1021/jacs.8b05143] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A method to directly arylate toluene derivatives with aryl bromides to generate diarylmethanes, which are important building blocks in drug discovery, is described. In this method, KN(SiMe3)2 in combination with a (NIXANTPHOS)Pd catalyst accomplished the deprotonative activation of toluene derivatives to permit cross-coupling with aryl bromides. Good to excellent yields are obtained with a range of electron-rich to neutral aryl bromides. Both electron-rich and electron-poor toluene derivatives are well tolerated, and even 2-chlorotoluene performs well, providing a platform for introduction of additional functionalization. This discovery hinges on the use of a main group metal to activate toluene for deprotonation by means of a cation-π interaction, which is secured by a bimetallic K(NIXANTPHOS)Pd assembly. Mechanistic and computational studies support acidification of toluene derivatives by the K+-cation- π interaction, which may prove pertinent in the development of other, new reaction systems.
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Affiliation(s)
- Sheng-Chun Sha
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Sergei Tcyrulnikov
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Minyan Li
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Bowen Hu
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Yue Fu
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Marisa C Kozlowski
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Patrick J Walsh
- Department of Chemistry, Roy and Diana Vagelos Laboratories , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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Pouya Karimi. Comparison of Cation-π and Anion-π Interactions by Way of Antiaromaticity. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418100254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sengupta A, Liu Y, Flood AH, Raghavachari K. Anion‐Binding Macrocycles Operate Beyond the Electrostatic Regime: Interaction Distances Matter. Chemistry 2018; 24:14409-14417. [PMID: 30036449 DOI: 10.1002/chem.201802657] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Arkajyoti Sengupta
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
- Current Address: Department of Chemistry Michigan State University East Lansing Michigan 48824 USA
| | - Yun Liu
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
- Current Address: Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Amar H. Flood
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
| | - Krishnan Raghavachari
- Department of Chemistry Indiana University 800 E. Kirkwood Avenue Bloomington Indiana 47405 USA
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46
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Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Proc Natl Acad Sci U S A 2018; 115:9992-9997. [PMID: 30224478 PMCID: PMC6176618 DOI: 10.1073/pnas.1811518115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite being evolved to process the four canonical nucleotides, DNA polymerases are known to incorporate and extend from modified nucleotides, which is the key to numerous core biotechnology applications. The structural basis for postincorporation elongation remained elusive. We successfully crystallized KlenTaq DNA polymerase in six complexes, providing high-resolution snapshots of the modification “moving” from the 3′ terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity. This highlights the unexpected plasticity of the system as origin of the broad substrate properties of the DNA polymerase and guide for the design of improved systems. DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification “moves” from the 3′-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.
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Wei D, Ma F, Wang R, Dou S, Cui P, Huang H, Ji J, Jia E, Jia X, Sajid S, Elseman AM, Chu L, Li Y, Jiang B, Qiao J, Yuan Y, Li M. Ion-Migration Inhibition by the Cation-π Interaction in Perovskite Materials for Efficient and Stable Perovskite Solar Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707583. [PMID: 29938843 DOI: 10.1002/adma.201707583] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/20/2018] [Indexed: 05/18/2023]
Abstract
Migration of ions can lead to photoinduced phase separation, degradation, and current-voltage hysteresis in perovskite solar cells (PSCs), and has become a serious drawback for the organic-inorganic hybrid perovskite materials (OIPs). Here, the inhibition of ion migration is realized by the supramolecular cation-π interaction between aromatic rubrene and organic cations in OIPs. The energy of the cation-π interaction between rubrene and perovskite is found to be as strong as 1.5 eV, which is enough to immobilize the organic cations in OIPs; this will thus will lead to the obvious reduction of defects in perovskite films and outstanding stability in devices. By employing the cation-immobilized OIPs to fabricate perovskite solar cells (PSCs), a champion efficiency of 20.86% and certified efficiency of 20.80% with negligible hysteresis are acquired. In addition, the long-term stability of cation-immobilized PSCs is improved definitely (98% of the initial efficiency after 720 h operation), which is assigned to the inhibition of ionic diffusions in cation-immobilized OIPs. This cation-π interaction between cations and the supramolecular π system enhances the stability and the performance of PSCs efficiently and would be a potential universal approach to get the more stable perovskite devices.
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Affiliation(s)
- Dong Wei
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Fusheng Ma
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Rui Wang
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Shangyi Dou
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Peng Cui
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Hao Huang
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Jun Ji
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Endong Jia
- Key Laboratory of Solar Thermal Energy and Photovoltaic System, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiaojie Jia
- Key Laboratory of Solar Thermal Energy and Photovoltaic System, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Sajid Sajid
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Ahmed Mourtada Elseman
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
- Electronic and Magnetic Materials Department, Central Metallurgical Research and Development Institute (CMRDI), PO Box 87 Helwan, 1, Elfelezat Street, El-Tebbin, 11421, Cairo, Egypt
| | - Lihua Chu
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Yingfeng Li
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Bing Jiang
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Juan Qiao
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yongbo Yuan
- Hunan Key Laboratory of Super-microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Hunan, 410083, P. R. China
| | - Meicheng Li
- State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
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Zhang Y, Chen S, Ying F, Su P, Wu W. Valence Bond Based Energy Decomposition Analysis Scheme and Its Application to Cation−π Interactions. J Phys Chem A 2018; 122:5886-5894. [DOI: 10.1021/acs.jpca.8b04201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Yang Zhang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Sifeng Chen
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Fuming Ying
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, iChEM, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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Bollini M, Leal ES, Adler NS, Aucar MG, Fernández GA, Pascual MJ, Merwaiss F, Alvarez DE, Cavasotto CN. Discovery of Novel Bovine Viral Diarrhea Inhibitors Using Structure-Based Virtual Screening on the Envelope Protein E2. Front Chem 2018; 6:79. [PMID: 29632860 PMCID: PMC5879447 DOI: 10.3389/fchem.2018.00079] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/08/2018] [Indexed: 02/04/2023] Open
Abstract
Bovine viral diarrhea virus (BVDV) is a member of the genus Pestivirus within the family Flaviviridae. BVDV causes both acute and persistent infections in cattle, leading to substantial financial losses to the livestock industry each year. The global prevalence of persistent BVDV infection and the lack of a highly effective antiviral therapy have spurred intensive efforts to discover and develop novel anti-BVDV therapies in the pharmaceutical industry. Antiviral targeting of virus envelope proteins is an effective strategy for therapeutic intervention of viral infections. We performed prospective small-molecule high-throughput docking to identify molecules that likely bind to the region delimited by domains I and II of the envelope protein E2 of BVDV. Several structurally different compounds were purchased or synthesized, and assayed for antiviral activity against BVDV. Five of the selected compounds were active displaying IC50 values in the low- to mid-micromolar range. For these compounds, their possible binding determinants were characterized by molecular dynamics simulations. A common pattern of interactions between active molecules and aminoacid residues in the binding site in E2 was observed. These findings could offer a better understanding of the interaction of BVDV E2 with these inhibitors, as well as benefit the discovery of novel and more potent BVDV antivirals.
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Affiliation(s)
- Mariela Bollini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad de Buenos Aires, Argentina
| | - Emilse S Leal
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad de Buenos Aires, Argentina
| | - Natalia S Adler
- Laboratory of Computational Chemistry and Drug Design, Instituto de Investigación en Biomedicina de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Partner Institute of the Max Planck Society, Ciudad de Buenos Aires, Argentina
| | - María G Aucar
- Laboratory of Computational Chemistry and Drug Design, Instituto de Investigación en Biomedicina de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Partner Institute of the Max Planck Society, Ciudad de Buenos Aires, Argentina
| | - Gabriela A Fernández
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad de Buenos Aires, Argentina
| | - María J Pascual
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, San Martín, Argentina
| | - Fernando Merwaiss
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, San Martín, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, San Martín, Argentina
| | - Claudio N Cavasotto
- Laboratory of Computational Chemistry and Drug Design, Instituto de Investigación en Biomedicina de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Partner Institute of the Max Planck Society, Ciudad de Buenos Aires, Argentina
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Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism. Cell Chem Biol 2018; 25:519-529.e4. [PMID: 29503207 DOI: 10.1016/j.chembiol.2018.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/13/2017] [Accepted: 02/05/2018] [Indexed: 11/22/2022]
Abstract
Sulfur incorporation in the biosynthesis of ergothioneine, a histidine thiol derivative, differs from other well-characterized transsulfurations. A combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation and a subsequent pyridoxal 5'-phosphate (PLP)-mediated C-S lyase reaction leads to the net transfer of a sulfur atom from a cysteine to a histidine. In this study, we structurally and mechanistically characterized a PLP-dependent C-S lyase Egt2, which mediates the sulfoxide C-S bond cleavage in ergothioneine biosynthesis. A cation-π interaction between substrate and enzyme accounts for Egt2's preference of sulfoxide over thioether as a substrate. Using mutagenesis and structural biology, we captured three distinct states of the Egt2 C-S lyase reaction cycle, including a labile sulfenic intermediate captured in Egt2 crystals. Chemical trapping and high-resolution mass spectrometry were used to confirm the involvement of the sulfenic acid intermediate in Egt2 catalysis.
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