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Journal articles on the topic 'Caged ligands'

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Author: Grafiati

Published: 25 May 2024

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1

Tadevosyan, Artavazd, Louis R. Villeneuve, Alain Fournier, David Chatenet, Stanley Nattel, and Bruce G. Allen. "Caged ligands to study the role of intracellular GPCRs." Methods 92 (January 2016): 72–77. http://dx.doi.org/10.1016/j.ymeth.2015.07.005.

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2

van de Graaff, Michel J., Timo Oosenbrug, Mikkel H. S. Marqvorsen, Clarissa R. Nascimento, Mark A. R. de Geus, Bénédicte Manoury, Maaike E. Ressing, and Sander I. van Kasteren. "Conditionally Controlling Human TLR2 Activity via Trans-Cyclooctene Caged Ligands." Bioconjugate Chemistry 31, no. 6 (June 8, 2020): 1685–92. http://dx.doi.org/10.1021/acs.bioconjchem.0c00237.

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3

Isa, Masayuki, Shigeyuki Namiki, Daisuke Asanuma, and Kenzo Hirose. "Spatiotemporal Control of Receptor Tyrosine Kinase Activity by Caged Ligands." Chemistry Letters 44, no. 2 (February 5, 2015): 150–51. http://dx.doi.org/10.1246/cl.140901.

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4

Mayer, Günter, Jens Müller, Timo Mack, Daniel F. Freitag, Thomas Höver, Bernd Pötzsch, and Alexander Heckel. "Differential Regulation of Protein Subdomain Activity with Caged Bivalent Ligands." ChemBioChem 10, no. 4 (February 2, 2009): 654–57. http://dx.doi.org/10.1002/cbic.200800814.

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5

Sansalone, Lorenzo, Joshua Bratsch-Prince, Sicheng Tang, Burjor Captain, David D. Mott, and Françisco M. Raymo. "Photopotentiation of the GABAA receptor with caged diazepam." Proceedings of the National Academy of Sciences 116, no. 42 (October 1, 2019): 21176–84. http://dx.doi.org/10.1073/pnas.1902383116.

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As the inhibitory γ-aminobutyric acid–ergic (GABAergic) transmission has a pivotal role in the central nervous system (CNS) and defective forms of its synapses are associated with serious neurological disorders, numerous versions of caged GABA and, more recently, photoswitchable ligands have been developed to investigate such transmission. While the complementary nature of these probes is evident, the mechanisms by which the GABA receptors can be photocontrolled have not been fully exploited. In fact, the ultimate need for specificity is critical for the proper synaptic exploration. No caged allosteric modulators of the GABAA receptor have been reported so far; to introduce such an investigational approach, we exploited the structural motifs of the benzodiazepinic scaffold to develop a photocaged version of diazepam (CD) that was tested on basolateral amygdala (BLa) pyramidal cells in mouse brain slices. CD is devoid of any intrinsic activity toward the GABAA receptor before irradiation. Importantly, CD is a photoreleasable GABAA receptor-positive allosteric modulator that offers a different probing mechanism compared to caged GABA and photoswitchable ligands. CD potentiates the inhibitory signaling by prolonging the decay time of postsynaptic GABAergic currents upon photoactivation. Additionally, no effect on presynaptic GABA release was recorded. We developed a photochemical technology to individually study the GABAA receptor, which specifically expands the toolbox available to study GABAergic synapses.

6

Specht, Alexandre, Maurice Goeldner, Jakob Wirz, and Ling Peng. "Characterization of Caged Cholinergic Ligands; Sulfonated Calix[4]arene Inclusion Complexes." Synlett 1999, Sup. 1 (December 31, 1999): 981–83. http://dx.doi.org/10.1055/s-1999-3108.

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7

Nielson, Alastair J., Chaohong Shen, and Joyce M. Waters. "A zirconium zwitterion containing a caged amine H atom." Acta Crystallographica Section C Crystal Structure Communications 59, no. 11 (October 31, 2003): m494—m496. http://dx.doi.org/10.1107/s0108270103022595.

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The crystallographically centrosymmetric zwitterion bis[tris(3,5-dimethyl-2-oxidobenzyl-κO)ammonium]zirconium(IV) crystallizes as the chloroform disolvate, [Zr(C27H31NO3)2]·2CHCl3, with the two molecules of chloroform closely associated with two of the aromatic rings. The Zr atom has a distorted octahedral geometry with three phenoxy O atoms from each of the two ligands coordinated to it. Charge balance is maintained by protonation of each N atom, which then forms intramolecular hydrogen-bonding interactions to all three adjacent O atoms.

8

STEVENSON, Thirza H., Aldo F. GUTIERREZ, Wendy K. ALDERTON, Lu-yun LIAN, and Nigel S. SCRUTTON. "Kinetics of CO binding to the haem domain of murine inducible nitric oxide synthase: differential effects of haem domain ligands." Biochemical Journal 358, no. 1 (August 8, 2001): 201–8. http://dx.doi.org/10.1042/bj3580201.

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The binding of CO to the murine inducible nitric oxide synthase (iNOS) oxygenase domain has been studied by laser flash photolysis. The effect of the (6R)-5,6,7,8-tetrahydro-l-biopterin (BH4) cofactor l-arginine and several Type I l-arginine analogues/ligands on the rates of CO rebinding has been evaluated. The presence of BH4 in the iNOS active site has little effect on the rebinding of protein-caged haem–CO pairs (geminate recombination), but decreases the bimolecular association rates 2-fold. Addition of l-arginine to the BH4-bound complex completely abolishes geminate recombination and results in a further 80-fold decrease in the overall rate of bimolecular association. Three of the Type I ligands, S-ethylisothiourea, l-canavanine and 2,5-lutidine, displaced the CO from the haem iron upon addition to the iNOS oxygenase domain. The Type I ligands significantly decreased the rate of bimolecular binding of CO to the haem iron after photolysis. Most of these ligands also completely abolished geminate recombination. These results are consistent with a relatively open distal pocket that allows CO to bind unhindered in the active site of murine iNOS in the absence of l-arginine or BH4. In the presence of BH4 and l-arginine, however, the enzyme adopts a more closed structure that can greatly reduce ligand access to the haem iron. These observations are discussed in terms of the known structure of iNOS haem domain and solution studies of ligand binding in iNOS and neuronal NOS isoenzymes.

9

Maier, Wolfgang, John E. T. Corrie, George Papageorgiou, Bodo Laube, and Christof Grewer. "Comparative analysis of inhibitory effects of caged ligands for the NMDA receptor." Journal of Neuroscience Methods 142, no. 1 (March 2005): 1–9. http://dx.doi.org/10.1016/j.jneumeth.2004.07.006.

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10

Slocik, Joseph M., Richard A. Kortes, and Rex E. Shepherd. "Developing Carrier Complexes for “Caged NO”: RuCl3(NO)(H2O)2 Complexes of Dipyridylamine, (dpaH), N,N,N'N'-Tetrakis (2-Pyridyl) Adipamide, (tpada), and (2-Pyridylmethyl) Iminodiacetate, (pida2-)." Metal-Based Drugs 7, no. 2 (January 1, 2000): 67–75. http://dx.doi.org/10.1155/mbd.2000.67.

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Delivery agents which can carry the {Ru(NO)}6 chromophore (“caged NO”) are desired for vasodilation and for photodynamic therapy of tumors. Toward these goals, complexes derived from [RuCl3(NO)(H2O)2]= (1) have been prepared using dipyridylamine (dpaH) as mono and bis adducts, [Ru(NO)Cl3(dpaH)] = (2) and [Ru(NO)Cl(dpaH)2]Cl2 = (3). The dpaH ligands coordinate cis to the Ru(NO) axis.The mono derivative is a model for a potential DNA groove-spanning binuclear complex {[Ru(NO)Cl3]2(tpada)} = (4) which has two DNA-coordinating RuII centers, photo-labile {Ru(NO)}6 sites, and a groove-spanning tether moiety.The binuclear assembly is prepared from the tethered dipyridylamine ligand N,N,N',N'-tetrakis(2-pyridylmethyl)adipamide (tpada) which has recently been shown to provide a binuclear carrier complex suited to transporting RuII and PdII agents. A related complex, [Ru(NO)Cl(pida)] = (5) with the {Ru(NO)}6 moiety bound to (2-pyridylmethyl) iminodiacetate (pida2-) is also characterized as a potential “caged NO” carrier. Structural information concerning the placement of the pyridyl donor groups relative to the {Ru(NO)}6 unit has been obtained from H1 and C13 NMR and infrared methods, noting that a pyridyl donor trans to NO+ causes “trans strengthening” of this ligand for [Ru(NO)Cl(pida)], whereas placement of pyridyl groups cis to NO+ causes a weakening of the N-O bond and a lower NO stretching frequency in the dpa-based complexes.

11

Sainlos, Matthieu, Wendy S. Iskenderian-Epps, Nelson B. Olivier, Daniel Choquet, and Barbara Imperiali. "Caged Mono- and Divalent Ligands for Light-Assisted Disruption of PDZ Domain-Mediated Interactions." Journal of the American Chemical Society 135, no. 12 (March 13, 2013): 4580–83. http://dx.doi.org/10.1021/ja309870q.

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12

Zhao, Jun, Tony D. Gover, Sukumaran Muralidharan, Darryl A. Auston, Daniel Weinreich, and Joseph P. Y. Kao. "Caged Vanilloid Ligands for Activation of TRPV1 Receptors by 1- and 2-Photon Excitation†." Biochemistry 45, no. 15 (April 2006): 4915–26. http://dx.doi.org/10.1021/bi052082f.

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13

Boer, Stephanie A., Winnie Cao, Bianca K. Glascott, and David R. Turner. "Towards a Generalized Synthetic Strategy for Variable Sized Enantiopure M4L4 Helicates." Chemistry 2, no. 3 (June 28, 2020): 613–25. http://dx.doi.org/10.3390/chemistry2030038.

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The reliable and predictable synthesis of enantiopure coordination cages is an important step towards the realization of discrete cages capable of enantioselective discrimination. We have built upon our initial report of a lantern-type helical cage in attempts to expand the synthesis into a general approach. The use of a longer, flexible diacid ligand results in the anticipated cage [Cu4(L1)4(solvent)4] with a similar helical pitch to that previously observed and a cavity approximately 30% larger. Using a shorter, more rigid ligand gave rise to a strained, conjoined cage-type complex when using DABCO as an internal bridging ligand, [{Co4(L2)4(DABCO)(OH2)x}2 (DABCO)]. The expected paddlewheel motif only forms for one of the Co2 units within each cage, with the other end adopting a “partial paddlewheel” with aqua ligands completing the coordination sphere of the externally facing metal ion. The generic approach of using chiral diacids to construct lantern-type cages is partially borne out, with it being apparent that flexibility in the core group is an essential structural feature.

14

Cheng, Weiyan, Shasha Li, Siyuan Han, Ruoyang Miao, Suhua Wang, Chunxia Liu, Han Wei, Xin Tian, and Xiaojian Zhang. "Design, synthesis and biological evaluation of the tumor hypoxia-activated PROTACs bearing caged CRBN E3 ligase ligands." Bioorganic & Medicinal Chemistry 82 (March 2023): 117237. http://dx.doi.org/10.1016/j.bmc.2023.117237.

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15

Jackson, Garrett D., Max B. Tipping, Christopher G. P. Taylor, Jerico R. Piper, Callum Pritchard, Cristina Mozaceanu, and Michael D. Ward. "A Family of Externally-Functionalised Coordination Cages." Chemistry 3, no. 4 (October 14, 2021): 1203–14. http://dx.doi.org/10.3390/chemistry3040088.

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New synthetic routes are presented to derivatives of a (known) M8L12 cubic coordination cage in which a range of different substituents are attached at the C4 position of the pyridyl rings at either end of the bis(pyrazolyl-pyridine) bridging ligands. The substituents are (i) –CN groups (new ligand LCN), (ii) –CH2OCH2–CCH (containing a terminal alkyne) groups (new ligand LCC); and (iii) –(CH2OCH2)3CH2OMe (tri-ethyleneglycol monomethyl ether) groups (new ligand LPEG). The resulting functionalised ligands combine with M2+ ions (particularly Co2+, Ni2+, Cd2+) to give isostructural [M8L12]16+ cage cores bearing 24 external functional groups; the cages based on LCN (with M2+ = Cd2+) and LCC (with M2+ = Ni2+) have been crystallographically characterised. The value of these is twofold: (i) exterior nitrile or alkene substituents can provide a basis for further synthetic opportunities via ‘Click’ reactions allowing in principle a diverse range of functionalisation of the cage exterior surface; (ii) the exterior –(CH2OCH2)3CH2OMe groups substantially increase cage solubility in both water and in organic solvents, allowing binding constants of cavity-binding guests to be measured under an increased range of conditions.

16

Pichugin, Alexander, Lindsey Ehrler, Sharvan Sehrawat, Theresa Funk, Cate Speake, Patrick Duffy, Hidde Ploegh, and Urszula Krzych. "Identification of Plasmodium berghei novel liver stage CD8 T cell epitopes by caged MHC class I tetramer technology (43.30)." Journal of Immunology 188, no. 1_Supplement (May 1, 2012): 43.30. http://dx.doi.org/10.4049/jimmunol.188.supp.43.30.

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Abstract Studies conducted in mice and humans have shown that IFN-γ+ CD8 T cell are the key effectors against liver-stage (LS) malaria; however, owing to complexities associated with the development of Plasmodia parasites, specificities of CD8 T cell effectors have been difficult to establish. Direct detection of Ag-specific CD8 T cells in high-throughput manner became possible with the development of caged MHC-tetramer technology, based on conditional photo-cleavable MHC class I ligands that can be displaced during UV induced exchange with a peptide of interest. On the basis of previously identified P. falciparum (Pf) genes expressed exclusively during LS infection, we identified P. berghei (Pb) orthologues of Pf genes and validated their expression by qRT-PCR in Pb infected C57Bl/6 mice. Several Pb LS antigens, administered as DNA vaccines, significantly reduced LS parasite burden in mice infected with Pb sporozoites. Using sequences of the 28 novel Pb LS genes we screened ~400 peptides by the caged MHC class I tetramer approach. Our preliminary results demonstrate that 2 H-2Kb- and 1 H-2Db-restricted Pb peptides that correspond to protective Pb LS Ags form MHC class I tetramers that specifically bound to CD8 T cells from mice immunized with radiation-attenuated Pb sporozoites. Identification of these epitopes is crucial towards resolving the role of antigen-specific CD8 T cell responses and establishing these responses as correlates of protection to Plasmodia infection.

17

Reyzer, Michelle L., Jennifer S. Brodbelt, Alan P. Marchand, Zhibing Chen, Zilin Huang, and I. N. N. Namboothiri. "Determination of alkali metal binding selectivities of caged crown ligands by electrospray ionization quadrupole ion trap mass spectrometry." International Journal of Mass Spectrometry 204, no. 1-3 (February 2001): 133–42. http://dx.doi.org/10.1016/s1387-3806(00)00332-8.

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18

Petit, Morgane, Guillaume Bort, Bich-Thuy Doan, Cécile Sicard, David Ogden, Daniel Scherman, Clotilde Ferroud, and Peter I. Dalko. "X-ray Photolysis To Release Ligands from Caged Reagents by an Intramolecular Antenna Sensitive to Magnetic Resonance Imaging." Angewandte Chemie International Edition 50, no. 41 (July 21, 2011): 9708–11. http://dx.doi.org/10.1002/anie.201102948.

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19

Petit, Morgane, Guillaume Bort, Bich-Thuy Doan, Cécile Sicard, David Ogden, Daniel Scherman, Clotilde Ferroud, and Peter I. Dalko. "X-ray Photolysis To Release Ligands from Caged Reagents by an Intramolecular Antenna Sensitive to Magnetic Resonance Imaging." Angewandte Chemie 123, no. 41 (July 21, 2011): 9882–85. http://dx.doi.org/10.1002/ange.201102948.

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20

Blair, Sheryl M., Jennifer S. Brodbelt, Alan P. Marchand, Kaipenchery A. Kumar, and Hyun-Soon Chong. "Evaluation of Binding Selectivities of Caged Crown Ligands toward Heavy Metals by Electrospray Ionization/Quadrupole Ion Trap Mass Spectrometry." Analytical Chemistry 72, no. 11 (June 2000): 2433–45. http://dx.doi.org/10.1021/ac991125t.

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21

Finazzi, Ilaria, Ioannis Bratsos, Teresa Gianferrara, Alberta Bergamo, Nicola Demitri, Gabriele Balducci, and Enzo Alessio. "Photolabile RuIIHalf-Sandwich Complexes Suitable for Developing “Caged” Compounds: Chemical Investigation and Unexpected Dinuclear Species with Bridging Diamine Ligands." European Journal of Inorganic Chemistry 2013, no. 27 (August 2, 2013): 4743–53. http://dx.doi.org/10.1002/ejic.201300792.

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22

Blair, Sheryl M., Jennifer S. Brodbelt, Alan P. Marchand, Hyun-Soon Chong, and Sulejman Alihodžić. "Evaluation of alkali metal binding selectivities of caged aza-crown ether ligands by microelectrospray ionization/quadrupole ion trap mass spectrometry." Journal of the American Society for Mass Spectrometry 11, no. 10 (October 2000): 884–91. http://dx.doi.org/10.1016/s1044-0305(00)00166-5.

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23

Yang, Yang, Yanfang Yang, Xiangyang Xie, Xingshi Cai, and Xingguo Mei. "Synergistic targeted delivery of payload into cancer cells using liposomes co-modified with photolabile-caged cell-penetrating peptides and targeting ligands." Journal of Controlled Release 213 (September 2015): e128. http://dx.doi.org/10.1016/j.jconrel.2015.05.216.

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24

Namanga, Jude E., Niels Gerlitzki, Volodymyr Smetana, and Anja-Verena Mudring. "Supramolecularly Caged Green-Emitting Ionic Ir(III)-Based Complex with Fluorinated C^N Ligands and Its Application in Light-Emitting Electrochemical Cells." ACS Applied Materials & Interfaces 10, no. 13 (November 30, 2017): 11026–36. http://dx.doi.org/10.1021/acsami.7b18159.

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25

Luo, Y., R. Cooke, and E. Pate. "A model of stress relaxation in cross-bridge systems: effect of a series elastic element." American Journal of Physiology-Cell Physiology 265, no. 1 (July 1, 1993): C279—C288. http://dx.doi.org/10.1152/ajpcell.1993.265.1.c279.

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Many experimental protocols employed in the study of muscle mechanics use tension transients as a probe of the magnitudes of the kinetic rates in the underlying cross-bridge dynamics. These transients could potentially be modified by the elastic elements that exist both within the fiber and at the points of attachment to the experimental apparatus. To better understand the magnitude of such modifications, we have used computer simulation to investigate the transients that would be expected for cross bridges acting on an actin filament attached to an elastic element. The original model of cross-bridge mechanics by A.F. Huxley was used (Prog. Biophys. 7: 255-318, 1957). After an isometric equilibrium is achieved, a tension transient is produced by changing the dissociation rate constant, g1, while holding the attachment rate constant, f1, fixed. This decreases the number of attached, force-producing cross bridges. We find that the tension transients are markedly slowed by the presence of even a few (> or = 2) nanometers of series elastic strain per half-sarcomere. Thus some rate constants inferred from mechanical transients (e.g., those induced by caged ligands) may underestimate the actual kinetic rates of the cross-bridge processes.

26

Petit, Morgane, Guillaume Bort, Bich-Thuy Doan, Cécile Sicard, David Ogden, Daniel Scherman, Clotilde Ferroud, and Peter I. Dalko. "Innentitelbild: X-ray Photolysis To Release Ligands from Caged Reagents by an Intramolecular Antenna Sensitive to Magnetic Resonance Imaging (Angew. Chem. 41/2011)." Angewandte Chemie 123, no. 41 (August 30, 2011): 9682. http://dx.doi.org/10.1002/ange.201105350.

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27

Petit, Morgane, Guillaume Bort, Bich-Thuy Doan, Cécile Sicard, David Ogden, Daniel Scherman, Clotilde Ferroud, and Peter I. Dalko. "Inside Cover: X-ray Photolysis To Release Ligands from Caged Reagents by an Intramolecular Antenna Sensitive to Magnetic Resonance Imaging (Angew. Chem. Int. Ed. 41/2011)." Angewandte Chemie International Edition 50, no. 41 (August 30, 2011): 9510. http://dx.doi.org/10.1002/anie.201105350.

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28

Rosair, Georgina M., Greig Scott, and Alan J. Welch. "The exopolyhedral ligand orientation (ELO) in 3-(nitrato-κO)-3,3-bis(triphenylphosphane-κP)-3-rhoda-1,2-dicarba-closo-dodecaborane(11) dichloromethane 2.2-solvate." Acta Crystallographica Section C Structural Chemistry 71, no. 6 (May 13, 2015): 461–64. http://dx.doi.org/10.1107/s2053229615008724.

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In the title compound, [Rh(C2H11B9)(NO3)(C18H15P)2]·2.2CH2Cl2, studied as a 2.2-solvate of what was assumed to be dichloromethane, the nitrate ligand liesciswith respect to both cage C atoms. Accordingly, the compound displays a pronounced preferred exopolyhedral ligand orientation (ELO) which is traced to both the greatertransinfluence of the cage B over the cage C atoms and the greatertransinfluence of the triphenylphosphane ligands over the nitrate ligand. The overall molecular architecture therefore agrees with that of a number of similar 3-L-3,3-L′2-3,1,2-closo-MC2B9H11species in the literature.

29

Frank, Marina, Lennard Krause, Regine Herbst-Irmer, Dietmar Stalke, and Guido H. Clever. "Narcissistic self-sorting vs. statistic ligand shuffling within a series of phenothiazine-based coordination cages." Dalton Trans. 43, no. 11 (2014): 4587–92. http://dx.doi.org/10.1039/c3dt53243g.

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30

Astakhov, Grigorii, Mikhail Levitsky, Alexander Korlyukov, Lidia Shul’pina, Elena Shubina, Nikolay Ikonnikov, Anna Vologzhanina, et al. "New Cu4Na4- and Cu5-Based Phenylsilsesquioxanes. Synthesis via Complexation with 1,10-Phenanthroline, Structures and High Catalytic Activity in Alkane Oxidations with Peroxides in Acetonitrile." Catalysts 9, no. 9 (August 21, 2019): 701. http://dx.doi.org/10.3390/catal9090701.

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Self-assembly of copper(II)phenylsilsesquioxane assisted by the use of 1,10-phenanthroline (phen) results in isolation of two unusual cage-like compounds: (PhSiO1,5)12(CuO)4(NaO0.5)4(phen)4 1 and (PhSiO1,5)6(PhSiO1,5)7(HO0.5)2(CuO)5(O0.25)2(phen)3 2. X-Ray diffraction study revealed extraordinaire molecular architectures of both products. Namely, complex 1 includes single cyclic (PhSiO1,5)12 silsesquioxane ligand. Four sodium ions of 1 are additionally ligated by 1,10-phenanthrolines. In turn, “sodium-less” complex 2 represents coordination of 1,10-phenanthrolines to copper ions. Two silsesquioxane ligands of 2 are: (i) noncondensed cubane of a rare Si6-type and (ii) unprecedented Si7-based ligand including two HOSiO1.5 fragments. These silanol units were formed due to removal of phenyl groups from silicon atoms, observed in mild conditions. The presence of phenanthroline ligands in products 1 and 2 favored the π–π stacking interactions between neighboring cages. Noticeable that in the case of 1 all four phenanthrolines participated in such supramolecular organization, unlike to complex 2 where one of the three phenanthrolines is not “supramolecularly active”. Complexes 1 and 2 were found to be very efficient precatalysts in oxidations with hydroperoxides. A new method for the determination of the participation of hydroxyl radicals has been developed.

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Mejuto, Carmen, Gregorio Guisado-Barrios, Dmitry Gusev, and Eduardo Peris. "First homoleptic MIC and heteroleptic NHC–MIC coordination cages from 1,3,5-triphenylbenzene-bridged tris-MIC and tris-NHC ligands." Chemical Communications 51, no. 73 (2015): 13914–17. http://dx.doi.org/10.1039/c5cc05114b.

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32

Pozzi, Cecilia, Flavio Di Pisa, Daniela Lalli, Camilla Rosa, Elizabeth Theil, Paola Turano, and Stefano Mangani. "Time-lapse anomalous X-ray diffraction shows how Fe2+substrate ions move through ferritin protein nanocages to oxidoreductase sites." Acta Crystallographica Section D Biological Crystallography 71, no. 4 (March 27, 2015): 941–53. http://dx.doi.org/10.1107/s1399004715002333.

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Ferritin superfamily protein cages reversibly synthesize internal biominerals, Fe2O3·H2O. Fe2+and O2(or H2O2) substrates bind at oxidoreductase sites in the cage, initiating biomineral synthesis to concentrate iron and prevent potentially toxic reactions products from Fe2+and O2or H2O2chemistry. By freezing ferritin crystals ofRana catesbeianaferritin M (RcMf) at different time intervals after exposure to a ferrous salt, a series of high-resolution anomalous X-ray diffraction data sets were obtained that led to crystal structures that allowed the direct observation of ferrous ions entering, moving along and binding at enzyme sites in the protein cages. The ensemble of crystal structures from both aerobic and anaerobic conditions provides snapshots of the iron substrate bound at different cage locations that vary with time. The observed differential occupation of the two iron sites in the enzyme oxidoreductase centre (with Glu23 and Glu58, and with Glu58, His61 and Glu103 as ligands, respectively) and other iron-binding sites (with Glu53, His54, Glu57, Glu136 and Asp140 as ligands) reflects the approach of the Fe2+substrate and its progression before the enzymatic cycle 2Fe2++ O2→ Fe3+—O—O—Fe3+→ Fe3+—O(H)—Fe3+and turnover. The crystal structures also revealed different Fe2+coordination compounds bound to the ion channels located at the threefold and fourfold symmetry axes of the cage.

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Hailu, Solomon Legese, Balachandran Unni Nair, Mesfin Redi-Abshiro, Rathinam Aravindhan, Isabel Diaz, and Merid Tessema. "Experimental and computational studies on zeolite-Y encapsulated iron(iii) and nickel(ii) complexes containing mixed-ligands of 2,2′-bipyridine and 1,10-phenanthroline." RSC Advances 5, no. 108 (2015): 88636–45. http://dx.doi.org/10.1039/c5ra14954a.

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Mixed ligand complexes of 2,2′-bipyridine and 1,10-phenanthroline with iron(iii) and nickel(ii) have been encapsulated into a zeolite cage by the reaction of zeolite exchanged metal ion with flexible ligands.

34

Li, Qiang. "A three-dimensional anionic metal–dicyanamide network in poly[ethyltriphenylphosphonium [tri-μ2-dicyanamidato-cadmium(II)]]." Acta Crystallographica Section C Structural Chemistry 71, no. 1 (January 1, 2015): 65–68. http://dx.doi.org/10.1107/s2053229614027090.

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The title compound, (C20H20P)[Cd(C2N3)3], consists of ethyltriphenylphosphonium (EtPh3P+) cations filling voids in a three-dimensional anionic cadmium dicyanamide network. In the structure, each CdIIatom is connected to six neighbouring CdIIatoms through six separate dicyanamide ligands, forming cube-shaped cages. The three-dimensional anionic network encloses a solvent-accessible void space of 1851 Å3, amounting to 69.3% of the unit-cell volume. Each cage accommodates only one EtPh3P+cation.

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Liu, Jing-Jing, Yue-Jian Lin, Zhen-Hua Li, and Guo-Xin Jin. "Self-assembled half-sandwich polyhedral cages via flexible Schiff-base ligands: an unusual macrocycle-to-cage conversion." Dalton Transactions 45, no. 35 (2016): 13675–79. http://dx.doi.org/10.1039/c6dt02393b.

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Half-sandwich M₆(L1)₄ octahedral and M₈(L2)₄ cubic cages have been assembled by flexible Schiff-base ligands upon coordination to Cp*Rh(iii) organometallic acceptors. In particular, the Rh(iii)-based half-sandwich M₂(HL1)₂ macrocycle rearranges in solution to give a M₆(L1)₄ cage.

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Min, Hyunsung, Alexander R. Craze, Takahiro Taira, Matthew J. Wallis, Mohan M. Bhadbhade, Ruoming Tian, Daniel J. Fanna, et al. "Self-Assembly of a Rare High Spin FeII/PdII Tetradecanuclear Cubic Cage Constructed via the Metalloligand Approach." Chemistry 4, no. 2 (May 26, 2022): 535–47. http://dx.doi.org/10.3390/chemistry4020038.

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Polynuclear heterobimetallic coordination cages in which different metal cations are connected within a ligand scaffold are known to adopt a variety of polyhedral architectures, many of which display interesting functions. Within the extensive array of coordination cages incorporating Fe(II) centres reported so far, the majority contain low-spin (LS) Fe(II), with high-spin (HS) Fe(II) being less common. Herein, we present the synthesis and characterisation of a new tetradecanuclear heterobimetallic [Fe8Pd6L8](BF4]28 (1) cubic cage utilising the metalloligand approach. Use of the tripodal tris-imidazolimine derivative (2) permitted the formation of the tripodal HS Fe(II) metalloligand [FeL](BF4)2·CH3OH (3) that was subsequently used to form the coordination cage 1. Magnetic and structural analyses gave insight into the manner in which the HS environment of the metalloligand was transferred into the cage architecture along with the structural changes that accompanied its occupancy of the eight corners of the discrete cubic structure.

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Rangarajan, Shalini, Owen A. Beaumont, Maravanji S. Balakrishna, Glen B. Deacon, and Victoria L. Blair. "Synthesis and Characterisation of Novel Bis(diphenylphosphane oxide)methanidoytterbium(III) Complexes." Molecules 27, no. 22 (November 9, 2022): 7704. http://dx.doi.org/10.3390/molecules27227704.

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Reaction of [YbCp2(dme)] (Cp = cyclopentadienyl, dme = 1,2 dimethoxyethane) with bis(diphenylphosphano)methane dioxide (H2dppmO2) leads to deprotonation of the ligand H2dppmO2 and oxidation of ytterbium, forming an extremely air-sensitive product, [YbIII(HdppmO2)3] (1), a six-coordinate complex with three chelating (OPCHPO) HdppmO2 ligands. Complex 1 was also obtained by a redox transmetallation/protolysis synthesis from metallic ytterbium, Hg(C6F5)2, and H2dppmO2. In a further preparation, the reaction of [Yb(C6F5)2] with H2dppmO2, not only yielded compound 1, but also gave a remarkable tetranuclear cage, [Yb4(µ-HdppmO2)6(µ-F)6] (2) containing two [Yb(µ-F)]2 rhombic units linked by two fluoride ligands and the tetranuclear unit is encapsulated by six bridging HdppmO2 donors. The fluoride ligands of the cage result from C-F activation of pentafluorobenzene and concomitant formation of p-H2C6F4 and m-H2C6F4, the last being an unexpected product.

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Dang, Li-Long, Tian Chen, Ting-Ting Zhang, Ting-Ting Li, Jun-Liang Song, Ke-Jia Zhang, and Lu-Fang Ma. "Size-Induced Highly Selective Synthesis of Organometallic Rectangular Macrocycles and Heterometallic Cage Based on Half-Sandwich Rhodium Building Block." Molecules 27, no. 12 (June 10, 2022): 3756. http://dx.doi.org/10.3390/molecules27123756.

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The controlled synthesis of organometallic supramolecular macrocycles cages remains interesting and challenging work in the field of supramolecular chemistry. Here, two tetranuclear rectangular macrocycles and an octuclear cage were designed and synthesized utilizing a rigid and functionalized pillar linker, 2,6-bis(pyridin-4-yl)-1,7-dihydrobenzo [1,2-d:4,5-d′]diimidazole (BBI4PY) based on three half-sandwich rhodium building blocks bearing different sizes. X-ray crystallography in combination with 1H NMR spectroscopy elucidated that the two building blocks with shorter spacers only result in rectangular macrocycles. However, the building block of bulkier size to avoid the π-π stacking interactions between two ligands BBI4PY led to the formation of an octuclear cage complex. The latter cage contains two types of metal ions, namely Rh3+ and Cu2+, showing significant characteristics of heterogeneous metal-assembling compounds. In addition, the cage accommodates two free isopropyl ether solvent molecules, thus displaying host–guest behavior.

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Ferrara, Skylar J., Bo Wang, and James P. Donahue. "An S4-symmetric mixed-valent decacopper cage comprised of [CuII(L-S2N2)] complexes bridged by CuI(MeCN)n (n = 1 or 2) cations." Dalton Transactions 45, no. 7 (2016): 2997–3002. http://dx.doi.org/10.1039/c5dt04359j.

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Oxidative addition of 1,2,11,12-tetrathia-5,8,15,19-tetra(N-methylamino)cycloicosane to [Cu(MeCN)₄][BF₄] yields an S₄-symmetric decacopper cage compound with four cupric ions in distorted square planar bis(amino) bis(thiolato) ligand environments bridged by six cuprous ions with MeCN ligands.

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Cuello-Garibo, Jordi-Amat, Michael S. Meijer, and Sylvestre Bonnet. "To cage or to be caged? The cytotoxic species in ruthenium-based photoactivated chemotherapy is not always the metal." Chemical Communications 53, no. 50 (2017): 6768–71. http://dx.doi.org/10.1039/c7cc03469e.

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Zhao, Yibo, Yunfeng Lu, Ao Liu, Zhi-Yuan Zhang, Chunju Li, and Andrew C. H. Sue. "Macrocycle with Equatorial Coordination Sites Provides New Opportunity for Structure-Diverse Metallacages." Molecules 28, no. 6 (March 10, 2023): 2537. http://dx.doi.org/10.3390/molecules28062537.

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Reported here is the synthesis of a macrocycle with equatorial coordination sites for the construction of self-assembled metallacages. The macrocycle is prepared via a post-modification on the equator of biphen[n]arene. Utilizing this macrocycle as a ligand, three prismatic cages and one octahedral cage were synthesized by regulating the geometric structures and coordination number of metal acceptors. The multi-cavity configuration of prismatic cage was revealed by single-crystal structure. We prove that a macrocycle with equatorial coordination sites can be an excellent building block for synthesizing structure-diverse metallacages. Our results provide a typical example and a general method for the design and synthesis of metallacages.

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Samantray, Sagarika, Sreenivasulu Bandi, and Dillip K. Chand. "Design of a double-decker coordination cage revisited to make new cages and exemplify ligand isomerism." Beilstein Journal of Organic Chemistry 15 (May 21, 2019): 1129–40. http://dx.doi.org/10.3762/bjoc.15.109.

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The complexation study of cis-protected and bare palladium(II) components with a new tridentate ligand, i.e., pyridine-3,5-diylbis(methylene) dinicotinate (L1) is the focus of this work. Complexation of cis-Pd(tmeda)(NO3)2 with L1 at a 1:1 or 3:2 ratio produced [Pd(tmeda)(L1)](NO3)2 (1a). The reaction mixture obtained at 3:2 ratio upon prolonged heating, produced a small amount of [Pd3(tmeda)3(L1)2](NO3)6 (2a). Complexation of Pd(NO3)2 with L1 at a 1:2 or 3:4 ratios afforded [Pd(L1)2](NO3)2 (3a) and [(NO3)2@Pd3(L1)4](NO3)4 (4a), respectively. The encapsulated NO3 – ions of 4a undergo anion exchange with halides (F–, Cl– and Br– but not with I–) to form [(X)2@Pd3(L1)4](NO3)4 5a–7a. The coordination behaviour of ligand L1 and some dynamic properties of these complexes are compared with a set of known complexes prepared using the regioisomeric ligand bis(pyridin-3-ylmethyl)pyridine-3,5-dicarboxylate (L2). Importantly, a ligand isomerism phenomenon is claimed by considering complexes prepared from L1 and L2.

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Grobe, Joseph, Kai Lütke-Brochtrup, Bernt Krebs, Mechtild Läge, Hans-Hermann Niemeyer, and Ernst-Ulrich Würthwein. "Alternativ-Liganden XXXVIII. [1] Neue Versuche zur Synthese von Pd(0)- und Pt(0)-Komplexen des Tripod-Phosphanliganden FSi(CH2CH2PMe2)3 / Alternative Ligands XXXVIII. [1] Further Attempts to Synthesize Pd(0) and Pt(0) Complexes with the Tripod Phosphane Ligand FSi(CH2CH2PMe2)3." Zeitschrift für Naturforschung B 62, no. 1 (January 1, 2007): 55–65. http://dx.doi.org/10.1515/znb-2007-0109.

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The tripod phosphane ligand FSi(CH2CH2PMe2)3 (1) has been prepared again and attempts to generate F3CSi(CH2CH2PMe2)3 (2) were undertaken for the preparation of transition metal cage compounds of the type A(CCP)3M or A(CCP)3M-L (A = FSi, F3CSi). The photochemical addition of dimethylphosphane to trifluoromethyl-trivinylsilane, however, gave 1 instead of the expected CF3Sitripod ligand 2, obviously due to difluorocarbene elimination. 1 was used to prepare the chromium carbonyl derivative (CO)3Cr[(Me2PCH2CH2)3SiF] (3) from Cr(CO)3CHT, and 3 was characterized by NMR and IR spectroscopy. The novel complex FSi(CH2CH2PMe2)3Pd (4) and its PPh3 derivative [FSi(CH2CH2PMe2)3Pd]PPh3 (5) have been obtained by reacting 1 with Pd(PPh3)4 and were characterized by NMR (4) and X-ray diffraction (5). The data prove the expected Pd→Si interaction by characteristic coordination shifts and a Pd-Si distance of 3.875 Å which is smaller than the Ni-Si distance in the corresponding nickel compound (3.92 Å ). The preparation of the analogous platinum complex from the precursors Pt(PPh3)4, Pt(C7H10)3, or (Ph3P)2Pt(η2-C2H4) failed, whereas the reaction of 1 with Pt(PEt3)4 was successful, but surprisingly led to the trinuclear complex [FSi(CH2CH2PMe2)3Pt]3(PMe2CH2CH2)3SiF (6) with three cages of type 4 and an additional ligand 1 as a bridging unit. Complex 6 was isolated and characterized spectroscopically. Quantum chemical calculations have been used to elucidate the coordination geometry expected for 4, 5 and the corresponding platinum cage 4′ in 6. The calculations support the structure of 5 within the expected limitations of the experimental and theoretical methods and - in spite of the extremely soft coordination sphere of the studied cages - are in accord with the spectroscopic results.

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Al Rasbi, Nawal K., and Michael D. Ward. "Synthesis and crystal structure of an M 4 L 6 tetrahedral cage with outward-facing pockets from a substituted pyrazolyl–pyridine ligand." Acta Crystallographica Section C Structural Chemistry 74, no. 8 (July 24, 2018): 961–66. http://dx.doi.org/10.1107/s2053229618009683.

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The self-assembly of metal–polydentate ligands to give supramolecular tetrahedral complexes is of considerable current interest. A new ligand, 4-benzyl-2-[1-(2-{[3-(4-benzylpyridin-2-yl)-1H-pyrazol-1-yl]methyl}benzyl)-1H-pyrazol-3-yl]pyridine (L), with chelating pyrazolyl–pyridine units substituted on the 4-position of the pyridyl ring with benzyl units, has been synthesized and fully characterized. The self-assembly of L with cobalt(II) gave rise to a tetrahedral cage (hexakis{μ-4-benzyl-2-[1-(2-{[3-(4-benzylpyridin-2-yl)-1H-pyrazol-1-yl]methyl}benzyl)-1H-pyrazol-3-yl]pyridine}perchloratotetracobalt(II) octakis(perchlorate) acetonitrile undecasolvate, [Co4(ClO4)(C38H32N6)6](ClO4)7·11CH3CN) with approximate T symmetry. The X-ray crystal structure of the cage, i.e. [Co4 L 6\subsetClO4](ClO4)7, shows that the substituted benzyl groups are oriented away from the centres of their respective ligands towards the CoII vertices, making small outward-facing pockets from three benzyl rings at the corners of the tetrahedron.

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Simon, Cory M., Efrem Braun, Carlo Carraro, and Berend Smit. "Statistical mechanical model of gas adsorption in porous crystals with dynamic moieties." Proceedings of the National Academy of Sciences 114, no. 3 (January 3, 2017): E287—E296. http://dx.doi.org/10.1073/pnas.1613874114.

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Some nanoporous, crystalline materials possess dynamic constituents, for example, rotatable moieties. These moieties can undergo a conformation change in response to the adsorption of guest molecules, which qualitatively impacts adsorption behavior. We pose and solve a statistical mechanical model of gas adsorption in a porous crystal whose cages share a common ligand that can adopt two distinct rotational conformations. Guest molecules incentivize the ligands to adopt a different rotational configuration than maintained in the empty host. Our model captures inflections, steps, and hysteresis that can arise in the adsorption isotherm as a signature of the rotating ligands. The insights disclosed by our simple model contribute a more intimate understanding of the response and consequence of rotating ligands integrated into porous materials to harness them for gas storage and separations, chemical sensing, drug delivery, catalysis, and nanoscale devices. Particularly, our model reveals design strategies to exploit these moving constituents and engineer improved adsorbents with intrinsic thermal management for pressure-swing adsorption processes.

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Avramov, Pavel V., Alex A. Kuzubov, Seiji Sakai, Manabu Ohtomo, Shiro Entani, Yoshihiro Matsumoto, Natalia S. Eleseeva, Vladimir A. Pomogaev, and Hiroshi Naramoto. "Atomic structure and physical properties of fused porphyrin nanoclusters." Journal of Porphyrins and Phthalocyanines 18, no. 07 (July 2014): 552–68. http://dx.doi.org/10.1142/s1088424614500291.

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The atomic and electronic structures, mechanical properties and potential barriers of formation of a set of meso–meso β–β fused porphyrin/metalloporphyrin nanopages, nanotapes, nanotubes and 2D nanofabrics were studied by GGA LC-DFT technique using cluster and PBC models. The porphyrin pages of the nanoclusters are connected with each other by graphene fragments formed by meso–meso β–β links. Fusion of all the edges of six porphyrin/metalloporphyrin units produces a novel ~ 1 nm sized molecule of cubic symmetry with a hollow cage inside. It was found that all studied nanoclusters are metastable with formation energies 0.36–7.57 kcal/mol per atom. Under applied mechanical stress, the nanoclusters exhibit superelastic and ultrastrong properties with binding graphene fragments being the weakest links for mechanical rupture. Depending on the spin-dependent reaction pathways, the hollow caged nanoclusters exhibit almost zero or low potential energy barriers (1–10 kcal/mol) during the initial stages of self-assembly. All nanoclusters exibit the main features of the electronic structures of the parent porphyrins, in particular the nature of HOMO/LUMO states and the relative energetic positions of the metal d states. The induced curvature of the hollow cage nanoclusters leads to admixture of more than 2% of the dπ⊥ states to the dσ energy region and formation of vacant superatomic molecular orbitals of d character in cubic ligand field. The Fe -derived hollow-caged nanoclusters reveal extremely high spin states with small energy differences between ferromagnetic and antiferromagnetic configurations, which can be utilized for quantum holonomic computations.

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Boer, Stephanie A., and David R. Turner. "Self-selecting homochiral quadruple-stranded helicates and control of supramolecular chirality." Chemical Communications 51, no. 98 (2015): 17375–78. http://dx.doi.org/10.1039/c5cc07422c.

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Suzuki, Mitsuaki. "Open-cage Fullerenes as Ligands." Journal of Synthetic Organic Chemistry, Japan 79, no. 10 (October 1, 2021): 968–70. http://dx.doi.org/10.5059/yukigoseikyokaishi.79.968.

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Harrowfield, Jack, and Pierre Thuéry. "Uranyl Ion Complexes of Polycarboxylates: Steps towards Isolated Photoactive Cavities." Chemistry 2, no. 1 (February 20, 2020): 63–79. http://dx.doi.org/10.3390/chemistry2010007.

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Consideration of the extensive family of known uranyl ion complexes of polycarboxylate ligands shows that there are quite numerous examples of crystalline solids containing capsular, closed oligomeric species with the potential for use as selective heterogeneous photo-oxidation catalysts. None of them have yet been assessed for this purpose, and some have obvious deficiencies, although related framework species have been shown to have the necessary luminescence, porosity and, to some degree, selectivity. Aspects of ligand design and complex composition necessary for the synthesis of uranyl ion cages with appropriate luminescence and chemical properties for use in selective photo-oxidation catalysis have been analysed in relation to the characteristics of known capsules.

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Luise, Chiara, Dina Robaa, and Wolfgang Sippl. "Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study." Journal of Computer-Aided Molecular Design 35, no. 6 (June 2021): 695–706. http://dx.doi.org/10.1007/s10822-021-00391-9.

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AbstractSome of the main challenges faced in drug discovery are pocket flexibility and binding mode prediction. In this work, we explored the aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction by means of in silico approaches. We first investigated the Spindlin1 aromatic cage plasticity by analyzing the available crystal structures and through molecular dynamic simulations. Then we assessed the ability of rigid docking and flexible docking to rightly reproduce the binding mode of a known ligand into Spindlin1, as an example of a reader protein displaying flexibility in the binding pocket. The ability of induced fit docking was further probed to test if the right ligand binding mode could be obtained through flexible docking regardless of the initial protein conformation. Finally, the stability of generated docking poses was verified by molecular dynamic simulations. Accurate binding mode prediction was obtained showing that the herein reported approach is a highly promising combination of in silico methods able to rightly predict the binding mode of small molecule ligands in flexible binding pockets, such as those observed in some reader proteins.