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“Preorganized” ligand

Xu Jing, Cheng He, Liang Zhao, Chunying Duan
Inspired by natural photosynthesis, researchers have designed symmetric metal-organic hosts with large inner pockets that are spontaneously generated through preorganized ligands and functionalized metallocorners to construct dye-containing host-guest systems. The abundant noncovalent interaction sites in the pockets of the hosts facilitated substrate-catalyst interactions for possible enrichment, fixation, and activation of substrates/reagents, providing special electron transfer pathways for regio- or stereoselectively photocatalytic chemical transformations...
December 26, 2018: Accounts of Chemical Research
Xiang-He Kong, Qun-Yan Wu, Jian-Hui Lan, Cong-Zhi Wang, Zhi-Fang Chai, Chang-Ming Nie, Wei-Qun Shi
Pyridylpyrazole ligands have shown excellent competence for partitioning actinides from lanthanides. As far as we know, the preorganization structure of the ligand has a great impact on the extraction separation ability. However, the mechanism that works well for some ligands but fails for others needs to be clearly elucidated. In this work, we designed three various pyridylpyrazole ligands, BPP, BPBP, and BPPhen, and further preorganized one or both side pyrazole rings of these ligands. The properties of these ligands and the coordination structures, bonding nature and thermodynamic behaviors of the related Am(III) and Eu(III) complexes have been systematically studied in a theoretical fashion...
November 9, 2018: Inorganic Chemistry
Amanda Li, Michael K Gilson
Calorimetric studies of protein-ligand binding sometimes yield thermodynamic data that are difficult to understand. Today, molecular simulations can be used to seek insight into such calorimetric puzzles, and, when simulations and experiments diverge, the results can usefully motivate further improvements in computational methods. Here, we apply near-millisecond duration simulations to estimate the relative binding enthalpies of four peptidic ligands with the Grb2 SH2 domain. The ligands fall into matched pairs, where one member of each pair has an added bond that preorganizes the ligand for binding and thus may be expected to favor binding entropically, due to a smaller loss in configurational entropy...
August 21, 2018: Journal of Chemical Physics
Ye Lu, Hai-Ning Zhang, Guo-Xin Jin
Over the last two decades, interlocked molecular species have received considerable attention, not only because of their intriguing structures and topological importance, but also because of their potential applications as smart materials, nanoscale devices, and molecular machines. Through judicious choice of metal centers and their adjoining ligands, a range of interesting interlocked structures have been realized by coordination-driven self-assembly. In addition, researchers have extensively developed synthetic methodologies for the construction of organized self-assemblies...
September 18, 2018: Accounts of Chemical Research
Peter Comba, Marion Kerscher, Katharina Rück, Miriam Starke
Very rigid tetra-, penta-, hexa-, hepta- and octadentate bispidine ligands are well preorganized for specific coordination geometries. The broad range of coordination numbers, geometries and donor sets allows one to design and prepare bispidines for many specific metal ions and applications. Major requirements for radiopharmaceuticals are efficient labeling, inertness under physiological conditions and easy functionalization of the ligands with biological vectors. The reasons why bispidines are among the most favorable chelators for radiopharmaceutical applications, a comprehensive list of bispidine ligands and a range of examples where bispidines have been used to develop radiopharmaceuticals for future applications in diagnosis and therapy are discussed...
July 17, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Sharrol T Bachas, Adrian R Ferré-D'Amaré
The large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn2+ . X-ray crystallography revealed a binuclear cation-binding pocket. This comprises one hexacoordinate site, with six oxygen ligands, which preorganizes the second, with five oxygen and one nitrogen ligands. The relatively soft nitrogen ligand was proposed to confer affinity for Mn2+ , but how this excludes other soft cations remained enigmatic...
August 16, 2018: Cell Chemical Biology
Wenqi Liu, Allen G Oliver, Bradley D Smith
Two macrocyclic tetralactam receptors are shown to selectively encapsulate anionic, square-planar chloride and bromide coordination complexes of gold(III), platinum(II), and palladium(II). Both receptors have a preorganized structure that is complementary to its precious metal guest. The receptors do not directly ligate the guest metal center but instead provide an array of arene π-electron donors that interact with the electropositive metal and hydrogen-bond donors that interact with the outer electronegative ligands...
June 6, 2018: Journal of the American Chemical Society
Jérémy Salaam, Lilia Tabti, Sylvana Bahamyirou, Alexandre Lecointre, Oscar Hernandez Alba, Olivier Jeannin, Franck Camerel, Sarah Cianférani, Embarek Bentouhami, Aline M Nonat, Loïc J Charbonnière
A series of polynuclear assemblies based on ligand L (1,4,7-tris[hydrogen (6-methylpyridin-2-yl)phosphonate]-1,4,7-triazacyclononane) has been developed. The coordination properties of ligand L with LnIII (Ln = La, Eu, Tb, Yb, Lu) have been studied in water (pH = 7.0) and in D2 O (pD = 7.0) by UV-absorption spectrometry, spectrofluorimetry, 1 H and 31 P NMR, DOSY, ESI-mass spectrometry, and X-ray diffraction. This nonadentate ligand forms highly stable mononuclear complexes in water and provides a very efficient shielding of the Ln cations, as emphasized by the very good luminescence properties of the Yb complex in D2 O, especially regarding its lifetime (τD2 O = 10...
May 21, 2018: Inorganic Chemistry
Sandra S Nurttila, Pim R Linnebank, Tetiana Krachko, Joost N H Reek
The hydroformylation reaction is one of the most intensively explored reactions in the field of homogeneous transition metal catalysis, and many industrial applications are known. However, this atom economical reaction has not been used to its full potential, as many selectivity issues have not been solved. Traditionally, the selectivity is controlled by the ligand that is coordinated to the active metal center. Recently, supramolecular strategies have been demonstrated to provide powerful complementary tools to control activity and selectivity in hydroformylation reactions...
April 6, 2018: ACS Catalysis
Ines Starke, Andreas Koch, Stefan Kammer, Hans-Jürgen Holdt, Heiko Michael Möller
The complex formation of the following diazaperylene ligands (L) 1,12-diazaperylene 1, 1,1'-bisisoquinoline 2, 2,11-disubstituted 1,12-diazaperylenes (alkyl = methyl, ethyl, isopropyl, 3, 5, 7), 3,3'-disubstituted 1,1'-bisisoquinoline (alkyl = methyl, ethyl, isopropyl, 4, 6, 8 and with R = phenyl, 11 and with pyridine 12), and the 5,8-dimethoxy-substituted diazaperylene 9, 6,6'-dimethoxy-substituted bisisoquinoline 10 with AgBF4 was investigated. Collision-induced dissociation measurements were used to evaluate the relative stabilities of the ligands themselves and for the [1:1]+ complexes as well as for the homoleptic and heteroleptic silver [1:2]+ complexes in the gas phase...
May 2018: Journal of Mass Spectrometry: JMS
Patrizia Rossi, Eleonora Macedi, Paola Paoli, Luca Giorgi, Mauro Formica, Vieri Fusi
The title compound, [CaCo2 (C22 H30 N4 O6 )2 ](ClO4 )2 ·1.36H2 O or {Ca[Co(H-2 L1 )]2 }·2ClO4 ·1.36H2 O {where L1 is 4,10-bis-[(3-hy-droxy-4-pyron-2-yl)meth-yl]-1,7-dimethyl-1,4,7,10-tetra-aza-cyclo-dodecane}, is a trinuclear complex whose asymmetric unit comprises a quarter of the {Ca[Co(H-2 L1 )]2 }2+ trinuclear complex, half of a perchlorate ion and 0.34-water mol-ecules. In the neutral [Co(H-2 L1 )] moiety, the cobalt ion is hexa-coordinated in a trigonal-prismatic fashion by the surrounding N4 O2 donor set...
December 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
Justin D Northrup, Giulia Mancini, Claire R Purcell, Christian E Schafmeister
Creating functional macromolecules that possess the diversity and functionality of proteins poses an enormous challenge, as this requires large, preorganized macromolecules to facilitate interactions. Peptoids have been shown to interact with proteins, and combinatorial libraries of peptoids have been useful in discovering new ligands for protein binding. We have created spiroligomer-peptoid hybrids that have a spirocyclic core that preorganizes functional groups in three-dimensional space. By utilizing spiroligomers, we can reduce the number of rotatable bonds between functional groups while increasing the stereochemical diversity of the molecules...
December 15, 2017: Journal of Organic Chemistry
Sarah Richard, Gaëtan Le Duc, Nicolas Le Poul, Yves Le Mest, Olivia Reinaud, Jean-Noël Rebilly
A new calix[6]arene scaffold bearing a tris-imidazole binding site at the small rim and three tetradentate aza ligands at the large rim was synthesized. The system binds three CuII ions at the large rim sites and is unable to bind a fourth one, which remains in solution. The charge repulsion between the complexes, together with the flexibility of the scaffold, disorganizes the small rim site for binding and prevents its use for host-guest studies. Although the presence of MeCN or DMF guests does not alter this state, the addition of a heptylamine guest, which further displays Brønsted basicity, restores its receptor ability by stabilizing the extra CuII ion at the tris-imidazole site with concomitant guest encapsulation and binding of an exo hydroxo ligand...
November 14, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
A S Saglam, D W Wang, M C Zwier, L T Chong
Many intrinsically disordered proteins, which are prevalent in nature, fold only upon binding their structured partner proteins. Such proteins have been hypothesized to have a kinetic advantage over their folded, preorganized analogues in binding their partner proteins. Here we determined the effects of ligand preorganization on the kon for a biomedically important system: an intrinsically disordered p53 peptide ligand and the MDM2 protein receptor. Based on direct simulations of binding pathways, computed kon values for fully disordered and preorganized p53 peptide analogues were within error of each other, indicating little if any kinetic advantage to being disordered or preorganized for binding the MDM2 protein...
November 2, 2017: Journal of Physical Chemistry. B
Yimu Hu, Elisabeth Drouin, Dominic Larivière, Freddy Kleitz, Frédéric-Georges Fontaine
Separating the rare earth elements (REEs) in an economically and environmentally sustainable manner is one of the most pressing technological issues of our time. Herein, a series of preorganized bidentate phthaloyl diamide (PA) ligands was synthesized and grafted on large-pore 3-dimensional (3-D) KIT-6 mesoporous silica. The synthesized sorbents were fully characterized by N2 physisorption, FT-IR, 13 C cross-polarization (CP) and 29 Si magic-angle spinning (MAS) NMR, thermogravimetric analysis-differential thermal analysis (TGA-DTA), and elemental analysis...
November 8, 2017: ACS Applied Materials & Interfaces
Mehdi Elsayed Moussa, Michael Seidl, Gábor Balázs, Manfred Zabel, Alexander V Virovets, Bianca Attenberger, Andrea Schreiner, Manfred Scheer
An AgI dimer capped with labile organometallic diphosphorus ligands [Cp2 Mo2 (CO)4 (η2 -P2 )] (Cp=C5 H5 ) acts as a highly pre-organized molecular precursor to direct the construction of 1D or 2D, and 3D organometallic-organic hybrid coordination polymers upon reaction with ditopic pyridine-based linkers. The formation of the supramolecular aggregates can be controlled by the stoichiometry of the organic molecules, and the mechanism is supported by DFT calculations.
November 16, 2017: Chemistry: a European Journal
Matthew J Bick, Per J Greisen, Kevin J Morey, Mauricio S Antunes, David La, Banumathi Sankaran, Luc Reymond, Kai Johnsson, June I Medford, David Baker
We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability...
September 19, 2017: ELife
H V Lavrov, N A Ustynyuk, P I Matveev, I P Gloriozov, S S Zhokhov, M Yu Alyapyshev, L I Tkachenko, I G Voronaev, V A Babain, S N Kalmykov, Yu A Ustynyuk
We have predicted earlier by DFT simulation that tridentate O,N,O-donor cyclic dilactams (B) belonging to the family of pyridine-2,6-dicarboxamides are much more selective and efficient extractants for the separation of lanthanides and actinides than open-structure pyridine-2,6-dicarboxamides due to the higher degree of "ligand preorganization". In the present work, three new ligands of type (B) were synthesized. Extraction experiments showed that, in line with the data from DFT simulation, these ligands have 5-6-fold higher selectivity for the separation of an Am3+ /Eu3+ pair and provide distribution coefficients D which are by three orders of magnitude higher than those for the related parent ligands with an open structure...
August 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
S Harikrishna, Saikiran Kotaru, P I Pradeepkumar
Stabilization of a G-quadruplex (G4) DNA structure in the proto-oncogene c-MYC using small molecule ligands has emerged as an attractive strategy for the development of anticancer therapeutics. To understand the subtle structural changes in the G4 structure upon ligand binding, molecular dynamics (MD) simulations of c-MYC G4 DNA were carried out in a complex with six different potent ligands: 3AQN, 6AQN, 3APN, 360A, Nap-Et, and Nap-Pr. The results show that the ligands 3AQN, 6AQN, 3APN, and 360A stabilize the G4 structure by making stacking interactions with the top quartet...
July 25, 2017: Molecular BioSystems
Santa Jansone-Popova, Alexander S Ivanov, Vyacheslav S Bryantsev, Frederick V Sloop, Radu Custelcean, Ilja Popovs, Madeline M Dekarske, Bruce A Moyer
We report a new family of preorganized bis-lactam-1,10-phenanthroline (BLPhen) complexants that possess both hard and soft donor atoms within a convergent cavity and show unprecedented extraction strength for the trivalent f-block metal ions. BLPhen ligands with saturated and unsaturated δ-lactam rings have notable differences in their affinity and selectivity for Am(III) over Eu(III), with the latter being the most selective mixed N,O-donor extractant of Am(III) reported to date. Saturated BLPhen was crystallized with five Ln(III) nitrates to form charge-neutral 1:1 complexes in the solid state...
May 15, 2017: Inorganic Chemistry
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