Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reversible Ligand Pairing and Sorting Processes Leading to Heteroligated Palladium(II) Complexes with Hemilabile Ligands.

ABSTRACT: Halide-induced ligand pairing and sorting processes have been observed in the context of Pd(II) complexes with hemilabile P,S and P,O ligands. Mixing of the ligands Ph₂PCH₂CH₂SMe (7) and Ph₂PCH₂CH₂SPh (8) with a Pd(II) precursor in CH₂Cl₂ results in a mixture of [(7)₂ClPd]Cl, [(8)₂Cl₂Pd], and [(7)(8)ClPd]Cl complexes at 20 °C. This equilibrium can be driven toward the heteroligated structure [(7)(8)ClPd]Cl by (1) cooling the mixture or (2) precipitation with hexanes, leading to the exclusive formation of semiopen heteroligated complex cis-[κ ²-(7)-κ ¹-(8)ClPd]Cl (9a), as confirmed by a single-crystal X-ray diffraction study and solid state CPMAS ³¹P{¹H} NMR spectroscopy. Dissolution of 9a in CH₂Cl₂ leads to the original mixture of complexes, which illustrates the reversible nature of this ligand pairing and sorting process. Similar processes occur when a combination of P,S and P,O ligands is used. The semiopen heteroligated complexes can be chemically manipulated in a reversible fashion to form closed complexes, allowing for control of the relative position and flexibility between neighboring substituents in these "tweezer"-like structures. Control experiments suggest these ligand sorting and pairing processes occur via a halide-induced ligand rearrangement (HILR) reaction.

SUBMITTER: Ulmann PA

PROVIDER: S-EPMC8386660 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Cooperative catalytic methoxycarbonylation of alkenes: uncovering the role of palladium complexes with hemilabile ligands.

Project description:Mechanistic studies of the catalyst [Pd2(dba)3/1,1'-bis(tert-butyl(pyridin-2-yl)phosphanyl)ferrocene, L2] for olefin alkoxycarbonylation reactions are described. X-ray crystallography reveals the coordination of the pyridyl nitrogen atom in L2 to the palladium center of the catalytic intermediates. DFT calculations on the elementary steps of the industrially relevant carbonylation of ethylene (the Lucite ?-process) indicate that the protonated pyridyl moiety is formed immediately, which facilitates the formation of the active palladium hydride complex. The insertion of ethylene and CO into this intermediate leads to the corresponding palladium acyl species, which is kinetically reversible. Notably, this key species is stabilized by the hemilabile coordination of the pyridyl nitrogen atom in L2. The rate-determining alcoholysis of the acyl palladium complex is substantially facilitated by metal-ligand cooperation. Specifically, the deprotonation of the alcohol by the built-in base of the ligand allows a facile intramolecular nucleophilic attack on the acyl palladium species concertedly. Kinetic measurements support this mechanistic proposal and show that the rate of the carbonylation step is zero-order dependent on ethylene and CO. Comparing CH3OD and CH3OH as nucleophiles suggests the involvement of (de)protonation in the rate-determining step.

| S-EPMC5912013 | biostudies-literature

Sterically and Electronically Flexible Pyridylidene Amine Dinitrogen Ligands at Palladium: Hemilabile cis/trans Coordination and Application in Dehydrogenation Catalysis.

Project description:Ligand design is crucial for the development of new catalysts and materials with new properties. Herein, the synthesis and unique hemilabile coordination properties of new bis-pyridylidene amine (bis-PYE) ligands to palladium, and preliminary catalytic activity of these complexes in formic acid dehydrogenation are described. The synthetic pathway to form cationic complexes [Pd(bis-PYE)Cl(L)]X with a cis-coordinated N,N-bidentate bis-PYE ligand is flexible and provides access to a diversity of PdII complexes with different ancillary ligands (L=pyridine, DMAP, PPh3 , Cl, P(OMe)3 ). The 1 H NMR chemical shift of the trans-positioned PYE N-CH3 unit is identified as a convenient and diagnostic handle to probe the donor properties of these ancillary ligands and demonstrates the electronic flexibility of the PYE ligand sites. In the presence of a base, the originally cis-coordinated bis-PYE ligand adopts a N,N,N-tridentate coordination mode with the two PYE units in mutual trans position. This cis-trans isomerization is reverted in presence of an acid, demonstrating a unique structural and steric flexibility of the bis-PYE ligand at palladium in addition to its electronic adaptability. The palladium complexes are active in formic acid dehydrogenation to H2 and CO2 . The catalytic performance is directly dependent on the ligand bonding mode, the nature of the ancillary ligand, the counteranion, and additives. The most active system features a bidentate bis-PYE ligand, PPh3 as ancillary ligand and accomplishes turnover frequencies up to 525 h-1 in the first hour and turnover numbers of nearly 1000, which is the highest activity reported for palladium-based catalysts to date.

| S-EPMC10092520 | biostudies-literature

Binuclear palladium(I) and palladium(II) complexes of ortho-functionalized 1,3-bis(aryl)triazenido ligands.

Project description:Three new bis(aryl)triazene ligands, Ar-NNNH-Ar' [Ar = o-C(6)H(4)-CO(2)Me, Ar' = p-C(6)H(4)-CH(3) (2); Ar = Ar' = o-C(6)H(4)-CO(2)Me (3); Ar = o-C(6)H(4)-SMe, Ar' = p-C(6)H(4)-CH(3)) (4)], have been synthesized. The reaction of 1-4 with PdCl(2)(NCCH(3))(2) in the presence of a base afforded a series of binuclear diamagnetic palladium complexes. In these reactions, ligands 1-3 afforded the palladium(I) complexes [Pd(I)(o-MeO(2)C-C(6)H(4)-NNN-o-C(6)H(4)-CO(2)Me)](2) (5, monoclinic, space group P21/c, a = 8.6070(10) Angstrom, b = 14.3220(10) Angstrom, c = 12.7310(10) Angstrom, beta = 100.2950(10) degrees, Z = 2), [Pd(I)(o-MeO-C(6)H(4)-NNN-o-C(6)H(4)-OMe)](2) (6, triclinic, space group P, a = 6.6288(5) Angstrom, b = 10.2631(10) Angstrom, c = 11.0246(11) Angstrom, alpha = 85.579(6) degrees, beta = 80.885(6) degrees, gamma = 74.607(6) degrees, Z = 1), and [Pd(I)(o-MeO(2)C-C(6)H(4)-NNN-p-C(6)H(4)-CH(3))](2) (7, tetragonal, space group I41/a, a = 20.866(3) Angstrom, b = 20.866(3) Angstrom, c = 13.156(2) Angstrom, Z = 8). In contrast, the reaction of ligand 4 with PdCl(2)(NCCH(3))(2) resulted in the formation of a palladium(II) dimer, [Pd(II)(o-MeS-C(6)H(4)-NNN-p-C(6)H(4)-CH(3))Cl](2) (8, orthorhombic, space group P2(1)2(1)2, a = 10.4058(5) Angstrom, b = 16.2488(8) Angstrom, c = 9.9500(5) Angstrom, Z = 2).

| S-EPMC2543110 | biostudies-literature

Aptamers as Reversible Sorting Ligands for Preparation of Cells in Their Native State.

Project description:Although antibodies are routinely used to label and isolate a desired cell type from a more complex mixture of cells, via either fluorescence-activated cell sorting (FACS) or magnetic-activated cell sorting (MACS), such antibody labeling is not easily reversible. We describe an FACS and MACS compatible method to reversibly label and purify cells using aptamers. Magnetic beads loaded with the epidermal growth factor receptor (EGFR)-binding antagonistic aptamer E07 specifically isolated EGFR-expressing cells, and pure, label-free cells were recovered via treatment with an "antidote" oligonucleotide complementary to the aptamer. Additionally, while FACS sorting cells with E07 or EGFR antibody yielded EGFR(+) cells with impeded EGFR signaling, stripping off the aptamer via antidote treatment restored receptor function, returning cells to their native state, which was not possible with the antibody. The ability to reversibly label or isolate cells without compromising their function is a valuable, versatile tool with important implications for both the laboratory and clinic.

| S-EPMC7038790 | biostudies-literature

Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies.

Project description:In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that 67 out of 80 pairs exhibit stable geometries and optimal deviations from their macromolecular crystal occurrences. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. QM calculated interaction energies of base:ligand pairs reveal a rich hydrogen bonding landscape, ranging from weak interactions (base:other, -3 kcal/mol) to strong (base:phosphate, -48 kcal/mol) contacts. The analysis was further extended to study the biological importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in the context of RNA:ligand recognition. This can, in turn, contribute toward current efforts to develop antimicrobials that target RNAs.

| S-EPMC6800475 | biostudies-literature

Hemilabile Ligands as Mechanosensitive Electrode Contacts for Molecular Electronics.

Project description:Single-molecule junctions that are sensitive to compression or elongation are an emerging class of nanoelectromechanical systems (NEMS). Although the molecule-electrode interface can be engineered to impart such functionality, most studies to date rely on poorly defined interactions. We focused on this issue by synthesizing molecular wires designed to have chemically defined hemilabile contacts based on (methylthio)thiophene moieties. We measured their conductance as a function of junction size and observed conductance changes of up to two orders of magnitude as junctions were compressed and stretched. Localised interactions between weakly coordinating thienyl sulfurs and the electrodes are responsible for the observed effect and allow reversible monodentate⇄bidentate contact transitions as the junction is modulated in size. We observed an up to ≈100-fold sensitivity boost of the (methylthio)thiophene-terminated molecular wire compared with its non-hemilabile (methylthio)benzene counterpart and demonstrate a previously unexplored application of hemilabile ligands to molecular electronics.

| S-EPMC6899542 | biostudies-literature

Melting thermodynamics of reversible DNA/ligand complexes at interfaces.

Project description:A variety of solution methods exist for analysis of interactions between small molecule ligands and nucleic acids; however, accomplishing this task economically at the scale of hundreds to thousands of sequences remains challenging. Surface assays offer a prospective solution through array-based multiplexing, capable of mapping out the full sequence context of a DNA/ligand interaction in a single experiment. However, relative to solution assays, accurate quantification of DNA/ligand interactions in a surface format must contend with limited understanding of molecular activities and interactions at a solid-liquid interface. We report a surface adaptation of a solution method in which shifts in duplex stability, induced by ligand binding and quantified from melting transitions, are used for thermodynamic analysis of DNA/ligand interactions. The results are benchmarked against solution calorimetric data. Equilibrium operation is confirmed through superposition of denaturation/hybridization transitions triggered by heating and cooling. The antibiotic compound netropsin, which undergoes electrostatic and sequence-specific minor groove interactions with DNA, is used as a prototypical small molecule. DNA/netropsin interactions are investigated as a function of ionic strength and drug concentration through electrochemical tracing of surface melt transitions. Comparison with solution values finds excellent agreement in free energy, though reliable separation into enthalpic and entropic contributions proves more difficult. The results establish key guidelines for analysis of DNA-ligand interactions via reversible melting denaturation at surfaces.

| S-EPMC3498581 | biostudies-literature

Non-Oxido-Vanadium(IV) Metalloradical Complexes with Bidentate 1,2-Dithienylethene Ligands: Observation of Reversible Cyclization of the Ligand Scaffold in Solution.

Project description:Derivatives of 1,2-dithienylethene (DTE) have superb photochromic properties due to an efficient reversible photocyclization reaction of their hexatriene structure and, thus, have application potential in materials for optoelectronics and (multi-responsive) molecular switches. Transition-metal complexes bearing switchable DTE motifs commonly incorporate their coordination site rather distant from the hexatriene system. In this work the redox active ligand 1,2-bis(2,5-dimethylthiophen-3-yl)ethane-1,2-dione is described, which reacts with [V(TMEDA)2 Cl2 ] to give a rare non-oxido vanadium(IV) species 3(M,M/P,P). This blue complex has two bidentate en-diolato ligands which chelate the VIV center and give rise to two five-membered metallacycles with the adjacent hexatriene DTE backbone bearing axial chirality. Upon irradiation with UVA light or prolonged heating in solution, the blue compound 3(M,M/P,P) converts into the purple atropisomer 4(para,M/para,P). Both complexes were isolated and structurally characterized by single-crystal X-ray diffraction analysis (using lab source and synchrotron radiation). The antiparallel configuration (M or P helicity) present in both 3(M,M/P,P) and 4(para,M/para,P) is a prerequisite for (reversible) 6? cyclization reactions. A CW EPR spectroscopic study reveals the metalloradical character for 3(M,M/P,P) and 4(para,M/para,P) and indicates dynamic reversible cyclization of the DTE backbone in complex 3(M,M/P,P) at ambient temperature in solution.

| S-EPMC7027510 | biostudies-literature

Polymer ligand-induced autonomous sorting and reversible phase separation in binary particle blends.

Project description:The tethering of ligands to nanoparticles has emerged as an important strategy to control interactions and organization in particle assembly structures. We demonstrate that ligand interactions in mixtures of polymer-tethered nanoparticles (which are modified with distinct types of polymer chains) can impart upper or lower critical solution temperature (UCST/LCST)-type phase behavior on binary particle mixtures in analogy to the phase behavior of the corresponding linear polymer blends. Therefore, cooling (or heating) of polymer-tethered particle blends with appropriate architecture to temperatures below (or above) the UCST (or LCST) results in the organization of the individual particle constituents into monotype microdomain structures. The shape (bicontinuous or island-type) and lengthscale of particle microdomains can be tuned by variation of the composition and thermal process conditions. Thermal cycling of LCST particle brush blends through the critical temperature enables the reversible growth and dissolution of monoparticle domain structures. The ability to autonomously and reversibly organize multicomponent particle mixtures into monotype microdomain structures could enable transformative advances in the high-throughput fabrication of solid films with tailored and mutable structures and properties that play an important role in a range of nanoparticle-based material technologies.

| S-EPMC5182054 | biostudies-literature

Intracellular Deprotection Reactions Mediated by Palladium Complexes Equipped with Designed Phosphine Ligands.

Project description:Discrete palladium(II) complexes featuring purposely designed phosphine ligands can promote depropargylation and deallylation reactions in cell lysates. These complexes perform better than other palladium sources, which apparently are rapidly deactivated in such hostile complex media. This good balance between reactivity and stability allows the use of these discrete phosphine palladium complexes in living mammalian cells, whereby they can mediate similar transformations. The presence of a phosphine ligand in the coordination sphere of palladium also provides for the introduction of targeting groups, such as hydrophobic phosphonium moieties, which facilitate the accumulation of the complexes in mitochondria.

| S-EPMC6038097 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data