The Fascinating Flexibility and Coordination Modes of a Pentamethylene Connected Macrocyclic CNC Pincer Ligand
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ABSTRACT:
SUBMITTER: Jordan R
PROVIDER: S-EPMC8002578 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Bidentate and tridentate coordination of a 2,4-di-tert-butyl-substituted bridging amine bis-(phenolate) ligand to a palladium(II) center are observed within the same crystal structure, namely di-chlorido-({6,6'-[(ethane-1,2-diylbis(methyl-aza-nedi-yl)]bis-(methyl-ene)}bis-(2,4-di-tert-butyl-phenol))palladium(II) chlorido-(2,4-di-tert-butyl-6-{[(2-{[(3,5-di-tert-butyl-2-hy-droxy-phen-yl)meth-yl](meth-yl)amino}-eth-yl)(meth-yl)amino]-meth-yl}phenolato)palladium(II) methanol 1.685-solvate 0.315-hydrate, [PdCl2(C34H56N2O2)][PdCl(C34H55N2O2)]·1.685CH3OH·0.315H2O. Both complexes exhibit a square-planar geometry, with unbound phenol moieties participating in inter-molecular hydrogen bonding with co-crystallized water and methanol. The presence of both ?2 and ?3 coordination modes arising from the same solution suggest a dynamic process in which phenol donors may coordinate or dissociate from the metal center, and offers insight into catalyst speciation throughout Pd-mediated processes. The unit cell contains di-chlorido-({6,6'-[(ethane-1,2-diylbis(methyl-aza-nedi-yl)]bis-(methyl-ene)}bis-(2,4-di-tert-butyl-phenol))palladium(II), {(L 2)PdCl2}, and chlorido-(2,4-di-tert-butyl-6-{[(2-{[(3,5-di-tert-butyl-2-hy-droxy-phen-yl)meth-yl](methyl)amino}eth-yl)(meth-yl)amino]-meth-yl}phenolato)palladium(II), {(L 2 X)PdCl}, mol-ecules as well as fractional water and methanol solvent mol-ecules.
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Project description:Large and flexible ligands gain increasing interest in the development of bioactive agents. They challenge the applicability of computational ligand optimization strategies originally developed for small molecules. Free energy perturbation (FEP) is often used for predicting binding affinities of small molecule ligands, however, its use for more complex ligands remains limited. Herein, we report the structure-based design of peptide macrocycles targeting the protein binding site of human adaptor protein 14-3-3. We observe a surprisingly strong dependency of binding affinities on relatively small variations in substituent size. FEP was performed to rationalize observed trends. To account for insufficient convergence of FEP, restrained calculations were performed and complemented with extensive REST MD simulations of the free ligands. These calculations revealed that changes in affinity originate both from altered direct interactions and conformational changes of the free ligand. In addition, MD simulations provided the basis to rationalize unexpected trends in ligand lipophilicity. We also verified the anticipated interaction site and binding mode for one of the high affinity ligands by X-ray crystallography. The introduced fully-atomistic simulation protocol can be used to rationalize the development of structurally complex ligands which will support future ligand maturation efforts.
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Project description:The mechanism for the borylation of an aromatic substrate by a cobalt pincer complex was investigated by density functional theory calculations. Experimental observations identified trans-(iPrPNP)CoH2(BPin) as the resting state in the borylation of five-membered heteroarenes, and 4-BPin-(iPrPNP)Co(N2)BPin as the resting state in the catalytic borylation of arene substrates. The active species, 4-R-(iPrPNP)CoBPin (R=H, BPin), were generated by reductive elimination of H2 in the former, through Berry pseudorotation to the cis isomer, and N2 loss in the latter. The catalytic mechanism of the resulting Co(I) complex was computed to involve three main steps: C-H oxidative addition of the aromatic substrate (C6H6), reductive elimination of PhBPin, and regeneration of the active complex. The oxidative addition product formed through the most favorable pathway, where the breaking C-H bond of C6H6 is parallel to a line between the two phosphine atoms, leaves the complex with a distorted PNP ligand, which rearranges to a more stable complex via dissociation and re-association of HBPin. Alternative pathways, ?-bond metathesis and the oxidative addition in which the breaking C-H bond is parallel to the Co-B bond, are predicted to be unlikely for this Co(I) complex. The thermodynamically favorable formation of the product PhBPin via reductive elimination drives the reaction forward. The active species regenerates through the oxidative addition of B2Pin2 and reductive elimination of HBPin. In the overall reaction, the flipping (refolding) of the five-membered phosphine rings, which connects the species with two phosphine rings folded in the same direction and that with them folded in different directions, is found to play an important role in the catalytic process, as it relieves steric crowding within the PNP ligand and opens Co coordination space. Metal-ligand cooperation based on the ligand's aromatization/dearomatization, a common mechanism for heavy-metal pincer complexes, and the dissociation of one phosphine ligand, do not apply in this system. This study provides guidance for understanding important features of pincer ligands with first-transition-row metals that differ from those in heavier metal complexes.
| S-EPMC6358283 | biostudies-literature
Project description:This report describes a synthetic protocols and the crystal structures involving a novel pincer-type H3[NNN] ligand, namely di-μ-bromido-μ-{2-(2,2-di-methylpropanimido-yl)-N-[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-bis-[(diethyl ether)lithium], [Li2Br2(C24H33N3)(C4H10O)2] (1) and a dinuclear metal complex, namely di-μ-bromido-2:3κ4Br:Br-bis-{2-(2,2-di-methylpropanimido-yl)-N-[2-(2,2-di-methyl-propanimido-yl)-4-methyl-phen-yl]-4-methylaniline}-1κ3N,N',N'';4κ3N,N',N''-tetra-μ-iso-propano-lato-1:2κ4O:O;3:4κ4O:O-diiso-propano-lato-1κO,4κO-2,3-dilithium-1,4-dititanium, [Li2Ti2Br2(C24H32N3)2(C3H7O)6] or {[NHNNH]Ti(O i Pr)3(LiBr)2}2 (2). Complex 1, which sits on a twofold rotation axis, is a rare example of a pincer-type ligand which bears ketimine side arms. A unique feature of complex 1 is that the ketimine N atoms have an LiBr(Et2O) fragment bonded to them, with the Li atom adopting a distorted tetra-hedral geometry. This particular fragment creates an LiBr bridge between the two ketimine sidearms, which leads to a cage-type appearance of the ligand. Complex 2 consists of the previously described ligand and a TiIV metal atom in an octa-hedral environment, and is located on an inversion center. Complex 2 crystallizes as a dinuclear species with the metal atoms being bridged by an LiBr entity [the Br atoms are disordered and refined in two positions with their site occupation factors refining to 0.674 (12)/0.372 (12)], and the Li cation being bonded to the isopropoxide O atoms (Li having a tetra-hedral coordination as in 1). The organic ligand of compound 2 exhibits disorder in its periphery groups; isopropyl and tert-butyl groups (occupation factors fixed at 0.6/0.4). The novel [NNN]H3 pincer-type ligand was characterized by multinuclear and multidimensional NMR, HRMS and X-ray crystallography. The dinuclear metal complex 2 was characterized by X-ray crystallography. Although each structure exhibits donor N-H groups, no hydrogen bonding is found in either one, perhaps due to the bulky groups around them. One of the ethyl groups of the ether ligand of 1 is disordered and refined in two parts with site-occupation factors of 0.812 (8) and 0.188 (8). One and a half toluene solvent mol-ecules are also present in the asymmetric unit of 2. The toluene mol-ecules were significantly disordered and could not be modeled properly, thus SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18] was used to remove their contributions to the overall intensity data.
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Project description:Based on previous work related to the design and application of rigid tridentate phosphine-pyridine-phenyl coordination offered by a PNC-pincer ligand upon cyclometalation to nickel, the synthesis, spectroscopic and solid state characterization and redox-reactivity of two NiII(PNC) complexes featuring either a methyl (2CH3 ) or CF3 co-ligand (2CF3 ) are described. One-electron oxidation is proposed to furnish C-C reductive elimination, as deduced from a combined chemical, electrochemical, spectroscopic and computational study. One-electron reduction results in a ligand-centered radical anion, as supported by electrochemistry, UV spectroelectrochemistry, EPR spectroscopy, and DFT calculations. This further attenuates the breadth of chemical reactivity offered by such PNC-pincer ligands.
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Project description:Pincer ligands have a remarkable ability to impart control over small molecule activation chemistry and catalytic activity; therefore, the design of new pincer ligands and the exploration of their reactivity profiles continues to be a frontier in synthetic inorganic chemistry. In this work, a novel, monoanionic NNN pincer ligand containing two phosphinimine donors was used to create a series of mononuclear Ni complexes. Ligand metallation in the presence of NaOPh yielded a nickel phenoxide complex that was used to form a mononuclear hydride complex on treatment with pinacolborane. Attempts at ligand metallation with NaN(SiMe3)2 resulted in the activation of both phosphinimine methyl groups to yield an anionic, cis-dialkyl product, in which dissociation of one phosphinimine nitrogen leads to retention of a square planar coordination environment about Ni. Protonolysis of this dialkyl species generated a monoalkyl product that retained the 4-membered metallacycle. The insertion of 2,6-dimethylphenyl isocyanide (xylNC) into this nickel metallacycle, followed by proton transfer, generated a new five-membered nickel metallacycle. Kinetic studies suggested rate-limiting proton transfer (KIE ≥ 3.9 ± 0.5) from the α-methylene unit of the putative iminoacyl intermediate.
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Project description:The bis-ortho-thioether 9,10-bis[(o-methylthio)phenyl]anthracene was synthesized as a syn-atropisomer, as revealed by X-ray diffraction. This alkylaryl thioether ligand (L) formed different macrocyclic complexes by coordination with silver(I) salts depending on the nature of the anion: M2L2 for AgOTf and AgOTFA, M6L4 for AgNO3. A discrete M2L complex was obtained in the presence of bulky PPh3AgOTf. These silver(I) complexes adopted similar structures in solution and in the solid state. As each sulfur atom in the ligand is prochiral, macrocycles L2M2 were obtained as mixtures of diastereoisomers, depending on the configurations of the sulfur atoms coordinated to silver cations. The X-ray structures of the two L2·(AgOTf)2 stereoisomers highlighted their different geometry. The catalytic activity of all silver(I) complexes was effective under homogeneous conditions in two tandem addition/cycloisomerization of alkynes using 0.5-1 mol % of catalytic loading.
| S-EPMC6808213 | biostudies-literature
Project description:Reactions of N'N'-bis(3-pyridylmethyl)oxalamide (L1), N'N'-bis(4-pyridylmethyl)oxalamide (L2), or N,N'-bis(3-pyridylmethyl)adipoamide) (L3) with angular dicarboxylic acids and Ni(II) salts under hydro(solvo)thermal conditions afforded a series of coordination polymers: {[Ni(L1)(OBA)(H2O)]·H2O}n (H2OBA = 4,4-oxydibenzoic acid), 1, {[Ni(L1)(SDA)(H2O)2]·H2O·CH3OH}n (H2SDA = 4,4-sulfonyldibenzoic acid), 2, {[Ni(L2)(OBA)]·C2H5OH}n, 3, {[Ni(L2)(OBA)]·CH3OH}n, 4, {[Ni2(L2)(SDA)2(H2O)3]·5H2O}n, 5, {[Ni2(L2)(SDA)2(H2O)3]·H2O·2C2H5OH}n, 6, {[Ni(L3)(OBA)(H2O)2]·2H2O}n, 7, {[Ni(L3)(SDA)(H2O)2]·2H2O}n, 8, and {[Ni(L3)0.5(SDA)(H2O)2]·0.5C2H5OH}n, 9, which have been structurally characterized by using single-crystal X-ray crystallography. Complex 1 exhibits an interdigitated 2D layer with the 2,4L2 topology and 2 is a 2D layer with the sql topology, while 3 and 4 are 3D frameworks resulting from polycatenated 2D nets with the sql topology and 5 and 6 are 2-fold interpenetrated 3D frameworks with the dia topology. Complexes 7 and 8 are 1D looped chains and 9 is a 2D layer with the 3,4L13 topology. The various structural types in 1-9 indicate that the structural diversity is subject to the flexibility and donor atom position of the neutral spacer ligands and the identity of the angular dicarboxylate ligands, while the role of the solvent is uncertain. The iodine adsorption of 1-9 was also investigated, demonstrating that that the flexibility of the spacer L1-L3 ligands can be an important factor that governs the feasibility of the iodine adsorption. Moreover, complex 9 shows a better iodine adsorption and encapsulates 166.55 mg g-1 iodine in the vapor phase at 60 °C, which corresponded to 0.38 molecules of iodine per formula unit.
| S-EPMC8998537 | biostudies-literature
Project description:Nitrile hydration provides access to amides that are important structural elements in organic chemistry. Here we report catalytic nitrile hydration using ruthenium catalysts based on a pincer scaffold with a dearomatized pyridine backbone. These complexes catalyze the nucleophilic addition of H2O to a wide variety of aliphatic and (hetero)aromatic nitriles in t BuOH as solvent. Reactions occur under mild conditions (room temperature) in the absence of additives. A mechanism for nitrile hydration is proposed that is initiated by metal-ligand cooperative binding of the nitrile.
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