THF-solvated Heavy Alkali Metal Benzyl Compounds (Na, Rb, Cs): Defined Deprotonation Reagents for Alkali Metal Mediation Chemistry.
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ABSTRACT:
SUBMITTER: Brieger L
PROVIDER: S-EPMC9298144 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The title alkali propano-ates poly[(?5-propano-ato)alkali(I)], M +(C2H5COO)-, with alkali/M + = Na+, K+, Rb+ and Cs+, show close structural similarity, which is manifested by the coordination of the cations by six oxygen atoms in a chessboard motif, forming a bilayer. This bilayer is situated between hydro-phobic layers composed of dangling ethyl chains from the carboxyl-ate groups. Stacking of these two-dimensional sandwiches, which are parallel to (001), forms the title structures. Each metal cation is coordinated by six O atoms in the form of a distorted trigonal prism. One pair of these oxygen atoms belongs to a bridging, bidentately coordinating carboxyl-ate anion, while each of the other four oxygen atoms belongs to different carboxyl-ate groups, which are in a bridging monodentate mode. Despite the close similarity, each of the studied alkali propano-ates crystallizes in a different space group. The atoms are in general positions, except for the cation in K+(C2H5COO)-, which is situated on a mirror plane. Positional disorder of the methyl groups that are disordered over two positions is present in the Na+ and K+ propano-ates, in contrast to the Rb+ and Cs+ propano-ates. In the Na+ compound, the occupational parameters of the disordered methyl groups are different compared to the K+ compound where they are equal. This difference results in doubling of the a unit-cell parameter of the Na+ compound with respect to that of the K+ compound, otherwise the structures are homeotypic. In Cs+ propano-ate, a disorder of the methyl H atoms is observed.
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Project description:Synergic combinations of alkali-metal hydrocarbyl/amide reagents were used to synthesise saturated N-heterocyclic carbene (NHC) ligands tethered to a fluorenide anion through deprotonation of a spirocyclic precursor, whereas conventional bases were not successful. The Li2 derivatives displayed a bridging amide between two Li atoms within the fluorenide-NHC pocket, whereas the Na2 and K2 analogues displayed extended solid-state structures with the fluorenide-NHC ligand chelating one alkali metal centre.
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Project description:Arylmethyl anions allow alkali-metals to bind in a σ-fashion to the lateral carbanionic centre or a π-fashion to the aryl ring or in between these extremities, with the trend towards π bonding increasing on descending group 1. Here we review known alkali metal structures of diphenylmethane, fluorene, 2-benzylpyridine and 4-benzylpyridine. Next, we synthesise Li, Na, K monomers of these diarylmethyls using polydentate donors PMDETA or Me6 TREN to remove competing oligomerizing interactions, studying the effect that two aromatic rings has on negative charge (de)localisation via NMR, X-ray crystallographic and DFT studies. Diphenylmethyl and fluorenyl anions maintain C(H)-M interactions regardless of alkali-metal, although the adjacent arene carbons engage in interactions with larger alkali-metals. Introducing a nitrogen atom into the ring (at the 2- or 4-position) encourages relocalisation of negative charge away from the deprotonated carbon and onto nitrogen. Phenyl(2-pyridyl)methyl moves from an enamide formation at one extremity (lithium) to an aza-allyl formation at the other extremity (potassium), while C- or N-coordination modes become energetically viable for Na and K phenyl(4-pyridyl)methyl complexes.
| S-EPMC9310864 | biostudies-literature
Project description:The structures of the alkali metal (K, Rb and Cs) complex salts with 4-amino-phenyl-arsonic acid (p-arsanilic acid) manifest an isotypic series with the general formula [M2(C6H7AsNO3)2(H2O)3], with M = K {poly[di-?3-4-amino-phenyl-arsonato-tri-?2-aqua-dipotassium], [K2(C6H7AsNO3)2(H2O)3], (I)}, Rb {poly[di-?3-4-amino-phenyl-arsonato-tri-?2-aqua-dirubidium], [Rb2(C6H7AsNO3)2(H2O)3], (II)}, and Cs {poly[di-?3-4-amino-phenyl-arsonato-tri-?2-aqua-dirubidium], [Cs2(C6H7AsNO3)2(H2O)3], (III)}, in which the repeating structural units lie across crystallographic mirror planes containing two independent and different metal cations and a bridging water mol-ecule, with the two hydrogen p-arsanilate ligands and the second water mol-ecule lying outside the mirror plane. The bonding about the two metal cations in all complexes is similar, one five-coordinate, the other progressing from five-coordinate in (I) to eight-coordinate in both (II) and (III), with overall M-O bond-length ranges of 2.694?(5)-3.009?(7) (K), 2.818?(4)-3.246?(4) (Rb) and 2.961?(9)-3.400?(10)?Å (Cs). The additional three bonds in (II) and (III) are the result of inter-metal bridging through the water ligands. Two-dimensional coordination polymeric structures with the layers lying parallel to (100) are generated through a number of bridging bonds involving the water mol-ecules (including hydrogen-bonding inter-actions), as well as through the arsanilate O atoms. These layers are linked across [100] through amine N-H?O hydrogen bonds to arsonate and water O-atom acceptors, giving overall three-dimensional network structures.
| S-EPMC5290566 | biostudies-literature
Project description:Quantum chemical calculations were carried out for deprotonated (P-) and protonated purine (PH+) and for adducts with one alkali metal cation (P-M+ and PM+, where M+ is Li+ or Na+) in the gas phase {B3LYP/6-311+G(d,p)}, a model of perfectly apolar environment, and for selected structures in aqueous solution {PCM(water)//B3LYP/6-311+G(d,p)}, a reference polar medium for biological studies. All potential isomers of purine derivatives were considered, the favored structures indicated, and the preferred sites for protonation/deprotonation and cationization reactions determined. Proton and metal cation basicities of purine in the gas phase were discussed and compared with those of imidazole and pyrimidine. Bond-length alternations in the P, PH+, P-M+, and PM+ forms were quantitatively measured using the harmonic oscillator model of electron delocalization (HOMED) indices and compared with those for P. Variations of the HOMED values when proceeding from the purine structural building blocks, pyrimidine and imidazole, to the bicyclic purine system were also examined. Generally, the isolated NH isomers exhibit a strongly delocalized ?-system (HOMED >?0.8). Deprotonation slightly increases the HOMED values, whereas protonation and cationization change the HOMED indices in different way. For bidentate M+-adducts, the HOMED values are larger than 0.9 like for the largely delocalized P-. The HOMED values correlate well in a comprehensive relationship with the relative Gibbs energies (?G) calculated for individual isomers whatever the purine form is, neutral, protonated, or cationized. When PCM-DFT model was utilized for P-, PH+, PM+, and P-M+ (M+?=?Li+) both electron delocalization and relative stability are different from those for the molecules in vacuo. The solvation effects cause a slight increase in HOMEDs, whereas the ?Es decrease, but in different ways. Hence, contribution of particular isomers in the isomeric mixtures of PH+, PM+, and P-M+ also varies. HOMED variations for the favored neutral, deprotonated, protonated, and lithiated forms of purine in the gas phase and aqueous solution.
| S-EPMC7256107 | biostudies-literature
Project description:The green compound poly[(tetra-hydro-furan)-tris-[?-?5:?5-1-(tri-methyl-sil-yl)cyclo-penta-dien-yl]caesium(I)ytterbium(II)], [CsYb(C8H13Si)3(C4H8O)] n or [(THF)Cs(?-?5:?5-Cp')3YbII] n was synthesized by reduction of a red THF solution of (C5H4SiMe3)3YbIII with excess Cs metal and identified by X-ray diffraction. The compound crystallizes as a two-dimensional array of hexa-gons with alternating CsI and YbII ions at the vertices and cyclo-penta-dienyl groups bridging each edge. This, based off the six-electron cyclo-penta-dienyl rings occupying three coordination positions, gives a formally nine-coordinate tris-(cyclo-penta-dien-yl) coordination environment to Yb and the Cs is ten-coordinate due to the three cyclo-penta-dienyl rings and a coordinated mol-ecule of THF. The complex comprises layers of Cs3Yb3 hexa-gons with THF ligands and Me3Si groups in between the layers. The Yb-C metrical parameters are consistent with a 4f 14 YbII electron configuration.
| S-EPMC7336790 | biostudies-literature
Project description:The complexes [LtBu Ni(OCO-κ2 O,C)]M3 [N(SiMe3 )2 ]2 (M=Li, Na, K), synthesized by deprotonation of a nickel formate complex [LtBu NiOOCH] with the corresponding amides M[N(SiMe3 )2 ], feature a NiII -CO2 2- core surrounded by Lewis-acidic cations (M+ ) and the influence of the latter on the behavior and reactivity was studied. The results point to a decrease of CO2 activation within the series Li, Na, and K, which is also reflected in the reactivity with Me3 SiOTf leading to the liberation of CO and formation of a Ni-OSiMe3 complex. Furthermore, in case of K+ , the {[K3 [N(SiMe3 )2 ]2 }+ shell around the Ni-CO2 2- entity was shown to have a large impact on its stabilization and behavior. If the number of K[N(SiMe3 )2 ] equivalents used in the reaction with [LtBu NiOOCH] is decreased from 3 to 0.5, the deprotonated part of the precursor enters a complex reaction sequence with formation of [LtBu NiI (μ-OOCH)NiI LtBu ]K and [LtBu Ni(C2 O4 )NiLtBu ]. The same reaction at higher concentrations additionally led to the formation of a unique hexanuclear NiII complex containing both oxalate and mesoxalate ([O2 C-CO2 -CO2 ]4- ) ligands.
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Project description:In this article, we predict the emergence of non-trivial band topology in the family of XX'Bi compounds having [Formula: see text] (# 189) space group. Using first principles calculations within hybrid functional framework, we demonstrate that NaSrBi and NaCaBi are strong topological insulator under controlled band engineering. Here, we propose three different ways to engineer the band topology to get a non-trivial order: (i) hydrostatic pressure, (ii) biaxial strain (due to epitaxial mismatch), and (iii) doping. Non-triviality is confirmed by investigating bulk band inversion, topological Z2 invariant, surface dispersion and spin texture. Interestingly, some of these compounds also show a three dimensional topological nodal line semi-metal (NLS) state in the absence of spin orbit coupling (SOC). In these NLS phases, the closed loop of band degeneracy in the Brillouin zone lie close to the Fermi level. Moreover, a drumhead like flat surface state is observed on projecting the bulk state on the [001] surface. The inclusion of SOC opens up a small band gap making them behave like a topological insulator.
| S-EPMC6345778 | biostudies-literature
Project description:Compared with the popularity of various C-centred radicals, the N-centred radicals remain largely unexplored in catalytic radical cascade reactions because of a lack of convenient methods for their generation. Known methods for their generation typically require the use of N-functionalized precursors or various toxic, potentially explosive or unstable radical initiators. Recently, visible-light photocatalysis has emerged as an attractive tool for the catalytic formation of N-centred radicals, but the pre-incorporation of a photolabile groups at the nitrogen atom largely limited the reaction scope. Here, we present a visible-light photocatalytic oxidative deprotonation electron transfer/2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediation strategy for catalytic N-radical cascade reaction of unsaturated hydrazones. This mild protocol provides a broadly applicable synthesis of 1,6-dihydropyradazines with complete regioselectivity and good yields. The 1,6-dihydropyradazines can be easily transformed into diazinium salts that showed promising in vitro antifungal activities against fungal pathogens. DFT calculations are conducted to explain the mechanism.
| S-EPMC4823831 | biostudies-other
Project description:Alkali (Li(+), Na(+), K(+), Rb(+), and Cs(+)) and halide (F(-), Cl(-), Br(-), and I(-)) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER-adapted Aqvist cation parameters. To provide a more appropriate balance, we reoptimized the parameters of the Lennard-Jones potential for the ions and specific choices of water models. To validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (LE) and lattice constants (LC) of alkali halide salt crystals. This is the first effort that systematically scans across the Lennard-Jones space (well depth and radius) while balancing ion properties like LE and LC across all pair combinations of the alkali ions and halide ions. The optimization across the entire monovalent series avoids systematic deviations. The ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically TIP3P, TIP4P EW, and SPC/E. In addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells.
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