Extending ligand field molecular mechanics to modelling organometallic π-bonded systems: applications to ruthenium-arenes

The ligand field molecular mechanics method has been extended to treat η(6)-arene ligands coordinated to a ruthenium(II) centre by employing a dummy atom located at the centroid of the arene ring and distributing the forces on the dummy to the arene carbon atoms. Angular overlap model parameters based on orbital energies derived from Kohn-Sham density functional theory (KS-DFT) calculations show that, relative to the Ru-dummy vector, the arene behaves as a very strong π donor and weak σ donor. Based on KS-DFT geometries, partial atomic charges and potential energy scans for a series of homoleptic and half sandwich complexes spanning arene, am(m)ine, imine, pyridyl, hydride and chloride ligands, a new LFMM force field has been developed which accurately reproduces the KS-DFT data. This FF was validated against 47 half-sandwich complexes obtained from the Cambridge Structural Database which, after minor corrections to account for the systematic errors between our chosen functional (BP86) and the experimental structures, yields a 'structurally tuned' FF where 93% of the Ru-L contacts are reproduced to 0.05 ? or better and all bar two bond lengths are within 0.1 ? of experiment. Over half the systems have non-hydrogen-atom rmsds of less than 0.5 ?. Larger differences are usually due to rotation of the arene moiety which is shown by ligand field molecular dynamics (LFMD) simulations to be an inherently low-energy process. Comparisons between LFMD and Car-Parrinello MD for [Ru(p-cymene)(ethylenediamine)Cl](+)show that LFMD is equally accurate but much faster enabling modelling of dynamic properties which occur on a timescale beyond the scope of CPMD.     

Assay Related Target Similarity (ARTS) - chemogenomics approach for quantitative comparison of biological targets

Computer-based chemogenomics approaches compare macromolecular drug targets based on their amino acid sequences or derived properties, by similarity of their ligands, or according to ligand-target interaction models. Here we present ARTS (Assay Related Target Similarity) as a quantitative index that estimates target similarity directly from measured affinities of a set of probe compounds. This approach reduces the risk of deducing artificial target relationships from mutually inactive compounds. ARTS implements a scoring scheme that matches intertarget similarity based on dose-response measurements. While all experimentally derived target similarities have a tendency to be data set-dependent, we demonstrate that ARTS depends less on the used data set than the commonly used Pearson correlation or Tanimoto index.     

False Results Caused by Solvent Impurity in Tetrahydrofuran for MALDI TOF MS Analysis of Amines

Tetrahydrofuran (THF) is one of the most frequently used solvents in the MALDI TOF MS analysis of synthetic compounds. However, it should be used with caution because a trace amount of 4-hydroxybutanal (HBA) might be generated and accumulated in THF during storage. Since only a tiny amount of analytes is required in MALDI MS measurements, a trace amount of HBA might have a significant effect on the MS results. It was found that HBA will quickly react with primary and secondary amino compounds, leading to false results about the sample composition with an extra series of ions with additional mass of 70 Da in between. The formation of HBA can be inhibited by butylated hydroxytoluene (BHT) antioxidant. Therefore, when THF is required as the solvent for sample preparation, it is strongly recommended to use a BHT-stabilized one, at least for the analysis of compounds with amino groups.

Sequential Hydroformylation/Diels–Alder Processes: One‐Pot Synthesis of Polysubstituted Cyclohexenes,Cyclohexadienes, and Phthalates from Alkynes

A novel, one‐pot hydroformylation/Diels–Alder sequence for the synthesis of multisubstituted cyclohexenes, cyclohexadienes, and phthalates has been developed. Various alkynes were efficiently converted into the corresponding products in good yields and with excellent diastereoselectivity through palladium‐catalyzed hydroformylation followed by an AAD‐type reaction (AAD: Amides–Aldehydes–Dienophiles). In view of the availability of the substrates, the atom‐efficiency of the overall process, and the convenient introduction of substituents in the cyclohexene ring, this method complements current methods for the preparation of polysubstituted cyclohexane derivatives.     

A Unified Mechanism on the Formation of Acenes,Helicenes, and Phenacenes in the Gas Phase

A unified low‐temperature reaction mechanism on the formation of acenes, phenacenes, and helicenes—polycyclic aromatic hydrocarbons (PAHs) that are distinct via the linear, zigzag, and ortho‐condensed arrangements of fused benzene rings—is revealed. This mechanism is mediated through a barrierless, vinylacetylene mediated gas‐phase chemistry utilizing tetracene, [4]phenacene, and [4]helicene as benchmarks contesting established ideas that molecular mass growth processes to PAHs transpire at elevated temperatures. This mechanism opens up an isomer‐selective route to aromatic structures involving submerged reaction barriers, resonantly stabilized free‐radical intermediates, and systematic ring annulation potentially yielding molecular wires along with racemic mixtures of helicenes in deep space. Connecting helicene templates to the Origins of Life ultimately changes our hypothesis on interstellar carbon chemistry.     

CaNa[Cr(OH)6] – A Layered Hydroxochromate(III) with Ordered Brucite Structure and its Thermal Decomposition

Green single-crystals of the hydroxochromate(III) CaNa[Cr(OH)₆] were grown under highly alkaline hydrothermal conditions at about 200 °C. The starting materials Ca(NO₃)₂ · 6H₂O and Cr(NO₃)₃ · 9H₂O were reacted in a mixture of water and sodium hydroxide with the molar ratio of 2.8:1. CaNa[Cr(OH)₆] crystallizes in the non-centrosymmetric trigonal space group R3 with the lattice parameters a = 583.86(2) pm and c = 1428.73(6) pm [T = 100(1) K]. Characteristically, the crystals are reverse-obverse as well as inversion twins. The crystal structure is a stack of uncharged metal hydroxide layers, which can be regarded as a cation-ordered rhombohedral variant of the Mg(OH)₂ (brucite) structure type. The oxidation state of chromium(III) and its coordination by hydroxide groups was confirmed by UV/Vis and IR spectroscopy, respectively. Temperature-dependent magnetic measurements revealed paramagnetic behavior with an effective moment of 3.82 μ_B per chromium atom. The thermal decomposition of CaNa[Cr(OH)₆] takes place at about 225 °C, where the fast elimination of 1.5 equivalents of water is followed by the oxidation of chromium(III) to chromium(VI). Upon further heating to 1000 °C and 1200 °C, the intermediate decomposition products CaCrO₄ and Na₂CrO₄ transform into the oxochromates(V) Ca₅(CrO₄)₃O_0.5 and Ca₃(CrO₄)₂, respectively.     

N-(4-(di-tert-butyl[F]fluorosilyl)benzyl)-2-hydroxy-N,N-dimethylethylammonium bromide ([F]SiFANBr): A novel lead compound for the development of hydrophilic SiFA-based prosthetic groups for F-labeling

¹⁸F-labeled compounds play a major role in the development of new in vivo imaging agents for Positron Emission Tomography (PET), a non invasive imaging modality depicting the biodistribution of radioactive compounds in humans. Recently we reported a new method for the introduction of fluorine-18 into a range of organic molecules exploiting the very fast ¹⁸F-¹⁹F isotope exchange of fluorosilanes (termed SiFA compounds). Here, we wish to report the labeling of the first charged SiFA molecule N-(4-(di-tert-butylfluorosilyl)benzyl)-2-hydroxy-N,N-dimethylethylammonium bromide (SiFAN⁺Br⁻) serving as a lead compound in the development of SiFA-based prosthetic groups of reduced lipophilicity for biomolecule labeling. Mild conditions for synthesis of [¹⁸F]SiFAN⁺Br⁻ and an easy purification procedure using simple C-18 solid phase cartridge have been developed yielding the [¹⁸F]SiFAN⁺Br⁻ in radiochemical yields of 34% (non-decay corrected) within 40 min. A series of kinetic experiments were performed that show high isotopic exchange rate constants. Low activation energy (15.7 kcal/mol) and a large preexponential factor (7.9 × 10¹³ M⁻¹ s⁻¹) were calculated for the isotopic exchange reaction from a corresponding Arrhenius plot. For comparison, the ¹⁸F-fluorination of ethyleneglycol-di-p-tosylate via the formation of a carbon-¹⁸F bond showed a 1.3 kcal/mol higher activation energy and a much lower preexponential factor of 2.9 × 10⁹ M⁻¹ s⁻¹. Moderate hydrophilicity (log D = 0.44), stability in aqueous media at pH up to 7.4 and a high specific activity of [¹⁸F]SiFAN⁺Br⁻ (SA = 20.4 GBq/μmol, 0.55 Ci/μmol) make this charged SiFA compound useful for the development of novel SiFA-based ¹⁸F-labeling synthons.     

Thermodynamically controlled synthesis of a chiral tetra-cavitand nanocapsule and mechanism of enantiomerization

The dynamic covalent synthesis, structure and conformational dynamics of a chiral polyimine nanocapsule 1a are reported. Reaction of four tetraformyl cavitands and eight H(2)N(CH(2))(2)NH(2) yields quantitatively 1a, which has a compact, asymmetrically folded, pseudo-C(2)-symmetric structure, as determined by X-ray crystallography, and encapsulates four CHCl(3) and three CH(3)OH guests in the solid state. In solution, 1a enantiomerizes by passing over a barrier of ΔG(298)(double dagger) = 21.5 ± 0.7 kcal mol(-1) via a refolding process.