Amino Acid Assisted Incorporation of Dye Molecules within Calcite Crystals

Biomineralisation processes invariably occur in the presence of multiple organic additives, which act in combination to give exceptional control over structures and properties. However, few synthetic studies have investigated the cooperative effects of soluble additives. This work addresses this challenge and focuses on the combined effects of amino acids and coloured dye molecules. The experiments demonstrate that strongly coloured calcite crystals only form in the presence of Brilliant Blue R (BBR) and four of the seventeen soluble amino acids, as compared with almost colourless crystals using the dye alone. The active amino acids are identified as those which themselves effectively occlude in calcite, suggesting a mechanism where they can act as chaperones for individual molecules or even aggregates of dyes molecules. These results provide new insight into crystal–additive interactions and suggest a novel strategy for generating materials with target properties.     

p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

Determining the net charge and protonation states populated by a small molecule in an environment of interest or the cost of altering those protonation states upon transfer to another environment is a prerequisite for predicting its physicochemical and pharmaceutical properties. The environment of interest can be aqueous, an organic solvent, a protein binding site, or a lipid bilayer. Predicting the protonation state of a small molecule is essential to predicting its interactions with biological macromolecules using computational models. Incorrectly modeling the dominant protonation state, shifts in dominant protonation state, or the population of significant mixtures of protonation states can lead to large modeling errors that degrade the accuracy of physical modeling. Low accuracy hinders the use of physical modeling approaches for molecular design. For small molecules, the acid dissociation constant (pK_a) is the primary quantity needed to determine the ionic states populated by a molecule in an aqueous solution at a given pH. As a part of SAMPL6 community challenge, we organized a blind pK_a prediction component to assess the accuracy with which contemporary pK_a prediction methods can predict this quantity, with the ultimate aim of assessing the expected impact on modeling errors this would induce. While a multitude of approaches for predicting pK_a values currently exist, predicting the pK_as of drug-like molecules can be difficult due to challenging properties such as multiple titratable sites, heterocycles, and tautomerization. For this challenge, we focused on set of 24 small molecules selected to resemble selective kinase inhibitors—an important class of therapeutics replete with titratable moieties. Using a Sirius T3 instrument that performs automated acid–base titrations, we used UV absorbance-based pK_a measurements to construct a high-quality experimental reference dataset of macroscopic pK_as for the evaluation of computational pK_a prediction methodologies that was utilized in the SAMPL6 pK_a challenge. For several compounds in which the microscopic protonation states associated with macroscopic pK_as were ambiguous, we performed follow-up NMR experiments to disambiguate the microstates involved in the transition. This dataset provides a useful standard benchmark dataset for the evaluation of pK_a prediction methodologies on kinase inhibitor-like compounds.     

Elucidation of the collision induced dissociation pathways of water and alcohol coordinated complexes containing the uranyl cation

Multiple-stage tandem mass spectrometry was used to characterize the dissociation pathways for complexes composed of (1) the uranyl ion, (2) nitrate or hydroxide, and (3) water or alcohol. The complex ions were derived from electrospray ionization (ESI) of solutions of uranyl nitrate in H2O or mixtures of H2O and alcohol. In general, collisional induced dissociation (CID) of the uranyl complexes resulted in elimination of coordinating water and alcohol ligands. For undercoordinated complexes containing nitrate and one or two coordinating alcohol molecules, the elimination of nitric acid was observed, leaving an ion pair composed of the uranyl cation and an alkoxide. For complexes with coordinating water molecules, MS(n) led to the generation of either [UO2(2+)OH-] or [UO2(2+)NO3(-)]. Subsequent CID of [UO2(2+)OH-] produced UO2(+). The base peak in the spectrum generated by the dissociation of [UO2(2+)NO3(-)], however, was an H2O adduct to UO2(+). The abundance of the species was greater than expected based on previous experimental measurements of the (slow) hydration rate for UO2(+) when stored in the ion trap. To account for the production of the hydrated product, a reductive elimination reaction involving reactive collisions with water in the ion trap is proposed.     

Detection of Zinc withβ-naphthoquinoline and thiocyanate

Summary -Naphthoquinoline with thiocyanate provides a sensitive crystal reaction for zinc in acid solution. Even at zinc concentrations as low as 1:200000, characteristic crystals of zinc hydrogen-naphthoquinoline thiocyanate are obtained in 2 N sulfuric acid solution. The test can be carried out in the presence of moderate amounts of barium (acetic acid solution of reagent), calcium, magnesium, beryllium, aluminum, chromium, cerium, lead (acetic acid solution), arsenic, manganese and nickel as well as the alkali metals. Cadmium in concentrations below 0,5 per cent does not interfere; ferric iron up to 1 per cent does not interfere if the test is carried out in 50 per cent phosphoric acid solution. Most other metals give precipitates with the reagent.

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Zusammenfassung -Naphthochinolin bildet im Verein mit Rhodanid ein empfindliches Kristallfällungsreagens auf Zink in saurer Lösung. Man erhält sogar noch bei Zinkkonzentrationen von 1:200000 charakteristische Kristalle von Zink-Hydro--Naphthochinolin-Rhodanid in 2n-schwefelsaurer Lösung. Der Nachweis kann in Gegenwart mäßiger Mengen von Barium (essigsaure Reagenslösung), Calcium, Magnesium, Beryllium, Aluminium, Chrom, Cer, Blei (essigsaure Lösung), Arsen, Mangan, Nickel sowie von Alkalimetallen ausgeführt werden. Cadmium stört in Konzentrationen unter 0,5% nicht; Eisen(III)-Ion bis zu 1% stört nicht, wenn der Nachweis in 50%ig phosphorsaurer Lösung ausgeführt wird. Die meisten anderen Metalle geben Fällungen mit dem Reagens.

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Résumé La-naphtol-chinoline forme avec le rhodanure un réactif de précipitation très sensible pour le zinc en solution acidulée. Même à une concentration de zinc de 1 : 200 000 des cristaux caractéristiques de zinc-hydro--naphtol-chinoline-rhodanure se forment en solution 2n-sulfurique. Cette réaction n'est pas troublée par la présence de petites quantités de barium (en solution acétée), de calcium, de magnésium, de béryllium, d'aluminium, de chrome, de cérium, de plomb (en solution acétée), d'arsénic, de manganèse, de nickel, d'alcali, de cadmium (concentration au-dessous de 0,5%), de ion de fer(III), (concentration au-dessous de 1%, en solution d'acide phosphorique de 50%). La plupart des autres métaux donnent des précipitations avec le réactif.

     

Nickel und Kobalt

Ohne Zusammenfassung     

PSEUDOROTATION IN MONOCYCLIC OXYPHOSPHORANES WHICH CONTAIN CHIRAL CENTERS

Abstract

Phenylbis[2-methyl-1-butoxy]phosphine has been allowed to react with butanedione to produce 2,2-bis[2-methyl-1-butoxy]-2-phenyl-4,5-dimethyl-1,3,2-dioxaphophol-4-ene. This material is a mixture of three diastereomers. It has been reported that 2,2-bis[tetrahydrofurfuyloxy]-2-phenyl-4,5-dimethyl-1,3,2-dioxaphosphol-4-ene is a mixture of only two diastereomers. The present work suggest that two of the diastereomers of the tetrahydrofurfuryloxy compound interconvert via hexacoordinated zwitterionic intermediates which involve addition of the oxygen of the tetrahydrofuran ring to phosphorus.     

Contrasting views of the internal dynamics of the HhaI methyltransferase target DNA reported by solution and solid-state NMR spectroscopy

Solution and solid-state NMR have been used conjointly to probe the internal motions of a DNA dodecamer containing the recognition site for the HhaI methyltransferase. The results strongly suggest that ns-mus motions contribute to the functionally relevant dynamic properties of nucleic acids during DNA methylation.