Testing an alternative search algorithm for compound identification with the ‘Wiley Registry of Tandem Mass Spectral Data,MSforID’

A tandem mass spectral database system consists of a library of reference spectra and a search program. State‐of‐the‐art search programs show a high tolerance for variability in compound‐specific fragmentation patterns produced by collision‐induced decomposition and enable sensitive and specific ‘identity search’. In this communication, performance characteristics of two search algorithms combined with the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS, John Wiley and Sons, Hoboken, NJ, USA) were evaluated. The search algorithms tested were the MSMS search algorithm implemented in the NIST MS Search program 2.0g (NIST, Gaithersburg, MD, USA) and the MSforID algorithm (John Wiley and Sons, Hoboken, NJ, USA). Sample spectra were acquired on different instruments and, thus, covered a broad range of possible experimental conditions or were generated in silico. For each algorithm, more than 30 000 matches were performed. Statistical evaluation of the library search results revealed that principally both search algorithms can be combined with the Wiley Registry MSMS to create a reliable identification tool. It appears, however, that a higher degree of spectral similarity is necessary to obtain a correct match with the NIST MS Search program. This characteristic of the NIST MS Search program has a positive effect on specificity as it helps to avoid false positive matches (type I errors), but reduces sensitivity. Thus, particularly with sample spectra acquired on instruments differing in their setup from tandem‐in‐space type fragmentation, a comparably higher number of false negative matches (type II errors) were observed by searching the Wiley Registry MSMS. Copyright © 2013 John Wiley & Sons, Ltd.     

Effect of Molecular Crowding on the Temperature–Pressure Stability Diagram of Ribonuclease A

FT‐IR spectroscopic and thermodynamic measurements were designed to explore the effect of a macromolecular crowder, dextran, on the temperature and pressure‐dependent phase diagram of the protein Ribonuclease A (RNase A), and we compare the experimental data with approximate theoretical predictions based on configuration entropy. Exploring the crowding effect on the pressure‐induced unfolding of proteins provides insight in protein stability and folding under cell‐like dense conditions, since pressure is a fundamental thermodynamic variable linked to molecular volume. Moreover, these studies are of relevance for understanding protein stability in deep‐sea organisms, which have to cope with pressures in the kbar range. We found that not only temperature‐induced equilibrium unfolding of RNase A, but also unfolding induced by pressure is markedly prohibited in the crowded dextran solutions, suggesting that crowded environments such as those found intracellularly, will also oppress high‐pressure protein unfolding. The FT‐IR spectroscopic measurements revealed a marked increase in unfolding pressure of 2 kbar in the presence of 30 wt % dextran. Whereas the structural changes upon thermal unfolding of the protein are not significantly influenced in the presence of the crowding agent, through stabilization by dextran the pressure‐unfolded state of the protein retains more ordered secondary structure elements, which seems to be a manifestation of the entropic destabilization of the unfolded state by crowding.     

Three salts from the reactions of cysteamine and cystamine with L‐(+)‐tartaric acid

Reaction between cysteamine (systematic name: 2‐aminoethanethiol, C₂H₇NS) and L‐(+)‐tartaric acid [systematic name: (2R,3R)‐2,3‐dihydroxybutanedioic acid, C₄H₆O₆] results in a mixture of cysteamine tartrate(1−) monohydrate, C₂H₈NS⁺·C₄H₅O₆⁻·H₂O, (I), and cystamine bis[tartrate(1−)] dihydrate, C₄H₁₄N₂S₂²⁺·2C₄H₅O₆⁻·2H₂O, (III). Cystamine [systematic name: 2,2′‐dithiobis(ethylamine), C₄H₁₂N₂S₂], reacts with L‐(+)‐tartaric acid to produce a mixture of cystamine tartrate(2−), C₄H₁₄N₂S₂²⁺·C₄H₄O₆²⁻, (II), and (III). In each crystal structure, the anions are linked by O—H...O hydrogen bonds that run parallel to the a axis. In addition, hydrogen bonding involving protonated amino groups in all three salts, and water molecules in (I) and (III), leads to extensive three‐dimensional hydrogen‐bonding networks. All three salts crystallize in the orthorhombic space group P2₁2₁2₁.     

Alkyl levulinates as `green chemistry' precursors: butane‐1,4‐diyl bis(4‐oxopentanoate) and hexane‐1,6‐diyl bis(4‐oxopentanoate)

Levulinic acid derivatives are potential `green chemistry' renewably sourced molecules with utility in industrial coatings applications. Suitable single crystals of the centrosymmetric title compounds, C₁₄H₂₂O₆ and C₁₆H₂₆O₆, respectively, were obtained with difficulty. The data for the latter hexane‐1,6‐diyl compound were extracted from the major fragment of a three‐component twinned crystal. Both compounds crystallize in similar‐sized unit cells with identical symmetry, utilizing the same weak nonconventional attractive C—H...O(ketone) hydrogen bonds via C(4) and C(5) motifs, which expand to R²₂(30) ring and C²₂(14) chain motifs. Their different packing orientations in similar‐sized unit cells suggest that crystal growth involving packing mixes could lead to intergrowths or twins.     

Efficacious Entry Into Substituted 5,6-Dihydro-4-Hydroxy-2H-Pyran-2-Ones and 2,3-Dihydro-4H-Pyran-4-Ones Utilizing Ketonic Dianions

Methyl acetoacetate and 2,4-pentanedione dianions were condensed with aldehydes and ketones to afford a 1,3,5-trioxygenated carboskeleton. Intramolecular cyclization of the aldol adducts delivered the title compounds in good yield.     

Conformational Isomerism in Monomeric,Low‐Coordinate Group 12 Complexes Stabilized by a Naphthyl‐Substituted m‐Terphenyl Ligand

The synthesis and characterization of the first series of low‐coordinate bis(terphenyl) complexes of the Group 12 metals, [Zn(2,6‐Naph₂C₆H₃)₂] ( 1 ), [Cd(OEt₂)(2,6‐Naph₂C₆H₃)₂] ( 2 ) and [Hg(OEt₂)(2,6‐Naph₂C₆H₃)₂] ( 3 ) (Naph=1‐C₁₀H₇) are described. The naphthyl substituents of the terphenyl ligands confer considerable steric bulk, and as a result of limited flexibility introduce multiple conformations to these unusual systems. In the solid state, complex 1 features a two‐coordinate Zn centre with the ligands oriented in a syn/anti conformation, whereas the three‐coordinate distorted T‐shaped complexes 2 and 3 feature the ligands in the syn/syn configurations. The results of DFT calculations are in good agreement with the solid‐state configurations for these complexes and support the spectroscopic measurements, which indicate several conformers in solution.     

Nanoscale Control of Polyoxometalate Assembly: A {Mn8W4} Cluster within a {W36Si4Mn10} Cluster Showing a New Type of Isomerism

Two near isomeric clusters containing a novel {Mn₈W₄} Keggin cluster within a [W₃₆Mn₁₀Si₄O₁₃₆(OH)₄(H₂O)8]^24? cluster are reported: K₁₀Li₁₄ [W₃₆Si₄O₁₃₆Mn^II₁₀(OH)₄(H₂O)₈] ( 1 ) and K₁₀Li1_3.5Mn_0.25[W₃₆Si₄O₁₃₆Mn^II₁₀(OH)₄(H₂O)₈] ( 1′ ). Bulk characterization of the clusters has been carried out by single crystal X‐ray structure analysis, ICP‐MS, TGA, ESI‐MS, CV and SQUID‐magnetometer analysis. X‐ray analysis revealed that 1′ has eight positions within the central Keggin core that were disordered W/Mn whereas 1 contained no such disorder. This subtle difference is due to a differences is how the two clusters assemble and recrystallize from the same mother liquor and represents a new type of isomerism. The rapid recrystallization process was captured via digital microscopy and this uncovered two “intermediate” types of crystal which formed temporarily and provided nucleation sites for the final clusters to assemble. The intermediates were investigated by single crystal X‐ray analysis and revealed to be novel clusters K₄Li₂₂[W₃₆Si₄Mn₇O₁₃₆(H₂O)₈]?56 H₂O ( 2 ) and Mn₂K₈Li₁₄[W₃₆Si₄Mn₇O₁₃₆(H₂O)₈]?45 H₂O ( 3 ). The intermediate clusters contained different yet related building blocks to the final clusters which allowed for the postulation of a mechanism of assembly. This demonstrates a rare example where the use X‐ray crystallography directly facilitated understanding the means by which a POM assembled.     

Minkowski content and fractal curvatures of self-similar tilings and generator formulas for self-similar sets

We study Minkowski contents and fractal curvatures of arbitrary self-similar tilings (constructed on a feasible open set of an IFS) and the general relations to the corresponding functionals for self-similar sets. In particular, we characterize the situation, when these functionals coincide. In this case, the Minkowski content and the fractal curvatures of a self-similar set can be expressed completely in terms of the volume function or curvature data, respectively, of the generator of the tiling. In special cases such formulas have been obtained recently using tube formulas and complex dimensions or as a corollary to results on self-conformal sets. Our approach based on the classical Renewal Theorem is simpler and works for a much larger class of self-similar sets and tilings. In fact, generator type formulas are obtained for essentially all self-similar sets, when suitable volume functions (and curvature functions, respectively) related to the generator are used. We also strengthen known results on the Minkowski measurability of self-similar sets, in particular on the question of non-measurability in the lattice case.