Epothilone Analogues with Benzimidazole and Quinoline Side Chains: Chemical Synthesis,Antiproliferative Activity,and Interactions with Tubulin

A series of epothilone B and D analogues bearing isomeric quinoline or functionalized benzimidazole side chains has been prepared by chemical synthesis in a highly convergent manner. All analogues have been found to interact with the tubulin/microtubule system and to inhibit human cancer cell proliferation in vitro, albeit with different potencies (IC₅₀ values between 1 and 150 nM ). The affinity of quinoline‐based epothilone B and D analogues for stabilized microtubules clearly depends on the position of the N‐atom in the quinoline system, while the induction of tubulin polymerization in vitro appears to be less sensitive to N‐positioning. The potent inhibition of human cancer cell growth by epothilone analogues bearing functionalized benzimidazole side chains suggests that these systems might be conjugated with tumor‐targeting moieties to form tumor‐targeted prodrugs.     

Altered Mascot search results by changing the <Emphasis Type="Italic">m</Emphasis>/<Emphasis Type="Italic">z</Emphasis> range of MS/MS spectra: analysis and potential applications

The Mascot search algorithm is one of the most commonly used tools for protein identification. Tandem mass spectrometry data searched against a protein sequence database is utilized for identifying peptides and proteins, each reported with a score. Higher Mascot scores are associated with lower chances of random hits. The process of peak selection performed by the search engine prior to the search is a critical aspect of the process. Here, we show that Mascot divides the MS/MS spectrum into fixed m/z regions for peak selection, starting at the lowest m/z value of the peak list. Therefore, modifying the m/z range of the peak lists by insertion of a dummy peak with low m/z value changes the ensemble of peaks used for searching. As a consequence, Mascot peptide scores and search results are altered significantly and a different subset of the peptides present in the sample is identified after processing. We further show that the effect can be exploited and additional proteins and peptides can be identified by repeating the search with a combined set of differently processed files, even when applying identical false-positive rates.     

Probing the reaction mechanism of spore photoproduct lyase (SPL) via diastereoselectively labeled dinucleotide SP TpT substrates

5-Thyminyl-5,6-dihydrothymine (commonly called spore photoproduct or SP) is the exclusive DNA photodamage product in bacterial endospores. It is generated in the bacterial sporulation phase and repaired by a radical SAM enzyme, spore photoproduct lyase (SPL), at the early germination phase. SPL utilizes a special [4Fe-4S] cluster to reductively cleave S-adenosylmethionine (SAM) to generate a reactive 5'-dA radical. The 5'-dA radical is proposed to abstract one of the two H-atoms at the C6 carbon of SP to initiate the repair process. Via organic synthesis and DNA photochemistry, we selectively labeled the 6-H(proS) or 6-H(proR) position with a deuterium in a dinucleotide SP TpT substrate. Monitoring the deuterium migration in enzyme catalysis (employing Bacillus subtilis SPL) revealed that it is the 6-H(proR) atom of SP that is abstracted by the 5'-dA radical. Surprisingly, the abstracted deuterium was not returned to the resulting TpT after enzymatic catalysis; an H-atom from the aqueous buffer was incorporated into TpT instead. This result questions the currently hypothesized SPL mechanism which excludes the involvement of protein residue(s) in SPL reaction, suggesting that some protein residue(s), which is capable of exchanging a proton with the aqueous buffer, is involved in the enzyme catalysis. Moreover, evidence has been obtained for a possible SAM regeneration after each catalytic cycle; however, such a regeneration process is more complex than currently thought, with one or even more protein residues involved as well. These observations have enabled us to propose a modified reaction mechanism for this intriguing DNA repair enzyme.     

Oxygen activation and intramolecular C-H bond activation by an amidate-bridged diiron(II) complex

A diiron(II) complex containing two μ-1,3-(κN:κO)-amidate linkages has been synthesized using the 2,2',2'-tris(isobutyrylamido)triphenylamine (H(3)L(iPr)) ligand. The resulting diiron complex, 1, reacts with dioxygen (or iodosylbenzene) to effect intramolecular C-H bond activation at the methine position of the ligand isopropyl group. The ligand-activated product, 2, has been isolated and characterized by a variety of methods including X-ray crystallography. Electrospray ionization mass spectroscopy of 2 prepared from(18)O(2) was used to confirm that the oxygen atom incorporated into the ligand framework is derived from molecular oxygen.     

Examining the robustness of first-principles calculations for metal hydride reaction thermodynamics by detection of metastable reaction pathways

First principles calculations have played a useful role in screening mixtures of complex metal hydrides to find systems suitable for H(2) storage applications. Standard methods for this task efficiently identify the lowest energy reaction mechanisms among all possible reactions involving collections of materials for which DFT calculations have been performed. The resulting mechanism can potentially differ from physical reality due to inaccuracies in the DFT functionals used, or due to other approximations made in estimating reaction free energies. We introduce an efficient method to probe the robustness of DFT-based predictions that relies on identifying reactions that are metastable relative to the lowest energy reaction path predicted with DFT. An important conclusion of our calculations is that in many examples DFT cannot unambiguously predict a single reaction mechanism for a well defined metal hydride mixture because two or more mechanisms have reaction energies that differ by a small amount. Our approach is illustrated by analyzing a series of single step reactions identified in our recent work that examined reactions with a large database of solids [Kim et al., Phys. Chem. Chem. Phys. 2011, 13, 7218].     

Formation and sigmatropic rearrangement of PhCOC(NO2)CH2 cycloadducts of 1,3-cyclohexadiene: a theoretical study

Competing cycloaddition pathways for the reaction of 2-nitro-1-phenyl-2-propen-1-one with 1,3-cyclohexadiene were investigated employing computational methods. A bifurcating pathway was found for formation of nitroketone 3 and nitronic ester 5. A second bifurcating pathway was found for the formation of nitroketone 4 and enol ether 6. Sigmatropic rearrangements of two cycloadducts, nitronic ester 5 and enol ether 6, were also studied computationally. The reaction pathways were mapped using the B3-LYP/6-311G(d) method and relative energies for species 3-6 were calculated at the same level. Solution-phase corrections were performed by the PCM method. The calculations for both bifurcating cycloaddition pathways indicate kinetic control with similar rate-determining activation energies. The nitroketone 3 is more stable than nitronic ester 5 by 5.3 kcal/mol and nitroketone 4 is more stable than enol ether 6 by 3.9 kcal/mol, consistent with the observed direction of sigmatropic rearrangement.     

Laser-based ion mobility spectrometer for the direct analysis of aromatic compounds in liquids

A laser-based ionization source for the direct analysis of liquid samples in ion mobility (IM) spectrometry is presented and characterized. Ionization of aromatic substances in liquids is achieved, analogous to atmospheric pressure laser ionization (APLI) in mass spectrometry, by vaporizing the liquid and subsequently ionizing the aromatic substances by resonance-enhanced multiphoton ionization (REMPI). The effects of parameters, such as composition and flow rate of the solvent as well as laser wavelength and pulse energy, are systematically investigated. The characterization of the IM spectrometer is carried out by means of selected substances from diverse fields of applications, e.g., polycyclic aromatic hydrocarbons (PAH), pesticides, wood preservatives and drug compounds. Limits of detection (LOD) down to 10 fmol and linear ranges up to three orders of magnitude are established. In addition to direct laser ionization, indirect laser ionization via dopants (toluene) for substances with low ionization efficiencies is investigated. Ionization occurs as a result of proton transfer from toluene radical cations to substances of sufficiently high proton affinities. As a result of indirect laser ionization, LOD could be decreased by up to two orders of magnitude. Ionization products are investigated by means of a combination of IM and mass spectrometer. Depending on the substance investigated primary ions (radical cations) and secondary ions (protonated molecules) resulting from ion molecule reactions are formed.     

Quantitative Bestimmung der Catechine und Hydroxyzimts?uren in pflanzlichen Lebensmitteln

Zusammenfassung Die Problematik der Bestimmung von Catechinen und Hydroxyzimtsäuren in pflanzlichen Lebensmitteln wird diskutiert und gezeigt, daß es notwendig ist, eine ausreichende Vorreinigung (Säulen-Chromatographie an Polyamid und Dünnschicht-Chromatographie an Cellulose bzw. Kieselgel) mit einem geeigneten Bestimmungsverfahren (Spektralphotometrie mit Vanillin/Salzsäure bzw. direkt) zu kombinieren. Beispiele werden beschrieben.Plenarvortrag anläßlich der Tagung Spurenanalyse, 2.–5. April 1973 in Erlangen.     

Beitr?ge zur Trennung und Bestimmung des Natriums und Kaliums

Zusammenfassung Es wurde die Trennung und Bestimmung des Natriums und Kaliums als Jodid untersucht. Als geeignetes Lösungsmittel erwies sich ein Gemisch von gleichen Raumteilen wasserfreien Isobutylalkohols und wasserfreien Äthers. Wenn man nach der angegebenen Vorschrift verfährt, enthält das ausgelaugte Natriumj odid nur Spuren von mitgelöstem Kaliumsalz, das zurückgebliebene Kaliumjodid gleichfalls nur Spuren von zurückgebliebenem Natriumsalz. Da aber die zwei entgegengesetzt wirkenden Fehler sich nur teilweise kompensieren, ist es empfehlenswert, eine empirische Korrektion von 0,6mg zu benutzen, welche Menge vom gefundenen Natriumoxyd abgezogen und zum gefundenen Kaliumoxyd hinzugezählt wird.Die Trennung des Natriums von Kalium als Jodid hat den prinzipiellen Vorteil, daß auch die Menge des Natriumsalzes unmittelbar bestimmt und nicht aus der Differenz des gefundenen Kaliumsatzes und des gesamten Salzgemisches berechnet wird. Ein praktischer Vorteil ist die Tatsache, daß Sulfatsalzgemische sich zur Trennung glatt in Jodide überführen lassen. Phosphat-Ion jedoch muß vor der Trennung zuerst abgeschieden werden.     

Solution of large configuration mixing matrices arising in partitioning technique and applications to the generalized eigenvalue problem

A method is presented that can be used (a) to determine the several lowest eigenvalues and eigenvectors of large symmetric matrices, (b) to solve the generalized eigenvalue problem associated with energy-dependent operators, that arises in computations involving energy-dependent many-body Green's functions and in the evaluation of the true parameters of the effective valence shell hamiltonian, and (c) to directly evaluate the matrices associated with resolvent operators. The applicability to large configuration mixing calculations arises when the N-electron basis functions can be easily broken down to a few dominant configurations (the primary block) and their complement. Using the partitioning technique, the effective hamiltonian within the primary block is directly evaluated. The method is extended to evaluation of the dynamical polarizability tensor, which effectively contains the contributions from all of the eigenstates of a hamiltonian matrix, without the necessity of explicitly calculating its eigenvalues and eigenvectors.