CASE via MS: Ranking Structure Candidates by Mass Spectra

Two important tasks in computer-aided structure elucidation (CASE) are the generation of candidate structures from a given molecular formula, and the ranking of structure candidates according to compatibility with an experimental spectrum. Candidate ranking with respect to electron impact mass spectra is based on virtual fragmentation of a candidate structure and comparison of the fragments’ isotope distributions against the spectrum of the unknown compound, whence a structure–spectrum compatibility matchvalue is computed. Of special interest is the matchvalue’s ability to distinguish between the correct and false constitutional isomers. Therefore a quality score was computed in the following way: For a (randomly selected) spectrum–structure pair from the NIST MS library all constitutional isomers are generated using the structure generator MOLGEN. For each isomer the matchvalue with respect to the library spectrum is calculated, and isomers are ranked according to their matchvalues. The quality of the ranking can be quantified in terms of the correct structure’s relative ranking position (RRP). This procedure was repeated for 100 randomly selected spectrum–structure pairs belonging to small organic compounds. In this first approach the RRP of the correct isomer was 0.27 on average

Families of Small Regular Graphs of Girth 5

In this paper we obtain $(q+3)$--regular graphs of girth 5 with fewer vertices than previously known ones for $q=13,17,19$ and for any prime $q \ge 23$ performing operations of reductions and amalgams on the Levi graph $B_q$ of an elliptic semiplane of type ${\cal C}$. We also obtain a 13-regular graph of girth 5 on 236 vertices from $B_{11}$ using the same technique

House of Graphs: a database of interesting graphs

In this note we present House of Graphs (http://hog.grinvin.org) which is a new database of graphs. The key principle is to have a searchable database and offer -- next to complete lists of some graph classes -- also a list of special graphs that already turned out to be interesting and relevant in the study of graph theoretic problems or as counterexamples to conjectures. This list can be extended by users of the database.Comment: 8 pages; added a figur

On bipartite graphs of defect at most 4

We consider the bipartite version of the degree/diameter problem, namely, given natural numbers {\Delta} \geq 2 and D \geq 2, find the maximum number Nb({\Delta},D) of vertices in a bipartite graph of maximum degree {\Delta} and diameter D. In this context, the Moore bipartite bound Mb({\Delta},D) represents an upper bound for Nb({\Delta},D). Bipartite graphs of maximum degree {\Delta}, diameter D and order Mb({\Delta},D), called Moore bipartite graphs, have turned out to be very rare. Therefore, it is very interesting to investigate bipartite graphs of maximum degree {\Delta} \geq 2, diameter D \geq 2 and order Mb({\Delta},D) - \epsilon with small \epsilon > 0, that is, bipartite ({\Delta},D,-\epsilon)-graphs. The parameter \epsilon is called the defect. This paper considers bipartite graphs of defect at most 4, and presents all the known such graphs. Bipartite graphs of defect 2 have been studied in the past; if {\Delta} \geq 3 and D \geq 3, they may only exist for D = 3. However, when \epsilon > 2 bipartite ({\Delta},D,-\epsilon)-graphs represent a wide unexplored area. The main results of the paper include several necessary conditions for the existence of bipartite $(\Delta,d,-4)$-graphs; the complete catalogue of bipartite (3,D,-\epsilon)-graphs with D \geq 2 and 0 \leq \epsilon \leq 4; the complete catalogue of bipartite ({\Delta},D,-\epsilon)-graphs with {\Delta} \geq 2, 5 \leq D \leq 187 (D /= 6) and 0 \leq \epsilon \leq 4; and a non-existence proof of all bipartite ({\Delta},D,-4)-graphs with {\Delta} \geq 3 and odd D \geq 7. Finally, we conjecture that there are no bipartite graphs of defect 4 for {\Delta} \geq 3 and D \geq 5, and comment on some implications of our results for upper bounds of Nb({\Delta},D).Comment: 25 pages, 14 Postscript figure

Using fluorescent lipids contributes to the active learning of principles underlying lipid signaling

The concepts of phospholipase activity is often taught in undergraduate biology and biochemistry classes and reinforced in laboratory exercises. However, very rarely does the design of these exercises allow students to directly gain experience in the use of modern instruments such as digital imaging systems and fluorescence spectrophotometers. The laboratory exercise described here involves the use of fluorescent lipids to evaluate phospholipase activity. Students use thin layer chromatography (TLC) to understand how lipids change under different conditions (i.e. abiotic and biotic stress). They explore strategies to separate, visualize and quantify lipids by TLC, digital imaging, and fluorometry. They also have increased opportunities for hands‐on practise with experimental design, liposome sample preparation, and implementation of instrumentation commonly used by experienced researchers; all while learning and applying fundamental concepts about lipids.Fil: Peppino Margutti, Micaela Yesica. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Reyna, Matias. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Villasuso, Ana Laura. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentin

1861-11-02 John W. Meringer recommends George W. Martin for promotion to captain

https://digitalmaine.com/cw_me_17th_regiment_corr/1016/thumbnail.jp

Computational Exploration of the Chemical Space Surrounding the Molecules of Life

How the transition of disorganized, inanimate matter to organized, living systems took place on our planet and might have occurred on other bodies of our solar system or elsewhere in the universe is one of the fundamental questions studied in the field of astrobiology. The only instance of life known so far is the terrestrial one, and all living organisms on Earth share many of the same biochemical foundations with respect to reproduction and metabolism. These biochemical foundations rely on a small pool of biomolecules, which represent a minute subset of plausible structural analogs, which themselves form only a very small fraction of all possible chemical compounds in chemical space. We believe that one key to understanding the origins of life is to study biomolecules in the context of their surrounding neighborhood in chemical space. Using unique software tools, so-called structure generators, we are able to exhaustively construct well defined subsets of chemical space. These virtual compound libraries are then computationally analyzed with respect to the physico-chemical properties of their constituents. In this talk some basic mathematical models and computational aspects of generating molecular structures are presented, results concerning the amino acid alphabet, nucleotide analogs and the core of intermediary metabolism are summarized, and perspectives of ongoing studies related to astrobiology exploration missions are outlined

Atmospheric methane with SCIAMACHY: Operational Level 2 data analysis and verification

SCIAMACHY is a passive imaging spectrometer mounted on board ESA’s ENVISAT satellite to probe a large number of atmospheric trace gas species, such as methane, and their global distribution and evolution. Methane (CH4) is particularly interesting as it is one of the most abundant greenhouse gas in the Earth atmosphere. To analyze SCIAMACHY methane measurements, we used the DLR BIRRA (Beer InfraRed Retrieval Algorithm) to retrieve nadir methane concentrations from its infrared spectra in channel 6. By integrating the DLR BIRRA code into ESAs operational Level 2 processor, we expanded it to include atmospheric CH4 column measurements. We have therefore performed an extensive test and verification operation. Our tests are based on separate comparisons with existing space and ground-based obtained measurements of methane column density. We present here our strategy for quality check of this first version of a CH4 product. We will further discuss specific geographical areas we used to validate the products

New Developments in the SCIAMACHY Level 2 Ground Processor Towards Version 7

SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric ChartographY) aboard ESA’s environmental satellite ENVISAT observed the Earth’s atmosphere in limb, nadir, and solar/lunar occultation geometries covering the UV-Visible to NIR spectral range. It is a joint project of Germany, the Netherlands and Belgium and was launched in February 2002. SCIAMACHY doubled its originally planned in-orbit lifetime of five years before the communication to ENVISAT was severed in April 2012, and the mission entered its post-operational phase. In order to preserve the best quality of the outstanding data recorded by SCIAMACHY, data processors are still being updated. This presentation will highlight three new developments that are currently being incorporated into the forthcoming Version 7 of ESA’s operational Level 2 processor: 1. Tropospheric BrO, a new retrieval based on the scientific algorithm of (Theys et al., 2011). This algorithm had originally been developed for the GOME-2 sensor and was later adapted for SCIAMACHY. 2. Improved cloud flagging using limb measurements (Liebing, 2015). Limb cloud flags are already part of the SCIAMACHY L2 product. They are currently calculated employing the scientific algorithm developed by (Eichmann et al., 2015). Clouds are categorized into four types: water, ice, polar stratospheric and noctilucent clouds. High atmospheric aerosol loadings, however, often lead to spurious cloud flags, when aerosols had been misidentified as clouds. The new algorithm will better discriminate between aerosol and clouds. It will also have a higher sensitivity w.r.t. thin clouds. 3. A new, future-proof file format for the level 2 product based on NetCDF. The data format will be aligned and harmonized with other missions, particularly GOME and Sentinels. The final concept for the new format is still under discussion within the SCIAMACHY Quality Working Group

High-precision frequency measurements: indispensable tools at the core of the molecular-level analysis of complex systems

This perspective article provides an assessment of the state-of-the-art in the molecular-resolution analysis of complex organic materials. These materials can be divided into biomolecules in complex mixtures (which are amenable to successful separation into unambiguously defined molecular fractions) and complex nonrepetitive materials (which cannot be purified in the conventional sense because they are even more intricate). Molecular-level analyses of these complex systems critically depend on the integrated use of high-performance separation, high-resolution organic structural spectroscopy and mathematical data treatment. At present, only high-precision frequency-derived data exhibit sufficient resolution to overcome the otherwise common and detrimental effects of intrinsic averaging, which deteriorate spectral resolution to the degree of bulk-level rather than molecular-resolution analysis. High-precision frequency measurements are integral to the two most influential organic structural spectroscopic methods for the investigation of complex materials—NMR spectroscopy (which provides unsurpassed detail on close-range molecular order) and FTICR mass spectrometry (which provides unrivalled resolution)—and they can be translated into isotope-specific molecular-resolution data of unprecedented significance and richness. The quality of this standalone de novo molecular-level resolution data is of unparalleled mechanistic relevance and is sufficient to fundamentally advance our understanding of the structures and functions of complex biomolecular mixtures and nonrepetitive complex materials, such as natural organic matter (NOM), aerosols, and soil, plant and microbial extracts, all of which are currently poorly amenable to meaningful target analysis. The discrete analytical volumetric pixel space that is presently available to describe complex systems (defined by NMR, FT mass spectrometry and separation technologies) is in the range of 108–14 voxels, and is therefore capable of providing the necessary detail for a meaningful molecular-level analysis of very complex mixtures. Nonrepetitive complex materials exhibit mass spectral signatures in which the signal intensity often follows the number of chemically feasible isomers. This suggests that even the most strongly resolved FTICR mass spectra of complex materials represent simplified (e.g. isomer-filtered) projections of structural space