Mass spectrometry in structural and stereochemical problems. Part 178 - The electron-impact promoted fragmentation of 1,2-cyclohexene oxide

Mass spectra of 1,2-cyclohexane oxide and three deuterium labeled analog

On the origin of terpenes in symbiotic associations between marine invertebrates and algae (zooxanthellae). Culture studies and an application of ^(13)C/^(12)C isotope ratio mass spectrometry.

^(13)C/^(12)C ratios of sets of compounds, algal sterols and terpenes, isolated from dinoflagellate symbiont (zooxanthellae)-bearing soft corals and gorgonians were determined. In most cases, a significant difference was found between the δ^(13)C values of the terpenes and of the algal sterols from the same set, the algal sterols containing less ^(13)C than the terpenes. These results can only be explained if terpenes are synthesized by the host. Cultured zooxanthellae, isolated from symbiotic associations, do not make terpenes. Algal sterols of the various sets do not all have the same δ^(13)C value: average values range from -18.2 to -24.3‰. A consistent difference of about 7‰ in the δ^(13)C values of sterols of cultured symbionts isolated from two of the gorgonians was found. This has potential applications for the taxonomy of zooxanthellae, most of which are believed by some specialists to be one discrete species

On the contact detection for contact-impact analysis in multibody systems

One of the most important and complex parts of the simulation of multibody systems with contact-impact involves the detection of the precise instant of impact. In general, the periods of contact are very small and, therefore, the selection of the time step for the integration of the time derivatives of the state variables plays a crucial role in the dynamics of multibody systems. The conservative approach is to use very small time steps throughout the analysis. However, this solution is not efficient from the computational view point. When variable time step integration algorithms are used and the pre-impact dynamics does not involve high-frequencies the integration algorithms may use larger time steps and the contact between two surfaces may start with initial penetrations that are artificially high. This fact leads either to a stall of the integration algorithm or to contact forces that are physically impossible which, in turn, lead to post-impact dynamics that is unrelated to the physical problem. The main purpose of this work is to present a general and comprehensive approach to automatically adjust the time step, in variable time step integration algorithms, in the vicinity of contact of multibody systems. The proposed methodology ensures that for any impact in a multibody system the time step of the integration is such that any initial penetration is below any prescribed threshold. In the case of the start of contact, and after a time step is complete, the numerical error control of the selected integration algorithm is forced to handle the physical criteria to accept/reject time steps in equal terms with the numerical error control that it normally uses. The main features of this approach are the simplicity of its computational implementation, its good computational efficiency and its ability to deal with the transitions between non contact and contact situations in multibody dynamics. A demonstration case provides the results that support the discussion and show the validity of the proposed methodology.Fundação para a Ciência e a Tecnologia (FCT

Science, performance and transformation: performance for a ‘scientific’ age?

This is an accepted manuscript of an article published by Taylor & Francis in International Journal of Performance Arts and Digital Media on 30/09/2014, available online: https://www.tandfonline.com/doi/full/10.1080/14794713.2014.946282 The accepted version of the publication may differ from the final published version.The ‘two cultures’ of science and the arts/humanities are often considered at odds, but digital technology, and the broader implications of digital culture, provides a model for more productive forms of exchange and hybridity. This article applies theories of intercultural theatre practice to performance that works across this cultural divide to explore the types of interaction that take place. Following a historical discussion of the science/art divide, a three-fold model is proposed and explored through case studies including Djerassi and Laszlo's 2003 NO, Eduardo Kac's 1999 Genesis, Reckless Sleepers' 1996/2006 Schrödinger's Box, and John Barrow's 2002 Infinities. It is argued that science operates through the creation of mathematical models of aspects of the physical world, whilst art similarly constructs different kinds of models for understanding the social/cultural and occasionally physical world. Digital technology expands the modelling possibilities both directly, through simulation, virtual reality and integration into ‘live’ activities of augmented and intermedia performance, and through the transformative nature of digital culture

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

BACKGROUND: Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas. RESULTS: An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries. CONCLUSION: The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65–81%. Corresponding software and supplemental data are available for downloads from the authors' website