DYNGA: a general purpose QM-MM-MD program. I. Application to water

We present a general purpose QM-MM-MD engine (DYNGA) designed to test alternative hybrid Hamiltonians geared towards the treatment of problems of interest in structural biology including the use of experimental data constraints. In this first presentation we use DYNGA to explore the behaviour of a traditional QM-MM approach in the treatment of the water—water interaction. We find the potential energy hypersurface for the water dimer computed with the HF 4–31G*/TIP3P hybrid Hamiltonian tends to be too flat. We also explore the effect of using traditional QM-MM techniques on proton wires and conclude there is a need for improvement, possibly addressed by using polarizable force fields.     

Synthesis and reduction of 5-halo-and 5-nitro-1-(benzofuran-3-yl)-2-phenylethanones

Novel 1-(2-alkylbenzofuran-3-yl)-2-(4-methoxyphenyl)ethanones having a halogen or nitro group in position 5 of the benzofuran ring were synthesized starting with the corresponding 2-(2-formylphenoxy)alkanoic acids. 1-(2-Alkylbenzofuran-3-yl)-2-phenylethanols containing bromine or chlorine atom were prepared in high yields by reduction of the corresponding ethanones with lithium aluminum hydride. Selective catalytic reduction of nitro 1-(2-alkylbenzofuran-3-yl)-2-(4-methoxyphenyl)ethanones to the corresponding amino compounds under Pd/C in room temperature was achieved. Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1158–1166, August, 2006.     

PAST AND FUTURE MANAGEMENT OF A COLLAPSED FISHERY: THE BAY OF BISCAY ANCHOVY

Abstract We analyze the efficiency of the international management of the Bay of Biscay anchovy. While a sharing agreement between France and Spain has been in place since 1992, the fish stock collapsed in 2005 and the fishery closed from 2005 to spring 2010. We consider differences in production technologies between both countries and calibrate our model using data from 1987 to 2009. Our results suggest two sources of rent dissipation under the existing sharing agreement: inefficient quota allocation and production inefficiencies due to inflexible national regulations. We discuss several alternatives to improve management.     

ConFlo III - an interface for high precision delta(13)C and delta(15)N analysis with an extended dynamic range

A newly developed interface coupling a CHN combustion device (elemental analyser 'EA') to an isotope ratio mass spectrometer is described and evaluated. The purpose of the device is to extend the dynamic range of delta(13)C and delta(15)N analysis from less than 2 orders of magnitude to more than 3 orders of magnitude. Carbon isotope ratio measurements of atropine as a model compound have been performed analysing between 1 μg to 5 mg C with acceptable to excellent precision (0.6 to 0.06 per thousand, delta-notation). The correction due to the blank signal is critical for sample amounts smaller than 4 μg C. The maximum sample weight is determined by the combustion capacity of the EA. Larger sample amounts are measured using dilution of a small part of the EA effluent with helium. The dilution mechanism works virtually free of isotope fractionation. Copyright 1999 John Wiley & Sons, Ltd.     

Spin-crossover behavior in a new series of iron (II) compounds based on the ligand 5-(2-pyridyl)-1,2,4-triazole

The title ligand (hereafter LL), is found to form an exciting new series of pseudo-octahedral Fe(II) compounds with formula Fe(LL)₃X₂. N Solvent, which exhibit conveniently studied spin-crossover transformations between nominal⁵T and¹A states of Fe(II). Mössbauer spectra indicate that the spin-crossover transformations for these new systems are probably of the continuous type. There is considerable variation in the degree of conversion to low spin with decreasing temperature depending on gegen ion, solvation and/or location of methyl substituent on the triazole - ligand. The Mössbauer spectra for particular complexes in this group show an absence of both noticeable hysteresis and mechanical grinding effects.     

Determination of esters in glycerol phase after transesterification of vegetable oil

In biodiesel production, glycerol is formed as a side product and it is contained in the glycerol phase. This phase contains (besides glycerol): water, soaps, alcohol, traces of catalyst and glycerides and the remaining esters. In this paper, a new method for the determination of esters in the glycerol phase is introduced. The determination enables the minimization of the losses of biodiesel within the production process. It is based on the gradient RP-LC method (water and acetonitrile) with refractometric detection. The analysis is easy and the samples do not need any treatment (only dilution by water) and has a low detection limit. The results of this method were compared with the results of two other published methods: isocratic HPLC and GC. The disadvantage of these two methods is that they need extensive treatment of the sample, which takes many hours, and they are able to determine only the sum of esters. The new method is reliable, much faster and able to differentiate esters of almost each higher fatty acid (e.g. linoleic, linolenic, strearic alkyl ester) in the glycerol phase.     

Gender Diversity in a STEM Subfield – Analysis of a Large Scientific Society and Its Annual Conferences

Speaking engagements, serving as session chairs, and receiving awards at national meetings are essential stepping stones towards professional success for scientific researchers. Studies of gender parity in meetings of national scientific societies repeatedly uncover bias in speaker selection, engendering underrepresentation of women among featured presenters. To continue this dialogue, we analyzed membership data and annual conference programs of a large scientific society (>7000 members annually) in a male-rich (~70% males), technology-oriented STEM subfield. We detected a pronounced skew towards males among invited keynote lecturers, plenary speakers, and recipients of the society’s Senior Investigator award (15%, 13%, and 8% females, respectively). However, the proportion of females among Mid-Career and Young Investigator award recipients and oral session chairs resembled the current gender distribution of the general membership. Female members were more likely to present at the conferences and equally likely to apply and be accepted for oral presentations as their male counterparts. The gender of a session chair had no effect on the gender distribution of selected applicants. Interestingly, we identified several research subareas that were naturally enriched (i.e., not influenced by unequal selection of presenters) for either female or male participants, illustrating within a single subfield the gender divide along biology-technology line typical of all STEM disciplines. Two female-enriched topics experienced a rapid growth in popularity within the examined period, more than doubling the number of associated researchers. Collectively, these findings contribute to the contemporary discourse on gender in science and hopefully will propel positive changes within this and other societies.

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