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.     

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.     

Inner-sphere oxidation of a ternary dipicolinatochromium(III) complex involving a malonic acid co-ligand

The oxidation of a ternary complex of chromium(III), [Cr^III(DPA)(Mal)(H₂O)₂]^?, involving dipicolinic acid (DPA) as primary ligand and malonic acid (Mal) as co-ligand, was investigated in aqueous acidic medium. The periodate oxidation kinetics of [Cr^III(DPA)(Mal)(H₂O)₂]^? to give Cr(VI) under pseudo-first-order conditions were studied at various pH, ionic strength and temperature values. The kinetic equation was found to be as follows: \( {\text{Rate}} = {{\left[ {{\text{IO}}_{4}^{ - } } \right]\left[ {{\text{Cr}}^{\text{III}} } \right]_{\text{T}} \left( {{{k_{5} K_{5} + k_{6} K_{4} K_{6} } \mathord{\left/ {\vphantom {{k_{5} K_{5} + k_{6} K_{4} K_{6} } {\left[ {{\text{H}}^{ + } } \right]}}} \right. \kern-0pt} {\left[ {{\text{H}}^{ + } } \right]}}} \right)} \mathord{\left/ {\vphantom {{\left[ {{\text{IO}}_{4}^{ - } } \right]\left[ {{\text{Cr}}^{\text{III}} } \right]_{\text{T}} \left( {{{k_{5} K_{5} + k_{6} K_{4} K_{6} } \mathord{\left/ {\vphantom {{k_{5} K_{5} + k_{6} K_{4} K_{6} } {\left[ {{\text{H}}^{ + } } \right]}}} \right. \kern-0pt} {\left[ {{\text{H}}^{ + } } \right]}}} \right)} {\left\{ {\left( {\left[ {{\text{H}}^{ + } } \right] + K_{4} } \right) + \left( {K_{5} \left[ {{\text{H}}^{ + } } \right] + K_{6} K_{4} } \right)\left[ {{\text{IO}}_{4}^{ - } } \right]} \right\}}}} \right. \kern-0pt} {\left\{ {\left( {\left[ {{\text{H}}^{ + } } \right] + K_{4} } \right) + \left( {K_{5} \left[ {{\text{H}}^{ + } } \right] + K_{6} K_{4} } \right)\left[ {{\text{IO}}_{4}^{ - } } \right]} \right\}}} \) where k ₆ (3.65 × 10^?3 s^?1) represents the electron transfer reaction rate constant and K ₄ (4.60 × 10^?4 mol dm^?3) represents the dissociation constant for the reaction \( \left[ {{\text{Cr}}^{\text{III}} \left( {\text{DPA}} \right)\left( {\text{Mal}} \right)\left( {{\text{H}}_{2} {\text{O}}} \right)_{2} } \right]^{ - } \rightleftharpoons \left[ {{\text{Cr}}^{\text{III}} \left( {\text{DPA}} \right)\left( {\text{Mal}} \right)\left( {{\text{H}}_{2} {\text{O}}} \right)\left( {\text{OH}} \right)} \right]^{2 - } + {\text{H}}^{ + } \) and K ₅ (1.87 mol^?1 dm³) and K ₆ (22.83 mol^?1 dm³) represent the pre-equilibrium formation constants at 30 °C and I = 0.2 mol dm^?3. Hexadecyltrimethylammonium bromide (CTAB) was found to enhance the reaction rate, whereas sodium dodecyl sulfate (SDS) had no effect. The thermodynamic activation parameters were estimated, and the oxidation is proposed to proceed via an inner-sphere mechanism involving the coordination of IO₄ ^? to Cr(III).     

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.     

Nondestructive neutron activation analysis of some soil clays of Egypt

Fourteen clay samples separated from calcareous, lacustrine, Nile alluvium and desert alluvium soils of Egypt were analyzed by pure instrumental neutron activation analysis. Elemental composition was determined by high resolution gamma-spectrometry on samples irradiated with reactor neutrons using the monostrandard technique. This was carried out in the nuclear research center of Karlsruhe, West Germany. As many as 17 trace elements, beside Ca, K, and Na, were quantitatively determined. The spectra of chosen activated clays are given. Data reveal that the content of the trace elements As, Cs, Hf, Sb, Sc, Sm, Yb, Th and U were found within a narrow range despite location and depths of clay samples. Nevertheless, the contents of some elements mainly Ce, Cr and La had a wide range. In brief, the presence of any elements in higher or lower levels in certain clays is contingent on the occurence of its bearing minerals, nature of parent sediments and depositional environments of these sediments.