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.     

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.     

Formation of oxygen-deficient type structural defects and state of ions in SiO2 glasses implanted with transition metal ions

The properties and concentrations of oxygen-deficient type structural defects in type III SiO₂ glasses implanted with Ti⁺, Cr⁺, Mn⁺, Fe⁺, or Cu⁺ to doses from 0.5×10¹⁶ to 6×100¹⁶ ions/cm² at an energy of 160 keV have been measured by using vacuum UV and EPR spectroscopies. An intense absorption band centered around 7.5 eV is observed in all the samples except for Cu-implanted ones and is attributed primarily to Si---Si homo-bonds with the bond distance close to that of the Si₂H₆ molecule. The homo-bond and implanted ion concentrations are of the same order of magnitude in the implanted layers. An E′ type center associated with the homo-bond is observed in all the samples except for Cu-implanted ones. Anomalous behaviors of the Cu-implanted samples are attributed to the formation of Cu-colloids. An enhanced formation of metallic particles or colloids is suggested for the samples implanted with Cr, Mn or Fe to doses higher than 3×10¹⁶ ions/cm².     

Intercalation of Toluidines into α-Zirconium Hydrogenphosphate

Intercalates of o-, m-, and p-toluidine into α-Zr(HPO₄)₂ · H₂O were prepared and characterized by powder X-ray diffraction, thermogravimetric analysis and infrared spectroscopy. As follows from IR, toludine molecules are protonated in the interlayer space. Toluidine molecules are arranged in a bimolecular way in the intercalates containing more than 1.5 toluidine molecules per Zr atom. On the other hand, a monolayer of the toluidine molecules is supposed in the intercalates with less than one toluidine molecule per Zr atom.     

Absolute Asymmetric Synthesis: The Origin, Control, and Amplification of Chirality

Biomolecular homochirality, the origin of which is still a puzzle, has challenged scientists to design chemical systems that provide chiral molecules through absolute asymmetric synthesis and to amplify a small stereochemical bias in such systems. The photoresolution of the enantiomers of helical-shaped, sterically overcrowded alkene 1 with circularly polarized light and the transduction of the stereochemical information by triggering the helical arrangement of a large collection of achiral molecules in a twisted nematic liquid crystalline phase (2) are examples of control and amplification of chirality.