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.     

Kinetic and thermochemical parameters of chlorine atom transfer reactions from CF3Cl,CF3CF2Cl,CF2ClCF2Cl,and CF2ClCFCl2 in gas phase

The following reactions: (1) were studied over the temperature ranges 533–687 K, 563–663 K, and 503–613 K for the forward reactions respectively and over 683–763 K, for the back reaction. Arrhenius parameters for chlorine atom transfer were determined relative to the combination of the attacking radicals. The ΔH_r°(1) = ?3.95 ± 0.45 kcal mol^?1 was calculated and from this value the ΔH∮(C₂F₅Cl) = ?2.66.3 ± 2.5 kcal mol^?1 and D(C₂F₅-Cl) = 82.0 ± 1.2 kcal mol^?1 were obtained. Besides, the ΔH_r°(2) was estimated leading to D(CF₂ClCF₂Cl) = 79.2 ± 5 Kcal mol^?1. The bond dissociation energies and the heat of formation are compared with those of the literature. The effect of the halogen substitutents as well as the importance of the polar effects for halogen transfer processes are discussed.     

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.     

Determination of a Gas-Phase Bimolecular Rate Coefficient Using a Discharge Flow Tube

A laboratory experiment for senior undergraduate students, the determination of the rate coefficient for the reaction of oxygen atoms with hexafluoropropene, is presented. This reaction has the advantage of not having any important secondary reactions. This laboratory experiment introduces the undergraduate physical chemistry student to advanced kinetic techniques and provides a test of the fundamental principles of chemical kinetics.     

Spectroscopic parameters of theJ π=1+,T=0 excited6Li level

An analysis of thed- coincidence spectra of the⁷Li(³He, d)⁴He reaction at incident energy of 5.0 MeV and at various detector angles has been carried out. The values of the spectroscopic parameters of theJ =1⁺,T=0⁶Li state at excitation energy of 5.65 MeV have been deduced. The results, considering the experimental errors, do not appear to be dependent on the geometry and are in line with the ones adopted in literature.     

Discharge flow‐chemiluminescence study of the rate coefficients for O(3P) + CF2CCl2 and O(3P) + CF3CFCF2 reactions at 298 K

The kinetics of the reactions O(³P) + CF₂CCl₂ and O(³P) + CF₃CFCF₂ were studied at room temperature in a discharge flow tube system. The overall rate constants based on the measured afterglow reactions were (3.10 ± 0.40) × 10⁻¹³ and (3.00 ± 0.60) × 10⁻¹⁴ cm³ molecule⁻¹ s⁻¹, respectively. The experiments were carried out under pseudo‐first‐order conditions with [O(³P)]₀ ≪ [alkene]₀. These results are compared with previous relative measurements using different experimental techniques. The effect of substituent atoms or groups on the overall rate constants is analyzed in comparison with other alkenes in the literature. © 1999 John Wiley & Sons, Inc. Int J Chem Kinet 31: 867–872, 1999