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.     

Exo-metal coordination by a tricyclic [(P(mu-N-2-NC5H4))2(mu-O)]2 dimer in [(P(mu-N-2-NC5H4))2(mu-O)]2(CuCl x (C5H5N)2)4 (2-NC5H4 = 2-pyridyl, C5H5N = pyridine)

The in situ reaction of the phosphazane dimer [CIP(mu-N-2-NC5H4)]2 (2) with CuCl in the presence of CsH5N/H2O gives the title complex [(P(mu-N-2-NC5H4))2(mu-O)]2(CuCl x (C5H5N)2)4 (1), containing a tricyclic [(P(mu-N-2-NC5H4))2(mu-O)]2 ligand which is isoelectronic with species of the type [(P(mu-NR))2NR]2.     

Steric control in the oligomerisation of phosphazane dimers; towards new phosphorus-nitrogen macrocycles

The reaction of [ClP(mu-NtBu)]2 (1) with H2O (1 : 2 equivalents) in the presence of excess Et3N gives the new chain compound [(mu-O)[P(mu-NtBu)2P(H)=O]2] (3), consisting of two P2N2 rings linked by a mu-O atom and terminating in P(V)(H)=O groups. A similar chain species is obtained from the reaction of the lithiate of [(tBuNH)P(mu-NtBu)2P(H)=O] (5) with [ClP(mu-NtBu)2P(NHtBu)] (2), the product being [(mu-O)[P(mu-NtBu)2P(NHtBu)]2] (6). Compounds 3 and 6 are the first examples of O-bridged chain phosphazanes and potential precursors to new phosphorus-nitrogen macrocycles. The syntheses and X-ray structures of 3, 5 and 6 are reported.     

A one-pot synthesis to [(Me3Si)3SiSb]4; a potential precursor for Sb42-

The reaction of (Me(3)Si)(3)SiK[middle dot]18-crown-6 with SbCl(3)(3 : 1 equiv.) provides a simple route to the title complex [(Me(3)Si)(3)SiSb](4). The potassium base initially acts as a nucleophile and then as a coupling agent, forming Sb-Sb bonds.     

Selection of the cis and trans phosph(III)azane macrocycles [{P(mu-NtBu)}2(1-Y-2-NH-C6H4)]2(Y=O, S)

The 1 : 1 reactions of [ClP(mu-NtBu)]2 with the difunctional aromatic amines 1,2-1-YH-2-NH2-C6H4 in the presence of Et3N give the dimeric phosph(III)azane macrocycles [{P(mu-NtBu)2(1-Y-2-HN-C6H4)]2, predominantly as the cis isomer in the case of Y=O (1.cis) and as the trans isomer for Y=S (2.trans). Model M.O. calculations suggest that the selection of the cis and trans isomers is not thermodynamically controlled. The alternative isomers 1.trans and 2.cis are generated exclusively by the deprotonation of the model intermediates [(1-Y-2-NH2-C6H4)P(mu-NtBu)]2[Y=O (3), S (4)] with nBuLi followed by cyclisation with [ClP(mu-NtBu)]2. The solid-state structures of 1.cis/trans(50 : 50), 2.cis, 3 and 4 are reported.     

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.     

Targeting large phosp(III)azane macrocyles [{P(mu-NR)}(2)(LL)](n) (n> or = 2)

The condensation reactions of the dimer [ClP(micro-NR)](2) with organic diacids [LL(H)(2)], possessing linear orientations of their organic groups, result in the formation of phospha(III)zane macrocyles of the type [{P(mu-NR)}(2)(LL)](n) of various sizes. The series of macrocycles [{P(mu-N(t)Bu)}(2){1,5-(NH)(2)C(10)H(6)}](3), [{P(mu-NCy)}(2)(1,5-O(2)C(10)H(6))](n) [n = 3; n = 4], [{P(mu-N(t)Bu)}(2){1,4-(NH)(2)C(6)H(4)}](4), [{P(mu-N(t)Bu)}(2)(1,4-O(2)C(6)H(4))], [{P(mu-NCy)}(2)(1,4-O(2)C(6)H(4))](3) and [{P(mu-N(t)Bu)}(2){(NH)C(6)H(4)OC(6)H(4)(NH)}](2) can be related to classical organic frameworks, like calixarenes.