A genetic algorithm for the structural optimization of Morse clusters

This article describes the application of a genetic algorithm for the structural optimization of 19–50-atom clusters bound by medium-range and short-range Morse pair potentials. The GA is found to be efficient and reliable for finding the geometries corresponding to the previously published global minima [Doye JPK, Wales DJ (1997) J Chem Soc Faraday Trans 93: 4233]. Using the genetic algorithm, only a relatively small number of energy evaluations and minimizations are required to find the global minima. By contrast, a simple random search algorithm often cannot find the global minima of the larger clusters, even after many thousands of searches. Received: 27 October 1999 / Accepted: 7 December 1999 / Published online: 19 April 2000     

Design of liquid crystals with "de Vries-like" properties: organosiloxane mesogen with a 5-phenylpyrimidine core

According to a new design strategy for "de Vries-like" liquid crystal materials, we report the synthesis and characterization of an organosiloxane mesogen with a 5-phenylpyrimidine core that forms SmA and SmC liquid crystal phases. This new material is characterized by a maximum layer contraction of 1.2% upon SmA-SmC phase transition and is comparable to the best "de Vries-like" materials reported heretofore.     

The synthesis of single enantiomers of meromycolic acids from mycobacterial wax esters

Three stereoisomers of a wax ester meromycolate have been prepared starting from mannitol. A detailed comparison of their NMR spectra with those reported for a homologous series of natural wax esters allows the relative configurations of the α-methyl group and adjacent trans-cyclopropane to be determined.     

Solvation in mixed aqueous solvents from a thermodynamic cycle approach

A novel approach is presented for interpreting and potentially predicting values of the isothermal, isobaric transfer free energy, entropy, and enthalpy (Deltamicrotr2, Deltastr2, and Deltahtr2) for a solute between water and water-cosolvent mixtures. The approach explicitly accounts for volumetric properties of the solvent and solute (the equation of state, EoS) and casts the overall transfer process as a thermodynamic cycle with two stages: (1) isothermal solvent exchange from pure water to the cosolvent composition of interest at fixed mass density; (2) isothermal expansion or compression at the final solvent composition to recover the pressure of the initial state. Using molecular simulations with methane as the solute, the analysis is illustrated over a wide range of cosolvent concentrations for sorbitol-, ethanol-, and methanol-water binary mixtures. The EoS contribution semiquantitatively or quantitatively captures Deltamicrotr2, Deltastr2, and Deltahtr2 in almost all cases tested, highlighting the importance of considering the effects of changes in solvent density on the overall transfer process. The results also indicate that apolar solvation at these length scales is dominated by the work of cavity formation across a range of cosolvent species and concentrations.     

Ligand-protein docking with water molecules

The presence of water molecules plays an important role in the accuracy of ligand-protein docking predictions. Comprehensive docking simulations have been performed on a large set of ligand-protein complexes whose crystal structures contain water molecules in their binding sites. Only those water molecules found in the immediate vicinity of both the ligand and the protein were considered. We have investigated whether prior optimization of the orientation of water molecules in either the presence or absence of the bound ligand has any effect on the accuracy of docking predictions. We have observed a statistically significant overall increase in accuracy when water molecules are included during docking simulations and have found this to be independent of the method of optimization of the orientation of water molecules. These results confirm the importance of including water molecules whenever possible in a ligand-protein docking simulation. Our findings also reveal that prior optimization of the orientation of water molecules, in the absence of any bound ligand, does not have a detrimental effect on the improved accuracy of ligand-protein docking. This is important, given the use of docking simulations to predict the binding modes of new ligands or drug molecules.     

Hyperconjugation and homoconjugation in alkyl radicals bearing β-phosphorus substituents

The isotropic ³¹P hyperfine splitting constants derived from the ESR spectra of a series of β-phosphorus-substituted alkyl radicals are in the order expected for hyperconjugative spin transmission.     

Thermal decomposition of poly(vinylidene chloride) prepared in presence of oxygen

The thermal decomposition of poly(vinylidene chloride) was studied for samples prepared in the presence of oxygen. The products from both mass and aqueous suspension polymerizations show two modes of thermal decomposition. A rapid initial mode varies in rate and extent with the amount of oxygen present. A slower mode is unaffected by oxygen and in similar in rate to the polymer made in the absence of oxygen. The chief volatile products are phosgene and formaldehyde for the rapid decomposition and hydrogen chloride for the slow decomposition. The rapid decomposition is interpreted to be an unzipping reaction of a vinylidene chloride–oxygen alternating copolymer initiated by homolysis of a peroxide bond. The absence of significant amounts of hydrogen chloride during this stage of decomposition shows that none of the free radicals generated are capable of initiating a chain reaction that would unzip hydrogen chloride from the poly(vinylidene chloride) backbone. The presence of oxygen during the aqueous suspension polymerization correlates with the generation of hydrochloric acid in the aqueous phase. By analogy with the high temperature decomposition, the hydrochloric acid is believed to result primarily from the hydrolysis of phosgene produced by partial decomposition of the polyperoxide. Initiation of the decomposition is believed due to a reaction of the chain propagating radical.     

International inter-comparison exercise on $${}^{153}\hbox {Sm}$$

Samarium-153 (\({}^{153}\hbox {Sm}\)) is a short-lived radionuclide that decays to stable europium-153 via beta emission, with subsequent de-excitation via gamma emission and internal conversion. Historical measurements of \({}^{153}\hbox {Sm}\) by gamma spectrometry and beta liquid scintillation counting have shown a low bias compared to beta proportional counting. In order to investigate this, four national laboratories jointly conducted an experimental inter-comparison exercise on a certified \({}^{153}\hbox {Sm}\) sample, created from neutron activation of samarium-152. Radiometric measurements were conducted using gamma spectrometry, liquid scintillation counting, gas proportional counting, and passivated implanted planar silicon detectors and compared across the four institutions against the certified value. The results from this experiment are presented together with a number of conclusions which suggest that the current published cumulative fission yield for \({}^{153}\hbox {Sm}\), as used by many laboratories, is approximately 15% high and is the likely cause of the previously observed bias.     

Comparing results of X-ray diffraction, µ-Raman spectroscopy and neutron diffraction when identifying chemical phases in seized nuclear material,during a comparative nuclear forensics exercise

Journal of Radioanalytical and Nuclear Chemistry - This work presents the results for identification of chemical phases obtained by several laboratories as a part of an international nuclear...