Restricted diffusion in silica particles measured by pulsed field gradient NMR

The restricted diffusion coefficient of water through porous silica is measured by pulsed field gradient (PFG) NMR as a function of loading in order to develop a model for self-diffusion at full pore filling in sol-gel-made porous silica particles. This model describes the pore or intraparticle diffusion coefficient as a function of particle porosity, tortuosity, and the steric hindrance applied on the molecules by the pore space. The particle morphology is characterized by nitrogen adsorption and an appropriate tortuosity model is chosen in comparison with literature data. To characterize the material, NMR relaxation and diffusion studies at different degrees of pore filling were carried out in relation to the silica/water adsorption isotherm.     

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin

The binding of a set of 10 triphenoxypyridine derivatives to two serine proteases, factor Xa and trypsin, has been used to analyze factors related to sampling and convergence in free energy calculations based on molecular dynamics simulation techniques. The inhibitors investigated were initially proposed as part of the Critical Assessment of Techniques for Free Energy Evaluation (CATFEE) project for which no experimental results nor any assessment of the predictions submitted by various groups have ever been published. The inhibitors studied represent a severe challenge for explicit free energy calculations. The mutations from one compound to another involve up to 19 atoms, the creation and annihilation of net charge and several alternate binding modes. Nevertheless, we demonstrate that it is possible to obtain highly converged results (+/- 5-10 kJ/mol) even for such complex multi-atom mutations by simulating on a nanosecond time scale. This is achieved by using soft-core potentials to facilitate the creation and deletion of atoms and by a careful choice of mutation pathway. The results show that given modest computational resources, explicit free energy calculations can be successfully applied to realistic problems in drug design.     

A facile and general route to 4-substituted-2 butenolides

Grignard reagents react with 7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylic anhydride and produce in high yields the corresponding substituted bicyclo-γ-butanolides. These lactones produce the title compounds by retro Diels-Alder reaction during distillation.     

Model for nucleon valence structure functions at allx,allp ⊥ and allQ 2 from the correspondence between QCD and DTU

We propose a simple parametrization of the nucleon valence structure functions at allx, allp _⊥ and allQ ². We use the DTU parton model to fix the parametrization at a reference point (Q ₀ ² =3 GeV²) and we mimic the QCD evolution by replacing the dimensioned parameters of the DTU parton model by functions depending onQ ². Excellent agreement is obtained with existing data.     

Thermotropic liquid crystalline properties of semiperfluoroalkyloxyphenyl and perfluoroalkylphenyl β-D-glucopyranosides

The synthesis of two series of semiperfluoroalkyloxyphenyl and perfluoroalkylphenyl β-D-glucopyranosides is described. Their mesomorphic properties are studied by DSC, polarized optical microscopy and X-ray diffraction. All mesophases are identified as smectic A with a bimolecular in-layer arrangement.     

Singular value decomposition of energy matrices in theoretical atomic structure calculations

The singular value decomposition, SVD, is applied to the linear eigenvalue problem in atomic structure calculations. By comparing with recent calculations of energy levels in neutral Ca, it is shown that the SVD can give quite accurate results and much faster than normal diagonalization techniques, even of the Davidson type. However, the energy levels calculated in this approach are more strongly bound than the real eigenvalues, and this is ascribed to an artefact of the SVD, caused by the use of a discretized continuum in the calculations. This effect can lead to fairly large errors if there is strong CI present. The property of the linear eigenvalue problem that the spectrum is unchanged when a constant is added to the diagonal does not apply to the SVD. This means that it is impossible to solve the problems connected with a discretized continuum simply by shifting the spectrum.