The Photoisomerization of cis-Stilbene Does Not Follow the Minimum Energy Path.

Thermal activation is not required for barrier crossing reactions in the photoisomerization of cis-stilbene, as demonstrated by computer simulations. The activation is achieved by using the excess energy from the photoexcitation. Moreover, the reaction proceeds with large energy transfers but small conformational changes. The reaction pathway is influenced by these effects and also by the solvent.

Reversing the perturbation in nonequilibrium molecular dynamics: an easy way to calculate the shear viscosity of fluids.

A nonequilibrium method for calculating the shear viscosity is presented. It reverses the cause-and-effect picture customarily used in nonequilibrium molecular dynamics: the effect, the momentum flux or stress, is imposed, whereas the cause, the velocity gradient or shear rate, is obtained from the simulation. It differs from other Norton-ensemble methods by the way in which the steady-state momentum flux is maintained. This method involves a simple exchange of particle momenta, which is easy to implement. Moreover, it can be made to conserve the total energy as well as the total linear momentum, so no coupling to an external temperature bath is needed. The resulting raw data, the velocity profile, is a robust and rapidly converging property. The method is tested on the Lennard-Jones fluid near its triple point. It yields a viscosity of 3.2-3.3, in Lennard-Jones reduced units, in agreement with literature results.

Estimating imprecision profiles in biochemical analysis.

We describe a computer program IMPROFIL which determines an imprecision profile of an analytical method from replicated measurements of samples. It calculates the variance function, the coefficient of variation, the power of definition, the critical limit, the limit of detection and the lower limit of quantification. The primary property, the variance function, is determined by two alternative methods: the conventional maximum approximate conditional likelihood method and the newly developed weighted absolute deviation method. For all quantities, confidence intervals are obtained using the bootstrap procedure. The program combines the use of robust numerical techniques, user-friendliness and integration into a spreadsheet program for data pre- and post-processing. The algorithms used are described in detail. Tests with synthetic data sets are used to validate the method and to establish its powers and limitations. Finally, its application to a practical analytical task (tumor marker CA 15-3 in human sera) is reported. For the method to yield a reliable estimate of the variance function and the derived properties, certain minimum requirements on the raw data must be met: They have to be spread throughout the concentration range of interest, there should not be less than three replicates per specimen, and there must be at least of the order of 25 (better at 50) specimens.

A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease.

Based on available three-dimensional structures of enzyme-inhibitor complexes, the mechanism of the reaction catalysed by HIV protease is studied using molecular dynamics simulations with molecular mechanics and combined quantum-mechanics/molecular-mechanics potential energy functions. The results support the general acid/general base catalysis mechanism, with Asp25' protonated in the enzyme-substrate complex. In the enzyme-substrate complex, the lytic water molecule binds at a position different from the positions of the hydroxyl groups in various aspartic protease-inhibitor complexes. The carboxyl groups at the active site also adopt a different orientation. However, when the lytic water molecule approaches the scissile peptide, the reaction centre changes gradually to a conformation close to that derived from X-ray diffraction studies of various enzyme-inhibitor complexes. The proton transfer processes can take place only after the lytic water molecule has approached the scissile peptide bond to a certain degree. Qualitatively, the free-energy barrier associated with the nucleophilic attack step, which takes place at physiological pH, is comparable with the acid or base-catalysed reactions of model systems. The structure of the tetrahedral intermediate resulting from the nucleophilic attack step also indicates a straightforward pathway of the next reaction step, i.e. the breaking of the C-N bond.

Cooperative effects in the transport of small molecules through an amorphous polymer matrix.

The transport of small molecules (penetrants) through polymer materials proceeds by a hopping mechanism: A penetrant typically dwells in a cavity of the polymer for a while and then performs a quick jump into an adjacent cavity. In this article we investigate a jump event in detail. Molecular graphics is used to identify if and how the motion of the penetrant is aided by the fluctuations of the polymer matrix. We employ both traditional molecular graphics techniques to show atomic motion and surface rendering methods to display the redistribution of penetrant-accessible volume in the polymer.