In this work, the thermodynamic scaling framework has been used to emphasize limitations of fully flexible coarse grained molecular models yield shear viscosity real liquids. particular, extensive dynamics simulations have confirmed that, while being reasonable describe short normal alkanes, Lennard-Jones and Mie chains force fields are inadequate capture density dependence medium long alkanes....

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, whic...

protonation of the reactive intermediates generated in the raction between dalkyl acetylenedicarboxylates and triphenylphosphine by isonitrosoacetophenone leads to vinyltriphenylphosphonium salts, which undergo intramolecular wittig reaction to produce dalkyl 4-phenyl-n-hydroxypyrrole-2,3-dicarboxylates in moderate yields.

The high force sensitivity of the atomic force microscope (AFM) has opened the possibility of measuring interand intramolecular forces of biomolecules on the single molecule level. Covalent binding of bioligands to AFM tips converts them into monomolecular biosensors by which cognate receptors can be localized on the sample surface and fine details of ligand-receptor interaction can be studied....

Bacteriorhodopsin is a model system for membrane proteins. This seven transmembrane helical protein is embedded within a membrane structure called purple membrane. Its structural stability against mechanical stress was recently investigated by atomic force microscopy experiments, in which single proteins were extracted from the purple membrane. Here, we study this process by all-atom molecular ...

> < ABSTRACT: The intramolecular helix backbone C O H— N hydrogen Ž . bonding energies in poly L-alanine a helices have been estimated both in vacuum and in an aqueous environment using the parameter sets of five of the most commonly used force fields for modeling biomolecules, namely AMBER, CHARMM, ECEPP, GROMOS, and OPLS. The relative capabilities of these force fields in describing the H-bon...

We describe the development of a coarse-grained (CG) force field for nylon-6 (polycaprolactam) and its application to the simulation of the structure and macromolecular dynamics within cylindrical fibres formed by this polymer, having diameters in the 14–28nm range. Our CG model is based on the MARTINI force field for the non-bonded interactions and on Boltzmanninverted gas-phase atomistic simu...

Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microsc...