Screening effects on hydrogen bonding in chain molecular fluids: Thermodynamics and kinetics

Development of a special molecular dynamics algorithm (discontinuous molecular dynamics with bonding) was previously reported for simulating molecules via potentials with small square-well potential bonding sites that mimic hydrogen bonding. The present study extends this approach to fluids composed of two new molecular models and focuses especially on the kinetics of bond associations and dissociations in addition to the equilibrium effects. The first molecular model comprises two repulsive sites and three bonding sites (simulated methanol). The second molecular model comprises five repulsive sites where bonding sites are placed at the end and the middle of the chain (a simulated 5-mer diamine). Equilibrium properties focus on the fractions of bonding sites that remain unbonded after extended equilibration. At moderate to high packing fractions, the equilibrium fraction of unbonded accepters for the middle site of the 5-mer is roughly equal to that of the end site. The fluid structures around end sites and middle sites are analyzed in order to suggest how the equilibrium effects may be analytically predicted. The rates of bond association and dissociation are studied for each type of bonding site as a function of temperature, molecular packing fraction, position along the chain, and bonding energy. The kinetic data more strongly suggest the presence of a mild screening effect by showing a shift in the rate constant. At all densities, the bonding in the 5-mer is higher than expected, indicating a stabilization effect that was not previously anticipated. These data point the way toward a fundamental theory of the kinetics of hydrogen bonding.