Computer simulations to calculate accurate molecular properties: are the widely reported densities of coumarin and indole erroneous?

摘要

Our recent research suggests a significant error in the widelynreported† density of coumarin, and a slightly smallerndiscrepancy for indole.nIn an effort to calculate various bulk properties of molecules,nand to test the validity of force fields, molecular dynamics simu-nlations were performed on a series of small organic molecules.nThe simulations were done under the NPT protocol where thennumber of particles (N), the pressure (P) and temperaturen(T) are kept constant, using the pressure control algorithmndeveloped by Berendsen and coworkers,n1n and applying temper-nature control using the stochastic collision approach ofnAndersen and coworkers.n2,3n This enables the simulated systemnto ‘find’ its own density and provides an excellent benchmarknfor testing the validity of the simulations and the force field.nThe main objective here is to compare the density obtainednfrom the simulations with the reported values. The force fieldnused was COMPASS,n4n a so-called ‘class II’ force field, whichnuses high level calculations to determine valence parameters,ncombined with experimental condensed phase PVT andncohesive property data to determine nonbond parameters, andnwhich includes coverage for a wide variety of organic systems.