No abstract

For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER-GAUSSIAN interface (AG-IF), which can be one of the simplest architectures. In the AG-IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG-IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG-IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces.

No abstract

FT-30, a typical aromatic polyamide membrane, is formed by interfacial polycondensation (IP) reaction between m-phenylenediamine (MPD) and benzene 1,3,5-tricarboxylic acid chloride (TMC) monomers. To investigate its microscopic characteristics, we performed an atomistic molecular simulation using the hybrid MC/MD reaction method modified to allow intercellular chemical bonds stretching over the periodic boundaries. Starting with appropriate monomer model systems, we succeeded in making membrane models by simulating a succession of condensation reactions. Through an analysis comparing our calculation results for the degrees of polymer cross-linking (DPC) and the composition ratios to the experimental results, we clarified the MPD/TMC mixing ratios in the near-surface active (NSA) and interior active (IA) regions associated with the reaction mechanism of IP. Further, we executed water diffusion simulations using the membrane model of the IA region and showed the calculated values of the total mass density of the hydrated membrane and the partition coefficient K to be in good agreement with the experimental ones. In conclusion, the present computationally modeled polyamide membrane has sufficient fidelity to the actual membrane and should be considered a stable spatial structure in the local equilibrium state under a nonequilibrium stationary state of permeation.