Dipole Switching by Intramolecular Electron Transfer in Single-Molecule Magnetic Complex [Mn12O12(O2CR)16(H2O)4].

We study intramolecular electron transfer in the single-molecule magnetic complex [Mn12O12(O2CR)16 (H2O)4] for R = -H, -CH3, -CHCl2, -C6H5, and -C6H4F ligands as a mechanism for switching of the molecular dipole moment. Energetics is obtained using the density functional theory (DFT) with onsite Coulomb energy correction (DFT + U). Lattice distortions are found to be critical for localizing an extra electron on one of the easy sites on the outer ring in which localized states can be stabilized. We find that the lowest-energy path for charge transfer is for the electron to go through the center via superexchange-mediated tunneling. The energy barrier for such a path ranges from 0.4 to 54 meV depending on the ligands and the isomeric form of the complex. The electric field strength needed to move the charge from one end to the other, thus reversing the dipole moment, is 0.01-0.04 V/Å.

PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems.

PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.

Comment on "A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation".

We comment upon the recent critique of use of the Program for User Package Interfacing and Linking (PUPIL) system for linking AMBER and GAUSSIAN in a multiscale quantum mechanical/molecular mechanics (QM/MM) simulation (Okamoto et al., J. Comput. Chem. 2011, 32, 932). Specifically, their method for computing forces on the MM particles from the QM region via the GAUSSIAN-03 electrical field was already implemented in PUPIL version 1.3, publicly available beginning December 2009. Some other doubtful characterizations of PUPIL are discussed briefly in the context of current awareness of open-source codes more generally.