Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Local structure of Mn in (La1-xHox) 2/3Ca1/3MnO3 studied by X-ray absorption fine structure

Results of X-ray absorption fine structure measurements in manganites (La1-xHox)2/3Ca1/3MnO3 with 0.15 < x < 0.50 are presented. When LaMnO3 is doped with a, divalent element such as Ca2+, substituting for La3+, holes are induced in the filled Mn d orbitais. This leads to a, strong ferromagnetic coupling between Mn sites. Ca ions in La1-xCa xMnO3 introduce a distortion of the crystal lattice and mixed valence Mn ions (Mn3+ and Mn4+). On the other hand, in manganites (La1-xHox)2/3Ca 1/3MnO3 the substitution of La for Ho causes a lattice distortion and induces a disorder, which reduces a magnetic interaction. The ferromagnetic transition temperature and conductivity decrease very quickly with increasing x. The magnetic and transport properties of compounds depend on the local atomic structure around Mn ions. The information on the bond lengths and Debye-Waller factor are obtained from the extended X-ray absorption fine structure (EXAFS) data analysis. The charge state of Mn is determined from the position of the absorption edge in X-ray absorption near edge structure (XANES) data. XAFS results are in good agreement with magnetic characteristics of the studied materials.