Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations

The application of hybrid quantum mechanical and molecular mechanical (QM/MM) potentials to the study of chemical reactions in enzymes is outlined. The discussion is general and addresses the difficulties encountered in an enzyme QM/MM study. First, general criteria for determining whether a particular enzyme is an appropriate candidate for a QM/MM approach are outlined. Methods for obtaining starting structures are detailed. The importance of choosing appropriate levels of ab initio or semiempirical theory is emphasized. Approaches for interfacing the QM and MM regions are briefly discussed, with greater detail given to describing our CHARMM-GAMESS interface. Techniques for partitioning the system into QM and MM regions are explored. Link atom placement, as distant from reacting atoms as possible within the confines of computational efficiency, is examined in some detail. Methods for determining reaction paths are also discussed. © 1996 John Wiley & Sons, Inc.     

Role of B-site ion on proton conduction in acceptor-doped Sm2B2O(7-δ) (B = Ti, Sn, Zr and Ce) pyrochlores and C-type compounds

Proton conduction in three pyrochlores, Sm(1.92)Ca(0.08)B(2)O(7-δ), B = Ti, Sn, Zr and one phase with a related C-type fluorite superstructure, B = Ce, has been investigated. The samples were prepared by solid state reaction. Infrared spectroscopy measurements and thermogravimetric analysis were carried out to study the extent of proton dissolution and determine its dependence on the B-site ion. Electrochemical impedance spectroscopy, performed on heating and cooling pre-hydrated samples, confirmed significant levels of proton conduction for Sm(1.92)Ca(0.08)Ti(2)O(7-δ) and Sm(1.92)Ca(0.08)Sn(2)O(7-δ) up to T～ 500 °C. In comparison the B = Zr and Ce samples revealed lower levels of proton conductivity, confined to temperatures below ～ 400 °C. Proton diffusion coefficients of 3.36 × 10(-8), 1.73 × 10(-9), 5.53 × 10(-10) and 2.78 × 10(-11) cm(2) s(-1) were determined at 300 °C for samples with B = Ti, Sn, Zr and Ce respectively. The proton mobility of Sm(1.92)Ca(0.08)Ti(2)O(7-δ) is therefore approximately one order of magnitude lower than that found in yttrium-doped perovskite phases such as BaZrO(3) and BaCeO(3).     

Intermediate temperature ionic conductivity of Sm1.92Ca0.08Ti2O7�C�� pyrochlore

The results of concentration cell electromotive force methods (EMF) and electrochemical impedance spectroscopy measurements on the pyrochlore system Sm_1.92Ca_0.08Ti₂O_7?C?? are presented. The data have been used to estimate total and partial conductivities and determine transport numbers for protons and oxide ions under various conditions. The EMF techniques employed include corrections for electrode polarisation resistance. The measurements were performed using wet and dry atmospheres in a wide $ {p_{{{{\rm{O}}_{{2}}}}}} $ range using mixtures of H₂, N₂, O₂, and H₂O in the temperature region where proton conductivity was expected (500?C300?°C). The impedance measurements revealed the conductivity to be mainly ionic under all conditions, with the highest total conductivity measured being 0.045?S/m under wet oxygen at 500?°C. Both bulk and grain boundary conductivity was predominantly ionic, but electronic conductivity appeared to play a slightly larger part in the grain boundaries. EMF data confirmed the conductivity to be mainly ionic, with oxide ions being the major conducting species at 500?°C and protons becoming increasingly important below this temperature.     

Intermediate temperature ionic conductivity of Sm1.92Ca0.08Ti2O7–δ pyrochlore

The results of concentration cell electromotive force methods (EMF) and electrochemical impedance spectroscopy measurements on the pyrochlore system Sm_1.92Ca_0.08Ti₂O_7–δ are presented. The data have been used to estimate total and partial conductivities and determine transport numbers for protons and oxide ions under various conditions. The EMF techniques employed include corrections for electrode polarisation resistance. The measurements were performed using wet and dry atmospheres in a wide \( {p_{{{{\rm{O}}_{{2}}}}}} \) range using mixtures of H₂, N₂, O₂, and H₂O in the temperature region where proton conductivity was expected (500–300 °C). The impedance measurements revealed the conductivity to be mainly ionic under all conditions, with the highest total conductivity measured being 0.045 S/m under wet oxygen at 500 °C. Both bulk and grain boundary conductivity was predominantly ionic, but electronic conductivity appeared to play a slightly larger part in the grain boundaries. EMF data confirmed the conductivity to be mainly ionic, with oxide ions being the major conducting species at 500 °C and protons becoming increasingly important below this temperature.