GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular Simulation software for (bio)molecular simulation. It contains more than 70 programs that can be used to prepare data for the production of molecular simulation trajectories and to analyze these. These programs are reviewed and the various structural, dynamic, and thermodynamic quantities that can be analyzed using time series, correlation functions, and distributions are described together with technical aspects of their implementation in GROMOS. A few examples of the use of GROMOS++ for the analysis of MD trajectories are given. A full list of all GROMOS++ programs, together with an indication of their capabilities, is given in the Appendix .

In the catalytic cycle of cytochrome P450cam, after molecular oxygen binds as a ligand to the heme iron atom to yield a ferrous dioxygen complex, there are fast proton transfers that lead to the formation of the active species, Compound I (Cpd I), which are not well understood because they occur so rapidly. In the present work, the conversion of the ferric hydroperoxo complex (Cpd 0) to Cpd I has been investigated by combined quantum-mechanical/molecular-mechanical (QM/MM) calculations. The residues Asp(251) and Glu(366) are considered as proton sources. In mechanism I, a proton is transported to the distal oxygen atom of the hydroperoxo group via a hydrogen bonding network to form protonated Cpd 0 (prot-Cpd0: FeOOH(2)), followed by heterolytic O-O bond cleavage that generates Cpd I and water. Although a local minimum is found for prot-Cpd0 in the Glu(366) channel, it is very high in energy (more than 20 kcal/mol above Cpd 0) and the barriers for its decay are only 3-4 kcal/mol (both toward Cpd 0 and Cpd I). In mechanism II, an initial O-O bond cleavage followed by a concomitant proton and electron transfer yields Cpd I and water. The rate-limiting step in mechanism II is O-O cleavage with a barrier of about 13-14 kcal/mol. According to the QM/MM calculations, the favored low-energy pathway to Cpd I is provided by mechanism II in the Asp(251) channel. Cpd 0 and Cpd I are of similar energies, with a slight preference for Cpd I.

What prompted you to investigate this topic? The increasing worldwide availability of naturala nd shale gas has stimulated aq uick technical shift to catalytic dehydrogena-tion of propane to propylene (PDH). However,t his technology relies on Pt-or CrO x-basedc atalysts and suffers from thermo-dynamic limitations and rapid catalystd eactivation by coking and sintering. Oxidative dehydrogenation (ODH) of propane offers ap romising alternative to industrialized PDH process, but selectivity control foro lefins is difficult, because of deep-oxidation reactions over conventional metal oxide catalysts that produce as ubstantial amount of undesired CO 2 .H ence, we have dedicated our efforts to the development of at her-mally stable and metal-free ODH catalyst, which can selectively cleave the CÀHb ond while preventing CO 2 formation. As presented in this paper,e dge-hydroxylated boron nitride addresses these issues. What new scientific questions/problems doest his work raise? This work represents af undamental breakthrough in chemistry because non-metallic, inert boron nitride was transformed into ac hemically active and selectivec atalystf or propaneO DH. We have identified the BÀOH groups at the edges of BN as active sites forp ropane ODH. However, aw ell-defined reaction pathway remainsu nclear.F uture studies should focus on theoretical simulations and the captureo fr eaction intermediates to illustrate the reactionm echanism under real reaction conditions.