Friday, April 29, 2011

Using clickers in lecture

Today's "educational seminar" (NB: in Danish) will be on the use of clickers and cards in lecture. Here are two videos that serve as a good introduction to the topic.

The first video is only 6 minutes long and is a good place to start. The second is more than an hour long, but much more informative. It is a lecture given by Eric Mazur who is a pioneer in the field.

Saturday, April 2, 2011

Discussion of the Ryde paper

The discussion page for the Ryde Paper:

"Reaction Mechanism of Manganese Superoxide Dismutase Studied by Combined Quantum and Molecular Mechanical Calculations and Multiconfigurational Methods", Martin Srnec, Francesco Aquilante, Ulf Ryde and Lubomír Rulíšek, J. Phys. Chem. B, 2009, 113, 6074–6086

Purpose of the study:

The aim of the study is to determine the correct reaction path during the two half cycles. For four proposed mechanisms intermediate structures, a region around the active site is QM/MM minimized and a more accurate single-point energy is calculated. For the rate limiting step, and adiabatic mapping is performed over two reaction coordinates in order to identify the saddle point and corresponding energy barrier.

General opinions on the methods involved (and the results obtained): 
The Ryde group use a three layer method, where the outer layer is frozen, a smaller layer is treated by MM and the inner layer is the QM layer in an ONIOM-like approach. The structures are QM/MM energy, and single point calculations are carried out. For a study that does not use MD snap-shots, a "frozen-outer-layer" approach has the advantage, that small differences in solvent molecule positions do not affect the energy difference between reactant and product calculations, since the positions are exactly the same. This has been a great concern for many of the papers we've seen in the QM/MM course.
The energy barrier for the suspected rate-limiting step is ~3 kcal/mol off the experimental value, which is very close in the context of QM/MM.

Points of discussion, concerning the amount of details given in the text:
  • The abstract and title of the paper suggests, that a lot of high-level CASPT2 single-point energy calculations are carried out and these play a central role in the study. However, only UB3LYP/6-311+G(2d,2p) energies are given, since these supposedly are in qualitative agreement with the spin-flip broken symmetry DFT energies.
  • It is also not clear, how initial structures are constructed for each intermediate structure of the enzymatic cycle.
  • An 45 ps MD simulation is carried out in order to identify possible second-sphere superoxide interaction sites, but literally no details are given on how the simulation is set up and what results are obtained from the simulation and how these are interpreted.
  • Not many details are given for the adiabatic scan, which reveals the transition state.
General conclusions:
Apart from the well known problem with lack of details in a QM/MM paper, the study replicates the experimental energy barrier well, and the structures obtained are in agreement with previous studies involving combined X-ray structures and QM calculations. If one does not want to use MD snapshots in a Yang-like approach, the general opinion was, that the frozen-outer-layer approach is a good way to avoid fluctuations in the reaction barrier height from artifacts arising from solvent interactions.