Peer instruction: entropy

Another post on peer instruction over at Molecular Modeling Basics

Peer instruction in MolStat

A new post on peer instruction on Molecular Modeling Basics.

Peer instruction without clickers

I have written about my first experience with peer instruction over at Molecular Modeling Basics.  Click here to read, and please leave any comments over there.

I have bought an instructors version of polleverywhere.  If anyone at KIKU or COMS is interested in using it, just contact me.

The importance of being indexed

Playing around with iAnnotate for iPad and talking about it with Jan, I realized the importance of being able to swiftly navigate through documents. While reading an article or reviewing a manuscript it is important to be able to check quickly the content of figure 3 and then jump back to where one was in the text. iAnnotate has the possibility of including personalized bookmarks to a PDF document, but it is extremely boring, tedious, and time consuming to go through an entire document first to mark all the important features. PDF documents can have an embedded outline, as well as cross references to figures and tables. I found out that latex can do that for you almost effortlessly! One just need to include the hyperref package in the preamble. For example here is what I used while preparing my latest manuscript:

\usepackage[hypertexnames=false, naturalnames=false, dvips, colorlinks=true, linkcolor=black, citecolor=black, hidelinks]{hyperref}

Automagically all your \section, \subsection, \begin{figure} etc. commands will also produce a cross referenced link. In the mentioned example I hid in the text any sign of the links, but it is also possible to specify to have differently colored links or with colored boxes around.
In order to be able to use the "hidelinks" option one has to use the very latest version of hyperref. Think about it when preparing your next manuscript!

Creating interactive chemistry ebooks

Well not quite. But I am getting started. See more in my latest post over at Molecular Modeling Basics. HTML experts especially welcome :).  Please leave any comments there.

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.

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.