Saturday, May 29, 2010

The Computational Microscope

A great title and an interesting talk about one of the fundamental roles of molecular modeling.

Saturday, May 8, 2010

Many-body effects in the water trimer

Figure 4.17. M06/6-31G(d) optimized geometry of the water trimer.
Click on the picture for an interactive version
From Molecular Modeling Basics CRC Press, 2010

In a previous post I showed how molecular electrostatic potentials can be used to illustrate polarization due intermolecular interactions. Polarization has an interesting and important consequence called the many-body effect, which occurs in systems with many relatively strong interactions such as the water trimer (Figure 4.17).

The many body effect is due to the fact that polarization of the charge density of, say, water molecule A due to the A–B hydrogen bond increases the strength of the A–C hydrogen bond, which lowers the energy further. As a result the binding energy of the water trimer (i.e. its energy relative to that of three free water molecules) is lower than the sum of the three hydrogen bond strengths.

The A–B hydrogen bond strength can be gotten by (1) deleting water C and computing the energy of the A-B dimer (don't re-optimize), and (2) comparing this energy to that of two free water molecules. And similarly for the A–C and B–C dimers. The coordinates can be extracted from the Jmol interactive figure as shown in a previous post, and this post shows how to perform the calculations with GAMESS.

The increased hydrogen bond strengths are also reflected in the hydrogen bond lengths, which are 0.09Å shorter in the trimer compared to the dimer. You can measure the distances between atoms in the Jmol interactive figure by double clicking on the atoms, and water dimer geometry can be found in a previous post.

Tuesday, May 4, 2010

Putting it out there

An inspiring post over at Noel O'Blog on sharing your PowerPoint presentations using Slideshare. Three of Noel's presentations (Quantum Chemistry I, II, and III)deserve special mention here because (a) they relate to teaching molecular modeling and (b) the third mention this blog prominently. So, of course, that gets embedded here.

Sunday, May 2, 2010

Rotating molecules in PowerPoint

Long-time MolModBasics reader/commenter NUChem posted the following question:

"One thing that I've been wondering for a while is creating movie files of optimized structures for presentations. Would it be possible for you to have a screen cast of how to take an optimized structure of cyclohexane and make a movie of the molecule rotating. Basically I have a few polycyclic molecules that I've optimized and I want to be able to have them rotating in my powerpoint presentation so my audience can see the whole molecule. Is there anyway to do this?"

I know of two ways of doing this that are relatively easy. One is to create an animated gif file using the Polyview3D web server, and inserting the file as a movie in Powerpoint. Here is a screencast of how to do this.

Another option is to set the molecule spinning in, for example, Avogadro and then simply record part of the screen using a screencasting program. Unfortunately, it looks as though you have to buy software to do this. There is a free screencasting program called Jing, but you can only save the movie file in the .swf file format, which Powerpoint can't read (and I haven't been able to find a free .swf to .mpeg converter). However, with JingPro ($15/year) you can save the file in the .mpeg format, which should work with Powerpoint, but I haven't tried it myself. I use ScreenFlow ($99) and really like it, but that only works on Macs.

UPDATE: Screencast-o-matic is free, and can make mp4 files, which can be included in Powerpoint.  See this new post for more information.

Of course, with the screencast option you can add animations to Powerpoint of anything, such as vibrations, IRCs, etc. in addition to rotation. However, for more complicated animations I usually switch between Powerpoint and Jmol (more precisely a browser showing an html file with Jmol embedded) during the presentation, ever since I found out I don't have to quit the Powerpoint presentation to switch to another program.