Online presentations: Intro to qualitative MO theory and Computational Organometallic Chemistry

Just came across these videos:

Wes Borden, University of North Texas
An Introduction to Qualitative Molecular Orbital Theory

Tom Cundari, University of North Texas
Computational Organometallic Chemistry

Computational Chemistry Highlights: August issue

The August issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach and Jan Jensen:

A grossly warped nanographene and the consequences of multiple odd-membered-ring defects

The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand

Nonamethylcyclopentyl Cation Rearrangement Mysteries Solved

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The Polarity and Solvation option in MolCalc

+Maher Channir, under the capable supervision of MolCalc designer +Jimmy Charnley Kromann, has added a great new feature to the Molecule Calculator, shown in the video below.



Some technical stuff
The solvation energy, molecular surface area, and dipole are computed using the PM3/PCM interface recently implemented in GAMESS by +Casper Steinmann.  The displayed surface, which is slightly different than that used by GAMESS, is computed by JSmol, which also computes the eletrostatic potential based on charges computed by OpenBabel when making a mol2 file.

Computational Chemistry Highlights: July issue

The July issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach, Ben Corry, Gerald Monard, Dean Tantillo, and Jan Jensen:

Towards First Principles Calculation of Electron Impact Mass Spectra of Molecules

Evaluation of Triplet Aromaticity by the Isomerization Stabilization Energy

Tunneling in the Bergman Cyclization

Enantioselective Thiourea-Catalyzed Intramolecular Cope-Type Hydroamination

Will molecular dynamics simulations of proteins ever reach equilibrium

Atomic-level simulations of current-voltage relationships in single-file ion channels

Interested in more? There are many ways to subscribe to CCH updates.

A python program for reading coordinates and gradients from a GAMESS output file

Some people liked the previous post on python, so I dusted off this python program for reading locating coordinates and gradients in a GAMESS log file and writing out and .xyz+vib file (to create this post).  I have only used it on this output file, but it should work for other files as well.

Even if you have no interest in .xyz+vib files, the program might be useful as an example of how to locate specific information in a file and read it in. If you have similar programs (or questions) please feel free to share them in the comments

Illustrating energy minimization: a simple python program

Here is a simple python program I wrote to illustrate energy minimization.  The program uses steepest descent and a force field to minimize the energy of a water molecule in internal coordinates.

If you have a Mac or Linux machine you already have python installed (Windows users please Google and/or leave a comment).  You can also get an invite for koding.com and run it there. You can run it by opening a terminal and typing "python Emin.py".

Things to play around with (once you have it running): change the starting geometry, step size (c), number of steps (n_steps), try printing out the geometry, energy and gradient for each step.

You can also try to write a similar program for other molecules (like methane), although once you have van der Waals interactions you will probably have to switch to Cartesian coordinates and things get complicated.

Related blog posts
The force is strong in this one
The autoopt tool in Avogadro

MOPAC/PCM interface in GAMESS

A new version of GAMESS was released recently.  Among the many new features is +Casper Steinmann's recent work on interfacing the PCM solvation method with the semiempirical methods AM1 and PM3.  So you can now simulate molecules in solution with AM1 and PM3.  

Casper also parallelized AM1 and PM3 (both in gas phase and solution), though molecules have to be pretty big before you see an appreciable speed up, as you can see from the figure below (on small proteins).

The work has been published in the open access journal PLoS ONE. +Jimmy Charnley Kromann is hard at work on implementing PM6.

This work is licensed under a Creative Commons Attribution 3.0