Natural Dipole Analysis with IPython Notebook

Understanding electrostatic interactions in molecules and molecular complexes provides the basis for interpretation of chemical reactions and molecular interactions. First of the series of "Analyzing NBO output with IPython notebook" is the example of decomposing NLMO dipole vectors into a vector path that can be displayed as images and further analyzed for intramolecular dipole components.

The first example is built around the molecule of formamide and can be followed in the book of Weinhold and Landis: Weinhold, F. and Landis, C.R. in Discovering Chemistry with Natural Bond Orbitals, pp. 147-152.

After extracting the dipole components from .nbo file output, variants of dipole decomposition are created and their plots saved as .png images. Below is one such example indication NLMO orbital numbers and the corresponding dipole vectors withing the planar molecule of formamide.

Since the analysis and accompanying description are done in IPython Notebook (now Jupyter notebook), it is more convenient to render such notebooks in specialized Python-driven web-builders, such as Pelican static site generator. 

Full version of this blog is available as Natural Dipole Analysis blog hosted at GitHub Pages. 

You can download the notebook and accompanying files from the latter link (click the "Download .zip" button at the right bottom).