Computational chemistry is an incredibly visual field, and much of the insight gained from running calculations comes from how the output of these calculations is visualized. Comparing the optimized ground-state geometry of different analogues can show how two rings sit out-of-plane differently, or how a key basic moiety is positioned well in one structure and poorly in another.
Unfortunately, it's difficult to superimpose two different structures using existing computational chemistry tools. While there are some visualization programs that allow users to superimpose and align two structures, these tools typically don't operate directly on the output of quantum chemistry software, necessitating a time-consuming file conversion step that impedes routine structure comparison.
Rowan changes this by making it painless and instant to superimpose two structures. In Rowan, any set of calculations or optimizations can be superimposed automatically. Rowan automatically detects any common substructures within the selected structures, aligns the structures based on this common substructure, and displays the result as a publication-quality line representation. If users want to align a specific region of their molecules, they can simply select the atoms in question before overlaying the molecules!
Here's a link to one such comparison in Rowan. It's easy to see the difference between the pyridyl amide, which is planar owing to an intramolecular hydrogen bond, and the other two compounds, which are twisted!
Rowan also makes it easy to overlay entire ensembles of conformations that result from a conformational search. Simply click "Overlay Conformers" and Rowan will automatically display all conformers at once, with a transparency that depends on the Boltzmann weight of the conformer! This makes it easy to survey complex mixtures of geometries at a glance and intuitively understand the conformational and geometric preferences of a given molecule in a holistic way.
