Hydrogen-Bonding: Guanine–Cytosine Base Pair

Usage

The adf.rkf file for this example can be downloaded here:

1. Download GC_basepair.adf.rkf

2. Open the PyOrbb application.

3. Drag the .adf.rkf file to the GUI.

Now the most important interactions will appear. To further study fragment orbitals that interact, the user will want to visualize the orbitals:

4. Select the orbital of interest.

5. Click on the orbital (\(\varphi\)).

Now the PyOrbb viewer window will open with many options for drawing the orbitals.

Once the previous steps have been completed, the user should be able to reproduce the following analysis [1] [2].

References

[1]

“The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance,” Chemistry - A European Journal 5 (1999): 3581–3594, https://doi.org/10.1002/(sici)1521-3765(19991203)5:12<3581::aid-chem3581>3.0.co;2-y.

[2]

Yuman Hordijk, Steven E. Beutick, Xiaobo Sun, Laurens Groot, Tori Gijzen, Jordi Poater, Trevor A. Hamlin, F. Matthias Bickelhaupt, Célia Fonseca Guerra, “PyOrbb – Automated Analyses of Orbital-Interaction Mechanisms” Journal of Computational Chemistry, 2026, e70512, DOI=https://doi.org/10.1002/jcc.70512.