Electronic properties of isolated molecules

Prev:LabQSM#Lecture 2: DFT simulations of Molecules

Calculation of molecules: Intro

File:Molecules.ong

Originals from [https://www.tf.uni-kiel.de/matwis/amat/td_kin_ii/index.html Thermodynamics and Kinetics II, Dr. J. Carstensen, Univ. Kiel]

At variance with bulk crystalline systems (fully periodic in 3D), molecules are finite isolated systems. Special care needs to be put in setting up calculations accordingly.

• scf + nscf: DFT calculations for molecules (or systems with reduced dimensionality in general) follow the same strategies discussed in the previous lectures, where scf calculations are followed by nscf runs (and perhaps by post-processing steps, as discussed below in Electronic properties of isolated molecules#Post processing tools).
• molecule isolation: when localised basis sets are used, this is usually the default option. Instead, when using plane-waves, periodic boundary conditions are automatically enforced and molecule isolation has to be achieved by, at least, including vacuum in the unit cell.
• including vacuum: for a molecule this means that the cell to be adopted needs to account for the size of the molecule to be studied plus extra space to avoid or reduce the interaction of the molecule with its periodic replica.

Exercises

Exercise1

Structural relaxation of the Guanine molecule

• Use a molecular builder to find the initial molecular structure. (Avogadro)
• Classical Force Field Relaxation (using a built-in engine)
• Quantum Mechanics Relaxation refinement (Quantum ESPRESSO) (thr=10^-3)
• Use the xcrysden software to visualize the relaxation path.

Solution