Introduction to Computational Quantum Chemistry
Intermolecular interactions
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 1 / 11
Intermolecular interactions
“Noncovalent” interactions
Usually weaker than covanlent bonding (thus reversible)
Hydrogen bonding, stacking, ion-ion, ion-dipole...
Halogen/chalcogen/pnicogen bonds (σ-hole)
Ion-π, π-hole ...
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 2 / 11
Stabilization energy
Upon formation of stable complex, energy is released:
∆E = Ecomplex − Emonomers (1)
Binding vs Interaction energy
Basis Set Superposition Error (BSSE)
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 3 / 11
Nature of stabilization
Mainly discussion of chemists
To what degree are Quantum or Classical stabilizations
responsible for the complex formation?
Consequences:
How the interactions with EM radiation differ?
Can the interaction be modeled by MM?
Can the electrostatic potential be used as guide to modeling?
Difficulty of transferring the properties between various systems
QM stabilization present for formally “noncovalent” interactions
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 4 / 11
Analysis of bonding
EDA-NOCV
NBO
SAPT
IQA
NCI
Electrostatic - Orbital - Dispersion - Pauli - Polarization - XC
All include certain degree of arbitrariness
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 5 / 11
Quantum Theory of “Atoms in Molecules” (QTAIM)
Works with electron density and its derivatives
Observable property
Lower dependence of results on basis set
No mathematical1 tricks (Transformations etc.)
Prone to overanalysis (properties of LCPs)
1
Read magical.
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 6 / 11
Task 1: σ-hole interactions
Analyze the σ-hole bonding between bromide and
pentafluorobromobenzene
Calculate the binding and interaction energies
Perform AIM calculation on the wavefunction (use output=wfn in
the route section of Gaussian job)
Use M062X/Def2TZVP level of theory
AIMAll package for the processing of wavefunction
http:
//aim.tkgristmill.com/manual/aimqb/aimqb.html
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 7 / 11
Inspection of AIM results
Going through the output (.sum)
Visualizing the molecular graph/contour maps/surfaces
Visualize the electron density and Laplacian of electron density
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 8 / 11
Extraction of numbers
Extract data from the .sum file:
Properties of LCP between bromines
Charge on bromide anion
Delocalization indices between atomic (bonded) pairs:
C-C
C-F
C-Br
Br-Br
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 9 / 11
NonCovalent Interactions (NCI)
Analysis of reduced density gradient:
RDG(ρ) =
1
2(3π2)1/3
| ρ|
ρ4/3
(2)
vs electron density multiplied by the sign of second eigenvalue of
Laplacian:
sign(λ2)ρ(r) (3)
Sign of λ2 is indicator of “attractive” (negative) vs “repulsive”
(positive) density
Manual of NCIplot:
http://www.lct.jussieu.fr/pagesperso/contrera/
nciplot-manual.pdf
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 10 / 11
Task 2: Perform NCI analysis on the .wfn
Calculate the NCI cube files
Visualize the cubes using the generated .vmd file
Plot the RDG vs ρ using gnuplot
Martin Novák (NCBR) Intermolecular interactions November 21, 2017 11 / 11