Introduction to Computational Quantum Chemistry
Intermolecular interactions
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 1 / 10
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 ...
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 2 / 10
Stabilization energy
Upon formation of stable complex, energy is released:
∆E = Ecomplex − Emonomers (1)
Binding vs Interaction energy
Basis Set Superposition Error (BSSE)
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 3 / 10
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
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 4 / 10
Analysis of bonding
EDA-NOCV
NBO
SAPT
IQA
NCI
Electrostatic - Orbital(Polarisation, charge transfer) - Pauli -
Dispersion
Alternative decomposition: Coloumb - Kinetic - Exchange
All include certain degree of arbitrariness
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 5 / 10
HOMEWORK: σ-hole interaction
Analyze the σ-hole bonding between bromide and C6F5Br.Br−
(structure
available in IS)
Calculate the interaction energy (M062X and B3LYP/def2tzvpp/BSSE in
Gaussian). Explain different DFT values.
Reoptimize the C6F5Br, calculate difference in single point energy of
both free and bound form and estimate deformation energy (use
Gaussian setup). What is the relation of interaction with bond
deformation?
Perform EDA analysis in ADF2019 using M062X/TZVP, compare the
individual terms (Electrostatic, Pauli, Orbital) with C6F6.Br−
. Input see
bellow.
Generate complex.wfn file from single-point calculation in Gaussian on
C6F5Br.Br−
(in *.com file keyword output=wfn and put name of wfn at
the end of *.com file), run NCI-analysis of reduced gradient of electron
density, prepare visualization of cube file in VMD (use session file vmd
-e *vmd). Input see bellow.. Interpret the results.
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 6 / 10
ADF-EDA
Input for adf_compl.inp
Atoms
C -3.0298060 0.6213630 -0.0000060 f=m
...
Br -1.7821970 6.2717390 0.0000290 f=n
End
ZlmFit
Quality good
End
charge -1
fragments
m t21.frag1
n t21.frag2
end
Basis
Type TZ2P
Core none
End
integration
accint 7
end
Symmetry Nosym
XC
MetaHybrid M062X
End
SAVE TAPE21
End Input
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 7 / 10
ADF-EDA run script
Input for run.sh
module add adf
adf < adf1.inp > adf1.out
mv TAPE21 t21.frag1
adf < adf2.inp > adf2.out
mv TAPE21 t21.frag2
adf < adf_compl.inp > adf_compl.out
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 8 / 10
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
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 9 / 10
NCI plot
Input for nci.sh
module add nciplot
nciplot < nci.inp > nci.out
Input for nci.inp
1
complex.wfn
CUTOFFS 1.0 1.0
Jan Novotny, Martin Novák (NCBR) Intermolecular interactions November 2, 2021 10 / 10