Exploring the Role of Substitution on the Formation of Se…O/N Noncovalent Bonds

1. Presentation on
Computational Chemistry
by Kunal Kishore
BS-MS 2014 Batch
Roll No. 14085

2. What we did?
• We studied the effect of various substituents (X) covalently bonded to the
chalcogen atom, Selenium(Se), which is already bonded covalently to either CH3
or H group on the interaction energies of the molecules bonded non- covalently
through chalcogen bond. Thus the interaction energies of the following four set
of molecules were studied by varying X:
• H(X)Se---OH2, H(X)Se---NH3, CH3(X)Se---OH2, CH3(X)Se---NH3

3. What are 'X'?
• H
• F
• CH3
• CF3
• H2C=CH2
Thus we studied 40 molecules in
total.
• Ph
• NH2
• CN
• NO2
• OH

4. Computational Methods
• All the calculations were performed using Gaussian 09 package at MP2/aug-cc-
pVTZ level of theory. (This level of theory involves larger basis set). What is Basis
set?
• Binding energies were calculated as the difference in energy between the
optimized complex and the sum of energies of the separately optimized
monomers. (What is Optimization?).
• Basis Set Superposition Error(BSSE) was removed by counterpoise
correction.(What is BSSE and Counterpoise Correction?).
• NBO analysis were performed to evaluate the 2nd order perturbation
energies(E2) using procedures contained within the context of the aug-cc-pVTZ
basis set.

5. BASIS SET
• Basis set in context of computational chemistry involves a set of
functions (basis functions) which are combined in linear combinations
to create molecular orbitals.
• Larger is the basis set higher will be the accuracy to obtain the wave
function (psi).

6. OPTIMIZATION
• Geometry optimization is the name for the procedure that attempts to find the
configuration of minimum energy of the molecule.
• If Δ(r) represents the electron density of the molecule and if r° represents the
position of maximum, minimum or saddle point then grad(Δ(r°))=0.
• Behavior of Δ(r) in the neighborhood of r° is given by Taylor series expansion of
Δ(r) about r°. Collection of nine 2nd order derivatives of Δ(r°) form Hessian
Matrix which is real and symmetrical and may be diagonalized to yield a set of
eigenvalues and eigenvectors.*
• If D>0 and Δ"(r°)>0 then r° is the point of minimum while if D>0 and Δ"(r°)<0 then
r° is the point of maximum.
• Critical points of charge distribution for a molecule at or in the neighborhood of
energetically stable nuclear configuration are all of rank(α) 3. A cp with α<3is said
to be degenerate.* A cp is labelled by (α,β) where α is the rank( number of non-
zero curvature) of the Hessian matrix while β is the sum of the algebraic signs of
the curvature.

8. Basis Set Superposition Error (BSSE)
• Most basis sets are centered on nucleus and are finite(not complete).This
introduces error in energies and these are geometry dependent.
• Simple example of dimer of water. To calculate Binding Energy of the
structure simplest approach is: ΔE(bind.)=E(dimer)- 2xE(monomer)*
• But there is a problem in this approach as in dimer basis functions on one
monomer compensate for the incompleteness of the basis set on the other
monomer
• Counterpoise correction is applied to correct the BSSE.*

9. What is Counterpoise Correction?

10. Natural Bond Orbital (NBO) Analysis
• Results from NBO calculations provide detailed insight into the
electronic structure of the molecule and helps to determine the
electronic configuration of an atom in the molecule i.e. number of
core, valence and rydberg electrons.
• It helps us determine the delocalization of electron density between
HOMO and LUMO leading to stabilization of donor-acceptor
interaction.

11. References
• 1. Effects of Charge and Substituent on the S···N Chalcogen Bond
Upendra Adhikari and Steve Scheiner
• 2. Atoms in Molecules, Richard F. W. Bader, McMaster University,
Hamilton, Ontario, Canada
• http://vergil.chemistry.gatech.edu/notes/cp.pdf
• 4. Topological and NBO analysis of hydrogen bonding interaction in
CH---O bonds, Gladis L. Sosa, Nelida M. Peruchena, Ruben H.
Contreras, Eduardo A. Castro.

12. THANK YOU