Presentation on Computational Chemistry

by Kunal Kishore

BS-MS 2014 Batch

Roll No. 14085

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

What are 'X'?

• H

• F

• CH3

• CF3

• H2C=CH2

Thus we studied 40 molecules in total.

• Ph

• NH2

• CN

• NO2

• OH

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.

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).

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.

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.*

What is Counterpoise Correction?

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.

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.

THANK YOU