SERC PRACTICALS

Each one of these classes especially III and IV could be easily expanded to two or three sessions. (Each week had one "theory" class to explain the experiment, a demonstration class and the practical)

The philosophy of this part of the course is to familiarize the student with software available at IISc and Free Software and enable them to get meaningful answers to problems they might face in their "LAB!".

Class I (familiarize the student with SERC facilities and open source software)

I Drawing Structures

1. Familiarisation of freeware resources (and Chemdraw for IISc users).

2. Drawing chemical structures ( 2D). Use ISIS or Chemsketch. Templates and their use.

3. Cleaning up figures in 2D (makes this neat looking and good for publication).

4. If you are using ACD, you can optimise a 3D structures in ACD (probably molecular mechanics)

5. Drawing molecules in 3D (Wedge bonds, Notations)

6. Rasmol / ACD / Jmol use it to measure distances.

7. Importing, exporting and File Save As

8. File format conversions (Using winBabel or OpenBabel)

II Molecular Mechanics - Hyperchem. / Tinker is freeware but I have not been able to set it up.

(a) Butane, dihedral angle driver.

(b) Cyclohexanes 1,2:1,3:14 disubstitution

What happens when you have a double bond as in cylohexene? Can you predict stability? Cholestrol (importing files), Ubiquitin

(c) DNA

In this session you:

Learn to manipulate molecules in silico

Measure: Distances, angles and torsion angles

Stability of molecules as predicted by MM.

Class II

Familiarization of users with HYPERCHEM

Using Hyperchem explore the following aspects.

PROBLEM I

Frontier orbitals : Their localization, symmetry and energy determine the chemistry of the molecule.

CO vs. ethylene

Comment on the bonding modes of CO, dinitrogen and acetylene with a metal Ni(0).

Instead of a metal, add a proton to both molecules; which is the more stable species. What is the stable geometry?

H⁺ + L = [HL]^{+ ,}

PROBLEM II

Examine the properties and energy of HOMO - LUMO in the following systems.

C₂F₄ vs C₂H₄

Isomers of C₂H₂F₂ (Cis1,2; Trans1,2; gem 1,1;)

- Which is the most stable one

- How do the shapes of HOMO and LUMO change?

Problem III

Olefin-Metal complexes have two stabilising interactions. Can you compare the relative importance of the two interactions from an EHT calculation? Use CACAO or HYPERCHEM.

Chemdraw 12.0 (to be checked)

Pd(0) olefin complexes

Pd(II) olefin complexes

Class III (Needs linux) Introduction to Cheminformatics

Chemical Databases USING CCDC (If the web version is available, there is no need for a particular OS)

(a) Coordination modes of anions

(b) Hydrogen bonding abilities of metal halides

(c) C-H- pi and pi - pi interactions in benzene rings.

(d) Coordination number preferences of various metal ions.

Class IV

MOPAC – Semiempirical Methods (Trace the history of Dewar's programs)

(a) Neopentane versus pentane versus iosopentane

Calculate the energy difference

(b) Conjugated and nonconjugated double bonds (check with PM3 and AM1)

Compare cyclobutadiene and methylene cyclopropene. (compare it with values from NIST web book)

(c ) Read the literature on the anomeric effect. Is there some way you can show the anomeric stabilization due to geminal OR groups CH₂(OMe)₂ Using isodesmic equations.

Class V

Ab initio

Write the Z-Matrix for a molecule

(i) Calculating charges & energies

Ab initio (do not use Hyperchem)

Use winGamess or Gaussian

What is the charge on O/F in the following molecules?

OH^-, NO₃^- , BF₄^-, PF₆^-

(ii) Dependence on basis sets. Carry out the calculation with different basis sets.

Class VI Intermolecular interactions (Weak) and computing reaction paths. (not developed).

Class VII MD and using VMD to analyze the results. (Prof. Debnath Pal was the guest lecturer)

EXAM:

One Molecular mechanics question.

One Electronic Structure Calculation

One database study.