Computational Chemistry

An Introduction to Computational Chemistry on a PC

Introduction

When Chemistry was a young science, most of the knowledge obtained about the structure and behaviour of molecules was determined through obsrevation. Most of the early observations were only able to indirectly reveal the properties of individual molecules, and the development of the predictive powers of the science of chemistry war slow. Direct methods for the observation of molecular properties, such as spectroscopy made it clear that molecules were complicated an bizaar little entities, and the 'rules' they followed were not that of common macroscopic objects, but that of a relatively new theory, Quantum Mechanics. As more and more detailed information on the the details of individual molecules was accrued, mathematical models of the behaviour of molecules were developed in the context of quantum mechanics. Most of these models appear to involve complex numerical approximations, as well as a tedious amount of 'bookkeeping' and are naturally applicable to modern digital computers. Such types of molecular theories are generally described as being in the realm of Computational Chemistry.

The types of computations performed on molecular systems fall into three main categories:

• Empirical These calculations are based on a database of experimental observations and work best at predicting molecules of the same class or type as those previously well characterized. Fast and Cheap. Example: AMBER, OPLS, etc...
• Semi-Empirical These calculations take advantage of the predictive power of a true quantum mechanical caculation but use empirically determined or fit values for parts of the calculation that are too hard to perform. Faster than ab initio and more accurate and predictive than empirical. Example ZINDO, AM1, etc...
• Ab Initio A full quantum mechanical calculation from first principles. Limited to small systems, the calculations are very time consuming but the most accurate that can be performed. Example: Gaussian 92, ACES II, etc...

'Experimental'

We will perform calculations using commercial software (HyperChem) which is installed on the suite of computers in PC teaching lab LEI 109. Your first task will be to load the software onto your computer from the server by clicking on the HyperChem icon in the program manager environment of Windows operating system. Then, once the software is running, familiarize yourself with the operation of the toolbar on the left and the menu bar across the top. Try loading a random molecule file (*.hin) from the disk and viewing the molecule from different aspects or rendering styles.

1. Open the periodic table by left clicking on the top icon in the tool bar. Select an element from the periodic table by a click and insert an atom of the element on the workspace by clicking where you want it. drop and drag to produce bonded atoms. Make a few molecules and save the *.hin files on a floppy on drive A: (your floppy).

Repeat steps 2-6 for each of the molecules on the following list:

HCO

Formaldyhyde (H₂CO)

d₂-Formaldyhyde (D₂CO)

HDCO

Phosgene (Cl₂CO)

H₂O

CO₂

2. Make the molecule of interest by constructing it from its atoms. Remember to get the double bonds in the structure by clicking on the bond that needs to be changed.

3. Optimize the structure of the target molecule using an empirical method (suggestion: MM+). Record the geometry of the optimized structure in terms of bond lengths and angles. Save a [*.hin] file with the 'force field' optimized structure.

4. Perform a 'single point' calculation of the energy of each target molecule using a semi-empirical method (suggestion: ZINDO/1). Record the energy and gradient resulting from this calculation.

5. Optimize the structure of the molecule using the same computational method as in part 4. Record the geometry and energy resulting from the calculation. Save another [*.hin] file with the semi-empiricly optimized structure.

6. Calculate the vibrational spectrum of the molecule. Record the frequencies of all of the vibrational transitions and indicate which bands are IR and Raman active. Describe the motion (normal mode) associated with each of the vibrational bands. Indicate the transition dipole moment direction (in the molecular frame) for each of the IR active modes.

Repeat Step 7 for HCO, H₂CO, and Cl₂CO, ONLY

7. Calculate the electronic spectrum of the molecule. This will involve recalculating the single point energy of the molecule using a semi-empirical method optimized for electronic transitions (suggestion: ZINDO/1). Record the new energy and geometry. Calculate and display the spectrum. Record the wavelengths of the lowest electronic transitions. Assign each of the electronic transitions by the symmetries of the orbitals that have changed in poulation from ground to excited state. You can visualize the orbital wavefunctions and even probability densities of results of the eletronic structure calculation. Save a few of these (like the HOMO and LUMO) on disk as bitmaps and add them to your notebook and paper

Keep your Results Organized.

Write down as many results as are important in your notebook as you perform the calculations. Name your files logically and remember to copy them to your floppy before you leave. (Nothing will remain on the hard drive for long.)

Data Analysis

• Critically compare the experimental (literature) structures of the above target molecules to those you calculated. What are the differences between the predictions made by the different levels (empirical vs semi-empirical) of calculations? Is the semi-empirical methoid woth the extra effort for the prediction of simple molecular structure?

• Use the calculated energies of the target molecules to calculate the heat of combustion of H₂CO. Use the literature values for the heat of formation of water and carbon dioxide to estimate the heats of formation of formaldyhde and phosgene. Is this estimate accurate? Critically compare calculations with and experimental (literature) values.

• Compare the electronic spectra calculated above with of experimental (literature) spectra.

• Compare the IR spectrum of formaldyhde to the experimental (literature) spectrum. Tabulate the vibrational frequencies for the three isotopic forms of this molecule. Do the isotope shifts in these frequencies make sense with respect to the motions of the normal modes? How does the IR spectrum help in determining the structure of molecules?