Computational Chemistry Formal Report

Computational Chemistry Formal Report

Additional Guidelines General Formal Report Guidelines

• See the general guidelines document • Note that the general guidelines are more geared towards a “wet experiment” but all the components

described in the general guidelines should be part of your report. Abstract

• Provide a synopsis of what you did and what you discovered. You have collected a lot of data and should not report all of it in the abstract, but you should report major findings. The abstract should not exceed one paragraph.

Introduction • The introduction should focus on background material. Do not discuss your results or explain how you

performed the experiment. • You should discuss what is meant by conformational analysis and how conformational preferences is

determined. o How are conformational preferences determined experimentally? What techniques are used? o How are conformational energies calculated (other than from computational chemistry methods) o Why is conformational analysis important (for example: possible applications to biochemistry)? o What structural factors influence conformational preference? o Butane is considered a prototype molecule for understanding conformational analysis. You

should discuss what we know about butane in terms of conformational preference and how this data is used to predict conformational equilibria for other structures.

Results

• Prepare a table organized by the conformations modeled for each compound. Provide the energy of the conformation (kJ/mol) determined by ab initio calculation, and the total strain energy calculated using values from Klein. In a separate column of the table, give the difference in energy between the higher and lower energy conformations. As well, when reporting the energy of the eclipsed conformations report the difference in energy between the lower energy staggered conformation and the eclipsed conformation. Use Newman projections in the table to identify the conformations.

Example: E (HF) ∆E Strain E

(Klein) ∆E

H

H CH3

CH3

HH

4.131×105 kJ/mol

3.68 kJ/mol 3.8 kJ/mol 3.8 kJ/mol

• Calculate the percent distribution of each conformer (see handout) based on your ab initio

computational data and report these results in a separate table. • Prepare a table that shows the following data from your HF calculations for each compound.

o For each staggered conformation of 2-methylbutane  C1-C2-C5 bond angle  H3-C3-C4 bond angle  C1-C4 dihedral angle  C2-C3 bond length

o For each staggered conformation of 2,3-dimethylbutane  C1-C2-C5 bond angle  C2-C3 bond length  For conformer A: both CH3∙CH3 dihedral angles  For conformer B: C1-C6 dihedral angle, C1-C4 dihedral angle and C5-C4 dihedral

angle

o For the eclipsed conformations, report the C2-C3 bond lengths Discussion

• Discuss the results of your calculations. Discuss each compound separately. o Which conformer is more stable? o Discuss any findings that deviate from expectations (such as deviations from ideal bond angles,

lengths, and dihedral angles) • Compare your ab initio calculations to the simple calculations using strain energy values from Klein. • Compare your results to any literature experimental results you were able to find (in addition to the

papers shared in canvas, you might consult the CRC handbook for bond angles and lengths). Experimental

• Describe the method used for your ab initio calculations Citations

• You should refer to the papers and textbook entry uploaded to Canvas. Perhaps start by reading the entry from more advanced textbook, then attempt to read the journal articles.

• The papers are challenging to read (and understand), but attempt to find the results so that you can use them as a point of comparison in your discussion.

Questions

• There are no additional questions for this report

1 2

3 4

5

1 2

3 4

5

6

H

H3C CH3

H

CH3H3C

A H

H3C CH3

CH3

CH3H

B

6 4 1

5

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