To begin, using a computational chemistry software package, draw the amino acid molecules bound to the reactive aldehydes derived from lipid peroxidation. Upon modification at the carboxyl group bend of the amino acid, draw the shape of the methylamine group. At the amino end, draw an acetyl group to emulate the peptide bonds of the modified amino acid.
Click on the clean icon to clean the structure. For structure optimization, click on calculate, followed by gaussian calculation setup. Then click on general and uncheck write connectivity.
From the job type, select optimization. In additional keywords, enter the indicated text. To change the basis set, go to method and select 631 G.For optimization, click on submit.
Then to optimize from gaussian terminal, enter the indicated command. Click on file, then save. Enter the file name and save the file as com.
Once the optimization is complete, open the output file and check that there are no error messages at the end of the document.
