Example of a Lab notebook: Chymotrypsin (download)(Back)

Computational chemistry lab notebooks should exist in a form that allows information to be examined easily; Microsoft Excel and Word are ideal for this purpose.  In practice, Excel is the more useful because it allows simple mathematical operations to be performed on computed results.

Excel Page 1  
  Chymotrypsin Mechanism: Stationary Intermediates  
Quantity Step 1 Step 2 Step 3 Step 4 Step 5 Step 6  
 
ΔHf -47899.77 -47902.31 -47904.60 -47895.48 -47895.17 -47905.48  
ΔHf relative to Step 1 0.00 -2.54 -4.83 4.29 4.60 -5.70  
An example of the type of information that can be useful in an Excel spreadsheet is provided by the work done on modeling the hydrolysis of a peptide bond by the enzyme chymotrypsin. 

The first page gives the calculated heats of formation for the six stable intermediates in the catalytic mechanism, and their values relative to that of Step 1.  By clicking on each of the hyperlinks, the appropriate system can be displayed and examined.  Errors in transcription are very easy to make, so it's very important to have an easy way to detect and correct such errors. By using hyperlinks and thereby having access to the unedited results of a computational simulation, the likelihood of transcription errors can be reduced.

If an error is found in a simulation, the error can be corrected and the notebook updated.

    Excel Page 2        
Chymotrypsin Mechanism: Transition States  
Quantity Step 1-2 Step 2-3 Step 1-3 Step 4-5 Step 5-6  
 
ΔHf -47881.85 -47882.20 -47863.92 -47885.80 -47879.41  
ΔHf relative to Step 1 17.93 17.58 35.86 13.97 20.36  
Barrier height 17.93 20.11 35.86 9.68 15.76  
 
Imaginary frequency 1035.0 734.7 359.2 1168.0 851.1  

The second page holds the calculated heats of formation for the five transition states and the differences between the ΔHf of the transition state and that of Step 1.

Transition states are validated by calculating the vibrational frequencies that involve atoms involved in the reaction.  As with the ΔHf, clicking on one of the imaginary vibrations displays the unedited results of a FORCETS calculation file.  For convenience, the file-names were modified by adding ".txt" to the end of the names.

Another very useful feature of Excel spreadsheets is the ability to add comments to individual cells.  Of course, only important comments, such as anything unusual about a specific simulation, should be made.

Individual files

Hyperlinks in Excel spreadsheets should point to files that contain results. To avoid clutter, these files should be in appropriately named sub-folders, in this case, GS, TS, and FORCE.  Other files might be needed, for example data-sets that were used in generating the results files.  These should also be in the sub-folders.  After a project has been underway for a while, these sub-folders can get quite crowded, so it's important to not store un-needed files, for example if a <file>.arc exists, the corresponding <file>.out is normally not needed.