OF ALL THE CHEMISTRY RELATED SOFTWARE

Transcription

1 ChemBioOffice Ultra A Great Benefit for Academia by Josh Kocher, Illinois State University OF ALL THE CHEMISTRY RELATED SOFTWARE that I have used in both an industrial and academic setting, ChemBioOffice Ultra 2010 is one of the best and most useful. On a scale of 1 to 5, the new software definitely rates a 5. It is laid out in a logical fashion, very easy to use, has helpful users guides, and is designed not just for the organic chemist but can be used by anyone in the vast scientific community. As an instrument for academia, the programs contained in ChemBioOffice s are of great benefit not just for graduate students and professors but for the undergraduate students as well. One particular program, ChemBioDraw, has practically limitless uses. Three programs will be reviewed here and they include: ChemBioDraw, E-Notebook, and CS Inventory. ChemBioDraw ChemBioDraw s many uses include undergraduate lab reports, instructional documents, general laboratory preparations, and as a tool for preparing documents of publishable quality. As an undergraduate student in the early part of this decade, I attended a university that had a site license for ChemOffice. I, as well as many of my classmates, started experimenting with the features of the software and including inserting ChemDraw images into our sophomore organic laboratory reports. The more professional appearance of the chemical structures, as opposed to hand drawn structures, was not only more appealing to eye and limited the number of mistakes made while drawing the structures. Though drawing structures is the most common use for the software, the present version has many other uses Shown in Figure 1 is a vacuum distillation setup. For the experienced student or industrial chemist, this may seem like a trivial setup, but to a sophomore organic student or an undergraduate performing research, this simple setup can be daunting. A simple drawing, such as this, showing the various pieces of glassware that are needed can greatly diminish the agony of a young student. Using ChemBioDraw, simple setups like this can be drawn and input into laboratory manuals or into SOP s for research groups.

2 Figure 1: A vacuum distillation apparatus was drawn using the glassware feature in ChemBioDraw. This drawing can be put into a laboratory manual for undergraduate students for a quick reference on what glassware is needed as well as the direction of flow of water in the condenser. One feature I found useful is the ability to draw TLC plates. Looking back to my undergraduate lab report days, I hated to draw TLC plates by hand. This feature, which very well could have been in older versions of the software, would have been put to great use. Along those same lines, the TLC plate shown in Figure 2 could easily be put into a laboratory manual, thesis, or a publication. Figure 2: An example of a TLC plate showing the Rf values for a two mixtures of compounds as well as the Rf values of pure compounds. I am sure I am not the only chemist who does not remember all of the IUPAC naming schemes for compounds. In ChemBioDraw, there is a tool that allows a chemical structure to be converted into a name and vice-versa with a chemical name being transformed into a chemical structure. One such example is shown in Figure 3. This particular structure was drawn to show how versatile the software is. In this compound, various different functional groups were included: a double bond, two stereocenters, a halogen, and a 6-membered ring. If we dissect the name given, we can account for these functional groups and stereocenters. However, for more complex structures or organometallic compounds such as ferrocene, the

3 naming feature does not always work. With the case of ferrocene, the software returns "inorganic compounds cannot yet be named." With my graduate working being in inorganic chemistry, I would like to see this feature added. I am sure someone at CambridgeSoft is currently working on this as you read this review. Figure 3: A simple ChemBioDraw structure showing the name of the chemical structure using the "Convert structure to name" feature. Another useful tool in ChemBioDraw is the "Predict NMR structure." Using this tool, both the 1H and 13C NMR spectra can be predicted. This tool, like most tools, works best for simpler compounds. This limitation can be expected, but as the software develops over time, I believe it will be able to handle more complex structures. Both the 1H and 13C of the compound shown in Figure 3 were predicted with the estimated chemical shifts being of good quality. For example, one complex compound in which the software does a mediocre job on is porphine, a simple porphyrin. For the external H s on the pyrrole rings, the estimated chemical shifts are predicted with a "good" estimation while the other H's are of "rough" quality. However, the protons of "rough" quality are the protons that are of most use. Perhaps the most useful aspects of ChemBioUltra is how it interfaces with Microsoft Word. A structure can easily be created in ChemBioDraw and then copied into a Word document that can be used for any number of uses. Once the structure has been embedded into the Word document, it can be edited as if you were using just ChemBioDraw. If, for example, in the final check of draft manuscript, a small error is discovered, it is much easier to edit the structure in Word than it would to open the drawing software and the redo the copy the and pasting. Examples showing the usefulness of this interface include writing a report, a manuscript or thesis, or creating structural diversity in examinations for students. E-Notebook One of the hardest, tedious, but also most important duties of any scientist is to keep an accurate, neat, and understandable laboratory notebook. With E-Notebook, this task has become much easier. Looking back through notebooks of past graduate students or colleagues in an industrial setting can be a daunting task. I am sure we have had our troubles trying to decipher another person s handwriting, even trying to re-

4 read your own notes can be troublesome, but with an electronic notebook, this dreadful task becomes very easy. While experimenting with the E-notebook, I have become a big fan. There are many potential uses for the E-notebook that I have just begun to learn. Figure 4 shows an example of a procedure in which I created an E-Notebook entry using a standard notebook preparation as a guide. A few of the particular useful applications are listed below: Ability to draw out reactions using ChemDraw Automatic molecular formula and molecular weight calculators Ability to input reaction conditions into an entry Ability to calculate the desired amount of reagents needed by entering in the mass of one reactant And the ever important ability to link spectra to a particular entry. One of the above features that I find useful is the ability of the software to do simple but time consuming mathematic calculations. However, if a data entry error is made, it will affect every variable in which that piece of information is used. By doing these calculations by hand, the software can be used as a check. On that same note, if a reaction is repeated time after time, the amount of reagents could simply be inserted into the entry saving a lot of time on calculations. The software also allows E-Notebook pages to be exported into Word documents and Adobe pdf files, as long as Adobe Professional is installed. This feature can be used for keeping hard copies of the notebook in case of accidental data loss or for distribution amongst research group members One limitation of the E-Notebook is, of course, having a valuable laptop or personal computer out on a bench top in a laboratory. I am sure that it would not take long for the computer to accidentally have some chemical spilled onto it or to be contaminated in some other aspect by being in a laboratory. This would be an easy way for the hard work of one individual to be lost due the carelessness of another. Thus, a pen and notepad would still be need to take notes and then to time would be needed to transpose that data to the software.

5 Figure 4: An example of a chemical synthesis taken from my graduate laboratory notebook that I made into an example for an E-Notebook entry. Take particular note of when a particular reagents mass is entered, the form entry can calculate the required mass of other reagents. CS Inventory One of the most important tasks in a laboratory is keeping an accurate inventory of not only the chemicals, but also the non-chemical items that keep a lab running. The CS Inventory software makes the task of updating or starting an inventory a much easier process. There is a very nice web tutorial using screen captures that walks a user through the setup progress. In the software, there is even a "test database" with data which can be used as an example when building a database that meets your labs overall needs for inventory control. This database, when created, can be kept on a single computer or can be networked to allow all members of the lab access to the data. The tier structure on which the inventory software is based on makes navigation as well as data entry simple progress. The user interface is set up showing the details of the material, its location, and the type of container in which it is found. Of course, the most important aspect, details of a particular substance, can be input into the database. Valuable information such as the supplier, CAS registry numbers, product codes, molecular formulas, molecular weights, and MSDS sheets can be easily created, linked or manipulated. Searching of the database is easy to do and searching of the ChemACX online database is included in certain versions of the software. Personally, I did not try to search the ChemACX database, but I feel it is certainly a desirable feature to have. Another valuable feature of CS Inventory is the printing labels and reports feature. Very professional labels and reports are easily created and maintained. On the labels, data such as lot number, bar codes and much more can easily be built into a template that can be tailored to individual uses. I feel the label making feature is of great value to both academia and industrial applications. Summary In summary, I feel that ChemBioOffice Ultra 2010 is a very easy to use software that has many potential uses in an academic laboratory as well as in an industrial setting. I give the software a rating of 5 out 5. The potential uses of ChemBioDraw alone make this software a necessity for a chemist. The drawing of chemical structures of extremely high quality is a must when creating reports, publication, and other documents. ChemBioDraw leads the way with the abilities that are built into the software such as the structure to name feature and NMR prediction tools. E-Notebook and CS Inventory are just two of the other very useful features incorporated into the software suite that makes the job of a scientist a much easier task. The interface of the various software packages is very user friendly and the software comes with extremely useful manuals to learn how to make best use of the software. In the short time that I have "played" with software, I continue to find new features that are of great utility for users.