Using SDBS Database For Identifying Unknowns

Using SDBS Database for Identifying Unknowns Table of Contents Note: Red arrows are used in the Figures to identify where buttons and functions are located. Use Zoom (under View) to read the details on any of the Figures. 200% magnification is usually enough. Figure Description Page Entering the SDBS Database 1 2 3 Entering Swain Library homepage Entering Chem 130 homepage Entering SDBS Homepage 2 2 2 Searching SDBS by CAS Registry No. and viewing spectra 4 5 6 7 Going to the SDBS Data entry page and entering CAS No. Viewing the results of a CAS No. search Viewing spectral data from results of a CAS No. search Viewing the assignment of H atoms to peaks in the chemical shift plot 3 3 3 4 Searching SDBS using spectral and atom data 8 9 10 Entering C13 NMR Spectral Peak Data Entering Atom Data Viewing the results of a search, and entering H NMR & IR spectral data 1 4 4 5

Using SDBS Database for Identifying Unknowns Action: Figure 1. Swain Home Page Go to the Swain Library home page: http://lib.stanford.edu/swain This will take you to Fig. 1. Next to Instruction, click on Course Pages [red arrow in Fig.1], then click on Chemistry 130. That will take you to the Chem 130 page shown in Fig. 2. The Chem 130 page has several links on the left side. To reach the SDBS database for spectra for organic compounds, click on Identifying Unknowns, Syntheses, & Reactions [red arrow in Fig. 2]. Figure 2. Chemistry 130 Page Action: Note: Then Click on SDBS Integrated Spectral Database for Organic Compounds. This will take you to Fig. 3. Figure 3. SDBS Database Homepage Action: 2 Scroll to the bottom of the page and accept the disclaimer. This will take you to Fig. 4.

Using SDBS Database for Identifying Unknowns Action: Figure 4. SDBS Data Entry Page You will typically enter either 1) a CAS Registry Number, or 2) enter 13C &/or 1H NMR &/or IR spectral data, plus elemental data, if known and needed, or 3) Molecular Formula [following the instructions under the entry box], and then click on Search to see if the “hit list” of compounds contains your compound of interest. The following are examples of each of the first 2 types of searches mentioned above. Action: Enter the CAS Registry No. 2243-42-7 into the field just below CAS Registry No.: (arrow), and click on Search at the bottom of the page (or hit “Enter” on keypad). You will see Fig. 5. Figure 5. Results of CAS Registry No. Search Note: Note: Figure 6. H NMR for o-phenoxyacetic acid 3 You will see a Y for Yes, under MS (Mass Spec), CNMR (C13 NMR), HNMR (H NMR), IR (Infra Red), and Raman, and an N for No under ESR (Electron Spin Resonance). Each Y is linked to an actual spectrum. Eg., if one clicks on Y under HNMR, one would see Fig. 6. You will see the actual spectrum in the middle of the page, and on the left are links to other spectral data, such as C13 NMR, and IR. If you scroll down you will see Fig. 7.

Using SDBS Database for Identifying Unknowns Figure 7. Peaks assigned to Hydrogens Note: Each hydrogen is labeled and assigned to a peak with a given chemical shift in ppm (parts per million). Return to the SDBS data entry page shown in Figure 4, using the “Back” arrow or by clicking on Return to Search. Next is an example of a search for an unknown using spectral data. Usually one would use C13 first, since lab data and literature values most often agree well. The C13 peak values from the spectrum are: 21.58, 124.90, 125.80, 126.84, 127.23, 127.58, 127.67, 128.05, 131.76, 133.72, and 135.29 The peak values above are then rounded to the nearest whole number, and entered in the field for C13 [red arrow, Fig. 8]. If one hit Enter, one would find 155 hits. This can be reduced by entering regions with no peaks. In the field to the right of the phrase No Shift Regions [blue arrow], enter the ranges with no C13 peaks (220 138,120 25,18 5). Note there is a space between the beginning and end of a range, and there is NO space after a comma if more than 1 range is used). Then click Search at the bottom of the page. This will generate a list of 14 hits. One can narrow it further by entering atom data. Here it is known that the compound has no hetero atoms ie only C, H, and possibly O. For the atoms known to be absent, one enters the range as 0 to 0, as shown in Fig. 9. For atoms which are not known, one can leave blanks, or guess a range. For atoms known to be present one can either enter a precise range [such as 1 to 1, or 2 to 2], or enter a wider range [such as 5 to 10], or leave blank. Then click on Search, or hit Enter. In this case, after entering the atom data, the hit list reduced to 12. The results are shown in Fig. 10. Action: Figure 8. Entering Spectral Data Action: Action: Figure 9. Entering Atom Data Action: 4

Using SDBS Database for Identifying Unknowns Action: Figure 10. Results of a spectral-plus-atom data search using SDBS One can see that 12 compounds met the search criteria. If H NMR and IR data had been used as well, one would have narrowed the list even further [IF those spectra were in the database]. Hence one must be cautious in entering data for more than one type of spectrum at the same time. For example, it is possible to have only IR data present, and then to miss the compound because H and/or C13 data were entered as well. H NMR data are entered in the same way as the C13 NMR. However, the default search range is /- 0.2 ppm, which is normally accepted. Hence, peaks are usually rounded to the nearest tenth when entered, and the search is /- 0.2 ppm from the value entered. If multiple peaks are used, they are separated by a comma with NO space after the comma. For multiplets, the midpoint is used. IR data can be entered as either peaks or ranges, in the box under IR Peaks (cm-1) , per the format shown under the box. One should accept the "allowance" of /- 10, although be aware that if only one peak differs from SDBS by greater than 10 cm -1, the compound will be dropped from the hit list. Also be aware that if the hit list is large, one can again reduce its size by entering hetero atom data, if given, for all elements except C, H, & O, and then one can often estimate ranges for C, H, & O, using spectral data. Eg. a range for H from HNMR integrals, or a range for C from the number of C13 peaks, and/or a range for O from C O, C-O peaks in IR, plus chemical test data. One should not use the small IR peaks because the "transmittance" is set by default to 80 % and small peaks usually have a transmittance of 80%. If one wants to use small peaks, one can set the transmittance to 90 for example, but then the hit list grows considerably as well. When viewing spectra or entering data, be aware that solvents can add peaks or shift peaks, both for H & C13 NMR. The values for the more common solvents are given in the course textbook. Using the IR and hetero atom data shown in Fig. 11, one obtains a hit list of 25 compounds. This can be quickly scanned to see if spectra match, or it can be reduced by entering a range for C using C13 data, and/or a range for H using H NMR data. Fig. 11 Search using IR data 5

Searching SDBS by CAS Registry No. and viewing spectra 4 Going to the SDBS Data entry page and entering CAS No. 3 5 Viewing the results of a CAS No. search 3 6 Viewing spectral data from results of a CAS No. search 3 7 Viewing the assignment of H atoms to peaks in the chemical shift plot 4 Searching SDBS using spectral and atom data