Information • Textbooks • Media • Resources edited by
computer bulletin board
Steven D. Gammon University of Idaho Moscow, ID 83844
Educational NMR Software
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Peter Lundberg* Department of Physical Chemistry, University of Umeå, S-901 87 Umeå, Sweden
Computers have been used for many years in teaching, but the availability and power of microcomputers have not, until relatively recently, allowed for more advanced simulations of NMR experiments (1, 2). One of the first such NMR programs is Principles of FT NMR, by J. W. Blunt (University of Canterbury, Christchurch, New Zealand), created in 1983 for Apple II+ (equipped with 48K memory!) (3). The program, which covered 11 different aspects of Fourier transform NMR, was well implemented and very inspiring, and perhaps it sparked the interest for the use of computers in NMR instruction. Background When I first taught a course in introductory NMR theory and methods to third-year university students in physics, the idea of inquiring what programs were used at other universities appeared. The worldwide electronic forum “Internet” was queried concerning what (and where) NMR software was available via a few specialists’ email user groups. Enough response was received to encourage the use of a few different simulations in the course, in the form of three computer lab exercises (pulse programs, spectral simulation, processing experimental data). After some time enough suggestions had been received to confuse even the most organized teacher, and the programs were typed into a simple list and categorized under different headings. Eventually the list grew to include 40–50 items, and the idea of giving something back to the helpful community of NMR spectroscopists, having been given the favor of teaching NMR at various levels, grew. In a somewhat humble attempt, the compilation of programs was offered to the original user groups in the anticipation of maybe 10– 15 requests. After a few days, several hundred requests had been received and the task of responding to each and every one was no little chore. Fortunately, a number of people offered their help, and copies of the compilation in a few different formats (ASCII, MacWord, and HTML) were placed at a few different file transfer protocol (FTP) and World Wide Web (WWW) sites. The Compilation When it comes to NMR, three principal categories of computer-based instruction are of perceived value. The first (I) is simulation and visualization of the physical phenomenon as such. In other words, this category includes simulations of the vector model of the macroscopic magnetic moment of a sample, as well as programs for using the product operator *Present address: Department of Radiation Physics, University of Linköping, 581 85 Linköping, Sweden. Correspondence to: Peter Lundberg, email:
[email protected] or
[email protected]; phone: (+46-13) 22 27 90; fax: (+46-13) 22 47 49. W Supplementary materials for this article are available on JCE Online at http://jchemed.chem.wisc.edu/Journal/Issues/1997/ Dec/index.html.
approach for the simulation of various pulse sequences. The second (II) is simulation of experimental data such as spectra, and the third (III) involves the analysis of actual experimental data. Additionally there are a few other more specialized types of applications. As of May 1996 there were more than 100 software items in the compilation. Public domain, freeware, shareware, and commercial software are all listed. I placed the programs under the heading I thought was most appropriate, although a few of them could equally well have been placed in other sections. The programs are divided into nine categories: 1. Introduction to NMR—Programs that simulate the operation of real spectrometers where the instrumental settings can be adjusted. Here are programs that simulate some of the basic experiments complete with generation and treatment of simple FIDs, and some programs in which other general aspects of NMR are simulated. “Complete” tutorial packages are also placed under this heading. 2. Simulation of NMR spectra—Programs that can be used to simulate NMR spectra (II) based on parameters such as J-coupling constants and chemical shifts. In general the scalar interactions between 5–8 spins can be simulated. 3. Spin simulation—Programs that simulate the physical background (I) of the NMR experiment at a more theoretical level than above. These include programs that simulate experiments using the common vector approach. The theoretically more useful product operator treatment is implemented in a few programs often based on the symbolic mathematics program Mathematica. 4. Processing and analyzing data—Programs intended mainly for processing experimental data (III). Some are commercial programs and some are freeware that can be obtained by simple FTP-file transfer. Several programs can be used for research as well as for education purposes. 5. Shift calculations—The programs in this section are mainly for calculating the chemical shifts of 13C using empirical or semi-empirical rules. Both in teaching and in some research it can be useful to calculate the expected chemical shifts of molecules of “arbitrary” structure. 6. Databases—A number of databases containing both 1 H and 13C experimental NMR spectra of some of the most common molecules, as well as of peptides and proteins. Each database contains between 50 and 700 spectra of authentic samples. Some of these programs are intended for introductory teaching, whereas others are research tools or are for advanced courses. 7. Imaging—Programs for medical NMR applications, especially imaging. There are programs for simulating the effects of different experimental parameters, simulations of imaging experiments, and processing software for imaging data. 8. Electron Spin Resonance—Programs for simulating ESR spectra and data processing are listed. 9. Other things—Includes X Windows client software,
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Information • Textbooks • Media • Resources utility programs, Internet sites of special interest to NMR spectroscopists, multimedia pictures, and special literature such as lecture notes.
Each item in the list is described with a title, a short summary of its application, what hardware is required, availability (electronically or otherwise), author, and for some programs, a reference to the literature. Use in Teaching The compilation includes programs that demonstrate simple to advanced concepts, as well as complete packages for a general introduction to the practical and theoretical aspects of NMR spectroscopy. One example of a complete tutorial package is the animated textbook Basics of NMR Spectroscopy (Rochester Institute of Technology, Rochester, NY), which includes 14 chapters discussing several theoretical and practical topics (4). Another program is Proton NMR Basics (JCE Software, Madison, WI), which is distributed on CD for Macintosh and PCs. It includes QuickTime movie sequences demonstrating an NMR spectrometer, spectral assignments, etc. Some programs emulate the actual hardware, the NMR spectrometer, producing realistic data based on the instrumental settings. Examples are the NMR Simulator (Falcon Software, Wentworth, NH, USA), and the Virtual NMR Spectrometer (Acorn NMR Inc, Freemont, CA). Other programs will calculate a spectrum, based on empirical parameters, corresponding to an entered structure of an organic molecule (e.g., the organic reaction program Beaker, Brooks/Cole, Pacific Grove, CA, and ACD/H-NMR by ACD, Toronto, Canada). In more advanced courses, programs that allow students to manipulate the product operators representing a spin system are extremely useful. These programs allow the introduction of very complicated experimental schemes and concepts. John Shriver’s Product Operator Mathematica Notebook (5, 6), POMA (7), and PENCIL (8) are examples of such programs. Another range of NMR program packages give a visual introduction to the use of MRI (Magnetic Resonance Imaging). These include MRI-Simulation (University of Pennsylvania, Philadelphia) and Basics of NMR Imaging (Rochester Institute of Technology, Rochester, NY) (9). In Conclusion The latest version of the list is called EduNMRSoft version 1.7.1. For reasons of accessibility the compilation has been placed at several sites around the world. The home site is
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http://www.chem.umu.se/divisions/fk/EduNMRSoft.html. Other sites are h t t p : / / t u t o r. o c . c h e m i e . t u - d a r m s t a d t . d e / nmrsoft.html http://www.chemistry.uakron.edu/MAGNET/ EduNMRSoft.html http://bmrl.med.uiuc.edu:8080/edusoft.html http://www.imt.liu.se/radiofysik/Information/ EduNMRSoft.html http://deane.bio.ucalgary.ca/EduNMRSoft.html http://www-nmr.chem.ruu.nl/Links.html Please feel free to pick up a copy, or to put it at your local site, or to simply make a link to the nearest site. The visiting statistics just for the site at the University of York indicate that the list has been received with great interest by NMR users. I hope that the list will be of some use, and that users will help in making it better. In particular I would be interested to learn how people use computer simulation in practice for teaching NMR. Acknowledgments There are many people whom I would like to thank for their willingness to share experience and information about suitable NMR software. I would like to thank the authors of various programs for sending them electronically or by mail, often without monetary compensation. I would like to thank the webmasters for allowing the distribution of this compilation as it develops, electronically around the world on the web or otherwise. Literature Cited 1. Jones, P. M.; Schneider, K. J. J. Ed. Multimedia Hypermedia 1996, 5(2), 151–178. 2. Jones, P. M.; Schneider, K. J. In Systems, Man, and Cybernetics; Proc. IEEE Int. Conf. (Le Toquet, France, Oct 1993); 1993, 1, 108– 113, France. 3. Blunt, J. W. J. Chem. Educ. 1983, 60, 97–98. 4. Agostinelli, R. M.; Browne, D. S.; Ellsworth, P. E.; Weigert, W. A.; Hornak, J. P. Abstracts of Papers, 202nd National Meeting of the American Chemical Society, New York, Aug 25–30, 1991; American Chemical Society: Washington, DC, 1991; Abstract CHED 123. 5. Shriver, J. Concepts Magn. Reson. 1992, 4, 1–33. 6. Shriver, J. J. Magn. Reson. 1991, 94, 612–616. 7. Güntert, P.; Schaefer, N.; Otting, G.; Wüthrich, K. J. Magn. Reson. A 1993, 101, 103–105; corrections in J. Magn. Reson. A 1993, 105, 328. 8. Callahan, J.; Mattiello, D.; Drobny, G. P. Bull. Magn. Reson. 1993, 14, 191–196. 9. Browne, D. S.; Ellsworth, P. E.; Hornak, J. P. J. Chem. Educ. 1989, 66, 647–649.
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