Interactive Visualization of Infrared Spectral Data: Synergy of

Information • Textbooks • Media • Resources edited by

Computer Bulletin Board

Steven D. Gammon

Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization, and Experiment for Learning Spectroscopy

University of Idaho Moscow, ID 83844

W

Paul M. Lahti* and Eric J. Motyka Department of Chemistry, University of Massachusetts, Amherst, MA 01003; *[email protected] Robert J. Lancashire Department of Chemistry, University of the West Indies, Mona, Kingston 7, Jamaica

One of the ongoing challenges in the teaching of spectroscopy is getting students to recognize the relationship between specific spectral transitions and molecular structural features. Traditionally, this is done through repetitive viewing of different spectra and identifying important features as being related to specific types of molecules or functional groups. The number of spectra available to the student often limits this approach. In addition, getting sufficient experience to identify the relationship between a spectral feature and a structural feature takes time—especially for IR spectra, in which peak shapes can be as important as peak positions. A common feature of many successful multimedia packages is a discovery-driven “point-and-click” system. This is particularly useful for spectroscopy, since the student can more easily become accustomed to finding the salient features of a spectrum and associating them with molecular structural features. IR spectroscopy can be explored by identification of bands in the functional group region and by specific bands in the fingerprint region, such as the out-of-plane C–H bending modes for alkenes and benzene rings. This process is considerably enhanced and facilitated by an interactive discovery-driven interface where the choice of a spectral band immediately displays information about the associated vibrational mode or functional group. Others have been exploring such interfaces for the teaching of IR spectroscopy. The Chemistry Hypermedia Project of Tissue, Bell, and colleagues (1) incorporates the interaction of spectroscopy and interpretation into their multimedia presentation. Rzepa and coworkers (2) developed Java–Applet-based applications such as jSPEC to allow the interactive display and manipulation of spectra (2d) through the Internet, linked such spectra to molecular displays, and discussed some of the comparisons between the use of plugins and Applets. The IR-Tutor tutorial-based software developed at Columbia University has an interactive point-andclick interface allowing the student to select an IR peak to visualize the associated vibration; the vibrational animation is not, however, interactive (3). A WWW tutorial page at the University of Illinois at Chicago includes a set of Java-driven spectroscopy problems, with interactive menus having static spectral displays (4). We attempted to incorporate multiple elements of the course curriculum of a typical second-year chemistry student into an interactive dual-display format that would make learning IR spectroscopy a more dynamic, student-controlled topic. In the following contribution, we describe a procedure

that extracts the descriptions of animated vibrational modes from the output files of any of several quantum computational chemistry programs and links the animation files to experimentally obtainable IR spectra stored electronically in any of the standard ASCII JCAMP-DX (5) formats. The JCAMP-DX files can then be edited to allow direct linkage of any portion of the spectrum to a specific vibrational animation, allowing both spectrum and animation to be simultaneously displayed. The characteristics of this dualdisplay format can be controlled using appropriate scripting commands in the Chime plug-in from MDL Information Systems Inc. (6), which is compatible with the WindowsNT/ 95/98 versions of the popular Netscape Navigator and Microsoft Internet Explorer WWW browsers. Both the spectra and the molecular displays can be interactively manipulated to allow maximum control by the user to assist with understanding what is being viewed. Software For computation of vibrational modes, several programs were used. Commercial programs included Spartan (Wavefunction Inc., Irvine, CA), Hyperchem (Hypercube Inc., Gainesville, FL), and Gaussian 94 or Gaussian 98 (Gaussian Inc., Pittsburgh, PA) (7). The program GAMESS (8), maintained by Gordon’s group and available at no cost, was also utilized. All these programs are able to compute vibrational modes and frequencies for various levels of theory, and the procedures described below are not dependent upon a specific choice of computational methodology. In a typical three-hour laboratory period, one can conveniently compute vibrational modes and frequencies for reasonably large molecules using semiempirical molecular orbital methods such as AM1 (9) or PM3 (10). Frequencies computed with semiempirical and Hartree–Fock ab initio methods typically are 15–20% higher than the experimental frequencies. This differential must be taken into account when using or explaining these programs in laboratory experiments and other demonstrations of computed vibrational spectral predictions. We found it convenient to extract the vibrational modes from the ASCII format files output by the various computational modeling programs. The program VIBREAD (11), written in Fortran 77 by P. M. Lahti, reads PC-Spartan, UnixSpartan, PC-Hyperchem, Unix-Hyperchem, Gaussian 90– Gaussian 98, or SGI-GAMESS output files and creates a set of files in XYZ format (12) that contain the data for vibra-

JChemEd.chem.wisc.edu • Vol. 77 No. 5 May 2000 • Journal of Chemical Education

649

Information • Textbooks • Media • Resources

tional animations. Each file is named for the computed mode frequency (degenerate modes trigger a request for an alternate name). The XYZ files are a setup of Cartesian coordinates representing a set of “snapshots” of stepwise distortion from the optimized molecular geometry along the computed vibrational modes. Visualization of both spectra and molecule animations used the Chime version 2.0 plug-in from MDL Information Systems Inc. A freeware version of this plug-in is available at the appropriate WWW URL (6 ); additional options are available in commercial versions of the plug-in. A variety of formats are supported for displaying molecules as stick, ball-and-stick, and space-filling models. Animations can be displayed in Chime using files that basically consist of concatenated geometry files. We chose to work with the XYZ Cartesian coordinate files described above for animations, owing to the convenience of generating them. A variety of options for controlling and displaying structures and animations are available and are described at the Chime WWW site. Occasionally the default bond display parameters in Chime can cause a bond to disappear if the vibrational distortion in the XYZ file is too large, so VIBREAD has an option to decrease the size of the distortion for any set of XYZ files that is extracted. Spectra stored in JCAMP-DX ASCII formats can be displayed in a standard Chime window, using methodology developed by R. J. Lancashire (13) and incorporated into Chime. A variety of options are available for spectral zooming, peak identification, and reversal (13). In addition, using command syntax that is presently implemented for Chime only on personal computers using the Windows95/98/NT operating system (14 ), it is possible to link a spectral display region to another Chime window displaying a user-controllable file. The various options available are described at the main Chime support WWW site (12). Appropriate examples of syntax will be given below.

the other Chime window. The JCAMP-DX file must nominate the name of the TARGET window in which the various XYZ files will be displayed. This is controlled by HTML EMBED tags so that one of the two Chime windows must be designated with the appropriate TARGET name, which will be referenced from the JCAMP-DX file. For example, let the Chime window displaying the molecular structure be designated by the TARGET name of MOLECULE. An example is given below of the HTML coding that would initially display acetophenone.pdb in the target window NAME=”MOLECULE” as part of a table, and display the JCAMP-DX spectrum acetoph.dx in the second Chime window. The example assumes that all files that will be used in the animation are present in one directory. Interactive display table for spectra and vibrations Molecule Display Window

Programming and File Structure

[Click a peak --
see upper right for position]
[Click right button
in window for options]

Various computational programs described earlier were used to carry out frequency calculations on fully optimized geometries of various molecules. VIBREAD was used to extract the XYZ files (12) that represent the various computed vibrations. Experimental spectra were obtained on a Midac 9000 Fourier transform infrared spectrometer interfaced with an Intel Pentium personal computer running the Grams/32 software (Galactic Industries Corp., Salem, NH), and were exported to JCAMP-DX format. These are the basic files required to create a pair of displays linking the experimental spectrum and the computed vibrational animations. The process of incorporating these files into interactive Hypertext Markup Language (HTML) files will be exemplified for the molecule acetophenone in the following discussion. A standard WWW display can be used with HTML EMBED tags to show both the JCAMP-DX format spectrum and any desired initial representation of the molecule being analyzed in separate Chime windows. A typical choice of initial display uses a Brookhaven Protein Databank Format file (e.g., acetophenone.pdb). The JCAMP-DX format spectral file must be edited to allow linkage of spectral abscissa ranges in one window to the display of a desired XYZ format file in 650

The various options within the EMBED statements are described elsewhere (12). The options within the first window will set up any files that will be displayed therein to be animated in a “loop” mode (animmode=”loop”), rather than in a “ping-pong” mode. This is important for smooth display of the XYZ files produced by VIBREAD. The following text is an excerpt from the edited JCAMPDX file acetoph.dx. The text given in italics is added manually; the rest is produced during the export of the FTIR spectrum to JCAMP-DX format by Grams/32: ##TITLE= Acetophenone ##JCAMP-DX= 4.24 $$Exported GRAMS Data File ##DATA TYPE= INFRARED SPECTRUM ##ORIGIN= UMass/Chemistry Dept. ##OWNER= Eric Motyka ##DATE= 98/05/06 ##TIME= 11:56:00 ##NPOINTS= 1868 ##XUNITS= 1/CM ##YUNITS= TRANSMITTANCE ##RESOLUTION= 4

Journal of Chemical Education • Vol. 77 No. 5 May 2000 • JChemEd.chem.wisc.edu

Information • Textbooks • Media • Resources ##FIRSTX= 400.00 ##LASTX= 3999.643 ##XFACTOR= 1.0 ##YFACTOR= 9.5367E-7 ##FIRSTY= 63.772 ##MAXY= 383.64 ##MINY= -1400.8 ##$ASSIGNMENT TYPE= Chime

##$CHIME TARGET= MOLECULE ##PEAK ASSIGNMENT= (XYWA) (3100, -1, 30, ) (3068, -1, 10, ) (3058, -1, 10, )

…portions of file deleted at this point… (687, -1, 20, ) (583, -1, 20, ) (2400, -1, 2000, ) ##XYDATA= (X++(Y..Y)) 399.19 66869742 52788072 75937442 199261863073669 2362042 410.76-6225005-5350244 5642315 23942268

15516653

28876131-

…portions of file deleted at this point… 3986.1 110470985 110238183 110070172 110056947 110094975 110014294 3997.7 110029423 110048682 ##END=

The lines referring to the targeting of Chime window “MOLECULE” are found just before the peak assignment code. For example, when abscissa value 3100 ± 30 (cm᎑1) is selected in the Chime window displaying acetoph.dx, the other Chime window “MOLECULE” will load the animation file 3198.xyz, which will be displayed in wireframe format with the animation of the file beginning at once upon display. Various spectral abscissa ranges can be linked to the corresponding computed XYZ animation files. Most of the assigned ranges have been omitted from the portion of the file shown above. The final line of the PEAK ASSIGNMENT code enables the reload of the initial acetophenone.pdb file whenever an abscissa region of the spectrum is selected that does not have a specific linkage to an XYZ animation file. The last few lines of the example show the XYDATA portion of a spectrum generated by exporting it from the spectrometer to JCAMP-DX format. Figure 1 shows a screen dump of a typical tutorial screen using the acetophenone example described above. The files used for this example are available in the supporting material; in addition, the example is available on the online version of this article.W The full display features of this example are only functional on Windows 9x/NT–based computers with Chime version 2.0, as of the writing of this article. The upper part of the figure contains a Chime display of a molecule that can be rotated, zoomed, and otherwise manipulated in a variety of manners appropriate for Chime; the lower part contains a Chime display of the acetophenone JCAMP-DX format spectral file. Using the point-and-click options available in Chime, one may select a portion of the IR spectrum for expansion, or point to a spectral feature and click to read the frequency of the feature in the upper right-hand portion of the spectral window. Clicking any peak that has been linked to a vibrational XYZ file will launch an animation of the vibration, which will replace whatever display is presently in

Figure 1. Identifying spectral modes. Screen capture for a typical dualwindow point-and-click simultaneous display of a molecular structure (upper window) and a JCAMP-DX spectrum (lower window), with both windows using the Chime plug-in for Windows. Both the upper and lower windows may be manipulated. This example is available in the electronic supporting material online.W HTML code by Eric Motyka and Paul M. Lahti. Chime Embed tags from MDL Inc. and Robert Lancashire. Vibrational modes computed with Hyperchem 5.0. AM1 fully optimized geometry, quantum print level = 9.


651


the upper part of the table. If a portion of the spectrum is clicked that is not linked to an XYZ file, a standard Chime display of acetophenone will be placed in the upper display. Naturally, the animation is far more effective than the static picture shown in Figure 1, but the figure shows the general layout of some of our tutorials, and gives a sense of the strategy for displaying both molecular structure and point-and-click spectra in the same display page.

letting students assist in creating their own spectral plus structure displays will enable them to find out more about both the power and the limitations of computational chemistry compared to experiment results. We hope that these procedures will expand the range of available WWW interactive IR spectroscopy tutorials.

Practical Considerations

Demonstrations of these techniques with example files may be found at two sites (accessed Feb 2000):

A major reason to follow a strategy such as ours is reproducibility. Given the same computational programs and digitized spectra, any person could readily reproduce another writer’s peak-to-vibration links. The animation of the vibrational modes is neither arbitrary nor artificial—all atom motions occur to the extent that is determined by the computation. This has a tremendous advantage over manual animation of molecular vibrations that do not benefit from computation. In addition, it would be straightforward to animate an overtone mode by simply increasing the speed of the Chime display animation to reflect frequency doubling or tripling. Combination bands, however, would not be produced by these methods. The production of these displays can be quite sophisticated, if desired. High levels of ab initio or density functional theory could be used to get the best possible vibrational mode predictions; of course, this strategy would be highly computerintensive and would take considerable time. In addition, the assignment of all modes in the fingerprint regions of relatively large molecules would be problematic. Unless mode assignments were made otherwise, it would be easiest to assign peaks sequentially according to the computational predictions. If this were done, there would be some uncertainty about the accuracy of the fingerprint region assignments. Still, the educational purpose of the displays would be served even if there were such uncertainty. Students can get a sense of the regions of the spectrum where typical fingerprint modes are found, such as olefinic and aromatic out-of-plane modes, polymethylene rocking modes or ester O–C=O modes. The ease of producing the displays would allow more time for the instructor to consider how to correlate peaks in the actual spectrum with vibrational modes, rather than working on the animations through specialized programming. Summary We have described a procedure for combining computational chemistry, freeware plug-ins, and experimental spectroscopy to create interactive displays of infrared spectra for use on the World Wide Web. In addition, JCAMP-DX spectral display files can be created by modification of a variety of ASCII XY-pair formats, allowing the importation of files obtained by digital scanning. Animated displays such as those described herein should help students to learn the relationship between experimental spectra and molecular vibrational assignments. The procedure is sufficiently straightforward to allow undergraduate students to participate in all phases of producing the displays. The ability to manipulate both the spectra and the molecular structural displays maximizes students’ ability to use the display interface. In addition, 652

Useful Electronic Resources

http://www.chem.umass.edu/~nermmw/Spectra, a Northeast Regional Molecular Modeling Workshops site. http://wwwchem.uwimona.edu.jm:1104/spectra/iranim/ index.html, a University of the West Indies site.

Additional useful information relevant to this paper can be found at the following sites (accessed Feb 2000): http://www.chem.umass.edu/~nermmw, information about various computational chemistry programs and exercises is found at the Northeast Regional Molecular Modeling Workshops WWW site. http://www.isas-dortmund.de/projects/jcamp/jcamp.htm, official site for the JCAMP-DX formats. http://www.mdli.com/support/chime/chimefree.htm, the official site for the MDL Chime plugin, including links to demonstrations of advanced uses of the plugin for various visualization modes. http://www2.ccc.uni-erlangen.de/services/vrmlvib/vib_intro. html is a site that allows online interactive computation and visualization. http://www.chem.umass.edu/~nermmw/Spectra/VIBREAD, download VIBREAD for Windows.

Acknowledgment This work was supported in part by the National Science Foundation as part of the Northeast Regional Molecular Modeling Workshops (DUE 9554634). The opinions expressed in this paper are ours and are not necessarily those of the Foundation. W

Supplemental Material

A set of files that will demonstrate the acetophenone animations described above, when used with an appropriate browser, plug-ins, and operating system, is available in this issue of JCE Online. Literature Cited 1. Tissue, B. M. Trends Anal. Chem. 1995, 14, 426. Tissue, B. B. J. Chem. Educ. 1996, 73, 65. See also the WWW site The Chemistry Hypermedia Project; http://www.chem.vt.edu/chem-ed/ (accessed Mar 2000). 2. (a) Casher, O.; Chandramohan, G.; Hargreaves, M.; Leach, C.; Murray-Rust, P.; Sayle, R.; Rzepa, H. S.; Whitaker, B. J. J. Chem. Soc., Perkin Trans. 2 1995, 7. (b) Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. J. Chem. Inf. Comp. Sci. 1998, 38, 976. (c) Rzepa, H. S. Displaying Molecules and Spectra

Journal of Chemical Education • Vol. 77 No. 5 May 2000 • JChemEd.chem.wisc.edu


3.

4. 5.

6.

7.

for Electronic Conferences in Organic Chemistry; http:// www.ch.ic.ac.uk/ectoc/echet98/pub/001/ (accessed Mar 2000). (d) Rzepa, H.; Locke, W.; Tonge, A. Molecular Animation on the Web using Chime™ and JavaScript; http://www.ch.ic.ac.uk/ aptonge/mdl/ (accessed Mar 2000); click on the button “IR Frequencies & Normal Mode Vibrations” to go directly to a tutorial that is similar in spirit to those described by us, at http://www.ch.ic.ac.uk/aptonge/mdl/normal_modes/main2.html (accessed Mar 2000). Information about IR Tutor is found at the following URLs (accessed Mar 2000): Abrams, C. Abrams Educational Software; http://users.aol.com/charlieabr/. IR Tutor Website; http:// www.columbia. edu/cu/chemistry/edison/IRTutor.html (accessed Mar 2000). Organic Chemistry OnLine Tutorial; http://homework.chem. uic.edu/NEXT.HTM# (accessed Mar 2000). For current information about the JCAMP-DX formats, see the WWW page by Davies, A. N. International Union of Pure and Applied Chemistry; Committee on Printed and Electronic Publications. Working Party on Spectroscopic Data Standards (JCAMP-DX); http://www.isas-dortmund.de/projects/jcamp/ jcamp.htm (accessed Mar 2000). For information about Chime, see the appropriate MDL Information Systems, Inc. WWW page; http://www.mdli.com/ support/chime/default.html (accessed Mar 2000). Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; AlLaham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A.; Gaussian 94 (Rev D.4), Gaussian Inc.: Pittsburgh, PA, 1995. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; AlLaham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J.

8.

9. 10. 11.

12.

13.

14.

B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian 98, Gaussian Inc.: Pittsburgh, PA, 1998. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347–1363. This program is available from the GAMESS Home Page; http:// www.msg.ameslab.gov/GAMESS/GAMESS.html (accessed Mar 2000). Dewar, M. J. S.; Zoebisch, E. G.; Healey, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1987, 107, 3902. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209, 221. Lahti, P. M. VIBREAD; Department of Chemistry, University of Massachusetts: Amherst, MA, 1998. This program is available at the VIBREAD Download Site; http:// www.chem.umass.edu/~nermmw/Spectra/VIBREAD as an executable file for PCs running the Intel chip set and clones (accessed Mar 2000). Details of file formats and command structure compatible with current versions of the Chime plug-in are available at the WWW site entitled Chime Plugin Support; http://www.mdli. com/support/chime/chimefree.htm (accessed Mar 2000). For details about development of the spectral viewer capability now incorporated into Chime, see the WWW site by Lancashire, R. J. JCAMP-DX Data Viewer for Windows (95 and NT); http://wwwchem.uwimona.edu.jm:1104/software/ jcampdx.html (accessed Mar 2000). The full range of capabilities required for spectral display and manipulation in our tutorials described at http://www. chem.umass.edu/~nermmw/Spectra or at http://wwwchem. uwimona.edu.jm:1104/spectra/iranim/index.html is at present available only in the Windows version of the Chime plug-in. Macintosh support for spectral JCAMP-DX features of Chime is not presently available: see http://www.mdli.com/support/chime/ relmain.html#15 (all accessed Mar 2000).


653

Interactive Visualization of Infrared Spectral Data: Synergy of

Recommend Documents