Applied Computational Chemistry for the Blind and Visually Impaired

Article pubs.acs.org/jchemeduc

Applied Computational Chemistry for the Blind and Visually Impaired Henry B. Wedler, Sarah R. Cohen, Rebecca L. Davis, Jason G. Harrison, Matthew R. Siebert,† Dan Willenbring,‡ Christian S. Hamann,§ Jared T. Shaw, and Dean J. Tantillo* Department of Chemistry, University of CaliforniaDavis, Davis, California 95616, United States S Supporting Information *

ABSTRACT: We describe accommodations that we have made to our applied computational−theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure−function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts written in-house, and three-dimensional printing in a process that allows a blind or visually impaired student to satisfy her or his curiosity about structure−function relationships with minimal assistance from sighted co-workers. KEYWORDS: Graduate Education/Research, Organic Chemistry, Computer-Based Learning, Inquiry-Based/Discovery Learning, Computational Chemistry, Laboratory Computing/Interfacing, Molecular Properties/Structure, Quantum Chemistry, Theoretical Chemistry, Undergraduate Research

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There are many references in this Journal that provide resources for teaching students with disabilities (for a summary see ref 1). In addition, pioneering work by Skawinski and co-workers on the use of stereolithography in fabricating molecular models derived from quantum chemical calculations2a−c and the recent development of a Web-based interface for processing of molecular structures2d have addressed several key aspects of applied computational−theoretical chemistry research by blind students. Nonetheless, none of the tasks listed above (as previously carried out in our working applied theoretical chemistry laboratory) was fully accessible to BVI researchers when the project described herein was initiated. Our approach has evolved over the course of many months of working closely with HBW and involves the use of the following adaptations: tactile drawings and molecular models for conveying the connectivity of molecules whose structures, energies, and other properties will be calculated; SMILES strings3 and the Open Babel software4 to convert connectivity into input files containing three-dimensional (3D) coordinates; existing computational chemistry software to carry out quantum chemical calculations; Bash and Perl scripts written in-house to collect relevant data from output files; and a 3D printer to construct physical models of computed structures. In short, our experience demonstrates that BVI students can perform applied computational−theoretical chemistry experiments, largely independently, when these tools are integrated appropriately.

n this paper, we address the issue of making applied computational chemistry research accessible to blind and visually impaired (BVI) students, an issue that came to our attention when chemistry faculty at our university were approached by a BVI student interested in pursuing chemical research. Herein, problems encountered and the solutions adopted are described, with comments from the blind student involved in this research (HBW, who initiated applied computational chemistry research as an undergraduate chemistry major and currently pursues such research as a chemistry graduate student) interspersed throughout. All accommodations found to be necessary (whether newly developed or previously reported) are described so as to present a complete picture of the changes made to the typical flow of research in applied computational chemistry to enable a BVI researcher to work independently. Remaining problems are also highlighted. To put the following discussion into perspective, the tasks generally associated with conducting applied computational chemistry research are first outlined: • Communication and discussion of the chemical question(s) to be addressed using computational methods. • Assimilation of structural information. • Conversion of organic structures to atomic coordinates and generation of input files for computational chemistry software. • Processing of output files (including geometry and frequency analysis information). • Organization and presentation of data (written, and poster and oral presentations). © 2012 American Chemical Society and Division of Chemical Education, Inc.

Published: September 7, 2012 1400

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Table 1. Representative SMILES Strings

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producing the figures knows Braille. Functional groups such as -N(CH3)2 are drawn in bond-line form, as numerical subscripts are difficult to decipher using one’s fingers. Although this approach is presented here in the context of initiating a research project, we have also used it in other contexts, such as a chemistry lecture environment.

COMMUNICATING INITIAL PROJECT DETAILS

Process

Anyone who has been through an introductory organic chemistry course likely understands that line drawings and common names (e.g., (−)-menthol, see Table 1) constitute the most frequently utilized modes of describing chemical structures in the organic chemistry community. However, common names often provide little, if any, specific information to help visualize a given structure if the structure in question has not been memorized previously. Although IUPAC nomenclature is unambiguous, official names for complex molecules (of the sort frequently encountered in applied theoretical chemistry research projects) are often cumbersome to generate. Consequently, alternative methods to convey structural information to BVI researchers were sought. This step is perhaps the most crucial step. Once a student understands the connectivity (and configuration if stereogenic centers are present) of the molecule to be subjected to quantum chemical calculations, she or he can carry out quantum chemical calculations on it with little to no sighted intervention. Although standard physical molecular model kits can be quite effective at conveying connectivity and stereochemical information, a faster, less expensive, and in many ways, easier-to-use method for communication of chemical structures is to convert line drawings to tactile graphics. Details of a method using a tracing wheel have been reported,5 but we favor a different method (additional ideas relating to tactile graphics are available at the Tactile Graphics Web site).6 Using a sheet of smooth 24-pound high-resolution laser printer paper (to maximize the signal-to-noise ratio), a regular ink pen (which doubles as a tactile stylus), and a notepad (to form a soft pad under the smooth paper), the person wishing to convey a structure to a BVI individual draws the molecular structure (usually as a standard organic chemistry line drawing7) on one side of the sheet of paper. The structure is drawn as large as possible so as to make up for the coarseness of tactile resolution compared to visual resolution. The sheet of paper is then flipped over, placed on the notepad, and the lines of the drawing are traced forcefully. This “double-flip” ensures that stereochemical information (if applicable) is communicated properly. A BVI student can then read the obverse using her or his fingers. For structures drawn in this fashion, print capital letters are used for atom labels; Braille atom labels may be used instead if the BVI individual prefers them and if the person

BVI Student Perspective

Learning my way around complex organic bond-line drawings was difficult before this method was developed. A reader or assistant would have to describe the molecules to me in words as well as she or he could, but nothing is as good as being able to feel the structures myself. In addition, this method can be used beyond chemistry (e.g., mathematics and tactile mapping) with most any sighted assistant who can write clear, unambiguous large-print letters and accurately reproduce a line drawing. If I can easily get the molecular structure and connectivity into my mind, thinking about the chemistry is easy. Perhaps the biggest challenge for BVI individuals is getting the chemistry (here, molecular structure) from the visual presentation into their mind, and this method is better than any I have used before for all subjects requiring visual information transfer.

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ASSIMILATING STRUCTURAL INFORMATION

Process

The use of SMILES (simplified molecular input line entry specification) strings3 for molecules constitutes a quick, simple, and portable format for recording structural information that is readily accessible to BVI researchers. SMILES strings are plain text strings that encode connectivity and stereochemical configurations for organic molecules. They are often used to construct large databases of organic molecules for myriad uses including virtual screening of molecules of biological interest.3b Readers are referred to ref 3 for additional details on the logic of constructing SMILES strings (see also Table 1 for examples). A SMILES string may be read by screen reading software (e.g., VoiceOver for Mac8 or JAWS for PC9), converted into a tactile line drawing, or converted into 3D coordinates. To produce a tactile line drawing from a SMILES string, the SMILES string is pasted into ChemDraw10,11 (or another similar program) and then printed via a Pictures in a Flash (PIAF) tactile graphics maker.12 The PIAF prints on special thermal paper, which is passed through a heating chamber. Tactile lines emerge wherever laser printer toner appears, allowing the student to feel the lines of the structural drawing. 1401

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BVI Student Perspective

The discovery that the use of SMILES strings allows one to input large chemical structures simply using a computer keyboard was a huge step forward on my road to becoming an independent computational chemist. Learning to use SMILES strings was relatively straightforward. I can input a SMILES structure, paste it into a chemical drawing program, print it on the PIAF paper, and run it through the PIAF to create a tactile printout of the structure with no assistance from sighted colleagues. If it is the correct structure, I cut and paste the SMILES string I generated to Open Babel to create a file that I can submit to our computer cluster for initiating quantum chemical calculations (see below). The drawback to this system is that no screen reader currently works with ChemDraw. Thus, I must memorize a sequence of keystrokes to perform this process successfully. Consequently, it often takes me a few tries to get the correct structure to print. Considering that each attempt takes approximately 15 min, this can be a timeconsuming process. Nonetheless, the use of SMILES strings is effective and will only become more so with advances in screenreader technology.

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Article

PROCESSING COMPUTATIONAL OUTPUT FILES

Process

Quantum chemical packages print their data into plain text files that are often tens- if not hundreds-of-thousands of lines long. Manually looking through such large text-only output files is possible, if cumbersome, but we instead favor using scripts that collect important information (such as geometries, energies, and frequency information) from the output file. For BVI researchers these standard scripts were adapted to produce text files that can be read by screen-reading software. These scripts (written for our lab’s preferred quantum chemical packages, but readily modifiable for use with other programs) are available as Supporting Information accompanying this paper.14,15 The data collected by such scripts can then be used to answer the chemical questions that prompted the computations. In some cases, text-based information (such as that collected by our scripts) is insufficient for answering a question of interest and examination of the optimized 3D geometry produced by the quantum chemistry program is necessary. Sighted chemists generally accomplish this task by using a GUI, that is, by viewing images of the computed structure on a computer screen. These images can be rotated at will and interatomic distances, bond angles, and dihedral angles are easily obtained by, for example, clicking on sequences of atoms. This process is obviously not accessible to a blind student. Consequently, an alternative process that would allow a blind student to obtain similar information was sought. Ultimately, a 3D printing approach (often used in rapid prototyping applications) was identified as the most promising lead.16 Using computer-aided design software (which, as of yet, is not fully accessible to a blind student, necessitating the assistance of a sighted co-worker for some operations), a 3D ball-and-stick model of a computed molecule can be printed (e.g., Figure 1, bottom). Methods of coding additional information (e.g., interatomic distances, Braille atom labels17,18) onto such models are now being examined.

CONVERTING ORGANIC STRUCTURES TO COORDINATES AND GENERATING COMPUTATIONAL INPUT FILES

Process

Conversion of SMILES strings to 3D coordinates is easily achieved using Open Babel,4 an open-source program. This program produces a reasonable guess at 3D coordinates for the molecule in question (to be used as an initial guess for a geometry optimization calculation). The file generated by Open Babel is a plain text file that can be edited (and most importantly read by a screen-reading program). A BVI researcher may freely edit this file in a word-processing program to produce the input file necessary to carry out a quantum chemical calculation (e.g., geometry optimization, frequency calculation, etc.). The quantum chemical calculation can then be run using this file, a process that can be accomplished via text alone in a Unix or Linux environment.13,14

BVI Student Perspective

Looking through an entire output file, whether one is blind or sighted, is time-consuming. The biggest challenge when looking at output files is not knowing what the optimized structure looks like on the screen. For instance, I have done unnecessary calculations and spent longer than necessary on projects when not knowing what an optimized molecule looked like. 3D printing allows me to feel how structures look. So far, printing three-dimensionally without assistance has been difficult both because I cannot independently set up and submit jobs to be printed and because the process of removing the model from the printer is currently largely inaccessible. Our printer produces models that are very brittle when first printed. Thus, removing structures from the printer is a delicate process, especially because our models have many thin bonds connecting atoms. We are examining other styles of 3D printers and accessible software for interfacing with these, in pursuit of versions of each with which I will be able to produce a tactile optimized structure completely independently. Still, even with its current limitations, the 3D printing system we employ allows me to visualize computed molecular structures that were previously inaccessible; this is another huge step forward in increasing my independence as a researcher and the efficiency of my research.

BVI Student Perspective

Using Open Babel and SMILES strings to create 3D atomic coordinates is a process that avoids the use of a graphical user interface (GUI). Creating files describing molecular structures and running calculations independently using these tools allows me to initiate research projects completely independently. The challenge with the current system is that the molecular structures are not always generated in a low energy conformation (or high energy, if that is what I desire for a particular experiment on, for example, a transition-state structure). For instance, two nonbonded oxygens positioned next to each other in space is not a low energy arrangement of atoms. I know this, but I am forced to use whatever geometry Open Babel generates if I do not want to involve sighted assistants. We are currently working to develop improvements in this area (a large project in its own right that will be described in due course) that will allow me to take advantage of my chemical intuition in creating appropriate input structures. 1402

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describe all figures in detail to an assistant when putting together a presentation. I then meticulously go through each and every slide with my assistant who describes everything present on the slide. I then think about the information and write a brief description of the slide on a sheet of Braille paper using a Perkins Brailler. This allows me to have a sheet of paper in front of me to remind me what each slide depicts. Though presentations using slideshows are useful for my audience, having figures and images displayed on slides puts me at a disadvantage, as the audience can rely on visuals to obtain information quickly and easily while I cannot. I prefer a situation where my audience and I are on the same page, so I have given many chemistry lectures using minimal to no visuals. Everything discussed is spoken aloud and the audience must listen carefully, as I do when I watch a presentation, to obtain all information. Describing chemical structures is not difficult provided the structures are not extremely complex. Feedback I have received on this type of lecture has been positive. Through questions asked and personal discussions with audience members, we find that this type of presentation challenges the audience and people often leave feeling that they acquired more information than they would have had the lecture been presented visually. As part of some talks, I bring three-dimensional models to show to the audience. These models are always received positively and many people have conveyed to me that holding a chemical model in hand helps them visualize the molecular structure without seeing it with their eyes. Thus, our 3D printing approach is useful not only for a BVI individual performing research, but also for an audience listening to her or him speak about her or his research results.

Figure 1. Typical workflow: from idea to quantum chemical calculation to printed 3D models of resulting structures. Despite resembling a model constructed with ball-and-stick pieces, this printed model is a single piece with bond lengths, bond angles, and dihedral angles determined using quantum chemical software.

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ORGANIZING AND PRESENTING DATA

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Process

There are many ways to organize one’s data, and many of these are accessible to BVI researchers. For example, various word processing and spreadsheet-generating programs can interface with screen-reading software. Regarding the presentation of research results, sighted students learn to present their research by studying visual and aural templates, reading research papers, attending lectures, and participating in poster sessions. BVI students do all of that, but without the visual component. While paper writing using word-processing software is accessible as described above, aspects of our approaches to preparing and presenting posters and lectures that are particularly relevant for BVI researchers are described here. To facilitate the construction of a poster describing research results, the typical apprentice approach is employed: studying a template, in this case manually, with a particular focus on the spatial arrangement of information. Making this process fully accessible is still ongoing, so sighted assistants are currently relied upon to facilitate the process. Nonetheless, the blind student selects the content, writes the text, identifies the types of images to be presented, and describes the layout desired. The same approach is used in constructing slides for lectures. Assistants provide the interface with graphic design software to create the actual poster or lecture slides. Because the blind student has a detailed knowledge of the content and the layout, she or he can present the work without assistants present.

SUMMARY

Instructors

By integrating existing technology used in other contexts molecular models, methods for tactile image generation, computational chemistry software, and 3D printing technologya blind student is able to carry out applied computational chemistry research projects with minimal sighted assistance. This approach is not limited to the particular software and equipment described herein; alternative computational chemistry software suites and 3D printers could be integrated into such a research program, although the ease of doing so will depend on the inherent accessibility of their user interfaces. BVI Student

Chemistry is, by nature, a visual subject and making it accessible to blind students certainly poses challenges. I learned early on that though I loved chemistry, working in an experimental setting was out of the question as I would require full-time assistance. Thus, not sure if science would fail me, I also received a degree in history and I was ready to submit graduate applications to various history departments; that is, until I discovered computational chemistry research. Without the accommodations described above, computational chemistry was no more accessible to me than experimental chemistry; to complete a project, I had to work with an assistant from start to finish, just like I would have worked with an experimental assistant full time in the wet chemistry lab. Until we made the theoretical lab accessible, I wondered how doing computational chemistry research as a blind person was any different than doing experimental research. Though there are still aspects of studying organic chemistry that are inaccessible, I have come to

BVI Student Perspective

Preparing lectures on my research is time-consuming but completely doable. When I use presentation software, I must know absolutely everything that is presented on my slides. Although creating lecture slides is still largely inaccessible due to the nature of available software, I compose all text and 1403

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Sousa, J.; Bonifacio, V. D. B.; Mata, P.; Lobo, A. M. J. Chem. Educ. 2011, 88, 361−362. (3) (a) Weininger, D.; Weininger, A.; Weininger, J. L. J. Chem. Inf. Mod. 1989, 29, 97 and references therein. (b) A recent application: Sutch, B. T.; Romero, R. M.; Neamati, N.; Haworth, I. S. J. Chem. Educ. 2012, 89, 45−51. (c) See also the Web resources mentioned in ref 2d. (4) (a) Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J. K.; Willighagen, E. J. Chem. Inf. Model. 2006, 46, 991−998. (b) Open Babel: The Open Source Chemistry Toolbox Home Page. http://openbabel.org/wiki/Main_ Page (accessed Aug 2012) (5) Supalo, C. J. Chem. Educ. 2005, 82, 1513. (6) Tactile Graphics Web site, http://tactilegraphics.org (accessed Aug 2012). (7) (a) Hoffmann, R.; Laszlo, P. Angew. Chem., Int. Ed. 1991, 30, 1− 16. (b) Mayo, P. M. Ph.D. Dissertation, Assessment of the Impact Chemistry Text and Figures Have on Visually Impaired Students’ Learning, Purdue University, 2004. (8) VoiceOver. http://www.apple.com/accessibility/voiceover/ (accessed Aug 2012). (9) JAWS. http://www.freedomscientific.com/products/fs/jawsproduct-page.asp (accessed Aug 2012). (10) ChemDraw. http://www.cambridgesoft.com/software/ chemdraw/ (accessed Aug 2012). (11) This process is still in development and can cause some problems, since the screen reader has to be turned off. For instance, the computer may be focused on the wrong program or the molecule may not cut and paste properly into the program without the blind student knowing, which results in printing a blank page. We are working to resolve this issue and will provide our solutions in due course. (12) PIAF Tactile. http://www.piaf-tactile.com/ (accessed Aug 2012). (13) (a) Frisch, M. J. et al. Gaussian03, revision D.01; Gaussian, Inc.: Pittsburgh, PA, 2003. See also: http://www.gaussian.com/ (accessed Aug 2012) (b) No cost access to computational chemistry software, including Gaussian, is available, for example, through education or startup grants from XSEDE (Extreme Science and Engineering Discovery Environment): https://portal.xsede.org/web/guest/ allocations (accessed Aug 2012). (14) Representative scripts for processing output (from both Gaussian and NWChem software) are included as Supporting Information. (15) Unfortunately, the screen reader JAWS does not read “standard output”. Standard output in Unix is text that is printed to the screen after a command is run but before the command prompt is returned. For example, when you type “ls”, the computer lists your files on the screen and then returns the command prompt. Workarounds are described in the Supporting Information. (16) (a) Johnson, R. D. Nat. Chem. 2012, 4, 338−339. (b) Jones, N. Nature 2012, 487, 22−23. (17) Braille Code for Chemical Notation Braille Authority of North America, American Print. House for the Blind: Louisville, KY, 1997 (18) Nemeth, A.The Nemeth Braille Code for Mathematics and Science Notation, 1972 Revision. Braille Authority of North America, American Print. House for the Blind: Louisville, KY, 1972.

realize that when thinking about chemistry, I use the same mental processes as I use for my survival as a blind traveler. When I think about the map of a campus or town, the layout of desks in a classroom, or the position of carbons in a benzene molecule, I use the same set of skills. Working in the theoretical lab has encouraged me to apply these skills, enhance them, and develop new approaches based on them. I discovered that the reason chemistry has been such a passion for me is because I have always used that part of my brain. Working in the laboratory has been challenging, exciting, and ultimately extremely rewarding. As a blind person, it is necessary to have a strong spatial sense so that once I understand the structure of a particular molecule I can make mental transformations, adjustments, and alterations to arrive at a new structure. The techniques mentioned herein provide a very useful way to go from a mental image of molecular connectivity to an optimized molecular geometry or take a figure from a textbook or research paper, get it into my mind, and then use it in the theoretical chemistry laboratory. Making the computational chemistry lab accessible to the blind has opened the door to the world of independent chemical research to me and other BVI individuals.

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ASSOCIATED CONTENT

S Supporting Information *

Standard scripts adapted to produce text files that can be read by screen-reading software. This material is available via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Present Addresses †

Department of Chemistry, Missouri State University, 901 S National Ave Springfield, MO 65897 ‡ Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 § Department of Chemistry & Biochemistry, Albright College, Reading, PA 19612 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We gratefully acknowledge the National Science Foundation and the UC Davis Department of Chemistry and Mathematics & Physical Sciences Dean’s Office for support of this research. We are also particularly grateful to Jon Huntoon at The Scripps Research Institute for assistance with converting atomic coordinates into files that can be used by a 3D printer.

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REFERENCES

(1) Clauss, A. J. Chem. Educ. 2009, 86, 591. (2) (a) Skawinski, W. J.; Busanic, T. J.; Ofsievich, A. D.; Venanzi, T. J.; Luzhkov, V. B.; Venanzi, C. A. J. Mol. Graphics 1995, 13, 126−135. (b) Skawinski, W. J.; Busanic, T. J.; Ofsievich, A. D.; Luzhkov, V. B.; Venanzi, T. J.; Venanzi, C. A. Inf. Technol. Disabil. 1994, 1 (No. 4), No. Article 6. The Free Library Hope Page. Chemistry by touch: blind scientist fashions new models of molecules. (c) http://www. thefreelibrary.com/ Chemistry+by+touch%3A+blind+scientist+fashions+new+models+of+ molecules.-a016723790 (accessed Aug 2012). (d) Pereira, F.; Aires-de1404

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