In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX–BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX–BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted—from published articles, via printed results of computational chemistry experiments, to 3D models—is now available to BVI scientists too. The possibilities offered by AsteriX–BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Price excludes VAT (USA)
Tax calculation will be finalised during checkout.
Paper presented at the Friday Discourse of the Royal Institution (7 Apr 1865) On the Combining Power of Atoms. In: Proceedings of the Royal Institution (1865), 4, No. 42:416
JAWS for Windows Screen Reading Software. http://www.freedomscientific.com/jaws-hq.asp. Accessed 30 Apr 2014
Humanware, developers of PIAF. http://www.humanware.com/. Accessed 23 Apr 2014
Wedler HB, Cohen SR, Davis RL, Harrison JG, Siebert MR, Willenbring D, Hamann CS, Shaw JT, Tantillo DJ (2012) Computational chemistry for the blind and visually impaired. J Chem Educ 89:1400–1404
Wedler HB, Boyes L, Davis RL, Flynn D, Franz AK, Hamann CS, Harrison JG, Lodewyk MW, Milinkevich KR, Shaw JT, Tantillo DJ, Wang SC (2014) Nobody can see atoms: science camps highlighting approaches for making chemistry accessible to blind and visually-impaired students. J Chem Educ 91:188–194
Skawinski WJ, Busanic TJ, Ofsievich AD, Venanzi TJ, Luzhkov VB, Venanzi CA (1995) The application of stereolithography to the fabrication of accurate molecular models. J Mol Gr 13:126–135
Skawinski WJ, Busanic TJ, Ofsievich AD, Luzhkov VB, Venanzi TJ, Venanzi CA (1994) The use of laser stereolithography to produce three-dimensional tactile molecular models for blind and visually-impaired scientists and students. Inf Technol Disabil 1 (No. 4 Article 6)
©Chemistry by touch: blind scientist fashions new models of molecules. http://www.thefreelibrary.com/Chemistry+by+touch%3A+blind+scientist+fashions+new+models+of+molecules.-a016723790. Accessed 30 Apr 2014
Lounnas V, Vriend G (2012) AsteriX: a web server to automatically extract ligand coordinates from figures in PDF articles. J Chem Inf Model 52 (2):568–576. doi:10.1021/ci2004303. http://www.ncbi.nlm.nih.gov/pubmed?term=Lounnas%20AsteriX
Schaftenaar G, Noordik JH (2000) Molden: a pre- and post-processing program for molecular and electronic structures. J Comput Aided Mol Design 14:123–134
ChemAxon Home Page. http://www.chemaxon.com/. Accessed 30 Apr 2014
Vigant F, Lee J, Hollmann A, Tanner LB, Akyol Ataman Z, Yun T, Shui G, Aguilar HC, Zhang D, Meriwether D, Roman-Sosa G, Robinson LR, Juelich TL, Buczkowski H, Chou S, Castanho M, Wolf MC, Smith JK, Banyard A, Kielian M, Reddy S, Wenk MR, Selke M, Santos NC, Freiberg AN, Jung ME, Lee B (2013) A mechanistic paradigm for broad-spectrum antivirals that target virus-cell fusion. PLoS Pathog 9(4):e1003297. doi:10.1371/journal.ppat.1003297
Cignoni P, Corsini M, Ranzuglia G (2008) Meshlab: an open-source 3d mesh processing system. Ercim news 73:45–46. http://vcg.isti.cnr.it/Publications/2008/CCR08/Cignoni%20Corsini%20Ranzuglia%20-%20MeshLab%20-%20Ercim%202008.pdf
Antonopoulos, K, Valet N, Spiratos D, Siragakis, G (2006) Olive oil and pomace olive oil processing Grasas Y Aceites 57:56–67
Stiti N, Triki S, Hartmann M (2007) Formation of triterpenoids throughout Olea europaea fruit ontogeny. Lipids 42(1):55–67
Frankel E (2010) Chemistry of extra virgin olive oil: adulteration, oxidative stability, and antioxidants. J Agric Food Chem 58(10):5991–6006
Vetter W, Schröder M, Lehnert K (2012) Differentiation of refined and virgin edible oils by means of the trans- and cis-phytol isomer distribution. J Agric Food Chem 60:6103–6107. doi:10.1021/jf301373k
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09 Revision B.02, Gaussian, Inc., Wallingford
Pereira F, Aires-de-Sousa J, Bonifácio VDB, Mata P, Lobo AM (2011) MOLinsight: a web portal for the processing of molecular structures by blind students. J Chem Educ 88:361–362. http://pubs.acs.org/doi/abs/10.1021/ed100723v
Fartaria RPS, Pereira F, Bonifácio VBD, Mata P, Aires-de-Sousa J, Lobo AM (2013) NavMol 2.0: a molecular structure navigator/editor for blind and visually impaired users. Eur J Org Chem 1415–1419. http://www.academia.edu/4413858/Navmol_2.0_A_molecular_structure_navigator_editor_for_blind_and_visually_impaired_users/
We gratefully acknowledge the US National Science Foundation (a graduate research fellowship to HBW, CHE-0957416 to DJT). VL travel expenses and accommodation during his stay at CMBI was supported by the WHAT IF foundation.
About this article
Cite this article
Lounnas, V., Wedler, H.B., Newman, T. et al. Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol. J Comput Aided Mol Des 28, 1057–1067 (2014). https://doi.org/10.1007/s10822-014-9782-7