Flexible, online teaching and assessment of organic chemistry using MarvinSketch and SMILES

O’Sullivan, Timothy P. and Hargaden, Gráinne C. (2013) Flexible, online teaching and assessment of organic chemistry using MarvinSketch and SMILES. In: 5th Eurovariety in Chemistry Education, University of Limerick, 3rd – 5th July 2013. “Smarter Teaching-Better Learning, Limerick, Ireland..


Learning by problem-solving is a key feature in the teaching of organic chemistry. In many institutions, this has traditionally taken the form of tutorials where students submit written answers which are assessed by a tutor with feedback given at a later date. However, current resource constraints have serious implications for this approach which is additionally aggravated by increasing student numbers. The use of online technologies to reinforce lecture material and to assess students is, therefore, increasingly attractive. A key requirement of any such system is the ability to draw and assess complex molecular structures. While commercial packages are available, they have several significant drawbacks. These include high access costs for the institution or student, limited scope of questions and an overall lack of flexibility. With assistance from the National Academy for Integration of Research, Teaching and Learning (NAIRTL) we have developed and tested a system which can be readily implemented, where a bank of questions can be drawn upon by the instructor who would have total control over content, breadth, emphasis and difficulty of the individual assignments. Our system can be integrated with commonly used web-based learning (WBL) technology systems such as Blackboard or Moodle. These platforms are not “chemically aware” and therefore do not natively support the drawing or checking of chemical structures. However, by exploiting the SMILES (simplified molecular input line entry specification) algorithm, we can convert chemical structures unambiguously to ASCII strings which are then machine readable. Therefore, a combination of a WBL system used in conjunction with a JAVA-based drawing application (MarvinSketch) enables students to draw structures and generate the corresponding SMILES string which can be submitted for machine reading. Such a system requires no special software, other than a standard web browser allowing students to work at their own pace and even from home. We describe how the above system is implemented and outline specific examples of the types of assessment employed. Additionally, we assess the impact of the system on students and evaluate the student feedback collated over the course of a year.

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