The courses Organic Chemistry I and II (Biol./Pharm. Sci./HST) are two first-year courses of the study programs Biology, Health Sciences and Technology, and Pharmaceutical Sciences (500 – 600 students). While OC I focuses on the structure of molecules, OC II introduces the basic types of organic reactions. The reactivity of molecules should be understood from their structure.
The courses consist of a lecture, an exercise section, and a study center. In addition, the students have a Moodle course with a broad range of online exercises at their disposal.
The present project relates to the online exercises. It is about a software tool (MOSFECCS) developed to allow the drawing of molecular structures and their encoding as alphanumeric strings (so-called SMILES), which can be entered as answers in text-based Moodle quizzes and scored by the system.
MOSFECCS = MOlecular Structural Formula Editor Calculating Canonical SMILES
SMILES = Simplified Molecular-Input Line-Entry System
Implementation of the Course During the Time of Distance Learning
The e-learning environment Moodle used at ETH is largely text-based, which is a serious shortcoming in chemistry, where the graphical generation and electronic processing of molecular structures are essential. Also, the learning effect for the students is considerably larger when they draw molecules from scratch rather than just make multiple-choice selections.
Out of this need, we have developed the structural formula editor MOSFECCS. Compared to existing SMILES generators, it has a number of technical and didactic advantages: the interconversion “structural formula ⇄ SMILES code” is bi-unique, the generated code is independent of the order in which atoms and bonds are drawn, the handling of so-called resonance structures has been greatly improved, there is no auto-correction of chemical errors, structures have to be drawn in full detail (there are no predefined building blocks), and finally, the source code is published.
The start of the project pre-dates the pandemic, but the increasing importance of online exercises in distance learning forced its development and optimization, so that the source code was ready for release in May 2021: https://github.com/mosfeccs-editor/MOSFECCS. The capabilities of the initial mere structure encoder MOSFECCS were extended to allow not only atoms and bonds but also lone electron pairs (→ complete Lewis structures) and electron displacement arrows (→ reaction mechanisms), and even entire reaction schemes to be drawn and converted to SMILES, ready to be entered as answers in Moodle quizzes.
If a molecular structure is requested as the answer in an online quiz, the students draw it using MOSFECCS and generate the corresponding SMILES code, which they copy into the answer field of the quiz. Upon submission, the code is matched against (a) stored (partially) correct answer(s). Depending on the concept of the quiz, intermediate feedbacks can be returned in case of partially correct answers and a new attempt will be allowed. After the final submission, the answer is graded as (partially) correct or wrong and scored. The final feedback includes a sample solution.
In the OC I and II courses, it became apparent that elaborate sample solutions are an important motivator for students to persevere with online exercises. If a solution is not easily comprehensible, students may give up and refrain from taking further quizzes. Therefore, in addition to optimizing MOSFECCS and expanding the range of exercises, the pandemic period was used to revise existing sample solutions and to unfold solution paths in detail.
Any remaining questions can be asked in a Moodle forum. Ideally, they will be answered by other students, or a discussion will ensue. If this is not the case, the lecturer will provide an answer. The forum also allows the reporting of errors or technical problems. Not surprisingly, prompt responses to any messages have a motivating effect on students.
Online exercises and self-assessments in OC I and II are optional and the grades issued by Moodle only serve as a feedback, i.e., they do not count as semester performance (lecturer’s decision). Participation in self-assessments is recommended at the beginning, in the middle, and at the end of the semester. The quizzes are organized according to the chapters of the course and the level of difficulty, but the students are free to decide which ones they take and when they do it (usually, there is an increased Moodle course activity during the exam preparation period).
In conclusion, the development of MOSFECCS has rendered possible a comprehensive treatment of the subject matter of Organic Chemistry I and II in Moodle online exercises through its capability to generate alphanumerically encoded molecular structures which can be entered into the largely text-based e-learning environment. The importance of MOSFECCS in the distance learning of chemistry is reflected, among other things, by a ca. 45% increase in students’ Moodle activity during the spring semester 2020. It was also MOSFECCS that allowed the switchover from paper to online exams in the above-mentioned 1st-year Organic Chemistry course with >500 participants.
Overall Concept of the Course before, during, and after the Pandemic
Before the pandemic:
The lecture courses Organic Chemistry I and II with lecture hall–to lecture hall video streaming impart the basic concepts of organic chemistry. The main media used are a beamer (slide presentation) and a document camera (in-class example problems, manipulation of molecular models). At home, the students deepen their knowledge using lecture notes, the lecture presentation, and textbooks.
This should enable them to solve the weekly problem set, which is discussed in detail during the exercise lesson (small groups of ca. 25 students per teaching assistant). In OC I, the lecturer regularly visits the exercise groups to give all the students (500–600 total) the opportunity to talk to him directly. In OC II, a study center is offered in addition to the exercise lesson.
Project-specific: Exercises being an extremely important part of this course, the students are provided with a broad range of extra online quizzes, self-assessments, and old online exams. This way, they become familiar from day one with the system (Moodle) and tools (MOSFECCS) used in the 1st-year online exam.
During the pandemic:
Because the OC I and II lectures are streamed from lecture hall to lecture hall by default, relatively few adjustments were necessary during the pandemic (internet livestream plus recording by the ETH Multimedia Service). Students were able to ask live questions in the eduApp chat, which the lecturer answered orally at the end of each section. Exercise lessons were held via Zoom.
Project-specific: The structural formula editor MOSFECCS, essential for the input of molecular structures in online exercises, was optimized and further developed, so that its source code could be published in May 2021. In addition, the range of online exercises was expanded (≥ 1000 individual questions). Together with the elaboration of detailed sample solutions, this led to a significant increase in usage (plus 30-45% in the 1st year of the pandemic).
After the pandemic:
Project-specific: MOSFECCS will continue to be further developed and intensively used in online exercises and exams. After the release of its source code, this is possible worldwide.
- Organic Chemistry I
- Fundamentals of Organic Chemistry: molecular structure. Bonding and functional groups; nomenclature; resonance and aromaticity; stereochemistry; conformation; bond strength; organic acids and bases; basic reaction thermodynamics and kinetcs; reactive intermediates: carbanions, carbenium ions and radicals.
- Understanding the basic concepts and definitions of organic chemistry. Knowledge of the functional groups and classes of compounds that are important in biological systems. Foundations for the understanding of the relationship between structure and reactivity.
Organic molecules: Isolation, separation and characterization of organic compounds. Classical structure theory: constitution, covalent bonding, bonding geometry, functional groups, classes of compounds, nomenclature. Electron delocalization: resonance, aromaticity. Stereochemistry: chirality, configuration, topicity. Conformational analysis. Bond energies, non-covalent interactions. Organic acids and bases. Basic reaction thermodynamics and kinetcs; reactive intermediates: carbanions, carbenium ions and radicals.
- Lecture (Excercice)
- Teaching Power:
- Session exam
- Organic Chemistry II
- The relationship between structure and reactivity of organic molecules is elaborated by studying the mechanisms of fundamental types of organic reactions. A basic synthesis repertoire is acquired.
- Understanding the mechanisms of the fundamental types of organic reactions. Particular emphasis is placed on the relationship between structure and reactivity. A basic repertoire for the synthesis of small organic molecules is acquired. Weekly problem solving lessons provide a deeper understanding of the concepts presented during the lecture.
- Session exam