Teaching Programming across the Chemistry Curriculum

Incorporating necessary skills for research and career success

Programming and computational science is an essential part of chemistry, yet some curricula still do not prioritize its inclusion. This work contains a collection of strategies, activities, and resources available to incorporate programming into all levels of the chemistry curriculum, with a focus on how the programming learning objectives are integrated with chemistry learning objectives. Chapters highlight best practices in software development, emphasize their importance to the future of computational molecular sciences, and describe challenges instructors might face in implementing programming in their own curriculum.

Ashley Ringer McDonald is an Associate Professor of Chemistry at California Polytechnic State University in San Luis Obispo. She received her bachelor's degree from Mississippi College and her Ph.D. from the Georgia Institute of Technology. Her research focuses on using multiscale modeling to study
molecular interactions in complex chemical contexts. She has a significant interest in discipline-specific programming education and helping all students develop the computational skills they need to succeed in the twenty-first century STEM workforce. McDonald is a sought-after speaker and workshop
leader in this area.

At Cal Poly, McDonald is involved in the Data Science Strategic Research Initiative where she works on outreach programming to teach the Cal Poly community about data science and programming. She is an Associate of the Molecular Sciences Software Institute (MolSSI) and a member of the MERCURY
Consortium. She also leads Psi4Education, the education and outreach program of the quantum chemistry software package Psi4, and serves as the Undergraduate Programming Chair for the Computers in Chemistry (COMP) division of the American Chemical Society.

Jessica Nash is a Software Scientist and the Education Lead at TheMolecular Sciences Software Institute (MolSSI) in Blacksburg, Virginia. She received her bachelor's degree in Chemistry from UNC Chapel Hill and her Ph.D. in Materials Science and Engineering from North Carolina State University. Her
research background is in soft materials and molecular dynamics simulations. As a Software Scientist at MolSSI, she works on project related to productivity and interoperability.

As the MolSSI Education Lead, Nash uses scientific domain knowledge and software design principles to build programming tutorials and resources for researchers in the computational molecular sciences. She has also designed and taught courses for industry and academic institutions including UC
Berkeley's Master of Molecular Science and Software Engineering program. Under her leadership, MolSSI's Education program has grown to be a valuable and well-recognized resource within the computational molecular sciences community.

Preface

Chapter 1: Teaching Programming across the Chemistry Curriculum: A Revolution or a Revival?, Ashley Ringer McDonald
Chapter 2: How Faculty with Minimal Programming Experience Implemented Jupyter Notebooks in Physical and General Chemistry Courses, Grace Yin Stokes
Chapter 3: Hiding the Vegetables: Teaching Programming to Chemists as a Professional Skill, Christopher E. Berndsen and Shveta Gupta
Chapter 4: Learning Programming through Chemistry in a First-Year Scientific Computing Course, Arun K. Sharma, Caecilia Thuermer, and Victor Ruan
Chapter 5: Introducing Students to Scientific Computing in the Laboratory through Python and Jupyter Notebooks, Charles J. Weiss and Andrew Klose
Chapter 6: The Compute-to-Learn Pedagogy and Its Implementation in the Chemistry Curriculum, Heidi P. Hendrickson, Kristina M. Lenn, Frank X. Vazquez, Kyle L. Williams, Blair A. Winograd, Ellen A. Mulvihill, and Eitan Geva
Chapter 7: Integrating Programming to Reinforce Quantum Mechanical Principles in Physical Chemistry, Danfei Hu, Janet N. Ahn, Alyssa Lakatos, Jose Bello, Jonathan McTague, and Jonathan J. Foley
Chapter 8: PSI4EDUCATION: Free and Open-Source Programing Activities for Chemical Education with Free and Open-Source Software, D. Brandon Magers, Victor H. Chávez, Benjamin G. Peyton, Dominic A. Sirianni, Ryan C. Fortenberry, and Ashley Ringer McDonald
Chapter 9: Integrating Python into an Undergraduate Mathematics for Chemists Course, Geoffrey R. Hutchison
Chapter 10: Teaching Computer-Aided Drug Design Using TeachOpenCADD, Dominique Sydow, Jaime Rodríguez-Guerra, and Andrea Volkamer
Chapter 11: Coding, Software Engineering, and Molecular Science — Teaching a Multidisciplinary Course to Chemistry Graduate Students, Jessica A. Nash and Benjamin P. Pritchard

Editors' Biographies
Author Index
Subject Index