What is MoleCalc?

MoleCalc is a Python-based web app and chemistry teaching tool that allows chemists to build small molecules and estimate key molecular properties using state-of-the-art quantum chemistry software. Currently, MoleCalc can provide, in a matter of minutes or seconds, a decent sense of the physical and chemical properties of a chosen molecule, such as

• energy-minimized molecular structure
• electronic structure and molecular orbitals
• thermochemical properties of the molecular gas form
• vibrational modes and their frequencies

Why do we need MoleCalc?

MoleCalc, which is being developed by the Yarger Research Group at Arizona State University for chemistry "cloud lab" courses in the School of Molecular Sciences at Arizona State University, is an evolution of the original MolCalc web app developed by the Jensen Group at the University of Copenhagen using the Pyramid Python web framework. MoleCalc has been ported to the Python (micro) web framework Flask, a very popular web framework that is remarkably easy to use and well-suited for a rapidly evolving web applications. In particular, rebuilding MoleCalc in Flask makes it even simpler for new developers to contribute to MoleCalc's ongoing development, including the incorporation of new features and integration with other Flask-based cloud apps used for online chemistry lab courses at ASU.

The original MolCalc web app was designed for teaching as opposed to research and, therefore, places an emphasis on running computations quickly. Indeed, so long as qualitative accuracy is sufficient, the speed of calculations is of primary importance since humans learn most effectively when real-time feedback is available. MoleCalc retains the spirit of the original app and is currently being stress-tested in the context of the upper-division CHM 343 lab course at ASU starting the Fall 2022 semester. However, the ASU MoleCalc project has broader and longer-term ambitions driven by the central goal of improving student engagement with fundamental concepts in chemistry and physics.

Emphasis on physical intuition

The broader ASU MoleCalc effort is focused on leveraging computational methods to deeply integrate physical intuition with real or simulated experimental data using clickable explanations, dynamic visualizations, and interactive data. A guiding focus of our development efforts is to make meaning transparent by leveraging a web interface that will provide succinct explanations in a visual context, thereby allowing the user to concentrate on concepts rather than deciphering complicated programs and arcane terminologies.

Cloud-based physics and chemistry

Like the original MolCalc project, MoleCalc will continue being developed as an open source interactive chemistry teaching tool. MoleCalc serves as the starting point for the development of a more comprehensive visual-centric interface for cloud-based physics and chemistry lab courses. The idea is to have students develop physical and chemical intuition about how molecular structure affects molecular properties, without performing the underlying calculations by hand (which would be near impossible for all but the simplest chemical systems). In particular, we envision developing a tool that establishes concrete conceptual pathways from representative experimental plots and data to the mechanistic physical/chemical picture that directly underlies that data.

What technologies does MoleCalc use?

MoleCalc uses standard HTML and CSS3, along with the technologies and software packages described below.

Front-end components

• JavaScript (jQuery)
• JSmol

Back-end components

• Python (Pyramid)
• SQLAlchemy
• JavaScript (jQuery)
• GAMESS
• Orca (coming soon!)

How does MoleCalc perform electronic structure calculations?

Great question! Currently, MoleCalc uses The General Atomic and Molecular Electronic Structure System (GAMESS), which is maintained by the Gordon research group at Iowa State University. We are also in the process of incorporating Orca as a user-selectable option for quantum chemistry calculation.

Development

Installation

Check out github.com/mscloudlab/molcalc for a developer's installation guide.

I found a bug or I have a feature request

Have suggestions about how MoleCalc might be improved? Awesome! Raise issues at github.com/mscloudlab/molcalc /issues.

How do I cite MoleCalc?

Please cite the original MolCalc paper by Jensen and Kromann, who have generously developed MolCalc as an open-source project under the MIT license for the benefit of the broader scientific community.

J. H. Jensen and J. C. Kromann. The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties, J. Chem. Educ., 2013, 90 (8), pp 1093–1095. DOI: 10.1021/ed400164n