Computational IR Spectroscopy of Plastic Monomers

Computational chemistry lesson. Students run DFT geometry-optimization and harmonic vibrational-frequency calculations in Turbomole/TmoleX on an HPC cluster to compute the IR spectra of two candidate monomer structures (Structure 1 and Structure 2), then identify which monomer an unknown plastic is made from by comparing the computed spectra with the experimental IR spectrum of the unknown (which shows a band near 1700 cm⁻¹). The cyberinfrastructure skills are remote HPC access via Open OnDemand and setting up/running a quantum-chemical calculation through a GUI. There is no wet-lab component in this lesson.

This README is the technical setup document: lesson information, instructor setup, software installation/licensing, and implementation notes. The student-facing lesson is student.md; the answer key, worked solution, and in-context teaching tips are in instructor.md.

Lesson Information

The Lesson Information below should be kept in sync with the student lesson.

Lesson Learning Outcomes

At the end of this lesson, students will be able to:

1. Build a molecular structure with the 2D editor and convert it to 3D in TmoleX.
2. Run a DFT geometry optimization and a harmonic vibrational-frequency calculation.
3. Compute an IR spectrum and read off vibrational frequencies and IR intensities.
4. Animate and characterize the vibrational normal modes behind individual IR bands.
5. Compare a computed IR spectrum with reference data to identify functional groups.

Cyberinfrastructure Prerequisites

• Ability to log in to an HPC cluster through an Open OnDemand web portal.
• Comfort launching a remote desktop session and using a graphical application within it.
• No programming is required; the lesson is a guided GUI workflow.

Content Prerequisites

• IR spectroscopy and the idea that functional groups absorb at characteristic wavenumbers (introductory organic/physical chemistry).
• Basic familiarity with molecular structure, bonding, and functional groups (e.g. esters, aromatics).
• DFT and harmonic vibrational frequencies are used as tools and explained conceptually; no prior quantum-chemistry coursework is assumed.

Resources

• Introduction to DFT (Grotjahn Lab)

Lesson Version & Intended Modality

A single student version is provided: student.md, written as a Markdown lab guide with GitHub-style alerts and screenshots. It is designed to be used in lab with an instructor present (guided inquiry); it can also support asynchronous review. There is no executable code; "running" the lesson means viewing/sharing the Markdown.

Instructor Setup

The computational part assumes a Turbomole/TmoleX installation reachable through an HPC Open OnDemand portal. The student lesson is written against SCU's WAVE cluster but is portable; no input files are required.

1. Accounts & network. Ensure each student has a cluster account and portal access, and knows the network requirement (at SCU: eduroam).
2. Resource profile. Identify the Open OnDemand interactive "Compute GUI" profile that exposes the TmoleX launcher, and tell students to select it (a different profile may hide the launcher). The default 2-CPU profile is sufficient because the jobs run locally and the monomers are small.
3. TmoleX availability. Confirm TmoleX starts from Applications → Other → TMOLEX. Identify the fallback launch path that students can type in the terminal /YOUR/INSTALLATION/PATH/TMOLEX/TmoleX/TmoleX25. Update this for your site.
4. No input files. Students build both monomers themselves with the 2D editor, so nothing needs to be distributed or staged.
5. Local execution. These jobs are small and run locally inside the GUI session (no queue/remote configuration needed), unlike the larger TDDFT lesson.

Obtaining a free educational Turbomole/TmoleX license

Turbomole offers a free educational license (TURBOMOLE 8.0 + the integrated TmoleX GUI) for teaching, coursework, and training:

1. Open the product page: https://store.turbomole.org/product/turbomole-8-0-educational/.
2. Download the educational license agreement (linked on that page), sign it electronically, and email the signed agreement to order@turbomole.org together with proof of student/educational status (enrollment certificate or student ID).
3. The license is free of charge and covers TURBOMOLE 8.0 for Linux, Windows, and macOS with the integrated TmoleX GUI, plus the standalone Linux build, with unlimited CPU/GPU cores.

Important

The educational license may not be used for scientific publishing (no publications, preprints, or conference proceedings). For published research, obtain a regular Turbomole license.

Installing Turbomole (command-line build)

Full instructions: https://manual.turbomole.org/v8.0/installation-of-turbomole/install-turbomole-command-line-version/. Summary for a shared multi-user install on a cluster or lab server:

1. Do not install or run Turbomole as root, because file ownership and permissions will be wrong. Unpack once as a normal user (ideally one whose group matches all course users) onto shared/network storage available on every machine:

   gunzip turbomole_80.tar.gz
   tar -xvf turbomole_80.tar
   # or, for the self-extracting installer:  ./turbolinux80.bin

2. Per-user environment. Point TURBODIR at the unpacked directory and source the setup file (add these to each user's .bashrc/.profile):

   export TURBODIR=/shared/software/TURBOMOLE
   source $TURBODIR/Config_turbo_env          # use Config_turbo_env.tcsh for csh/tcsh

3. Verify the install:

   cd $TURBODIR/TURBOTEST
   TTEST

Student access options

Both options work for this lesson because the jobs are small and run locally inside the TmoleX session.

• Option A: Local TmoleX install on university computers (simplest here). Install the educational TmoleX package (Linux/Windows/macOS) on managed lab/university machines from the license download, and have students run TmoleX locally. The geometry optimization and frequency jobs in this lesson are small enough to run on a typical desktop/laptop.
• Option B: Browser access via Open OnDemand. Install Turbomole/TmoleX on an HPC cluster that runs Open OnDemand and expose an interactive "Compute GUI" desktop app. Students open the portal in a web browser, launch the remote desktop, and run TmoleX there, with no local installation. This is the workflow the lesson screenshots show, and it keeps both modules on one platform. Ensure the chosen resource profile exposes the TmoleX launcher (see step 2 above).

Calculation settings

• Build: Draw 2D → Get SMILES and close → SMILES to 3D.
• Job 1: Geometry Optimization, Ground state, default method/basis (DFT, BP86, def2-SV(P)), accepting the defaults by clicking Continue through the advanced menus.
• Job 2: Spectra & Excited States → IR & vibrational frequencies, from the optimized geometry.
• Neutral molecules (no charge change), gas phase (no solvation).
• Execution: Run (local).
• Spectrum display: standard deviation 40, 1000 sampling points, x-axis 600–4000 cm⁻¹.

Answer Key & Worked Solution

Important

The answer key, the formative-question answers, the worked solution (computed spectra, frequencies, and mode interpretation), and the in-context teaching tips now live in instructor.md, a single self-contained instructor document that mirrors the student lesson. Keep instructor.md out of any student-facing branch. This README holds the technical setup only.

Implementation Notes (for adopting instructors)

• Lesson timing: about 1.5 to 2 hours of computational work during the lab session.
• Group size / facilitator ratio: piloted with 1 instructor and 1 TA for 22 students in a single lab session.