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INSTRUCTIONAL MATERIALS

 

 

Teaching with Q-Chem:

Q-Chem can help you to enhance students' learning experience. Calculations and visualizations can be used to illustrate basic and advanced concepts in quantum mechanics, molecular structure, chemical bonding, and spectroscopy.

Getting Started

The first step is to download IQmol, a free graphic interface that handles building molecules, setting up calculations, visualization of the results, local and remote job submission. Windows, Mac, and Linux versions are available from www.iqmol.com. Every student in a class can install a fully functional version of IQmol on his/her laptop for free.

Once IQmol is installed, instructors have two options of using Q-Chem in classes:

1. Use IQmol and Q-Chem server.

Short jobs can be submitted jobs through IQmol to the Q-Chem server. This is a default configuration of IQmol. This is a free option. It is recommended for low-volume use of Q-Chem (e.g., simple illustrative calculations, jobs shorter than 5 min, class sizes 25 students or less).

2. Use existing Q-Chem license or purchase a new Q-Chem license.

For larger volume of calculations and for more advanced projects, we recommend that you use a dedicated computational resource such as a local cluster or university computing center. Of course, Q-Chem can also be installed on instructor's and students' laptops.

Using dedicated local computational resource requires purchasing a Q-Chem license (check with your department or HPCC if you already have one). One installation of Q-Chem on an adequate machine is sufficient for serving the entire class. IQmol can be configured to submit jobs to any machine on which you have an account.

 

Instructor Resources

Getting started with IQmol

Online presentations (can be used for classroom presentation or for independent study at home):

IQmol Server Setup and Job Submission: pdf
IQmol - Intro-I (Recommended for everyone) pdf ppt
IQmol-Intro-II (Advanced) pdf ppt
IQmol Troubleshooting (Advanced) pdf ppt


IQmol User Guide





Computational Labs

GROUP 1: EQUILIBRIUM STRUCTURES AND TRANSITION STATES, MOLECULAR VIBRATIONS, CALCULATION OF REACTION ENERGIES, ISOMERS, VIBRATIONAL AND NMR SPECTRA

GROUP 2: MOLECULAR ORBITAL THEORY

GROUP 3: ELECTRONICALLY EXCITED STATES

GROUP 4: ADVANCED MOLECULAR ORBITAL THEORY AND BONDING CONCEPTS




GROUP 1: EQUILIBRIUM STRUCTURES AND TRANSITION STATES, MOLECULAR VIBRATIONS, CALCULATION OF REACTION ENERGIES, ISOMERS, VIBRATIONAL AND NMR SPECTRA

"Introduction to IQmol: Exploring potential energy surfaces"

  • Lab Handout

  • Description: Students learn how to build molecules and perform basic electronic structure calculations using IQmol and Q-Chem while reviewing the key concepts of potential energy surfaces (stationary points, minima, saddle points) and their relation to stable molecular structures and transition states.

    Suggested level: Beginning graduate

    Learning objectives: Learn how to build and manipulate molecules; understand concepts of stable molecular structures, transition states, and reaction coordinates; learn basic standards of reporting electronic structure calculations.


"IR and NMR Spectra"

  • Lab Handout

  • Description: In this lab we will be computing molecular properties by considering derivatives of the energy. In particular, we will calculate the IR and NMR spectra of several small organic molecules, and use the calculated spectra to help identify an unknown molecule.

    Suggested level: graduate/advanced undergraduate

    Learning objectives: Learn how compute IR and NMR spectra and how to relate them to molecular structure; review harmonic and anharmonic oscillators; review point group symmetry of molecular structures and vibrations.


"Reaction Mechanics and Transition States"

  • Lab Handout

  • Description: In this lab we will consider the SN1 and SN2 reaction mechanism for nucleophilic substitution. By considering transition structures, intermediates and solvation effects we will determine which pathway is favored for the reactions involving CN- attack of bromomethane and t-butyl bromide.

    Suggested level: Graduate/advanced undergraduate

    Learning objectives: Learn how compute stable structures, reaction intermediates, and transition states; review concepts of enthalpy, entropy, and Gibbs free energy; learn how to incorporate solvent in calculations.


"Predicting Trends in Ring Strain of Cycloalkanes"

  • Lab Handout

  • Description: In this experiment we will estimate the amount of ring strain in cycloalkanes, and use our estimates to order the molecules from cyclopropane to cyclooctane from most to least strained.

    Suggested level: Beginning graduate/advanced undergraduate

    Learning objectives: Learn how to build and manipulate molecules; how to optimize molecular geometry; how to compute energy di erences from total energies. Review basic concepts of structure of organic molecules containing sp3-hybridized carbon atoms.


GROUP 2: MOLECULAR ORBITAL THEORY

. "Bonding and Molecular Orbitals"

Description: Students learn how to compute and visualize molecular orbitals using
IQmol and review the key concepts of the MO-LCAO picture of bonding and symmetry of
electronic wave functions.

Suggested level: Beginning graduate

Learning objectives: Learn how to compute and visualize molecular orbitals and how
to assign their characters (bonding, lone pairs, antibonding); review symmetry concepts.


. "Interpreting the Results of Hartree-Fock Calculations: Ionized States and Koopmans Theorem"

Description: Students learn how to interpret the results of Hartree-Fock calculations. The focus of this lab is on physical significance of the canonical molecular orbitals and their energies.

Suggested level: Beginning graduate

Learning objectives: Learn how to compute and visualize molecular orbitals and how to connect the computed orbital energies with experimental observables such as ionization energies (IEs). By analyzing the shapes of the MOs, make predictions about anticipated shapes of photoelectron spectra. Learn how to determine symmetry of the ionized states.


GROUP 3: ELECTRONICALLY EXCITED STATES

. "Electronically Excited States: Calculations by Configuration Interaction Singles Method"

Description: Students learn how to describe electronically excited states in terms of their electronic configurations. They compare the prediction of the Koopmans theorem with the results of CIS calculations.

Suggested level: Beginning graduate

Learning objectives: Learn how to use Koopmans theorem to predict the character of low-lying excited states. Learn how to perform CIS calculations and analyze the results. Learn about diffuse orbitals and Rydberg states.


. "Calculating Excited States"

Description: In this lab we will compute the excited states of several poly-aromatic molecules and try to predict the frequency at which they phosphoresce.

Suggested level: Graduate/advanced undergraduate

Learning objectives: Learn how compute electronically excited states and their structures; review concepts of Stokes shift, spin-symmetry, optically dark and bright states.


GROUP 4: ADVANCED MOLECULAR ORBITAL THEORY AND BONDING CONCEPTS

. "Natural Bond Orbital (NBO) Analysis: Formaldehyde Example"

Description: Students learn how to execute NBO calculations, interpret the output by extracting various chemical data such as natural charges, bond types and order (Lewis structure), hybridization, and how to visualize natural bond orbitals. Students will compare NBO and Mulliken charges and their basis set dependence. Students will use Mulliken and NBO atomic charges to compute dipole moments and compare them with proper dipole moments computed using the original densities.

Suggested level: Beginning graduate

Learning objectives: Learn how to derive bonding picture from quantum chemical calculations. By visualizing the shape of NBOs and MOs, students can compare localized (NBO-based) versus delocalized (canonical MO) representation of the electronic density. By comparing dipole moments computed using point charges with the dipole moments computed using the original density, students will learn the limitations of point charges.


. "Calculating Walsh Diagrams"

Description: In this lab you will calculate Walsh diagrams for several rst row hydrides, and use these to predict their equilibrium structures.

Suggested level: Advanced graduate/advanced undergraduate; introductory organic chemistry is required.

Learning objectives: Learn how to use molecular-orbital diagrams to predict trends on molecular structure.


Help Resources

Q-Chem offers a broad spectrum of educational resources for beginners and seasoned computational chemists.

IQmol Resources:

Basic and advanced features of IQmol

Q-Chem Resources

  • Q-Chem Manual: Everything you need to know about Q-Chem. Includes theoretical background and examples of sample jobs
  • Q-Chem YouTube Channel: Collection of webinars on basic and advanced topics (can be used as guest lectures in the class)