Computational Physical Chemistry ‘Labs’

The field of computational biophysical chemistry is so large that entire courses don’t even do it justice.  However, it would be a huge omission not to at least introduce a few of the more important and practically used computational methods in biophysical chemistry.   Lets start with the books Prof. Yarger recommends most for developing an understanding of molecular level computational modeling:

There are a lot of computational chemistry online resources, tutorials, and both commercial and open-source software.  There are way too many different methods for molecular modeling and associated software and computer programs/code for each type of molecular modeling to provide a thorough list here. Listed below are a few specific links to software and programs that are directly useful for CHM 341 and 343 (pchem) students.

• MolCalc (and the associated J. Chemical Education paper: molcalc_JCE2013)
• GAMESS (open-source molecular electronic structure system)
• ORCA (Electronic Structure program)
• Gaussian (commercial electronic structure software – ASU has Linux/MacOS Site License)
• Spartan (commercial molecular modeling software)
• Cresset (Software for molecular design, Prof. Yarger has a teaching license for Torch, Forge and Spark that can be used for BCH 341)
• NAMD (Scalable Molecular Dynamics, open-source)
• MS2 (Molecular Simulation Program for Thermodynamic Properties)
• eQuilibrator (open source web interface for thermodynamic analysis of biochemical systems)

Computational chemistry plays an ever important role in physical chemistry.  Most theorists rely heavily on computers for numerical and iterative mathematics that are only possible because of the processing power of computers.  Also, experimentalists often do ‘virtual experiments’ on computers either instead of doing real-world experiments or as a way of texting variables and idea systems out on a computer before doing the real-world experiment in the lab.   The rapid development of AI, Machine Learning algorithms, quantum computation, etc. indicate that computers and computational methods will continue to grow in significance for all practical and fundamental science. Some links are provided below to some physical chemistry computational textbooks.

• Schrier, Introduction to Computational Physical Chemistry.
• Cramer, Essentials of Computational Chemistry.
• Leach, Molecular Modelling: Principles and Applications.
• Frenkel & Smit, Understanding Molecular Simulations.
• Forescman & Frisch, Exploring Chemistry with Electronic Structure Methods

ASU ONLINE CHM343 Students – Pchem ‘Cloud’ Computing

The primary resource for students is GaussView6 (using X11 forwarding) and Gaussian16 on the ASU Research Computing Cluster, Agave (ASU has a site license to the linux and mac versions of GaussView and Gaussian. Students can also use WebMO and ASU Research Computing Cluster – Agave (WebMO Link) (Primary Agave Link) as a more general alternative to GaussView6 (WebMO can work as a GUI for numerous quantum chemistry calculation programs). Students will need to be connected to the ASU VPN (Cisco ASU VPN found at myapps.asu.edu) to access the WebMO server and the Agave research computer cluster. All CHM343 computational components can be completed using WebMO as a user interface (UI) and Gaussian 16 on Agave as the quantum computational program for ab initio electronic structure calculations (primarily energy, optimization and vibrational calculations to provide thermochemical computational data).

As a backup or alternative, Prof. Yarger has created a CHM343 account and AnyDesk alias to a Mac Pro system at ASU that has Gaussview 6 and Gaussian 16 installed and available.  However, this computer is not near as capable as the computer cluster ASU-Agave.  The AnyDesk alias for this alternative/backup is yargermacpro@ad and the password is the standard password for ASU-ONLINE CHM343.

Lastly, there are many open source ab initio software packages available for students to run computational chemistry ‘experiments’ on their own computer hardware.  Examples of open source Gaussian alternatives are ORCA, OpenMOLCAS, Psi4, NWChem and GAMESS.  Examples of open source Gaussview (WebMO) alternatives are Gabedit, Avogadro, ECCE, Vesta, and QuantumATK (Article, PDF). This is discussed generally in the previous section.