Chemistry I Spring 2010

– Understand what CSM is – Be able to apply WebMO in learning chemistry

Computational Science & Modeling Use of computers to help gain scientific understanding (Brent Krueger, Hope College) Example Weather forecasting

CSM is key component of scientific discovery – Formerly: theory and experiment – Now: theory, experiment, and CSM (Three Pillars) Allows both very difficult problems and simple problems on very large/complex systems Essential in nearly all disciplines – Used by faculty in every science dept. at Hope (chem, bio, physics, engineering, computer science, math, nursing, psychology) Students interested in science must have basic understanding of what CSM is.

Most Chem CSM is either classical mechanics or quantum mechanics – Classical mechanics is simpler model (ignores electrons) – used to study motions in very large systems (Molecular Dynamics) – Quantum mechanics involves a full treatment of all electrons in system using Schr ö dinger Equation. Apply using sophisticated computer programs (Gaussian, MOPAC, GAMESS, NWChem, HyperChem, etc.) These programs are notoriously difficult to use and often expensive (though some are free)

 Hardware, Software, Experience ◦ Hardware provided by the Midwest Undergraduate Computational Chemistry Consortium (MU3C) ◦ Software (e.g. Gaussian) provided by MU3C ◦ Experience will come as you practice using WebMO

 Where else is CSM applied in everyday life?

 Traffic flow modeling  Genome sequencing (e.g. Human Genome Project)  Fluid dynamics (aircraft and ship design)  Epidemiology  Drug discovery (modeling target protein, designing drug molecule itself, and modeling interaction)  Chemistry (classical molecular dynamics of molecules and quantum calculations of structure and molecular properties)

 WebMO is web-based ‘front-end’ that makes interaction with Gaussian and other research- grade computational chemistry tools easier. ◦ Used for doing quantum mechanics, such as viewing molecular orbitals  Doesn’t actually do calculation ◦ Prepares input file ◦ Submits job to ‘engine’ (e.g. Gaussian) ◦ Sifts through output file  Created at Hope by Dr. Will Polik ◦ ◦ Used in many research labs worldwide in addition to classrooms ◦ Free version available. We will use fancier pay version  Provided by MU3C

 Login to WebMO running on cluster via web browser on your PC (anywhere) ◦ ◦ Login: harpercreek2 Password: gobeavers  Build molecule and tell WebMO what you want to know (anywhere)  WebMO creates proper input file and submits job to cluster’s queuing system (cluster)  Cluster runs difficult QM calculation (cluster)  WebMO collects results and displays (some of) them beautifully in your browser (anywhere)