1. Computational Chemistry, WebMO, and Energy Calculations
Lecture CompChem 1 Chemistry 347 Hope College

2. Chemistry 347: Chemical Modeling Lab
Overall Goal: Use mathematical and computer models to understand and predict chemical structure, properties, and reactivity
Methods:
Gaussian98: Most popular research-level computer program for computing electronic structure and properties of molecules
WebMO: Web-based interface for preparing, submitting, and visualizing computational chemistry jobs

3. Computational Chemistry
Computer-based calculation of chemical structure, properties, and reactivity
Usefulness
Complements and explains experimental results
Goes where experiment cannot (transition states, intermediates)
Makes predictions and can guide experiments

4. Computational Chemistry (con’t)
History
Past: Mainframe computers (limited to a few specialists due to difficult interface)
Present: Desktop workstations (still inaccessible to many due to system requirements, cost, and licensing)
Future: WWW (readily available to all chemists)

5. WebMO Quick Start WebMO: curie.chem.hope.edu/~chem347
Login: Username=Last Name, Password = Student ID # (with leading zeroes)
Job Manager: Create New Job
Build Molecule: Open Editor, Build HFCO, Close Editor
Choose Engine: Gaussian
Job Options: Single Point, Hartree-Fock, Basic, Preview Input File
Preview Gaussian Input File: Submit Job
Job Manager: View

6. Chemical Models Plastic models for organic chemistry structures
Lewis structures and electron pushing for organic reactions
Computational chemistry models for structure and reactivity

7. Computational Chemistry Approaches
Molecular Mechanics
Classical mechanics
Parameters kr, r0, kq, q0, ... chosen to fit observed data
No explicit treatment of electrons
Very fast

8. Computational Chemistry Approaches (con’t)
Electronic Structure Methods
Quantum Mechanics
Electrons (molecular orbitals) explicitly calculated
Much slower, but more general

9. Electronic Structure Methods
Semi-empirical (MOPAC, AMPAC, HyperChem)
use parameters to evaluate integrals
relatively fast
ab initio (Gaussian, Spartan, GAMESS)
evaluate integrals from first principles
slow
scales poorly with size

10. Electronic Structure Methods (con’t)
Density Functional Theory (Gaussian, GAMESS)
similar to ab initio
includes electron correlation
electron density calculated, not orbitals
not as slow

11. Model Chemistry Methods Basis Set Open vs. Closed Shell
Hartree-Fock (HF), Møller-Plesset (MP2), B3LYP
Basis Set
STO-3G, 3-21G, 6-31G(d), ...
Open vs. Closed Shell
unrestricted (U) if unpaired electrons exist
restricted (default) when all electrons are paired
Compound Methods
geometry at lower theory; energy at higher theory

12. Running Calculations WebMO User Interface
Build molecule – Submit job
Choose engine – Monitor progress
Select job options – View results
WebMO behind-the-scenes actions
Create input file
Queue and run job
Format output file

13. Gaussian Input File Route (job options) blank line Title
Charge and Multiplicity
Geometry Specification
#N HF/3-21G SP
HFCO
0 1 C O F H

14. Z-Matrix C O F H

15. Z-Matrix (con’t)
Z-Matrix is chemically intuitive (atom distance, bond angle, dihedral angle)
Z-Matrix is efficient because it has only 3N-6 coordinates (vs. 3N for Cartesian coordinates)
Many possible Z-matrices due to different ordering of atoms
Near linear molecules have poorly defined dihedral angles

16. Gaussian Output File Geometry Energy Molecular Orbitals and Energies
Standard orientation:
Energy
SCF Done: E(RHF) =
Molecular Orbitals and Energies
Molecular Orbital Coefficients
EIGENVALUES

17. Gaussian Output File (con’t)
Atomic Charges
Total atomic charges:
Dipole Moment
Dipole moment (Debye): Tot =
NMR Shifts
GIAO Magnetic shielding tensor (ppm): C Isotopic =

18. WebMO Easier input creation, job management, and result viewing
Project is stable, but always under development
Over 2000 international downloads to date
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