Computational Chemistry, WebMO, and Energy Calcul

Computational Chemistry, WebMO, and Energy Calculations : Computational Chemistry, WebMO, and Energy Calculations Modified from ‘Lecture CompChem 1 Chemistry 347 Hope College’

Chemistry 347: Chemical Modeling Lab : Chemistry 347: Chemical Modeling Lab Overall Goal: Use mathematical and computer models to understand and predict chemical structure, properties, and reactivity Methods: WebMO/Gaussian/GaussView: Use existing, state-of-the-art computer models to calculate molecular properties Mathcad(optional, use your own): Develop your own models for thermodynamic quantities, reactivity, and kinetics

Computational Chemistry : 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

Computational Chemistry (con’t) : 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)

WebMO Quick Start : WebMO Quick Start WebMO: rep.kaist.ac.kr/webmo/login.cgi Login: Username=guest, Password = guest 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

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

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

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

Electronic Structure Methods : 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

Electronic Structure Methods (con’t) : 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

Model Chemistry : Model Chemistry Methods 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

Running Calculations : 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 Most can be done more conveniently by GaussView Use WebMo from remote site

Gaussian Input File : Gaussian Input File #N HF/3-21G SP HFCO 0 1 C O 1 1.50 F 1 1.49 2 120.0 H 1 1.09 2 120.0 3 180.0 Route (job options) blank line Title blank line Charge and Multiplicity Geometry Specification

Z-Matrix : Z-Matrix C O 1 1.50 F 1 1.49 2 120.0 H 1 1.09 2 120.0 3 180.0

Z-Matrix (con’t) : 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

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

Gaussian Output File (con’t) : 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 =

WebMO : WebMO Easier input creation, job management, and result viewing Project is stable, but always under development About 200 international downloads to date We want and value your feedback!!! www.chem.hope.edu/webmo