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Computational Chemistry, WebMO, and Energy Calculations

Computational Chemistry, WebMO, and Energy Calculations. Lecture CompChem 1 Chemistry 347 Hope College. Chemistry 347: Chemical Modeling Lab. Overall Goal: Use mathematical and computer models to understand and predict chemical structure, properties, and reactivity Methods:

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Computational Chemistry, WebMO, and Energy Calculations

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  1. Computational Chemistry, WebMO, and Energy Calculations Lecture CompChem 1Chemistry 347Hope 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 • 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 blank line Charge and Multiplicity Geometry Specification #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

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

  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 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 • We want and value your feedback!!! www.chem.hope.edu/webmo

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