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An Introduction to Molecular Orbital Theory

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Title: Semi-empirical Molecular Orbital Theory Last modified by: martinn Created Date: 2/10/1997 4:34:26 PM Document presentation format: On-screen Show – PowerPoint PPT presentation

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Title: An Introduction to Molecular Orbital Theory


1
An Introduction to Molecular Orbital Theory
2
Levels of Calculation
  • Classical (Molecular) Mechanics
  • quick, simple accuracy depends on
    parameterization no consideration of orbital
    interaction not MO theory)
  • Molecular Orbital Theory (Quantum Mechanics)
  • Ab initio molecular orbital methods...much more
    demanding computationally, generally more
    accurate.
  • Semi-empirical molecular orbital methods
    ...computationally less demanding than ab initio,
    possible on a pc for moderate sized molecules,
    but generally less accurate than ab initio,
    especially for energies.

3
Relative Computation Cost
  • Molecular mechanics...cpu time scales as square
    of the number of atoms...
  • Calculations can be performed on a compound of
    MW 300 in a few minutes on a Pentium computer,
    or in a few seconds on the SGI.
  • This means that larger molecules (even peptides)
    and be modeled by MM methods.

4
Relative Computation Cost
  • Semi-empirical and ab initio molecular orbital
    methods...cpu time scales as the cube (or fourth
    power) of the number of orbitals (called basis
    functions) in the basis set.
  • Semi-empirical calculations on MW 300 compound
    take 10 minutes on a Pentium pc, less
    than one minute on our SGIs, a second on a
    supercomputer.

5
Semi-Empirical Molecular Orbital Theory
  • Uses simplifications of the Schrödinger equation
    E? H ? to estimate the energy of a system
    (molecule) as a function of the geometry and
    electron distribution.
  • The simplifications require empirically derived
    (not theoretical) parameters (fudge factors) to
    bring calculated values in agreement with
    observed values, hence the term semi-empirical.

6
Properties Calculated by Molecular Orbital Theory
  • Geometry (bond lengths, angles, dihedrals)
  • Energy (enthalpy of formation, free energy)
  • Vibrational frequencies, UV-Vis spectra
  • NMR chemical shifts
  • IP, Electron affinity (Koopmans theorem)
  • Atomic charge distribution (...ill defined)
  • Electrostatic potential (interaction w/ point )
  • Dipole moment.

7
History of Semi-Empirical Molecular Orbital
Theory
  • 1930s Hückel treated ? systems only
  • 1952 Dewar PMO first semi- quantitative
    application
  • 1960s Hoffmann Extended Huckel included
    ??bonds
  • 1965 Pople CNDO first useful MO program
  • 1967 Pople INDO

8
History...
  • 1975 Dewar MINDO/3 was widely used
  • 1977 Dewar MNDO
  • 1985 Dewar AM1 added vdW attraction
    H-bonding
  • 1989 Stewart PM3 larger training set
  • 1970s Zerner ZINDO includes transition
    metals, parameterized for calculating
    UV-Vis spectra

9
Basis of Molecular Orbital Theory
  • Schrödinger equation
  • E ? H ?
  • (can be solved exactly for the Hydrogen atom,
  • but nothing larger)
  • P.A.M. Dirac, 1929 The underlying physical
    laws necessary for the mathematical theory of a
    large part of physics and the whole of chemistry
    are thus completely known.

10
Basis of M.O. Theory...
  • Simplifying assumptions are employed to solve
    the Schrödinger equation approximately
  • Born-Oppenheimer approximation allows separate
    treatment of nuclei and electrons
  • Hartree-Fock independent electron approximation
    allows each electron to be considered as being
    affected by the sum (field) of all other
    electrons.
  • LCAO Approximation
  • Variational Principle

11
Born-Oppenheimer Approx.
  • States that electron motion is independent of
    nuclear motion, thus the energies of the two are
    uncoupled and can be calculated separately.
  • Derives from the large difference in the mass of
    nuclei and electrons, and the assumption that the
    motion of nuclei can be ignored because they move
    very slowly compared to electrons
  • Htot a (Tn) Te Vne Vn Ve
  • Kinetic energy
    Potential energy
  • (Tn is omitted this ignores relativistic
    effects, yielding the electronic Schrödinger
    equation.)

12
Hartree-Fock Approximation
  • Assumes that each electron experiences all the
    others only as a whole (field of charge) rather
    than individual electron-electron interactions.
  • Introduces a Fock operator F
  • F????????
  • which is the sum of the kinetic energy of an
    electron, a potential that one electron would
    experience for a fixed nucleus, and an average of
    the effects of the other electrons.

13
LCAO Approximation
  • Electron positions in molecular orbitals can be
    approximated by a Linear Combination of Atomic
    Orbitals.
  • This reduces the problem of finding the best
    functional form for the molecular orbitals to the
    much simpler one of optimizing a set of
    coefficients (cn) in a linear equation
  • ? c1 f1 c2 f2 c3 f3 c4 f4
  • where ? is the molecular orbital wavefunction
    and fn represent atomic orbital wavefunctions.

14
Variational Principle
  • The energy calculated from any approximation of
    the wavefunction will be higher than the true
    energy.
  • The better the wavefunction, the lower the energy
    (the more closely it approximates reality).
  • Changes are made systematically to minimize the
    calculated energy.
  • At the energy minimum (which approximates the
    true energy of the system), dE 0.

15
Basis sets
  • A basis set is a set of mathematical equations
    used to represent the shapes of spaces (orbitals)
    occupied by the electrons and their energies.
  • Basis sets in common use have a simple
    mathematical form for representing the radial
    distribution of electron density.
  • Most commonly used are Gaussian basis sets, which
    approximate the better, but more complicated
    Slater-Type orbitals (STO).

16
Slater-type orbitals (STO)
  • Slater-type orbitals describe the electron
    distribution fairly well, but they are not simple
    enough to manipulate mathematically.
  • Several Gaussian-type orbitals can be added to
    approximate the STO. Four GTOs mimic one STO.

17
Basis Sets
  • STO-3G (Slater-type orbitals approximated by 3
    Gaussian functions)minimal basis set, commonly
    used in Semi-Empirical MO calculations.

(L-click here)
18
Hartree-Fock Self-Consistent Field (SCF) Method...
  • Computational methodology
  • guess the orbital occupation (position) of an
    electron
  • guess the potential each electron would
    experience from all other electrons (taken as a
    group)
  • solve for Fock operators to generate a new,
    improved guess at the positions of the electrons
  • repeat above two steps until the wavefunction for
    the electrons is consistent with the field that
    it and the other electrons produce (SCF).

19
Semi-empirical MO CalculationsFurther
Simplifications
  • Neglect core (1s) electrons replace integral for
    Hcore by an empirical or calculated parameter
  • Neglect various other interactions between
    electrons on adjacent atoms CNDO, INDO, MINDO/3,
    MNDO, etc.
  • Add parameters so as to make the simplified
    calculation give results in agreement with
    observables (spectra or molecular properties).

20
Steps in Performing a Semi-empirical M O
Calculation
  • Construct a model or input structure from MM
    calculation, X-ray file, or other source
    (database)
  • optimize structure using MM method to obtain a
    good starting geometry
  • select MO method (usually AM1 or PM3)
  • specify charge and spin multiplicity (s n 1)
  • select single point or geometry optimization
  • set termination condition (time, cycles,
    gradient)
  • select keywords (from list of gt100).

21
Comparison of Results
  • Mean errors relative to experimental
    measurements
  • MINDO/3 MNDO AM1 PM3
  • ?Hf, kcal/mol 11.7 6.6 5.9 --
  • IP, eV -- 0.69 0.52 0.58
  • ?, Debyes -- 0.33 0.24 0.28
  • r, Angstroms -- 0.054 0.050 0.036
  • ???degrees -- 4.3 3.3 3.9

22
More results...
  • Enthalpy of Formation, kcal/mol
  • MM3 PM3 Expt
  • ethane -19.66 -18.14 --
  • propane -25.32 -23.62 -24.8
  • cyclopropane 12.95 16.27 12.7
  • cyclopentane -18.87 -23.89 -18.4
  • cyclohexane -29.95 -31.03 -29.5

23
Some Applications...
  • Calculation of reaction pathways (mechanisms)
  • Determination of reaction intermediates and
    transition structures
  • Visualization of orbital interactions (formation
    of new bonds, breaking bonds as a reaction
    proceeds)
  • Shapes of molecules including their charge
    distribution (electron density)

24
more Applications
  • QSAR (Quantitative Structure-Activity
    Relationships)
  • CoMFA (Comparative Molecular Field Analysis)
  • Remote interactions (those beyond normal
    covalent bonding distance)
  • Docking (interaction of molecules, such as
    pharmaceuticals with biomolecules)
  • NMR chemical shift prediction.
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