Computational Flashcards
Which model is most suitable for TM?
B3LYP/6-31G*
Which model is most suitable for unsaturated organics?
MP2/6-31G* or B3LYP/6-31G*
Which model is most suitable for weakly associated dimers?
HF/G-311+G*
Which model is most suitable for compounds with electronegative elements or lone pairs?
MP2/6-311+G*
MM
How are electrons treated?
They are ignored
Advantages of MM?
2 points
- Quick not computationally demanding
- Applicable to very large systems
Disadvantages of MM?
4 points
- Electrons are ignored
- Bond energies, molecular orbitals, electron densities, excited states are not calculated
- Primary function of force field is structure optimisation
- Calculations depend on the force field used.
Describe MD calculations
- Take forces calculated on atoms
- Apply Newton 2nd Law
- Define time step
- Output molecular trajectory
MD
What is a typical time step?
1 fs
MD
What do force fields define?
Potential energy surface
MD
How are force fields calculated?
From the gradient of the potential energy surface
What is the principle of Ab initio calculation?
MO theory approach to finding solutions to Schrödinger’s equation
Ab initio
How are electrons treated?
Explicitly
Ab initio
What does Hamiltonian operator describe?
KE & PE terms of matter
Ab inito
How is the Hamiltonian operator approximated?
Using a level of theory Hartree-Fock or DFT
Schrödinger equation
What is E?
Proportionality constant (the Eigenvalue)
Schrödinger equation
What does the wavefunction describe?
Size and shapes of atomic and molecular orbitals
Schrödinger equation
How is the wavefunction approximated?
Using a basis set. Linear combination of simple functions like Gaussian
Born-Oppenheimer approximation of Hamiltonian operator
What happens to KE of electron
Worked out
Born-Oppenheimer approximation of Hamiltonian operator
What happens to KE of nucleus
=0, as molecule is fixed in space for geometry optimisation
Born-Oppenheimer approximation of Hamiltonian operator
What hapens to PE of electron to electon
Worked out
Born-Oppenheimer approximation of Hamiltonian operator
What happens to PE of nucleus to nucleus
Calculated using Coulomb’s law
Born-Oppenheimer approximation of Hamiltonian operator
What happens to PE of nucleus to electron
Calculated
Which level(s) of theory approximate electron to electron correlation
DFT, Hybrid DFT
Which level(s) of theory ignore electron to electron correlation
HF theory
Which level(s) of theory approximate electron to electron exchange
DFT
Which level(s) of theory get exact electron to electron exchange
HF theory, Hydrid DFT
Describe Hartree theory
Replaces the insolvable many electron problem with the solvable single electron problem. Each electron modelled as a moving in an effective uniform field
What is the disadvantage of HF theory
Missing electron correlation energy
For what molecules is the missing electron correlation energy significant?
Significant for molecules with high electron density (aromatics)
How many variable s per electron are used in HF?
4
3 positional + spin
Variation theorem
Define basis set
Collection of Gaussian functions
Variaiton theorem
Define polarisation function
One higher angular momentum function
Variation theorem
Describe the process of variation theorem
- Generate a trial wavefunction based on random weighting coefficients
- Determine its energy
- Vary weighting coefficients to get a new wavefunction. Is the new energy lower?
- Repeat until the electronic ground state (minimum is found)
Basis sets
What is the meaning of dash?
Treat core electrons separate from valence electrons
Basis sets
What is the meaning of star?
Polarisation function (two stars — polarisation on the hydrogen as well as heavy; one star — only heavy, not hydrogen)
Basis sets
What is the meaning of plus?
Diffuse function. Larger versions of ‘s’ and ‘p’ orbitals. Important for atoms that carry extra charge
What is the difference between semi-empirical calculations and ab initio?
- Remove core electrons from calculations
- Use minimal basis set
- Zero differential overlap
What is zero differential overlap?
Ovelap integral between many atoms assumed to be zero
MD
What is to be calculated to get the nature of the stationary point on the potential energy surface?
Nedd to calculate 3N-6 force constant
MD, PES stationary points
What makes a minimum?
If all 3N-6 vibrational frequencies are real numbers
MD, PES stationary points
What makes a saddle point?
If one freq is imaginary and the rest are real, 1st order transition state
What is the main difficulty in calculating NMR with DFT?
Need specially constructued split-valence basis sets with enhanced descriptors for core electrons
What can calculating EPR with DFT show?
By comparing plots from experimental you can verify the model and then assume that the molecular orbitals are shown correctly
Electron correlation
Describes how the electric field/movement of one electron is influenced by the electric field/movement of all other electrons. It’s a manifestation of the many-body effect.
Electron exchange
Describes the energy lowering obtained when spin up (alpha) electrons pair upwith spin down (beta) electrons
