molecular modelling Flashcards
what is a wavefunction
describe the chemical system, and contain info about the probability of where the particle is
what is Hartree Fock theory and the assumptions
a computational method to approximate the behaviour of many electron-systems
assumes motions of electron to be independent of the dynamics of other electrons
what are slater determinants
describes the arrangement of electrons with a molecular system
what is variational principle
shows HF theory approximate energy must be higher than the true ground state
what does the fock operator do
set of one e- equation that produce the orbital of HF many-electron wavefunction
explain the HF method
- set system and basis set
- choose initial orbital coefficient (Cp)
- build fock operator
- solve fock equation
- did converge (no => step 3)
- wavefunction and energy obtained
what do you get from hartree fock
- overall wavefunction
- the molecular orbital (their energies)
- total energy
cons with Hartree Fock theory
- neglects electron correlation (not accurate)
- performs bad when bonds are broken
3.computationally expensive - no account for dispersion
- HF always gives higher then true ground state energy
what are basis sets and name some examples
math fuctions used to describe the behaviour of electrons
double zeta
valence double zeta
def2-nZVP
cc-pVn2
what is the Ci expansion method
- HF calculation to get occupied and virtual orbitals
- choose level (truncation) of Ci
- variational principle to solve ci equations
- add excited determinants
cons of Ci expansion
its not size consistent = A method is size consistent if its energies scale linearly with the number of molecules, enabling accurate calculations for larger systems.
what is correlation energy
the energy due to instantaneous repulsion between pairs of electrons
what different about density functional theory
ground state is determined by electron density p
pros and cons of the couple cluster method
pros
- size consistency
cons
- very slow
- not variational
- expensive
how to approximate the Exc value
- fit parameters to reproduce theoretical or experimental
2.
cons of B3LYP
-underestimates barrier heights
- doesn’t account for dispersion
- often unreliable for transition M
how do semi-empirical methods work
replaces integral with a set of parameters
pros and cons of semi empirical methods
pros
- very very fast
-not super accurate
cons
-requires training data
-can be bias
-could break anytime
what is the Hooke’s law eqaution
E = 1/2k(X-X_0)^2
E = energy
k = force constant
x = distance
what are the pros and cons of the hooke’s law
pros:
- simple form
- easy to calculate
- accurate when r is close to r_0
cons
- does not describe dissociation
- does not describe anharmonicity
what is the morse potential
E_str = D[1-exp[-a(r-r_0)]]^2
D= dissociation energy
a= strength of potential
difference between proper and improper torsion
proper not restricted with 360 rotation
improper is restricted
whats the electrostatic equation
E = 1/(4πε_0ε_r) x qq/r
r = distance
ε_0 = dielectric permittivity
ε_r = relative dielectric permittivity
q =charge on atom
what is the lennard jones potential
E = 4ε[(σ/r)^12 - (σ/r)^6]
r = distance
sigma = distance when E=0
epsilon = interaction energy
what is a force field
parameter to determine the strength of interaction
pros and cons of coarse grain ff
atoms are grouped into larger particles
pros
-fewer atoms => fewer interaction => faster calculation
can ignore less movement
cons
-loss of info
-map coarse grain back into structure
what is optimisation
finding the minimum energy structure
what are molecular dynamics
simulates the movement of atoms/molecules
-thermal energy allow for overcoming potential energy barriers
what is the improved verlet algorithm
x(t+Δt) = x + v *Δt + 1/2a *(Δt)^2
what are ensembles
the combination of multiple models to improve accuracy
what is the procedure of MD
- choose appropiate FF
- build several starting structures
- choose simulation parameters
- run
- analyse results
what is annealing
metals are heated to remove defects then cooled
this explores the potential energy surfaces
what is monte carlo method
follows the evolution of a system by trial and error of randomly chosen movements
finds the minima and follows the evolution of the system
metropolis MC -goes toward the lowest energy
kinetic MC- info on energy barrier
what is replica exchange
- carries out multiple MD at the same time
eg simulates same system with different temps
finds energy minima and tension
metadynamics
used for exploring and constructing potential energy surfaces
things QM can model
- intermolecular interactions
- energies of reactants and products separately
- model transition states
- electronic structure of molecules.
