molecular modelling

Question 1

what is a wavefunction

Answer 1

describe the chemical system, and contain info about the probability of where the particle is

Question 2

what is Hartree Fock theory and the assumptions

Answer 2

a computational method to approximate the behaviour of many electron-systems

assumes motions of electron to be independent of the dynamics of other electrons

Question 3

what are slater determinants

Answer 3

describes the arrangement of electrons with a molecular system

Question 4

what is variational principle

Answer 4

shows HF theory approximate energy must be higher than the true ground state

Question 5

what does the fock operator do

Answer 5

set of one e- equation that produce the orbital of HF many-electron wavefunction

Question 6

explain the HF method

Answer 6

1. set system and basis set
2. choose initial orbital coefficient (Cp)
3. build fock operator
4. solve fock equation
5. did converge (no => step 3)
6. wavefunction and energy obtained

Question 7

what do you get from hartree fock

Answer 7

1. overall wavefunction
2. the molecular orbital (their energies)
3. total energy

Question 8

cons with Hartree Fock theory

Answer 8

1. neglects electron correlation (not accurate)
2. performs bad when bonds are broken
   3.computationally expensive
3. no account for dispersion
4. HF always gives higher then true ground state energy

Question 9

what are basis sets and name some examples

Answer 9

math fuctions used to describe the behaviour of electrons

double zeta
valence double zeta
def2-nZVP
cc-pVn2

Question 10

what is the Ci expansion method

Answer 10

1. HF calculation to get occupied and virtual orbitals
2. choose level (truncation) of Ci
3. variational principle to solve ci equations
4. add excited determinants

Question 11

cons of Ci expansion

Answer 11

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.

Question 12

what is correlation energy

Answer 12

the energy due to instantaneous repulsion between pairs of electrons

Question 13

what different about density functional theory

Answer 13

ground state is determined by electron density p

Question 14

pros and cons of the couple cluster method

Answer 14

pros
- size consistency
cons
- very slow
- not variational
- expensive

Question 15

how to approximate the Exc value

Answer 15

1. fit parameters to reproduce theoretical or experimental
   2.

Question 16

cons of B3LYP

Answer 16

-underestimates barrier heights
- doesn’t account for dispersion
- often unreliable for transition M

Question 17

how do semi-empirical methods work

Answer 17

replaces integral with a set of parameters

Question 18

pros and cons of semi empirical methods

Answer 18

pros
- very very fast
-not super accurate
cons
-requires training data
-can be bias
-could break anytime

Question 19

what is the Hooke’s law eqaution

Answer 19

E = 1/2k(X-X_0)^2
E = energy
k = force constant
x = distance

Question 20

what are the pros and cons of the hooke’s law

Answer 20

pros:
- simple form
- easy to calculate
- accurate when r is close to r_0
cons
- does not describe dissociation
- does not describe anharmonicity

Question 21

what is the morse potential

Answer 21

E_str = D[1-exp[-a(r-r_0)]]^2

D= dissociation energy
a= strength of potential

Question 22

difference between proper and improper torsion

Answer 22

proper not restricted with 360 rotation
improper is restricted

Question 23

whats the electrostatic equation

Answer 23

E = 1/(4πε_0ε_r) x qq/r
r = distance
ε_0 = dielectric permittivity
ε_r = relative dielectric permittivity
q =charge on atom

Question 24

what is the lennard jones potential

Answer 24

E = 4ε[(σ/r)^12 - (σ/r)^6]
r = distance
sigma = distance when E=0
epsilon = interaction energy

Question 25

what is a force field

Answer 25

parameter to determine the strength of interaction

Question 26

pros and cons of coarse grain ff

Answer 26

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

Question 27

what is optimisation

Answer 27

finding the minimum energy structure

Question 28

what are molecular dynamics

Answer 28

simulates the movement of atoms/molecules
-thermal energy allow for overcoming potential energy barriers

Question 29

what is the improved verlet algorithm

Answer 29

x(t+Δt) = x + v *Δt + 1/2a *(Δt)^2

Question 30

what are ensembles

Answer 30

the combination of multiple models to improve accuracy

Question 31

what is the procedure of MD

Answer 31

1. choose appropiate FF
2. build several starting structures
3. choose simulation parameters
4. run
5. analyse results

Question 32

what is annealing

Answer 32

metals are heated to remove defects then cooled
this explores the potential energy surfaces

Question 33

what is monte carlo method

Answer 33

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

Question 34

what is replica exchange

Answer 34

• carries out multiple MD at the same time
  eg simulates same system with different temps

finds energy minima and tension

Question 35

metadynamics

Answer 35

used for exploring and constructing potential energy surfaces

Question 36

things QM can model

Answer 36

1. intermolecular interactions
2. energies of reactants and products separately
3. model transition states
4. electronic structure of molecules.