Intro QM PDF

Molecular Modeling
Quantum Mechanics
• Basics
• The Schrödinger equation
• Hartree-Fock theory (HF)
• Electron correlation
• Semi-empirical theory (SE)
• Density Functional Theory (DFT)
UWI-Mona Per-Ola Norrby University of Gothenburg

March 2011 Department of Chemistry
Modeling methods
Quantum Mechanics (QM) Reaction mechanisms

Small model systems
• Accurate: <100 atoms
Molecular Mechanics (MM) Structure, conformational energies

• Nonbonded interactions
• Potentially accurate, large size
• Needs parameters
QM/MM QM reaction center, MM outside

• Potential QM accuracy, large size
• Slow compared to MM

Quantum mechanics A functional: An operator transforming
The Schrödinger equation a function into another function.
Example: H = (1/m)∂ 2/∂ x2
The Hamiltonian
A functional describing the Total
interaction of each particle energy
with every other particle
^
H Ψ= E Ψ
The wavefunction
The spatial distribution of all nuclei and electrons.
The function gives a number for each region in space. The square of
that number is the probability to find a particle in the region.
Usually divided into separate functions for each electron, orbitals.
The wavefunction is the total of all molecular orbitals.

The Born-Oppenheimer approximation
The electrons move several orders of magnitude faster than the nuclei
For each small move of the nuclei, the electrons have time to find equilibrium
⇒ Positions of electrons and nuclei can be calculated separately
Quantum mechanics: From fixed nuclear positions, calculate electron

distribution, giving all properties.
Molecular mechanics: Ignore all electrons, assume that they find their
optimum position. Use empirical rules to
calculate the energies of the nuclei.

When Born-Oppenheimer breaks down
Nuclei should in reality be described by very small orbitals (probability distributions),

smaller the heavier the nucleus is.
— For 1H, the distribution width can be non-negligible, and larger than 2H.
We get tunneling and extreme isotope effects (kH/kD > 7).
Extremely rare for non-hydrogen, only at very low temperature.
2H
1H

^
Atomic Orbitals H Ψ= E Ψ
Solving the Schrödinger equation for a single atom yields

the familiar shapes of atomic orbitals:
1s 2s 2px 2py 3dxy 3dz 2
Why? And what are these?

Solving a simple Schrödinger equation
Hˆ " = E " Hˆ = 1 #2
m #x 2
1 #2 "
$ E " = 0 % " = cos Ax
m #x 2
Illustrated as: Electron density:

!

Overlap and orthogonality H Ψ= E Ψ
Negative
overlap Overlap: multiply the values at
All orbitals are orthogonal!
every point in space, add together
Atomic orbitals, s and p: Positive If sum = 0 : orthogonal!
overlap
1s 2s 2px 2py 3dxy 3dz 2
At short distances, orbitals overlap: no longer

Orbitals at long distance
don’t overlap: still valid valid, form orthogonal orbitals by combination
H H !
Large
distance, H H
negligible
overlap H H !*

Quantum mechanics H Ψ= E Ψ
Approximate solutions
With more than one electron in the system, we cannot find exact solutions.
The best possible wavefunction is the one that gives the lowest energy in the Schrödinger
equation. The problem is variational.
Guess a wavefunction, that is, enough molecular orbitals (MOs) to accommodate all
electrons (two electrons with opposite spin in each orbital). Usually, but not always, the
orbitals are linear combinations of atomic orbitals (the LCAO approximation), ϕj=∑cijφi
Ensure that all MOs are orthogonal (diagonalize the overlap matrix).
Make a small variation in the MOs. If the energy goes down, the new wavefunction is
better. Continue until no more improvement can be obtained (the wavefunction is
converged).
– Same type of problem as geometry optimization.

– Use derivatives of the energy with respect to orbital coefficients cij.

Basis sets
Wavefunction (electron distribution) H Ψ= E Ψ
Composed of filled, orthogonal molecular orbitals ψ1 ψ2 ψ3...
In turn made up of atomic orbitals (LCAO) c1φ1+c2φ2+c3φ3...
Self Consistent Field (SCF): vary cn, keep orthogonality, minimize E
Atomic orbitals from exact solution for one-electron system (H)
φn: 1s 2s 2px 2py 3dxy 3dz 2
Functions with value everywhere in space, 90% within the surfaces shown

Actual basis sets
AOs (atomic orbitals) from Gaussian functions
• Wrong shape, use several
• Easy math
AOs variable in size

• Hard math, combine several of different size +
• Example: anions
AOs can change shape

• Polarization functions +
• Example: π-bonds
Costly!
• With N orbitals, at least N2.7 resources (HF, DFT)
• High accuracy methods worse, typically N7

Basis set nomenclature
Minimum basis sets: one set of AOs up to the valence shell
Split basis sets, zeta (ζ) = number of functions/actual AO

• Allow size change, different sizes of each AO to choose from
• Double-ζ (DZ), Triple-ζ (TZ), ... , DZV (split valence only)
• Diffuse (very large): mostly anions, “aug-” or “+”
Polarization, “P”, “*”, or explicit (3d2fg,2pd)

• Allow shape change +
• Mix in higher order AOs (p+d, s+p)
Standard: Double-ζ valence with polarization, possibly not on H

• Examples: DZVP, pDZ, 6-31G*, MIDI!
Correlation-consistent (cc), allows extrapolation to infinity

• cc-DZ (d), cc-TZ (2df), cc-QZ (3d2fg) => ∞Z)
Pople style: 6-31G* (DZVP), 6-311+G** (aug-TZVP)

Extrapolation with basis sets
R Model:
better basis larger system Real:
R
it
il m
Extrapolated value
∞
Model Real
Property[Real,6-311+G(2df,p)] ≈
6-31G* Property[Real,6-31G*]
it + Property[Model,6-311+G(2df,p)]
lim
6-311+G(2df,p) – Property[Model,6-31G*]
∞

Hartree-Fock theory
Major approximation: each electron interacts with the

average field of all other electrons (and the nuclei).
Guess an initial electron distribution.
Calculate the best (=lowest energy) distribution for
each electron in the average field of all other particles.
The new distribution for the electron becomes part of
the new average field for the other electrons.
Vary all distributions until no further change can
decrease the energy (Self Consistent Field, SCF).
Accounts for 99% of the total energy!
Electron density is the square of an orbital. Interactions between two electrons thus require
integration over four orbitals (two for each electron). The time and space requirement for the
calculation is proportional to N4, where N is the number of basis functions.
In practice, products with low overlap are ignored, the real requirement is proportional to N2.7

Electron correlation
The major error in HF comes from violation of the Pauli principle: “Two electrons with the same spin
cannot be at the same position at the same time”.
Wherever an electron is, HF will give a non-zero average density of other electrons.
One solution is to “punch a hole” in the average electron density where the electron of interest is located.
Correlated wavefunctions are always more diffuse (spread out) than HF wavefunctions.
This can be done by mixing in HF excited states, configuration interaction (CI). Variational mixing of
all excited states (full CI) will yield the final truth about life, the universe and everything. Not practical.
Correlation energy is defined as the difference between HF and reality, that is, full CI.
Møller-Plesset: pertubation theory, non-variational “hole-punching”, MP2,
MP3, MP4, ... Also called MBPT.
Coupled cluster (CC): MP partially extended to infinity.
Quadratic CI (QCI): a subset of CC.
Complete active space or multiconfigurational SCF (CASSCF, MCSCF): mix
with selected excitations, optimize these variationally.
Can be limited to single, double, triple, or quadruple excitations (SDTQ).
Popular methods: MP2, CIS (spectroscopy), CISD, CCSD, MP4SDQ,
CCSD(T), RASSCF. Active space methods can be combined with pertubation:
Time-consuming!
CASPT2.
Extrapolation more correlation
Full CI
Combining contributions
better basis
it
Using a good basis set at a high level of theory lim
might be too costly, but can be simulated using Extrapolated value
three affordable calculations. Example:
∞
“MP4/TZ” ≈ MP4/DZ + MP2/TZ – MP2/DZ
The slash / separates level of theory from basis set. Solvation and vibration
contributions might be calculated at lower levels:
G(MP4/TZ) ≈ E(“MP4/TZ”) + ∆Gvib(HF/DZ) + ∆Gsol(HF/DZ)
The geometry is sometimes calculated at a lower level than the energy. This is
indicated by a double slash. MP2/TZ//HF/DZ indicates a HF geometry.
CBS methods (complete basis set): calculation with correlation-consistent basis sets
(eg., cc-DZVP) allow extrapolation to what the results would be with an infinite basis.
Other contributions added as above.
Several other fixed-recipe extrapolations exist, for example, G2 and G3.

Semi-empirical theory (SE)
QM can be applied to anything, but it is time-consuming! Several approximations to HF are possible.
The most time-consuming part of HF is calculating 4-center integrals. Some of these can be assumed to be
constant throughout a chemical reaction, and are replaced by empirical parameters. This is called “neglect
of differential overlap”, NDO, and is used in most popular SE methods (CNDO, INDO, ZINDO, MINDO).
The most modern style, NDDO (Neglect of Differential Diatomic Overlap), is a family of methods
including MNDO, AM1, and PM3 (recently also PM5), differing only in details of parameterization.
Further approximations:
— Treat the core as a constant charge, include only valence orbitals.
— No splitting, only one size of orbitals available (singe-ζ).
Through the empirical parameterization, some correlation is included (right results for the wrong reason).
Correlation can be explicitely added to SE, but be aware of double-counting. Many systematic errors are
known, experience is essential in evaluating the results.
ZINDO-CIS is popular for spectroscopy.
AM1 and PM3 are standard methods for “quick-and-dirty” calculations, or systems that are so large that no
other QM methods can be applied (proteins).
A few methods can handle d-orbitals (transition metals and hypervalent systems): MNDO-d, PM3(tm)
Simpler approach: Hückel, only find orthogonal orbitals, no variational energy improvement.
Unrestricted calculations
For most simple systems, all electrons are paired (closed shell). This is usually imposed as a
restriction in many calculations (RHF, RB3LYP, ...).
– Impossible for open-shell systems (radicals, high-spin metals), homolysis reactions.
Two possible approaches:
Restricted open-shell (RO): all orbitals orthogonal,

either doubly or singly occupied.
– Spin pure, theoretically sound
– Does not account for correlation
ROHF, ROB3LYP, ...
– Hard to implement
Unrestricted (U): α and β treated separately, need

not be orthogonal to each other, just within each set.
– Spin-contaminated, not a true solution
– Includes some static correlation
– Easy to implement UHF, UB3LYP, ...
– Usually better results than RO
Quantum mechanics
Excited states, UV/VIS spectroscopy
E=0 ≈hν
≈IP
Cation Ground Excited Triplet ground

state Excited states triplet state state (O2)
(from CIS) (from UHF)
Ionization potential and excitation energies can be crudely approximated with orbital
energies (trends). For better accuracy, the excited states must be calculated explicitly.
The SCF procedure will cause the electrons to return to the lowest possible energy. The
simplest way to obtain explicit excited states is by configuration interaction (CIS).
The SE method ZINDO gives good accuracy/cost ratio.
Density functional theory
The Schrödinger equation for wavefunctions is exact, but hard to solve. There is a similar,
unknown equation that uses electron densities directly, we can guess what it should look like.
The equations we solve in DFT are approximate, but they are easier to solve than the
Schrödinger equation, and the solutions include some of the electron correlation directly.
First generation: Local DFT (LDA), uses only the density at each point.
Examples: Xα, SVWN
Second generation: Nonlocal DFT (NLDA), uses also the immediate surrounding
(the density gradient). Examples: BP, BLYP
Third generation: Mix between DFT and HF, using a few empirical parameters.
Examples: B3LYP, B3PW91
Other approaches: Include time dependence (TDDFT; necessary for excited states).
Dispersion corrections (Grimme, M06, ...)
Current concerns in DFT
The B3LYP method has been dominant for a decade, but is it the best?
- Dependent on cancellation of errors
Self interaction error, results may be invalid when investigating:

- Multiple spin states
- Charge transfer complexes
Lack of dispersion (vdW attraction)

- May invalidate large systems with significant interactions, DFT is too repulsive
- Can be added explicitly, empirically (Grimme)
- Can be addressed by reparameterization: M06 family
Advice: validate method before starting

- Calculate experimentally known, important observable
? Will changing the method change the property significantly ?
- Use methods isodesmically, try to achieve systematic cancellation of errors!

Quantum mechanics SE Semi-empirical methods
AM1, PM3, MNDO, …
QM methods
HF Hartree-Fock (SCF)
Molecular mechanics DFT Density functional theory
LDA, BP, B3LYP, …
N
MP2 Møller-Plesset perturbation
Hückel
Proteins MP4 to order 2, 4, …
N2 SE CASSCF Multi-determinant SCF.
Complete active space
Mw 1000 DFT CASPT2 CASSCF with perturbation
HF CI Configuration interaction
N4
Rapid
QCI Quadratic CI
N5 MP2 CC Coupled cluster
MP4 SDTQ With the above, which
Mw 100
CA
CISD excitations are included

SS
Slow
(single, double, …)
N7
CF
QCISD(T)
CCSD(T)
CA
SP
T2
Mw 10
N! Full CI
Accuracy
Potential energy surfaces
Good level: B3LYP/6-311G**, Continuum solvation, Harmonic vibrations, Conformations
Typical barrier: ∆E‡ ≈ 100 kJ/mol ; Needed: error ε < ∆∆E‡ (Quant: ε < 2 kJ/mol)
Chemoselectivity Isomeric selectivity
Expected accuracy
!!E ‡AB
‡
!!E AA'
Diastereomers Chemoselectivity: 10-100 kJ/mol
Regioisomers
Isomeric selectivity: 1-10 kJ/mol
!E B‡
!EA‡ A' !!E‡RS Ground states: 1-10 kJ/mol
B Reactant Enantiomers
A
Common approximation Cost in accuracy

Gas phase 20-200 kJ/mol, more if changed charge
Gas phase geometries 2-20 kJ/mol, possibly more
Ignore ZPE 2-20 kJ/mol
Smaller basis (6-31G*) 2-20 kJ/mol
Ignore entropic contributions 1-10 kJ/mol + ca 30 kJ/mol molecularity
Single conformation 1-10 kJ/mol

QM/MM
Etot = EQM + EMM + EQM/MM

QM/MM outer
coupling inner MM
Easiest: QM molecule, MM solvent
QM Otherwise bond broken in coupling
Components of EQM/MM : Electrostatics and vdW; MM with QM charges

Polarization of MM
Polarization of QM
ONIOM (and IMOMM):
Etot = EQM(inner) + EMM(all) - EMM(inner)

Continuum: cavity with
Solvation compensating surface charges
O PCM, COSMO
H3 N
!" !+ !+
O !"
!" !+
O
H3 N
!+
!"
!" O !+
Born: Free energy gain from exposed !" !+
Gas phase
surface of polar atoms, SM2, SM3,... !+ !+
O
O O Explicit solvation (QM/MM)

H3 N
N H
H2
O
O O
H3 N H3 N
Micro-
O
solvation O

Car-Parinello
Dynamics at the QM level
Acceleration of QM to allow dynamics in a reasonable time frame.
Never converge the wave function!
Calculate the gradient of the wavefunction (a

“force”).
When the geometry is updated in time, also

update the wavefunction in the direction of the
“force”.
Free energy reaction profiles can

be obtained by constrained dynamics.

Molecular Energy
Total energy: separate all electrons and nuclei completely (QM)
Atomization energy, heat of formation: separate into component atoms (SE)
— Bond energy: separate molecule into two fragments.
Potential energy: relative to an arbitrary state defined as zero
— Steric energy: relative to a hypothetical unstrained conformation (MM)

— Conformational energy: relative to lowest energy conformation
Isodesmic energy: energy of a reaction where all atoms and bonds stay the same.
Systematic errors tend to cancel, low-quality calculations
can be used for trends (SE).
Example:
NH2 + NH3 NH + NH4

Frontier Orbitals
Most chemical reactions include interaction between a high-energy filled orbital (lone pair, π),
and a low-energy empty (virtual) orbital (σ*, π*).
Nu
HOMO LUMO HOMO
Lp !* Lp
R R'
LUMO
N Cl O !*
H H
H H
Frontier orbitals are easily calculated even by low-level methods, and can be made for qualitative
(or semi-quantitative) predictions about reactivity, especially relative reactivity
LUMO HOMO
!* !
LUMO
!*
Calculated Frontier Orbitals O O
HOMO
LUMO

Isodensity Surfaces O O
All points w. density < 0.002 e–/Å3

inside the surface
Good model of van der Waals surface

Approximate contact distance

Mapping FMO on surfaces O O
LUMO
Also LUMO site,
why not reactive?
LUMO mapped
on ID surface
Possible Nu– attack

Mapping FMO on surfaces O O
HOMO
HOMO mapped
on ID surface

NH2 O
More isodensity surfaces

H2N N O
H

NH2 O
Electrostatic potential
Mapped on isodensity surface H2N N
H
O
Strongly negative
Strongly positive Good interaction
Good interaction with cations
with anions

NH2 O
Solid representation H2N N
H
O

NH2 O
Negative only H2N N
H
O

NH2 O
Positive only H2N N
H
O

Use of electrostatic potential
• Determining charges
- Find the set of atomic charges that reproduces the calculates potential
- CHELPG, ESP, MK
• Interaction sites (complementarity, ligands and receptors)
• Determination of relative reactivity and pKa for related compounds
H
O
X H R3N H
O

QM vs. MM, What to choose?
Quick-and-dirty anything SE
Simple structures MM
“New” systems QM
Large, flexible systems MM
Large, “new” systems QM/MM, or MM parameterization
Solvation
Large biosystems MD/MM, explicit
Small molecules QM, continuum
Medium-size SE, continuum
Mechanisms QM
Reaction selectivity QM/MM, or MM parameterization
Electronic structure QM (SE)
van der Waals attraction MM, or QM/MM.

Example: Dynamic NMR
Conformational equilibria, assignment problem
Leishmania inhibitors isolated from Rubiaceous plants.
Dihydrocorynantheine Corynantheine
N N
N N
H H H H H H
Only difference
H H
MeO OMe MeO OMe
O H O H
Unusual dynamic behavior in 1H NMR

Dynamic NMR Dihydrocorynantheine
Conformational equilibria
Methoxy signals:
N
N
H H H Dynamic (line-fitting):
∆H‡ = 71 kJ/mol
H
MeO OMe Equilibrium (–40°C):
∆G = 1.1 kJ/mol
O H
Population 1:1.7

Dynamic NMR Corynantheine
Methoxy signals:
N
N Population 1:2
H H H Dynamic (line-fitting):
∆H‡ = 60 kJ/mol
H
MeO OMe Equilibrium (–45°C):
∆G = 1.3 kJ/mol
O H

Dynamic NMR Chair-boat or chair-chair?
Inversion?
N
Which process can be slow enough at room N
H H H
temperature to give coalescence? And why
the large difference between ethyl and vinyl?
H Rotation?
MeO OMe
Conformational searches (Monte Carlo in Maestro)
– MMFF: Wide parameterization base, high-quality data, O H
including N-inversion parameters.
– Amber*: Good non-bonded interactions & solvation
Reoptimization in solvent (GB/SA)
Unusual push-pull-system, possibly bad parameters
– Verify by B3LYP/6-31G*
R R
MeO OMe MeO OMe
O H O H
Dynamic NMR
N
N
H H H
COOMe MeO H
H
MeO OMe
O H H OMe
COOMe
Can be identified by low-temperature NOE to MeO-groups. Also: two conformations with
inverted nitrogen, slightly higher in energy by all methods.
– R=ethyl, Amber* identifies the correct major isomer, ∆E = 1.4 kJ/mol (exp. ∆G=1.1 kJ/mol).
Wrong major isomer from the other two methods, B3LYP: 0.1 kJ/mol; MMFF: 2.8 kJ/mol).
– R=vinyl, Amber* good, B3LYP OK, MMFF wrong by ca 10 kJ/mol !
Ester cis-MeO
Dynamic NMR eclipses R eclipses R
Inversion?
N
N
H H H
H Rotation?
MeO OMe
O H
Solvent has negligible effect
Amber*, kJ/mol R=Ethyl R=Vinyl
Observed process 71 60
Rotation ∆E‡ 54 43 <<< Right trend
N-inversion ∆E‡ 33 31
Mechanisms from QM calculations
Tamao-Fleming oxidation
R SiMe2X
H2O2 or R'OOH
or R OH
F–
R SiMeX2
X can be alkoxide, fluoride. The Fleming protocol starts with an aryl silane, and
uses electrophilic substitution to replace Ar with F or AcO on Si.
The mechanism is assumed to go via hypervalent silicon. Penta- or hexa-valent?

Are there hypervalent intermediates, or just transition states? Does the oxidant
react in neutral or anionic form? When starting from alkoxides, several
equivalents of fluoride (or strong base) are needed, why?

Basic level: HF/6-31G* + continuum solvation (single point) + ∆Gtherm

Higher levels tested at the HF geometries
Initial model systems: Me X

Si X=Me or X=F
Me2SiF2 or Me3SiF Me F
H2O2 or HOO–
F– HOO– F–
Locate all X !" F !" F !"2

Me X F– Me F – Me HOO– Me F
Si Si F Si F Si
intermediates Me OOH Me
O HOO– Me
X
Me
X
O OH
OH
and products;
screen geometries F– HOOH
–
- OH– - OH - H2O - OH–
using MNDO-d
Me X F– F !"
F
Si Me Si
MeO F X
OMe

Me X
Si X=Me or X=F
Me F All intermediates and
–
HOO transition states in this study
–F–
HOO– F–
X !" F !" F ! "2

Me X F– Me F– Me HOO– Me F
Si Si F Si F Si
Me OOH Me HOO– Me Me O OH
O X X
OH
F– HOOH
F !" ‡ " ‡ F " ‡ F ‡

F !
"2
Me X ! Me Me F !
Me Si F Si Si
Si X Me O O
Me O Me O Me
X OH X OH
OH OH H
- OH– - OH– - H2O - OH–
Me X F !"
F– F
Si Me Si
MeO F X
OMe

At HF/6-31G* geometries:
Me X !
" ‡
Me
F
F
!" ‡ B3LYP/6-31+G* and
Si
Si F
Me O
MP2/6-311+G** similar
Me O
OH
X
H
OH – converged level
Lower levels not accurate

enough.
B3LYP/6-31+G* is the
same optimized as with
HF/6-31G* geometries, so
the structures are good
enough.
Pentavalent intermediates
preferred (gas phase).
Which TS is most favored?

Tamao-Fleming oxidation Me X
Si
Preferred path: Me F
HOO–
X !"
Me
Si F
Me
O
OH
" ‡
Me X !
Si F
Me O
OH
Me X
Si
MeO F
F–
F !"
F
Me Si
OMe
X

Extended model systems,

Tamao oxidation: Me2Si(OMe)2
All pre- and post-equilibria with F–
Both possible transition states
Free energies at B3LYP/6-31+G*
(incl. SP solvation)

a: no F
b: 1 F
c: 2 F
d: 3 F
e: 4 F

Summary, Quantum Mechanics
Can address anything!
Time constraints
Method choice
- Standard: B3LYP/6-31G* (DFT, double-ζ basis)
Beyond potential energies:

- Vibrational free energies
- Solvation
Combine different levels
Validate!

Not recommended reading
"Every attempt to employ mathematical methods in

the study of chemical questions must be considered
profoundly irrational and contrary to the spirit of
chemistry. If mathematical analysis should ever hold
a prominent place in chemistry - an aberration which
is happily almost impossible - it would occasion a
rapid and widespread degeneration of that science.”
A. Comte (1830)


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Molecular Modeling

UWI-Mona Per-Ola Norrby University of Gothenburg

Quantum Mechanics (QM) Reaction mechanisms

Molecular Mechanics (MM) Structure, conformational energies

QM/MM QM reaction center, MM outside

UWI-Mona Per-Ola Norrby University of Gothenburg

UWI-Mona Per-Ola Norrby University of Gothenburg

⇒ Positions of electrons and nuclei can be calculated separately

Quantum mechanics: From fixed nuclear positions, calculate electron

UWI-Mona Per-Ola Norrby University of Gothenburg

Nuclei should in reality be described by very small orbitals (probability distributions),

UWI-Mona Per-Ola Norrby University of Gothenburg

Solving the Schrödinger equation for a single atom yields

1s 2s 2px 2py 3dxy 3dz 2

Why? And what are these?

UWI-Mona Per-Ola Norrby University of Gothenburg

Illustrated as: Electron density:

UWI-Mona Per-Ola Norrby University of Gothenburg

1s 2s 2px 2py 3dxy 3dz 2

At short distances, orbitals overlap: no longer

UWI-Mona Per-Ola Norrby University of Gothenburg

– Same type of problem as geometry optimization.

UWI-Mona Per-Ola Norrby University of Gothenburg

In turn made up of atomic orbitals (LCAO) c1φ1+c2φ2+c3φ3...

Self Consistent Field (SCF): vary cn, keep orthogonality, minimize E

Atomic orbitals from exact solution for one-electron system (H)

φn: 1s 2s 2px 2py 3dxy 3dz 2

UWI-Mona Per-Ola Norrby University of Gothenburg

AOs variable in size

AOs can change shape

UWI-Mona Per-Ola Norrby University of Gothenburg

Split basis sets, zeta (ζ) = number of functions/actual AO

Polarization, “P”, “*”, or explicit (3d2fg,2pd)

Standard: Double-ζ valence with polarization, possibly not on H

Correlation-consistent (cc), allows extrapolation to infinity

Pople style: 6-31G* (DZVP), 6-311+G** (aug-TZVP)

UWI-Mona Per-Ola Norrby University of Gothenburg

UWI-Mona Per-Ola Norrby University of Gothenburg

Major approximation: each electron interacts with the

UWI-Mona Per-Ola Norrby University of Gothenburg

Several other fixed-recipe extrapolations exist, for example, G2 and G3.

Two possible approaches:

Restricted open-shell (RO): all orbitals orthogonal,

Unrestricted (U): α and β treated separately, need

Cation Ground Excited Triplet ground

Self interaction error, results may be invalid when investigating:

Lack of dispersion (vdW attraction)

Advice: validate method before starting

UWI-Mona Per-Ola Norrby University of Gothenburg

CISD excitations are included

Common approximation Cost in accuracy

UWI-Mona Per-Ola Norrby University of Gothenburg

Etot = EQM + EMM + EQM/MM

Components of EQM/MM : Electrostatics and vdW; MM with QM charges

ONIOM (and IMOMM):

Etot = EQM(inner) + EMM(all) - EMM(inner)

UWI-Mona Per-Ola Norrby University of Gothenburg