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BGSU

Introduction to Computational
Chemistry
Target: Computer simulations are employed to study the
structure and reactivity of single molecules and molecular
systems (molecule in solution, in a macromolecular cavity,
in a membrane or in a crystal).

Tools: We use a series of hardware and software

technologies to describe the electronic and geometrical
structure of molecules and their time evolution.

(visit http://www.lcpp.bgsu.edu) courses

A. Leach, Molecular Modeling (2nd Edition) textbooks

F. Jensen, Introduction to Computational Chemistry (2nd Edition)
I. N. Levine, Quantum Chemistry (7th Edition)
n PLEASE, TAKE NOTES!
UNISI
eng

The Mulliken’s dream

BGSU

Robert Mulliken, Nobel Lecture, 1966

“…In conclusion, I would like to emphasize

strongly my belief that the era of computing
chemists, when hundreds if not thousands of
chemists will go to the computing machine instead
of the laboratory for increasingly many facets of
chemical information, is already at hand…”

Software: Language (Fortran, C, C++, etc.), Compilers, Parallelization

Theories: Molecular Orbitals rather than Atomic Orbitals for the description of the electronic structure of molecules

Faster computations Slower computations

 UNISI
eng
BGSU Hardware Technologies
Computer Speed:
No. of Transistors
MIPS (Millions of Instructions/Sec)
FLOPS (Floating Point Operations/Sec)
Benchmarks (http://www.spec.org/)

IBM RoadRunner, 1 petaflops

R. Mulliken (6,912 AMD Opteron 2210 + 12,960
IBM Power XCell), November, 2008.

Present speed

Dual-core Intel Xeon Woodcrest 64 CPUs

30 gigaflop each, 2006

CRAY Y-MP C90, 16 CPUs 1 gigaflop each

LCPP@BGSU
PostDoc in London
IBM 701 was formally announced on May 21, 1952.
It could perform more than 16,000 addition or subtraction
operations a second.
 What is the course about ?
UNISI
eng
BGSU

Part 1

Organic Chemistry: organocatalysis

10-10 (1 Å) - 10-9 m

Part 2

Bioorganic Chemistry: peptide conformations

Part 3 10-9 - 10-8 m

Photochemistry & Photobiology: olefins, vision & switches

Tutorial (Hands-on)

> 10-8 m (proteins)

 Part 1.The Aldol Reaction

UNISI
eng
BGSU

(using the computer to investigate reaction

mechanisms)
- O

M + https://en.wikipedia.org/wiki/Aldol_reaction

R1

O O O OH
M +
+
R1 H R2 R1 * * R2
-
enolate aldehyde
β-hydroxyketone
(reactant) (substrate)
UNISI
eng
BGSU

The (1957) Zimmerman-Traxler 


Transition State 

Counterion (e.g. Li+)

R1 ‡ R1
‡
R2 O OH
H δ- M + δ- M +
O
Me O
or Me
δ- O δ-
H
O
R1 * * R2
R2
H H
Me

Disfavored racemate
Favored (1,3-diaxial repulsion)
 The Intramolecular Proline

UNISI
eng
BGSU

Catalyzed Direct Asymmetric Aldol

1970 - Hajos et al. (La Roche) & Eder et al. (Schering)

* CO2H

N
H

CH3CN

racemate single enantiomer

yield (95-100%)
e.e. (90-96%)
Expression for yield ?
Expression for e.e. ?
BGS
U The Intermolecular Proline

BGSU

Catalyzed Direct Asymmetric Aldol

2000 - List et al.
* CO2H

N
H

CRAM ?

single enantiomer
UNISI
eng
BGSU

The Catalyst
Structure
Requirements
Five membered ring
required
 The Catalyst Structural
UNISI
eng
BGSU

Requirements

(5,5-dimethyl thiazolidinium-4-carboxylate)
BGS
U

The Mechanism
Water is not well tollerated: unperturbed intramolecular
hydrogen bonding through -COOH must be important.
UNISI

Aldolase I and II
eng
BGSU

R1
N
Enamine M O Enolate
Me δ+ δ-
R1 H

Me
H

nucleophilic attack
UNISI
BGSU
eng

Entiomeric Zimmerman-Traxler 

Transition States 

Counterion (e.g. Li+)
H
δ- ‡
R1 ‡ R1
M +
H O OH
δ- M + R2
O
O
Me O
or Me
δ- O δ- R1 * * R2
R2
H H
Me

Attack on Re face Attack on the Si face

Major Enatiomer
Favored Disfavored (mirror image). How ?

Requires a chiral molecular environment

 The Proposed Mechanism for Proline Catalyzed
UNISI
eng
BGSU Aldol Reaction

Proline (chiral catalyst)

* * *
aldehyde O
(substrate)
ketone O

N H

*
O
*
*
*
Zimmerman-Traxler-type
chiral enamine
(new reactant)
Nonacyclic TS
*
*
chiral β-hydroxyketone

rate determining
step
 The Enantioselectivity
UNISI
BGSU
eng

Two Zimmerman-Traxler type nonacyclic TS’s:

Target: predict computationally the enantioselectivity.

*
O

anti OH
O

R Re face
H *
anti,Re
*
*

syn,Si
O
* *
H
Si face
R
*
O

syn N
OH
UNISI

The Curtin-Hammett Principle

eng
BGSU

kA→C KAB kB→D

C A B D

anti,Re TSB→D
ΔG TSA→C syn,Si
ΔG‡B→C A ΔG‡B→D
B

weakly bounded D
C complexes

Reaction Coordinate

Target: compute the free energy difference between TSA→C and TSB→D
UNISI
eng
BGSU

The Curtin-Hammett Principle

Nu → Re face

TSA→C A
B
ΔG
C TSB→D
Nu → Si face

n
tio
sa
con D
en

for.
chan
nd

ge
co
UNISI

Enantioselectivity and

eng
BGSU

Potential Energy Barriers

The Curtin-Hammett principle states that:

D:C = kB→D[B]:kA→C[A] = kB→D[B]:(kA→C/KAB)[B] =

ΔG ‡
The rate constant kT − RT
D
−1 expression is: k= e
e.e. = C #D &
×100 % ≥ 1( h
D $C '
+1
C

€ D:C = exp[(ΔG‡B→C-ΔG‡B→D)/RT] homework !

€
UNISI
BGSU

The Curtin-Hammett Principle

eng

ΔG‡B→C-ΔG‡B→D

TSB→D
ΔG TSA→C
A B ΔG‡B→D
ΔG‡ B→C

D
C

Reaction Coordinate

Target: compute the free energy difference between TSA→C and TSB→D
 No

Enantioselectivity and

UNISI
eng
BGSU

Potential Energy Barriers

change in order/organization

ΔG‡=ΔH‡-TΔS‡

if ΔSB→C‡ ≈ ΔSB→D‡ then

ΔGB→C‡-ΔGB→D‡ = ΔHB→C‡-ΔHB→D‡
change in size

if ΔVolB→C‡ ≈ ΔVolB→D‡ then

ΔHB→C‡-ΔHB→D‡ = ΔUB→C‡+PΔVolB→C‡- ΔUB→D‡-PΔVolB→D‡=

ΔUB→C‡- ΔUB→D‡
 UNISI
BGSU
eng Enantioselectivity and Potential
Energy Barriers
Only final formula

3m− 6
ΔU = ΔV + Δ
$1 '
∑ &% 2 hν i )(
i
change in bonding (except reaction coordinate)

3m−6 3m−6
%1 ( ‡ %1 (
if B→C‡ ∑ & 2 i *) ≈
' − h ν B→ D ∑ & 2 i *) then
€ ' − h ν
i i

UB→C‡- UB→ D‡= VB→ C ‡- VB→ D ‡

€ €
in conclusion:

D:C = exp[(VB→C ‡- VB→ D ‡)/RT]

Ratio between the
velocities of the two
competing reactions
UNISI
eng
BGSU

The Potential Energy V(R)

Molecules are nuclei + electron gases

electron density

Experimental (x-ray crystallography) Computed (HF method)

 UNISI
eng
BGSU

The Potential Energy V(R)

Molecules are nuclei + electron gases

Proton 2 Electron 2

H H
Electron 1 Proton 1

The Scrhödinger Equation (time-independent)

Erwin Schrödinger
(1887-1961) HΨ = EΨ

kinetic energy
H = [T(r1) + T(r2) + T(R1) + T(R2)] +
[V(r1,r2)+V(R1,R2)+V(R1,r1)+V(R1,r2)+V(R2,r1)+V(R2,r2)] potential energy
UNISI

The Potential Energy V(R)

eng
BGSU

Proton 2 Electron 2

R2 Electron 1
r2
R1
r1 Proton 1

kinetic energy operator

T= -1/2m ∇2
V= -Z1Z2 / d12 d12=R1-R2
Erwin Schrödinger
potential energy operator
(1887-1961)

not separable
H = [T(r1) + T(r2) + T(R1) + T(R2)] +
[V(r1,r2)+V(R1,R2)+V(R1,r1)+V(R1,r2)+V(R2,r1)+V(R2,r2)]
UNISI
eng
BGSU

The Potential Energy V(R)

Born-Oppenheimer Approximation

Nuclear part of the Schrödinger Equation:

[Tn(R) + Vnn(R) + Eel(R)] χ = Etot χ
nuclear coord.
V (R) ← Potential Energy

Electronic part of the Schrödinger Equation:

[Te(r) + Vee(r) + Ven(r,R)] ψ = Eel(R) ψ
electronic coord.
R = parameter
 UNISI
eng
BGSU

The Potential Energy V(R)

Nuclear part of the Schrödinger Equation:

[Tn(R) + Vnn(R) + Eel(R)] χ = Etot χ
nuclear coord.
V (R) ← Potential Energy

H H Eel(R) V12(R)+Eel(R)
bond
Proton 2 bond length
Proton 2 Proton 2 angle
Electron 2

Electron 1 Proton 1 Proton 1 Proton 1

Molecular
V12(R) Structure

Forces along 3n-6

coordinates
UNISI
eng
BGSU
The (3N-6 Dimensional)

Potential Energy Surface

of a Chemical Reaction

[Tn(R) + Vnn(R) + Eel(R)] χ

UNISI

Transition State
eng
BGSU

http://www.hyle.org/journal/issues/8-2/bio_nye.html

Computational chemistry: methods (software)

In 1929 he developed with Henry Eyring the

procedure that came to be called the semi-empirical
quantum chemistry method for predicting activation
energies (potential energy barriers) for chemical
reactions…….Eyring and Polanyi co-authored paper
presented the first potential energy surface for
chemical reactions, using a new language of the
saddle-points or cols, valleys, barriers, and passes
Michael Polanyi for understanding the energy transition from
reactants to products.
(1891-1976)
Computational chemistry: concepts

Evans, M.G.; Polanyi M. (1935) Trans. Faraday Soc. 31: 875.

Eyring, H. (1935) J. Chem. Phys. 3: 107.
UNISI
eng
BGSU

Stationary Points:
Gradient

and 

Hessian

of V(R) in a
“2D molecule”
UNISI
eng
BGSU Stationary Points: Force Constants

Hessian Matrix

of V(R)

H11 H12 H1n

H21 H22

HN1 HNN
in a
Hij
“hypothetic 2D molecule”
UNISI
eng
BGSU Stationary Points: Force Constants
redo

potential energy
x1,y1,z1
d1= C-H1
H1 H1
a1= H1-C-H2 C C x3,y3,z3
H2 H2
d2= C-H2 x2,y2,z2
internal coordinates (3N-6) cartesian coordinates (3N)

geometrical structure or
in a geometry
“2D molecule”
 BGSU
Stationary Points: Force Constants
Hessian matrix in internal: 3N x 3N where N=3n-6 (n=number of nuclei)

H11 H12 H13 H1N H11 0 0 0

𝛿2V H21 H22 H23 0 H22 0 𝛿2V
Hij = Hii=
𝛿qi𝛿qi H31 H32 H33 0 0 H33 𝛿Qi2

HN1 HNN 0 HNN

Hessian computed using Hessian computed using

mass-weighted mass-weighted
internal (arbitrary) or in mass-weighted normal
cartesian coordinates: coordinates:
d1= C-H1
H1
q1=d1 Q1=d1+d2
C
H2
q2=d2 Q2=d1-d2
d2= C-H2
BGSU
Stationary Points: Force Constants

In order to find the normal coordinates we need to find the 3N-6 molecular
displacement that correspond to independent (uncoupled) vibrational motions
within a quadratic (local) representation of the potential energy surface:

Mass-weighted
internal coordinates q=
i
mi x i Etot
(internal or cartesians)

Normal Coordinates Etot

see classification
of stationary points

Normal coordinates are linear combination of mass-waighted internal or cartesian

coordinates
Stationary Points for a “2D Molecule”:
UNISI
eng
BGSU

Force Constants
in mass-weighted
internal (arbitrary) or
q2 cartesian coordinates
q1
H12 q=i
mi x i

q1
H21 H22
in mass-weighted
€ normal coordinates Qi
q2
1
ωi = FKiii
H11 2π
H22 vibrational frequency

€
Ki = Hii
(eigenvectors) (eigenvalues)
UNISI

Vibrations of a “3D Molecule”

eng
BGSU

basis
q1 q2 q3
𝛿2V
H q1=d1 q1 H11 H12 H13 Hij=
𝛿qi𝛿qi
q3=a1 C
q2 H21 H22 H23
H q2=d2
q3 H31 H32 H33
Methylene
force constant (scalar)

H11 H12 H13 c1 c1 Eigenvalue problem:

H21 H22 H23 c2 = k c2

Hc=kc
H31 H32 H33 c3 c3
Matrix
Matrix Vector Scalar
Orthonormal basis forms a Vector
UNISI

Vibrations of a “3D Molecule”

eng
BGSU

Eigenvalue problem:

H11 H12 H13 c1 c1 H11- k H12 H13 c1 0

H21 H22 H23 c2 = k c2 H21 H22- k H23 c2 = 0
H31 H32 H33 c3 c3 H31 H32 H33- k c3 0

System of linear equation:

(H11- k) c1 + H12c2 + H13c3 = 0 for n linear equation in n unknown

H21c1 + (H22- k) c2 + H23c3 = 0 use Cramer’s Theorem

H31c1 + H32c2 + (H33- k) c3 = 0 C1=C2=C3=0 is a trivial solution

UNISI

Vibrations of a “3D Molecule”

eng
BGSU

from Cramer’s Theorem

Secular equation:

H11- k H12 H13

3rd degree polynomial
Det H21 H22- k H23 =0 equation (three solutions
or roots)
H31 H32 H33- k

Eigenvalues (non-trivial solutions of the Secular equation):

k = k1 k = k2 k = k3
UNISI

Vibrations of a “3D Molecule”

eng
BGSU

Eigenvector computation

(H11- k1) c1 + H12c2 + H13c3 = 0 Q1=d1+d2

H
H21c1 + (H22- k1) c2 + H23c3 = 0 Eigenvalue k1
C Eigenvector 1
H31c1 + H32c2 + (H - k1) c = 0 𝛿2V
33 3
k1 = H + d2
𝛿Q12
(H11- k2) c1 + H12c2 + H13c3 =0 Eigenvector 2
H
H21c1 + (H22- k2) c2 + H23c3 =0 Eigenvalue k2
H31c1 + H32c2 + (H - k2) c Q3=d1-d2 C
=0 𝛿2V
33 3
k2 = H
𝛿Q22
(H11- k3) c1 + H12c2 + H13c3 =0 Eigenvector 3
H21c1 + (H22- k3) c2 + H23c3 H
=0 Eigenvalue k3
H31c1 + H32c2 + (H - k3) c =0 C
33 3 𝛿2V Q2=a1
k3 = H
𝛿Q32
Stationary Points for a “2D Molecule”:
UNISI
eng
BGSU

Saddle Point
redo
Transition vector

H11= K1 H22= K2 >0

H 22

𝛿2V 𝛿2V
k1 = k2 =
𝛿Q12 𝛿Q22
UNISI

The Reaction Coordinate “s“

eng
BGSU

Requires the Hessian at TS in mass-weighted coordinates qi

R(s)= c1(s) q1 + c2(s) q2

dR(s) g(R) when g(R) is 0 (at TS) then:

=−
ds g(R) dR(s)/ds = Q1 or - Q1
Q1

q2
€ dV
dqi (s) dq i = 1,3N
=− i
ds dV
dqi

q1 € to the curve “R(s)”

Tangent (unit) vector
UNISI
eng
BGSU The Reaction Coordinate “s“
Reaction Path, R(s) = q1(s), q2(s) q1 and q2 in mass-weighted
coordinates:
Reaction Coordinate, s

B dq1(s)/ds=-dV(q1,q2)/dq1
H dq2(s)/ds=-dV(q1,q2)/dq2
C
after integration:
H TS C
H q2=d1 q1(s), q2(s)

d1H R(s)
q2(s)
a1 C R(s)
q1(s)
H A Tangent (unit) vector to curve “R(s)”

q1=a1
UNISI

Vibrations of a “3D Molecule”

eng
BGSU

Rewriting the Hessian using the eigevectors as new coordinates (a new orthonormal basis):

Q1 Q2 Q3
H11- k 0 0
Q1 H11 0 0
Det 0 H22- k 0 =0
Q2 0 H22 0
0 0 H33- k
Q3 0 0 H33
molecular vibrations

Eigenvalues (solutions):

H11 = k1 H22 = k2 H33 = k3 k1

k2
for an energy minimum:

H11 > 0 H22 > 0 H33 > 0 Q1

Q2
UNISI

Vibrations of a “3D Molecule”

eng
BGSU

An equilibrium three-atomic molecule has an Hessian matrix of the following form (in mass-
weighted internal coordinates (kcal mol-1)2 / amu Å2

q2
q1 q2 q3 q1 q3

q1 2 0.0 0.0
find:

q2 0.0 5 -1 a) if the molecule is located in a V(R) minimum

b) its vibrational frequencies
q3 0.0 -1 4 c) its vibrational modes

2- k 0 0 (2- k)(5-k)(4-k)-(2-k)=0
Det 0 5- k -1 =0 ……. continue
0 -1 4- k homework !
UNISI

V(R) Mapping → Chemistry

eng
BGSU

d2V (R)/dR2

Optimization methods

Energy Profile along

the Reaction Path
dV(R)/dR

V(R)

dR(s)/ds=-dV(R)/dR =s
 UNISI
eng
BGSU
Computational Chemistry Technologies

(and Model Chemistries) for getting V(R)

Classical
Biomolecules
Molecular Mechanics (Part 2)
(MM2, Amber, Charmm, …)

Semiempirical e.g. Polanyi

Computational (ZINDO, AM1, MNDO, …)
Cost organic and organometallic
Quantum

chemistry
DFT
(B3LYP, PBE, BPW91…) excited states
(Part 3)

Ab initio (first principle or HF-based)

(HF, CISD, CASSCF, … , MRCI, FCI)
LCPP@BGSU Exact
UNISI
eng
BGSU

The Potential Energy V(R)

Nuclear part of the Schrödinger Equation:

[Tn(R) + Vnn(R) + Eel(R)] χ = Etot χ
nuclear coord.
V (R) ← Potential Energy

H H Eel(R) V12(R)+Eel(R)
Proton 2
Proton 2 Electron 2 Proton 2

Electron 1 Proton 1
Proton 1 Proton 1

V12(R)
 UNISI
eng
BGSU
The Electronic Energy: Quantum
Chemical Technologies
Electronic part of the Schrödinger Equation:

Hel [Te(r) + Vee(r) + Ven(r,R)] ψ = Eel(R) ψ

The correct wavefunction ψtrue:

e-
Homolysis (degenerate electronic states)
e- e- Fermi hole e-

Coulomb hole
ψtrue (r1, s1, r2, s2, ... , rN, sN)
describes the simultaneous e-

motion of many electrons in the e-

e-

electrostatic field of fixed nuclei

Nuclear Cusp
(charge density)
 The Electronic Energy: Quantum
UNISI
eng
BGSU

Chemical Technologies
Physics: Total Charge Density
2
δ (r) = N ∑ ...∑ ∫ dr1 ... ∫ drN ψ ( r1,s1,r2 ,s2 ...rN ,sN )
s1 sN

Technology (man-made): all-electron wavefunction

€ ψtrial = ( ,..., , )
mathematical formulation of the: MOs
Wavewfunction AOs

The “technological” wavefunction is mathematical formulation of the AOs:

a mathematical expression
containing “hydrogen-like orbitals” Basis Set
UNISI Ab initio (from first principles) Quantum Chemical
eng
BGSU Technologies: The Pople Diagram

Better description of the HF Coulomb hole and

Nuclear cusps
Atomic Basis Set (Atomic Orbitals)

e- EXACT
infinite b asis s et

6-311+ + G **

6-311G ** increa sing acc urac y,

increa sing c pu time
6-311G * inc reas ing
size of Fermi hole
3-21G * bas is s et
e- e-
3-21G

ST O -3G
Homolysis
ST O inc reas ing level o f theory

full e - e-
e- HF CI S CIS D CIS DT M P2 MP3 MP4 co rrelation FCI
e-
Fermi hole e- ca. DFT
Mathematical expression (level of theory) of the Coulomb hole
Wavefunction
 How to get a good wavefunction (good charge density): The
UNISI
eng
BGSU
Eigenvalue Problem

Electronic part of the Schrödinger Equation:

Hel [Te(r) + Vee(r) + Ven(r,R)] ψ = Eel(R) ψ

linear operator function constant

Hel ψ = Eel(R) ψ
r) + Ven(r,R)] Eigenvalue problem:

Hc=kc
Scalar
Matrix representation
Vector representation
Approximate Eigenvalue
Exact Eigenvalue
ψtrial ∼ ψtrue
Eigenvector
ψ trial H el ψ trial
Eigenvalue E el ( R) trial = ≥ E el ( R) true
ψ trial | ψ trial
 How to get a good wavefunction (good charge density): The
UNISI
eng
Variational Principles
BGSU

Schrödinger’s Electronic Wavefuction:

Physics
(unkown ψtrue)
ψ trial H el ψ trial HF
E el ( R) trial = ≥ E el ( R) true
Technology ψ trial | ψ trial methods
(man made ψtrial)
Hohenberg and Khon’s proofs (1964): Existence and
Variation
€
For the ground state there is a one-to-one correspondence
between charge (electron) density δ and the electronic
energy E and therefore:
δtrial(R) δtrue(R)
DFT
E el (δ ) trial ≥ E el (δ ) true
methods
 UNISI How to get a good wavefunction:

eng
The Variational Principle
BGSU

nuclear coord.

ψ trial H el ψ trial
E el ( R) trial = ≥ E el ( R) true
ψ trial | ψ trial
variational param.
vector of variational parameters
Rayleigh ratio

trial
E(R,c)

best

ctrial cbest c
UNISI How to get a good wavefunction:

eng
BGSU
The Variational Principle

ψ trial H el ψ trial Basis of the HF and Post-

E el ( R) trial = ≥ E el ( R) true HF Methods:
ψ trial | ψ trial
variational coefficient
Linear trial function with
respect to Ci
ψ trial H el ψ trial
E el ( R) trial = ψ trial = ∑ c iξi Orthonormal set
ψ trial | ψ trial i function of the electronic coordinates

Basis functions (fixed)

Variational coefficients (variable) Integrals (fixed)
Matrix Elements (fixed)

∑ c c €ξ H
i j iξj el ∑ c ic j H ij
E el ( R) trial =
ij
E el ( R) trial = ij Notice that ξi = any basis
∑ c ic j ξi | ξ j ∑ c ic j Sij function. It can be an
ij ij atomic orbital, a Slater
determinant or a CSF
UNISI
eng
BGS
BGSU How to get a good wavefunction:

U
The Variational Principle

Basis functions (a complete set of Matrix elements of the Hamiltonian operator

orthonormal functions)

Linear variational coefficients

∑c c i j ξ i H el ξ j ∑c c H i j ij
ij ij
E el (R) trial = =
∑c c i j ξi | ξ j ∑c c S i j ij
ij ij
Overlap matrix of the basis
BGS One way of getting a good wavefunction:

UBGSU
The Independent Particle Model

Hel =
2

i
+

Hel =
2

i
+

Hel = i
2
= hel(ri) N
φ i = ∑ c ijξ j
j

hel(ri) =
2 Hartree product Molecular Orbitals
i uncorrelated electronic motion
Pauli’s exclusion principle is not
satisfied
€
ψ trial = ∑ c iξi =
i
 UNISI Electronic Energy Computation with the Independent
eng
Particle Model: HF
BGSU

The Fermi hole is correctly described in Hartree-Fock wavefunction but the Coulomb hole and the
Homolysis are poorly described (> 5% of the electron-electron repulsion is missing).

Electrons are Far to large for chemical accuracy

indistinguishable.
Therefore we have to
basis set
replace the Hartree
product with the

…
Slater determinant:
φ1 (1)α (1) φ1 (1)β (1) ... φ n (1)β (1)
2
φ1 (2)α (2) φ1 (2)β (2) ... φ n (2)β (2)

n0 electrons
ψ HF = Det 2
... ... ... ...
φ1 ( n )α ( n ) φ1 ( n )β ( n ) ... φ n ( n )β ( n )

…
2
the n=electrons

wavefunction N
φ i = ∑ c ijξ j
€ N=atomic orbitals
the MOs j

variational atomic basis = AOs

coefficients
 BGS
UUNISI

The Slater Determinant

eng

is a n x n matrix (n = number of electrons)

monoelectronic wavefunction
Satisfies the Pauli exclusion principle
(molecular orbital)
electronic coordinates
spin wavefunction
spin coordinate
spin-orbital
φ1 (1)α (1) φ1 (1)β (1) ... φ n (1)β (1)
2
φ1 (2)α (2) φ1 (2)β (2) ... φ n (2)β (2)
ψ HF = Det 2
... ... ... ...
φ1 ( n )α ( n ) φ1 ( n )β ( n ) ... φ n ( n )β ( n )
2
n=electrons
simplified
notations
€
2n 2n or
BGSU
Electronic Energy Computation: HF
UNISI
eng
Describe the relationship between the
variational principle and the Fock equations.
nel of occupied spin orbitals constructed with N basis set functions

Nel electrons
φ1 (1)α (1) φ1 (1) β(1) ... φ n (1) β(1)
φ (2)α (2) φ1 (2) β(2) ... φ n2(2) β(2)
ψ HF = Det 1
... ... ... 2 ...
φ1 ( n )α ( n ) φ1 ( n ) β( n ) ... φ n ( n ) β( n )
2
n=electrons

ψ HF H el ψ HF
€ E el ( R) HF = ≥ E el ( R) true VMF (i)
ψ HF | ψ HF
replace

Hel =
2
+
i
Vladimir Fock €
December 22, 1898–December 27, 1974 Main idea: replace the two electron term with a
potential of mean force VMF depending on the sum
of functions. In turn, each function in the sum is
depending from the coordinates of one electron.
 Electronic Energy Computation: HF
BGSU
UNISI
eng
Describe the relationship between the
variational principle and the Fock equations.
n0 spin orbitals constructed with N basis set functions

n0 electrons
φ1 (1)α (1) φ1 (1) β(1) ... φ n (1) β(1)
φ (2)α (2) φ1 (2) β(2) ... φ n2(2) β(2)
ψ HF = Det 1
... ... ... 2 ...
φ1 ( n )α ( n ) φ1 ( n ) β( n ) ... φ n ( n ) β( n )
n=electrons 2

€ Hel = fk ?
k
fk = Fock operators

k=1,Nel
ˆf = − 1 ∇ 2 − ∑ Z i + V HF {kj}
k k i
Vladimir Fock 2 i rki
December 22, 1898–December 27, 1974
k function depending from the space coordinates of one electron
size of basis set
(one equation for each molecular orbital)
 UNISI
BGSU
Electronic Energy Computation: HF

How to compute the molecular orbitals efficiently ?

There are N MOs

fˆkφ k = ε kφ k Fermi hole

Occupied MOs
Fock operator (for each orbital k) Exchange
total number of nuclei total number of occupied MOs

⌢ 1 2 M
Zi N
ˆf = − 1 ∇ 2 − ∑ Z i + V HF {kj}
fkk = − ∇ k − ∑ + ∑ ( 2Jk j ( k2) −kK j (i kr)ki i )
2 i rki
€ j
electron in orbital k interacting with electron in orbital j Coulomb average
e-
e-
Mean field electrostatic interaction:
€ Mean field exchange interaction:

1 1
Jji (k) = ∫ ∫ φjiφji r φkφk dr1dr2 Kji (k) = ∫ ∫ φjiφk r12
φjiφ k dr1dr2
12
 UNISI Electronic Energy Computation: HF
BGSU

A physical picture of Coulomb and Exchange interactions:

J1,2= ∫ |φ1(r)|2 e2/|r-r’||φ2(r’)|2 dr dr’ = ∫ J1(r) |φ2(r’)|2 dr’ = ∫ |φ1(r)|2 J2(r’) dr

(-)
Electrostatic Repulsion

e-
Coulomb operator e- (-)
operates on Φj (r’)

K1,2= ∫ φ1(r) φ2(r’) e2/|r-r’|φ2(r) φ1(r’)dr dr’

Exchange operator
operates on Φj (r’) and Φk (r’)
BGSU Electronic Energy Computation: HF
UNISI
eng
MO energies
one equation for N
each MO fˆk φ k = ε k φ k MOs φ i = ∑ c ijξ j
matrix elements of the j
matrix representation of
the Fock operator
molecular orbitals εn φn = cn,0ξ0 + cn,1ξ1 +… + cn,µ ξ µ … + …
Secular equations: €
N € basis = atomic orbitals

…
φ i = ∑ c ijξ j
j

‘
f µν = ξ f ξ ‘ ‘ ‘ ε1 φ1 = c1,0ξ0 + c1,1ξ1 +… + c1,µξµ …+…
µ ν Sµν = ξ ξµ ν
=0
Atomic orbital
(basis functions)
fc = εc Hc=kc
Eigenvalue Problem ε0 φ0 = c0,0ξ0 + c0,1ξ1 +… + c0,µξµ …+…
Fock matrix
€ The number of orbitals
equal the number of basis functions
(“atomic” orbitals).
Molecular orbitals coefficients (eigenvectors)
Molecular orbital energies (eigenvalues)
 Electronic Energy Computation: HF
UNISI
BGSU

Orbital energies: kinetic energy of the electron + the energy resulting from the averaged
interaction of the electron with the other 2N-1 electrons.

total number of orbitals total number of occupied orbitals

N Nocc
E el ( R) = ∑[2εk − ∑ (2J kj − K kj )]
k=1 j=1

N
2
Electron density ρ = ∑ φk
k
€ Orbitals: linear combinations of atomic orbitals with cik
being the variational coefficients.
UNISI
eng Electronic Energy Computation: HF
BGSU

ENIAC, short for Electronic Numerical Integrator

and Computer

Douglas Hartree
27 March 1897 – 12 February 1958
UNISI
BGSU
Density Functional Theory
Hohenberg-Kohn existence theorem:

Kohn-Sham approximate solution (1965):

3 ρ (1) ρ (2) Z i ρ(1)
E el ( R) = (3π 2 ) 2 / 3 ∫ ρ 5 / 3 dr + ∫∫ drk dri − ∑ + E xc
10 rki i
Rik
2 unknown
1 ρ = ∑ φk ηk
− ∑ ∫ ηi∇ 2ηi dr k
2 i commonly used expression with Kohn-Sham MO (ηk)

The Generalized€ Gradient Approximation (GGA):

1
€
9$ 3' 3 4
E xc = − & ) 0.7 ∫ ρ ( ri ) 3 dτ i + Corr.Term(∇ρ)
8%π (
Fitting sets!
 (Hybrid) Density Functional Theory
UNISI
BGSU
How to compute the electron density efficiently ?

There are n Kohn-Sham MOs

Fˆkηk = ε kηk
average No Kij:
e
-

no exact Fermi hole

The Kohn-Sham Operator (1965) Coulomb e-

ˆ €1 2 Zi ∂E xc
F(rk ) = − ∇ k − ∑ + ∑ J j (rk ) + Vxc Vxc =
2 i rki j ∂ρ

ηk = ∑ ckj ξj The basis set

j
The Kohn-Sham
MO
€
 UNISI
BGSU
Summary: HF vs. DFT
Variational principle Variational principle
ψ H el ψ
E el (ψ ) trial = ≥ E el (ψ ) true E el (δ ) trial ≥ E el (δ ) true
ψ |ψ
2
ρ = ∑ ηk
Slater Determinants
k

€ Kohn-Sham Orbitals and Orbital Energies

Molecular Orbitals and Orbital Energies

variational
variational € coefficient
coefficients

Ritz method (eigenvalues and eigenvectors) Ritz method (eigenvalues and eigenvectors)

fˆkφ k = ε kφ k solution Fˆkηk = ε kηk solution

N N
1 ρ (1) ρ (2) Z ρ(1)
E el ( R) = ∑[2εk − ∑ (2J kj − K kj )] E el ( R) = − ∑
2 i
∫ ηi∇ 2ηi dr + ∫∫ rki
drk dri − ∑ i
R
+ E xc
k=1 j=1 € i ik
BGS
U (Dynamic) Electron Correlation

ˆf = − 1 ∇ 2 − ∑ Z i + V HF { j}
k k i
2 i
rki

In the HF theory the interaction between electrons is treated

in an average way not in an instantaneous way
€
Error = H-HHF = Ve,e – (J-K).

infinite basis set calc.

H He

EHF = -0.50000 au EHF = -2.86168 au

Eexact= -0.50000 au Eexact= -2.90372 au (FCI)
Error=26 kcal mol-1 (ca. 1 eV)
BGS

(Dynamic) Electron Correlation

U

ˆ 1 2 Zi
F(rk ) = − ∇ k − ∑ + ∑ J j (rk ) + Vxc Vi HF { j}
2 i rki j

In the KS implementation, DFT also employ a one-electron

formalism to compute densities/energies. The
€ true Vxc is
know only for model systems.
€

infinite basis set calc.

H He

EDFT = -0.49997 au EDFT = -2.89283 au

Eexact= -0.50000 au Eexact= -2.90372 au (FCI)
Error=7 kcal mol-1 (ca. 0.3 eV)
UNISI Ab-initio Quantum Chemical Technologies:

BGSU
The Pople Diagram
Better description of the HF Coulomb hole and
Nuclear cusps

e- EXACT
infinite b asis s et
Basis Set (Atomic Orbitals)

6-311+ + G ** N

6-311G **
φ i = ∑ c ijξ j increa sing acc urac y,
j increa sing c pu time
6-311G * inc reas ing
size of Fermi hole
3-21G * bas is s et Part 3
e- e-
3-21G
€
ST O -3G
Homolysis
ST O inc reas ing level o f theory

full e - e-
e- HF CI S CIS D CIS DT M P2 MP3 MP4 co rrelation FCI
e-
Fermi hole e- Wavefunction ca. DFT
Coulomb hole
UNISI

How to Compute the Potential Energy

eng
BGSU

Molecular Mechanics
(only conformational changes) Classical
Part 2

Quantum
V(R) = Vnn(R) + Eel(R)

ZiZ j Need
Vnn (R) = ∑ Quantum Chemical
i≤ j Rij
(Electronic Structure)
Methods

Hartree-Fock theory or Density Functional Theory

UNISI
BGSU
”Atomic” Basis (Basis Sets)

ξ i must form a ≈ complete set of orthonormal functions

φ i = ∑ cij ξj
€ j

variational coefficients
HOMO (benzene)
Hydrogen-like orbitals
€

n principal quantum number →shell n≥1

l angular momentum →sub-shell 0 ≤ l ≤ n-1
ml projection of l →energy shift -l ≤ ml ≤ l
 UNISI
BGSU
” Atomic” Basis (Basis Sets)
one-center
two-centers
ξ i must form a ≈ complete set of orthonormal functions three-centers
four-centers

M basis
1 1
J kj = φ k (1)φ j (2)
r1 − r2
φ k (1)φ j (2) ∑ cαkcγj c βk cδj ξα (1)ξγ (2)
r1 − r2
ξ β (1)ξδ (2)
αβγδ

€
Coulomb atomic integrals ! no
variational coefficients
€ variational
€ coefficients
(disk storage or direct)

φ i = ∑ cij ξj
j

HOMO (benzene)
 UNISI
BGSU
” Atomic” Basis (Basis Sets)
three-centers Shape
four-centers (spherical harmonics):
Integrals
are very time-consuming to compute Yl,m l (θ,ϕ )
with the STO radial part

Hydrogen-like orbitals Slater Type Orbitals (STO):

€
n−1 −ςr Z−s
ξς ,n,l,m l (r,θ,ϕ ) = NYl,m l (θ,ϕ )r e ς=
n screening
constant
No radial nodes zeta
radial behavior (critical) exponent determined
Integrals (Jkj and Kkj) variationally
are slow to compute
but accurate€
€ Integrals (Jkj and Kkj) STO
are fast to compute GTO
but not accurate

r (distance from nucleus)

UNISI
BGSU
” Atomic” Basis (Basis Sets)

Gaussian Type Orbitals (GTO):

2n−2−l −ςr 2
ξς ,n,l,m l (r,θ,ϕ ) = NYl,m l (θ,ϕ )r e
Radial nodes

€ Smaller exponent (ζ)

more diffuse
Larger exponent (ζ)
less diffuse
UNISI
BGSU
” Atomic” Basis (Basis Sets)

https://en.wikipedia.org/wiki/Gaussian_orbital

The use of Gaussian orbitals in electronic structure theory (instead of the more physical Slater-
type orbitals) was first proposed by Boys in 1950. The principal reason for the use of Gaussian
basis functions in molecular quantum chemical calculations is the 'Gaussian Product Theorem',
which guarantees that the product of two GTOs centered on two different atoms is a finite
sum of Gaussians centered on a point along the axis connecting them. In this manner,
four-center integrals can be reduced to finite sums of two-center integrals, and in a next step to
finite sums of one-center integrals. The speedup by 4—5 orders of magnitude compared to
Slater orbitals more than outweighs the extra cost entailed by the larger number of basis
functions generally required in a Gaussian calculation.
For reasons of convenience, many quantum chemistry programs work in a basis of Cartesian
Gaussians even when spherical Gaussians are requested, as integral evaluation is much easier
in the cartesian basis, and the spherical functions can be simply expressed using the cartesian
functions.

77
 ” Atomic” Basis (Basis Sets)
UNISI
BGSU

John Edward Lennard-Jones (Cambridge, UK)

1894-1854

Samuel Francis Boys

was born in 1911, he died in 1972.

S.F. Boys, G.B. Cook, C.M. Reeves and I.

Shavvitt,

Automatic fundamental calculations of molecular

structure.

Nature 178, 1207 (1958).

UNISI
BGSU ” Atomic” Basis (Basis Sets)
Decreasing ζ STO

STO-3G Chemistry
GTO-2
GTO-1
GTO-3
1 2 3 4 5
distance from nucleus (au)

Minimal Basis: enough functions to accommodate all the electrons

all ξ contains 3 Gaussian primitives

H (1S) ξ6 (9 different molecular orbitals, 27 gaussians in total)

H C (1S) + (2S) + (2Px,2Py,2Pz) φ i = ∑ c ijξ j

H H ξ1 ξ2 ξ3 ξ4 ξ5 j

STO-3G Basis Set contraction

 UNISI
BGSU ” Atomic” Basis (Basis Sets)
Split Valence - Double ζ (i.e. double exponent) Basis Set: more functions to describe
different bonding
higher accuracy z π
Poor for describing the π-bond
decrease compute. cost
σ
A split-valence basis uses only one basis x
function for each core AO, and a larger basis H C
for the valence AO’s

OK for describing the σ-bond

H (1S) + (2S)

H C (1S) + (2S) + (2Px,2Py,2Pz)

H H
+ (3S) + (3Px,3Py,3Pz)
Smaller values of the
radial function exponent ζ
 UNISI ” Atomic” Basis (Basis Sets)
BGSU

Split Valence Double-Zeta (DZ) Basis Set with Polarization Functions:

to better describe the anisotropy in the electron density

z π
Larger z
density
σ allow for a better
y x description of the
H H C electron motion
Lower
density better

H (1S) + (2S) + (2Px,2Py,2Pz)

H C (1S) + (2S) + (2Px,2Py,2Pz) 3dxy

H 3dxz
H
(3S) + (3Px,3Py,3Pz) + 3dyz,
+
3dx2-y2
3dz2
 UNISI ” Atomic” Basis (Basis Sets)
BGSU
Split Valence Double-Zeta (DZ) Basis Set with Polarization Functions and
Diffuse Functions: to better describe the structure of the electron density.
Important for dynamic correlation (description of the Coulomb Hole).

Radial correlation (diffuse function on H)

= very small exponent
Angular correlation = very small exponent
(diffuse function on C)
z π z

σ
x y
H CH3 H

Diffuse functions, usually s-, p-functions with very small exponents ζ (s,p for C and s for hydrogens):
• Calculations on anions.
• Dipole moment
• Polarizability
UNISI ” Atomic” Basis (Basis Sets)
BGSU

Split-Valence Double-Zeta (DZ) Basis Set with Polarization Functions and

Diffuse Functions: to better describe high electron densities

-
(1S) + (2S) + (2Px,2Py,2Pz) 3dxy
H C
3dxz
H H 3dyz,
+ (3S) + (3Px,3Py,3Pz) +
3dx2-y2
3dz2

+ (4S) + (4Px,4Py,4Pz) allow for a description of

the electron motion far
from the nuclei
UNISI ” Atomic” Basis (Basis Sets)
BGSU

Basis set contraction leads to John Pople’s style basis sets

1S (uncontracted) 1S (contracted)

one variational
three contraction (fixed) coefficient
coefficients

3 primitive GTO = 3 Ci 1 contracted GTO = 1Ci

(PGTO) (fixed linear combination of 3 PGTO)

Example: STO-3G
contraction
 ” Atomic” Basis (Basis Sets)
UNISI
BGSU

Basis set contraction leads to (C7,C8,C9)

John Pople’s style basis sets
3P z

contraction sizes
(C4,C5,C6)
6-31G variational
coefficients of the
2P 1S
C (C1 )
carbon atom 2S
(C2 )

1S 2S 2P 3S 3P 3S
(C3 )
GTO of the inner shell (core) formed by contraction of 6 PGTO
GTO of the first outer shell (valence) formed by contraction of 3 PGTO
GTO of the second outer shell (double-ζ) formed by 1 PGTO

GTO of the first outer shell

fixed contraction
variational
coefficient
C7 (c1 PGTO1+ c2 PGTO2 + c3 PGTO3) coefficients
UNISI ” Atomic” Basis (Basis Sets)
BGSU

Basis set contraction leads to John Pople’s style basis sets

polarization functions for

6-31+G* heavy atoms (*)

diffuse functions for

heavy atoms (+)

3-21G*
How many

6-311+G* variational
coefficients (orbitals)
homework !

for methylene ?
6-311++G**
diffuse functions for heavy and light
(++) atoms
UNISI ” Atomic” Basis (Basis Sets)
BGSU

John Pople, Nobel Prize for Chemistry in 1998

Pioneered the development of ab initio HF

quantum chemistry methods, that use basis
sets of either Slater type orbitals or Gaussian
orbitals. He was instrumental in the
development the most widely used
computational chemistry packages, the
"GAUSSIAN", including coauthorship of the
first version, Gaussian 70. One of his most
important original contributions is the concept
of a model chemistry whereby a method is
rigorous evaluated across a range of
molecules.

October 31, 1925 – March 15, 2004

UNISI

V(R) Mapping → Chemistry

eng
BGSU

d2V (R)/dR2

Optimization methods

Energy Profile along

the Reaction Path
dV(R)/dR

V(R)

dR(s)/ds=-dV(R)/dR =s
 Geometry Optimization
quadratic representation of the potential energy surface
region of interest

V(R) = [d2V (R-Ra)/d(R-Ra)2]Ra R2

V(R) = [d2V (R-Rb)/d(R-Rb)2]Rb R2

stationary points
V(R)

complex V(R) function

Ra Rb
R
UNISI
BGSU
Geometry Optimization
need an analytical (e.g. polynomial) representation of the
potential energy surface region of interest

quartic region

cubic region

quadratic region
cubic trust radius

stationary point (target)

quadratic trust radius
 Geometry Optimization
UNISI
BGSU

quadratic representation of the energy surface

point representation
quadratic representation

linear representation

R0
point linear quadratic

∂V(R) 1 ∂2V(R)
V(R) = V(R0 )+ ∑i (Ri − Ri 0 )+ ∑i ∑ (Ri − Ri 0 )(Rj − Rj 0 )
∂Ri R 2 j
∂Ri∂Rj R
0 o

Energy
(value) homework !
= + Δ + 1Δ t t
V(R) V(R0 ) g R R HR0 ΔR R0
2 Hessian
Gradient (curvature)
(slope)
UNISI
BGSU
Computational Cost
The hessian is computationally very expensive
(Intel Xeon Woodcrest (2 GHz))

663
HF/6-31G* B3LYP/6-31G*

CPU time (sec)

CPU time (sec)

energy

gradient
hessian
174
152 123
78
41

energy +gradient +hessian energy +gradient +hessian

UNISI
BGSU
Geometry Optimization
quadratic representation of the energy surface

t
V(R0 ) gR0 HR0

Energy
V
(value)
ideal step
V(R) (perfect method)

Gradient
(slope) R0 R0

geometry change
UNISI
BGSU

Classification
i ) Methods that use only the value of the function (i.e., in our
case, the potential energy at R0). One example is that of the
Simplex method.
i i ) Methods that use the energy and the gradient of the function.
For instance the steepest-descent and conjugated-gradient
methods.
iii) Methods that use the energy, first and second derivative of the
function (e.g. in our case the potential energy its gradient and
its hessian at R0). An example is the Newton-Raphson method.

iv) Local or Global.

UNISI
BGSU Classification
step
dn = (d1n, d 2n)
component
Rn = (R1n, R2n)
step n=1
direction of
the step (dn)
guess
size of
step n=2
the step (Rn)

termination
(thresholds)
UNISI
BGSU Classification

local vs. global

guess

crown
chair
UNISI
Simplex Method
BGSU
a 3D case
R1 A D (V1)
Step 1 Step Direction:
(orthogonal to the contour level)
B n
ΔR = −cg n
C
D’ (V2) if VD > VC > VB >VA then D D’

R2
R3 € if VC > VB > VD’ >VA then C E

R1 A
Step 2
E (V2) ΔR = −cg n
n
Step Size:
B (proportional to the energy difference)
C (V1)
D’
€
ΔR n = c|V
−cg1n-V2|
R2
R3
UNISI
BGSU Steepest Descent Method

Step Direction:
(orthogonal to the contour level)

Target ∂V (R n )
n ∂Ri
n=3 di = −
gn
n=2

n=1 Start Step Size:

(proportional to the gradient)

n n
€ ΔR n = −cg n
ΔR = −cg
UNISI Conjugated Gradient Method
BGSU

conjugated steepest descent Step :

gradient (orthogonal to the contour level)

n ∂V (R)
d =−
i + β n din−1
∂Ri
Target
gn gn
βn = (Fletcher-Reeves)
n−1 n−1
g g

dn €
€
Step Size:
βdn-1 n (proportional to the gradient)
dn-1
ΔR n = −cd n
Start
UNISI
BGSU
The Newton-Raphson Method
1 t t
V(R) = V(R0 )+ g ΔR + ΔR H R0 ΔR
R0
2
∂V(R) t t
= gR0 + ΔR H R0 = 0
∂R Is this a good time for revising
some elementary linear algebra ?
€
requirement for Step Direction and Size:
a stationary point (not orthogonal to the contour level)
(either Min or TS)
One-dimensional:
€ General: 3N-6 dimensional: dV

ΔR = − H R−10 gR0 ΔR = − dR
d 2V
HR0 HR0-1= 1 dR 2
UNISI
BGSU
The Newton-Raphson Method:

Search for an Energy Min

V(R) dV
ΔR = − dR
1 d 2V
2
positive (concave) curvature dR
2
3
€

3 21 R
n
 The Newton-Raphson Method:

UNISI
BGSU

Search for a TS

negative (convex) curvature

2
dV
dV
=0
dR 2
ΔR = − dR
d 2V
dR 2
€

€
n
UNISI
BGSU
Termination: multiple thresholds
Termination Step:
(four criteria)

Elements of gR0
# ∂V (R) &
Maximum force % ( < t max
$ ∂Ri ' max

2
# ∂V (R) &
RMS force 1
N
∑%$ ∂R (' < t RMS
€ i i

Elements of ΔRR0

Maximum step size (ΔRi) max < dmax

€
2

RMS step size

1
N
∑ (ΔRi ) < dRMS
i
€
 The Newton-Raphson Method:

UNISI
BGSU
eng

Search for an Equilibrium Geometry

V = (α −120) 2 + 0.63(α −120) 3 + (r −1.34) 2 + 0.04(r −1.34)3
guess geometry ΔRR0 = (2.0, 112.0) Step direction and size Gradient

−1
H H
ΔR = − H g R0 R0
r
α inverse Hessian

H H
HR0 HR0-1= 1

€
What is the predicted
r geometry after 3
hαα hαr hiαα hiαr 1 0
optimization steps ? = 0
hrα hrr hirα hirr 1
homework !
α
UNISI
BGSU
Change in Curvature
“NR” directions d 2V
2 =0
dR2
TS2 Max usually small regions
2
TS1
dV
2 =0
dR1
€

R1
TS3
R1
R2 R2

We need to control the direction and size of the step

 Step Control:

Trust Radius (Newton-Raphson) Methods
Hessian Shift parameter (to be assigned)

−1
ΔR = − H g −1
R0 R0 ΔR = −( H − λI ) R gR 0
0

Normal modes Direction and size

t EIgenvalues and
Qi (Q gR 0 )
i
eigenvectors of the

€ ΔR = −∑ Hessian in mass-
weighted coord.: bi,
i bi − λ Qi

Trust radius
Force constants
t 2
(Q gR 0 )
i
τ = −∑
2
2
€
Validity of the Second i (bi − λ)
Order Taylor Expansion
 Step Direction Control:

Trust Radius (Newton-Raphson) Methods

Qi (Qit g)R0
ΔR = − ∑ λ controls of the
i bi − λ sign of the denominator

λ <€b1 < b2, b3, … , b3m-6 look for a Min

b1 < λ < b2, b3, … , b3m-6 look for a TS

b1, b2 < λ < b3, … , b3m-6 look for a

saddle point of
index 2
 Step Control:

Trust Radius (Newton-Raphson) Methods

Effect of the shift par. λ

(for a TS search) old
new
UNISI
BGSU
Quasi Newton-Raphson Methods (QN)

QN Methods use Hessian updating formulas

The most commonly used updating scheme in QN methods is based on the

Broyden-Fletcher-Goldfarb-Shanno (BFGS) updating:
OUTER PRODUCT

t old t old
ΔgΔg H ΔRΔR H
H new = H old + t t −
ΔRΔg ΔR t H old ΔR
DOT or INNER PRODUCT

the BFGS updating produces positive definite hessians it cannot obviously

be used when attempting a TS optimization. For this reason one has to
use a different scheme such as the Murtaugh-Sargent (MS) formula
€
UNISI
Optimization Efficiency:

Hessian Quality
BGSU

Initial Hessian computed with a more approximate

C 6H 4N 4
Quantum Chemical Method or with a Molecular
C8H10N4O2 Mechanics Method

C5H6N2O2S
most efficient
C5H10N3 Initial steepest descent
C12H12N2 with updating best (cost/efficiency) compromise
UNISI
BGSU ……..in practice

Organic
1. Create a guess geometry for the transition states (TSs)
Chemistry

2. Prepare the approximate Hessian for the guess Quantum Chemistry

3. Search for the TS Optimization Method

4. Calculate the exact Hessian at the TSs Quantum Chemistry

5. Comparing results for TSs to confirm the expected stereoselectivity

Organic
Chemistry

QC- Software: (i) Gaussian (commercial), (ii) Molcas

(commercial), (iii) Gamess-USA (free), (iv) ADF (commercial) …
many other…
 The Enantioselectivity
UNISI
BGSU
eng

Two Zimmerman-Traxler type nonacyclic TS’s:

Target: predict computationally the enantioselectivity.

*
O

anti OH
O

R Re face
H *
anti,Re
*
*

syn,Si
O
* *
H
Si face
R
*
O

syn N
OH
 UNISI
BGSU
Results (B3LYP/3-21G*)
O O
δ δ δ δ
N O O
N
δ O H δ O H δ
δ
CH3 H3 C
H3 C H H CH3

H3 C CH3

1.130 Å
anti syn
1.323 Å
1.094 Å

1.398 Å
C--C 2.107 Å
C--C 2.164 Å

TSanti-re TSsyn-si
UNISI
BGSU
Results (B3LYP/3-21G*)

si

re syn

anti

TS#ar& TS#ss&
UNISI

Results (B3LYP/3-21G*)
BGSU
 UNISI

Results (B3LYP/3-21G*)
BGSU

(gas-phase) TSanti-re is 2.3 kcal mol-1 lower than TSsyn-si

Houk et al. calculated the gas-phase activation enthalpies of activation have the
smallest error (standard deviation ± 0.4 kcal/mol) when compared with the
experimental enantioselectivities (Bahmanyar, Houk et al., JACS, 2003, 125, 2475-2479).
The predicted product ratios from ΔH‡298 values, in our case confirm the
stereoselectivity of the reaction:

Product Ratio
Structure
Calculated Experimental
TSanti-re 0.0 ~96-99%
TSsyn-si 2.3 ~4-1%
UNISI
eng Hardware Technologies

Instruction Cycle https://en.wikipedia.org/wiki/Instruction_cycle

(fetch-decode-execute cycle)

The processor checks the program counter to see which

instruction to run next.

The program counter gives an address value in the

memory of where the next instruction is.

The processor fetches the instruction value from this

memory location.

Once the instruction has been fetched, it needs to be

decoded and executed. For example, this could
involve taking one value, putting it into the ALU,
then taking a different value from a register and
adding the two together.

Once this is complete, the processor goes back to the

program counter to find the next instruction.
This cycle is repeated until the program ends.
UNISI

CPU performance:
eng

No. of Transistors and MIPs

Intel CPU

Name Date Transistors Microns Clock Speed MIPS

8080 1974 6,000 6 2 MHz 0.64

8088 1979 29,000 3 5 MHz 0.33
80286 1982 134,000 1.5 6 MHz 1
80386 1985 275,000 1.5 16 MHz 5
80486 1989 1,200,000 1 25 MHz 20
Pentium 1993 3,100,000 0.8 60 MHz 100
Pentium II 1997 7,500,000 0.35 233 MHz ~300
Pentium III 1999 9,500,000 0.25 450 MHz ~510
Pentium IV 2000 42,000,000 0.18 1.5 GHz ~1,700
UNISI
eng
BGSU
Hardware and Software
Moor’s Law (empirical)

transistor count:
doubles approximately every two years

MIPS and FLOPS increases of one

order of magnitude every 5 years

Motorola
Intel
 UNISI
eng

Hardware Speedup
BGSU

(beyond FLOPS)
Standard Performance Evaluation Corp.

Benchmarks (http://www.spec.org/cpu2006/results/)

Standardized Collection of Programs

used to evaluate hardware performance
Intel Xeon
19 3 GHz

Cfp2006 Base
Harpertown
Execution − timebefore
Speedup
Speedup
used = Clowertown
Execution − timeafter 17

Speedup = 1.26 15 Woodcrest

'06 '07 '08

Year
UNISI
eng
BGSU
Hardware and Software Speedup
Amdahl’s Law
Fraction of the Software USING the
Improved Hardware
(e.g. program uses all cores )

Execution − timebefore 1
Speedupobserved = =
Execution − timeafter Frac used
Frac unused +
Speedupused
Fraction of the Software NOT USING Improved Hardware
the Improved Hardware (e.g. when using all cores )
(e.g. program uses a single core)

Computer Technology
Conclusion: It is important to have faster computer and faster methods and programs

e.g. using MOs instead of AOs e.g. parallelization

Quantum Chemistry Computer Science
The End

(of Part 1)

 The Variational Principle:
the Ritz Method
BGS
BGSU
U
No

Linear variational coefficients (variable)

if the coefficients are not linear (e.g.

exponential) the Ritz method cannot be
applied

∑ c ic j ξ i H el ξ j ∑ cc
∑ cH
c i
i
j
j
ij
ξ i H el ξ j ∑c c H i j
ij ij
E el ( R) trial = ij E el ( R) trial == ij =
∑c c i j ξi | ξ j ∑∑
c ccSic j ξ i | ξ j
i j ij ∑ c ic j S
matrix representation of the
ij ij
ij ij
Hamiltonian operator

€ vector of coefficients

€
The matrix S for a set of orthonormal basis
functions = the Unit matrix
 The Variational Principle:
the Ritz Method (valid for linear variational coeff)
BGS
BGSU
U
No

small and arbitrary variation of c

Hel is Hermitian, δc arbitrary

Secular Equation

non-trivial solution only if

Det
 BGS The Variational Principle: the Ritz Method
BGSU
U
No

∑c c H
i j ij
ij
E el ( R) trial =
∑c c S
i j ij
ij

€
H11 − E el (R) trial H12 ... H1n
H 21 H 22 − E el (R) trial ... H 2n
Det =0
... ... ... ...
H n1 Hn 2 ... H nn − E el (R) trial

eigenvectors &
diagonalization
€ eigenvalues
BGS
U
The Secular Equation
No

A is a NxN matrix AC=eC C is a N-dimensional vector

e is a scalar

eigenvalue
eigenvector associated
A11 A12 A1N C1 C1 to e
A21 A22 C2 C2
= e

AN1 AN2 ANN CN CN

equivalent to:

A11-e A12 A1N C1 0

A21 A22-e C2 0
=
set of linear equations
AN1 AN2 ANN-e CN 0
BGS
U
The Secular Equation
No

A11-e A12 A1N C1 0

A21 A22-e C2 0
=

AN1 AN2 ANN-e CN 0

1 0 0

0 1
A-e1=0 1=
0 0 1 secular equation

non-trivial solution
for a set of linear equations Det |A - e 1| = 0
 BGS
U
The Secular Equation
No

Det |A - e 1| = 0

Matrix diagonalization:

A11 A12 A1N D11 0 0

A21 A22 0 D22

G is a NxN matrix G-1 G =

AN1 AN2 ANN 0 0 DNN

similarity transformation

N eigenvalues:

e = D1, D2, D3, ..., DN

BGS
U The Secular Equation
No

a specific eigenvalue

A11-Di A12 A1N C1 0

A21 A22-Di C2 0
= set of linear equations for Di

AN1 AN2 ANN-Di CN 0

(A11-Dii)C1 + A12C2 + .. + A1NCN = 0 The eigenvector

A11C1+ (A12-Dii)C2 + .. + A1NCN = 0 corresponding to Di:

C1i, C2i, C3i, ..., CNi

A11C1+ A12C2 + .. + (A1N-Dii)CN = 0
BGS How to Construct the Matrix Elements of the
Hamiltonian using an MO (Φi) basis
U

Hel = i
2
+

F (one-electron) G (two-electrons)

| > and | ' > are identical determinants and F and G are one-electron and two-
electron additive operators
BGS
U

The Slater-Condon Rules for Identical Determinants

(i) If two
determinants | > and | ' > are identical and F and G are one-electron
and two-electron additive operators, then:

<|F+G|>= Σi < Φi | F | Φi > +Σi>j [< ΦiΦj | G | ΦiΦj > - < ΦiΦj | G | ΦjΦi >]
(ii) If | > and | ' > differ by a single spin-orbital ( Φp≠Φ'p ),

<|F+G|'>= < Φp | F | Φ'p > +Σj [< Φp Φj | G | Φ'p Φj > - < Φp Φj | G | Φj'Φp >]

(iii) If | > and | ' > differ by two ( Φp≠Φ'p and Φq≠Φ'q),

<|F+G|'>= < Φp Φq | G | Φ'p Φ'q > - < Φp Φq | G | Φ'q Φ'p >

(iv) If | > and | ' > differ by three or more spin orbitals, then

<|F+G|'>=0
(v) For the identity operator I, < | I | ' > = 0 if | > and | ' > differ by one or more spin-orbitals.
 BGS Electronic Energy Computation: HF
U

How does one find a good VMF? One way is the Single (Slater) Determinant trial function
ψ= |φ1 φ2 φ3 ...φn|, and write down <ψ | Hel | ψ> using the Slater-Condon rules

VMF <ψ | Hel | ψ> = Σk=occ.< φk|Te + Ve,n| φk> +

1/2 Σk,j=occ. [< φk(1) φj(2)|e2/r1,2| φk(1) φj(2)> - < φk(1) φj(2)|e2/r1,2| φj(1) φk(2)>]

and observe that Coulomb (Jk,j) and exchange (Kk,j) integrals among occupied orbitals arise.

If one minimizes this energy with respect to the φJ’s coefficients (c), with the constraint that

< φJ| φK> = δJ,K

one obtains the HF system of equations:

f φJ = εJ φJ = [Te + Ve,n] φJ + Σk [< φk(1)|e2/r1,2| φk(1)> φJ(2) - < φk(1)|e2/r1,2| φJ(1)> φk(2)]

therefore f contains the Jk (1) = < φk(1)|e2/r1,2| φk(1)> and Kk (1) = < φk(1)|e2/r1,2| φJ(1)> integral
operators.

operate on the coordinates of one-electron

 BGS Electronic Energy Computation: HF
U

H = Te + Ve,n + Ve,e

One can define VMF in terms of the J and K interactions. This is the Hartree-Fock definition of VMF.

It has the characteristic that

EHF = <ψ | HHF | ψ > ≥ Etrue
if HHF is defined as
HHF = Te + Ve,n + (J-K).
In this case,
Error = H-HHF = Ve,e – (J-K).
Poor description of the Coulomb hole

electron correlation energy

Notice that it is by making a mean-field model that our (chemists’) concepts of molecular
orbitals φJ and of electronic configurations (e.g., 1s α1s β 2s α 2s β 2p1 α) arise.
3
 BGSU Electronic Energy Computation: HF
UNISI
eng
MO energies
one equation for N
each MO fˆk φ k = ε k φ k MOs φ i = ∑ c ijξ j
matrix elements of the j
Fock operator
molecular orbitals
εn φn = cn,0ξ0 + cn,1ξ1 +… + cn,µ ξ µ … + …

Secular equations: €
€

…
f µν = ξφµµ f ξφνν Sµν = ξφµµ ξφνν

ε1 φ1 = c1,0ξ0 + c1,1ξ1 +… + c1,µξµ …+…

∑( f µν − εel Sµν )c µ = 0
Atomic orbital
µ € (basis functions)
ε0 φ0 = c0,0ξ0 + c0,1ξ1 +… + c0,µξµ …+…
The number of orbitals
equal the number of basis functions
(“atomic” orbitals).
Molecular orbitals coefficients (eigenvectors)
Molecular orbital energies (eigenvalues)