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Comp Chem8
Comp Chem8
eng
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).
Theories: Molecular Orbitals rather than Atomic Orbitals for the description of the electronic structure of molecules
Present speed
Part 1
Part 2
Tutorial (Hands-on)
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
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
* CO2H
N
H
CH3CN
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
* * *
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
anti OH
O
R Re face
H *
anti,Re
*
*
syn,Si
O
* *
H
Si face
R
*
O
syn N
OH
UNISI
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
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
ΔG ‡
The rate constant kT − RT
D
−1 expression is: k= e
e.e. = C #D &
×100 % ≥ 1( h
D $C '
+1
C
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
ΔG‡=ΔH‡-TΔS‡
ΔGB→C‡-ΔGB→D‡ = ΔHB→C‡-ΔHB→D‡
change in size
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
H H
Electron 1 Proton 1
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
Proton 2 Electron 2
R2 Electron 1
r2
R1
r1 Proton 1
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
Born-Oppenheimer Approximation
H H Eel(R) V12(R)+Eel(R)
bond
Proton 2 bond length
Proton 2 Proton 2 angle
Electron 2
Transition State
eng
BGSU
http://www.hyle.org/journal/issues/8-2/bio_nye.html
Stationary Points:
Gradient
and
Hessian
of V(R) in a
“2D molecule”
UNISI
eng
BGSU Stationary Points: Force Constants
Hessian Matrix
of V(R)
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)
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)
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
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)
Eigenvalue problem:
k = k1 k = k2 k = k3
UNISI
Eigenvector computation
Saddle Point
redo
Transition vector
𝛿2V 𝛿2V
k1 = k2 =
𝛿Q12 𝛿Q22
UNISI
q2
€ dV
dqi (s) dq i = 1,3N
=− i
ds dV
dqi
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
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):
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:
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
d2V (R)/dR2
Optimization methods
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, …)
chemistry
DFT
(B3LYP, PBE, BPW91…) excited states
(Part 3)
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:
Coulomb hole
ψtrue (r1, s1, r2, s2, ... , rN, sN)
describes the simultaneous e-
Chemical Technologies
Physics: Total Charge Density
2
δ (r) = N ∑ ...∑ ∫ dr1 ... ∫ drN ψ ( r1,s1,r2 ,s2 ...rN ,sN )
s1 sN
€ ψtrial = ( ,..., , )
mathematical formulation of the: MOs
Wavewfunction AOs
e- EXACT
infinite b asis s et
6-311+ + G **
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
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
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
∑ 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
∑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).
…
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
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
⌢ 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
(-)
Electrostatic Repulsion
e-
Coulomb operator e- (-)
operates on Φj (r’)
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.
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
Douglas Hartree
27 March 1897 – 12 February 1958
UNISI
BGSU
Density Functional Theory
Hohenberg-Kohn existence theorem:
ˆ €1 2 Zi ∂E xc
F(rk ) = − ∇ k − ∑ + ∑ J j (rk ) + Vxc Vxc =
2 i rki j ∂ρ
variational
variational € coefficient
coefficients
Ritz method (eigenvalues and eigenvectors) Ritz method (eigenvalues and eigenvectors)
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
ˆ 1 2 Zi
F(rk ) = − ∇ k − ∑ + ∑ J j (rk ) + Vxc Vi HF { j}
2 i rki j
H He
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
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
φ i = ∑ cij ξj
€ j
variational coefficients
HOMO (benzene)
Hydrogen-like orbitals
€
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
2n−2−l −ςr 2
ξς ,n,l,m l (r,θ,ϕ ) = NYl,m l (θ,ϕ )r e
Radial nodes
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
STO-3G Chemistry
GTO-2
GTO-1
GTO-3
1 2 3 4 5
distance from nucleus (au)
H (1S) + (2S)
z π
Larger z
density
σ allow for a better
y x description of the
H H C electron motion
Lower
density better
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
-
(1S) + (2S) + (2Px,2Py,2Pz) 3dxy
H C
3dxz
H H 3dyz,
+ (3S) + (3Px,3Py,3Pz) +
3dx2-y2
3dz2
1S (uncontracted) 1S (contracted)
one variational
three contraction (fixed) coefficient
coefficients
Example: STO-3G
contraction
” Atomic” Basis (Basis Sets)
UNISI
BGSU
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
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
d2V (R)/dR2
Optimization methods
V(R)
dR(s)/ds=-dV(R)/dR =s
Geometry Optimization
quadratic representation of the potential energy surface
region of interest
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
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*
energy
gradient
hessian
174
152 123
78
41
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.
termination
(thresholds)
UNISI
BGSU Classification
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 n
€ ΔR n = −cg n
ΔR = −cg
UNISI Conjugated Gradient Method
BGSU
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
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
−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
−1
ΔR = − H g −1
R0 R0 ΔR = −( H − λI ) R gR 0
0
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
t old t old
ΔgΔg H ΔRΔR H
H new = H old + t t −
ΔRΔg ΔR t H old ΔR
DOT or INNER PRODUCT
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
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
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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
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
CPU performance:
eng
transistor count:
doubles approximately every two years
Motorola
Intel
UNISI
eng
Hardware Speedup
BGSU
(beyond FLOPS)
Standard Performance Evaluation Corp.
Benchmarks (http://www.spec.org/cpu2006/results/)
Cfp2006 Base
Harpertown
Execution − timebefore
Speedup
Speedup
used = Clowertown
Execution − timeafter 17
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
∑ 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
Secular Equation
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
eigenvalue
eigenvector associated
A11 A12 A1N C1 C1 to e
A21 A22 C2 C2
= e
equivalent to:
A21 A22-e C2 0
=
set of linear equations
AN1 AN2 ANN-e CN 0
BGS
U
The Secular Equation
No
A21 A22-e C2 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:
N eigenvalues:
a specific eigenvalue
A21 A22-Di C2 0
= set of linear equations for Di
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
(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),
(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
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
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.
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.
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