+ All Categories
Home > Documents > Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum...

Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum...

Date post: 03-Jun-2020
Category:
Upload: others
View: 5 times
Download: 0 times
Share this document with a friend
56
Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr¨ odinger equation. Molecular orbital theory expresses the solution as a linear combination of atomic orbitals. Density functional theory (DFT) attempts to solve for the electron density function. Semi-empirical methods use approximate Hamiltonians that are partly parameterized using experimental data. Molecular mechanics uses Newtonian mechanics and empirically parameterized force fields. Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 1 / 56
Transcript
Page 1: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Theory

Computational Chemistry

Ab initio methods seek to solve the Schrodinger equation.

Molecular orbital theory expresses the solution as a linear combinationof atomic orbitals.Density functional theory (DFT) attempts to solve for the electrondensity function.

Semi-empirical methods use approximate Hamiltonians that are partlyparameterized using experimental data.

Molecular mechanics uses Newtonian mechanics and empiricallyparameterized force fields.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 1 / 56

Page 2: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Theory

The Time-Dependent Schrodinger Equation

The time-dependent Schrodinger equation can be written as

i~∂Ψ(x , t)

∂t= HΨ(x , t)

where

~ = 1.055× 10−34J s is the reduced Planck’s constant;

the operator H is the system Hamiltonian;

Ψ(·, t) is the wavefunction of the system at time t.

The modulus of the wavefunction, |Ψ(·, t)|2, is often interpreted as theprobability density of the system at time t.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 2 / 56

Page 3: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Theory

The Time-Independent Schrodinger Equation

If H is time-indepedent, then we can seek an eigenfunction expansion

Ψ(x , t) =∞∑

n=1

cnΨn(x)e−i En~ t

where Ψn satisfies the eigenvalue problem

HΨn = EnΨn

and En is interpreted as the energy of the stationary configuration Ψn.The eigenfunction Ψ0 corresponding to the smallest eigenvalue E0 is calledthe ground state of the system.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 3 / 56

Page 4: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Theory

The Hamiltonian of a Molecule

The Hamiltonian H can be written as the sum of the kinetic and potentialenergy operators

H = T + V,

where for a (non-relativistic) molecule

T = −~2

2

∑i

1

mi

(∂2

∂x2i

+∂2

∂y2i

+∂2

∂z2i

)V =

1

4πε0

∑i<j

eiej

rij(electrostatic potential).

Here i , j range over nuclei and electrons, mi and ei are the mass andcharge of the i ’th particle, and ε0 is the vacuum permittivity.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 4 / 56

Page 5: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hydrogen-like atom

Hydrogen-like Atom

In a few cases, Schrodinger’s equation can be solved analytically. For asingle nucleus with mass M and charge +Ze with a single electron (ofmass m), we have:(

− ~2

2(M + m)∇2

CM −~2

2µ∇2 − Ze2

4πε0r

)Ψ = EΨ,

where

∇2CM is the Laplacian for the center-of-mass coordinates

RCM =Mra + mre

M + m

∇2 is the Laplacian for the coordinates of the electron relative to thenucleus: r = re − ra

µ is the reduced mass µ = (M−1 + m−1)−1 ≈ m.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 5 / 56

Page 6: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hydrogen-like atom

Reduction of Dimension

Because the potential energy depends only on the distance of the electronto the nucleus, the center-of-mass can be separated out of the previousequation, leaving

− ~2

2µ∇2Ψ− Ze2

4πε0rΨ = EΨ

where r = |r|. Transforming to polar coordinates (r , θ, φ) gives

− ~2

2m

1

r2 sin(θ)

[sin(θ)

∂r

(r2 ∂

∂r

)+

∂θ

(sin(θ)

∂θ

)+

1

sin(θ)

∂2

∂φ2

− Ze2

4πε0rΨ = EΨ.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 6 / 56

Page 7: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hydrogen-like atom

Separation of Variables

The last equation can be solved by separation-of-variables and leads tothe following set of eigenfunctions and eigenvalues

Ψnlm(r , θ, φ) = CnlRnl(r)Y ml (θ, φ)

Enlm = −(

Ze2

2ε0h

)2µ

2n2,

which are indexed by

the principal quantum number n = 1, 2, 3, · · · ;the azimuthal quantum number l = 0, 1, 2, · · · , n − 1;

the magnetic quantum number m = −l ,−l + 1, · · · , l − 1, l .

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 7 / 56

Page 8: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hydrogen-like atom

Radial Component

The radial part of the wavefunction is

Rnl(r) =

(2r

n

)l

L2l+1n+l

(2r

n

)e−r/n

where

the associated Laguerre polynomial Lβα(x) is defined by

Lβα(x) =dβ

dxβLα(x)

Lα(x) = ex dα

dxα[xαe−x

]r = (µe2Z/mε0h

2)r ;

Cnl is a normalization constant chosen so that∫|Ψnlm|2dr = 1.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 8 / 56

Page 9: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hydrogen-like atom

Angular Component

The angular part of the wavefunction is a spherical harmonic:

Y ml (θ, φ) = P

|m|l (cos(θ))

1

2πe imφ,

where the associated Legendre polynomial Pml (x) is defined by

Pml (x) = (1− x2)|m|/2

d |m|

dx |m|Pl(x)

Pl(x) =1

2l l!

d l

dx l

[(x2 − 1)l

].

Notice that, in general, this function is complex except when l = 0.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 9 / 56

Page 10: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hydrogen-like atom

s-orbitals

When l = 0, we must also have m = 0. In this case, the wavefunctionΨn,0,0 is radially-symmetric and is said to represent the ns orbital.

Notice that as n increases:

the energy increases;

the diffuseness of theorbital also increases;

nodes appear.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 10 / 56

Page 11: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hydrogen-like atom

p-orbitals

For larger values of l , radial symmetry is lost. For example, if l = 1, thenm = −1, 0, 1 and there are three p orbitals that can be aligned along thecoordinate axes. If n = 2, then these have the following appearance:

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 11 / 56

Page 12: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Separation of timescales

Born-Oppenheimer Approximation

Since analytical solutions are usually unavailable, we try to simplify theproblem. The Born-Oppenheimer approximation assumes that:

the nuclei are fixed on the timescale of electronic motion (since nucleiare much heavier than electrons);

we can treat the electronic wavefunction and energy as functions ofthe nuclear coordinates R;

the total wavefunction can be factored as

Ψtot(r,R) = Ψel(r,R)Ψnuc(R).

This leads to the electronic Schrodinger equation:

Hel(R)Ψel(r,R) = E el(R)Ψel(r,R).

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 12 / 56

Page 13: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Separation of timescales

The Electronic Hamiltonian

The electronic Hamiltonian Hel is equal to the sum of the electronickinetic energy and the coulomb potential energy:

T el = − ~2

2m

elec∑i

(∂2

∂x2i

+∂2

∂y2i

+∂2

∂z2i

)

Vel =1

4πε0

− elec∑i

nuc∑s

Zse2

ris+

elec∑i<j

e2

rij

where Zi is the atomic number of the i ’th nucleus.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 13 / 56

Page 14: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Separation of timescales

Effective Potential Energy Surface

Typically, we are interested in the electronic ground state energy, E el0 (R),

which can be used to estimate the potential energy surface for the nuclearconfiguration:

Enuc(R) ≈ E el0 (R) +

1

4πε0

nuc∑s<t

ZsZte2

Rst

This can be used to:

identify the minimum energy molecular structure;

characterize reaction trajectories;

solve for the nuclear wavefunction: HnucΨnuc(R) = EtotΨnuc(R).

However, even with this approximation, the Schrodinger equation stillmust be solved numerically.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 14 / 56

Page 15: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Molecular Orbital Theory

Molecular orbital theory attempts to approximate the full wavefunctionΨ using a collection of one electron functions called spin orbitalsχ(x , y , z , ξ). These usually have the form

ψ(x , y , z)α(ξ) or ψ(x , y , z)β(ξ)

where ξ denotes the spin angular momentum of the electron along thez-axis and the spin wavefunctions for spin-up and spin-down particles are

α

(+

1

2

)= 1, α

(−1

2

)= 0

β

(+

1

2

)= 0, β

(−1

2

)= 1.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 15 / 56

Page 16: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Fermi-Dirac Statistics

Because electrons have half-integer spin, the following two conditionsmust be satisfied:

The wavefunction must be antisymmetric: if πij(X) denotes theconfiguration obtained by permuting the positions and spins of thei ’th and j ’th electrons, then

Ψ(πij(X)) = −Ψ(X).

Pauli exclusion principle: no two electrons can occupy the samespin orbital function. Thus each spatial orbital function can containat most two electrons, one with spin +1/2 and the other with spin−1/2.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 16 / 56

Page 17: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Slater Determinants

Given a collection of linearly independent spin orbitals, χ1, · · · , χn, anantisymmetric n-electron wavefunction can be constructed by setting

Ψdet =1√n!

∣∣∣∣∣∣∣∣∣χ1(X1) χ2(X1) · · · χn(X1)χ1(X2) χ2(X2) · · · χn(X2)

......

...χ1(Xn) χ2(Xn) · · · χn(Xn)

∣∣∣∣∣∣∣∣∣=

1√n!

∑π∈Sn

(−1)|π|n∏

i=1

χi (Xπ(i))

where Xi = (xi , yi , zi , ξi ) denotes the location and spin of the i ’th electron.Ψdet is called a Slater determinant.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 17 / 56

Page 18: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Basis Set Expansions

In practice, the molecular orbitals ψi (x) are expressed as linearcombinations of one-electron functions known as basis functions,

ψi (x) =N∑

s=1

csiφs(x), 1 ≤ i ≤ N,

where the csi are the molecular orbital expansion coefficients.

Notice that

2N ≥ n, if we allow for double occupancy of orbitals;

if 2N > n, then there are unoccupied orbitals that do not appearin the Slater determinant.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 18 / 56

Page 19: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Linear Combination of Atomic Orbitals

Usually, the basis elements φs are taken to be ‘atomic orbitals’ associatedwith individual nuclei present in the molecule (LCAO method). In thiscase, a set of orbitals is assigned to each nucleus such that these orbitals

are centered at the nucleus;

depend on the type of nucleus (e.g., H vs. C);

allow for symmetric and polarized electron distributions.

It is often the case that several such basis elements are used to representan ‘actual’ atomic orbital, for example, by allowing for different degrees ofdiffuseness of the orbital about the nucleus.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 19 / 56

Page 20: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Slater-type atomic orbitals

One choice for the basis functions are the Slater-type orbitals (STOs):

φ1s =

(ζ31

π

)1/2

exp(−ζ1r)

φ2s =

(ζ52

96π

)1/2

r exp(−ζ2r/2)

φ2px =

(ζ52

32π

)1/2

x exp(−ζ2r/2)

...

where ζ1, ζ2, · · · are parameters that control the size of the orbitals. WhileSTOs are good approximations for atomic orbitals, integrals of theirproducts must be evaluated numerically.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 20 / 56

Page 21: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Gaussian-type atomic orbitals

Gaussian orbital functions are polynomials multiplied by exp(−αr2):

gs =

(2α

π

)3/4

exp(−αr2)

gx =

(128α5

π3

)1/2

x exp(−αr2)

gy =

(128α5

π3

)1/2

y exp(−αr2)

...

Although integrals involving Gaussian-type functions can be evaluatedexplicitly, these functions are poor approximations for atomic orbitals.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 21 / 56

Page 22: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Molecular orbital theory

Contracted Gaussians

A compromise can be reached by using linear combinations of Gaussianfunctions (called contracted Gaussians):

φs(x) =∑α

dsα gα(x)

where each gα(x) is a Gaussian function and the coefficients dsα are fixedin advance, i.e., do not depend on the Hamiltonian. One approach is tochoose the coefficients to minimize the least squares distance betweenthe contracted Gaussian and a STO:

εnl =

∫ (φSTO

nl − φCGnl

)2dx.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 22 / 56

Page 23: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hartree-Fock theory

Hartree-Fock Theory

Having chosen a set of basis functions, Hartree-Fock theory seeks toestimate the ground state energy E0 by finding a determinantalwavefunction Φ that minimizes the quantity:

E ′ =

∫Φ∗HΦdX ≥ E0.

This leads to variational conditions on the expansion coefficients

∂E ′

∂cri= 0 1 ≤ r , i ≤ N.

Thus, we have reduced an infinite-dimensional linear problem to afinite-dimensional non-linear one (see below).

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 23 / 56

Page 24: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hartree-Fock theory

Roothan-Hall Equations

For a closed-shell system (i.e., two electrons per orbital), the variationalconditions lead to a system of non-linear equations

N∑s=1

(Frs − εiSrs)csi = 0 1 ≤ r , i ≤ N,

where εi is the one-electron energy of molecular orbital ψi and Srs is theoverlap of the atomic orbitals φr and φs :

εi =

∫ψ∗i (x)Hψi (x)dx

Srs =

∫φ∗r (x)φs(x)dx.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 24 / 56

Page 25: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hartree-Fock theory

The Fock matrix

The Fock matrix F = (Frs) is defined as

Frs = hrs +AO∑p,q

Pqp

[(rp|sq)− 1

2(rp|qs)

]where the summation goes over atomic orbitals and hrs is a component ofthe one-electron energy in a field of bare nuclei:

hrs =

∫φ∗r (x)h(1)φs(x)dx

h(1) = − ~2

2m∇2 − 1

4πε0

Nuc∑a

Za

ra1.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 25 / 56

Page 26: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hartree-Fock theory

Bond-order Matrix

The matrix P = (Ppq) is called the bond-order matrix or theone-electron density matrix:

Pqp = 2MO∑

i

c∗picqi ,

where the summation is over occupied molecular orbitals and the factor of2 reflects the closed-shell assumption.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 26 / 56

Page 27: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hartree-Fock theory

Two-electron Integrals

Much of the computational burden in the H-F theory comes from the needto compute the two-electron repulsion integrals

(rp|sq) =

∫ ∫φ∗r (x1)φ∗p(x2)

(1

r12

)φs(x1)φq(x2)dx1dx2,

where r12 = |x2 − x1|.

Because the elements of the Fock matrix are themselves functions of themolecular orbital expansion coefficients, the Roothan-Hall equations arenon-linear and must be solved iteratively (e.g., Newton-type methods).

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 27 / 56

Page 28: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Hartree-Fock theory

Self-Consistent Field Method

A simple iterative scheme for solving for the coefficient matrix c is:

1 Use c(n) to form the bond-order matrix P(n).

2 Use P(n) to form the Fock matrix F(n).

3 Find c(n+1) and ε(n+1) by solving the secular equation(F(n) − ε(n+1)S

)c(n+1) = 0.

4 Choose the N/2 molecular orbitals of lowest energy to be occupied.

5 Repeat steps (1)-(4) until ||c(n+1) − c(n)|| < δ.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 28 / 56

Page 29: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Electron Correlation

There are two sources of negative correlation between the locations ofdifferent electrons.

The Coulomb hole results from electrostatic repulsion.

The exchange hole is a consequence of the Pauli exclusionprinciple: electrons with the same spin cannot occupy the sameorbital.

The most important limitation of the H-F method is that it fails toaccount for the Coulomb hole. This is particularly problematic whenmodeling large molecules, for which about half of the interaction energycan be due to electron correlation.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 29 / 56

Page 30: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Hartree-Fock wavefunction of H2

Example: The H-F wave function for the hydrogen molecule H2 withdouble occupancy of a single molecular orbital φ(·) is

ψ(1, 2) =1√2

∣∣∣∣ χ1(1) χ2(1)χ1(2) χ2(2)

∣∣∣∣=

1√2φ(x1)φ(x2)

[α(ξ1)β(ξ2)− β(ξ1)α(ξ2)

],

where (xi , ξi ) is the location and spin of electron i , ξ2 = −ξ1, and α(·)and β(·) are the spin-up and spin-down functions introduced earlier.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 30 / 56

Page 31: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

The H-F wave function for H2 neglects electronic correlation.

The joint probability density of the locations of the two electrons is

|ψ(1, 2)|2 = Cφ2(x1)φ2(x2)

where C is a normalizing constant. Since this density factors into theproduct of two one-electron densities, it follows that under the H-F wavefunction, the locations of the two electrons are independentof one another.

This result is unphysical, but is also observed in H-F calculations formore complicated molecules.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 31 / 56

Page 32: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Post-Hartree-Fock Methods

Several methods have been devised to better account for electroniccorrelation:

Configuration Interaction (CI) method

Coupled Cluster (CC) method.

Many Body Perturbation Theory (MBPT), including theMøller-Plesset perturbation theory.

However, these are even more computationally intensive than the H-Fmethod.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 32 / 56

Page 33: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Occupancy

Given a collection of spin-orbitals, χ1, χ2, · · · and a Slater determinantΨ, we define the occupancy of spin-orbital χi to be

ni =

{1 if χi appears in Ψ0 otherwise ,

and we write Ψ = Ψn(n1, n2, · · · ). Here we require that

∞∑k=1

nk = n.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 33 / 56

Page 34: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Creation and Annihilation Operators

The creation and annihilation operators are defined as:

k†Ψn(· · · nk · · · ) = θk(1− nk)Ψn+1(· · · 1− nk · · · ),kΨn(· · · nk · · · ) = θknkΨn−1(· · · 1− nk · · · ),

where θk = (−1)P

j<k nj . Thus k† creates an electron and places itin the unoccupied spin-orbital χk , while k annihilates the electron inthe occupied spin-orbital χk .

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 34 / 56

Page 35: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Configuration Interaction

In the CI method, the H-F wave function is replaced by a linearcombination of Slater determinants formed from different sets of nspin-orbitals:

ΨCI = c0Ψ0 +∑a,p

cap p†aΨ0 +

∑a<b,p<q

cabpq q†p†abΨ0 + · · · .

Here, Ψ0 is usually the H-F wave function and the coefficients cap , · · · are

chosen to minimize the energy:

ECI =

∫Ψ∗CIHΨCIdX ≤

∫Ψ∗0HΨ0dX ≡ EHF .

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 35 / 56

Page 36: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Partial Configuration Interaction

As a rule, the full CI calculation is not feasible, since(2N

n

)different

n-electron determinants can be formed from a set of N molecular orbitalsand we usually take N � n. Instead, the CI expansion is usually restrictedto lower order terms (called excitations):

CID includes all doublet excitations cabpq q†p†abΨ0;

CISD includes all singlet and doublet excitations;

frozen shell CI only allows outer shell orbitals to be substituted.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 36 / 56

Page 37: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Coupled Cluster Method

The coupled cluster method seeks to find an operator T such that theexact ground state wave function can be written as

Ψ = eT Ψ0

where Ψ0 is usually the H-F wave function and the cluster operator T isa sum of excitation operators

T = T1 + T2 + T3 + · · ·

with

T1 =∑a,r

tra r†a (single excitations)

T2 =1

4

∑a,b,r ,s

trsab s†r †ab (double excitations).

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 37 / 56

Page 38: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

The amplitudes tra , · · · can be characterized in the following way. First, we

writeHeT Ψ0 = EeT Ψ0

which, upon multiplying both sides by e−T , gives

e−THeT Ψ0 = EΨ0.

Next, we use the commutator expansion to write

e−THeT = H+ [H, T ] +1

2![[H, T ], T ] +

1

3![[[H, T ], T ] , T ]

+1

4![[[[H, T ], T ] , T ] , T ]

where [A,B] ≡ AB − BA. The key observation is that the commutatorexpansion terminates because H only has two-particle interactions.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 38 / 56

Page 39: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Calculating the CC Amplitudes

If we then substitute the commutator expansion into (*) and multiply bythe function

Ψm1···mla1···al

= m†l · · · m†1a1 · · · alΨ0

and finally integrate over the spin and spatial coordinates, then we obtainthe identity∫ (

Ψm1···mla1···al

)∗(H+ [H, T ] + · · ·+ 1

4![[[[H, T ], T ] , T ] , T ]

)Ψ0dX = 0.

The right-hand side vanishes because Ψ0 and Ψm1···mla1···al

are orthogonal.

This leads to a system of fourth-order polynomial equations in the CCamplitudes which in principle can be solved iteratively. As with CI, thecluster expansion is usually truncated to obtain CCD or CCSD.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 39 / 56

Page 40: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

Møller-Plesset (MP) Perturbation Theory

In the Møller-Plesset perturbation theory, we write the Hamiltonian as

H = H(0) +H(1) =∞∑i=0

εi i† i +H(1),

where εi is the one-electron energy of the i ’th molecular orbital and theH-F wave function Ψ0 is the ground state eigenfunction for H(0). We canthen expand the true ground state wave function and energy as series

Ψ0 =∞∑

n=0

Ψ(n)0 , E0 =

∞∑n=0

E(k)0

where the terms in these series can be evaluated recursively, usually up tosecond (MP2) or sometimes fourth (MP4) order.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 40 / 56

Page 41: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Electron correlation

More formally, if Ψ(0)k and E

(0)k form a complete set of eigenvalues and

eigenfunctions for H(0), then we can define the reduced resolvent

R0 =∞∑

n=1

(1

E(0)0 − E

(0)n

)Pn.

where Pn is the orthogonal projection onto Ψ(0)n . It can then be shown that

Ψ0 =∞∑

n=0

SnΨ(0)0

E0 = E(0)0 + 〈Ψ(0)

0 ,H(1)∞∑

n=0

SnΨ(0)0 〉,

where S ≡ R0(E(0)0 − E0 +H(1)). The difficulty here is that S also

depends on E0.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 41 / 56

Page 42: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Sponer et al. (2004). Accurate Interaction Energies of Hydrogen-BondedNucleic Acid Base Pairs. JACS 126: 10142-10151.

Background

Base pair interactions in DNA and RNA depend largely on H-bonding.

Experimental measurement of the H-bond energies is difficult.

This motivates ab initio calculations of these energies.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 42 / 56

Page 43: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Interaction Energies

The interaction energy of dimer A · · ·B is defined as

∆EA···B = EA···B − (EA + EB) + EDef

where

EA···B is the energy of the optimized dimer;

EA,EB are the energies of the isolated bases, with the geometriesof the optimized dimer, calculated using the dimer basis set;

EDef is the deformation energy of the two isolated bases.

Thus, the interaction energy is equal to the energy of the H-bonds lessthe energy required to deform the geometries of the isolated bases.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 43 / 56

Page 44: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Deformation Energy

The deformation energy of dimer A · · ·B is defined as

EDef = (EA′ − EA′mon) + (EB′ − EB′

mon)

where

EA′,EB′

are the energies of the isolated bases, with the geometriesof the optimized dimer, calculated using the monomer basis sets

EA′mon,E

B′mon are the energies of the isolated bases, with the geometries

optimized in isolation using the monomer basis sets.

Here the monomer basis sets are used in both calculations to avoid basisset superposition error (BSSE).

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 44 / 56

Page 45: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Extrapolated Energies

Extrapolation of energies to the complete basis set (CBS) limit wasdone using Helgaker’s formula

E corrX = E corr

CBS + BX−3

where

E corrCBS is the extrapolated energy;

X is the number of basis functions used to represent each valenceorbital (X = 2, 3, 4);

E corrX is the calculated energy, using the MP2 perturbation theory

with an aug-cc-pVXZ basis set;

The aDZ → aTZ values reported in Table 2 were obtained byextrapolating from X = 2 and X = 3.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 45 / 56

Page 46: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Results

dimer ∆EA···B ∆ESCF ∆E corr EDef AMBER

GC (WC) -27.5 -20.0 -7.4 3.6 -28.0

AT (WC) -15.0 -7.0 -8.0 1.5 -12.8

GU (wobble) -15.8 -9.7 -6.1 3.0 -16.0

GA 1 -17.5 -8.2 -9.3 1.9 -14.7

AA 1 -13.1 -5.1 -8.0 1.4 -10.8

AMBER is a molecular mechanics package that uses a particular set offorce fields.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 46 / 56

Page 47: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Conclusions

Comparison with higher-order extrapolations suggests that theaDZ → aTZ are within ∼ 1 kcal/mol of the true values.

Electron correlation (dispersion attraction + intramolecularcorrelation) contributes significantly to the interaction energies.

H-bond energies estimated using AMBER are within ∼ 3 kcal/mol ofthe the QM estimates, with greater discrepancies for weak base pairs.

Base pair stability is mainly determined by electrostatic interactionsthat can be approximated by atom-centered charges.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 47 / 56

Page 48: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Schreier et al. (2007). Thymine Dimerization in DNA Is an UltrafastPhotoreaction. Science 315: 625-9.

Boggio-Pasqua et al. (2007). Ultrafast Deactivation Channel for ThymineDimerization. JACS 129: 10996-7.

Background

Thymine dimerization occurs through UV irradiation of DNAsequences containing adjacent thymine bases (TT dinucleotides).

Thymine dimers are usually repaired by photoreactivation or bynucleotide excision pathways.

Unrepaired dimers are mutagenic and are believed to be a majorcontributor to melanoma.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 48 / 56

Page 49: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Photocycloaddition

Absorption of a photon by thymineexcites a π electron to a π∗ orbital.This can then:

Return to the ground state(S0) via internal conversionof the excitation energy toheat.

Attack the double bond on anadjacent thymine, leading todimerization.

Thermal activation of the cycloaddition reaction has low yield because ofimproper symmetry of the interacting orbitals.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 49 / 56

Page 50: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Femtosecond Time-Resolved IR Spectroscopy

Schreier et al. (2007) studied thymine dimerization in UV-irradiated(dT )18 using IR spectroscopy.

This indicates that TD formation occurs within 3 ps of UV absorption.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 50 / 56

Page 51: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Quantum Mechanical Analysis of Thymine Dimerization

Boggio-Pasqua et al. (2007) used molecular orbital theory to characterizethe likely reaction pathways for thermal and photochemical thyminedimerization.

The QM calculations used multi-configurational SCF (CASSCF) andperturbation theory (CASPT2) to calculate energies of intermediatestates.

These methods allow for electron excitation to higher-energy orbitals.

The potential energy surface near the UV-excited state has thegeometry of a conical intersection (CI).

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 51 / 56

Page 52: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

Thermally-driven TD formation has low yield.

The thermal reaction pathway passes through two transition states to leadto a thymine dimer that is higher in energy than the TT dinucleotide.Thymine dimerization is unlikely to occur through this mechanism.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 52 / 56

Page 53: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

The photochemical reaction is barrierless.

In contrast, following photon absorption, the excited system will relax to aCI from which it can either rapidly relax to the thymine dimer or return tothe TT ground state.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 53 / 56

Page 54: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Applications

The conical intersection.

Relaxation of the excited state occurs so rapidly that the neighboringdimers must have a suitable conformation at the time of photoexcitationfor thymine dimerization to occur.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 54 / 56

Page 55: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Summary

Quantum Chemistry: Scope and Limitations

Quantum mechanical calculations are important whenever:

Empirical data relevant to molecular energetics are lacking or havequestionable accuracy;

We wish to study processes involving bond formation and breaking(chemical reactions).

However, all of these methods are computationally intensive and so areusually restricted to aperiodic systems containing at most a tens of atoms.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 55 / 56

Page 56: Computational Chemistry Ab initio methods seek to solve ...jtaylor/teaching/Fall2010/... · Quantum Chemistry Theory Computational Chemistry Ab initio methods seek to solve the Schr

Quantum Chemistry Summary

References

Hehre, W. J., Radom, L., Schleyer, P. v. R., and Pople, J. A. (1986)Ab Initio Molecular Orbital Theory. Wiley.

Piela, L. (2007) Ideas of Quantum Chemistry. Elsevier.

Jay Taylor (ASU) APM 530 - Lecture 3 Fall 2010 56 / 56


Recommended