II.

Quantum Chemistry and Spectroscopy

1. The Quantum Theory [Chapter 9] 2. Chemical Bonding [Chapter 9] 3. Weak interactions [Chapter 9] 4. Spectroscopy [Chapter 10] 5. X-Ray Diffraction [Chapter 12]

II.1a. Version date: Oct. 15, 2008.

(to end of harmonic oscillator)

Figures from Engel, Quantum Chemistry and Spectroscopy (except as noted)

Syllabus

I. Thermodynamics: To react or not to react?

1. The First Law: Energy Is Conserved. [Chapter 2] 2. The Second Law: The Entropy of the Universe Increases. [Chapter 3] 3. The Chemical Potenial and Chemical and Physical Equilibria. [Chapters 4 & 5]

II. Quantum Chemistry and Spectroscopy: Structure at the molecular level

1. The Quantum Theory [Chapter 9] 2. Chemical Bonding [Chapter 9] 3. Weak interactions [Chapter 9] 4. Spectroscopy [Chapter 10] 5. X-Ray Diffraction [Chapter 12]

III. Kinetics: How Fast?

1. Molecular Motion and Transport Properties. [Chapter 6] 2. Rates Laws. [Chapter 7] 3. Molecular Distributions and Statistical Thermodynamics. [Chapter 11] 4. How to Calculate Reaction Rates. [Chapter 7] 5. Examples. [Chapter 7] 6. Enzyme Kinetics. [Chapter 8]

Classical Theory
Matter
Newton s Laws of Motion: F=ma Need to know the initial conditions Follow the trajectores of objects such as baseballs, satellites, etc. A particle is localized in space. Determine the position and momentum of each particle at each moment in time.

The Quantum Theory

Matter
Has wave-like properties which are especially apparent for light particles on small length scales. Wave-particle duality: Still has some particlelike properties.

Light

Light

Behaves like a wave. Behaves like a particle. Obeys a Wave Equation (coutesy of Maxwell) Comes in packets called photons. Need to know the boundary conditions. Wave-particle duality: Still has some wavelike properties. Waves are spread out in space.

Department of Chemistry Seminar Tuesday, October 7, 2008

3:20 -5:00 pm - MGH 111 Refreshments 3:05 pm

Biological Molecules In and Out of Water: Mass Spectrometry, Optical Spectroscopy and Computational Studies Rebecca Jockusch, Ph.D. University of Toronto

Single slit diffraction pattern

Interference of waves

Two slit diffraction pattern

Standing waves on a string

Number the different standing waves: u(x,t)

n=1

n=2

n=3

n=4
Figs from D.A. McQuarrie, Quantum Chemistry

A vibrating drum is a 2D standing wave

D.A. McQuarrie, Quantum Chemistry

Blackbody radiation
particle-like properties of light

Photon energy:

E = h

Photoelectric effect
particle-like properties of light

Photoelectric effect
particle-like properties of light

Emax = h -
Photon energy:

E = h

For bound particles, energy is quantized!

Atomic line spectra of Hydrogen

electrons in atoms can only have certain energies

"#

& 1 1 1 ) = %R H ( 2 % 2 + $ n1 * ' n2

n1 and n2 are integers. For Balmer series above n1 = 2. RH = 109, 677.581 cm-1

!
Silberberg Chermistry 4th ed, 2006, Fig. 7.8, p 264.

ALSO: The heat capacities of solids at low temperatures show that atomic vibrations can only have certain energies.

Electron diffraction
wave-like properties of electrons

DeBroglies relationship give the wavelength of matter-waves as = h/p

Wave - Particle Duality

Is light both a wave AND a particle? What about electrons?

GFP
Glowing proteins - a guiding star for biochemistry
The remarkable brightly glowing green fluorescent protein, GFP, was first observed in the beautiful jellyfish, Aequorea victoria in 1962. Since then, this protein has become one of the most important tools used in contemporary bioscience. With the aid of GFP, researchers have developed ways to watch processes that were previously invisible, such as the development of nerve cells in the brain or how cancer cells spread.

Heisenberg Uncertainty Principle

follows directly from the wave nature of matter.

"x # "p $ 1 h 2

The POSTULATES of the Quantum Theory

The amplitude of our matter wave is specied by a wave amplitude function, (r, t)
The probability of nding the particle at the position r is |(r, t)|2
POSTULATE 1: The state of a quantum-mechanical system is completely specified by a continuous, single-valued function (r,t) that depends on the coordinates of the particles, r = (x1, y1, z1, x2, y2, z3, ) and on time, t. This function, called the wave function or state function, has the property that *(r,t) (r,t)d is the probability that the particle lies is a volume element, d = dx1dy1dz1dx2dy2dz2, located at r and time t. Note: Since the total probability of finding the particle(s) anywhere in space is 1, the wave function must be normalized such that all space *(r,t) (r,t)d = 1. If there is only 1 dimension, x, then this becomes

*( x, t )( x,t )dx = 1

Williams-Sonoma $100

To extract information about the particle from the wave function, we use the operator that corresponds to the property of interest.

POSTULATE 2: To every observable in classical mechanics, there corresponds a linear, Hermitian operator in quantum mechanics. The operator for the position coordinate x is x , which means multiply by x. The operator for the px, the momentum in the x direction, is px = ih . x

Definition: A linear operator has the property that (c1 1+c2 2) = c1( 1)+c2( 2) where c1 and c2 are any real or complex numbers and functions obeying postulate 1.

1 and

2 are

any two

Warranty and how to get one.

POSTULATE 2: To every observable in classical mechanics, there corresponds a linear, Hermitian operator in quantum mechanics. The operator for the position coordinate x is x , which means multiply by x. The operator for the px, the momentum in the x # direction, is px = "ih . #x Definition: A Hermitian operator satisfies all space * d = all space ( )*d ! The Hermitivity property assures that all observable quantities will be real.
Note: Most other operators can be derived from x and px using the appropriate classical expressions. For example, the kinetic energy T for motion in the x direction is classically T = px2/2m. The corresponding quantum mechanical operator is 2 1 $ # '$ # ' "h 2 # 2 p "ih )& "ih ) = T= x = ! . & 2m 2m % #x (% #x ( 2m #x 2 For motion in 3 dimensions 2 2 p 2 px + py + pz2 = T= 2m 2m ! # '$ #' $ # '$ #' $ # '$ # '1 *$ = ,& "ih )& "ih ) + &"ih )& "ih ) + &"ih )&"ih )/ 2m +% #x (% #x ( % #y (% #y ( % #z (% #z (.

#2 # 2 ' "h 2 2 "h 2 $ # 2 + + 0 = & )= 2m % #x 2 #y 2 #z 2 ( 2m

A model for every need.

More Operators

Instructions for use.

How operators are used.

Sometimes a property has a denite value
POSTULATE 3: For any measurement of the observable associated with the operator , the only values that will ever be observed are the eigenvalues a, which satisfy the eigenvalue equation, = a . Note: An eigenvalue is a just a real number. That is when the application of the operator to the function gives a multiple of the same function (a times ), then is an eigenfunction of the operator and a is the eigenvalue. The Hemitivity property of the operators ensures that the eigenvalues will always be real. When an observable has a definite value, that value of the observable is the eigenvalue.

sometimes you can only get an average value.

POSTULATE 4: If the system is in a state described by a normalized wavefunction average value of the observable corresponding to is given by A = # " * A"d$
all space

, then the

POSTULATE 5: The wavefunction evolves in time according to the time-dependent Shrdinger equation, ! %" H" = ih %t = T + V is the Hamiltonian operator equal to the sum of the kinetic and where t is time and H potential energies.

!
!

How to get them

POSTULATE 4: If the system is in a state described by a normalized wavefunction average value of the observable corresponding to is given by A = # " * A"d$

How to nd the wave function

all space

, then the

POSTULATE 5: The wavefunction evolves in time according to the time-dependent Shrdinger equation, ! %" H" = ih %t where t is time and H = T + V is the Hamiltonian operator equal to the sum of the kinetic and potential energies.

For dynamics, we need to use the above differential equation, but mostly we are ! interested in the stationary structure of atoms and molecules, so we want to nd the standing wave pattern for the electrons, etc., which is just the spatial part of the wavefunction, (r). For this purpose, we can use the time-independent ) Schoedinger equation:

H" (r ) = E" (r )

This is also a differential equation, because H has derivatives with respect to the coordinates, but at least the time derivative is gone.

In nearly all practical cases, the Schroedinger equation cannot be solved exactly, so approximate methods must be used. Commercial software is available for this purpose and is often used. For example, the Student P Chem version of Spartan is available in KNCL 314. The computational power required increases dramatically with the size of the molecule and large biomacromolecules are still out of reach.

Too big!

Particle in a 1-Dimensional Box

The Potential The Wavefunctions & Energies
En = n h 8ma 2
2 2

Remember the vibrating string! The standing wave patterns are exactly the same!

u(x,t)

The Probability Distributions

P( x) = "( x)
2

n = 1,2,3,4,...

n=4

n=3

nodes

2 "h 2 d # ( x ) = E# ( x ) 2m dx 2

n=2

Boundary Conditions: (x) = 0 at x = 0 and x = a

n=1

Correspondence Principle
Particle in a 1-D Box In the limit of high quantum numbers, the classical result is obtained.

prophyrin

Remember the vibrating drum!

Particle in a 2-Dimensional Box

y
Square a a box
a a

x
E ( n x ,n y ) 8ma 2 n x ,n y = 1,2,3,4,...
a

(n =

2 x

2 + n y )h 2

a a

Particle in a nite depth box

Boundary Conditions: Tunnelling:

Innite depth box

Smooth join at the boundaries

Wavefunctions extend into the forbidden regions

Quantum-Mechanical Tunnelling through a barrier

Examples: Radiaoactive decay Proton-transfer reactions The tunnelling rate decreases exponentially with the particle mass and the height and width of the barrier.

Scanning Tunnelling Microscopy

http://www.physics.berkeley.edu/research/crommie/figures/STM_Figure_1.jpg Graphite 52 A x 52 A: www.its.caltech.edu/~yehgroup/stm/2952.html

DNA STM image and STS on bare gold.

Errez Shapir, Hezy Cohen, Arrigo Calzolari, Carlo Cavazzoni, Dmitry A. Ryndyk, Gianaurelio Cuniberti, Alexander Kotlyar, Rosa Di Felice & Danny PorathNature Materials 7, 68 - 74 (2008) Published online: 25 November 2007

Vibrational Potential of a Diatomic Molecule

V(r) Harmonic potential 2 V ( r) = 1 k ( r " re ) 2
V ( x ) = 1 kx 2 2

m1
r

m2

Use the reduced mass,

1 1 1 = + m1 m2
as the effective mass when both atoms are vibrating.

Realistic potential

re Let x = r - re

Harmonic Oscillator Wavefunctions & Probability Distributions

2 "h 2 d # ( x ) 1 2 + kx # ( x ) = E# ( x ) 2m dx 2 2

E n = (n +

1 2

)h"

with n = 0, 1, 2, 3,
"=
1 2# k

Boundary Conditions: (x) 0 at x =

!
!

Harmonic Oscillator and the Correspondence Principle