Transcript Slide 1

While we wait for everyone to arrive, please jot down your
syntheses numbers for weeks 1 and 2. Your protocols can
be picked up from the lab before you leave.
mon-22
wk
1
wk
2
tues - 21
wk
1
wk
2
Berkowitz, Silas John
8
41
Aguilera, Alexya Nicole
8
41
Chau, Steven Minh
8
41
Baken, Erica Karin
8
41
Eggers, Hilary Helen
8
41
Buchholz, Adam Lane Zukoski
8
41
Buck, Olivia
11
47
Choi, Elaine Young
11
47
Franks, Jennifer Marie
11
47
Cody, Evan William
11
47
Heo, James Muyoung
11
41
Colantuoni, Deborah Elise
11
47
Kryder, William Christian
23
10
Coreas, Bryan
23
10
Marich, Martha Elizabeth
23
10
Crabo, Anders Gustaf
23
10
Mazer, Benjamin Aaron
24
10
Fong, Aaron Yeu Wah
24
42
McHugh, Keith Michael
24
8
Henderson, Carolyn Jordan
24
10
Metcalf, Kathryn Bishop
44
8
Jones, Jennifer Julia
44
8
Meyer, Ryan Luther Nai-Ming
44
8
Kim, Daeho
44
8
Misra, Rahul
10
46
Kistler, Kathryn Elise
10
46
Mokkarala, Sameera
10
46
Koh, Sukjin
10
46
Murphy, Kellyann Marie
10
46
Leonard, Heidi
10
42
Quinn, Andrew McDonough
12
42
Ssembajjwe, Brian Sekabira
12
42
Simmons, Amina Yasmeen
12
42
Tran, Annie Marie
12
42
Toscano, Ashley
41
44
Ventrudo, Lauren Unell
41
44
Tseng, Joseph James
41
44
Washington, Niger
41
44
VanDerGeest, Kori Ann
42
12
Wilairat, Nathan Taketo
42
12
Zarafshar, Shahriyar Shahpour
42
12
LaBriola, Joseph
42
12
Xu, Zhen Zhen Jane
42
12
While we wait for everyone to arrive, please jot down your syntheses numbers for weeks
1 and 2. Your protocols can be picked up from the lab before you leave.
wed -15
w1
w2
Clarke, Cornelia Ann
8
41
Cleveland, Thomas Josiah
8
Garcia, Paloma Elizabeth
thurs - 12
w1
w2
fri-21
w1
w2
Chestler, Shelley Renee
8
41
Bahl, Luke Ari
8
41
41
Course, Meredith Marie
8
41
Burgess, Lucia Goodwin
8
41
11
47
Friedman, Gabriel Nathan
11
47
Cherney, Joseph David
11
47
Groth, Alexander E.
11
47
Lewis, John Edwin
11
47
Davila, David
11
47
Kinicki, Sarah Elizabeth
23
10
Min-Venditti, Claire Elien
23
10
Dodds, Eric McVoy
23
10
Lawrence, Katherine Elizabeth
23
10
Olsson, Chase Robert
23
10
Green, Eldridge M.,, Jr.
23
10
Lee, Donghyung
24
8
Smith, Zipporah
24
12
He, Jixi
44
46
Lee, Joyce Danbee
24
8
Williford, John Alden
24
12
Helms, Stefan Kristoffer
44
46
Lee, Rachel Minji
42
12
Wright, Christopher Lyle
44
46
Ichikawa, David Matthew
10
23
McCormack, Ellen
42
12
Wu, Julie Jiabin
44
46
Jensen, Kelsey Marie
10
23
McOmber, Kristina Ru
44
46
deBoisblanc, Jenna Suzanne
10
42
Jones, Tera Jeneil
10
24
Pang, Samuel Wei Kean
44
46
Ekaireb, Rachel Ingrid
10
42
Koenig, Michael John
12
42
Nako, John-David Akio
10
42
Lindbergh, Kristen Marie
12
42
Park, Matthew YunJoon
12
42
Liu, Albert Yen
41
44
Pegeron, Andre Marc
12
46
Ly, Thuy Minh
41
44
42
10
Roh, Seo Young
42
10
Sahl, Anna Helen
46
8
Snyder, Hannah Greenlick
46
8
Taylor, Katherine Anne
47
11
Zhao, Danyang
47
11
McKinney, Andrew Michael
Introduction to Molecular
Modeling
The 1998 Nobel Prize in Chemistry
Walter Kohn, UC Santa Barbara
"for his development of the
density-functional theory“
John Pople, Northwestern
"for his development
of computational methods
in quantum chemistry"
“Chemistry is not only test tubes and chemicals. In
quantum chemistry, quantum mechanics is used to compute the
properties of molecules and their interaction. This year's laureates
have made it possible to use the complex equations of quantum
mechanics to study molecules and chemical processes with the
help of computers.”
- from the Nobel Press Release
http://nobelprize.org/nobel_prizes/chemistry/laureates/1998/illpres/computers.html
Applications
• Academic Research
– models to explain
chemical
phenomena at the
molecular level
• Protein folding
• Active sites of enzymes
• Industry/Pharmaceuticals
– drug mechanism and/or
metabolism
– product improvement
Avoid costly
experiments
($, time, safety)
Objectives for today…what kind of information can
you obtain from molecular modelling?
Stick
Tube
Space filling
Ball & Stick
(Simple Pictures/Not realistic representations)
• Structure (bond lengths, bond angles, & molecular geometry)
• Energy (enthalpy of formation & MOs)
• Reactivity (electron rich or poor parts of the molecule & dipoles)
• Spectroscopic properties: Vibrational (IR)
*(UV-Vis) & (NMR) also possible, but not done today
More realistic picture with electrons from all occupied molecular orbitals
Where you start.
Hartree-Fock models useful for predicting structure, energy
and property calculations, in particular for organic molecules
ĤΨ = εΨ
Two energy forms must be accounted for:
1) Potential energy
• Electrostatic attraction b/w electrons & nucleus (usual view of bonding)
• Electrostatic repulsion b/w nuclei
• minimize by finding equilibrium bond length
2) Kinetic energy
• e- movement
• minimize by allowing for delocalization in a larger space (i.e. create an MO
larger than the AO)
Total energy is the heat of a hypothetical reaction that creates a molecule
from a collection of separated nuclei and electrons.
3-21G ab initio Hartree- Fock calculation
Schrodinger equation ĤΨ = εΨ
describes molecules in terms of motions and
interactions of nuclei and electrons
solvable for a 1-electron atom only
use approximations to simplify the equations to be solved
Born-Oppenheimer Approximation
nuclei >>> electrons
nuclear kinetic energy = 0
Hartree-Fock Approximation
electrons move independently of each other
In the calculation, one electron is selected and the Schrodinger equation is solved in
the presence of a field (replacing individual e-e interactions) containing the remaining
electrons. This is repeated for each electron until convergence.
Ab Initio
from the beginning, without empirical data
MO-LCAO: Molecular Orbital – Linear Combination of Atomic Orbitals
Atomic Orbitals just mathematical functions {e.g., Ψ1s = 1s = ce-Zr/a◦}
Basis Set: Atomic orbitals approximated by Gaussian functions (easier to  )
3 represents the
number of functions
used to construct
core atomic orbitals.
The basis set is divided into
core and valence sets of
Gaussian functions describing
all of the electrons.
f(r) = a e-ζr2/a◦2
3-21G basis set
“Two – one” describes the
number of functions summed
to construct the valence
atomic orbitals.
{These two functions are different
because they have different
exponent arguments (ζ).}
HOMO & LUMO
electron pair donor/acceptor orbitals
The exercise will ask you to analyze the HOMO of two
ligands and determine the preferential site of attack.
Highest Occupied Molecular Orbital
HOMO
Lowest Unoccupied Molecular Orbital
&
LUMO
electron pair donor/acceptor orbitals
“frontier orbitals,” important for chemical reactions
What sort of
orbital is this?
Delocalized π*
+
–
–
–
+
+
LUMO of formamide
What are the limits of your chosen model?
• Hartree-Fock models tend to overestimate energies and
underestimate bond lengths. Methods exist to correct HF
calculations.
• IR frequencies tend to be 12% higher than experimental
values.
• No single method is ideal for all applications.
• Models and basis sets are chosen based on the properties,
problems, level of confidence, and practicality.
• Improved technology allow for advances in modeling.
Some final reminders…
Do the examples in pairs and then individually do the exercises to
be turned in.
The updated Spartan ’08 info is on the course website. It remains
largely the same as what is in your manual for ‘06.
The online info contains a copy of the report to be completed. Info
can be cut and pasted into the document, printed, and turned in.
The department has 15 licenses, so if your calculation fails at first,
try again.
Pick up protocol for first synthesis before leaving!