Computational biophysics:
concepts and methods
Lectures 1 & 2: Quantum Chemistry
Jochen Hub
Computational Molecular Biophysics Group
[email protected]
http://cmb.bio.uni-goettingen.de/
Before we start
•
Access to CIP-Pool of physics faculty. ☞ Paper forms to fill out
• Lectures / computer practicals in weekly turns
!
• Practicals in Seminar room 1
•
!
Exams: 30 minutes oral exams
August 4, 5, 6, 20, 21
Schedule
Only an overview...
Books on quantum chemistry
!
• Szabo and Ostlund: Modern
Quantum Chemistry
!
• Leach: Molecular Modelling
!
• Jensen: Introduction to
Computational Chemistry
Chemistry on a computer
chemical reactions
substitution
understand & predict
reactant
transition state
F-
product
F
Cl-
0 kJ/mol
17 kJ/mol
-204 kJ/mol
Br-
0 kJ/mol
65 kJ/mol
-181 kJ/mol
Observe while it happens: bacteriorhodopsin
catching the photo-isomerization of retinal in the act
bR: multiconfigurational QM/MM MD strajectory
Radiation damage: UV absorption in DNA
thymine dimerization
base stack (TT)
CASSCF(8,8)/6-31G
diabatic surface hop
Simulations conducted by G. Groenhof
Radiation damage: UV absorption in DNA
thymine dimerization
cell death?
mutation?
Atomic orbitals
n=1
n=2
http://www.orbitals.com/orb/orbtable.htm
n=3
n=4
n=5
n=6
n=7
n=8
n=9
l =0
m=0
l =1
m=0
l =1
m=1
l =2
m=0
l =2
m=1
Complete set: any function can be expanded in
(r, ✓, ) =
X X nX1 m=+l
X
i
n=1 l=0 m= l
cinlm
(r, ✓, ):
nlm (r, ✓,
)
n=10