Molecular Devices
Chennai, September 14, 2005
K.L. Sebastian
IPC Department, IISc
http://ipc.iisc.ernet.in/~kls
Outline
• Motivation – examples from biology
• Molecular Rollers and Rocker
• Molecular Wheel
• Molecular Rattle
. Fluxionality for Rotational Motion
• Nature does it very well! (Biological Molecular Motors)
• Synthetic Molecular Motors
• Light driven molecular motor
Is that a
flower?
It is a
motor
Height ~ 8 nm
Width ~ 10 n
MOLECULAR
Can one design
molecules that would
prefer to roll on a
surface?
What do you
mean?
ROLLER
Seems rather difficult,
perhaps we can try to use
fluxionality!
Consider Hypostrophene-it is
fluxional -perhaps we can use
this property!
God! He
crazy!!
is
To explain, let us start with
Pentaprismane
H
Pentaprismane (C10H10)
D5h
hypostrophene
Hypostrophene
C2v
pentaprismane
Symmetry is broken! It
can be broken in FIVE
different ways!
Five degenerate minima!
It should be possible to
jump from one to the
other
It does! Known as
Degenerate Cope
Rearrangement
Degenerate Cope Rearrangement for
Hypostrophene
Activation energy
B3LYP/6-31G**
(kcal/mol)
25.31
GS
TS
Rate constant
Rate constant ~ 1.8 X 10-5 sec-1
Activation
energy
Q and Q* are the
partition functions
of GS and TS
Think of Hypostrophene
adsorbed on Al(100)
Rolling Motion
Rolling-TS
Eact ~ 18 kcal/mol
Translation-TS:
Eact ~ 65.5 kcal/mol
Molecular Roller
Same thing can happen
with syn-TOD!
Cubane
Syn-TOD
C2v
Td
Activation energy
B3LYP/6-31G**
(kcal/mol)
GS
TS
24.25
Activation energy
13.6 kcal/mol
(B3LYP/6-31G** C,H and 321G for Al)
TS
MOLECULAR ROLLERS
We conclude that:
Hypostrophene and tricyclooctadiene when chemisorbed
on Al(100) surface should behave as ‘Molecular roller’
Bidisa Das, K.L Sebastian, Chemical Physics Letters, 330, 433 (2000).
MOLECULAR ROCKER
Cope Rearrangement of
Semibullvalene
GS
GS
TS
Activation energy
B3LYP/6-31G**
(kcal/mol)
5.5
Semibullvalene on Al(100)
Metal surface: cluster of 14 or 32 Al atoms in two layers
Hydrogen atoms at the edges.
B3LYP/Al:3-21G, C,H:6-31G**
Ea = 21.8 kcal/mol
MOLECULAR
ROCKER
Fluxionality for Rotational Motion
Fe(CO)3
Fe(CO)3 moving around
hypostrophene
Hypostrophene
203i cm-1
4.3
kcal/mol
33.6
kcal/mol
Molecular wheel
MOLECULAR WHEEL
C5H5Ge(CH3)3 is known
to be fluxional!
Eact ~ 16.0 kcal/mol
The activation barriers and rate constants
Eact
(kcal/mol)
rate constant at
298.15 K
(sec-1)
Si (C,H: 6-31G** &
Si: 6-31G**)
14.04
3.2X102
Ge (C,H: 6-31G**
& Ge: 6-31G**)
12.21
1.6X103
Sn (C,H: 6-31G**
& Sn: 3-21G)
5.74
3.7X108
M atom bonded to
Cp and basis-sets
used
Cyclopentadienyl adsorbed
on Ge surface, should move
like a wheel!
Hopping onto
adjacent Ge
atoms
Adsorbed to the
same site!
Eact ~ 11.9 kcal/mol
M atom
bonded to Cp
and basis-sets
used
Eact
(kcal/mol)
Rate constant
(sec-1)
298.15 K
Si (C,H: 631G** & Si:
6-31G**)
13.45
8.5X102
Ge (C,H: 631G** & Ge:
6-31G**)
11.90
1.9X104
Sn (C,H: 631G** & Sn:
3-21G)
5.97
2.5X108
Molecular Wheel
That is not bad!
Why don’t you call it a
molecular “seal”?
Sn
Ea = 5.97 kcal/mol
B. Das and K.L. Sebastian: CPL 357, 25 ( 2002)
We conclude that :
The cyclopentadienyl co-adsorbed with hydrogen on
Si/Ge/Sn (111) surfaces would form a system
where the five membered ring can undergo spinning
motion with low activation energies.
Bidisa Das, K.L Sebastian, Chemical Physics Letters, 357, 25 (2002).
Molecular Rattle
A
B
B
A
B
A
H
H
H+
-
H
H
H
H
Does not happen!
Ionization potential of
H too large!
Perhaps, in an excited
state, this might happen
H+
Replace H with Li!
Li+
-
Ring too small
-
Li+
Eact~42.4
kcal/mol
Eact
a:315 kcal/mol
b:36.6kcal/mol
c:33.6kcal/mol
These are the molecules that we studied but activation
energies for the ‘umbrella inversion’ kind of motion was
found to be high.
M. Oda, Pure & Appl. Chem. 58, 7 (1986), T.Z. Ktaz, P. A. Garratt, J. Am. Chem. Soc. 85, 2852 (1963).
C9H9-
Molecular Rattle
Ea = 11.7 kcal/mol
B. Das and K.L. Sebastian: CPL, 365, 320
(2002)
Proton going
through benzene
(C6H7+)
Mahapatra, Sathyamurthy, Current
Science, 1995
Cyclononatetraenyllithium
The activation barrier for
the ‘umbrella inversion’ in
this case is ~11.5
kcal/mol
Normal mode analysis: 276 cm-1(GS), 274i cm-1(TS)
1D through ring motion calc.: 277 cm-1(GS), 267i cm-1 (TS)
Nature does it well!
Biological Molecular Motors
We know of
several, efficient
molecular motors!
All of them occur in
BIOLOGICAL
systems
Figure from:
http://ccgb.umn.edu/~mwd/cell.html
Energy from
photosynthesis
Figures and animation from:
http://www.sp.uconn.edu/~terry/images/anim/ATPmito.html
ATP Synthase (Rotary)
Most powerful
known motor
ATP Synthase
Synthesizes ATP.
Rotates while it
does this!
Kinesin (Walker)
Proteins that
WALK!
Works like a
PORTER at the
railway station
See animation at
http://mc11.mcri.ac.uk/wrongtrousers.html
Myosin
Proteins that
PUSH!
Myosin
For an animation, see the CD of the
book: Molecular Biology of the Cell by B.
Alberts et. Al.
See also:
http://www.rpi.edu/dept/bcbp/molbioch
em/MBWeb/mb2/part1/myosin.htm
Synthetic Molecular Motors
NO WAY near
the natural ones!
shuttle
station
station
Rotaxane
stopper
Electron Removal
+e
-e
Proton Addition
- H+
+ H+
Either electron
removal or
proton addition
Catenanes
2-catenane
3-catenane
Switching by Oxidation-Reduction
Reations
-e
+e
Catenanes – how to have light
driven motor?
station
shuttle
Leigh et. al. Nature, 424, 174 (2003)
Excitation of the station leads
to unbinding!
Light induced excitation of the
shuttle is better!
K.L. Sebastian: Current Science, 87, 232 (2004)
Can one have……?
Light induced conformational
change driving translation!
Cis-trans isomerization as in
Azobenzene could be useful
Molecular Ratchets, Second Law
and Detailed Balance
Brownian motion would drive the
ratchet! But it can rotate only in one
direction! So thermal, random motion
can be used to drive the ratchet in
one direction!
Axle
[4]helicene
triptycene
A molecular ratchet was
Synthesized and studied by
Kelly et. al. Angewandte
Chemie 109, 1969 (1997).
It can undergo ratchet-like
internal rotation!
To probe rotational
motion use NMR
That is clever!
Second Law
verified!
But wait! Let us
think about this!
There he
goes! As
mad as a
coot!
The fact that you can
see rotation means that
your initial state is a
non-equilibrium one!
So even if you had seen net
rotation, that would not
violate the second law!
But you do not see any net
rotation! What does that
mean?
Because of Detailed
Balance!
K.L. Sebastian, Physical Review E61, 937 (2000)
CONCLUSIONS
Molecular Roller, Wheel,
Rocker, Rattle!
Fluxional behavior can be
used to get interesting
mechanical motion
Ratchets, Light driven
motor……
Acknowledgements
Dr. Bidisa Das
Prof. Ashoka Samuelson