k.l. sebastian ipc department, iisc kls chennai, september 14, 2005 molecular devices

K.L. Sebastian

IPC Department, IISc

http://ipc.iisc.ernet.in/~kls

Chennai, September 14, 2005

Molecular Devices

• 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

Outline

Height ~ 8 nm Width ~ 10 n

Is that a flower?

It is a motor

Can one design molecules that would

prefer to roll on a surface?

Seems rather difficult, perhaps we can try to

use fluxionality!

What do you mean?

ROLLERMOLECULAR

To explain, let us start with Pentaprismane

Consider Hypostrophene-it is fluxional -perhaps we

can use this property!

!!

Pentaprismane (C10H10)

D5h

Hypostrophene

C2v

Symmetry is broken! It can be broken in FIVE different ways!

hypostrophene

pentaprismane

H

Five degenerate minima! It should be possible to jump from

one to the other

It does! Known as Degenerate Cope Rearrangement

Rate constant

Degenerate Cope Rearrangement for Hypostrophene

GS TS

Activation energy

Q and Q* are the partition functions of GS and TS

Rate constant ~ 1.8 X 10-5 sec-1

Activation energy

25.31

B3LYP/6-31G** (kcal/mol)

Think of Hypostrophene

adsorbed on Al(100)

Rolling-TS Eact ~ 18 kcal/mol

Translation-TS:Eact ~ 65.5 kcal/mol

Rolling Motion

Same thing can happen with syn-

TOD!

Molecular Roller

GS TS

Activation energy

24.25

B3LYP/6-31G**(kcal/mol)

Syn-TOD

C2v

Cubane

Td

Activation energy

13.6 kcal/mol

(B3LYP/6-31G** C,H and 3-21G for Al)

TS

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 ROLLERS

MOLECULAR ROCKER

GS GS

Cope Rearrangement of Semibullvalene

Activation energy

5.5

B3LYP/6-31G**(kcal/mol)

TS

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

Fe(CO)3

Fe(C

O) 3

Fe(C

O)3

Fe(CO)3 moving around

hypostrophene

Fluxionality for Rotational Motion

Hypostrophene

33.6

kcal/mol

4.3 kcal/mol

203i cm-1

Molecular wheel

C5H5Ge(CH3)3 is known to be fluxional!

Eact ~ 16.0 kcal/mol

MOLECULAR WHEEL

The activation barriers and rate constants

3.7X1085.74Sn (C,H: 6-31G**

& Sn: 3-21G)

1.6X10312.21Ge (C,H: 6-31G** & Ge: 6-31G**)

3.2X10214.04Si (C,H: 6-31G** & Si: 6-31G**)

rate constant at 298.15 K

(sec-1)

Eact

(kcal/mol)M atom bonded to Cp and basis-sets used

Cyclopentadienyl adsorbed on Ge surface,

should move like a

wheel!

Eact ~ 11.9 kcal/mol

Adsorbed to the same site!

Hopping onto adjacent Ge

atoms

2.5X1085.97

1.9X10411.90

8.5X10213.45

Rate constant(sec-1)

298.15 KEact

(kcal/mol)

Sn (C,H: 6-31G** & Sn:

3-21G)

Ge (C,H: 6-31G** & Ge:

6-31G**)

Si (C,H: 6-31G** & Si:

6-31G**)

M atom bonded to Cp and basis-sets used

Molecular Wheel

Sn

Ea = 5.97 kcal/mol

B. Das and K.L. Sebastian: CPL 357, 25 ( 2002)

That is not bad!Why don’t you call it a molecular “seal”?

We conclude that :

Bidisa Das, K.L Sebastian, Chemical Physics Letters, 357, 25 (2002).

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.

Molecular Rattle

A

B

B B

A

A

H

H

HHH

H

Does not happen! Ionization potential of

H too large!

Perhaps, in an excited state, this

might happen

H+

-

H+

-

Replace H with Li! Li+

-

Ring too small

Li+

-

These are the molecules that we studied but activation energies for the ‘umbrella inversion’

kind of motion was found to be high.

Eact~42.4 kcal/mol

Eact

a:315 kcal/mol

b:36.6kcal/mol

c:33.6kcal/mol

M. Oda, Pure & Appl. Chem. 58, 7 (1986), T.Z. Ktaz, P. A. Garratt, J. Am. Chem. Soc. 85, 2852 (1963).

C9H9-

Ea = 11.7 kcal/mol

B. Das and K.L. Sebastian: CPL, 365, 320 (2002)

Molecular Rattle

Proton going through benzene (C6H7

+)Mahapatra, Sathyamurthy, Current

Science, 1995

Cyclononatetraenyl-lithium

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

Synthesizes ATP.Rotates while it

does this!

Most powerful known motor

ATP Synthase (Rotary)

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/molbiochem/MBWeb/mb2/part1/myosin.htm

Synthetic Molecular Motors

NO WAY near the natural

ones!

Rotaxane

shuttlestationstopper

station

-e+e

Electron Removal

+ H+

- H+

Proton Addition

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?

Leigh et. al. Nature, 424, 174 (2003)

Excitation of the station leads to unbinding!

station

shuttle

Light induced excitation of the shuttle is better!

K.L. Sebastian: Current Science, 87, 232 (2004)

Light induced conformational change driving translation!

Cis-trans isomerization as in Azobenzene could be

useful

Can one have……?

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!

Molecular Ratchets, Second Law and Detailed Balance

[4]helicene

triptycene

Axle

It can undergo ratchet-like internal rotation!

A molecular ratchet was Synthesized and studied by Kelly et. al. Angewandte Chemie 109, 1969 (1997).

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