MOC 5.

MOLECULAR COMPUTERS

1. PRINCIPLE: MOLECULAR-LEVEL SWITCHES FOR COMPUTING

2. MEMORIES
3. LOGIC GATES
 MOC 5. MOLECULAR COMPUTERS
CONVENTIONAL SILICON-BASED COMPUTERS
Data are processed electronically by microprocessor systems and are exchanged
optically between remote locations
Data processing and communication is based on enconding the information in electrical
and optical signals in the form of binary digits (0 and 1)
Treshold value and logic convention are established for each signal:
positive logic convention – 0 (~ 1 V, bellow treshold voltage 2 V)
1 (~ 3 V, over threshold voltage 2 V)
negative logic convention – reversed asignment
Logic circuits of microprocessor systems process binary data trough sequences of logic
gates
Data are stored also in binary code

MOLECULAR COMPUTERS
Although it is not inevitable, effort is devoted to their design to operate based on the same
principle (binary encoding for storing and processing information)
Strategies prefere to use optoelectronic molecular devices (molecular-level switches) with
propagation of optic signals

Optic transport of information (via optic fibers) can transport several independent signals
(noninteracting light beams of different wavelengths) in contrary to electric wire which can
transport single signal only
Optical signal is then converted into electric signals
 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
Lecture 3: switches as molecular-level devices that can reversibly interrupt the
movement of the electrons or electronic energy across it in response to
external stimuli

Here: switches as molecular-level systems that can be reversibly switched between

two or more states with different optical properties (absorption, emission or
chiroptical) by use of external stimuli (photochemical, thermal, electrical, chemical
→ photochromic, thermochromic, electrochromic, ... systems).
For storing information (memories) and perform logic operations (logic gates)
→ molecular computers based on binary logic

Principle of bistable photochromic system

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
CHEMOSENSOR (supramolecular chemistry)
Output (purpose): molecular recognition – signaling (indicating) the presence of
particular molecules or ions

MOLECULAR-LEVEL SYSTEM SWITCHABLE BY CHEMICAL STIMULUS

Output: switching of optical properties (switching between states 0 and 1)
Input: molecular recognition – target addition of particular molecules of ions

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
IRREVERSIBLE SYSTEMS (permanent memories)
photography, chemodosimetry

REVERSIBLE SYSTEMS
2nd state is unstable – switch is “on“ (or “off“) only upon presence of stimulus –
switches under thermodynamic control (very low activation barrier for
conversion)
(switches for conductance)

2nd state is metastable – after being switched it is slowly converted to more stable one
– switches under thermodynamic control (medium activation barrier for
conversion)
(short-term memories)

2nd state is sufficiently stable – another stimulus is necessary to switch it back to

primary state (operation times from picoseconds to years) – switches under
kinetic control (sufficiently high activation barrier to prevent back thermal
conversion)
(erasable permanent memories, logic gates, switches for conductance)

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING

Classification based on input:

1. PHOTOCHROMIC SYSTEMS (photonic input) – easy switchable
2. THERMOCHROMIC SYSTEMS (thermal input)
3. ELECTROCHROMIC SYSTEMS (redox input) – easy switchable
4. CHEMICALLY SWITCHABLE SYSTEMS (chemical input)

Classification based on output:

A. CHROMOGENIC SWITCHES (change in absorption characteristics)
B. FLUORESCENT SWITCHES (change in emission characteristics)
C. CHIROPTICAL SWITCHES (change in chiroptical properties)

Threshold intensity (analogous to silicon based computers)

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)

1867 Giacomo Ciamician: 1st report on phototropic substance

1960 commercial photochromic glasses (lenses, windows, filters)
Nature biological photoreceptors (rhodopsin, phytochrome, etc.)

T-type thermally reversible

P-type photochemically reversible

Important factors:
quantum yield
responce time (diarylethenes: picoseconds)
fatigue resistance – undesired side reactions (diarylethenes: high; satisfactory
performance after more than 104 cycles)

For side reaction with quantum yield of 0.001: 63% decomposition after 103 cycles
Molecular Devices and Machines
 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Most important families of photochromic compounds
P-type photochemically reversible

Diarylethenes
very fast conrotatory ring-closure/opening (picoseconds)
high fatigue resistance (satisfactory performance after over 104 cycles)

Fulgides

T-type thermally reversible

Spiropyranes
Molecular Devices and Machines
 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Most important families of photochromic compounds
T-type thermally reversible

Diaryldiazenes

Dihydroazulenes

Chalcone-Flavylium Systems

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Fluorescent Switches

Fulgides

Colorless Colored
Diarylethenes

Luminiscence excitation at 400-500 nm

does not cause ring-closure –
information (“data“) can be read
without destroying it
Molecular Devices and Machines
 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Chiroptical Switches

Overcrowded alkenes

–OMe –OMe

Detected by CD signal at 262 nm

10% racemization after 20 cycles

–OMe –OMe

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Chiroptical Switches

Diarylethenes

Diastereomers, excellent reversibility

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Chiroptical Switches
Chromenes

Switching performance 50 μm
polystyrene film

M. Putala et al. New J. Chem. 2010

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Chiroptical Switches
Diazenes

Δd = 2Å
Δθ = 38°

105° 7Å 67° 5Å

M. Putala et al. J. Phys. Chem. C 2015

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
1. PHOTOCHROMIC SYSTEMS (photonic input)
Chiroptical Switches
Diazenes
Conformational analysis
(Z)
67° (Z)

(Z)

(E)
105° (E)

(E)

N=N θ (binaphthalene) Δθ -CO-NH- azobenzene

(E)-1 105° (E,E) (M)
-38°
(Z)-1 67° (Z,Z) (M)

M. Putala et al. J. Phys. Chem. C. 2015

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
3. ELECTROCHROMIC SYSTEMS (redox input)
Two (or more) oxidation states have different absorption and other characteristics

Electrochromic systems can be

switched on/off rapidly
(submicroseconds),
but slower than photochromic
systems (up to femtoseconds)

Molecular Devices and Machines

 5.1. MOLECULAR-LEVEL SWITCHES FOR COMPUTING
3. ELECTROCHROMIC SYSTEMS (redox input)
Two (or more) oxidation states have different absorption and other characteristics

Chiroptical Switches

CD band at 501 nm disappears upon two electron reduction

(to bisradical anion)

Molecular Devices and Machines

 5.2. MEMORIES
PHOTOCHROMIC (OPTICAL) MEMORY SYSTEMS

Nondestructive read proccess

Diarylethenes

Luminiscence excitation at 400-500 nm

does not cause ring-closure –
information (“data“) can be read
without destroying it
Molecular Devices and Machines
 5.2. MEMORIES
PHOTOCHROMIC (OPTICAL) MEMORY SYSTEMS

Destructive read proccess

Three state systems (A, B, C):

Cycles write-lock-read-unlock-erase

Nondestructive read proccess

I(2): second stimulus (lock-unlock)

proton, electron, etc.

Molecular Devices and Machines

 5.2. MEMORIES
THREE-STATE MEMORIES WITH WRITE-LOCK-READ-UNLOCK-ERASE CYCLES

Diarylethenes

Electrochemical lock-unlock (oxidation-reduction)

Colored quinone form is not light sensitive

Molecular Devices and Machines

 5.2. MEMORIES
THREE-STATE MEMORIES WITH WRITE-LOCK-READ-UNLOCK-ERASE CYCLES

4’-Methoxyflavylium

Acid-base lock-unlock
(pH 1 – pH 5)
Flavylium form AH+ is
not light sensitive

Energy level diagram

Molecular Devices and Machines, Molecular Switches

 5.2. MEMORIES
THREE-STATE MEMORIES WITH WRITE-LOCK-READ-UNLOCK-ERASE CYCLES

4’-Methoxyflavylium

Fluorescence spectra of Ct (pH 4), AH+ (pH 1)

Time-dependence of Ct solution absorbance (pH 3)

after photoexcitation at 365 nm (dashed lines)
followed by dark periods
- short-term (shallow) memory

Molecular Devices and Machines

 5.2. MEMORIES
THREE-STATE MEMORIES WITH WRITE-LOCK-READ-UNLOCK-ERASE CYCLES

Unsubstituted flavylium

a) Thermodynamic equilibrium at pH 1
d) Thermodynamic equilibrium at pH 4

Energy level diagram

Hydraulic analogy for pH jump

Molecular Devices and Machines, Molecular Switches
 5.2. MEMORIES
THREE-STATE MEMORIES WITH WRITE-LOCK-READ-UNLOCK-ERASE CYCLES

Unsubstituted flavylium

Hydraulic analogy for photochemical reaction

a) Thermodynamic equilibrium at pH 4 (before irradiation)
d) Immediately after photon flash

Energy level diagram

Molecular Devices and Machines, Molecular Switches

 5.2. MEMORIES
MOLECULAR SHIFT REGISTER
Set of memory sets (registers) connected into series

S – sending electrode (cathode)

P – identical polymer chains
R – receiving electrode (anode)
M – indentical monomer units consisting of donor (D) and acceptors (A1, A2)

Molecular Devices and Machines

 5.2. MEMORIES
MOLECULAR SHIFT REGISTER
Electrochemical
reduction of donor by
adjacent cathode
followed by spontanoeus
electron transfer up to
acceptor A2

Excited state resulting

from photoexcitation of
reduced acceptor A2
followed by reduction of
donor of next monomer
unit (or competitive
error back electron
transfer)

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Conversion of signal

Truth table
Inverted conversion
of signal

Inverted OR, AND →

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

OR except AND Inverted XOR

COMBINATIONIAL LOGIC GATES

Combinations of basic logic gates

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Excellent sensor for intracellular

Ca2+ concentration
Emission is quenched by
alkoxyaniline donor

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Free:  = 0.13
Protonated:  = 0.003

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Excitation by absorption at 304 nm

Phenantridine triplet excited state
is quenched by molecular oxygen
only of its protonated form

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Blue-green fluorescence
of 92+ is quenched by
formation of red charge-
transfer complex

Molecular Devices and Machines

 5.3. LOGIC GATES
BASIC LOGIC GATES

Oxidation of tetrathiafulvalene 10 or reduction of

bipyridinium cyclophane 114+ does not allow
formation of colored charge-transfer
pseudorotaxane complex

Molecular Devices and Machines

 5.3. LOGIC GATES
COMBINATIONAL LOGIC GATES

OR AND

SDS – sodium dodecyl sulphate forms micelles

where it traps hydroxychalcone 13 and
concentrates protons locally

Molecular Devices and Machines

 5.3. LOGIC GATES
COMBINATIONAL LOGIC GATES
ADDER

BINARY ADDITIONS DECIMAL

0 + 0 = 00 0+0=0
0 + 1 = 01 0+1=1
1 + 0 = 01 1+0=1
1 + 1 = 10 1+1=2

Molecular Devices and Machines

 5.3. LOGIC GATES
MOLECULE-BASED ELECTRONIC CIRCUITS

3 nm x 4 nm – milion times smaller than semiconductor

logic element fabricated on a semiconductor chip
using transistor based circuits

Diode-diode, OR logic gate

Molecular Devices and Machines