Supramolecular Information/Programming

from a Boolean Perspective

A. Prasanna de Silva
Queens University, Belfast, UK

1 Introduction
2 Illustrative Examples of Molecular Information
Handlers
3 Conclusion
Acknowledgments
References

161
161
165
165
165

INTRODUCTION

Molecules have been dealing reliably with information ever

since life became self-sustaining. The case of information
handling by nucleobase pair recognition in DNA has
been celebrated often.1 The advent of supramolecular
chemistry2 has made clear that the recognition between
reacting/interacting molecules must involve information
handling at its heart. While (supra)molecular information
handling involves writing, storing, reading, processing, and
erasing,3, 4 we concentrate mostly (but not entirely) on
processing and the Boolean aspects thereof.
Booles seminal contribution to information processing5
is widely appreciated. Following his analysis of language
in terms of the truth or falsehood of elementary statements,
the representation of truth or falsehood with the symbols
0 and 1 allowed algebraic manipulation and analysis so
that Aristotles classical logic could be greatly extended.
Subsequently, these ideas evolved into Boolean logic where

different logic operations could be characterized in terms

of their truth tables. The materialization of these operations
within semiconductor-based devices led to logic gates that
powered the information technology revolution,69 which
we have all witnessed. While each of these logic gates
can perform elementary algorithms, larger gate arrays were
built into information-handling machines, which could be
controlled by operator-written algorithms of considerable
complexity, to perform previously challenging tasks.
Whether covalently bound or noncovalently assembled,
supramolecular systems can be programmed to perform
simple computing operations. In most cases, supramolecular interactions between the device and the input species
are crucial. The algorithms are simple, that is, to perform
the Boolean AND logic operation10 or to add two very
small numbers.11 Nevertheless, these ideas have been developed within molecules to the extent that a population of
small objects can be individually identified12 or a game like
tic-tac-toe can be played successfully against a human
opponent.13, 14 In most cases, the program is frozen within
the molecule.

ILLUSTRATIVE EXAMPLES OF
MOLECULAR INFORMATION
HANDLERS

Figure 1 lays out the truth tables of some Boolean logic

gates relevant to our discussion. Molecular-level examples
of some of these have been detailed in a companion review
titled Molecular Logic Gates, Supramolecular Devices,15
as well as in other reference works.1630 Therefore, that
exercise is not repeated here. Instead, we discuss logic gates

Supramolecular Chemistry: From Molecules to Nanomaterials, Online 2012 John Wiley & Sons, Ltd.
This article is 2012 John Wiley & Sons, Ltd.
This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons, Ltd.
DOI: 10.1002/9780470661345.smc011

Concepts

Output

Input
0

NOT

PASS 1

YES

Input1

Input2

0
0
1
1

0
1
0
1

Output
0
0
0
1
AND

0
1
1
1

1
0
0
0

OR

NOR

Figure 1 Truth tables for single-input YES, NOT, and PASS 1

logic gates and for double-input AND, OR, and NOR logic gates.
The NOT OR function of the NOR gate can be noted by referring
to the truth tables for NOT and OR logic.

and appropriate procedures are set in train by doctors and

nurses.

2.2

Fluorescent sensor device for blood

electrolytes

The literature on fluorescent molecular sensors stretches

back over a century3740 from the present day.41, 42 We
consider just one case here. How does a duty nurse measure
the level of an electrolyte like Na+ in the blood sample of
a patient in a critical care unit of a hospital?
Compound 143 is immobilized on a cellulose-based fiber
substrate.44 The fiber substrate filters the blood so that only
the serum interacts with 1, The higher the concentration of
Na+ in serum, the higher the fraction of 1Na+ . This form is
fluorescent, whereas 1 itself is significantly less fluorescent.
The fluorescence intensity then produces, with appropriate
calibration, the blood Na+ level.
HN
O

and gate arrays which achieve particular purposes, as well

as their underlying concepts.

2.1

Sensors

Sensors are common in various fields of engineering and

science.3133 They report on environmental parameters of
various kinds. Owing to their small size, molecular versions can operate in very restricted spaces such as a cellular
organelle.34, 35 Since sensors produce a significant quantitative response to a small change in the value of a physical property or the concentration of a chemical species,
they are analog devices. Molecular versions are no different in this respect. However, the analog behavior depends
on the molecular sensor having two clearly distinguishable statesone when the sensor is free of the target and
the other when the sensor is saturated with the target. The
readout of the molecular device is controlled by the ratio
between the populations of target-free and target-bound sensor molecules, which in turn is controlled, for instance,
by the concentration of the chemical target species. Taken
together, these two states of a given molecular sensor offer
evidence of its binary digital heart. Boolean YES logic
applies when the response signal increases with increasing
target species concentration. NOT logic applies to the opposite behavior.36 Furthermore, results from molecular sensors
are often used in a binary digital manner for yes/no
decisions by professionals. If the blood hemoglobin concentration is lower than normal, the patient is treated as anemic

NH

CH3O
N
O

O
1

Compound 1 is poorly fluorescent because the emission has to compete with photoinduced electron transfer
(PET)4547 from the N-arylaza-15-crown-5 ether receptor
to the aminonaphthalimide fluorophore across the dimethylene spacer. This receptor48 successfully binds Na+ at the
concentrations found in normal blood and is sufficiently
selective against other ions like K+ and H+ .49, 50
How does the Na+ binding cause stronger fluorescence?
Once bound to the receptor of 1, Na+ not only retards
PET processes that take the electron away from the crown
due to electrostatics51, 52 but also causes a rotation of
about 60 about the aromatic CN bond such that the
nitrogen electron pair is deconjugated from the benzene
ring -system.53 Such conformational effects are known
to substantially raise oxidation potentials so that PET is
seriously retarded.53, 54 The receptor within 1 can also be
developed into an absorptiometric sensor for Na+ .55

Supramolecular Chemistry: From Molecules to Nanomaterials, Online 2012 John Wiley & Sons, Ltd.
This article is 2012 John Wiley & Sons, Ltd.
This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons, Ltd.
DOI: 10.1002/9780470661345.smc011

Information/programming from a Boolean perspective

2.3

Sensors with improved selectivity

Boolean methods can help increase the selectivity of

sensing in the following way. Molecular AND logic gates
produce a high output signal only if two chemical inputs are
applied at a high level.10 While early examples employed
separate chemical species as inputs, there is no reason why
these two species cannot be covalently linked. But then we
need to ensure that the receptor modules in the AND gate
are correctly positioned so that they can receive and bind
the two species at the same time. Such AND gates will then
signal the presence of the linked pair of species with higher
efficiency than a simple mixture of the separate species due
to the advantage of intramolecular effects56 in the former
case. Suitable sensing targets would be molecules with two
(or more) functional groups.
Glucosamine57 (2) is one such multifunctional molecular
target which is detected and measured by the fluorescent
sensor 3. Sensor 3 responds to relatively low concentrations
of 2 owing to the chelate effect.56 The azacrown ether
receptor and the aminomethylboronic acid receptor within
3 serve as the two claws that capture 2 by binding the
(protonated) amine and a diol unit of 2, respectively. The
electron pairs of the nitrogen atoms in the two receptors
are PET donors to the anthracene fluorophore. Even one
PET process is sufficient to knock out fluorescence. This
is why glucosamine at neutral pH successfully achieves a
strong fluorescence enhancement of 3 by blocking both PET
processes at once.

positives are funneled to the doctors who can pick out the
real patients for treatment.
Medical professionals use their education and experience
to deduce the disease from the results of clinical laboratory
tests. Their particular focus is on the set of parameters
which are higher or lower than the normal. A Boolean
logic-based combination of these leads the doctors to the
disease. We illustrate a case of a molecule where three
ion concentrations need to be high in order to create
a fluorescence enhancement. This would be a three-input
AND logic gate. High here means higher than the
reciprocal of the binding constant of the molecular device
with regard to the particular ion. The knowledge of normal
concentration level of an ion allows the molecular designer
to choose the appropriate receptor. Using three receptors
within the device, three high ion concentrations are
detected with one strong fluorescence signal. We note that
the ion concentrations themselves are not part of the output.
We focus on three-input AND gate 458 to illustrate
the concepts discussed above, though there are newer
cases aimed at more biological targets.59, 60 Compound
4 possesses three receptors which select Na+ , H+ , and
Zn2+ as inputs. Benzo-15-crown-5-ether, tertiary amine,
and phenyliminodiacetate61 are the three receptors. Each
of these receptors is a PET donor toward the anthracene
fluorophore. In that sense, 4 is a conceptual continuation of
3. Again, fluorescence enhancement is seen only when all
three PET processes are knocked out. Table 1 details the
numbers involved.
O
O
O

NCH3 B(OH)2

OH
O

NH2

H2N

OH
NCH3

NH2

O
N

O
O

O
O

O
O

2.4

O
4

Lab-on-a-molecule systems

Programming a molecule to perform, even in a rudimentary

way, the functions of a clinical laboratory and a medical practitioner is useful because health services are overworked in many countries at the best of times. The overload
can go to the breaking point when a pandemic or crisis
situation arrives. Then, doctors will not have the time to
analyze the clinical data from the large body of potential
patients. Some molecules step in to screen the large population. The (hopefully) smaller number of positives and false

2.5

Molecular computational identification

(MCID) tags

Our penultimate example applies molecular logic in a situation inaccessible to semiconductor devices. The problem
is to identify all small objects in a large population.12 There
is a process for the identification of an object concerning

Supramolecular Chemistry: From Molecules to Nanomaterials, Online 2012 John Wiley & Sons, Ltd.
This article is 2012 John Wiley & Sons, Ltd.
This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons, Ltd.
DOI: 10.1002/9780470661345.smc011

Concepts

Table 1

Truth table for three-input AND gate 4.a

Input1
Na+
0
0
0
0
1
1
1
1

(0 M)
(0 M)
(0 M)
(0 M)
(5 M)
(5 M)
(5 M)
(5 M)

Input2
H+
0
1
0
1
0
1
0
1

(109.5 M)
(106.0 M)
(109.5 M)
(106.0 M)
(109.5 M)
(106.0 M)
(109.5 M)
(106.0 M)

Input3
Zn2+
0
0
1
1
0
0
1
1

Output
Fluorescenceb

(0 M)
(0 M)
(104.8 M)
(103.1 M)
(0 M)
(0 M)
(104.8 M)
(103.1 M)

0
0
0
0
0
0
0
1

(0.001)
(0.001)
(0.002)
(0.003)
(0.006)
(0.007)
(0.006)
(0.020)

105 M in water.
b
Quantum yields; exc 379 nm; em 410, 435, and 458 nm.

acidic conditions the resulting protonation of the amine

causes the PET process to halt and fluorescence to resume.

N
CH3 O

NH
O
6

2.6

NH

Random access memory

its face or tag. A series of questions need to be asked and

answers need to be obtained to those. For example, the set
of answers could be as follows. The best excitation wavelength is 368 nm and the optimal emission wavelength is
422 nm. The binary logic type is NOT in terms of the
fluorescence intensity pattern that is obtained as output
in response to H+ input. The number of distinguishable
answers could be many, since four single-input, singleoutput and 16 double-input, single-output logic types, and
so on8, 9 are available even for a given set of wavelengths
and inputs. The number of answers climbs sharply, especially if combinations of gates, that is, two tags, are used on
one object. This is molecular computational identification
(MCID).12
The availability of several dye tags with several distinguishable excitation and emission has already been
exploited for purposes of identifying combinatorial chemistry libraries on beads,62, 63 but the broad nature of molecular absorption and emission spectra puts a bandwidth limit
on the number of dyes that can be practically applied. The
logic approach mentioned in the previous paragraph can
increase the diversity available with a single color combination manifold times.
As a specific example, we can consider H+ -driven YES
and PASS 1 logic gates 5 and 6, respectively,12 both
of which carry the same fluorophore, that is, the same
excitation and emission colors. However, tag 5 switches
on its fluorescence as pH is reduced to low values while 6
shows pH-independent fluorescence. This is the distinction
between the two tags. Many other distinctions, that is, other
Boolean logic actions, can be built up in similar ways. The
different pH-dependent fluorescence behavior of 5 and 6
arises from the presence of the tertiary amine receptor in
5 and its absence in 6. As seen in the previous sections,
the amine is the donor component in the PET process
whereas the anthracene fluorophore serves as the acceptor.
Thus, fluorescence is minimal in neutral solutions, but under

We finish with a case of sequential logic, that is, where

memory is involved and where history determines the logical outcome. Some of best established molecular memories
are photochromics. Amazingly, this possible relevance to
computer science was noted as far back as 1956.64 Newer
systems such as Iries celebrated dithienylethenes65 have
been honed to a high degree of usefulness. These function
at the single molecule level66 and, when embedded in polymer matrices, allow robust, fatigue-free operation for up to
104 readwrite cycles.67 These systems can be written to
their colored state with ultraviolet light doses. The colored
state can be erased with a dose of visible light. The colored
(or colorless) state can be read by interrogation with a weak
beam of visible light.
A semiconductor electronic analog of the above is the
RS flip-flop (or setreset latch),6, 7 prepared from two
cross-wired and fed-back NOR gates (Figure 2), where the
states of the inputs R (reset) and S (set) allow a memory to
be held and read along the output lines A and B, according
to the truth table (Table 2).
InputR = 0 and InputS = 1 produce one held memory
state, whereas swapping the inputs around (InputR = 1 and
InputS = 0) produces the other memory state. It is notable
that the condition InputR = 0 and InputS = 0 simply holds
the previous memory state. The fourth condition (InputR =
1 and InputS = 1) is usually avoided by adding a small
logic array before the device to act as a guard.
van der Booms electrochromic 7 allows this general
goal of the RS flip-flop to be achieved, even though
the persistence of written memory states is limited to
25 min for now. His group achieved this by using chemical
redox agents68 or electrode potentials69 with mono-68 or

Figure 2
flop.

InputR

OutputA

InputS

OutputB

Electronic engineering representation of an RS flip-

Supramolecular Chemistry: From Molecules to Nanomaterials, Online 2012 John Wiley & Sons, Ltd.
This article is 2012 John Wiley & Sons, Ltd.
This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons, Ltd.
DOI: 10.1002/9780470661345.smc011

Information/programming from a Boolean perspective

Table 2

Truth table for the RS flip-flop.

Chronology
1
2
3

InputR

InputS

0
0
1

0
1
0

OutputA

OutputB

Holds previous state

1
0
0
1

multi-69 layer systems on glass. The chemical agents are

Cr2 O7 2 in water, at pH < 1, for oxidation (InputR )
and Co(C5 H5 )2 in dry acetonitrile for reduction (InputS ).
Though the solvents are not mutually compatible, careful
drying steps between input applications allow the system
to function as required. The electrode potential approach
avoids this problem anyway. Naturally, each of the redox
states of 7 is stable in the absence of inputs or in the presence of the appropriate input (R or S). This is the memory
aspect. The application of the other input naturally changes
the existing redox state. This is the flip-flop aspect.

2+

N+

ACKNOWLEDGMENTS
We thank the Department of Employment and Learning,
UK, and the Almac Trust for support.

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CONCLUSION

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Supramolecular Chemistry: From Molecules to Nanomaterials, Online 2012 John Wiley & Sons, Ltd.
This article is 2012 John Wiley & Sons, Ltd.
This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons, Ltd.
DOI: 10.1002/9780470661345.smc011

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Supramolecular Chemistry: From Molecules to Nanomaterials, Online 2012 John Wiley & Sons, Ltd.
This article is 2012 John Wiley & Sons, Ltd.
This article was published in the Supramolecular Chemistry: From Molecules to Nanomaterials in 2012 by John Wiley & Sons, Ltd.
DOI: 10.1002/9780470661345.smc011