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V. Bojinov, N. Georgiev

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Journal of the University of Chemical Technology and Metallurgy, 46, 1, 2011, 3-26

MOLECULAR SENSORS

AND MOLECULAR LOGIC GATES

(REVIEW)


University of Chemical Technology and Metallurgy

8 Kl. Ohridski, 1756 Sofia, Bulgaria

E-mail: [email protected]

ABSTRACT

Current computers are based on semiconductor logic gates which perform binary arithmetic and logical opera-

tions. However, trend of device miniaturization will reach its molecular-scale ultimate in the near future. Therefore the

design and construction of molecular systems capable of performing complex logic functions is of great scientific interest

now. Logic operations from the simplest to small-scale integrated cases are now available on molecular level, including

those with arithmetic capability. The ideas of supramolecular switches can be a useful way of advancing molecular logic

and computation. Here we illustrate and discuss recent progress of this research area.

Keywords: molecular sensors, molecular logic gates, molecular computers, half-adder, full-adder, half-subtractor,

full-subtractor, digital magnitude comparator.

Received 20 January 2011

Accepted 18 February 2011

INTRODUCTION

Computers have enhanced human life to a great

extent. The speed of conventional computers is achieved

by miniaturizing electronic components to a very small

micron-size scale so that those electrons need to travel

only very short distances within a very short time. Fur-

ther miniaturization of lithography introduces several

problems such as dielectric breakdown, hot carriers, and

short channel effects [1]. All of these factors combine

to seriously degrade device reliability. Even if develop-

ing technology succeeded in temporarily overcoming

these physical problems, we will continue to face themas long as increasing demands for higher integration

continues. Therefore, a dramatic solution to the prob-

lem is needed, and unless we gear our thoughts toward

a totally different pathway, we will not be able to fur-

ther improve our computer performance for the future.

The concept of a macroscopic logic device can

be extended to the molecular level by designing and

synthesizing molecular species capable of performing

specific functions. Further miniaturization on molecu-

lar level will not only decrease the size and increase the

power of computers, but is also expected to open the wayto new technologies, such as nanorobotics [2]. Supra-

molecular chemistry, also known as the chemistry be-

yond the molecules, provides the best route for molecular

nanotechnology, allowing the design of versatile functional

nanomaterials conveying the remarkable characteristics of

the molecular centers, including their electronic, opti-

cal and chemical properties [3]. Molecular devices op-

erate via electronic and/or nuclear rearrangements and,

like macroscopic devices, need energy to operate and

signals to communicate with the operator. The energy

needed to make a device work can be supplied as chemi-cal energy, electrical energy, or light. Luminescence is

one of the most useful techniques to monitor the op-

eration of molecular-level devices. The logic operations

are based on Boolean algebra, which is in the back-

ground of the modern computers dealing with 0 and

1 binary code. Molecular or supramolecular sensors

and switches are promising candidates for the realiza-

tion of innovative materials for information technology

[4]. Molecular sensors show large changes in their


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Journal of the University of Chemical Technology and Metallurgy, 46, 1, 2011

4

photophysical and electromagnetic properties so called

off and on states, where off and on state would

be presented as 0 and 1, consequently they can per-

form logic operations.

MOLECULAR SENSORS

There is currently great interest within the field

of supramolecular chemistry in developing miniatur-

ized molecular devices that mimic or mirror the action

of macroscopic devices such as switches, motors and

other machinery [5-8]. Supramolecular devices that

show large changes in their so called off and on

states, where their states refer to their luminescence,

magnetic, or electronic properties, are of particular inter-

est as these can be modulated, or tuned, by employing

external sources, or inputs, such as ions, molecules,

light, etc. [9-18].

The simplest common definition of a sensor is

that a sensor is something that senses, i.e., receives in-

formation and transforms it into a form compatible with

our perception, knowledge and understanding. The man-

made sensors are often called chemical sensors and

those of them that involve biology-related compounds

and/or biospecific target binding biosensors. The sen-

sor has two functions [19]. The first is to provide interac-

tion with the target in a highly selective way, recognizing

it from other objects of similar structure and properties

that can be present in the probed system. The structure

responsible for that is called recognition unit or recep-

tor. The other function is to visualize this interaction,

to report about it by providing a signal that can be ana-

lyzed and counted. The structure responsible for the

generation of this signal is called a reporter.

Molecular receptors are defined as organic struc-

tures held by covalent bonds that are able to bind se-

lectively ionic or molecular substrates by means of

various intermolecular interactions, leading to an as-

sembly of two or more species, a supramolecule. Thechemistry of artificial receptor molecules represents

generalized coordination chemistry, not limited to tran-

sition-metal ions but extending to all types of sub-

strates: cationic, anionic, or neutral species of or-

ganic, inorganic, or biological nature [8,18]. In order

to obtain high recognition, the non-covalent forces

must be taken into account in the design of the recep-

tor. Design principles are therefore applied in order

to achieve the desired intermolecular interaction, with

a number of factors being used to increase the strength

of the intended host-guest complex.

The sensing function can actually be incorporated

at a molecular level. This is achieved by combining a

binding site and a reporter group in one molecule. The

reporter group is chosen to have electrochemical or spec-

troscopic properties that are altered by proximate host-

guest interaction. This electrochemical or spectroscopic

output can therefore be used to quantitatively detect spe-

cific guests [20]. The most common type of optical sen-

sors is based on the fluorescence phenomenon.

Fluorescence was first used as an analytical tool

to determine the concentrations of various species, ei-

ther neutral or ionic. When the analyte is fluorescent,

direct determination is possible; otherwise, a variety

of indirect methods using derivatization, formation of

a fluorescent complex or fluorescence quenching have

been developed. Fluorescence sensing is the method

of choice for the detection of analytes with a very high

sensitivity, and often has an outstanding selectivity

thanks to specially designed fluorescent molecular sen-

sors.

In fluorescent molecular sensors, the fluorophore

is the signaling species, i.e. it acts as a signal transducer

that converts the information (presence of an analyte)

into an optical signal expressed as the changes in the

photophysical characteristics of the fluorophore. In prin-

ciple, a fluorescent molecular sensor is the analyte-re-

sponsive (supra)molecular moiety, involving a fluorophore

that signals the presence of an analyte by changes in its

fluorescence characteristics [21,22]. In contrast, in an

electrochemical sensor, the information is converted into

an electrical signal.

The success of fluorescence detection over other

methods can be explained by the distinct advantages in

terms of sensitivity, selectivity, high speed (response time),

local observation (e.g. by fluorescence imaging spectros-

copy), and safety.The design of fluorescent sensors is of major

importance because of the high demand in analytical

chemistry, clinical biochemistry, medicine, the environ-

ment, etc. Numerous chemical and biochemical analytes

can be detected by fluorescence methods: cations (H+,

L+, N+, K+, Ca2+, Mg2+, Zn2+, Pb2+, Cd2+, Al3+, Cr3+,

etc.), anions (halide, citrates, carboxylates, phosphates,

etc.), neutral molecules (sugars, e.g. glucose, etc.) and

gases (O2, CO

2, NO, etc.).


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Molecular systems in which fluorescence switches

between on and off states when driven by chemical

stimuli can be designed according to a few principles

photoinduced electron transfer (PET), photoinduced

charge transfer (PCT), energy transfer (ET) and excimer

formation, with emphasis on the first category [23]. These

designs open the way to sharp signaling of small chemi-

cal species that perform critical biological functions.

Fluorescent sensors based on photoinduced electron

transfer (PET)

The most widely used mode of fluorescence

modulation is the decrease or increase of fluorescence

intensity at a single emission wavelength upon analyte

binding. One of the mostly used phenomena in supramo-

lecular recognition by chemosensors is photoinduced

electron transfer. The photoinduced electron transfer

(PET) using the fluorophore-spacer-receptor format

is the most commonly exploited approach for the de-

sign of the fluorescent sensors and switchers [23-26].

In photoinduced electron transfer, absorption of

light by a molecule causes an electron to jump to an-

other molecule or component of a composite system.

Once the electron has jumped, a molecular radical ion

pair is formed or in an organic/semiconductor

nanostructure, an electron-hole pair is created. These

ions or electron hole pairs have a finite lifetime after

which they recombine (mostly geminate recombination)

through radiative or nonradiative channels.

This type of system consists of a fluorophore

linked to a donor atom (usually amino nitrogen). Upon

Fig. 1. PET mechanism.

excitation of fluorophore, an electron transfer occurs

from the HOMO of the donor to the low-lying HOMO

of the acceptor (fluorophore). Thus fluorescence doesnt

take place. When cation binds to the recognition moi-

ety where the donor atom is present, the energy of the

HOMO of the ion receptor is lowered so that the pho-

toinduced electron transfer cant happen from HOMO

of the donor to the fluorophore (Fig. 1). This is dis-

played as enhancement in fluorescence [27].

Many of the fluorescent chemosensors work with

this principle. Selectivity for ions is achieved by the

correct choice of recognition moiety for the desired ion.

A classical example is compound 1 [28]. The recogni-

tion moiety is not necessary to be crown ether. Podands

like 2 [29,30], cryptands 3 [31] and 4 [32], chelating 5

[33,34], calixarene [35,36] type receptors can also serve

as ion binding sites (Scheme 1).

Naphthalimide derivatives are a special class of

environmentally sensitive fluorophores [37,38]. Because

of their good photophysical properties and strong fluo-

rescence the 1,8-naphthalimide derivatives have found

application in a number of areas including colouration

and photostabilization of polymers [39-49], laser active

media [50,51], fluorescent markers in biology [52], an-

ticancer agents [53] and analgesics in medicine [54],

light emitting diodes [55,56], electroluminescent mate-

rials [57,58], liquid crystal displays [59], solar cells [60].

They are well studied class of luminophores that have

already found application as signal fragment in fluores-

cent sensor systems for protons [61-63], ions [64,65]

and neutral molecules [66].


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Recently a new fluorescent bis-1,8-disubstituted

naphthalimide 6 have been synthesized where the two

1,8-naphthalimide fragments are substituted with N,N-

dimethylaminoethylamino receptor groups [67]. Novelcompound show very good sensor properties in the pres-

ence of protons and transition metal ions due to the

quenching of PET processes in the 1,8-naphthalimide

fluorophores (Scheme 2). Because of the deprotonation

of the amino moiety at C-4 position in the 1,8-

naphthalimide units caused by OH anions, compound

6 changes its colour from yellow to red in alkaline me-

dia and could be used as a naked eye sensor for hy-

droxyl anions as well.

The fluorescent sensors photostability is a very

important characteristic with regard to their practical us-age. With that end of view a series of highly photostable

1,8-naphthalimide-based fluorescent sensors, containing

a hindered amine light stabilizer (HALS) fragment 7-11

[68-70] as well as containing simultaneously HALS frag-

ment and 2-hydroxyphenyl-benzotriazole 12-15 [71,72]

or 2-hydroxyphenyl-1,3,5-triazine 16-19 [73,74] UV ab-

sorber moieties have been synthesized (Scheme 3).

The combination of 2,2,6,6-tetramethylpiperidine

radical scavenger (HALS) fragment with an UV absorber

moiety in the dyes molecules synergistically improved

in large extent their photostability in respect to other

similar fluorescent dyes, not containing either an UV

absorber or a HALS component. Due to the incorpo-rated allyl function compounds 9-11 and 16-19 are able

for simultaneously chemically fluorescent dyeing and

photostabilization of polymers in the production of solid

stable to solvents fluorescent sensors.

All compounds in Scheme 3 are designed to act

as photostable detectors of environment pollution by tran-

sition metal cations and protons. They are configured on

the fluorophore-spacer-receptor model (Fig. 1), where

the 4-amino-1,8-naphthalimide or 4-oxy-1,8-

naphthalimide moiety is the fluorophore and the 2,2,6,6-

tetramethylpiperidine N-amine or 4-methylpiperazineN-amine in the C-4 substituent is the analyte receptor.

The hydrocarbon part of the piperazine

(tetramethylpiperidine) fragment serves as a spacer that

covalently separates the two units. In these particular

cases a PET process (an electron transfer from the re-

ceptor to the excited state of the fluorophore) quenches

fluorescence emission of the 1,8-naphthalimide unit.

This represents the off-state of the system. The proto-

nation or respective metal complex formation of the

Scheme 1. Some examples of PET based fluorescent chemosensors.

Scheme 2. PET process in bis-1,8-naphthalimide 6.


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Scheme 3. PET-based photostable 1,8-naphthalimide sensors.

Scheme 4. PET process in 1,8-naphthalimide 16.


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piperidine amine or piperazine N-amine increases the

oxidation potential of the receptor, and as such, ther-

modynamically disallow the electron transfer [63,75].

Consequently the emission is switched on. Thus, the

fluorescence is strong in acidic media and transition

metal cations environment.

As a typical example, protonation of the alky-

lated amine donor (receptor) of compound 16 drasti-

cally alters the electron-donating properties and conse-

quently switching of the PET path from the alkylated

amine donor to the 4-amino-1,8-naphthalimide moiety

(Scheme 4).

The typical naphthalimide emission band of16

in water/DMF (4:1, v/v) is blue-shifted upon protona-

tion and red-shifted upon deprotonation. Compared with

the fluorescence in the basic medium, protonation of

the alkylated amine results in the fluorescence enhance-

ment of the 4-amino-1,8-naphthalimide fluorophore by

46.37 times (Fig. 2).

All of compounds 7-19 (Scheme 3) show approxi-

mately the same behaviour throughout the coordina-Fig. 2. Fluorescence enhancement of16 as a function of

pH.

Scheme 5. Type of coordination of15 and 16 (1:1 metal/ligand complex).

Scheme 6. Type of coordination of 7, 8 and 17 (3:2 metal/ligand complex).

tion process with different transition metal ions as that

in the presence of protons the coordination of the dye

receptor with the metal ion results in fluorescence en-

hancement. However, the titration plot of compound

16 differs from the plot of the similar compound 17

and provides for a 1:1 metal/ligand complex coordina-


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tion. In consent to this assumption, a hypsochromic shift

(F

= 11 nm) of the dye fluorescence maxima in the

presence of metal ions has been observed, which indi-

cates a bidentat chelation to both nitrogen atoms in the

lower piperazine moiety, as it is shown in Scheme 5.

The same type of coordination (1:1 metal/ligand

complex) manifest sensors 11, 13 and 15, containing

2,2,6,6-tetramethylpiperidine receptor at C-4 position

of 1,8-naphthalimide moiety (Scheme 5).

The titration plot of compounds 7, 8 and17, con-taining upper piperidine nitrogen (see Scheme 3),

provides for a 3:2 metal/ligand complex coordination.

This supposes chelation to the piperidine nitrogen in

two different molecules in addition to the bidentat che-

lation of the piperazine or tetramethylpiperidine moi-

ety at 1,8-naphthalimide C-4 position (Scheme 6).

Compounds 9, 10, 12, 14, 18 and 19, containing

only piperidinyloxy receptor at 1,8-naphthalimide C-4

position (see Scheme 3), provides for a 1:2 metal/ligand

complex. This supposes chelation to the piperidine ni-

trogen in two different molecules (Scheme 7).

The results described reveal a very good sensor

activity of the yellow-green emitting 1,8-naphthalimide

fluorophores 7-19, indicating their potential as highly

efficient off-on switchers for protons and transition

metals ions.

The presented basic scheme (Fig.1.) is not only

PET mechanism. In some cases PET sensors involve in

their signaling mechanism formation eximers [76-78]or energy transfer [79]. With transition metals, electron

transfer may occur from fluorescent chemosensor to the

coordinated metal ion or vice versa [80]. This results in

quenching of the fluorescence by non-radiative energy-

transfer according to Dexter mechanism. PET may some-

times occur from acceptor to donor, and then it is called

oxidative PET (Fig. 3).

In some instances, after the prevention of PET

by metal binding, excitation energy is transferred from

Scheme 7. Type of coordination of 9, 10, 12, 14, 18 and 19 (1:2 metal/ligand complex).

Fig. 3. Oxidative PET mechanism.


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the fluorophore through ligand to another bound cat-

ion like Eu3+ or Tb3+. This transfer is seen as the dis-

appearance of emission signal from the fluorescent

cations. An example for oxidative PET is

borondipyrromethene dye 20 [81]. Dye 20 typically

displays very high quantum yield and bright-green fluo-

rescence (Scheme 8). After binding the cation at addi-

tion of zinc fluorescence is quenched via oxidative PET

mechanism.

Fluorescent sensors based on photoinduced charge

transfer (PCT)

In contrast with PET systems, in the PCT

chemosensors the receptor is directly attached to the

electron-donating/withdrawing unit that is conjugated

to the fluorophore an electron-withdrawing/electron-

donating unit. The difference is that in the latter case,

this process occurs within the same electronic system.

During excitation of the system the fluorophore under-

goes donor-acceptor intramolecular charge transfer

(ICT) from the donor to the acceptor. The electronic

states achieved in this reaction are not charge-sepa-

rated but charge-polarized states. The excited-state

charge transfer makes the electron-donor site strongly

positively charged. The subsequent change in the di-

pole moment results in a Stokes shift that depends on

the microenvironment of the fluorophore. Thus it can

be predicted that the presence of a guest near by the

donor/acceptor moiety will change the photophysical

properties of the fluorophore because it will affect the

efficiency of ICT [82].

When a group (like an amino group) playing the

role of an electron donor within the fluorophore inter-

acts with a cation, the latter reduces the electron-donat-

ing character of this group; owing to the resulting re-

Fig. 4. PCT sensors based on cation interaction with an electron-donating or electron-withdrawing group.

Scheme 8. An example of oxidative PET-based fluorescent

sensor.


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duction in polarization, a blue shift of the absorption

spectrum is expected, together with a decrease in the

molar absorption coefficient. Conversely, a cation

interactig with the acceptor group enhances the elec-

tron-withdrawing character of this group; the absorp-

tion spectrum is thus red-shifted and the molar absorp-

tion coefficient is increased (Fig. 4). The fluorescence

spectra are in principle shifted in the same direction as

the absorption spectra. An anion produces the opposite

effect. In addition to these shifts, changes in quantum

yields and lifetimes are often observed [19].

The above-explained general principles of effi-

cient usage of the ICT mechanism in sensing is well

demonstrated by the example of 1,8-naphthalimide based

sensor 21 for Cu2+ ion [83]. The pronounced spectral

variations, particularly the largely red shifted ICT ab-

sorption by Cu2+, are consistent with the expected in-

crease in the ICT interaction mediated by the electron

donation from the probable donor perimidine nitrogens

along with amide carbonyl of the naphthalimide sub-

unit, acting as an acceptor (Fig. 5).

Using this concept a various sensors for

cationdetection are obtained. For instance sensors 22, 23,

24, and 25 show high selectivity in respect of Hg2+ [84],

Zn2+ [85], Ca2+ [86], Pb2+ [87], respectively (Scheme 9).

The PCT based chemosensors are able to detect

not only cations but anions as well [88,89]. Gunnlaugssonpresented that the PCT effect in compounds 26-28 is a

useful tool for F determination [90]. Compounds 26-

28 are based on the 4-amino-1,8- naphthalimide struc-

ture. Such compounds are highly coloured, as well as

being fluorescent, emitting typically with max

: 550Fig. 5. ICT sensing mechanism and spectral variations for

sensor 21 interacting with Cu2+.

Scheme 9. Some examples of PCT based chemosensors.

Scheme 10. PCT based chemosensors for determination of

fluorine ions.


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nm, as they possess large excited state dipole moments

due to their internal charge transfer (ICT) excited state

nature (Scheme 10).

Upon addition of AcO-, H2PO

4-, Cl-, Br- and F-

anions (as their (C4H

9)

4N+ salts), only F- gave rise to

changes in the absorption bands of examine compounds

due to the deprotonation of the 4-amino moiety. This

causes a significant increase in the charge density on theamino nitrogen with associated enhancement in the push-

pull character of the ICT transition, bathochromically

shifting the absorption (colour changes of28 from green

to purple, Scheme 11).

Fluorescent sensors based on energy transfer (ET)

Another important process that occurs in the

excited state is resonance energy transfer. This process

occurs whenever the emission spectrum of a fluorophore,

called the donor, overlaps with the absorption spectrum

of another molecule, called the acceptor. The acceptordoes not need to be fluorescent. It is important to un-

derstand that resonance energy transfer does not involve

emission of light by the donor. Resonance energy trans-

fer is not the result of emission from the donor being

absorbed by the acceptor [91]. Such reabsorption pro-

cesses are dependent on the overall concentration of

the acceptor, and on non-molecular factors such as

sample size, and are thus of less interest. There is no

intermediate photon in resonance energy transfer. The

donor and acceptor are coupled by a dipole-dipole in-

teraction. For these reasons, the term resonance energy

transfer is preferred to the term fluorescence resonance

energy transfer (FRET), which is also in common use.

The extent of energy transfer is determined by the dis-

Scheme 11. Deprotonation of the donating 4-amino moiety and colour change in dye 28.

Scheme 12. Energy transfer after complexation of29 with metal ions.

Scheme 13. ET-based anthracene sensors for Cu2+.


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tance between the donor and acceptor and the extent of

spectral overlap.

Fluorescent chemosensor 29 with two different

fluorophores (naphthalene and anthracene) at the both

ends of polyether was synthesized (Scheme 12). This

compound based on 9-anthryl aromatic amide adopted

naphthalene as a TICT (twisted intramolecular charge

transfer) controller and an intramolecular energy trans-

fer source. Compound 29 shows high fluorescence effi-

ciency upon complexation with metal ions due to the

close interaction between both fluorophores [92].

Other useful energy transfer pathway for sensing

is based on fluorophore-analyte interaction. This con-

cept is well demonstrated by anthracene based sensors

30-33 for Cu2+ detection. The remarkable high selective

detection in this system is due to the Dexter energy trans-

fer from anthracene exited state to the Cu2+ resulting in

strong fluorescence quenching effect (Scheme 13) [30].

Fluorescent sensors based on combination of PET, PCT

and ET effects

The combination of above commented basic

chemosensing principles (PET, PCT and ET) provide

sensor compounds with new and interesting properties.

On Scheme 14 is illustrated a pH sensing dyad 34 in

which an energy transfer between a PET based 1,8-

naphthalimide and Rhodamine 6G is used [93]. Com-

pared with the separated 1,8-naphthalimide and

Rhodamine 6G units, dyad 34 shows remarkable high

fluorescence amplified in acidic media. After careful

titration from pH ca. 9 to pH ca. 2 the emission inten-Scheme 14. Combination of PET and ET in dyad 34.

Scheme 15. PAMAM light harvesting dendrons.


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sity of focal Rhodamine 6G in dyad 34 had enhanced

about 43 times.

To improve the absorption ability of chemosensing

system a number of 1,8-naphthalimide PAMAM light

harvesting dendrons have been synthesized [94-98]. Two

typical examples of such systems are presented on Scheme

15. On the first view the both system 35 and 36 are the

same but PET process is realizable by different ways.The remarkable difference in the behaviour of the recep-

tors in C-4 and N-position of the core can be easily ra-

tionalized according to Scheme 15. The 4-

aminonaphthalimide core in antennae is a push-pull

-electron system with 4-amino donor and 1,8-

naphthalimide acceptor. This leads to strong internal

charge transfer (ICT) in the lowest excited singlet state

and considerable dipole character (positive pole at 4-

amino terminus). A large dipole moment in the excited

state gives rise to a strong photogenerated electric field.

Such a molecular electric field can, depending on its signand magnitude, inhibit or accelerate a transiting electron

in the 1,8-naphthalimides. Thus the PET fluorescence

quenching is observed only if the electron leaving the

unprotonated amine donor can enter the space of the 4-

amino-1,8-naphthalimide fluorophore across the C-4

position with its attractive electric field (dendron 35).

The corresponding PET path from the unprotonated

amino receptor in N-position is just as feasible thermody-

namically but requires the electron to enter the fluorophore

across the imide moiety with its repulsive electric field

and is not observed [63]. Furthermore the 4-alkylamino

core substituent possesses higher electron donating abil-

ity in comparison with the peripheral 4-alkyloxy sub-

stituent. Consequently the negative repulsion field in

Scheme 16. Combination of PET and PCT in pH sensing mechanism of sensor 37.

Fig. 6. Range of the on-state (pH-window) for compound

37.


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peripheral imide groups is weaker compared with the

negative repulsion field in core imide. That is why the

PET process from the tertiary amine in dendron bone

(upper receptor) is thermodynamically favorable in

large extent to the periphery of the system 36.

A nice combination of simultaneous PCT and

PET processes for pH-detection is demonstrated by 1,8-

naphthalimide derivative 37 [99]. The pH-chemosensing

mechanism of sensor 37 is illustrated in Scheme 16.

In neutral and alkaline media the fluorescence

emission of sensor 37 is in off-state, which is due to

the PET quenching from ester-branching amine recep-

tor to the fluorophore excited state. After acidification

to ca. pH 5, the PET process is thermodynamically dis-

allowed because of the protonation of the amine recep-

Fig. 7. Range of the on-state (pH-window) for compound

38.

Fig. 8. Chemical system 10 (P) which performs the YES logic operation under the action of one chemical input (H+) and the

corresponding truth table.

tor and the fluorescence of37 is switched-on. Fur-

ther acidification caused protonation of the imine ni-

trogen (C=N), which quench the emission of the sensor

again and fluorescence is switched-off. That is why

sensor 37 shows off-on-off pH switching properties

with on-state between pH 6 and pH 4. The simulta-

neous PET and PCT sensing properties in 37 (Fig. 6)

lead to tight onpH-window (about 2 pH units). As an

example, the similar off-on-off sensor 38 (Fig. 7) based

only on PCT shows on-state in wide pH-window of

about 5 pH units [100].

MOLECULAR LOGIC GATES

In computers, information processing is based

on Boolean algebra. Booles (binary) algebra (from the

name of the English mathematician George Boole) is a

system for the mathematical analysis of logic. Logic gates

are the devices used to perform basic logic operations.

In semiconductor devices the logic gates work using

binary logic, where the signals are encoded as 0 and 1

(low and high current). Developments in supramolecu-

lar chemistry and nanotechnology shows great interest

in the construction of simple electronic or photonic

driven systems and network that function as molecular

level devices which are working by logic gates [101-

104]. This process is executable on molecular level by

several ways, but the most common are based on the

optical properties of the molecule switches encoding

the low and high concentrations of the input guest mol-

ecules and the output absorption and/or fluorescent in-

tensities with binary 0 and 1, respectively [4, 105-107].

The first proposal to execute logic operations at the

molecular level was made in 1988 [108], but the field


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developed only five years later when the analogy be-

tween molecular switches and logic gates was experi-

mentally demonstrated by de Silva [75].

Molecule logic based on single inputs

With single input (e.g., analyte binding) and single

output (e.g., switch-on of fluorescence intensity) only

two simple operations are possible, YES when input is

0 or 1 and the output is the same, and NOT, which is

the opposite - when input is 0 or 1, the output is 1 or 0.

Fluorescent off-on sensors where an analyte causes a

fluorescence enhancement (FE) can be understood as

YES logic gates (Fig. 8) [69]. A logical inverter, some-

times called a NOT gatereverses the logic state and itwould be implement on molecular level using on-off

sensors which fluorescence is quenched in the presence

of an analyte (Fig. 9) [109].

Molecule logic based on two inputs

More complicated logical operations are possible

with two inputs such as two different ions bound to two

different sites. There are six basic logic gates that oper-

ate with two inputs and one output: AND, OR, XOR,

Fig. 9. Chemical system 39 (P) which performs the NOT logic operation under the action of one chemical input (Zn2+) and the

corresponding truth table.

Fig. 10. Chemical system 40 (P) which performs the AND logic operation under the action of two chemical inputs (H+ and

Na+) and the corresponding truth table.

Fig. 11. AND logic gate 41 with two inputs (H+ and Na+)

and singlet oxygen as output.


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NAND, NOR and XNOR. And all of this logic gates

were achieved by molecules [110-112].

The AND gate is so named because, if 0 is called

false and 1 is called true, the gate acts in the same

way as the logical and operator. The output is true

when both inputs are true. Otherwise, the output is

false. The first case of a molecule scale logic gate

designed of primary importance was the de Silvas AND

gate [75]. This molecule 40 (Fig. 10) displayed the prop-

erty that two possible PET channels from the receptorsneeded to be suppressed if a strong fluorescence output

was to be obtained. This was arranged by providing the

two guest species that these two receptors were selec-

tive. The amine unit required H+ (input 1) whereas the

benzocrown ether moiety required Na+ (input 2).

Using the above fluorophore-spacer1-receptor

1-

spacer2-receptor

2 format several AND molecular logic

gates were obtained [113-115]. An useful AND logic

gate based nanobot for selective cellular acting agent in

photodynamic therapy was demonstrated by Akkaya

[115]. Photodynamic therapy is a noninvasive method-

ology used for the treatment malignant tumors and age

related macular degeneration. The cytotoxic agent thus

produced within the target region is singlet oxygen. In

the tumor tissues, the pH can be quite acidic, especially

in the intracellular large acidic vacuoles (LAV) it can

drop below 4, and intracellular sodium ion concentra-

tion is also significantly higher (up to three times) than

normal tissues. Thus, in the proposed logic system 41the chemical inputs are Na+ and H+ (Fig. 11).

An OR gate performs the logic sum between

Boolean variables; the output is 1 at least one of the

inputs is 1. The OR gate requires a set of nonselective

receptors gives a positive optical response upon cation

binding. As a rule, the less selective receptors provide

the operationally better OR action. In the first inten-

tionally designed logic OR gate 42 Ca2+ and Mg2+ pro-

duce essentially identical fluorescence enhancements

Fig. 12. Chemical system 42 (P) which performs the OR logic operation under the action of two chemical inputs (Mg2+ and

Ca2+) and the corresponding truth table.

Fig. 13. Chemical system 43 (P) which performs the XOR logic operation under the action of two chemical inputs (I1and I

2)

and the corresponding truth table.


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18

(Fig. 12) [34]. Fluorescence switching on in the pres-

ence of Ca2+ or Mg2+ in sufficient concentrations to bind

the receptor of42 arises because of an increased oxida-

tion potential of the receptor and PET suppression.

The XOR (exclusive-OR) gate acts in the sameway as the logical either/or. The output is true if

either, but not both of the inputs are true. The output

is false if both inputs are false or if both inputs are

true. Another way of looking at this circuit is to ob-

serve that the output is 1 if the inputs are different, but

0 if the inputs are the same. XOR is the one of the

hardest logic gate to proceed chemically. The first XOR

gate design came from the laboratories of Balzani and

Stoddart [116]. This used the ingenious strategy of acid-

base neutralization as a means of achieving the required

cancellation of inputs. The pseudorotaxane 43 results

from self-assembly of the electron-accepting 2,7-

dibenzyldiazapyrenium dication (Input 1) with the

crown ether which contains two 2,3-dioxynaphthalene

units (Input 2). Because of the electron donor/acceptor

interaction, a low energy CT excited state is formed

which is responsible for (i) the presence of a weak and

broad absorption band and (ii) the disappearance of the

strong fluorescence exhibited by two separated compo-

nents (Fig. 13).

The NOR gate is a combination of OR gate fol-

lowed by an inverter. Its output is true if both inputs

are false. Otherwise, the output is false. Fluorescence

from 44 is switched off by Cu2+. Similar action of H+

can also be seen (Fig. 14) [117].The XNOR (exclusive-NOR) gate is a combina-

tion of XOR gate followed by an inverter. Its output is

true if the inputs are the same and false if the in-

puts are different.

Since the receptor 45 shows optical sensing to-

wards Fe3+ and F- ions, it was investigated the on-off

switching behaviour of the receptor between Fe3+ and

F- ions [118]. The addition of Fe3+ ions to the solution

of receptor 45 leads to fluorescence quenching, that is,

off-state. The addition of F- ions to the solution of

45-Fe3+ complex (off-state), results in the revival of

fluorescence emission (on-state). The revival in fluo-

rescence emission with the addition of F- ion indi-

cates that Fe3+ has more affinity for F- ions than with

the receptor. The fluorescence was quenched again,

that is, off-state when Fe3+ was titrated into the so-

lution of45-Fe3+-F- complex. This reversible onoff

switching process of receptor could not be observed

with other anions indicating the high selectivity of45-

Fe3+complex towards fluoride ion. Such fluorescence

Fig. 14. NOR logic gate 44 with two chemical inputs (Cu2+

and H+) and the corresponding truth table.

Fig. 15. XNOR logic gate 45 with two chemical inputs (Fe3+

and F-) and the corresponding truth table.


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19

changes upon the actions of two chemical inputs mimic

the performance of an exclusive-NOR (XNOR) logic

gate (Fig. 15).

A NAND logic gate can be understood as an

integration of NOT and AND gates. It acts in the man-

ner of the logical operation and followed by nega-

tion. The output is false if both inputs are true.

Otherwise, the output is true. Nice molecular example

is compound 46 [119]. Addition of either inputs Fe2+

or NOBF4

individually has no effect on the emission

and the fluorescent output of the gate remains high as

output 1. Conversely, the presence of both Fe2+ and

NOBF4

inputs leads to fluorescence quench, which is

due to the sequential quenching effect of Fe3+ from the

oxidation of Fe2+ by NOBF4

(Fig. 16).

The INHIBIT gate involves a particular combina-

tion of the logic functions AND and NOT. Gunnlaugsson

et al. [120] produced the first two-input INHIBIT gate

using a tetraazamacrocyclic Tb(III) complex47. This

complex shows a high luminescence output only in an

O2-free acidic solution, while all other combinations of

inputs yield virtually no emission whatsoever. The bind-

ing of H+

to sensitizer unit of the tetraazamacrocyclicligand allows sufficient light absorption and subsequent

electronic energy transfer (EET) to turn on the lumi-

nescence of the metal, but only when O2

has been re-

moved to prevent triplet quenching (Fig. 17).

Molecule logic based on multichannel inputs and mul-

tichannel outputs

Currently molecule devices that can perform more

complex logical operation are on great inters. At present

time were introduced various molecular sensors capable

to execute more than one simultaneous logic operationdue to their multichannel inputs and/or multichannel

outputs (color change and fluorescence variation) [121-

126]. For instance compound 48 implement YES, NOT,

OR, INH, NOR logic gates using H+, Cu2+, Zn2+, Hg2+,

Ag+ as inputs [127] and compound 49 perform XOR,

XNOR, AND using sodium dodecylsulfate as input

[128] (Scheme 17).

A key requirement of digital computers is the

ability to use logical functions to perform arithmetic

operations. The basis of this is addition. If we can add

two binary numbers, we can just as easily subtract them,

or get a little fancier and perform multiplication and

division. Two one-bit binary numbers can be added with

so called half adder. An electronic half-adder circuit

has two inputs and two output channels which is the

basis of number processing in most electronic comput-

ers. Addition needs an AND logic gate for the carry

digit and an XOR logic gate for the sum digit [129]. As

shown in the truth table (Fig. 18), the four rows for a

half-adder show binary addition of 0 (input A) and 0

Fig. 16. NAND logic gate 46 with two chemical inputs (Fe2+

and NOBF4) and the corresponding truth table.

Fig. 17. INHIBIT logic gate 47 with two chemical inputs (H+

and O2) and the corresponding truth table.

Scheme 17. Multichannel molecular devices 48 and 49.


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20

(input B) to give 00 (output), 0 and 1 to give 01, 1 and

0 to give 01, 1 and 1 to give 10. In the more common

decimal numbering these operations become the kin-

dergarten classics: 0 + 0 = 0; 0 + 1 = 1; 1 + 0 = 1 and

1 + 1 = 2 (the final sum is 2Carry+ Sum).

Qian and coworkers demonstrated a simple mol-

ecule 50 able to perform multiple logic functions (AND,

NAND, OR, NOR, XNOR, INH, YES, NO, Pass 1,

Pass 0) [130]. In absorption regime using 400 nm and

425 nm as outputs and sodium dodecylsulfate as input

compound 50 executes simultaneous XNOR and AND

logic gates. For obtaining a half-adder the authors use

the ingenious idea to transform absorption XNOR in

the necessary XOR logic gate changing the absorption

channel at 400 nm with the transmission. This logic

inversion is possible due to the fact that the absorption

is inverse proportion to the transmission (Fig. 18).

The half-subtractor is a combinational circuit

which is used to perform subtraction of two bits. Sub-

traction needs INH logic for the borrow digit and XOR

for the difference digit [131]. The truth table of the half-

subtractor is presented in Fig. 19.

Lu and Zong reported that a phenylalanine de-

rivative 51 may be used as a fluorescent and absorption

dual-modal sensor, which is highly sensitive and selec-

tive to copper ion at physiological pH interval [132].

Fig. 18. Half-adder 50 (AND and XOR logic gates) and corresponding truth table.

Scheme 18. The four ionization states of Fluorescein 52.


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21

Fig. 19. Half-subtractor 51 (INHIBIT and XOR logic gates) and corresponding truth table.

Fig. 20. Truth tables for half-adder and half-subtractor based on Fluorescein 52.

Furthermore, the authors pay attention to the use of its

copper complex to acquire a half-subtractor with par-

allel operating INHIBIT and XOR logic gates, by moni-

toring fluorescence and absorbance as output signals,

respectively (Fig. 19).

Tree or more binary numbers can be added and

subtract with combinational circuit full-adder and full-

subtractor. Using commercially available fluorescein 52,

acid and base inputs, integration of a full-adder and a

full-subtractor is demonstrated in an even simpler man-

ner by Margulies et al. [133]. Fluorescein is well known

to exist in four ionization states (+1, 0, -1, -2) each

with its own signature absorption spectrum (Scheme 18).

Authors have expanded the operations of fluo-

rescein to suggest the possibility of a molecular-scale

calculator (a moleculator) with full-adder and full-

subtractor capabilities. Previous ideas such as mutual

annihilation of inputs, degeneracy of inputs, switching

between positive and negative logic with absorbance and

transmittance outputs are combined for the first time

in this fine paper (Fig. 20).

Two binary numbers can be compared using com-

binational logic circuit called digital magnitude com-

parator. In fact XOR and XNOR are able to compare

binary numbers and give information are they equal, but

not which is higher. Compound 53 can mimic the func-

tion of digital magnitude comparators [134]. Starting from

the neutral species with base (B) and acid (A) as two

inputs, the fluorescent output at 410 nm is eq (equal)

digit and the output at 550 nm is gt (greater than) digit

(Fig. 21). With no or both inputs present, i.e. when B =

A, the output eq is 1. When adding the base, i.e. B>A,

the output gt is 1. The addition of an acid, i.e. B


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22

logic operation. An electronic device recovers its ini-

tial state immediately once electricity current is cut off.

However, a molecular device retains its binding state

even when the input signals are cut off, and thus pre-

vents further operation, as the molecular system has been

remaining in thermodynamic equilibrium with the in-

put introduced. Therefore, the effect of the input sig-

nals must be removed or neutralized to restore the ini-

tial state of the molecular device, enabling the system

to execute new logic operations [135].

Usually, the resetting reagents are often intro-

duced to recover the initial state of the molecular de-

vices, the operation principle of which is based on the

fact that the recognition reactions driving molecular logic

devices, such as protonation, coordination, or redox

reactions, are usually chemically reversible, which re-

veals that the direction of recognition reaction can be

reversed if some reagents are introduced to consume

the previous input signals. According to this strategy,

the protonated product can be reset to the initial state

when an equivalent amount of base is introduced [136].

A nice example of Reset function using EDTA

(ethylenediaminetetraacetic acid) was demonstrated.

EDTA is a good chelating agent which can be well co-

ordinated with metal ions and its effect with some mo-

lecular function systems have also been developed in

recent years [137-140]. Wang et al. prepared a binaphthyl

molecular device 54 capable to implement simultaneous

AND and INH logic gates [137]. The logic gates were

executed using Cu2+ and Zn2+ as inputs and absorption

at 410 nm and emission at 500 nm as outputs (Fig. 22).

Afterward, the addition of EDTA gradually re-

covered both absorption and emission spectra to the

original spectra of54, suggesting that the chemosensor

could be returned to original state. Moreover, individual

action of EDTA caused no obvious spectra change to

the 54 solution, indicating that no structural changes

could be generated by the addition of EDTA.

Fig. 22. Binaphthyl-derived device 54 (AND and INH logic gates) with Reset function and corresponding truth table.

Fig. 21. Digital comparator based on 8-hydroxyquinoline 53 and corresponding truth table.


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23

CONCLUSIONS

The realization of computing devices with ex-

tremely small size and unprecedented performance is a

strong motivation for the search of molecule-based in-

formation processing. Recent literature is a testament to

the general significance of logic interpretations based on

supramolecular phenomena. The field has developed from

simple switches to produce more complex molecular

systems that are capable of performing a variety of clas-

sical logic functions, including extensions to arithmetic

devices such as half-adder, full-adder, half-subtractor,

full-subtractor and digital magnitude comparator.

Acknowledgements

This work was supported by the National Science

Foundation of Bulgaria (project DVU-10-0195). Authors

also acknowledge the Science Foundation at the University

of Chemical Technology and Metallurgy (Sofia, Bulgaria).

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