Fluorescence based Molecular Logic Gates

The ultimate goal of miniaturisation is to use molecular assemblies as memory, processing and mechanical devices. To acieve these goals, it is essential to transform molecular structures between two or more states in response to external signals such as photonic, chemical, electrochemical, or magnetic stimuli, and to tailor readable output(s) such as electronic or optical signals that reflect the molecular state. Electronically transduced photochemical switching is possible in organic monolayers and thin films, enzyme monolayers, redox-enzymes tethered with photoisomerisable groups, enzymes reconstituted onto photoisomerisable FAD-cofactors etc. Photoinduced electron transfer process (PET) in many organic compounds, leads to OFF-ON and ON-OFF mechanism. Numerous organic molecules can follow this simple signal transduction protocol, and execute simple

NOT and YES operations. For example, pyrazole derivative 1 emits only when the concentration of H+ is low. Photoinduced electron transfer from the central pyrazoline unit to the pendant benzoic acid quenches the fluorescence of the protonated form. Thus, the emission intensity switches from a high to low value when the concentration of the H+ changes from low to high value. This inverse relation between the chemical input (concentration of H+) and the optical output (fluorescence intensity) corresponds to a NOT operation (de Silva 1993). On the contrary, PET process in molecule 2 executes a YES operation, where the fluorescence of anthracene is turned ON with presence of H+.


In OR gates the output is 0 only when both the inputs are 0 and the output will be 1 in all the other three cases. To execute this operation compounds should be able to respond to two input signals i.e., they have to produce a detectable signal when one or both the inputs are applied. This can be readily realised by many photophysical processes, which have been an active area of current photochemistry process study. For example, compound 3 generates an optical output (fluorescence) in response to one or two chemical inputs (K+ and Rb+ metal cations). In the absence of metal cations, PET from the tertiary amino groups to the anthracene appendage quenches the fluorescence (de Silva 1993).

In another example, the cryptand compound 4 containing three anthryl moieties is capable of functioning as a very efficient multi-input OR logic gate. The fluorophores in these systems do not show any fluorescence due to an efficient PET from nitrogen lone pairs to the anthracene moiety. However, the fluorescence is recovered to different extents in the presence of transition metal ions like Cu(II) and Ni(II), inner-transition metal ions like Eu(III) and Tb(III) ions along with H+

and Zn(II) (Ghosh 1996). The first fluorescence based molecular AND gate was introduced by de Silva in his work on Na+ detection (de Silva 1997). Molecule 5 fluoresces when amine receptor is bound to H+ and benzo-15-crown-5 ether to Na+. This is the ON state with high fluorescence intensity emitted from the anthracene moiety. When the amine group is proton-free, it serves as an efficient PET donor (AGPET ~ -0.1 eV) to the fluorophore, which is separated by only a methylene group. In the presence of protons in sufficient concentration and in the absence of Na+, the protonated amino methyl moiety behaves as an electron-withdrawing group on the anthracene fluorophore permitting rapid PET from the benzocrown ether moiety (AGPET ~ -0.1 eV) a short distance away and resulted in the quenching of the fluorescence of 5. The ion-induced fluorescence emission spectral behavior of these systems is illustrated in Fig. 12.3, giving an excellent example for a digital AND logic gate (de Silva 1997). Compound 6 also generates an optical output (fluorescence) only when both two chemicals exist (H+ and K+ or Na+ metal cation) (AND gate) (de Silva 1993).

Fig. 12.3. Fluorescence emission spectra of gate 5 in MeOH excited at 377 nm under the four ionic conditions necessary to test its digital AND logic gate function. The PET processes are also shown

Fluorescence intensity / arbitrary units

Fluorescence intensity / arbitrary units

Fig. 12.3. Fluorescence emission spectra of gate 5 in MeOH excited at 377 nm under the four ionic conditions necessary to test its digital AND logic gate function. The PET processes are also shown


This molecule exhibited an unique logic gate system that combines an AND gate and an INHIBIT gate as described in Fig. 12.4 by two representations. For example, 2 combines an AND gate and an INHIBIT gate with the input notations IN1, IN2, and IN3 signifying presence (1) or absence (0) of potassium ion (K+), proton (H+), and sodium ion (Na+) in solution.


output output

Truth table


Fig. 12.4. Schematic representation of 7 showing an AND gate and an INHIBIT gate logics switched by H+. Inset shows the truth table for this logical gating performance

Monoaza-18-crown-6 ether and boronic acid receptor linked compound 8 shows selective fluorescent enhancement with D-glucosamine hydrochloride in aqueous solution at pH 7.18. This system also behaves like an AND logic gate where in the fluorescence recovery is observed only when ammonium cation and a diol compound are supplied (Cooper 1997).

Flavylium derivative 9 can exist in more than two forms (multistate) that can be interconverted by more than one type of external stimulus (multifunctional). This can be taken as the basis for an optical memory system with multiple storage and non-destructive readout capacity. For the 4'hydroxyflavylium compound, light excitation and pH jumps can be taken as inputs, and fluorescence as outputs that exhibits an AND logic function (Pina 1998, 1999).

(Structural transformations of 4'hydroxyflavylium compound)

Single molecules with several functional groups can be used for mimicking complicated multi logical functions. For example, compound 10 converts two chemical inputs into an optical output mimicking a NAND function. At neutral

pH, the anthracene fluorophore emits fluorescence. After the addition of either H+ or adenosine triphosphate (ATP), the fluorescence remains but the optical output diminishes in intensity when both chemical inputs (H+ and ATP) are applied. Protonation of the aligoamino arm leads to the association of 10 with ATP resulting in the quenching phenomenon (Albelda 1999).

Similar to OR gate, NOR gate can readily be realised. The photophysical properties of metal complexes using lanthanide ions as emitting moieties can also be used to develop luminescent molecular level devices. Compound 11 converts two chemical inputs into an optical output according to a NOR operation. For Terbium complex 11, H+ and O2 are the chemical inputs and lanthanide luminescence is the output. In the presence of H+, excitation at 304 nm is followed by the fluorescence of the phenanthridine appendage. In the absence of H+, the excitation of the phenanthridine fragment is followed by intersystem crossing, electron transfer to the Tb center and delayed emission from the lanthanide. In the presence of O2, the tripled state of the phenanthridine appendage is quenched and the Tb emission is not observed. Thus, the optical output (Tb emission) is detected only when the two chemical inputs (H+ and O2) are not applied (Parker 1998).

In another example, the anthracene fluorescence of compound 12 under neutral pH conditions can be observed only in the absence of Cu2+ and Ni2+ (chemical inputs). The binding of one of the cations to the aligoamino arm efficiently quenches the anthracene fluorescence. The behavior of the compound 12 corresponds to molecular NOR gate (Alves 2001).


Another two NOR gate systems are shown in Fig. 12.5. Complexation or input of either H+ or Zn2+ cation with 13 is expected to quench fluorescence output. Molecule 14 is a spatially overlapping "fluorophore-receptor" system. Its receptor, which is reminiscent of 2,2'; 6',2''-terpyridyl, complexes H or Hg2+. The fluorescence output of 14 is seriously quenched by either cation and the NOR truth table is satisfied. The mechanism of fluorescence quenching with Hg2+ involves a nonemissive ligand-to-metal charge transfer (LMCT) excitation (de Silva 1999a).

/ ultraviolet ^ violet / ultraviolet ^blue

Fig. 12.5. Molecular-scale implementation of NOR logic gates

/ ultraviolet ^ violet / ultraviolet ^blue

13 14

Fig. 12.5. Molecular-scale implementation of NOR logic gates

Tb(III) based quinolyl derived macrocyclic 1,4,7,10-tetraazacyclododecane (cyclen) conjugate 15, executes the INHIBIT function with H+ and O2 as the chemical inputs and Tb luminescence being the optical output. Under basic conditions, the complex 32 has a weak emission band at 548 nm in either aerated or degassed solutions. After the addition of H+, the emission intensity dramatically increases in the absence of O2. The protonation of the quinoline fragment facilitates the energy transfer from the quinoline excited state to the lanthanide excited state, enhancing the emission intensity. The presence of O2 supresses the energy transfer process. Thus the emission intensity is high only when the concentration of H+ is high and that of O2 is low. If a positive logic convention is applied to the system, the signal transduction of the 32 translates into the truth table of the INHIBIT circuit (Gunnlaugsson 2000, 2001).


Functional integration also succeeded in achieving a more complex INHIBIT logic operation with a rather simple supramolecule 16 (Fig. 12.6) (de Silva 1999).

Fig. 12.6. Molecular-scale implementation of INHIBIT logic gates

Photochromic spiropyrans (SP) via proton transfer or energy transfer is another logical gate system (Fig. 12.7). Oxidation potential of Fe2+ is significantly reduced after coordination with the open form of spiropyran, thus, the electron transfer between the tetrathiafulvalene (TTF) unit and Fe3+ can be photocontrolled in the presence of SP. Radical cation of fluorescein formed by oxidation with ferric ion can be reduced to the corresponding neutral species upon UV light irradiation in the presence of SP (Scheme 1), just like the TTF+. Radical cation of fluorescein shows strong emission at 480 nm when excited at 410 nm compared to its neutral form. Hence, a promising redox fluorescence switch based on fluorescein can be constructed. A redox fluorescence switch based on fluorescein and a photochromic molecular switch based on spiropyran through the Fe(II)/Fe(III)

redox couple is realised. The concatenation of these two molecular switches can mediate the transduction of two kinds of external inputs into one kind of optical output, which corresponds to the function of an INHIBIT logic gate (Guo 2004).

Fig. 12.l. Photochromic switch of spiropyran

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