Molecular logic gate

A molecular logic gate is a molecule that performs a logical operation based on one or more physical or
chemical inputs and a single output. The field has advanced from simple logic systems based on a single
chemical or physical input to molecules capable of combinatorial and sequential operations such as
arithmetic operations i.e. moleculators and memory storage algorithms.

For logic gates with a single input, there are four possible output patterns. When the input is 0, the output
can be either a 0 or 1. When the input is 1, the output can again be 0 or 1. The four output bit patterns that
can arise corresponds to a specific logic type: PASS 0, YES, NOT and PASS 1. PASS 0 always outputs 0,
whatever the input. PASS 1 always outputs 1, whatever the input. YES outputs a 1 when the input is 1 and
NOT is the inverse YES – it outputs a 0 when the input is 1. An example of a YES logic gate is the
molecular structure shown below. A "1" output is given only when sodium ions are present in solution ("1"
input).

Molecular logic gates work with input signals based on chemical processes and with output signals based on
spectroscopy. One of the earlier water solution-based systems exploits the chemical behavior of compounds
A and B in scheme 1.[1]

Compound A is a push-pull olefin with the top receptor containing four carboxylic acid anion groups (and
non-disclosed counter cations) capable of binding to calcium. The bottom part is a quinoline molecule which
is a receptor for hydrogen ions. The logic gate operates as follows. Without any chemical input of Ca2+ or
H+, the chromophore shows a maximum absorbance in UV/VIS spectroscopy at 390 nm. When calcium is
introduced a blue shift takes place and the absorbance at 390 nm decreases. Likewise addition of protons
causes a red shift and when both cations are in the water the net result is absorption at the original 390 nm.
This system represents a XNOR logic gate in absorption and a XOR logic gate in transmittance.

In compound B the bottom section now contains a tertiary amino group also capable of binding to protons.
In this system fluorescence only takes place when both cations available. The presence of both cations
hinders photoinduced electron transfer (PET) allowing compound B to fluoresce. In the absence of both or
either ion, fluorescence is quenched by PET, which involves an electron transfer from either the nitrogen
atom or the oxygen atoms, or both to the anthracenyl group. When both receptors are bound to calcium ions
and protons respectively, both PET channels are shut off. The overall result of Compound B is AND logic,
since an output of "1" (fluorescence) occurs only when both Ca2+ and H+ are present in solution, that is,
have values as "1". With both systems run in parallel and with monitoring of transmittance for system A and
fluorescence for system B the result is a half-adder capable of reproducing the equation 1+1=2.

In a modification of system B not two but three chemical inputs are simultaneously processed in an AND
logic gate.[2] An enhanced fluorescence signal is observed only in the presence of excess protons, zinc and
sodium ions through interactions with their respective amine, phenyldiaminocarboxylate and crown ether
receptors. The processing mode operates similarly as discussed above – fluorescence is observed due to the
prevention of competing photoinduced electron transfer reactions from the receptors to the excited
anthracene fluorophore. The absence of one, two or all three ion inputs results in a low fluorescence output.
Each receptor is selective for its specific ion as an increase in the concentration of the other ions does not
yield a high fluorescence. The specific concentration threshold of each input must be reached to achieve a
fluorescent output in accordance with combinatorial AND logic. This prototype could potentially be
extended to point-of-care medical diagnostics application for disease screening in the future.

In a similar set-up, the molecular logic gate illustrated below demonstrates the advancement from redox-
fluorescent switches to multi-input logic gates with an electrochemical switch.[3] This two-input AND logic
gate incorporates a tertiary amine proton receptor and a tetrathiafulvelene redox donor. These groups, when
attached to anthracene can simultaneously process information concerning acid concentration and oxidizing
ability of the solution.

The INHIBIT logic gate illustrated below as provided by Gunnlaugsson et al. incorporates a Tb3+ ion in a
chelate complex.[4] This two-input logic gate is the first of its kind and displays non-commutative behaviour
with chemical inputs and a phosphorescence output. Whenever dioxygen (input 1) is present, the system is
quenched and no phosphorescence is observed (output 0). The second input, H+, must also be present for an
output "1" to be observed. This is understood from a two-input INHIBIT truth table.
In another XOR logic gate system the chemistry is based on the pseudorotaxane[5] depicted in scheme 3. In
organic solution the electron deficient diazapyrenium salt (rod) and the electron rich 2,3-dioxynaphthalene
units of the crown ether (ring) self-assemble by formation of a charge transfer complex.

An added tertiary amine like tributylamine forms a 1:2 adduct with the diazapyrene and the complex gets
dethreaded. This process is accompanied by an increase in emission intensity at 343 nm resulting from freed
crown ether. Added trifluoromethanesulfonic acid reacts with the amine and the process is reverted. Excess
acid locks the crown ether by protonation and again the complex is dethreaded.

A full adder system based on fluorescein[6] is able to compute 1+1+1=3.

Molecular sequential logic is exemplified by D. Margulies et al., where they demonstrate a molecular
keypad lock resembling the processing capabilities of an electronic security device which is equivalent to
incorporates several interconnected AND logic gates in parallel.[7] The molecule mimics an electronic
keypad of an automated teller machine (ATM). The output signals are dependent not only on the
combination of inputs but also on the correct order of inputs: in other words the correct password must be
entered. The molecule was designed using pyrene and fluorescein fluorophores connected by a siderophore,
which binds to Fe(III), and the acidic of the solution changes the fluorescence properties of the fluorescein
fluorophore.

Further development in this field might also see molecular logic gates replace semiconductors in the IT
industry. Such molecular systems can theoretically overcome the problems arising when semiconductors
approach nano-dimensions. Molecular logic gates are more versatile than their silicon counterparts, with
phenomena such as superposed logic unavailable to semiconductor electronics. Dry molecular gates such as
the one demonstrated by Avouris and colleagues prove to be possible substitutes for semiconductor devices
due to their small size, similar infrastructure and data processing abilities. Avouris revealed a NOT logic
gate composed of a bundle of carbon nanotubes. The nanotubes are doped differently in adjoining regions
creating two complementary field effect transistors. The bundle operates as a NOT logic gate only when
satisfactory conditions are met.

New potential applications of chemical logic gates continue to be explored. A recent study[8] illustrates the
application of a logic gate for photodynamic therapy. A bodipy dye attached to a crown-ether and two
pyridyl groups separated by spacers (as shown below) works according to an AND logic gate. The molecule
works as a photodynamic agent upon irradiation at 660 nm under conditions of relatively high sodium and
proton ion concentrations by converting triplet oxygen to cytotoxic singlet oxygen. This prototypical
example would take advantage of the higher sodium levels and lower pH in tumor tissue compared to the
levels in normal cells. When these two cancer-related cellular parameters are satisfied, a change is observed
in the absorbance spectrum. This technique could be useful for the treatment of malignant tumors as it is
non-invasive and specific.

A molecular logic gate can processes modulators much like the set up seen in de Silva’s ‘Proof-of-principle’
but incorporating different logic gates on the same molecule. Such a function is called integrated logic and is
exemplified by the BODIPY-based, half-subtractor logic gate illustrated by A. Coskun, E. U. Akkaya and
their colleagues (as shown below).[9] When monitored at two different wavelengths, 565 and 660 nm, XOR
and INHIBIT logic gates are obtained at the respective wavelengths. Optical studies of this compound in
THF reveal an absorbance peak at 565 nm and an emission peak at 660 nm. Addition of an acid results in a
hypsochromic shift of both peaks as protonation of the tertiary amine results in an internal charge transfer.
The colour of the emission observed is yellow. Upon addition of a strong base, the phenolic hydroxyl group
is rendered deprotonated, resulting in a photoinduced electron transfer, which in turn renders the molecule
non-emissive. Upon addition of both an acid and a base, the emission of the molecule is observed as red, as
the tertiary amine would not be protonated while the hydroxyl group would remain protonated resulting in
the absence of both PET and ICT. Due to the great difference in emission intensity, this single molecule is
capable of carrying out an arithmetic operation; subtraction at a nanoscale level.
See also
Chemical computer
Biological computer
Quantum computer

References
1. ^ A. Prasanna de Silva and Nathan D. McClenaghan. Proof-of-Principle of Molecular-Scale
Arithmetic J. Am. Chem. Soc. 2000, 122, 16, 3965–3966. doi:10.1021/ja994080m (https://doi.o
rg/10.1021%2Fja994080m)
2. ^ David C. Magri, Gareth J. Brown, Gareth D. McClean and A. Prasanna de Silva.
Communicating Chemical Congregation: A Molecular AND Logic Gate with Three Chemical
Inputs as a "Lab-on-a-Molecule" Prototype J. Am. Chem. Soc. 2006, 128, 4950–4951.
(Communication)doi:10.1021/ja058295 (https://doi.org/10.1021%2Fja058295)
3. ^ David C. Magri. A fluorescent AND logic gate driven by electrons and protons. New J. Chem.
2009, 33, 457–461.
4. ^ T. Gunnlaugsson, D.A. MacDonail and D. Parker, Chem. Commun. 2000, 93.
5. ^ Alberto Credi, Vincenzo Balzani, Steven J. Langford, and J. Fraser Stoddart. Logic
Operations at the Molecular Level. An XOR Gate Based on a Molecular Machine J. Am.
Chem. Soc. 1997,119, 2679–2681.(Article) doi:10.1021/ja963572l (https://doi.org/10.1021%2Fj
a963572l)
6. ^ David Margulies, Galina Melman, and Abraham Shanzer. A Molecular Full-Adder and Full-
Subtractor, an Additional Step toward a Moleculator J. Am. Chem. Soc. 2006, 128, 4865–
4871. (Article) doi:10.1021/ja058564w (https://doi.org/10.1021%2Fja058564w)
7. ^ David Margulies, Galina Melman, and Abraham Shanzer. A molecular keypad lock: A
photochemical device capable of authorizing password entries. J. Am. Chem. Soc. 2007, 129,
347–354.
8. ^ S. Oslem and E.U. Akkaya. Thinking outside the silicon box: molecular AND logic as an
additional layer of selectivity in singlet oxygen generation for photodynamic therapy. J. Am.
Chem. Soc. 2009, 131, 48–49.
9. ^ A. Coskun, E. Deniz and E.U. Akkaya. Effective PET and ICT switching of
boradiazaindacene emission: A unimolecular, emission-mode, molecular half-subtractor with
reconfigurable logic gates. Org. Lett. 2005 5187–5189.

External links
A Molecular Photoionic AND Gate Based on Fluorescent Signaling (http://www.nature.com/nat
ure/journal/v364/n6432/pdf/364042a0.pdf)
 The 3rd International Conference on Molecular Sensors & Molecular Logic Gates (MSMLG)
was held on July 8–11, 2012 at Korea University in Seoul, Korea. [10] (https://archive.is/20130
503073134/http://msmlg2012.org/calix/main)

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