Molecular logic gate

Last updated

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). [1] Molecular logic gates work with input signals based on chemical processes and with output signals based on spectroscopic phenomena.

Contents

Logic gates are the fundamental building blocks of electrical circuits. They can be used to construct digital architectures with varying degrees of complexity by a cascade of a few to several million logic gates, and are essentially physical devices that produce a singular binary output after performing logical operations based on Boolean functions on one or more binary inputs. The concept of molecular logic gates, extending the applicability of logic gates to molecules, aims to convert chemical systems into computational units. [2] [3] The field has evolved to realize several practical applications in molecular electronics, biosensing, DNA computing, nanorobotics, and cell imaging, among others.  

Working principle

Select single-input logic gates with truth tables Table 1. Select single-input logic gates with truth tables.png
Select single-input logic gates with truth tables

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 correspond to a specific logic type: PASS 0, YES, NOT, and PASS 1. PASS 0 and PASS 1 always outputs 0 and 1, respectively, regardless of input. YES outputs a 1 when the input is 1, and NOT is the inverse of YES – it outputs a 0 when the input is 1.[ citation needed ]

AND, OR, XOR, NAND, NOR, XNOR, and INH are two-input logic gates. The AND, OR, and XOR gates are fundamental logic gates, and the NAND, NOR, and XNOR gates are complementary to AND, OR, and XOR gates, respectively. An INHIBIT (INH) gate is a special conditional logic gate that includes a prohibitory input. When the prohibitory input is absent, the output produced depends solely on the other input.[ citation needed ]

Select dual-input logic gates with symbols and truth tables Table 2. Select dual-input logic gates with truth tables.png
Select dual-input logic gates with symbols and truth tables
Block structure of a dual-input combinational molecular logic gate with metal ions as inputs (input "1") and fluorescence emission as output (output "1") Figure 1. Block structure of a dual-input combinational molecular logic gate.png
Block structure of a dual-input combinational molecular logic gate with metal ions as inputs (input "1") and fluorescence emission as output (output "1")

History and development

One of the earliest ideas for the use of π-conjugated molecules in molecular computation was proposed by Ari Aviram from IBM in 1988. [5]

Schematic of a proposed molecular electronic switch by Aviram Figure 2. Schematic of a proposed molecular electronic switch by Aviram.png
Schematic of a proposed molecular electronic switch by Aviram

The first practical realization of molecular logic was courtesy of de Silva and coworkers in their seminal work, in which they constructed a molecular photoionic AND gate with a fluorescent output. [6] While a YES molecular logic gate can convert signals from their ionic to photonic forms, they are singular-input-singular-output systems. To build more complex molecular logic architectures, two-input gates, namely AND and OR gates, are needed. Some early works made some progress in this direction, but they could not realize a complete truth table as their protonated ionic forms could not bind to the substrate in every case. [7] [8] De Silva et al. constructed an anthracene-based AND gate made up of tertiary amine and benzo-18-crown-6 units, both of which were known to show photoinduced electron transfer (PET) processes. In the system shown, they both acted as receptors, connected to the anthracene-based fluorophore by alkyl spacers. The PET is quenched upon coordination with protons [9] and sodium ions, [10] respectively, for the two receptors, and would cause the anthracene unit to fluoresce.

A molecular AND gate Figure 3. A molecular AND gate.png
A molecular AND gate

Examples of molecular logic gates

YES molecular logic gate

An example of a YES logic gate comprises a benzo-crown-ether connected to a cyano-substituted anthracene unit. An output of 1 (fluorescence) is obtained only when sodium ions are present in the solution (indicating an input of 1). Sodium ions are encapsulated by the crown ether, resulting in a quenching of the PET process and causing the anthracene unit to fluoresce. [11]

A YES molecular logic gate A YES molecular logic gate.png
A YES molecular logic gate

AND molecular logic gate

This molecular logic gate illustrates the advancement from redox-fluorescent switches to multi-input logic gates with an electrochemical switch, detecting the presence of acids. This two-input AND logic gate incorporates a tertiary amine proton receptor and a tetrathiafulvalene redox donor. These groups, when attached to anthracene, can simultaneously process information concerning the concentration of the acid and oxidizing ability of the solution. [12]

A two-input AND molecular logic gate sensor for protons and electrons Two-input AND molecular logic gate sensor for protons and electrons.png
A two-input AND molecular logic gate sensor for protons and electrons

OR molecular logic gate

De Silva et al. constructed an OR molecular logic gate using an aza-crown ether receptor and sodium and potassium ions as the inputs. Either of the two ions could bind to the crown ether, causing the PET to be quenched and the fluorescence to be turned on. Since either of the two ions (input “1”) could cause fluorescence (output “1”), the system resembled an OR logic gate. [6]

A two-input molecular OR logic gate Figure 6. A two-input molecular OR gate.png
A two-input molecular OR logic gate

INH molecular logic gate

The INH logic gate incorporates a Tb3+ ion in a chelate complex. This two-input logic gate displays non-commutative behavior 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. [13]

A two-input molecular INH logic gate INHIBIT molecular logic gate by Gunnlaugsson.png
A two-input molecular INH logic gate

NAND molecular logic gate

Parker and Williams constructed a NAND logic gate based on turning on strong emission from a terbium complex of phenanthridine. When acid and oxygen (the two inputs) are absent (input “0”), the fluorescence from the terbium center is turned on (output “1”). [14]

A two-input molecular NAND logic gate Figure 8. A two-input NAND molecular logic gate.png
A two-input molecular NAND logic gate

NOR molecular logic gate

Akkaya and coworkers demonstrated a molecular NOR gate using a boradiazaindacene system. Fluorescence of the highly-emissive boradiazaindacene (input “1”) was found to be quenched in the presence of either a zinc salt [Zn(II)] or trifluoroacetic acid (TFA). [15]

A two-input molecular NOR logic gate Figure 9. A two-input molecular NOR logic gate.png
A two-input molecular NOR logic gate

XOR and XNOR molecular logic gates

Redshift (shift to longer wavelengths) and blueshift (shift to shorter wavelengths) Redshift blueshift.svg
Redshift (shift to longer wavelengths) and blueshift (shift to shorter wavelengths)

De Silva and McClenaghan designed a proof-of-principle arithmetic device based on molecular logic gates. 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 hypsochromic shift (blue shift) takes place and the absorbance at 390 nm decreases; likewise, an addition of protons causes a bathochromic shift (red shift). When both cations are in water, the net result is absorption at the original 390 nm wavelength. This system represents an XNOR logic gate in absorption and an XOR logic gate in transmittance. [16]

In another XOR logic gate system, the chemistry is based on pseudorotaxane. 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 the complex is de-threaded again. [17]

A pseudorotaxane-based logic gate RotaxaneLogicGate.png
A pseudorotaxane-based logic gate

Half-adder and half-subtractor molecular circuits

A. A multi-functional dual-input XNOR/XOR molecular logic gate; B. A triple-input half-adder system based on AND gates. Moleculators de silva13 02.png
A. A multi-functional dual-input XNOR/XOR molecular logic gate; B. A triple-input half-adder system based on AND gates.

In compound B, the bottom section contains a tertiary amino group that is capable of binding to protons. In this system, fluorescence only occurs when both cations are present. The presence of both cations hinders PET, allowing compound B to fluoresce. In the absence of 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 running in parallel and the 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. [16]

In a modification of system B, three chemical inputs are simultaneously processed in an AND logic gate. 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 PET reactions from the receptors to the excited anthracene fluorophore. The absence of any ion input 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. [18]

A triple-input half-adder system based on AND gates Three-input AND logic gate.png
A triple-input half-adder system based on AND gates

More complex molecular logic circuits

A molecular logic gate can processes modulators much like the setup seen in de Silva’s proof-of-principle, [16] but incorporating different logic gates on the same molecule is challenging. Such a function is called integrated logic and is exemplified by the BODIPY-based, half-subtractor logic gate illustrated by Coskun, Akkaya, and their colleagues. When monitored at two different wavelengths, 565 and 660 nm, XOR and INH logic gates operations are realized at the respective wavelengths. Optical studies of this compound in tetrahydrofuran 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 color of the emission observed is yellow. When a strong base is added, the phenolic hydroxyl group is deprotonated, effecting a PET that renders the molecule non-emissive. When an acid and base are added, the molecule is observed to give off a red emission, as the tertiary amine would not be protonated while the hydroxyl group would remain protonated, resulting in the absence of both PET and intramolecular charge transfer (ICT). Due to the great difference in emission intensity, this single molecule is capable of carrying out subtraction at a nanoscale level. [19]

An integrated logic gate An integrated logic gate by A. Coskun.png
An integrated logic gate

A full adder system based on fluorescein has also been constructed by Shanzer et al. The system is able to compute 1+1+1=3. [1]

Potential applications

Over the years, the utility of molecular logic gates has been explored in a wide range of fields such as chemical and biological detection, the pharmaceutical and food industries, and the emerging fields of nanomaterials and chemical computing. [20] [21] [22] [23] [24]

Chemical detection of ions

Fluoride (F-) and acetate (CH3COO-) anions are among the most important ones in the context of human health and well-being. The former, used extensively in health care, is known for its toxicity and corrosiveness. The latter can cause alkalosis and affect metabolic pathways beyond a certain concentration. Hence, it is crucial to develop methods to detect these anions in aqueous media. Bhat et al.. constructed an INH gate with receptors that bind selectively to F‑ and CH3COO- anions. The system used changes in absorbance as a colorimetric-based output to detect the concentration of anions. [25]  

Wen and coworkers designed an INH molecular logic gate with Fe3+ and EDTA as the inputs and a fluorescent output for the detection of ferric ions in solutions. The fluorescence of the system is quenched if and only if Fe3+ input is present and EDTA is absent. [26]

Heavy metal ions are a persistent threat to human health because of their inherent toxicity and low degradability. Several molecular logic gate-based systems have been constructed to detect ions such as Cd2+, [27] Hg2+/Pb2+, [28] and Ag+. [29] In their work, Chen et al. demonstrated that logic gate-based systems could be used to detect Cd2+ ions in rice samples. [27]

Biological applications

The effectiveness of methods such as chemotherapy to treat cancer tends to plateau after some time, as the cells undergo molecular changes that render them insensitive to the effect of anticancer drugs, [30] making the early detection of cancerous cells important. A biomarker, microRNA (miRNA), is crucial in this detection via its expression patterns. [31] Zhang et al. have demonstrated an INH-OR gate cascade for the purpose, [32] Yue et al. used an AND gate to construct a system with two miRNA inputs and a quantum dot photoluminescence output, [33] and Peng et al. also constructed an AND gate-based dual-input system for the simultaneous detection of miRNAs from tumor cells. [34]

Akkaya et al. illustrated the application of a logic gate for photodynamic therapy in their work. A BODIPY dye attached to a crown ether and two pyridyl groups separated by spacers 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 uses 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. [35]

Two-input AND logic gate with photodynamic therapeutic applications. AND logic gate by Akkaya.png
Two-input AND logic gate with photodynamic therapeutic applications.

DNA computing and logic calculation

The concept of DNA computing arose from addressing storage density issues because of the increasing volumes of data information. Theoretically, a gram of single-stranded DNA is capable of storing over 400 exabytes of data at a density of two bits per nucleotide. [36] Leonard Adleman is credited with having established the field in 1994. [37] Recently, molecular logic gate systems have been utilized in DNA computing models. [38]

Massey and coworkers constructed photonic DNA molecular logic circuits using cascades of AND, OR, NAND, and NOR molecular logic gates. [39] They used lanthanide complexes as fluorescent markers, and their luminescent outputs were detected by FRET-based devices at the terminals of DNA strands. Works by Campbell et al. on demonstrating NOT, AND, OR, and XNOR logic systems based on DNA crossover tiles, [40] Bader and co. on manipulating the DNA G-quadruplex structure to realize YES, AND, and OR logic operations, [41] and Chatterjee and coworkers on constructing logic gates using reactive DNA hairpins on DNA origami surfaces are some examples of logic gate-based DNA computing. [42]

Nanorobotics and advanced machines

Nanorobots have the potential to transform drug delivery processes and biological computing. [43] Llopis-Lorente and co. developed a nanorobot that can perform logic operations and process information on glucose and urea. [44] Thubagere and coworkers designed a DNA molecular nanorobot capable of sorting chemical cargo. The system could work without additional power as the robot was capable of walking across the DNA origami surface on its two feet. It also had an arm to transport cargo. [45]  

Margulies et al. demonstrated molecular sequential logic, where they created 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. The molecule mimics an electronic keypad of an automated teller machine. The output signals are dependent not only on the presence of inputs but also on a correct order; i.e. 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 acidity of the solution changes the fluorescence properties of the fluorescein fluorophore. [46]

Molecular logic gate 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. [24] 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, and the bundle operates as a NOT logic gate only when satisfactory conditions are met. [47]

See also

Related Research Articles

<span class="mw-page-title-main">DNA computing</span> Computing using molecular biology hardware

DNA computing is an emerging branch of unconventional computing which uses DNA, biochemistry, and molecular biology hardware, instead of the traditional electronic computing. Research and development in this area concerns theory, experiments, and applications of DNA computing. Although the field originally started with the demonstration of a computing application by Len Adleman in 1994, it has now been expanded to several other avenues such as the development of storage technologies, nanoscale imaging modalities, synthetic controllers and reaction networks, etc.

<span class="mw-page-title-main">Fluorescent tag</span>

In molecular biology and biotechnology, a fluorescent tag, also known as a fluorescent label or fluorescent probe, is a molecule that is attached chemically to aid in the detection of a biomolecule such as a protein, antibody, or amino acid. Generally, fluorescent tagging, or labeling, uses a reactive derivative of a fluorescent molecule known as a fluorophore. The fluorophore selectively binds to a specific region or functional group on the target molecule and can be attached chemically or biologically. Various labeling techniques such as enzymatic labeling, protein labeling, and genetic labeling are widely utilized. Ethidium bromide, fluorescein and green fluorescent protein are common tags. The most commonly labelled molecules are antibodies, proteins, amino acids and peptides which are then used as specific probes for detection of a particular target.

Nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and analyzed. There are several ways proposed today to make nanosensors; these include top-down lithography, bottom-up assembly, and molecular self-assembly. There are different types of nanosensors in the market and in development for various applications, most notably in defense, environmental, and healthcare industries. These sensors share the same basic workflow: a selective binding of an analyte, signal generation from the interaction of the nanosensor with the bio-element, and processing of the signal into useful metrics.

<span class="mw-page-title-main">Förster resonance energy transfer</span> Photochemical energy transfer mechanism

Förster resonance energy transfer (FRET), fluorescence resonance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through nonradiative dipole–dipole coupling. The efficiency of this energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor, making FRET extremely sensitive to small changes in distance.

<span class="mw-page-title-main">Host–guest chemistry</span> Supramolecular structures held together other than by covalent bonds

In supramolecular chemistry, host–guest chemistry describes complexes that are composed of two or more molecules or ions that are held together in unique structural relationships by forces other than those of full covalent bonds. Host–guest chemistry encompasses the idea of molecular recognition and interactions through non-covalent bonding. Non-covalent bonding is critical in maintaining the 3D structure of large molecules, such as proteins and is involved in many biological processes in which large molecules bind specifically but transiently to one another.

<span class="mw-page-title-main">Molecular machine</span> Molecular-scale artificial or biological device

Molecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes. For the last several decades, scientists have attempted, with varying degrees of success, to miniaturize machines found in the macroscopic world. The first example of an artificial molecular machine (AMM) was reported in 1994, featuring a rotaxane with a ring and two different possible binding sites. In 2016 the Nobel Prize in Chemistry was awarded to Jean-Pierre Sauvage, Sir J. Fraser Stoddart, and Bernard L. Feringa for the design and synthesis of molecular machines.

<span class="mw-page-title-main">Ligand (biochemistry)</span> Substance that forms a complex with a biomolecule

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from Latin ligare, which means 'to bind'. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure.

<span class="mw-page-title-main">Molecular motor</span> Biological molecular machines

Molecular motors are natural (biological) or artificial molecular machines that are the essential agents of movement in living organisms. In general terms, a motor is a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work. In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors. One important difference between molecular motors and macroscopic motors is that molecular motors operate in the thermal bath, an environment in which the fluctuations due to thermal noise are significant.

<span class="mw-page-title-main">Fluorine-18</span> Isotope of fluorine emitting a positron

Fluorine-18 (18F) is a fluorine radioisotope which is an important source of positrons. It has a mass of 18.0009380(6) u and its half-life is 109.771(20) minutes. It decays by positron emission 96.7% of the time and electron capture 3.3% of the time. Both modes of decay yield stable oxygen-18.

<span class="mw-page-title-main">Molecular beacon</span>

Molecular beacons, or molecular beacon probes, are oligonucleotide hybridization probes that can report the presence of specific nucleic acids in homogenous solutions. Molecular beacons are hairpin-shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid sequence. This is a novel non-radioactive method for detecting specific sequences of nucleic acids. They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes.

<span class="mw-page-title-main">Molecular sensor</span>

A molecular sensor or chemosensor is a molecular structure that is used for sensing of an analyte to produce a detectable change or a signal. The action of a chemosensor, relies on an interaction occurring at the molecular level, usually involves the continuous monitoring of the activity of a chemical species in a given matrix such as solution, air, blood, tissue, waste effluents, drinking water, etc. The application of chemosensors is referred to as chemosensing, which is a form of molecular recognition. All chemosensors are designed to contain a signalling moiety and a recognition moiety, that is connected either directly to each other or through a some kind of connector or a spacer. The signalling is often optically based electromagnetic radiation, giving rise to changes in either the ultraviolet and visible absorption or the emission properties of the sensors. Chemosensors may also be electrochemically based. Small molecule sensors are related to chemosensors. These are traditionally, however, considered as being structurally simple molecules and reflect the need to form chelating molecules for complexing ions in analytical chemistry. Chemosensors are synthetic analogues of biosensors, the difference being that biosensors incorporate biological receptors such as antibodies, aptamers or large biopolymers.

<span class="mw-page-title-main">Transition metal dinitrogen complex</span> Coordination compounds with N2

Transition metal dinitrogen complexes are coordination compounds that contain transition metals as ion centers the dinitrogen molecules (N2) as ligands.

<span class="mw-page-title-main">Nucleic acid analogue</span> Compound analogous to naturally occurring RNA and DNA

Nucleic acid analogues are compounds which are analogous to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. An analogue may have any of these altered. Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties of the chain . Nucleic acid analogues are also called xeno nucleic acids and represent one of the main pillars of xenobiology, the design of new-to-nature forms of life based on alternative biochemistries.

<span class="mw-page-title-main">BODIPY</span> Parent chemical compound of the BODYPY fluorescent dyes

BODIPY is the technical common name of a chemical compound with formula C
9H
7BN
2F
2, whose molecule consists of a boron difluoride group BF
2 joined to a dipyrromethene group C
9H
7N
2; specifically, the compound 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene in the IUPAC nomenclature. The common name is an abbreviation for "boron-dipyrromethene". It is a red crystalline solid, stable at ambient temperature, soluble in methanol.

Nanoclusters are atomically precise, crystalline materials most often existing on the 0-2 nanometer scale. They are often considered kinetically stable intermediates that form during the synthesis of comparatively larger materials such as semiconductor and metallic nanocrystals. The majority of research conducted to study nanoclusters has focused on characterizing their crystal structures and understanding their role in the nucleation and growth mechanisms of larger materials.

Lanthanide probes are a non-invasive analytical tool commonly used for biological and chemical applications. Lanthanides are metal ions which have their 4f energy level filled and generally refer to elements cerium to lutetium in the periodic table. The fluorescence of lanthanide salts is weak because the energy absorption of the metallic ion is low; hence chelated complexes of lanthanides are most commonly used. The term chelate derives from the Greek word for “claw,” and is applied to name ligands, which attach to a metal ion with two or more donor atoms through dative bonds. The fluorescence is most intense when the metal ion has the oxidation state of 3+. Not all lanthanide metals can be used and the most common are: Sm(III), Eu(III), Tb(III), and Dy(III).

<span class="mw-page-title-main">Small molecule sensors</span>

Small-molecule sensors are an effective way to detect the presence of metal ions in solution. Although many types exist, most small molecule sensors comprise a subunit that selectively binds to a metal that in turn induces a change in a fluorescent subunit. This change can be observed in the small molecule sensor's spectrum, which can be monitored using a detection system such as a microscope or a photodiode. Different probes exist for a variety of applications, each with different dissociation constants with respect to a particular metal, different fluorescent properties, and sensitivities. They show great promise as a way to probe biological processes by monitoring metal ions at low concentrations in biological systems. Since they are by definition small and often capable of entering biological systems, they are conducive to many applications for which other more traditional bio-sensing are less effective or not suitable.

Excited state intramolecular proton transfer (ESIPT) is a process in which photoexcited molecules relax their energy through tautomerization by transfer of protons. Some kinds of molecules could have different minimum-energy tautomers in different electronic states, and if the molecular structure of minimum-energy tautomer in the excited state is proton-transferred geometry between neighboring atoms, proton transfer in excited state can occur. The tautomerization often takes the form of keto-enol tautomerism.

<span class="mw-page-title-main">Fluorescence imaging</span> Type of non-invasive imaging technique

Fluorescence imaging is a type of non-invasive imaging technique that can help visualize biological processes taking place in a living organism. Images can be produced from a variety of methods including: microscopy, imaging probes, and spectroscopy.

<span class="mw-page-title-main">Anthony Czarnik</span> American biochemist and inventor (born 1957)

Anthony William Czarnik is an American chemist and inventor. He is best known for pioneering studies in the field of fluorescent chemosensors and co-founding Illumina, Inc., a biotechnology company in San Diego. Czarnik was also the founding editor of ACS Combinatorial Science. He currently serves as an adjunct visiting professor at the University of Nevada, Reno.

References

  1. 1 2 Margulies, David; Melman, Galina; Shanzer, Abraham (2006-04-01). "A Molecular Full-Adder and Full-Subtractor, an Additional Step toward a Moleculator". Journal of the American Chemical Society. 128 (14): 4865–4871. doi:10.1021/ja058564w. ISSN   0002-7863. PMID   16594723.
  2. ↑ de Silva, A Prasanna (2012-11-29). Molecular Logic-based Computation. The Royal Society of Chemistry. doi:10.1039/9781849733021. ISBN   978-1-84973-148-5.
  3. ↑ Kompa, K. L.; Levine, R. D. (2001-01-16). "A molecular logic gate". Proceedings of the National Academy of Sciences. 98 (2): 410–414. Bibcode:2001PNAS...98..410K. doi: 10.1073/pnas.98.2.410 . ISSN   0027-8424. PMC   14599 . PMID   11209046.
  4. ↑ He, Xiaojun; Xie, Qi; Fan, Jinyi; Xu, Chuchu; Xu, Wei; Li, Yahui; Ding, Feng; Deng, Hui; Chen, Hong; Shen, Jianliang (2020). "Dual-functional chemosensor with colorimetric/ratiometric response to Cu(II)/Zn(II) ions and its applications in bioimaging and molecular logic gates". Dyes and Pigments. 177: 108255. doi:10.1016/j.dyepig.2020.108255. S2CID   213144762.
  5. ↑ Aviram, Ari. (1988). "Molecules for memory, logic, and amplification". Journal of the American Chemical Society. 110 (17): 5687–5692. doi:10.1021/ja00225a017. ISSN   0002-7863.
  6. 1 2 de Silva, Prasanna A.; Gunaratne, Nimal H. Q.; McCoy, Colin P. (1993). "A molecular photoionic AND gate based on fluorescent signaling". Nature. 364 (6432): 42–44. Bibcode:1993Natur.364...42D. doi:10.1038/364042a0. ISSN   0028-0836. S2CID   38260349.
  7. ↑ Huston, Michael E.; Akkaya, Engin U.; Czarnik, Anthony W. (1989). "Chelation enhanced fluorescence detection of non-metal ions". Journal of the American Chemical Society. 111 (23): 8735–8737. doi:10.1021/ja00205a034. ISSN   0002-7863.
  8. ↑ Hosseini, Mir Wais; Blacker, A. John; Lehn, Jean Marie (1990). "Multiple molecular recognition and catalysis. A multifunctional anion receptor bearing an anion binding site, an intercalating group, and a catalytic site for nucleotide binding and hydrolysis". Journal of the American Chemical Society. 112 (10): 3896–3904. doi:10.1021/ja00166a025. ISSN   0002-7863.
  9. ↑ de Silva, A. Prasanna; Rupasinghe, R. A. D. Dayasiri (1985). "A new class of fluorescent pH indicators based on photo-induced electron transfer". Journal of the Chemical Society, Chemical Communications (23): 1669–1670. doi:10.1039/c39850001669. ISSN   0022-4936.
  10. ↑ de Silva, A. Prasanna; Sandanayake, K. R. A. Samankumara (1989). "Fluorescent PET (photo-induced electron transfer) sensors for alkali metal ions with improved selectivity against protons and with predictable binding constants". Journal of the Chemical Society, Chemical Communications (16): 1183–1185. doi:10.1039/c39890001183. ISSN   0022-4936.
  11. ↑ Magri, David C.; de Silva, A. Prasanna (2010). "From PASS 1 to YES to AND logic: building parallel processing into molecular logic gates by sequential addition of receptors". New Journal of Chemistry. 34 (3): 476. doi:10.1039/b9nj00564a. ISSN   1144-0546.
  12. ↑ Magri, David C. (2009). "A fluorescent AND logic gate driven by electrons and protons". New J. Chem. 33 (3): 457–461. doi:10.1039/B820313J. ISSN   1144-0546.
  13. ↑ Gunnlaugsson, Thorfinnur; Mac Dónail, Dónall A.; Parker, David (2000). "Luminescent molecular logic gates: the two-input inhibit (INH) function". Chemical Communications (1): 93–94. doi:10.1039/a908951i. ISSN   1359-7345.
  14. ↑ Parker, David (1998). "Taking advantage of the pH and pO2 sensitivity of a luminescent macrocyclic terbium phenanthridyl complex". Chemical Communications (2): 245–246. doi:10.1039/a707754h.
  15. ↑ Turfan, Bilge; Akkaya, Engin U. (2002-08-01). "Modulation of Boradiazaindacene Emission by Cation-Mediated Oxidative PET". Organic Letters. 4 (17): 2857–2859. doi:10.1021/ol026245t. ISSN   1523-7060. PMID   12182573.
  16. 1 2 3 Prasanna de Silva, A.; McClenaghan, Nathan D. (2000-04-01). "Proof-of-Principle of Molecular-Scale Arithmetic". Journal of the American Chemical Society. 122 (16): 3965–3966. doi:10.1021/ja994080m. ISSN   0002-7863.
  17. ↑ Credi, Alberto; Balzani, Vincenzo; Langford, Steven J.; Stoddart, J. Fraser (1997-03-01). "Logic Operations at the Molecular Level. An XOR Gate Based on a Molecular Machine". Journal of the American Chemical Society. 119 (11): 2679–2681. doi:10.1021/ja963572l. ISSN   0002-7863.
  18. ↑ Magri, David C.; Brown, Gareth J.; McClean, Gareth D.; de Silva, A. Prasanna (2006-04-01). "Communicating Chemical Congregation: A Molecular AND Logic Gate with Three Chemical Inputs as a "Lab-on-a-Molecule" Prototype". Journal of the American Chemical Society. 128 (15): 4950–4951. doi:10.1021/ja058295+. ISSN   0002-7863. PMID   16608318.
  19. ↑ Coskun, Ali; Deniz, Erhan; Akkaya, Engin U. (2005-10-18). "Effective PET and ICT Switching of Boradiazaindacene Emission: A Unimolecular, Emission-Mode, Molecular Half-Subtractor with Reconfigurable Logic Gates". Organic Letters. 7 (23): 5187–5189. doi:10.1021/ol052020h. ISSN   1523-7060. PMID   16268534.
  20. ↑ de Silva, A. Prasanna; Uchiyama, Seiichi (2007). "Molecular logic and computing". Nature Nanotechnology. 2 (7): 399–410. Bibcode:2007NatNa...2..399D. doi:10.1038/nnano.2007.188. ISSN   1748-3387. PMID   18654323.
  21. ↑ Andréasson, Joakim; Pischel, Uwe (2015). "Molecules with a sense of logic: a progress report". Chemical Society Reviews. 44 (5): 1053–1069. doi:10.1039/C4CS00342J. ISSN   0306-0012. PMID   25520053.
  22. ↑ Erbas-Cakmak, Sundus; Kolemen, Safacan; Sedgwick, Adam C.; Gunnlaugsson, Thorfinnur; James, Tony D.; Yoon, Juyoung; Akkaya, Engin U. (2018). "Molecular logic gates: the past, present and future". Chemical Society Reviews. 47 (7): 2228–2248. doi:10.1039/C7CS00491E. ISSN   0306-0012. PMID   29493684.
  23. ↑ Andréasson, Joakim; Pischel, Uwe (2010). "Smart molecules at work—mimicking advanced logic operations". Chem. Soc. Rev. 39 (1): 174–188. doi:10.1039/B820280J. ISSN   0306-0012. PMID   20023848.
  24. 1 2 Liu, Lijun; Liu, Pingping; Ga, Lu; Ai, Jun (2021-11-16). "Advances in Applications of Molecular Logic Gates". ACS Omega. 6 (45): 30189–30204. doi:10.1021/acsomega.1c02912. ISSN   2470-1343. PMC   8600522 . PMID   34805654.
  25. ↑ Bhat, Mahesh P.; Vinayak, Shraddha; Yu, Jingxian; Jung, Ho-Young; Kurkuri, Mahaveer (2020-11-13). "Colorimetric Receptors for the Detection of Biologically Important Anions and Their Application in Designing Molecular Logic Gate". ChemistrySelect. 5 (42): 13135–13143. doi:10.1002/slct.202003147. ISSN   2365-6549. S2CID   228845587.
  26. ↑ Wen, Xiaoye; Yan, Li; Fan, Zhefeng (2021). "Multi-responsive fluorescent probe based on AIE for the determination of Fe3+, total inorganic iron, and CN- in aqueous medium and its application in logic gates". Journal of Photochemistry and Photobiology A: Chemistry. 405: 112969. doi:10.1016/j.jphotochem.2020.112969. S2CID   225121769.
  27. 1 2 "Versatile Sensing Platform for Cd2+ Detection in Rice Samples and Its Applications in Logic Gate Computation". doi:10.1021/acs.analchem.0c01022.s001 . Retrieved 2023-02-15.{{cite journal}}: Cite journal requires |journal= (help)
  28. ↑ Zou, Qiang; Li, Xin; Xue, Tao; Zheng, Jia; Su, Qi (2019). "SERS detection of mercury (II)/lead (II): A new class of DNA logic gates". Talanta. 195: 497–505. doi:10.1016/j.talanta.2018.11.089. PMID   30625575. S2CID   58583843.
  29. ↑ Wang, Luhui; Zhang, Yingying; Dong, Yafei (2018-09-29). "A Multifunctional Molecular Probe for Detecting Hg2+ and Ag+ Based on Ion-Mediated Base Mismatch". Sensors. 18 (10): 3280. Bibcode:2018Senso..18.3280W. doi: 10.3390/s18103280 . ISSN   1424-8220. PMC   6211076 . PMID   30274296.
  30. ↑ "How cancer cells learn to resist chemotherapy". Nature. 579 (7799): 323. 2020-03-13. Bibcode:2020Natur.579R.323.. doi:10.1038/d41586-020-00722-0. ISSN   0028-0836. S2CID   212742239.
  31. ↑ Yue, Renye; Chen, Mi; Ma, Nan (2020-07-22). "Dual MicroRNA-Triggered Drug Release System for Combined Chemotherapy and Gene Therapy with Logic Operation". ACS Applied Materials & Interfaces. 12 (29): 32493–32502. doi:10.1021/acsami.0c09494. ISSN   1944-8244. PMID   32573191. S2CID   219982593.
  32. ↑ Zhang, Siqi; Cheng, Jiaxi; Shi, Wei; Li, Kai-Bin; Han, De-Man; Xu, Jing-Juan (2020-04-21). "Fabrication of a Biomimetic Nanochannel Logic Platform and Its Applications in the Intelligent Detection of miRNA Related to Liver Cancer". Analytical Chemistry. 92 (8): 5952–5959. doi:10.1021/acs.analchem.0c00147. ISSN   0003-2700. PMID   32207618. S2CID   214628829.
  33. ↑ Yue, Renye; Li, Zhi; Wang, Ganglin; Li, Junying; Ma, Nan (2019-01-25). "Logic Sensing of MicroRNA in Living Cells Using DNA-Programmed Nanoparticle Network with High Signal Gain". ACS Sensors. 4 (1): 250–256. doi:10.1021/acssensors.8b01422. ISSN   2379-3694. PMID   30520293. S2CID   54486452.
  34. ↑ Peng, Ying; Zhou, Wenjiao; Yuan, Ruo; Xiang, Yun (2018). "Dual-input molecular logic circuits for sensitive and simultaneous sensing of multiple microRNAs from tumor cells". Sensors and Actuators B: Chemical. 264: 202–207. Bibcode:2018SeAcB.264..202P. doi:10.1016/j.snb.2018.02.043. S2CID   103487434.
  35. ↑ Ozlem, Suriye; Akkaya, Engin U. (2009-01-14). "Thinking Outside the Silicon Box: Molecular AND Logic As an Additional Layer of Selectivity in Singlet Oxygen Generation for Photodynamic Therapy". Journal of the American Chemical Society. 131 (1): 48–49. doi:10.1021/ja808389t. hdl:11693/22855. ISSN   0002-7863. PMID   19086786. S2CID   207134456.
  36. ↑ Church, George M.; Gao, Yuan; Kosuri, Sriram (2012-09-28). "Next-Generation Digital Information Storage in DNA". Science. 337 (6102): 1628. Bibcode:2012Sci...337.1628C. doi:10.1126/science.1226355. ISSN   0036-8075. PMID   22903519. S2CID   934617.
  37. ↑ Adleman, Leonard M. (1994-11-11). "Molecular Computation of Solutions to Combinatorial Problems". Science. 266 (5187): 1021–1024. Bibcode:1994Sci...266.1021A. doi:10.1126/science.7973651. ISSN   0036-8075. PMID   7973651.
  38. ↑ Okamoto, Akimitsu; Tanaka, Kazuo; Saito, Isao (2004-08-01). "DNA Logic Gates". Journal of the American Chemical Society. 126 (30): 9458–9463. doi:10.1021/ja047628k. ISSN   0002-7863. PMID   15281839.
  39. ↑ Massey, Melissa; Medintz, Igor L.; Ancona, Mario G.; Algar, W. Russ (2017-08-08). "Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR". ACS Sensors. 2 (8): 1205–1214. doi:10.1021/acssensors.7b00355. ISSN   2379-3694. PMID   28787151.
  40. ↑ Campbell, Eleanor A.; Peterson, Evan; Kolpashchikov, Dmitry M. (2017-03-24). "Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles". ChemPhysChem. 18 (13): 1730–1734. doi:10.1002/cphc.201700109. ISSN   1439-4235. PMID   28234410.
  41. ↑ Bader, Antoine; Cockroft, Scott L. (2018-03-07). "Simultaneous G-Quadruplex DNA Logic". Chemistry - A European Journal. 24 (19): 4820–4824. doi:10.1002/chem.201800756. ISSN   0947-6539. PMID   29446498.
  42. ↑ Chatterjee, Gourab; Dalchau, Neil; Muscat, Richard A.; Phillips, Andrew; Seelig, Georg (2017-07-24). "A spatially localized architecture for fast and modular DNA computing". Nature Nanotechnology. 12 (9): 920–927. Bibcode:2017NatNa..12..920C. doi:10.1038/nnano.2017.127. ISSN   1748-3387. PMID   28737747.
  43. ↑ Tregubov, Andrey A.; Nikitin, Petr I.; Nikitin, Maxim P. (2018-10-24). "Advanced Smart Nanomaterials with Integrated Logic-Gating and Biocomputing: Dawn of Theranostic Nanorobots". Chemical Reviews. 118 (20): 10294–10348. doi:10.1021/acs.chemrev.8b00198. ISSN   0009-2665. PMID   30234291. S2CID   206542327.
  44. ↑ Llopis-Lorente, Antoni; de Luis, Beatriz; García-Fernández, Alba; Jimenez-Falcao, Sandra; Orzáez, Mar; Sancenón, Félix; Villalonga, Reynaldo; Martínez-Máñez, Ramón (2018-08-08). "Hybrid Mesoporous Nanocarriers Act by Processing Logic Tasks: Toward the Design of Nanobots Capable of Reading Information from the Environment". ACS Applied Materials & Interfaces. 10 (31): 26494–26500. doi:10.1021/acsami.8b05920. hdl:10251/143326. ISSN   1944-8244. PMID   30016064. S2CID   206485516.
  45. ↑ Thubagere, Anupama J.; Li, Wei; Johnson, Robert F.; Chen, Zibo; Doroudi, Shayan; Lee, Yae Lim; Izatt, Gregory; Wittman, Sarah; Srinivas, Niranjan; Woods, Damien; Winfree, Erik; Qian, Lulu (2017-09-15). "A cargo-sorting DNA robot". Science. 357 (6356): eaan6558. doi:10.1126/science.aan6558. ISSN   0036-8075. PMID   28912216. S2CID   20233341.
  46. ↑ Margulies, David; Felder, Clifford E.; Melman, Galina; Shanzer, Abraham (2007-01-01). "A Molecular Keypad Lock: A Photochemical Device Capable of Authorizing Password Entries". Journal of the American Chemical Society. 129 (2): 347–354. doi:10.1021/ja065317z. ISSN   0002-7863. PMID   17212414.
  47. ↑ Derycke, V.; Martel, R.; Appenzeller, J.; Avouris, Ph. (2001-09-01). "Carbon Nanotube Inter- and Intramolecular Logic Gates". Nano Letters. 1 (9): 453–456. Bibcode:2001NanoL...1..453D. doi:10.1021/nl015606f. ISSN   1530-6984.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.