Molecular logic circuits

Programmable Biomolecule-Mediated Processors

Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle computational problems. It is of great significance to investigate the various issues of programmable biomolecule-mediated processors that are capable of automatically processing, storing, and displaying information. This Perspective provides several conceptual designs of programmable biomolecule-mediated processors and provides some insights into potential future research directions for programmable biomolecule-mediated processors.

A Tutorial Review on the Fluorescent Probes as a Molecular Logic Circuit-Digital Comparator

The rapid progress in the field of fluorescent probes and fluorescent sensing material extended this research area toward more complex molecular logic gates capable of carrying out a variety of sensing functions simultaneously. These molecules are able to calculate a composite result in which the analysis is not performed by a man but by the molecular device itself. Since the first report by de Silva of AND molecular logic gate, all possible logic gates have been achieved at the molecular level, and currently, utilization of more complicated molecular logic circuits is a major task in this field. Comparison between two digits is the simplest logic operation, which could be realized with the simplest logic circuit. That is why the right understanding of the applied principles during the implementation of molecular digital comparators could play a critical role in obtaining logic circuits that are more complicated. Herein, all possible ways for the construction of comparators on the molecular level were discussed, and recent achievements connected with these devices were presented.

A Highly Water-Soluble and Solid State Emissive 1,8-Naphthalimide as a Fluorescent PET Probe for Determination of pHs, Acid/Base Vapors, and Water Content in Organic Solvents

A new highly water-soluble 1,8-naphthalimide fluorophore designed on the “fluorophore-spacer-receptor1-receptor2” model has been synthesized. Due to the unusually high solubility in water, the novel compound proved to be a selective PET-based probe for the determination of pHs in aqueous solutions and rapid detection of water content in organic solvents. Based on the pH dependence of the probe and its high water solubility, the INH logic gate was achieved using NaOH and water as chemical inputs, where NaOH is the disabler and the water is an enabler. In addition, the probe showed effective fluorescence “off-on” reversibility on glass support after exposure to acid and base vapors, which defines it as a promising platform for rapid detection of acid/base vapors in the solid-state, thus extending the molecular sensing concept from solution to the solid support.

Temperature and solvent-dependent photoluminescence quenching in [Ru(bpy)2(bpy-cc-AQ)]2

I have herein investigated the solvent-dependent photoluminescence quenching mechanism of [Ru(bpy)₂(bpy-cc-AQ)]²⁺ using variable temperature emission spectroscopies. The photophysics of this complex are dominated by an excited-state thermal equilibrium between a photoluminescent ³MLCT state and a charge-separated state that lies higher in energy relative to the ³MLCT state in low polarity solvents and approximately isoenergetic in high polarity solvents. Furthermore, an unusual photoluminescence temperature-dependence in high polarity solvents is shown to arise from competition between enthalpic factors favouring the charge-separated state and entropic factors favouring the photoluminescent ³MLCT state, analogous to the molecular light-switch effect of [Ru(bpy)₂(dppz)]²⁺. The solvent-dependent photoluminescence quenching of [Ru(bpy)₂(bpy-cc-AQ)]²⁺ is attributed to two key solvent-dependent factors: (1) the excited-state equilibrium position and (2) the rate of charge-recombination from the charge-separated state.

Molecular switches and dual channel detection of Cd2+ and Fe3+ ions based on a multipodand system

Multipodand conjugates were designed and synthesized and incorporated 5-chloro-8-hydroxyquinoline for efficient performance and fine tuning to behave as molecular switches by the addition of metals ions, protonation, and their combination in CH₃ CN and CH₃ CN-H₂ O. Dipodand 3 and tetrapodand 4 showed a switching 'ON' of fluorescence (λ_em = 435-445) with Zn²⁺ and Cd²⁺ (OR logic) and switching 'OFF' of fluorescence (λ_em = 402) in the presence of Cu²⁺ , Co²⁺ and Ni²⁺ (NOR logic). 4 showed switching 'OFF' of fluorescence at 402 nm at low concentrations of Ag⁺ , Pb²⁺ , Hg²⁺ and Fe³⁺ and, on further accumulation of these metal ions, excimer bands at 432 nm (Ag⁺ ) and 510 nm (Pb²⁺ , Hg²⁺ and Fe³⁺ ) provided the opportunity for 'ON-OFF-ON' switching. In contrast, 3 showed no change with Ag⁺ , while Pb²⁺ caused only 'ON-OFF' switching and Hg²⁺ and Fe³⁺ ions caused similar 'ON-OFF-ON' switching. The H⁺ -induced 'ON-OFF-ON' molecular switch was combined with Cu²⁺ that persuaded NOR logic to mimic inhibit (INH) logic. The compound also exhibited a H⁺ /Cu²⁺ -induced 'OFF-ON-OFF' type of signalling pattern. These proton-induced multiple outputs provide opportunities for YES, NOT logic gates. 3 showed selective 'ON-OFF' behaviour with Fe³⁺ ions and 'OFF-ON' behaviour with Cd²⁺ ions in 20% HEPES buffer-CH₃ CN.

When Molecular Magnetism Meets Supramolecular Chemistry: Multifunctional and Multiresponsive Dicopper(II) Metallacyclophanes as Proof-of-Concept for Single-Molecule Spintronics and Quantum Computing Technologies?

Molecular magnetism has made a long journey, from the fundamental studies on through-ligand electron exchange magnetic interactions in dinuclear metal complexes with extended organic bridges to the more recent exploration of their electron spin transport and quantum coherence properties. Such a field has witnessed a renaissance of dinuclear metallacyclic systems as new experimental and theoretical models for single-molecule spintronics and quantum computing, due to the intercrossing between molecular magnetism and metallosupramolecular chemistry. The present review reports a state-of-the-art overview as well as future perspectives on the use of oxamato-based dicopper(II) metallacyclophanes as promising candidates to make multifunctional and multiresponsive, single-molecule magnetic (nano)devices for the physical implementation of quantum information processing (QIP). They incorporate molecular magnetic couplers, transformers, and wires, controlling and facilitating the spin communication, as well as molecular magnetic rectifiers, transistors, and switches, exhibiting a bistable (ON/OFF) spin behavior under external stimuli (chemical, electronic, or photonic). Special focus is placed on the extensive research work done by Professor Francesc Lloret, an outstanding chemist, excellent teacher, best friend, and colleague, in recognition of his invaluable contributions to molecular magnetism on the occasion of his 65th birthday.

Fluorescence for biological logic gates

Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli-responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.

Multiple logic operations based on chemically triggered upconversion fluorescence switching

The development of upconversion nanoparticles based logic systems, especially integrated logic systems is still a challenge until now. In this work, an upconversion nanocomposite system is developed and studied for the sensing abilities toward hydrion, hydroxyl ions, metal ions and anions (S^2-, I^-) by taking the advantages of turn-on and turn-off upconversion fluorescence switching response. Triggering by different kinds of ions, the upconversion system can act as a fluorescence switch due to the specific recognition abilities of Rhodamine 6G functionalized PEI for specific ions and the energy transfer process from upconversion nanoparticles to recognition molecules. Based on these results, multiple molecular logic gates, including single-input logic operation (YES, NOT), double-inputs logic operation (OR, AND, NOR, INHIBIT) and multiple-input integrative logic operation (INHIBIT+OR) are developed by employing hydrion, hydroxyl ions, metal ions and anions as inputs and the changes in the upconversion fluorescence intensity as output. The multiple logic operations are of great significance for the applications in biomedicine and molecular calculation.

A Personal Journey across Fluorescent Sensing and Logic Associated with Polymers of Various Kinds

Our experiences concerning fluorescent molecular sensing and logic devices and their intersections with polymer science are the foci of this brief review. Proton-, metal ion- and polarity-responsive cases of these devices are placed in polymeric micro- or nano-environments, some of which involve phase separation. This leads to mapping of chemical species on the nanoscale. These devices also take advantage of thermal properties of some polymers in water in order to reincarnate themselves as thermometers. When the phase separation leads to particles, the latter can be labelled with identification tags based on molecular logic. Such particles also give rise to reusable sensors, although molecular-scale resolution is sacrificed in the process. Polymeric nano-environments also help to organize rather complex molecular logic systems from their simple components. Overall, our little experiences suggest that researchers in sensing and logic would benefit if they assimilate polymer concepts.

A Janus-inspired amphichromatic system that kills two birds with one stone for operating a "DNA Janus Logic Pair" (DJLP) library

Although DNA computing has exhibited a magical power across diverse areas, current DNA logic gates with different functions are always separately operated and can only produce hard-to-visualize output. The fussy/obligatory gates' redesign/reconstruction and the non-intuitive output cause the wastage of time and costs, low efficiency and practicality. Herein, inspired by the ancient Roman mythical God Janus, for the first time, we propose the concept of "DNA Janus Logic Pair" (DJLP) to classify the DNA logic gates with contrary functions into "Positive + Negative" gates (DJLP = Pos + Neg). Based on the biocatalytic property of G-quadruplex DNAzyme (G4zyme) and the luminescence quenching ability of oxidized 3,3',5,5'-tetramethylbenzidine (OxTMB) towards the upconversion (UC) particles, we fabricated a universal amphichromatic platform that kills two birds with one stone for operating a versatile DJLP library. Different from the previous DNA logic systems, the "Pos + Neg" gates of each DJLP in this study were concomitantly achieved via the same one-time DNA reaction, which avoided the gates' redesign/reoperation and reduced the operating costs/time of the DNA gates by at least half. Besides, both the amphichromatic outputs (Visual-blue and UC luminescent-green) can be visualized under harmless-NIR, thus bringing greatly enhanced practicality to the method. Moreover, we constructed various concatenated logic circuits via logically modulating the G4zyme's biocatalytic property with glutathione, thus enabling the largely improved computing complexity. Furthermore, taking the circuit "YES-INH-1-2 decoder" as the "computing core", we designed an "antioxidant indicator" with ratiometric logical responses that could recognize the presence of antioxidants smartly (output changed from "10" to "01"), which provided a typical prototype for potential intelligent bio-applications.

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

A Uniform Molecular Low-Density Parity Check Decoder

Error correction codes, such as low-density parity check (LDPC) codes, are required to be larger scale to meet the increasing demands for reliable and massive data transmission. However, the construction of such a large-scale decoder will result in high complexity and hinder its silicon implementation. Thanks to the advantages of natural computing in high parallelism and low power, we propose a method to synthesize a uniform molecular LDPC decoder by implementing the belief-propagation algorithm with chemical reaction networks (CRNs). This method enables us to flexibly design the LDPC decoder with arbitrary code length, code rate, and node degrees. Compared with existing methods, our proposal reduces the number of reactions to update the variable nodes by 42.86% and the check nodes by 47.37%. Numerical results are presented to show the feasibility and validity of our proposal.

A reversible fluoride chemosensor for the development of multi-input molecular logic gates

A reversible chemosensor for the development of a multi-input molecular logic gate was shown.

Nanopore Decoding of Oligonucleotides in DNA Computing

In conventional DNA-computation methods involving logic gate operations, the output molecules are detected and decoded mainly by gel electrophoresis or fluorescence measurements. To employ rapid and label-free decoding, nanopore technology, an emerging methodology for single-molecule detection or DNA sequencing, is proposed as a candidate for electrical and simple decoding of DNA computations. This review describes recent approaches to decoding DNA computation using label-free and electrical nanopore measurements. Several attempts have been successful in DNA decoding with the nanopore either through enzymatic reactions or in water-in-oil droplets. Additionally, DNA computing combined with nanopore decoding has clinical applications, including microRNA detection for early diagnosis of cancers. Because this decoding methodology is still in development and not yet widely accepted, this review aims to inform the scientific community regarding usefulness.

New insights into the photoswitching mechanisms of normal dithienylethenes

The photoswitching and competitive processes of the referent photochromic diarylethene derivative 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (DTE) and a novel bridged analog DTE-m5 have been investigated by state-of-the-art TD-DFT calculations and ultrafast spectroscopy supported by advanced chemometric data treatments. Focusing on DTE, the overall deactivation pathway of both antiparallel (AP) and parallel (P) conformers of the open form (OF) (1 : 1 in solution) has been resolved and rationalized starting from the Franck-Condon (FC) region to the ground state recovery. For the photo-excited P conformer, after ultrafast relaxation (∼200 fs) towards the S₁ relaxed state, an expected ISC occurred (55 ps) to produce a triplet state, ³P, the latter relaxing within 2.5 μs. Concerning the AP conformer, the photocyclization reaction is reported to proceed immediately (100 fs) starting from the FC region while the relaxed singlet state is populated in parallel. For the first time, we discovered that the latter state evolves through an unexpected ISC process (1 ps) giving rise to a second triplet state,³AP. For DTE-m5, by slightly constraining the molecule with the bridge, this triplet becomes reactive and participates in the formation of 10% of closed form (CF) probably through an adiabatic mechanism. Concerning the photoreversion, in accordance with the literature, we report on a two-step process, a 190 fs vibrational relaxation followed by a 6 ps ring-opening reaction. For the overall species at the singlet or triplet manifold, the use of advanced MCR-ALS allows us to obtain specific spectral signatures. This study is therefore a new step within the comprehension of DTE photochemistry.

BINOL-based differential chromo-fluorescent sensor and its application in miniaturized 1-2/4-2 bit encoders and decoders

A BINOL (1,1′-bi-2-naphthol)-based probe 1 with a diamide group has been synthesized and investigated for its photophysical behavior towards various cations and anions.

Berberine as a novel light-up i-motif fluorescence ligand and its application in designing molecular logic systems

Berberine is reported as a light-up fluorescence ligand for i-motif structures, which enables the development of label-free DNA-based logic gates.

Multiple and configurable optical logic systems based on layered double hydroxides and chromophore assemblies

Multiple and configurable fluorescence logic gates were fabricated via self-assembly of layered double hydroxides and various chromophores. These logic gates were operated by observation of different emissions with the same excitation wavelength, which achieve YES, NOT, AND, INH and INHIBIT logic operations, respectively.

Taking baby steps in molecular logic-based computation

Constructs of fluorophores, receptors, spacers, ¹O₂ sensitizers, enzymes and oligonucleotides play their part in advancing the field of molecular logic-based computation.

Molecular computing by PNA:PNA duplex formation

Molecular computing is potentially one of the most powerful tools for the development of massive parallel computing protocols. In the present paper, a first example of the use of PNA:PNA interactions in molecular computing is described. A series of short PNA sequences have been designed with a four base stretch coding for variables and solutions. Hybridization of the components in different combinations was tested both in solution and in a microarray format. A series of PNA representing the solutions were spotted on a microarray surface in order to simulate the hardware. A series of PNA representing the variables, labeled with TAMRA, were used to interrogate the device enabling to solve non-deterministic logic operations. The system was shown to be able to solve a two-variable equation with a high signal to noise ratio. This paper intends to provide a proof of principle that PNA, on account of their stability and specificity of binding, are most suitable for constructing organic-type computers.

Synthesis and antibacterial activities of antibacterial peptides with a spiropyran fluorescence probe

In this report, antibacterial peptides 1-3 were prepared with a spiropyran fluorescence probe. The probe exhibits a change in fluorescence when isomerized from a colorless spiro-form (spiropyran, Sp) to a colored open-form (merocyanine, Mc) under different chemical environments, which can be used to study the mechanism of antimicrobial activity. Peptides 1-3 exhibit a marked decrease in antimicrobial activity with increasing alkyl chain length. This is likely due to the Sp-Mc isomers in different polar environments forming different aggregate sizes in TBS, as demonstrated by time-dependent dynamic light scattering (DLS). Moreover, peptides 1-3 exhibited low cytotoxicity and hemolytic activity. These probe-modified peptides may provide a novel approach to study the effect of structural changes on antibacterial activity, thus facilitating the design of new antimicrobial agents to combat bacterial infection.

INHIBIT logic operations based on light-driven β-cyclodextrin pseudo[1]rotaxane with room temperature phosphorescence addresses

INHIBIT logic gates based on light-driven β-cyclodextrin pseudo[1]rotaxane were fabricated conveniently utilizing reversible ICD and RTP as output addresses respectively.

A switchable peptide sensor for real-time lysosomal tracking

A bis-spiropyran functionalized peptide1, which exhibits good cell-permeability, biocompatibility and low cytotoxicity, has been developed for lysosomal tracking.

Implementing conventional logic unconventionally: photochromic molecular populations as registers and logic gates

In this paper we detail experimental methods to implement registers, logic gates and logic circuits using populations of photochromic molecules exposed to sequences of light pulses. Photochromic molecules are molecules with two or more stable states that can be switched reversibly between states by illuminating with appropriate wavelengths of radiation. Registers are implemented by using the concentration of molecules in each state in a given sample to represent an integer value. The register's value can then be read using the intensity of a fluorescence signal from the sample. Logic gates have been implemented using a register with inputs in the form of light pulses to implement 1-input/1-output and 2-input/1-output logic gates. A proof of concept logic circuit is also demonstrated; coupled with the software workflow describe the transition from a circuit design to the corresponding sequence of light pulses.

Redox control of molecular motion in switchable artificial nanoscale devices

The design, synthesis, and operation of molecular-scale systems that exhibit controllable motions of their component parts is a topic of great interest in nanoscience and a fascinating challenge of nanotechnology. The development of this kind of species constitutes the premise to the construction of molecular machines and motors, which in a not-too-distant future could find applications in fields such as materials science, information technology, energy conversion, diagnostics, and medicine. In the past 25 years the development of supramolecular chemistry has enabled the construction of an interesting variety of artificial molecular machines. These devices operate via electronic and molecular rearrangements and, like the macroscopic counterparts, they need energy to work as well as signals to communicate with the operator. Here we outline the design principles at the basis of redox switching of molecular motion in artificial nanodevices. Redox processes, chemically, electrically, or photochemically induced, can indeed supply the energy to bring about molecular motions. Moreover, in the case of electrically and photochemically induced processes, electrochemical and photochemical techniques can be used to read the state of the system, and thus to control and monitor the operation of the device. Some selected examples are also reported to describe the most representative achievements in this research area.

A photoswitchable bichromophoric oxazine with fast switching speeds and excellent fatigue resistance

In search of strategies to regulate the photochemical and photophysical properties of photochromic oxazines, we designed a multichromophoric compound incorporating 3H-indole, benzooxazine, and 2-(4-dimethylaminophenyl)ethynyl fragments. We synthesized this molecule in two steps in an overall yield of 51%, starting from commercial precursors. The ultraviolet irradiation of this photochrome opens a [1,3]oxazine ring in less than 6 ns to generate a zwitterionic isomer with a quantum yield of 0.10. In particular, the photoinduced ring opening generates a 4-nitrophenolate anion and a 3H-indolium cation. Additionally, this process brings the 2-(4-dimethylaminophenyl)ethynyl appendage into conjugation with the 3H-indolium cation. As a result, two distinct bands for the anionic and cationic fragments of the photogenerated zwitterion appear in the visible region of the absorption spectrum. The photogenerated isomer has a lifetime of 2 µs and switches back to the original form with first-order kinetics. Furthermore, this bichromophoric photochrome tolerates hundreds of switching cycles with no sign of degradation and can be operated within rigid polymer matrices. Thus, this particular structural design can lead to the development of a new family of bichromophoric photochromes and photoresponsive materials with microsecond switching times and excellent fatigue resistances.