Molecular Implementation of Sequential and Reversible Logic Through Photochromic Energy Transfer Switching

Designing Unconventional Molecular Ternary INHIBIT Logic Gate and Crafting Multifunctional Molecular Logic Systems

The paper describes an improved method for building flexible interswitchable logic gates such as rare-type molecular ternary INHIBIT and combinational logic circuits using a specially designed pyridine-end oligo-p-phenylenevinylene compound featuring alkyl substituents (-C16H33) in a THF medium. The probe molecule showed distinct opto-chemical signals upon interaction with Cu(II) and Hg(II) in THF medium. It is interesting to note that the presence of certain anions (S2-, I-, and CN-) could specifically mask the interaction of either of these metal ions or both. The most exciting thing is that we used a completely new gate design technique to construct a rare-type ternary INHIBIT logic gate using Cu(II), Hg(II), and CN- ions as three chemical inputs. With the identical set of chemical inputs, two more ternary combinational logic circuits were created out of these case-specific, independent reversible and irreversible spectroscopic studies. Finally, we were able to design adaptive molecular logic systems composed of several logic gates, including NOR, AND, IMPLICATION, INHIBIT, TRANSFER, and COMPLEMENT, that in this specific situation change the sort of logic sense by effortless optical toggling.

A Modern Look at Spiropyrans: From Single Molecules to Smart Materials

Photochromic compounds of the spiropyran family have two main isomers capable of inter-switching with UV or visible light. In the current review, we discuss recent advances in the synthesis, investigation of properties, and applications of spiropyran derivatives. Spiropyrans of the indoline series are in focus as the most promising representatives of multi-sensitive spirocyclic compounds, which can be switched by a number of external stimuli, including light, temperature, pH, presence of metal ions, and mechanical stress. Particular attention is paid to the structural features of molecules, their influence on photochromic properties, and the reactions taking place during isomerization, as the understanding of the structure-property relationships will rationalize the synthesis of compounds with predetermined characteristics. The main prospects for applications of spiropyrans in such fields as smart material production, molecular electronics and nanomachinery, sensing of environmental and biological molecules, and photopharmacology are also discussed.

Molecules for security measures: from keypad locks to advanced communication protocols

The idea of using molecules in the context of information security has sparked the interest of researchers from many scientific disciplines. This is clearly manifested in the diversity of the molecular platforms and the analytical techniques used for this purpose, some of which we highlight in this Tutorial Review. Moreover, those molecular systems can be used to emulate a broad spectrum of security measures. For a long time, molecular keypad locks enjoyed a clear preference and the review starts off with a description of how these devices developed. In the last few years, however, the field has evolved into something larger. Examples include more complex authentication protocols (multi-factor authentication and one-time passwords), the recognition of erroneous procedures in data transmission (parity devices), as well as steganographic and cryptographic protection.

Spironaphthoxazine switchable dyes for biological imaging

Recent developments in super-resolution microscopy have significantly expanded the requirements for switchable dyes, leading to demand for specially designed molecular switches. We report the synthesis and characterization of a spironaphthoxazine photochromic switch (a derivative of palatinate purple) displaying high photoconversion (85-95%) under readily accessible 405 nm light, broad absorption in the visible, and excellent fatigue resistance. The indole substituent on this spironaphthoxazine is twisted out of conjugation with the naphthalene unit, yet it is crucial for activation with visible light. The open colored merocyanine form of the spironaphthoxazine reverts to the closed form with a lifetime of 4.7 s in dichloromethane at 20 °C; this thermal reversion is even faster in more polar solvents. The photochemical quantum yields for ring-opening and ring-closing are approximately 8% and 1%, respectively, in dichloromethane. The ring-opening and ring-closing reactions have been characterized by time-resolved infrared and transient absorption spectroscopies. Ring opening occurs rapidly (τ = 2.1 ns) and efficiently (∼90%) from the singlet excited state to form an intermediate (assigned as a cisoid merocyanine), which returns to the closed ground state (τ = 4.5 ns) in competition with relaxation to the transoid open form (τ = 40 ns). Photochemical ring closing is a faster and simpler process: the excited state proceeds to the closed spirooxazine with a time constant of 0.28 ns. This photochromic switch can be used in conjunction with commercial fluorescent dyes to create a small-molecule switchable fluorescent dyad that shows high contrast and good fatigue resistance in living cells. These properties make the dyads suitable for application in RESOLFT microscopy.

Novel fluorescent anthracene–bodipy dyads displaying sensitivity to pH and turn-on behaviour towards Cu(ii) ions

The effect of the nature of the spacer in three new bichromophoric compounds showing intramolecular PET and EET processes has been studied.

A Chiroptical Logic Circuit Based on Self-Assembled Soft Materials Containing Amphiphilic Spiropyran

A chiral logic circuit is proposed based on the multiple chiroptical responsiveness of a supramolecular gel material. The gel is fabricated by mixing a chiral gelator and a spiropyran derivative. Chiral responsiveness including the chiral switch and the logic gate is realized through the combined chirality transfer, photochromism, and acidichromism of the system.

Monomolecular pyrenol-derivatives as multi-emissive probes for orthogonal reactivities

Chameleons in a test tube: up to four easily distinguishable emission colors result from conversion by two hydrolytic enzymes at opposite reaction sites.

A photoswitchable diarylethene heterodimer for use as a multifunctional logic gate

A photoswitchable diarylethene heterodimer was prepared and its applications to logic gates were successfully demonstrated.

An enzyme-based reversible CNOT logic gate realized in a flow system

An enzyme system organized in a flow device was used to mimic a reversible Controlled NOT (CNOT) gate with two input and two output signals. Reversible conversion of NAD(+) and NADH cofactors was used to perform a XOR logic operation, while biocatalytic hydrolysis of p-nitrophenyl phosphate resulted in an Identity operation working in parallel. The first biomolecular realization of a CNOT gate is promising for integration into complex biomolecular networks and future biosensor/biomedical applications.

Enzyme-based logic gates switchable between OR, NXOR and NAND Boolean operations realized in a flow system

The enzyme-based system performing a biocatalytic cascade reaction was realized in a flow device and was used to mimic Boolean logic operations. Chemical inputs applied to the system resulted in the activation of additional reaction steps, allowing the reversible switch of the logic operations between OR, NXOR and NAND gates for processing of two other biomolecular inputs.

Biomolecular Computing Realized in Parallel Flow Systems: Enzyme-Based Double Feynman Logic Gate

An enzyme system organized in a flow device with three parallel channels was used to mimic a reversible Double Feynman Gate (DFG) with three input and three output signals. Reversible conversion of NAD+ and NADH cofactors was used to perform XOR logic operations, while biocatalytic oxidation of NADH resulted in Identity operation working in parallel. The first biomolecular realization of a DFG gate is promising for integrating into complex biomolecular networks operating in future unconventional biocomputing systems, as well as for novel biosensor applications.

Joint spectroscopic and theoretical investigation of cationic cyanine dye Astrazon Orange-R: solvent viscosity controlled relaxation of excited states

In this paper, the first study of cationic cyanine dye Astrazon Orange-R by combined spectroscopic and theoretical investigation is presented.

Molecules with a sense of logic: a progress report

Ones and zeros can be handled by molecules through the input-control of their signaling features. The progress in this exciting field during the last five years is covered in this tutorial review.

Inorganic-organic hybrid nanoprobe for NIR-excited imaging of hydrogen sulfide in cell cultures and inflammation in a mouse model

Hydrogen sulfide (H2S) is an important gaseous signaling agent mediated by many physiological processes and diseases. In order to explore its role in biological signaling, much effort has been focused on developing organic fluorescent probes to image H2S. However, these downconversion H2S probes are impractical for bio-imaging beyond a certain depth because of the short tissue penetration of UV/visible light (as an excitation source). In most circumstance, these probes are also not suitable for long-term assay due to photo-bleaching. Herein, a new design to detect H2S based on the coumarin-hemicyanine (CHC1)-modified upconversion nanophosphors is reported. This inorganic-organic integrated nanoprobe is demonstrated to display a fast response time with a large ratiometric upconversion luminescence (UCL) enhancement, and extraordinary photo-stability. CHC1-UCNPs not only can be used for ratiometric UCL monitoring of pseudo-enzymatic H2S production in living cells, but can also be used to identify the risk of endotoxic shock through ratiometric UCL imaging of tissue and measurement of endogenous H2S levels in plasma. The first ratiometric UCL H2S nanoprobe reported here may be further developed as the next-generation diagnostic tool for the detection of inflammatory-related diseases.

Modulating short wavelength fluorescence with long wavelength light

Two molecules in which the intensity of shorter-wavelength fluorescence from a strong fluorophore is modulated by longer-wavelength irradiation of an attached merocyanine-spirooxazine reverse photochromic moiety have been synthesized and studied. This unusual fluorescence behavior is the result of quenching of fluorophore fluorescence by the thermally stable, open, zwitterionic form of the spirooxazine, whereas the photogenerated closed, spirocyclic form has no effect on the fluorophore excited state. The population ratio of the closed and open forms of the spirooxazine is controlled by the intensity of the longer-wavelength modulated light. Both square wave and sine wave modulation were investigated. Because the merocyanine-spirooxazine is an unusual reverse photochrome with a thermally stable long-wavelength absorbing form and a short-wavelength absorbing photogenerated isomer with a very short lifetime, this phenomenon does not require irradiation of the molecules with potentially damaging ultraviolet light, and rapid modulation of fluorescence is possible. Molecules demonstrating these properties may be useful in fluorescent probes, as their use can discriminate between probe fluorescence and various types of adventitious "autofluorescence" from other molecules in the system being studied.

Characterization of the thermal and photoinduced reactions of photochromic spiropyrans in aqueous solution

Six water-soluble spiropyran derivatives have been characterized with respect to the thermal and photoinduced reactions over a broad pH-interval. A comprehensive kinetic model was formulated including the spiro- and the merocyanine isomers, the respective protonated forms, and the hydrolysis products. The experimental studies on the hydrolysis reaction mechanism were supplemented by calculations using quantum mechanical (QM) models employing density functional theory. The results show that (1) the substitution pattern dramatically influences the pKa-values of the protonated forms as well as the rates of the thermal isomerization reactions, (2) water is the nucleophile in the hydrolysis reaction around neutral pH, (3) the phenolate oxygen of the merocyanine form plays a key role in the hydrolysis reaction. Hence, the nonprotonated merocyanine isomer is susceptible to hydrolysis, whereas the corresponding protonated form is stable toward hydrolytic degradation.

An all-photonic molecule-based parity generator/checker for error detection in data transmission

The function of a parity generator/checker, which is an essential operation for detecting errors in data transmission, has been realized with multiphotochromic switches by taking advantage of a neuron-like fluorescence response and reversible light-induced transformations between the implicated isomers.

A multiaddressable photochromic bisthienylethene with sequence-dependent responses: construction of an INHIBIT logic gate and a keypad lock

A photochromic bisthienylethene derivative (BIT) containing two imidazole units has been synthesized and fully characterized. When triggered by chemical ions (Ag(+)), protons, and light, BIT can behave as an absorbance switch, leading to a multiaddressable system. BIT exhibits sequence-dependent responses via efficient interaction of the specific imidazole unit with protons and Ag(+). Furthermore, an INHIBIT logic gate and a keypad lock with three inputs are constructed with the unimolecular platform by employing an absorption mode at different wavelengths as outputs on the basis of an appropriate combination of chemical and photonic stimuli.

Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates

The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a construction of the logically reversible Toffoli and Fredkin gates by implementing a library of predesigned Mg(2+)-dependent DNAzymes and their respective substrates. Although the logical reversibility, for which each set of inputs uniquely correlates to a set of outputs, is demonstrated, the systems manifest thermodynamic irreversibility originating from two quite distinct and nonrelated phenomena. (i) The physical readout of the gates is by fluorescence that depletes the population of the final state of the machine. This irreversible, heat-releasing process is needed for the generation of the output. (ii) The DNAzyme-powered logic gates are made to operate at a finite rate by invoking downhill energy-releasing processes. Even though the three bits of Toffoli's and Fredkin's logically reversible gates manifest thermodynamic irreversibility, we suggest that these gates could have important practical implication in future nanomedicine.

Design of a universal reversible bidirectional current switch based on the fullerene-phthalocyanine supramolecular system

A novel bidirectional current ON-OFF switch controlled by electron injection and deprivation was proposed on the basis of the density functional theory (DFT) calculation over a fullerene-phthalocyanine supramolecular system PcCoC(60) for the first time. The electron density for PcCoC(60) was revealed to move from fullerene to phthlocyanine only in the oxidized form and from phthlocyanine to fullerene only in the reduced form, reaching the control of electron movement direction by changing the oxidation state of this supramolecular system.

An all-photonic molecule-based D flip-flop

The photochromic fluorescence switching of a fulgimide derivative was used to implement the first molecule-based D (delay) flip-flop device, which works based on the principles of sequential logic. The device operates exclusively with photonic signals and can be conveniently switched in repeated cycles.

Synthesis and photochromism of naphthopyrans bearing naphthalimide chromophore: predominant thermal reversibility in color-fading and fluorescence switch

Two novel photochromic naphthopyrans containing naphthalimide moieties (Nip1 and Nip2) were studied in solution under flash photolysis conditions, exhibiting highly photochromic response, rapid thermal bleaching rate and good fatigue-resistance. Owing to the different N-substituted imide groups at the naphthalimide units, the thermal bleaching rate of Nip2 bearing phenyl on the naphthalimide unit is found to be approximately 2 times that of Nip1 bearing n-butyl, indicating that the photochromic properties can be modulated with introduction of different functional groups on the naphthalimide unit. In Nip1 and Nip2, the strong electron-withdrawing effect of the imide group incorporated at the naphthalimide moiety maintains several merits: (i) shifting absorption bands to longer wavelength, (ii) beneficial to an enhancement in the ratio of transoid-cis (TC) isomer and an increase in the transformation rate from transoid-trans (TT) to TC with respect to reference compound NP, and (iii) resulting in a preferable color bleaching rate and fading absolutely to their colorless state with thermal reversibility. As demonstrated in the system of NP, the slow transformation process from TT to TC might be the predominant dynamic step in thermal back process, leading to the residual color of NP being only faded to its original colorless state by visible light irradiation. The optical densities of colored forms for Nip1 and Nip2 are dependent upon the intensity of incident light, ensuring a possible application in the manufacture of ophthalmic lenses and smart windows. Moreover, the fluorescence of Nip1 and Nip2 can be switched on and off by photoinduced conversion between the closed and open forms.

OFF-ON-OFF fluorescence switch with T-latch function

A novel molecular system with characteristics of an OFF-ON-OFF fluorescence switch was designed to integrate the function of a T-latch. In detail, a receptor(1)-fluorophore-receptor(2) architecture was adopted to achieve fluorescence switching upon addition of protons.