Molecular-scale logic gates

Currently available approaches to molecular-scale logic gates are summarized and compared. These include: chemically-controlled fluorescent and transmittance-based switches concerned with small molecules, DNA oligonucleotides with fluorescence readout, oligonucleotide reactions with DNA-based catalysts, chemically-gated photochromics, reversibly denaturable proteins, molecular machines with optical and electronic signals, two-photon fluorophores and multichromophoric transient optical switches. The photochemical principles of electron and energy transfer are involved in several of these approaches. More complex molecular logic systems with reconfigurability and superposability provide contrasts with current semiconductor electronics. Integration of simple logic functions to produce more complex ones is also discussed in terms of recent developments.     

Unprecedented gas-phase chiroselective logic gates

The gas-phase encounters between 2-aminobutane and proton-bound chiral resorcin[4]arene/nucleoside complexes behave in the gas phase as supramolecular "chiroselective logic gates" by releasing the nucleoside depending on the resorcin[4]arene and the 2-aminobutane configurations.     

Molecular photonic logic gates

The possibility of performing logical operations at the molecular level is being actively investigated at present with the aim of developing molecular logic gates, which can be used in information technologies. In this minireview, the design algorithm of molecular logic gates is considered and the requirements on molecular systems for use as logic gates are specified. Examples of molecular logic gates performing different logical operations are given. Attention is focused on all-photonic molecular logic gates, in which light is used as an input signal for transferring the system from one state to another and for reading the output signal by absorption or luminescence. In addition, optoelectronic devices with light as the input signal and electric current as the output signal are briefly discussed.     

DNA logic gates

A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine ((MD)A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an (MD)A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite (MD)A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through (MD)A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple (MD)A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.     

Effective PET and ICT switching of boradiazaindacene emission: a unimolecular, emission-mode, molecular half-subtractor with reconfigurable logic gates

[reaction, structure: see text] We report a unimolecular system functioning as a combinatorial logic circuit for half-subtractor. The emission characteristics can be modulated by chemical inputs, and when followed at two different wavelengths, two functionally integrated logic gates XOR and INHIBIT are obtained. Both logic gates function in the emission mode, and with very large differences in the signal intensity allowing unequivocal assignment of logic-0 and logic-1.     

Synthesis of cyano-bridged magnetic nanoparticles using room-temperature ionic liquids

A principally new exploit of ionic liquids as an alternative reaction medium in the synthesis of cyano-bridged coordination-polymer nanoparticles is reported. Stable colloid solutions containing nanoparticles of cyano-bridged molecule-based magnets, M)[Fe(CN)6]2/[RMIM][BF4] (M2+=Ni, Cu, Co) and Fe4[Fe(CN)6]3/[RMIM][BF4] (R=1-butyl (BMIM), 1-decyl (DMIM)), were prepared in the corresponding 1-R-3-methylimidazolium tetrafluoroborate [RMIM][BF4], which acts as both a stabilising agent and a solvent. By varying the length of the N-alkyl chain on the imidazolium cation of [RMIM]+ and the temperature, the growing process can be controlled to produce nanoparticles of different sizes. By studying the magnetic properties of frozen colloids it is shown that the relaxation of magnetisation is strongly influenced by interparticle interactions, which leads to the appearance of spin-glass-like dynamics in these systems.     

Modular multi-level circuits from immobilized DNA-based logic gates

One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals.     

Deoxyribozyme-based logic gates

We report herein a set of deoxyribozyme-based logic gates capable of generating any Boolean function. We construct basic NOT and AND gates, followed by the more complex XOR gate. These gates were constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxyribozymes. Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in solution. The operation of these gates is conveniently connected to a fluorescent readout.     

DNA-based photonic logic gates: AND,NAND, and INHIBIT

Conventional microprocessors use elementary logic gates to perform complex computational tasks. Mimicking such computational processes using purely molecular systems has been limited in most cases by the lack of design generality or potential addressability of existing molecular logic gates. Herein we report that by employing the universal recognition properties of DNA simple photonic logic gates can be created that are capable of AND, NAND, and INHIBIT logic operations.     

Photonic logic gates based on control of FRET by a solvatochromic perylene bisimide

New perylenebisimide derivatives hydroxyperylenebisimide and naphthoperylenebisimide were obtained and applied to construct a new solvatochromic dyad 9. The solvatochromic behavior of hydroxyperylenebisimide was studied, and the structure of naphthoperylenebisimide was determined by X-ray crystallography. The spectral studies indicated that the hydroxyperylenebisimide and naphthoperylenebisimide units of dyad 9 were strongly coupled in the ground state, and as a result the fluorescence of the naphthoperylenebisimide unit was almost quenched and that of the hydroxyperylenebisimide unit was greatly enhanced due to the fluorescence resonance energy transfer (FRET). As we expected, this FRET process could be tuned with the addition of protons, base, and ferric ions. This behavior of dyad 9 could be interpreted by a two-input INH logic gate, while in the presence of Fe(III), the ion complex of 9 could execute a two-input XOR logic gate. By changing the output signal, a combinational logic circuit with three inputs could also be interpreted.     

Quantum design rules for single molecule logic gates

Recent publications have demonstrated how to implement a NOR logic gate with a single molecule using its interaction with two surface atoms as logical inputs [W. Soe et al., ACS Nano, 2011, 5, 1436]. We demonstrate here how this NOR logic gate belongs to the general family of quantum logic gates where the Boolean truth table results from a full control of the quantum trajectory of the electron transfer process through the molecule by very local and classical inputs practiced on the molecule. A new molecule OR gate is proposed for the logical inputs to be also single metal atoms, one per logical input.     

Deoxyribozyme-based ligase logic gates and their initial circuits

A complete set (YES, NOT, AND, and ANDNOT) of molecular scale logic gates based on ligase deoxyribozymes was constructed. The activity of these gates was visualized through the formation of cascades with downstream phosphodieseterase YES gates, which performed fluorogenic cleavage.     

AND molecular logic gates based on host-guest complexation operational in live cells

We report supramolecular AND logic gates based on host-guest complexation between acid-labile acyclic cucurbit[n]uril(CB[n]) molecular container and Na Cl O-responsive dye. Supramolecular AND logic gate is turned on due to acid-triggered degradation of molecular container and the release of the dye, followed by Na Cl O-induced fluorescence “switch on” effect of the dye. The reason for AND molecular logic gate is discovered to be the combination of oxidation inhibition and fluorescence “switch of...     

Photonic Boolean logic gates based on DNA aptamers

We designed a pair of DNA-based logic gates that sense single-stranded DNAs and aptamer ligands to produce fluorescence outputs according to Boolean logic functions AND and OR.     

Switchable electrode controlled by Boolean logic gates using enzymes as input signals

Application of Boolean logic operations performed by enzymes to control electrochemical systems is presented. Indium–tin oxide (ITO) electrodes with the surface modified with poly-4-vinyl pyridine (P4VP) brush were synthesized and used as switchable electrochemical systems. The switch ON and OFF of the electrode activity were achieved by pH changes generated in situ by biocatalytic reactions in the presence of enzymes used as input signals. Two logic gates operating as AND/OR Boolean functions were designed using invertase and glucose oxidase or esterase and glucose oxidase as input signals, respectively. The electrode surface coated with a shrunk P4VP polymer at neutral pH values was not electrochemically active because of the blocking effect of the polymer film. The positive outputs of the logic operations yielded a pH drop to acidic conditions, resulting in the protonation and swelling of the P4VP polymer allowing penetration of a soluble redox probe to the conducting support, thus switching the electrode activity ON. The electrode interface was reset to the initial OFF state, with the inhibited electrochemical reaction, upon in situ pH increase generated by another enzymatic reaction in the presence of urease. Logically processed biochemical inputs of various enzymes allowed reversible activation–inactivation of the electrochemical reaction.     

Modulation of boradiazaindacene emission by cation-mediated oxidative PET

[reaction: see text] Bright green boradiazaindacene fluorescence is quenched by an oxidative photoinduced electron transfer (PET) from the excited state fluorophore to the bipyridyl unit complexed to metal cations. The closed shell diamagnetic cation Zn(II) is one of the most effective quenchers of fluorescence in this system, demonstrating that the quenching is not simply related to the facilitated intersystem crossing. The molecule also acts as a NOR logic gate with two chemical inputs, TFA and Zn(II).     

Chemical approaches to molecular logic elements for addition and subtraction

Molecular and supramolecular logic gates are candidates for computation at the nanoscale level. Nowadays all common logic operations can be mimicked with molecular devices based on chemical approaches. One step further towards molecular systems with increased logic capabilities is the addition or subtraction of binary digits. This Minireview describes recent developments to attain this goal, including bioinspired systems based on DNA and enzymes. Furthermore, chemical molecular logic gates are discussed and compared critically with regard to alternative concepts.     

Redox chemistry of [Fe2(CN)10]4−. Part 5. Reaction with thiourea

The reaction of the dimeric iron(III) complex [Fe2(CN)10]4– with a large excess of thiourea, tu, takes place in a series of stages, the first two of which have been examined in detail. The first stage is a one equivalent outer sphere electron transfer to form [Fe2– (CN)10]5– and the radical cation tu+· which dimerises to form the disulfide tu22+. There is kinetic evidence for the formation of a significant proportion of a precursor complex [Fe2(CN)10]4–·tu at high concentrations of tu. The second stage involves cleavage of the mixed valence dimer to yield [Fe(CN)5tu]2– and [Fe(CN)5H2O]3–. On standing, substitution of H2O by tu and oxidation by air occurs slowly, and finally all of the original iron is observed as [Fe(CN)5tu]2–.     

Dicyanomethylene-4H-pyran chromophores for OLED emitters, logic gates and optical chemosensors

Dicyanomethylene-4H-pyran (DCM) chromophores are typical donor-π-acceptor (D-π-A) type chromophores with a broad absorption band resulting from an ultra-fast internal charge-transfer (ICT) process. In 1989, Tang et al. firstly introduced a DCM derivative as a highly fluorescent dopant in organic electroluminescent diodes (OLEDs). Integration of ICT chromophore-receptor systems based on DCM chromophores with ion-induced shifts in absorption or emission is a convenient method to perform the logic expression for molecular logic gates. In recent years, various DCM-type derivatives have been explored due to their excellent optical-electronic properties and diverse structural modification. This feature article provides an insight into how the structural modification of DCM chromophores can be utilized for OLED emitters, logic gates and optical chemosensors. In addition, the aggregation-induced-emission (AIE) of DCM derivatives for further optical applications was also introduced.     

A calix(4)arene pyridine derivative and its monomeric component: structural and thermodynamic aspects of their complexation with metal cations

The interaction of a calix(4)arene derivative, namely 5,11,17,23-tetra-tert-butyl-25,26,27,28-tetra[2-(4-pyridyl)methoxy]calix(4)arene, 1a, and its monomeric component, p-tert-butylphenoxy-4-pyridine, 1b, with metal cations has been investigated in acetonitrile and methanol. (1)H NMR measurements carried out in CD(3)CN show the primary role played by the pyridyl nitrogens in their complexation with metal cations. Conductance measurements demonstrated that for all cations (except mercury) the composition of the metal ion complexes of 1a is 1:1 (ligand:metal cation). However, 1a hosts two mercury cations per unit of ligand. For the monomer 1b, complexes of 2:1 (ligand:metal cation) stoichiometries are formed with the exception of Pb(2+) (1:1 composition). The thermodynamics of complexation of these systems are reported in acetonitrile. Data in methanol are limited to stability constant values for mercury(II) and these ligands. This paper demonstrates for the first time that thermodynamic data for the complexation of the monomeric component of the ligand and metal cations contribute significantly to the interpretation of systems involving cation-calixarene interactions in solution.