Development Of Molecular Sensors Research Articles

Aryl-Extended and Super Aryl-Extended Calix[4]pyrroles: Design, Synthesis, and Applications.

ConspectusProteins exhibit high-binding affinity and selectivity, as well as remarkable catalytic performance. Their binding pockets are hydrophobic but also contain polar and charged groups to contribute to the binding of polar organic molecules in aqueous solution. In the past decades, the synthesis of biomimetic receptors featuring sizable aromatic cavities equipped with converging polar groups has received considerable attention. "Temple" cages, naphthotubes, and aryl-extended calix[4]pyrroles are privileged examples of synthetic scaffolds displaying functionalized hydrophobic cavities capable of binding polar substrates. In particular, calix[4]pyrroles are macrocycles containing four pyrrole rings connected through their pyrrolic 2- and 5-positions by tetra-substituted sp3 carbon atoms (meso-substituents). In 1996, Sessler introduced the meso-octamethyl calix[4]pyrrole as an outstanding receptor for anion binding. Independently, Sessler and Floriani also showed that the introduction of aryl substituents in the meso-positions produced aryl-extended calix[4]pyrroles as a mixture of configurational isomers. In addition, aryl-extended calix[4]pyrroles bearing two and four meso-aryl substituents (walls) were reported. The cone conformation of "two-wall" αα-aryl-extended calix[4]pyrroles features an aromatic cleft with a polar binding site defined by four converging pyrrole NHs. On the other hand, "four-wall" αααα-calix[4]pyrrole isomers possess a deep polar aromatic cavity closed at one end by the converging pyrrole NHs. Because of their functionalized interior, aryl-extended calix[4]pyrroles are capable of binding anions, ion-pairs, and electron-rich neutral molecules in organic solvents. However, in water, they are restricted to the inclusion of neutral polar guests.Since the early 2000s, our research group has been involved in the design and synthesis of "two-wall" and "four-wall" aryl-extended calix[4]pyrroles and their derivatives, such as aryl-extended calix[4]pyrrole cavitands and super aryl-extended calix[4]pyrroles. In this Account, we mainly summarize our own results on the binding of charged and neutral polar guests with these macrocyclic receptors in organic solvents and in water. We also describe the applications of calix[4]pyrrole derivatives in the sensing of creatinine, the facilitated transmembrane transport of anions and amino acids, and the monofunctionalization of bis-isonitriles. Moreover, we explain the use of calix[4]pyrrole receptors as model systems for the quantification of anion-π interactions and the hydrophobic effect. Finally, we discuss the self-assembly of dimeric capsules and unimolecular metallo-cages based on calix[4]pyrrole scaffolds. We comment on their binding properties, as well as on those of bis-calix[4]pyrroles having a fully covalent structure.In molecular recognition, aryl-extended calix[4]pyrroles and their derivatives are considered valuable receptors owing to their ability to interact with a wide variety of electron-rich, neutral, and charged guests. Calix[4]pyrrole scaffolds have also been applied in the development of molecular sensors, ionophores, transmembrane carriers, supramolecular protecting groups and molecular containers modulating chemical reactivity, among others. We believe that the design of new calix[4]pyrrole receptors and the investigation of their binding properties may lead to promising applications in many research areas, such as supramolecular catalysis, chemical biology and materials science. We hope that this Account will serve to spread the knowledge of the supramolecular chemistry of calix[4]pyrroles among supramolecular and nonsupramolecular chemists alike.

Tracking twisted intramolecular charge transfer and isomerization dynamics in 9-(2,2-dicyanovinyl) julolidine using femtosecond stimulated Raman spectroscopy

Understanding the mechanism of how micro-environments affect molecular rotors helps the design and development of molecular sensors. Here, we utilized femtosecond stimulated Raman spectroscopy, helped by quantum chemical calculation, to study the structural dynamics of 9- (2,2-dicyanovinyl) julolidine in cyclohexane, THF, and DMSO solvents. The obtained hydrogen out-of-plane (HOOP) mode and symmetric/anti-symmetric stretching of two nitriles (C≡N) indicate the rotation of the C7=C8 double bond and C4–C7 single bond in the excited-state which provide two non-radiative decay channels to effectively quench the excited-state population on local excited (LE) state via isomerization and twisted intramolecular charge transfer (TICT). In nonpolar solvent, the excited molecule in the LE state radiatively relaxes to the ground state or performs rotation motions via isomerization and TICT to deactivate fluorescence in the LE state. In the polar solvent, the isomerization plays a role to quench the LE state population; simultaneously, an ultrafast intramolecular charge transfer (ICT) from LE state to emissive ICT state was followed by an TICT between ICT state and dark ICT’ state.

Molecular robots with sensors and intelligence.

CONSPECTUS: What we can call a molecular robot is a set of molecular devices such as sensors, logic gates, and actuators integrated into a consistent system. The molecular robot is supposed to react autonomously to its environment by receiving molecular signals and making decisions by molecular computation. Building such a system has long been a dream of scientists; however, despite extensive efforts, systems having all three functions (sensing, computation, and actuation) have not been realized yet. This Account introduces an ongoing research project that focuses on the development of molecular robotics funded by MEXT (Ministry of Education, Culture, Sports, Science and Technology, Japan). This 5 year project started in July 2012 and is titled "Development of Molecular Robots Equipped with Sensors and Intelligence". The major issues in the field of molecular robotics all correspond to a feedback (i.e., plan-do-see) cycle of a robotic system. More specifically, these issues are (1) developing molecular sensors capable of handling a wide array of signals, (2) developing amplification methods of signals to drive molecular computing devices, (3) accelerating molecular computing, (4) developing actuators that are controllable by molecular computers, and (5) providing bodies of molecular robots encapsulating the above molecular devices, which implement the conformational changes and locomotion of the robots. In this Account, the latest contributions to the project are reported. There are four research teams in the project that specialize on sensing, intelligence, amoeba-like actuation, and slime-like actuation, respectively. The molecular sensor team is focusing on the development of molecular sensors that can handle a variety of signals. This team is also investigating methods to amplify signals from the molecular sensors. The molecular intelligence team is developing molecular computers and is currently focusing on a new photochemical technology for accelerating DNA-based computations. They also introduce novel computational models behind various kinds of molecular computers necessary for designing such computers. The amoeba robot team aims at constructing amoeba-like robots. The team is trying to incorporate motor proteins, including kinesin and microtubules (MTs), for use as actuators implemented in a liposomal compartment as a robot body. They are also developing a methodology to link DNA-based computation and molecular motor control. The slime robot team focuses on the development of slime-like robots. The team is evaluating various gels, including DNA gel and BZ gel, for use as actuators, as well as the body material to disperse various molecular devices in it. They also try to control the gel actuators by DNA signals coming from molecular computers.

Surface-Confined Assemblies and Polymers for Molecular Logic

Stimuli responsive materials are capable of mimicking the operation characteristics of logic gates such as AND, OR, NOR, and even flip-flops. Since the development of molecular sensors and the introduction of the first AND gate in solution by de Silva in 1993, Molecular (Boolean) Logic and Computing (MBLC) has become increasingly popular. In this Account, we present recent research activities that focus on MBLC with electrochromic polymers and metal polypyridyl complexes on a solid support. Metal polypyridyl complexes act as useful sensors to a variety of analytes in solution (i.e., H(2)O, Fe(2+/3+), Cr(6+), NO(+)) and in the gas phase (NO(x) in air). This information transfer, whether the analyte is present, is based on the reversible redox chemistry of the metal complexes, which are stable up to 200 °C in air. The concurrent changes in the optical properties are nondestructive and fast. In such a setup, the input is directly related to the output and, therefore, can be represented by one-input logic gates. These input-output relationships are extendable for mimicking the diverse functions of essential molecular logic gates and circuits within a set of Boolean algebraic operations. Such a molecular approach towards Boolean logic has yielded a series of proof-of-concept devices: logic gates, multiplexers, half-adders, and flip-flop logic circuits. MBLC is a versatile and, potentially, a parallel approach to silicon circuits: assemblies of these molecular gates can perform a wide variety of logic tasks through reconfiguration of their inputs. Although these developments do not require a semiconductor blueprint, similar guidelines such as signal propagation, gate-to-gate communication, propagation delay, and combinatorial and sequential logic will play a critical role in allowing this field to mature. For instance, gate-to-gate communication by chemical wiring of the gates with metal ions as electron carriers results in the integration of stand-alone systems: the output of one gate is used as the input for another gate. Using the same setup, we were able to display both combinatorial and sequential logic. We have demonstrated MBLC by coupling electrochemical inputs with optical readout, which resulted in various logic architectures built on a redox-active, functionalized surface. Electrochemically operated sequential logic systems such as flip-flops, multivalued logic, and multistate memory could enhance computational power without increasing spatial requirements. Applying multivalued digits in data storage could exponentially increase memory capacity. Furthermore, we evaluate the pros and cons of MBLC and identify targets for future research in this Account.

Molecular dyes used for the detection of biological and environmental heavy metals: Highlights from 2004 to 2008

The coordination chemistry of heavy metals, for example, Fe3 + , Pb2 + , Cd2 + , Hg2 + , Cu2 + and Zn2 + , is of interest, in part because of their hazards and toxicity in biological, industrial and agricultural applications. Additionally, there is much interest in the detection and quantification of trace metals in the products of chemical synthesis, in particular sensors for detecting Pd2 + . There has been plethora of new molecular sensors for the detection of heavy metals, which utilise colorimetric or fluorescence mechanisms. This mini-review covers recent advances (2004–2008) in the development of molecular sensors that is restricted to molecular dyes. Other methods for the detection of heavy metals, for example, conjugated polymers and gold nanoparticles are omitted.

Fluorescent Sensors for the Detection of Chemical Warfare Agents

Along with biological and nuclear threats, chemical warfare agents are some of the most feared weapons of mass destruction. Compared to nuclear weapons they are relatively easy to access and deploy, which makes them in some aspects a greater threat to national and global security. A particularly hazardous class of chemical warfare agents are the nerve agents. Their rapid and severe effects on human health originate in their ability to block the function of acetylcholinesterase, an enzyme that is vital to the central nervous system. This article outlines recent activities regarding the development of molecular sensors that can visualize the presence of nerve agents (and related pesticides) through changes of their fluorescence properties. Three different sensing principles are discussed: enzyme-based sensors, chemically reactive sensors, and supramolecular sensors. Typical examples are presented for each class and different fluorescent sensors for the detection of chemical warfare agents are summarized and compared.

Electrochemical control of CO/NO ligand exchange in a triruthenium cluster monolayer assembled on a gold electrode surface.

A highly selective ligand exchange reaction is realized in the self-assembled monolayer (SAM) of a triruthenium cluster on a gold electrode surface under precise electrochemical potential control. CO as well as NO molecules, which are known to play key roles in many chemical, biological, and environmental systems, can be efficiently introduced into the SAM by electrochemically tuning the electronic state of the Ru site. These unique surface reactions are more convenient and efficient than conventional ligand exchange reactions in solution and could be used for the elucidation of the electron-transfer mechanism in a biological system as well as in the development of molecular sensors and devices.

NaCN-induced chemical hypoxia is associated with altered gene expression.

Sodium cyanide (NaCN)-induced chemical hypoxia is known to increase intracellular free calcium concentration and reduce cell survival, but its effect on gene expression has not been studied. In this study, we designed primers to conduct a rapid and reliable assay for the expression of mRNA of inducible nitric oxide synthase (iNOs), tumor suppressor protein p53, Bcl-2, heat shock protein 70 (HSP-70), and beta-actin in human intestinal epithelial T84 cells and Jurkat T cells. NaCN-induced chemical hypoxia increased iNOs and HSP-70 mRNA in both types of cells, whereas p53 and Bcl-2 mRNA were singularly induced in T84 cells and Jurkat T cells, respectively. In both cell types, treatment of hypoxic cells with a reversible selective iNOs inhibitor, Now-nitro-L-arginine (LNNA), blocked iNOs, Bcl-2, and HSP-70 mRNA, but increased p53. The NaCN-induced hypoxia was also found to increase caspase-3 cellular activity in both cell types. Treatment with LNNA alone decreased the basal caspase-3 cellular activity. A prior treatment of LNNA significantly inhibited the NaCN-induced increase in the cellular activity of this apoptotic enzyme. This is the first report to show that NaCN-induced chemical hypoxia alters both stress-related gene expression and caspase-3 cellular activity and can be regulated by the iNOs inhibitor LNNA. Since NaCN has been included in the 'National chemical terrorism threat' list, by the US Department of Defense, our studies provide useful insight in the development of molecular sensors to detect early exposure to this chemical terrorism threat.