Modulation of Energy Conversion Processes in Carbonaceous Molecular Bearings

The energetics and photodynamics of carbonaceous molecular bearings with discrete molecular structures were investigated. A series of supramolecular bearings comprising belt‐persistent tubular cycloarylene and fullerene molecules accepted photonic stimuli to afford charge‐separated species via a photoinduced electron transfer process. The energy conversion processes associated with the photoexcitation, however, differed depending on the molecular structure. A π‐lengthened tubular molecule allowed for the emergence of an intermediary triplet excited state at the bearing, which should lead to an energy conversion to thermal energy. On the other hand, low‐lying charge‐separated species induced by an endohedral lithium ion in fullerene enabled back electron transfer processes to occur without involving triplet excited species. The structure–photodynamics relationship was analyzed in terms of the Marcus theory to reveal a large electronic coupling in this dynamic supramolecular system.     

Artificial molecular-level machines

The concept of "machine" can be extended to the molecular level by designing supramolecular species capable of performing mechanical-like movements as a consequence of an appropriate energy supply. Molecular-level machines operate via electronic and nuclear rearrangements, for example, through some kind of chemical reaction. Like macroscopic machines, they are characterized by: (i) the kind of energy input supplied to make them work, (ii) the kind of movement performed by their components, (iii) the way in which their operation can be controlled and monitored, (iv) the possibility to repeat the operation at will and establish a cyclic process, (v) the time scale needed to complete a cycle of operation, and (vi) the function performed. A crucial issue is that concerning energy supply. Artificial machines powered by chemical energy ("fuels") produce waste products whose accumulation compromises the operation of the machine unless they are removed from the system. Photochemical and electrochemical energy inputs, however, can be used to make a machine work without formation of waste products. Examples of chemically, electrochemically, and photochemically powered machines investigated in our laboratory are reviewed, and future directions for the construction of novel machines are illustrated. The two most interesting kinds of applications of molecular-level machines are related to the mechanical aspect, which can be exploited, for example, for molecular-level transportation purposes, and the logic aspect, which can be exploited for information processing at the molecular level and, in the long run, for the construction of molecular level (chemical) computers.     

Redox-responsive carbometalated ruthenium and osmium complexes

Organometallic conjugated complexes have become an important type of stimuli-responsive materials because of their appealing electrochemical properties and rich photonic, electronic, and magnetic properties. They are potentially useful in a wide range of applications such as molecular wires, molecular switches, molecular machines, molecular memory, and optoelectronic detections. This review outlines the recent progress on the molecular design of carbometalated ruthenium and osmium complexes and their applications as redox-responsive materials with visible and near-infrared (NIR) absorptions and electron paramagnetic resonance as readout signals. Three molecule systems are introduced, including the symmetric diruthenium complexes, metal-amine conjugated bi-center system, and multi-center redox-active organometallic compounds. Because of the presence of a metal-carbon bond on each metal component and strong electronic coupling between redox sites, these compounds display multiple reversible redox processes at low potentials and each redox state possesses significantly different physical and chemical properties. Using electrochemical potentials as input signals, these materials show reversible NIR absorption spectral changes, making them potentially useful in NIR electrochromism and information storage.     

A new conduction phenomenon observed in polyethylene and epoxy resin: Ultra‐fast soliton conduction

A new conduction mechanism in polyethylene and epoxy resin is presented and discussed in this article. This mechanism is based on the presence of charge pulses that can be seen as solitons (solitary waves) crossing dielectrics with mobility 4–5 orders of magnitude larger than that of conventional charge carriers. The nature of this new process that is characterized by charge pulses with such high mobility requires a completely different mechanism for transport to be theorized with respect to that, mediated by trap sites, of conventional charge carriers. It is speculated in this article that injection and transport of positive and negative solitons occurs through the coupling of space charge and relaxation processes involving molecular chains, but of different nature for negative or positive solitons. Observation of space charge shows the existence of such solitons for at least two families of materials, polyethylene, and epoxy resin. In addition, it has been observed that nanostructuration, which is able to modify mechanical properties, affects also the presence and size of the solitons. In this article, we not only seek to demonstrate the existence of this new phenomenon, but attempt to provide an explanation and a kind of qualitative–quantitative model, which shows that the assumption of a pulsive conduction mechanism mediated by chain relaxation processes, transport in free volume (for negative solitons), and reverse‐tunneling between macromolecular chains (positive solitons) seems to fit quite well with the experimental observations. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

GTKDynamo: A PyMOL plug‐in for QC/MM hybrid potential simulations

Hybrid quantum chemical/molecular mechanical (QCMM) potentials are very powerful tools for molecular simulation. They are especially useful for studying processes in condensed phase systems, such as chemical reactions that involve a relatively localized change in electronic structure and where the surrounding environment contributes to these changes but can be represented with more computationally efficient functional forms. Despite their utility, however, these potentials are not always straightforward to apply since the extent of significant electronic structure changes occurring in the condensed phase process may not be intuitively obvious. To facilitate their use, we have developed an open‐source graphical plug‐in, GTKDynamo that links the PyMOL visualization program and the pDynamo QC/MM simulation library. This article describes the implementation of GTKDynamo and its capabilities and illustrates its application to QC/MM simulations. © 2013 Wiley Periodicals, Inc.     

Molecular reactors and machines: applications, potential, and limitations

Molecular reactors are miniature vessels for the assembly of reactants at the molecular level, in order to change the nature of chemical transformations. It seems probable that those that will find most immediate applications are those that change product ratios or give products which would not readily form in the absence of the reactors, and thereby afford easy access to materials that are otherwise difficult to obtain. Molecular machines consist of interrelated parts with separate functions and perform some kind of work, at the molecular level. Practical examples are likely to be relatively uncomplicated and not based on individual functions of single-molecule devices. Instead they will probably rely on extensive redundancy of the molecular components and their interactions and reactions, as well as of the machines themselves.     

Single-step electron transfer on the nanometer scale: ultra-fast charge shift in strongly coupled zinc porphyrin-gold porphyrin dyads

The synthesis, electrochemical properties, and photoinduced electron transfer processes of a series of three novel zinc(II)-gold(III) bisporphyrin dyads (ZnP--S--AuP(+)) are described. The systems studied consist of two trisaryl porphyrins connected directly in the meso position via an alkyne unit to tert-(phenylenethynylene) or penta(phenylenethynylene) spacers. In these dyads, the estimated center to center interporphyrin separation distance varies from 32 to 45 A. The absorption, emission, and electrochemical data indicate that there are strong electronic interactions between the linked elements, thanks to the direct attachment of the spacer on the porphyrin ring through the alkyne unit. At room temperature in toluene, light excitation of the zinc porphyrin results in almost quantitative formation of the charge shifted state (.+)ZnP--S--AuP(.), whose lifetime is in the order of hundreds of picoseconds. In this solvent, the charge-separated state decays to the ground state through the intermediate population of the zinc porphyrin triplet excited state. Excitation of the gold porphyrin leads instead to rapid energy transfer to the triplet ZnP. In dichloromethane the charge shift reactions are even faster, with time constants down to 2 ps, and may be induced also by excitation of the gold porphyrin. In this latter solvent, the longest charge-shifted lifetime (tau=2.3 ns) was obtained with the penta-(phenylenethynylene) spacer. The charge shift reactions are discussed in terms of bridge-mediated super-exchange mechanisms as electron or hole transfer. These new bis-porphyrin arrays, with strong electronic coupling, represent interesting molecular systems in which extremely fast and efficient long-range photoinduced charge shift occurs over a long distance. The rate constants are two to three orders of magnitude larger than for corresponding ZnP--AuP(+) dyads linked via meso-phenyl groups to oligo-phenyleneethynylene spacers. This study demonstrates the critical impact of the attachment position of the spacer on the porphyrin on the electron transfer rate, and this strategy can represent a useful approach to develop molecular photonic devices for long-range charge separations.     

分子基逻辑材料*

在适当的条件下分子开关将输入的信息转换为输出信号,利用这一特点,可在分子体系根据二进位布尔逻辑规则实现信号转换。目前,用化学体系进行基本的布尔逻辑功能执行 (PASS、YES、NOT、AND、NAND、OR、NOR、XNOR和INH)都已成为可能。在此基础上,逻辑门的整合与编程,以及更进一步的复杂分子运算开始受到人们的关注。迄今为止,以高灵敏性的荧光输出信号为主,人们在分子水平上设计实现了多种复杂的逻辑电路,包括组合逻辑电路和时序逻辑电路等,并开始涉及信息处理的安全平台设计。本文主要介绍了近年来利用分子荧光开关体系模拟数字逻辑电路过程中所取得的最新进展,对分子逻辑电路研究的热点和问题进行了展望。     

Two-dimensional electronic conjugation: statics and dynamics at structural domains beyond molecular wires

Chemical architectures supporting a high degree of electronic conjugation serve as important functional components in devices and materials for advanced electronic and photonic applications. Increasing the spatial dimensionality of such constructs can fundamentally modify their optoelectronic properties and significantly alter intra- and intermolecular interactions that are crucial for understanding and controlling charge/energy-transfer processes. In this article, emerging design principles in the construction of well-defined conjugated platforms beyond molecular wires are highlighted. Both covalent and noncovalent approaches can be strategically employed to position one-dimensional (1D) substructures in a spatially well-defined manner in order to enhance both structural and functional complexity in a two-dimensional (2D) setting. A predictable and controllable switching mechanism can be designed and implemented with mobile 2D electronic conjugation that operates by correlated motions of inherently rigid 1D subunits. This emerging "dynamic" approach complements and challenges the prevailing "static" paradigm of conjugated chemical architectures.     

Influence of Intermolecular Vibrations on the Electronic Coupling in Organic Semiconductors: The Case of Anthracene and Perfluoropentacene

We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure.     

Photoinduced proton exchange between molecular switches

The identification of strategies to establish communication between independent molecules is an essential requirement for the development of operating principles to manipulate information at the molecular level. In this context, we have devised a strategy to exchange signals between pairs of complementary molecular switches. It is based on the photoinduced ring closing of a merocyanine to produce a spiropyran with the concomitant release of a proton. The liberated proton is captured by either one of two pyridine derivatives with the formation of their conjugate acids. This transformation induces a significant increase in chemical shift for the resonances of the pyridyl protons and, in one instance, also a pronounced color change. The overall process is fully reversible and the pair of communicating molecules reverts to the original state in the dark. Relying on this mechanism, an optical input is transduced into a detectable spectroscopic output after the controlled intermolecular exchange of protons. A simple analysis of the signal transduction operated by the communicating molecular switches reveals that a binary digit is passed unaltered from the input to the output even although the nature of the signal carrying the information changes at each step. Furthermore, the different nature of input and output implies that the state of the ensemble of molecules can be probed non-destructively at any point in time. The timescales of the switching steps, however, are seriously limited by the slow reaction kinetics. The photoinduced transformation occurs within minutes, but the thermal reaction reverts the switch state only after several hours.     

Digital processing with a three-state molecular switch

Certain molecular switches respond to input stimulations producing detectable outputs. The interplay of these signals can be exploited to reproduce basic logic operations at the molecular level. The transition from simple logic gates to complex digital circuits requires the design of chemical systems able to process multiple inputs and outputs. We have identified a three-state molecular switch that responds to one chemical and two optical inputs producing two optical outputs. We have encoded binary digits in its inputs and outputs applying positive logic conventions and demonstrated that this chemical system converts three-digit input strings into two-digit output strings. The logic function executed by the three-state molecular switch is equivalent to that of a combinational logic circuit integrating two AND, two NOT, and one OR gate. The three states of the molecular switch are a colorless spiropyran, a purple trans-merocyanine, and its yellow-green protonated form. We have elucidated their structures by X-ray crystallography, (1)H NMR spectroscopy, COSY and NOE experiments, as well as density functional calculations. The three input stimulations controlling the interconversion of the three states of the molecular switch are ultraviolet light, visible light, and H(+). The two outputs are the absorption bands in the visible region of the two colored states of the molecular switch. We have monitored the switching processes and quantified the associated thermodynamic and kinetic parameters with the aid of (1)H NMR and visible absorption spectroscopies.     

Specific interactions and binding free energies between thermolysin and dipeptides: molecular simulations combined with ab initio molecular orbital and classical vibrational analysis

Thermolysin (TLN) is a metalloprotease widely used as a nonspecific protease for sequencing peptide and synthesizing many useful chemical compounds by the chemical industry. It was experimentally shown that the activity and functions of TLN are inhibited by the binding of many types of amino acid dipeptides. However, the binding mechanisms between TLN and dipeptides have not been clarified at the atomic and electronic levels. In this study, we investigated the binding mechanisms between TLN and four dipeptides. Specific interactions and binding free energies (BFEs) between TLN and the dipeptides were calculated using molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital (FMO) methods. The molecular systems were embedded in solvating water molecules during calculations. The calculated BFEs were qualitatively consistent with the trend of the experimentally observed inhibition of TLN activity by binding of the dipeptides. In addition, the specific interactions between the dipeptides and each amino acid residue of TLN or solvating water molecules were elucidated by the FMO calculations.     

Weakly coupled molecular photonic wires: synthesis and excited-state energy-transfer dynamics

Molecular photonic wires, which absorb light and undergo excited-state energy transfer, are of interest as biomimetic models for photosynthetic light-harvesting systems and as molecular devices with potential applications in materials chemistry. We describe the stepwise synthesis of four molecular photonic wires. Each wire consists of an input unit, transmission element, and output unit. The input unit consists of a boron-dipyrrin dye or a perylene-monoimide dye (linked either at the N-imide or the C9 position); the transmission element consists of one or three zinc porphyrins affording short or long wires, respectively; and the output unit consists of a free base (Fb) porphyrin. The components in the arrays are joined in a linear architecture via diarylethyne linkers (an ethynylphenyl linker is attached to the C9-linked perylene). The wires have been examined by static absorption, static fluorescence, and time-resolved absorption spectroscopy. Each wire (with the exception of the C9-linked perylene wire) exhibits a visible absorption spectrum that is the sum of the spectra of the component parts, indicating the relatively weak electronic coupling between the components. Excitation of each wire at the wavelength where the input unit absorbs preferentially (typically 480-520 nm) results in emission almost exclusively from the Fb porphyrin. The static emission and time-resolved data indicate that the overall rate constants and quantum efficiencies for end-to-end (i.e., input to output) energy transfer are as follows: perylene-(N-imide)-linked short wire, (33 ps)(-1) and >99%; perylene-(C9)-linked short wire, (26 ps)(-1) and >99%; boron-dipyrrin-based long wire, (190 ps)(-1) and 81%; perylene-(N-imide)-linked long wire, (175 ps)(-1) and 86%. Collectively, the studies provide valuable insight into the singlet-singlet excited-state energy-transfer properties in weakly coupled molecular photonic wires.     

Multi‐Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues

Theoretical‐computational modeling with an eye to explaining experimental observations in regard to a particular chemical phenomenon or process requires choices concerning essential degrees of freedom and types of interactions and the generation of a Boltzmann ensemble or trajectories of configurations. Depending on the degrees of freedom that are essential to the process of interest, for example, electronic or nuclear versus atomic, molecular or supra‐molecular, quantum‐ or classical‐mechanical equations of motion are to be used. In multi‐resolution simulation, various levels of resolution, for example, electronic, atomic, supra‐atomic or supra‐molecular, are combined in one model. This allows an enhancement of the computational efficiency, while maintaining sufficient detail with respect to particular degrees of freedom. The basic challenges and choices with respect to multi‐resolution modeling are reviewed and as an illustration the differential catalytic properties of two enzymes with similar folds but different substrates with respect to these substrates are explored using multi‐resolution simulation at the electronic, atomic and supra‐molecular levels of resolution.     

In silico engineering of tailored ink-binding ability at molecular printboards.

Molecular recognition between guest ink molecules and beta-cyclodextrin (beta-CD) cavities at self-assembled monolayers provides a molecular printboard for nanopatterning applications. We recently used molecular dynamics (MD) simulations to describe the specificity of ink-printboard binding and here extend the simulations to include charged cyclodextrin hosts, necessary to broaden the chemistry of molecular printboards and bind charged inks such as the ferrocenium cation. Shifting to high pH, or alternatively grafting a charged sidearm onto beta-CD, created three distinct types of anionic beta-CD cavity and we used electronic structure calculations and MD simulations to measure host-guest charge transfer and binding strengths. We find that steric recognition of uncharged organic molecules is retained at the charged printboards, and that improved guest-host electrostatic contacts can strengthen binding of larger inks while penalising small inks, enhancing the level of discrimination. A prudent choice of complementary host-guest shape and charge states thus provides a means of tuning both ink binding strength and specificity at molecular printboards.     

Resonant Scattering of X Rays as a Probe of Valence and Hybridization in Solids

With the advent of the very intense 3rd generation synchrotron sources of X rays, new powerful spectroscopic techniques, requiring the detection of very low cross section phenomena, have come of age. Among them Resonant Inelastic X-Ray Scattering (RIXS) is rapidly becoming a major probe of the electronic structure of solids. RIXS measures the decay radiation that follows the excitation of core electrons into states located in a narrow region above the Fermi level. It shares with other core-level spectroscopies a remarkable chemical sensitivity and provides specific information on selected elements in a compound. Since photons are used to excite the process and photons are detected, truly bulk-sensitive information can be obtained. RIXS is sensitive to the nature of the ground state and of the characteristic excitations of a material, and can separately measure their energies, because exciting atoms with different atomic configuration leaves the solid in final states of different total energy. Therefore, it can discriminate different chemical environments and valence states of the same element. In this paper, we outline the basic principles of RIXS, with special emphasis on electronic excitations, and discuss the relevance of this information for studies of hybridization and valence in materials science, by referring to recent experiments.     

Redox-Guest-Induced Multimode Photoluminescence Switch for Sequential Logic Gates in a Photoactive Coordination Cage

Molecular or supramolecular level photoluminescence (PL) modulation combining chemical and photonic input/output signals together in an integrated system can provide potential high-density data memorizing and process functions intended for miniaturized devices and machines. Herein, a PL-responsive supramolecular coordination cage has been demonstrated for complex interactions with redox-active guests. PL signals of the cage can be switched and modulated by adding or retracting Fc derivatives or converting TTF into different oxidation states through chemical or photochemical pathways. As a result, reversible or stepwise PL responses are displayed by these host–guest systems because of the occurrence of photoinduced electron-transfer (PET) or fluorescence resonance energy transfer (FREnT) processes, providing unique nanodevice models bearing off/on logic gates or memristor-like sequential memory and Boolean operation functions.     

Synthesis,Crystal Structures,and Properties of 6,12‐Diaryl‐Substituted Indeno[1,2‐b]fluorenes

Fused polycyclic indeno[1,2‐b]fluorene derivatives with aryl substituents at the 6,12‐positions have been prepared as a potential antiaromatic 20π electronic system. They showed strong absorptions in the visible region and amphoteric redox properties. The quinoid‐type molecular structures were revealed by X‐ray crystal‐structure analysis, which indicated that the bond lengths of the quinoid unit depend on the aryl substituents. Whereas nucleus‐independent chemical shift NICS(1) calculations indicate the antiaromatic nature of the s‐indacene core, they have higher stability than substituted acene derivatives. The derivatives with difluorophenyl or anthryl groups were stable in solution. Vapor‐deposited thin films showed ambipolar carrier transportation in the field‐effect transistor devices.