Control of the Structure and Functions of Biomaterials by Light

Vision and other light-triggered biochemical transformations in plants and living organisms represent a sophisticated biological processes in which optical signals are recorded and transduced as (physico)chemical events. Photoswitchable biomaterials are a new class of substances in which optical signals generate discrete “On” and “Off” states of biological functions, resembling logic gates that flip between 0 and 1 states in response to the changes in electric currents in computers. The (photo)chemistry of photochromic materials has been extensively developed in the past four decades. These materials isomerize reversibly upon light absorption, and the discrete photoisomeric states exhibit distinct spectral and chemical features. Integration of photoisomerizable (or photochromic) units into biomaterials allow their secondary functions such as biocatalysis, binding, and electron transfer to be tailored so that they can be switched on or off. This can be accomplished by chemical modification of the biomaterial by photoisomerizable units and by integration of biomaterials in photoisomerizable microenvironments such as monolayers or polymers. The photoswitchable properties of chemically modified biomaterials originate from the light-induced generation or perturbation of the biologically active site, whereas in photoisomerizable matrices they depend upon the regulation of the physical or chemical features of the photoisomerizable assemblies of polymers, monolayers, or membranes. Light-triggered activation of catalytic biomaterials provides a means of amplifying the recorded optical signal by biochemical transformations, and photostimulated biochemical redox switches allow its electrochemical transduction and amplification. The field of photoswitches based on biomaterials has developed extensively in the past few years within the general context of molecular switching devices and micromachinery. The extensive knowledge on the manipulation of biomaterials through genetic engineering and the fabrication of surfaces modified by biologically active materials enables us to prepare biomaterials with improved optical-switching features. Their application in optoelectronic or bioelectronic devices has been transformed from fantasy to reality. The use of photoswitchable biomaterials in information storage and processing devices (biocomputers), sensors, reversible immunosensors, and biological amplifiers of optical signals has already been demonstrated, but still leaves important future challenges.     

Metal-assembled anion receptors

This review describes the self-assembly of anion receptors from organic ligands and transition metal ions. These metal-assembled anion receptors can be synthesised from a number of different species; bidentate ligands with metals that prefer octahedral coordination geometries and monodentate ligands with metals that prefer square planar geometries are common. Anion binding transition metal helicates and systems where the coordination of metal ions results in the formation of an anion receptor by conformational locking are also reported. The effect of anion binding on the different properties of these complexes is discussed.     

Grid-type metal ion architectures: functional metallosupramolecular arrays

Recent advances in supramolecular coordination chemistry allow access to transition-metal complexes of grid-type architecture comprising two-dimensional arrays of metal ions connecting a set of organic ligands in a perpendicular arrangement to generate a multiple wiring network. General design principles for these structures involve the thermodynamically driven synthesis of complex discrete objects from numerous molecular components in a single overall operation. Such supramolecular metal ion arrays combine the properties of their constituent metal ions and ligands, showing unique optical, electrochemical, and magnetic behavior. These features present potential relevance for nanotechnology, particularly in the area of supramolecular devices for information storage and processing. Thus, a dense organization of addressable units is represented by an extended "grid-of-grids" arrangement, formed by interaction of grid-type arrays with solid surfaces.     

多功能二噻吩乙烯光致变色光分子开关材料

光致变色材料是一类在不同波长的光交替照射下,产生两种可进行可逆转换的光致异构体并伴随明显的光物理和光化学性能变化的材料。基于其特殊的光致异构性质,人们已开发出多种光致变色功能材料并将其广泛应用于超高密度光信息存储、分子开关、分子逻辑门、分子导线、光电材料、多光子器件、表面/纳米器件、液晶材料、化学传感、生物成像、自组装、聚集诱导发光、光控生物体系等诸多领域。其中,二噻吩乙烯类化合物因其出色的热稳定性、优良的耐疲劳性、快的响应速率、高的转化率和量子产率以及出色的固相反应活性而成为理想的光致变色材料之一。本文主要围绕近期本研究组研究成果着重介绍近几年二噻吩乙烯类化合物从溶液体系到功能化表面体系的研究进展,探讨当前该领域存在的问题并对其前景和发展方向进行展望。     

Conformational changes of DNA molecules in interactions with bioactive compounds. II. DNA complexes with coordination compounds of cobalt and ruthenium

A comparative analysis is made of the character of conformational changes of the DNA molecule in its interaction with coordination compounds of cobalt and ruthenium with different ligand sets in the coordination sphere of the ion. It is shown that during complexation global conformational changes of DNA (e.g., the reduction of its volume) practically do not depend on the location and on the binding mode of the complex ion, but are primarily determined by its charge, whereas local conformational changes of the macromolecule are very sensitive to the type of the complex being formed, as indicated by the change of spectral properties of DNA. An assessment of sizes of the particles that are formed as a result of DNA condensation due to its binding with trivalent ions of cobalt and ruthenium was performed with the use of dynamic light scattering.     

Figure eights, Möbius bands, and more: conformation and aromaticity of porphyrinoids

The aromatic character of porphyrins, which has significant chemical and biological consequences, can be substantially altered by judicious modifications of the parent ring system. Expansion of the macrocycle, which is achieved by introducing additional subunits, usually increases the so‐called free curvature of the ring, leading to larger angular strain. This strain is reduced by a variety of conformational changes, most notably by subunit inversion and π surface twisting. The latter effect creates a particularly convenient access to Möbius aromatic molecules, whose properties, predicted over 40 years ago, are of considerable theoretical importance. The conformational processes occurring in porphyrin analogues are often coupled to other chemical phenomena, and can thus be exploited as a means of constructing functional molecular devices. In this Review, the structural chemistry of porphyrinoids is discussed in the context of their conformational dynamics and π‐electron conjugation     

Electrospray ionization mass spectrometry of biotin binding to streptavidin

Stepwise binding of biotin to streptavidin via several intermediates was monitored with electrospray ionization mass spectrometry (ESIMS). Protein ligand interactions that result in conformational changes could be recognized with ESIMS by a mass shift and a change of the average multiple charge state of this protein. In addition, mass spectrometry for the ions in the gas phase revealed a much greater strength of the noncovalent bonds between the streptavidin subunits in the tetrameric complex than between the streptavidin and biotin molecules and remarkable differences in stability for the different charge states of the biotin-streptavidin noncovalent complex.     

Electrochemical functions of metallosupramolecular nanomaterials

Self-assembly of metal ions and organic ligands results in the formation of extended or discrete metallosupramolecular structures. In case of neutral ditopic ligands such as bisterpyridines, extended metallosupramolecular coordination polyelectrolytes (MEPEs) are formed. Metal ion-induced self-assembly of 1,4-bis(2,2':6',2'-terpyridin-4'-yl)benzene with Fe(II) or Co(II) results in MEPEs with interesting electrochemical properties. These MEPEs reversibly change their color when oxidized or reduced. The heterometallic MEPE consisting of Fe(II) and Co(II) combines the properties of the individual MEPEs and therefore shows their different states: red-purple, blue, and transparent. On the other hand, complexation of cyclic phenylazomethines with metal ions results in discrete metallosupramolecular structures. We find that metal ion assembly to the organic module occurs in a stepwise fashion because of a difference in the basicity of the imine conformers, and the metal ion assembly can be controlled electrochemically. This example illustrates how metal ion binding can be controlled by the conformation of the receptor, an important step toward assembling organic ligands and metal ions in predictable ways.     

Sequential Logic Operations with a Molecular Keypad Lock with Four Inputs and Dual Fluorescence Outputs

A novel coumarin–rhodamine conjugate was prepared, and its metal binding properties were studied by UV/Vis and fluorescence spectroscopy. The conjugate serves as a ratiometric and highly selective fluorescent sensor for Hg²⁺ ions. Its metal‐responsive spectral properties were utilized to construct a molecular keypad lock with four inputs and dual fluorescence outputs. The complexity of this molecular logic network can greatly enhance the security level of this device.     

Theoretical investigations on electronic structures and photophysical properties of N-heteroaryl carbazole derivatives as host materials

The carbazole-endcapped host molecules with tailoring different heteroaryl core and meta-position linkage mode have great potential on phosphorescent organic light-emitting diodes. To provide a profound view on structure?Cproperty relationships, new linear-shaped counterparts have been designed based on the existing molecular composition and the linkage at para-position (p-type molecules). A series of studies about the influence of the linkage mode on optical and electronic properties of these carbazole derivatives have carried out via density functional theory and time-dependent density functional theory calculations. The geometric and the electronic structure of these molecules in the ground states, ions states, and lowest triplet states have been calculated especially focusing on the analysis of highest occupied molecular orbitals, lowest unoccupied molecular orbitals, energy gaps, triplet energies, ionization potentials, electron affinities, reorganization energies, triplet exciton-formation fraction, and absorption spectra. These optoelectronic properties can be effectively tuned by the chemical modifications of different linkage pattern. The good coordination between our calculated results and the available experimental data has been observed. The study reveals that the designed p-type molecules show great promise as new high-performance red host materials with large triplet energy, narrow energy gap, good electron and hole-transport properties, and high triplet exciton-formation fraction.     

Multiple expression of molecular information: enforced generation of different supramolecular inorganic architectures by processing of the same ligand information through specific coordination algorithms

The multisubunit ligand 2 combines two complexation substructures known to undergo, with specific metal ions, distinct self-assembly processes to form a double-helical and a grid-type structure, respectively. The binding information contained in this molecular strand may be expected to generate, in a strictly predetermined and univocal fashion, two different, well-defined output inorganic architectures depending on the set of metal ions, that is, on the coordination algorithm used. Indeed, as predicted, the self-assembly of 2 with eight CuII and four CuI yields the intertwined structure D1. It results from a crossover of the two assembly subprograms and has been fully characterized by crystal structure determination. On the other hand, when the instructions of strand 2 are read out with a set of eight CuI and four MII (M = Fe, Co, Ni, Cu) ions, the architectures C1-C4, resulting from a linear combination of the two subprograms, are obtained, as indicated by the available physico-chemical and spectral data. Redox interconversion of D1 and C4 has been achieved. These results indicate that the same molecular information may yield different output structures depending on how it is processed, that is, depending on the interactional (coordination) algorithm used to read it. They have wide implications for the design and implementation of programmed chemical systems, pointing towards multiprocessing capacity, in a one code/ several outputs scheme, of potential significance for molecular computation processes and possibly even with respect to information processing in biology.     

Probing conformational variations at the ATPase site of the RNA helicase DbpA by high-field electron-nuclear double resonance spectroscopy

The RNA helicase DbpA promotes RNA remodeling coupled to ATP hydrolysis. It is unique because of its specificity to hairpin 92 of 23S rRNA (HP92). Although DbpA kinetic pathways leading to ATP hydrolysis and RNA unwinding have been recently elucidated, the molecular (atomic) basis for the coupling of ATP hydrolysis to RNA remodeling remains unclear. This is, in part, due to the lack of detailed structural information on the ATPase site in the presence and absence of RNA in solution. We used high-field pulse ENDOR (electron-nuclear double resonance) spectroscopy to detect and analyze fine conformational changes in the protein's ATPase site in solution. Specifically, we substituted the essential Mg(2+) cofactor in the ATPase active site for paramagnetic Mn(2+) and determined its close environment with different nucleotides (ADP, ATP, and the ATP analogues ATPγS and AMPPnP) in complex with single- and double-stranded RNA. We monitored the Mn(2+) interactions with the nucleotide phosphates through the (31)P hyperfine couplings and the coordination by protein residues through (13)C hyperfine coupling from (13)C-enriched DbpA. We observed that the nucleotide binding site of DbpA adopts different conformational states upon binding of different nucleotides. The ENDOR spectra revealed a clear distinction between hydrolyzable and nonhydrolyzable nucleotides prior to RNA binding. Furthermore, both the (13)C and the (31)P ENDOR spectra were found to be highly sensitive to changes in the local environment of the Mn(2+) ion induced by the hydrolysis. More specifically, ATPγS was efficiently hydrolyzed upon binding of RNA, similar to ATP. Importantly, the Mn(2+) cofactor remains bound to a single protein side chain and to one or two nucleotide phosphates in all complexes, whereas the remaining metal coordination positions are occupied by water. The conformational changes in the protein's ATPase active site associated with the different DbpA states occur in remote coordination shells of the Mn(2+) ion. Finally, a competitive Mn(2+) binding site was found for single-stranded RNA construct.     

Aminoanthraquinone-based chemosensors: colorimetric molecular logic mimicking molecular trafficking and a set-reset memorized device

The synthesis, photophysical properties, protonation and metal-ion coordination features of a family of four (3-6) anthraquinone-based schiff base derivatives are reported. The outstanding UV-vis absorption properties of the 1-aminoanthraquinone chromophore allowed the efficient visual detection and quantification of Cu(2+) and/or Ni(2+) in buffered aqueous solution. Analysis of spectrophotometric data with SPECFIT yielded the macroscopic and microscopic stability constants of the complexes. Furthermore, the different optical output signals (i.e. absorbance) observed with addition of various metal ions to a solution of 6 can be used for mimicking the operation of a traffic signal and "Set-Reset" molecular level information processing device.     

Characterization of the polymorphic states of copper(II)‐bound Aβ(1–16) peptides by computational simulations

Understanding the polymorphic states of metal amyloid β (Aβ) interactions helps to elucidate metal‐mediated events in the pathogenesis of Alzheimer's disease. Systematic investigations on the effects of metal ions such as Cu²⁺ and Zn²⁺ on the structural and thermodynamic properties of Aβ at the molecular lever seem desirable. In this study, a set of new AMBER force field parameters was developed to model various Cu²⁺ coordination spheres of Aβ. These parameters including force constants and partial charges obtained using restrained electrostatic potential method were then validated in replica‐exchange molecular dynamics simulations on six Cu²⁺‐Aβ(1–16) systems. The Cu²⁺ coordination geometry differs depending on the Cu²⁺ binding fashions. The structural analyses reveal that Aβ(1–16) prefers turn conformations, which provides a geometrical favor to establish multiple Cu²⁺ coordination modes in solution at physiological pH. The relative stability of different Cu²⁺‐Aβ(1–16) complexes was estimated by free energy calculations. The Cu²⁺ ligands in the most stable Cu²⁺‐Aβ(1–16) structure involve Glu³, His⁶, His¹³ and His¹⁴ in terms of MM/3D‐RISM (molecular mechanics/three‐dimensional reference interaction site model). The solvation free energy and conformational entropy calculated by 3D‐RISM method suggest that the binding of Cu²⁺ within Aβ(1–16) is a spontaneous process. The overlap of the preparation free energy distributions demonstrates the heterogeneous states of Aβ(1–16) conformations that are ready for Cu²⁺ binding whereas the populations of such polymorphic states may shift at differing pH. © 2013 Wiley Periodicals, Inc.     

Structural transitions in ion coordination driven by changes in competition for ligand binding

Transferring Na(+) and K(+) ions from their preferred coordination states in water to states having different coordination numbers incurs a free energy cost. In several examples in nature, however, these ions readily partition from aqueous-phase coordination states into spatial regions having much higher coordination numbers. Here we utilize statistical theory of solutions, quantum chemical simulations, classical mechanics simulations, and structural informatics to understand this aspect of ion partitioning. Our studies lead to the identification of a specific role of the solvation environment in driving transitions in ion coordination structures. Although ion solvation in liquid media is an exergonic reaction overall, we find it is also associated with considerable free energy penalties for extracting ligands from their solvation environments to form coordinated ion complexes. Reducing these penalties increases the stabilities of higher-order coordinations and brings down the energetic cost to partition ions from water into overcoordinated binding sites in biomolecules. These penalties can be lowered via a reduction in direct favorable interactions of the coordinating ligands with all atoms other than the ions themselves. A significant reduction in these penalties can, in fact, also drive up ion coordination preferences. Similarly, an increase in these penalties can lower ion coordination preferences, akin to a Hofmeister effect. Since such structural transitions are effected by the properties of the solvation phase, we anticipate that they will also occur for other ions. The influence of other factors, including ligand density, ligand chemistry, and temperature, on the stabilities of ion coordination structures are also explored.     

Squaraines as reporter units: insights into their photophysics, protonation, and metal-ion coordination behaviour

The synthesis, photophysical properties, protonation, and metal-ion coordination features of a family of nine aniline-based symmetrical squaraine derivatives are reported. The squaraine scaffold displays very attractive photophysical properties for a signalling unit. These dyes show absorption and weakly Stokes-shifted, mirror-image-shaped emission bands in the visible spectral range and there are no hints of multiple emission bands. The mono-exponential fluorescence decay kinetics observed for all the derivatives indicate that only one excited state is involved in the emission. These data stress the interpretation that squaraines can be regarded as polymethine-type dyes. From a coordination chemistry point of view, the squaraines possess four potential binding sites; that is, two nitrogen atoms from the anilino groups and two oxygen atoms from the central C(4)O(2) four-membered ring. These coordination sites are part of a cross-conjugated pi-system and coordination events with protons or certain metal ions affect the electronic properties of the delocalised pi-system dramatically, resulting in a rich modulation of the colour of the squaraines. The absorption band at around 640 nm is blue-shifted when coordination at the anilino nitrogen atoms occurs, whereas coordination to the C(2)O(4) oxygen atoms results in the development of red-shifted bands. Addition of more than one equivalent of protons or metal cations could additionally entail mixed N,O- or N,N-coordinated complexes, manifested in the development of a broad band at 480 nm or complete bleaching in the visible range, respectively. Analysis of the spectrophotometric titration data with HYPERQUAD yielded the macroscopic and microscopic stability constants of the complexes. Theoretical modelling of the various protonated species by molecular mechanics methods and consideration of some of the title dyes within the framework of molecular chemosensing and molecular-scale "logic gates" complement this contribution.     

Hidden Conformations in Aspergillus niger Monoamine Oxidase are Key for Catalytic Efficiency

Enzymes exist as an ensemble of conformational states, whose populations can be shifted by substrate binding, allosteric interactions, but also by introducing mutations to their sequence. Tuning the populations of the enzyme conformational states through mutation enables evolution towards novel activity. Herein, Markov state models are used to unveil hidden conformational states of monoamine oxidase from Aspergillus niger (MAO‐N). These hidden conformations, not previously observed by any other technique, play a crucial role in substrate binding and enzyme activity. This reveals how distal mutations regulate MAO‐N activity by stabilizing these hidden, catalytically important conformational states, but also by modulating the communication pathway between both MAO‐N subunits.     

Concentration of sodium ion as the determining factor for the association of dansyl amino acids with the teicoplanin molecule in reversed-phase liquid chromatography

The mechanism of the binding of D,L dansyl amino acids to teicoplanin was investigated. Na+ was used as an indicator of the interactions between the solutes and teicoplanin. The number (n) of sodium ions, Na+, excluded from the solute-teicoplanin interface when analyte transfer occurred was determined. A thermodynamic study and enthalpy-entropy compensation were performed to further explore the interaction mechanism. From these results, it was shown that teicoplanin was balanced between 2 conformational states characterized by distinct enantioselective properties. This approach indicates that liquid chromatography (LC) is a useful tool to extract physicochemical and molecular information from retention data. Thus, LC can be used as a complementary technique with the conventional techniques of molecular interaction analysis.     

Constitutional self-selection of [2 x 2] homonuclear grids from a dynamic mixture of copper(I) and silver(I) metal complexes

This paper describes the controlled self-selection and quantitative parallel amplification of the homonuclear grid architectures derived from the same ligand 1 of different conformational geometries and Cu+ and Ag+ metal ions of different coordination behavior and ionic size.     

Photochemically and electrochemically triggered Au nanoparticles "sponges"

Stimuli-triggered wettability of surfaces and controlled uptake and release of substrates by "smart" materials are essential for drug delivery and microfluidic control. A composite "sponge" consisting of bis-aniline-bridged Au nanoparticles (NPs), functionalized with photoisomerizable nitrospiropyran/nitromerocyanine that includes selective imprinted molecular recognition sites for N,N'-bis(3-sulfonatopropyl)-4,4'-bipyridinium (PVS) was electropolymerized on a Au electrode. The system is triggered by photonic and/or electrical signals to yield four different states exhibiting variable binding/release capacities for PVS and controlled wettability of the surface. The electrical/optical uptake and release of PVS to and from the Au NPs "sponge", respectively, is followed by CdSe/ZnS quantum dots, acting as an auxiliary photonic label.