Molecular Spacer Research Articles

Label-free, zeptomole cancer biomarker detection by surface-enhanced fluorescence on nanoporous gold disk plasmonic nanoparticles.

We experimentally demonstrate a label-free biosensor for the ERBB2 cancer gene DNA target based on the distance-dependent detection of surface-enhanced fluorescence (SEF) on nanoporous gold disk (NPGD) plasmonic nanoparticles. We achieve detection of 2.4 zeptomole of DNA target on the NPGD substrate with an upper concentration detection limit of 1 nM. Without the use of molecular spacers, the NPGD substrate as an SEF platform was shown to provide higher net fluorescence for visible and NIR fluorophores compared to glass and non-porous gold substrates. The enhanced fluorescence signals in patterned nanoporous gold nanoparticles make NPGD a viable material for further reducing detection limits for biomolecular targets used in clinical assays. With patterned nanoporous gold disk (NPGD) plasmonic nanoparticles, a label-free biosensor that makes use of distance-dependent detection of surface-enhanced fluorescence (SEF) is constructed and tested for zeptomole detection of ERBB2 cancer gene DNA targets.

Synthesis of a ditopic homooxacalix[3]arene for fluorescence enhanced detection of heavy and transition metal ions

A pyrene-appended ratiometric fluorescent chemosensor L based on a synthetic approach of insulating the fluorophore from the ionophore by a specific molecular spacer has been synthesised and characterised. The fluorescence spectra changes of L suggested that the chemosensor can detect heavy and transition metal (HTM) ions ratiometrically and with variable sensitivity according to the substituents present. 1H NMR titration experiments indicated that the three triazole ligands prefer binding with Hg2+, Pb2+ and Zn2+, resulting in a conformational change that produces monomer emission of the pyrene accompanied by the excimer quenching. However, the addition of Fe3+, which may be accommodated by the cavity of L, makes the pyrene units move closer to each other, and a discernible increase in the emission intensity of the static excimer is observed. Therefore, it is believed that the ditopic scaffold of the calix[3]arene as a specific molecular spacer here plays an important role in the blocking of the heavy atom effect of HTM ions by insulating the fluorophore from the ionophore given the long distance between the metal cation and the pyrene moiety.

Unified picture of the doping dependence of superconducting transition temperatures in alkali metal/ammonia intercalated FeSe

In the recently synthesized ${\mathrm{Li}}_{x}{({\mathrm{NH}}_{2})}_{y}{({\mathrm{NH}}_{3})}_{z}{\mathrm{Fe}}_{2}{\mathrm{Se}}_{2}$ family of iron chalcogenides, a molecular spacer consisting of lithium ions, lithium amide, and ammonia separates the layers of FeSe. It has been shown that upon variation of the chemical composition of the spacer layer, superconducting transition temperatures can reach ${T}_{c}\ensuremath{\sim}44\phantom{\rule{0.28em}{0ex}}\mathrm{K}$, but the relative importance of the layer separation and effective doping to the ${T}_{c}$ enhancement is currently unclear. Using state of the art band structure unfolding techniques, we construct eight-orbital models from ab initio density functional theory calculations for these materials. Within an RPA spin-fluctuation approach, we show that the electron doping enhances the superconducting pairing, which is of ${s}_{\ifmmode\pm\else\textpm\fi{}}$ symmetry and explain the experimentally observed limit to ${T}_{c}$ in the molecular spacer intercalated FeSe class of materials.

Adsorption studies of divalent, dinuclear coordination complexes as molecular spacers on SWCNTs.

In order to enhance the electrical energy storage capabilities of nanostructured carbon materials, inter-particle spacer strategies are needed to maintain ion-accessible surface area between the nanoparticles. This paper presents a comparison between different classes of divalent, dinuclear coordination complexes which both show strong adsorption to SWCNTs and have molecular spacer properties that maintain electrochemical activity. We find that a novel, dinuclear zinc hydrazone complex binds as an ion-pair at very high loading while not inducing significant aggregation as compared to our previously studies of dinuclear ruthenium complexes. These conclusions are supported by conductivity and dispersion stability data. Moreover, since zinc is an earth abundant metal, these complexes can be used as components in sustainable energy storage materials. Binding kinetics and binding equilibrium data are presented. Modeling of the adsorption isotherm is best fit with the BET model. Kinetics data support an independent binding model. Preliminary capacitance and membrane resistance data are consistent with the complexes acting as molecular spacers between the SWCNTs in a condensed thin film.

Unfolding the contents of sub-nm plasmonic gaps using normalising plasmon resonance spectroscopy.

Plasmonic coupling of gold nanoparticles to a gold surface creates intense plasmonic hot spots with large electromagnetic field-enhancements within the cavity formed by the two metallic surfaces. The localised field in such structures is extremely sensitive to morphological fluctuations and subtle changes in the dielectric properties of the cavity contents. Here, we present an optical method that pins down the properties of the gap contents with high sensitivity, termed normalising plasmon resonance (NPR) spectroscopy. We use this on a variety of ultrathin molecular spacers such as filled and empty cucurbiturils, and graphene. Clear differences in the spectral positions and intensities of plasmonic modes observed in the scattering spectrum resolve thickness differences of 0.1 nm, and refractive index changes from molecular filling.

Rapid identification of environmental NTM species using molecular genotyping

Background and objectiveNontuberculosis mycobacteria (NTM) are free-living saprophytes that are found in water, soil, animals and dairy products. During recent years, advances in molecular biology improved the recovery and accuracy of NTM identification. In the present study, similar approaches were used to differentiate environmental NTM. For this reason, the prevalence of environmental NTM in soil and water in two densely populated areas of Tehran were investigated. Material and methodsA total of 2,540 samples were collected from soil (n=1237) and water (n=1303) resources. For the soil sample: digestion and decontamination were performed using modified Engbaeks method, and for the water sample: decontamination followed with ethylpyridinium chloride (CPC; final concentration of 0.05%) and standard protocol. The phenotypic and genotyping tests were performed on all positive cultures. For molecular tests, both 16S-23S RNA and hsp65 genes spacer PCR-RFLP were used. ResultsOf the 2,540 collected samples, 285 (12%) were positive for mycobacterium. One hundred and sixty-nine (169; 60%) belonged to a slow growing mycobacteria (SGM) and 116 (41%) were rapid growing mycobacteria (RGM). The most frequent NTM were identified as Mycobacterium farcinogenes (51/485; 10.5%) and Mycobacterium fortuitum (38/485; 7.8%). However, M. farcinogenes is found to be dominant in both studied areas, but the frequency of RGM was different. In Shahre-ray, Mycobacterium senegalense was identified as the most frequent RGM (22/65; 34%), while in Varamin, M. fortuitum (20/51; 40%) had the most frequency. ConclusionThe molecular genotyping methods facilitate the rapid identification of environmental NTM. As the higher prevalence of NTM within a region increases the risk of human infection, this study outlines the importance of further investigation.

Interfacial characterization of epoxy/silica nanocomposites measured by fluorescence

Fluorescence labeling was used as a tool for the interfacial characterization of nanocomposites. The solvatochromic probe dansyl chloride was employed as interfacial reporter in epoxy/silica nanocomposites. Molecular spacers (organosiloxanes and polyetheramines) of different lengths were used to vary the location of the chromophore at the interface. The steady state and time resolved fluorescent responses reflect a rigid polar interface. Fluorescence changes during heating at a constant rate were analyzed for determining the local glass transition (Tg) at the interface region. The fluorescence results were then compared to the Tg obtained from differential scanning calorimetry and the results showed the existence of a gradient interface of a few nanometers thick having different properties than the bulk matrix. The thickness of this interface is small but its altered dynamics due to strong interactions with the nanofiller spreads its influence throughout the whole matrix.

Electronic Structure of Self-Assembled Monolayers Modified with Ferrocene on a Gold Surface: Evidence of Electron Tunneling

The electron transfer mechanism for the prototypical system ferrocenoyl-glycylcystamine (Fc-Gly-CSA) on Au(111) is investigated within the framework of density functional theory. Different Fc-Gly-CSA/Au systems, including the explicit methanol solvent and sodium perchlorate counterion, are studied. As seen from the partial density of states, electronic contributions close to the Fermi energy are found to derive only from the ferrocene units and gold atoms, while the contributions from electronic states located on the molecular spacers (Gly-CSA) are detected at lower energies, with or without the effects of the environment. These results strongly indicate a direct ferrocene-to-gold tunneling as the electron transfer mechanism across the interface.

Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures.

In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The peptoids can be realized with cis amide bond if the side chain of ith residue can engage the carbonyl group of ith-1 residue in CH--O interactions. Simulations studies both in water and DMSO have been carried out. The peptoid Ac-(N(tle))(7) -NMe(2) can adopt degenerate conformations with alternate φ, ψ values of inverse PP-I and PP-I type structure's, or vice versa in water. In DMSO, Ac-(N(tle))(7)-NMe(2) also adopts inverse PP-I type structure. Like polyproline, molecule adopting a rigid structure can be used as molecular markers or spacers in biological studies.The peptoid Ac-(N(ala)-N(tle))(3)-NMe(2) with alternate trans and cis amide bond geometry for N(ala) and N(tle) residue corresponding to inverse PP-II/PP-II type and for N(tle) residue of PP-I type.

Distinguishing localized surface plasmon resonance and Schottky junction of Au-Cu₂O composites by their molecular spacer dependence.

The surface plasmon resonance (SPR) and Schottky effects are important photocatalytic activity boosters in metallic cocatalyst/photocatalyst systems, but it is difficult to differentiate them. In this report, we design a simple method to distinguish the two effects by utilizing a distance-tunable self-assembled monolayer (SAM) in a gold (Au)-Cu2O composite in conjunction with UV and visible-light sources, by which we had only the SPR or Schottky effect identified in the visible or UV light, respectively. Cysteine (cys) and mercaptoundecanoic acid (MUA) SAMs as linkers were used respectively for making Au-cys-Cu2O and Au-MUA-Cu2O composites. Au-citrate-Cu2O as a mild linker was also synthesized. Under UV-light irradiation, Au-Cu2O showed only the Schottky effect, while Au-MUA-Cu2O and Au-cys-Cu2O showed neither of the two effects. Under visible-light irradiation, Au-MUA-Cu2O and Au-cys-Cu2O showed clearly only the localized SPR (LSPR) effect, while Au-Cu2O demonstrated the coexistence of the two effects, which was further confirmed by their LSPR enhancement factor.

Suitability of the molecular subtyping methods intergenic spacer region, direct genome restriction analysis, and pulsed-field gel electrophoresis for clinical and environmental Vibrio parahaemolyticus isolates.

Vibrio parahaemolyticus is the leading cause of infectious illness associated with seafood consumption in the United States. Molecular fingerprinting of strains has become a valuable research tool for understanding this pathogen. However, there are many subtyping methods available and little information on how they compare to one another. For this study, a collection of 67 oyster and 77 clinical V. parahaemolyticus isolates were analyzed by three subtyping methods--intergenic spacer region (ISR-1), direct genome restriction analysis (DGREA), and pulsed-field gel electrophoresis (PFGE)--to determine the utility of these methods for discriminatory subtyping. ISR-1 analysis, run as previously described, provided the lowest discrimination of all the methods (discriminatory index [DI]=0.8665). However, using a broader analytical range than previously reported, ISR-1 clustered isolates based on origin (oyster versus clinical) and had a DI=0.9986. DGREA provided a DI=0.9993-0.9995, but did not consistently cluster the isolates by any identifiable characteristics (origin, serotype, or virulence genotype) and ∼ 15% of isolates were untypeable by this method. PFGE provided a DI=0.9998 when using the combined pattern analysis of both restriction enzymes, SfiI and NotI. This analysis was more discriminatory than using either enzyme pattern alone and primarily grouped isolates by serotype, regardless of strain origin (clinical or oyster) or presence of currently accepted virulence markers. These results indicate that PFGE and ISR-1 are more reliable methods for subtyping V. parahemolyticus, rather than DGREA. Additionally, ISR-1 may provide an indication of pathogenic potential; however, more detailed studies are needed. These data highlight the diversity within V. parahaemolyticus and the need for appropriate selection of subtyping methods depending on the study objectives.

Electron Transfer Dynamics of Supramolecular Solar Cells

Habtom B. Gobeze and Francis D’Souza*Department of Chemistry, University North Texas, 1155, Union Circle, #305070, Denton, TX 76203-5017, USAFrancis.DSouza@unt.eduThe relation between energy positioning and adsorption geometry on the electron transfer dynamics of donor-acceptor photosynthetic model compounds immobilized mesoporous TiO2 surface will be presented. Novel Zn-porphyrin (ZnP) and Zn-phthalocyanine (ZnPc) electron-donor and fullerene (C60) electron-acceptor bearing photosynthetic model compounds are designed to build supramolecular dye-sensitized solar cells (DSSC). It has been found that the solar cell efficiencies normalized for surface coverage (ηrel) are affected by the molecular spacer connecting the porphyrin sensitizer to the TiO2 surface, orientation of the dye molecule, the sensitization conditions (solvent and time) and dye aggregation. Ultrafast transient absorption spectroscopy shows that the forward and reverse electron transfer rates are strongly dependent on the spacer and sensitization conditions. These results also indicate that the electron transfer between sensitizer and TiO2 occurs “through-space” rather than “through-molecular spacer”. Implications of these findings for optimized solar energy/fuel production, and future sensor/biosensor development will be discussed.

Nacre Protein Sequence Compartmentalizes Mineral Polymorphs in Solution

The Japanese pearl oyster (Pinctada fucata) n16 framework matrix protein is an integral part of the growth and formation of the mollusk shell biomineralization mechanism. It is a required component of the extracellular matrix with a dual mineralization role, as an anchor component to synchronize the assembly of the beta-chitin and N-series, Pif-series protein extracellular matrix for aragonite formation and as a regulator of aragonite formation itself. However, the mechanism by which this protein controls aragonite formation is not understood. Here, we investigate the mineralization potential and kinetics of the 30 AA N-terminal portion of the n16 protein, n16N. This sequence has been demonstrated to form either vaterite or aragonite depending upon conditions. Using in situ potentiometric titration methods, we find that n16N is indeed responsible for the self-assembly characteristics found in vivo and in vitro but is not involved with active Ca2+ binding or mineral nucleation processes. Upon the basis of time- and peptide concentration-dependent sampling of mineral deposits that form in solution, we find that n16N is responsible for controlling where mineralization occurs in bulk solution. This protein sequence acts as a molecular spacer that organizes the mineralization space and promotes the formation of mineral constituents that contain ACC, vaterite, and aragonite. Without the concerted action of the n16N assemblage, unregulated calcite formation occurs exclusively. Thus, the n16 protein provides the regulation needed to have the characteristic polymorph, crystalline orientations, and related mechanical properties associated to the microstructure of mollusk shells.

Universal self-assembly of organosilanes with long alkyl groups into silicone nanofilaments

Recently, a new group of nanostructures called “silicone nanofilaments (SNs)” were prepared via polymerization of organosilanes with small alkyl groups. Organosilanes with long alkyl groups tend to form self-assembled monolayers and cannot form SNs because of their bulky steric hindrance. Here we report the one-step self-assembly of organosilanes with long alkyl groups into SN coatings at room temperature by using tetraethyl orthosilicate (TEOS) or tetrachlorosilane (TCS) as the molecular spacer. The SNs should grow according to a “limiting growth” mechanism via a “seeding-asymmetric growth-further growth” process. The growth of SNs could be controlled simply by the composition of the precursor and the water concentration (Cwater) in toluene. All the precursors studied can form SNs successfully under proper conditions, indicating universality of this method. The wettability of the SN coatings ranges from hydrophilic to superhydrophobic and even to superamphiphobic. Moreover, these coatings are transparent and can be easily applied onto various substrates besides the glass slide. This facile fabrication of SNs using organosilanes with long alkyl groups will shed light on their application in generating unique nanostructures besides self-assembled monolayers.

Reprogramming an ATP-Driven Biological Machine into a Light-Gated Protein Nanocage

Supramolecular protein assemblies are attractive materials for engineering nanoscale machines with controllable functions. Protein monomers have been engineered to self-assemble into symmetrical complexes, metal-templated structures and cage-like architectures. The mechanistic complexity of protein machines, however, has made it difficult to engineer assemblies with not only new architectures but also desired functions. Here we describe an approach to controlling functional states of a protein assembly with light. The approach uses covalently attached molecular spacers that reversibly switch interatomic distances upon illumination. We applied this strategy to convert an ATP-dependent homo-oligomeric group II chaperonin to a light-driven machine that undergoes large-scale conformational changes between open and closed states visualized by single particle cryo-electron microscopy. The resulting light-gated nanocontainer can capture and release non-native cargos. The design principle of alternately stabilizing conformational states by switching atomic distances illuminates the cooperativity of evolved protein assemblies and provides a strategy for engineering other light-controlled biologically inspired machines.View Large Image | View Hi-Res Image | Download PowerPoint Slide

Effect of motional restriction on the unfolding properties of a cytochrome c featuring a His/Met–His/His ligation switch

The K72A/K73H/K79A variant of cytochrome c undergoes a reversible change from a His/Met to a His/His axial heme ligation upon urea-induced unfolding slightly below neutral pH. The unfolded form displays a dramatically lower reduction potential than the folded species along with a pseudo-peroxidase activity. We have studied electrochemically the effects of urea-induced unfolding on the protein electrostatically immobilized on an electrode surface functionalized by means of a negatively charged molecular spacer. The latter mimics the electrostatic interaction with the inner mitochondrial membrane. This behavior has been compared with the unfolding of the same species in solution. This system constitutes a model to decipher the role of the above electrostatic interaction in the unfolding of cytochrome c at physiological pH upon interaction with the membrane component phospholipid cardiolipin in the early stages of the apoptosis cascade. We found that immobilization obstacles protein unfolding due to structural constraints at the interface imposed by protein-SAM interaction.

Database of protein complexes with multivalent binding ability: Bival‐bind

Phenomena of multivalent binding of ligands with receptors are ubiquitous in biology and of growing interest in material sciences. Multivalency can enhance binding affinity dramatically. To understand the mechanism of multivalent binding in more detail model systems of bi- and multivalent receptors are needed, but are difficult to find. Furthermore it is useful to know about multivalent receptors, which can serve as targets to design multivalent drugs. The present contribution tries to close this gap. The Bival-Bind database (http://agknapp.chemie.fu-berlin.de/bivalbind) provides a relatively complete list - 2073 protein complexes with less than 90% sequence identity - out of the protein database, which can serve as bi- or multivalent receptors. Steric clashes of molecular spacers - necessary to connect the monomeric ligand units - with the receptor surface can diminish binding affinity dramatically and, thus, abolish the expected enhancement of binding affinity due to the multivalency. The potential multivalent receptors in the Bival-Bind database are characterized with respect to the receptor surface topography. A height profile between the receptor binding pockets is provided, which is an important information to estimate the influence of unfavorable spacer receptor interaction.

Reduction of open circuit voltage loss in a polymer photovoltaic cell via interfacial molecular design: Insertion of a molecular spacer

Loss to the open circuit voltage (Voc) in organic photovoltaic cells is a critical bottleneck to achieving high power conversion efficiency. We demonstrate that the insertion of multilayers of a poly(phenylene ethynylene) spacer into the planar heterojunction between poly(3-hexylthiophene) and phenyl-C61-butyric acid methyl ester incrementally escalates the Voc of a polymer solar cell from 0.43 V to 0.9 V. Through a combination of light intensity and temperature dependent measurements, we show that this control over the molecular structure local to the interface increases Voc by raising the polaron pair energy and by suppressing the dark-diode current.

Multiple, consecutive, fully‐extended 2.05‐helix peptide conformation

The peptide 2.0(5)-helix does exist. It has been experimentally authenticated both in the crystalline state (by X-ray diffraction) and in solution (by several spectroscopic techniques). It is the most common conformation for C(α)-tetrasubstituted α-amino acids with at least two atoms in each side chain, provided that cyclization on the C(α)-atom is absent. X-Ray diffraction has allowed a detailed description of its geometrical and three-dimensional (3D)-structural features. The infrared absorption and the nuclear magnetic resonance parameters characteristics of this multiple, consecutive, fully-extended structure have been described. Conformational energy calculations are in agreement with the experimental findings. As the contribution per amino acid residue to the length of this helix is the longest possible, its exploitation as a molecular spacer is quite promising. However, it is a rather fragile 3D-structure and particularly sensitive to solvent polarity. Interestingly, in such a case, it may reversibly convert to the much shorter 3(10)-helix, thus generating an attractive molecular spring.

Spacer effect on nanostructures and self-assembly in organogels via some bolaform cholesteryl imide derivatives with different spacers

In this paper, new bolaform cholesteryl imide derivatives with different spacers were designed and synthesized. Their gelation behaviors in 23 solvents were investigated, and some of them were found to be low molecular mass organic gelators. The experimental results indicated that these as-formed organogels can be regulated by changing the flexible/rigid segments in spacers and organic solvents. Suitable combination of flexible/rigid segments in molecular spacers in the present cholesteryl gelators is favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle and belt to fiber with the change of spacers and solvents. Spectral studies indicated that there existed different H-bond formations between imide groups and assembly modes, depending on the substituent spacers in molecular skeletons. The present work may give some insight into the design and character of new organogelators and soft materials with special molecular structures.