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1.  Polymerization or Cyclic Dimerization: Solvent Dependent Homo-Coupling of Terminal Alkynes at HOPG Surface 
Scientific Reports  2014;4:3899.
Surface reactivity has become one of the most important issues in surface chemistry over the past few years. In this work, we, for the first time, have investigated the homo-coupling of a special terminal alkyne derivative on the highly oriented pyrolitic graphite (HOPG) surface. Using scanning tunneling microscopy (STM) technique, we have found that such coupling reaction seriously depends on the supramolecular assembly of the monomer on the studied substrate, whereas the latter appears an obvious solvent effect. As a result, the reaction in our system undergoes polymerization and cyclic dimerization process in 1-phenyloctane and 1,2,4-trichlorobenzene, respectively. That is to say, the solvent effect can be extended from the two-dimensional (2D) supramolecular self-assembly to surface chemical reactions, and the selective homo-coupling has been successfully achieved at the solid/liquid interface.
doi:10.1038/srep03899
PMCID: PMC3904147  PMID: 24469357
2.  Surface Confined Metallosupramolecular Architectures: Formation and STM Characterization 
Accounts of chemical research  2009;42(2):249-259.
CONSPECTUS
Metallosupramolecular compounds have attracted a great deal of attention over the past two decades largely because of their unique, highly-complex structural characteristics, the fact that they can be prepared with relative ease using coordination-driven self-assembly techniques, and their potential electronic, magnetic, optical, and catalytic properties. In particular, the use of electron-poor square planar Pt(II) transition metals in conjunction with rigid, electron-rich pyridyl donors had enabled the spontaneous self-assembly of a rich library of 2D metallacyclic and 3D metallacage assemblies via the directional-bonding approach. With the tremendous progress that has been made in the preparation and characterization of metallosupramolecules, much attention is now being turned toward fully exploring and developing their materials properties.
Assembling metallosupramolecular compounds on solid supports represents a vitally important step toward developing their materials properties. Surfaces provide a means of uniformly aligning and orienting these highly symmetric metallacycles and metallacages, which increases the level of coherence between molecules above that which can be achieved in the solution phase and affords a means of integrating adlayers into a solid-state materials setting. The dynamic nature of kinetically labile Pt(II)-N coordination bonds, however, requires that deposition and imaging conditions be appropriate to retain the assemblies' stability. Toward these aims it is imperative to understand the factors that govern surface self-assembly and the interactions that influence the structure and stability of the resulting adlayer. Such insight can be obtained from Scanning Tunneling Microscopy (STM), which has emerged as a powerful technique for the imaging and characterization of self-assembled adlayers.
This account describes the means by which 2D rectangular and square metallacycles and 3D trigonal bipyrimidal and chiral trigonal prism metallacages can be deposited on Highly Oriented Pyrolytic Graphite (HOPG) and Au(111) substrates such that the assemblies remain intact and result in ordered adlayers. The effects of varying the size, symmetry, and dimensionality of supramolecular adsorbates, the choice of substrate, the use of a molecular template, and the effects of chirality have been investigated. These systematic investigations provide much insight into the various adsorbate-adsorbate and substrate-adsorbate interactions that largely determine the architecture of each assembly and affect their performance in a materials setting. Exhibiting the ability to rationally control adlayer formation and structure will greatly enhance the potential of these supramolecules to be used in a variety of applications such as in host-guest sensing/diagnostic systems, molecular electronic devices, and in heterogeneous stereoselective synthesis and catalysis.
doi:10.1021/ar800117j
PMCID: PMC2654282  PMID: 19072706
3.  Septipyridines as conformationally controlled substitutes for inaccessible bis(terpyridine)-derived oligopyridines in two-dimensional self-assembly 
Summary
The position of the peripheral nitrogen atoms in bis(terpyridine)-derived oligopyridines (BTPs) has a strong impact on their self-assembly behavior at the liquid/HOPG (highly oriented pyrolytic graphite) interface. The intermolecular hydrogen bonding interactions in these peripheral pyridine units show specific 2D structures for each BTP isomer. From nine possible constitutional isomers only four have been described in the literature. The synthesis and self-assembling behavior of an additional isomer is presented here, but the remaining four members of the series are synthetically inaccessible. The self-assembling properties of three of the missing four BTP isomers can be mimicked by making use of the energetically preferred N–C–C–N transoid conformation between 2,2'-bipyridine subunits in a new class of so-called septipyridines. The structures are investigated by scanning tunneling microscopy (STM) and a combination of force-field and first-principles electronic structure calculations.
doi:10.3762/bjnano.2.46
PMCID: PMC3190612  PMID: 22003448
oligopyridines; self-assembled monolayer; STM
4.  Nanopatterning of Donor/Acceptor Hybrid Supramolecular Architectures on HOPG: An STM Study 
Journal of the American Chemical Society  2008;130(40):13433-13441.
Hybrid supramolecular architectures have been fabricated with acceptor 1,4-bis(4-pyridylethynyl)-2,3-bis-dodecyloxy-benzene (PBP) and donor 2,6-bis(3,4,5-tris-dodecyloxy-phenyl)dithieno[3,2-b:2′,3′-d]thiophene (DTT) compounds on highly oriented pyrolytic graphite (HOPG) surfaces and their structures and molecular conductance are characterized by scanning tunneling microscopy/spectroscopy (STM/STS). Stable, one-component adlayers of PBP and DTT are also investigated. The coadsorption of two-component mixtures of PBP and DTT results in a variety of hybrid nanopattern architectures that differ from those of their respective one-component surface assemblies. Adjusting the acceptor/donor molar ratio in mixed adlayer assemblies results in dramatic changes in the structure of the hybrid nanopatterns. STS measurements indicate that the HOMO and LUMO energy levels of PBP and DTT on an HOPG surface are relatively insensitive to changes in the hybrid supramolecular architectures. These results provide important insight into the design and fabrication of two-dimensional hybrid supramolecular architectures.
doi:10.1021/ja8040515
PMCID: PMC2653624  PMID: 18783221
5.  The Self-Assembled Behavior of DNA Bases on the Interface 
A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.
doi:10.3390/ijms15021901
PMCID: PMC3958828  PMID: 24473140
DNA base; self-assembly; interface chemistry; scanning tunneling microscopy
6.  Dimer/tetramer motifs determine amphiphilic hydrazine fibril structures on graphite 
Summary
Fibril structures are produced at a solvent–graphite interface by self-assembly of custom-designed symmetric and asymmetric amphiphilic benzamide derivatives bearing C10 aliphatic chains. Scanning tunnelling microscopy (STM) studies reveal geometry-dependent internal structures for the elementary fibrils of the two molecules that are distinctly different from known mesophase bulk structures. The structures are described by building-block models based on hydrogen-bonded dimer and tetramer precursors of hydrazines. The closure and growth in length of building units into fibrils takes place through van der Waals forces acting between the dangling alkyl chains. The nanoscale morphology is a consequence of the basic molecular geometry, where it follows that a closure to form a fibril is not always likely for the doubly substituted hydrazine. Therefore, we also observe crystallite formation.
doi:10.3762/bjnano.3.75
PMCID: PMC3458612  PMID: 23019562
fibrils; graphite; hydrazide; hydrazine; interface; self-assembly; STM
7.  Modification of Hydrophilic and Hydrophobic Surfaces Using an Ionic-Complementary Peptide 
PLoS ONE  2007;2(12):e1325.
Ionic-complementary peptides are novel nano-biomaterials with a variety of biomedical applications including potential biosurface engineering. This study presents evidence that a model ionic-complementary peptide EAK16-II is capable of assembling/coating on hydrophilic mica as well as hydrophobic highly ordered pyrolytic graphite (HOPG) surfaces with different nano-patterns. EAK16-II forms randomly oriented nanofibers or nanofiber networks on mica, while ordered nanofibers parallel or oriented 60° or 120° to each other on HOPG, reflecting the crystallographic symmetry of graphite (0001). The density of coated nanofibers on both surfaces can be controlled by adjusting the peptide concentration and the contact time of the peptide solution with the surface. The coated EAK16-II nanofibers alter the wettability of the two surfaces differently: the water contact angle of bare mica surface is measured to be <10°, while it increases to 20.3±2.9° upon 2 h modification of the surface using a 29 µM EAK16-II solution. In contrast, the water contact angle decreases significantly from 71.2±11.1° to 39.4±4.3° after the HOPG surface is coated with a 29 µM peptide solution for 2 h. The stability of the EAK16-II nanofibers on both surfaces is further evaluated by immersing the surface into acidic and basic solutions and analyzing the changes in the nanofiber surface coverage. The EAK16-II nanofibers on mica remain stable in acidic solution but not in alkaline solution, while they are stable on the HOPG surface regardless of the solution pH. This work demonstrates the possibility of using self-assembling peptides for surface modification applications.
doi:10.1371/journal.pone.0001325
PMCID: PMC2117347  PMID: 18091996
8.  Diffusion of hydrophobin proteins in solution and interactions with a graphite surface 
BMC Biophysics  2011;4:9.
Background
Hydrophobins are small proteins produced by filamentous fungi that have a variety of biological functions including coating of spores and surface adhesion. To accomplish these functions, they rely on unique interface-binding properties. Using atomic-detail implicit solvent rigid-body Brownian dynamics simulations, we studied the diffusion of HFBI, a class II hydrophobin from Trichoderma reesei, in aqueous solution in the presence and absence of a graphite surface.
Results
In the simulations, HFBI exists in solution as a mixture of monomers in equilibrium with different types of oligomers. The oligomerization state depends on the conformation of HFBI. When a Highly Ordered Pyrolytic Graphite (HOPG) layer is present in the simulated system, HFBI tends to interact with the HOPG layer through a hydrophobic patch on the protein.
Conclusions
From the simulations of HFBI solutions, we identify a tetrameric encounter complex stabilized by non-polar interactions between the aliphatic residues in the hydrophobic patch on HFBI. After the formation of the encounter complex, a local structural rearrangement at the protein interfaces is required to obtain the tetrameric arrangement seen in HFBI crystals. Simulations performed with the graphite surface show that, due to a combination of a geometric hindrance and the interaction of the aliphatic sidechains with the graphite layer, HFBI proteins tend to accumulate close to the hydrophobic surface.
doi:10.1186/2046-1682-4-9
PMCID: PMC3114038  PMID: 21595866
9.  Local Electronic and Chemical Structure of Oligo-acetylene Derivatives Formed Through Radical Cyclizations at a Surface 
Nano Letters  2014;14(5):2251-2255.
Semiconducting π-conjugated polymers have attracted significant interest for applications in light-emitting diodes, field-effect transistors, photovoltaics, and nonlinear optoelectronic devices. Central to the success of these functional organic materials is the facile tunability of their electrical, optical, and magnetic properties along with easy processability and the outstanding mechanical properties associated with polymeric structures. In this work we characterize the chemical and electronic structure of individual chains of oligo-(E)-1,1′-bi(indenylidene), a polyacetylene derivative that we have obtained through cooperative C1–C5 thermal enediyne cyclizations on Au(111) surfaces followed by a step-growth polymerization of the (E)-1,1′-bi(indenylidene) diradical intermediates. We have determined the combined structural and electronic properties of this class of oligomers by characterizing the atomically precise chemical structure of individual monomer building blocks and oligomer chains (via noncontact atomic force microscopy (nc-AFM)), as well as by imaging their localized and extended molecular orbitals (via scanning tunneling microscopy and spectroscopy (STM/STS)). Our combined structural and electronic measurements reveal that the energy associated with extended π-conjugated states in these oligomers is significantly lower than the energy of the corresponding localized monomer orbitals, consistent with theoretical predictions.
doi:10.1021/nl403791q
PMCID: PMC4022646  PMID: 24387223
Conducting polymers; C1−C5 thermal enediyne cyclization; radical step-growth polymerization; noncontact atomic force microscopy (nc-AFM); scanning tunneling microscopy (STM); density functional theory (DFT)
10.  Binding Modes of Thioflavin T Molecules to Prion Peptide Assemblies Identified by Using Scanning Tunneling Microscopy 
ACS Chemical Neuroscience  2011;2(6):281-287.
The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.
doi:10.1021/cn200006h
PMCID: PMC3369759  PMID: 22778872
GNNQQNY; thioflavin T; binding mode; amyloid; labeling molecule; scanning tunneling microscopy
11.  Beta-Strand Interfaces of Non-Dimeric Protein Oligomers Are Characterized by Scattered Charged Residue Patterns 
PLoS ONE  2012;7(4):e32558.
Protein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual β-strands (β-interfaces), but are otherwise unrelated. The results show that the β-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each one has its own characteristics which can be associated to a distinct role. The secondary structure of the β-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular β-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charged residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular β-strands, of intramolecular β-strands and of β-strands forming β-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the β-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a β-interface formation. Such β-strands could be considered as ‘assemblons’, independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development.
doi:10.1371/journal.pone.0032558
PMCID: PMC3322119  PMID: 22496732
12.  STM visualisation of counterions and the effect of charges on self-assembled monolayers of macrocycles 
Summary
Despite their importance in self-assembly processes, the influence of charged counterions on the geometry of self-assembled organic monolayers and their direct localisation within the monolayers has been given little attention. Recently, various examples of self-assembled monolayers composed of charged molecules on surfaces have been reported, but no effort has been made to prove the presence of counterions within the monolayer. Here we show that visualisation and exact localisation of counterions within self-assembled monolayers can be achieved with scanning tunnelling microscopy (STM). The presence of charges on the studied shape-persistent macrocycles is shown to have a profound effect on the self-assembly process at the liquid–solid interface. Furthermore, preferential adsorption was observed for the uncharged analogue of the macrocycle on a surface.
doi:10.3762/bjnano.2.72
PMCID: PMC3201620  PMID: 22043456
counterions; liquid–solid interface; macrocycles; scanning tunnelling microscopy; self-assembly
13.  Molecular Engineering of Supramolecular Scaffold Coatings that Can Reduce Static Platelet Adhesion 
Novel supramolecular coatings that make use of low molecular weight ditopic monomers with guanine end groups are studied using fluid tapping AFM. These molecules assemble on highly oriented pyrolytic graphite (HOPG) from aqueous solutions to form nano-sized banding structures whose sizes can be systematically tuned at the nano-scale by tailoring the molecular structure of the monomers. The nature of the self-assembly in these systems has been studied through a combination of the self-assembly of structural derivatives and molecular modeling. Furthermore, we introduce the concept of using these molecular assemblies as scaffolds to organize functional groups on the surface. As a first demonstrationof this concept, scaffold monomers that contain a monomethyl triethyleneglycol branch were used to organize these “functional” units on a HOPG surface. These supramolecular grafted assemblies have been shown to be stable in biologically-relevant environments and even have the ability to significantly reduce static platelet adhesion.
doi:10.1021/ja0775927
PMCID: PMC2536642  PMID: 18177047
nanopattern; nanotechnology; surface assembly; supramolecular polymerization; surface thrombosis; biomaterial coating
14.  Structure, morphology, and magnetic properties of Fe nanoparticles deposited onto single-crystalline surfaces 
Summary
Background: Magnetic nanostructures and nanoparticles often show novel magnetic phenomena not known from the respective bulk materials. In the past, several methods to prepare such structures have been developed – ranging from wet chemistry-based to physical-based methods such as self-organization or cluster growth. The preparation method has a significant influence on the resulting properties of the generated nanostructures. Taking chemical approaches, this influence may arise from the chemical environment, reaction kinetics and the preparation route. Taking physical approaches, the thermodynamics and the kinetics of the growth mode or – when depositing preformed clusters/nanoparticles on a surface – the landing kinetics and subsequent relaxation processes have a strong impact and thus need to be considered when attempting to control magnetic and structural properties of supported clusters or nanoparticles.
Results: In this contribution we focus on mass-filtered Fe nanoparticles in a size range from 4 nm to 10 nm that are generated in a cluster source and subsequently deposited onto two single crystalline substrates: fcc Ni(111)/W(110) and bcc W(110). We use a combined approach of X-ray magnetic circular dichroism (XMCD), reflection high energy electron diffraction (RHEED) and scanning tunneling microscopy (STM) to shed light on the complex and size-dependent relation between magnetic properties, crystallographic structure, orientation and morphology. In particular XMCD reveals that Fe particles on Ni(111)/W(110) have a significantly lower (higher) magnetic spin (orbital) moment compared to bulk iron. The reduced spin moments are attributed to the random particle orientation being confirmed by RHEED together with a competition of magnetic exchange energy at the interface and magnetic anisotropy energy in the particles. The RHEED data also show that the Fe particles on W(110) – despite of the large lattice mismatch between iron and tungsten – are not strained. Thus, strain is most likely not the origin of the enhanced orbital moments as supposed before. Moreover, RHEED uncovers the existence of a spontaneous process for epitaxial alignment of particles below a critical size of about 4 nm. STM basically confirms the shape conservation of the larger particles but shows first indications for an unexpected reshaping occurring at the onset of self-alignment.
Conclusion: The magnetic and structural properties of nanoparticles are strongly affected by the deposition kinetics even when soft landing conditions are provided. The orientation of the deposited particles and thus their interface with the substrate strongly depend on the particle size with consequences regarding particularly the magnetic behavior. Spontaneous and epitaxial self-alignment can occur below a certain critical size. This may enable the obtainment of samples with controlled, uniform interfaces and crystallographic orientations even in a random deposition process. However, such a reorientation process might be accompanied by a complex reshaping of the particles.
doi:10.3762/bjnano.2.6
PMCID: PMC3045938  PMID: 21977415
epitaxy; iron; magnetic nanoparticles; Ni(111); RHEED; spontaneous self-alignment; STM; W(110); XMCD
15.  Quinacridone on Ag(111): Hydrogen Bonding versus Chirality 
Quinacridone (QA) has recently gained attention as an organic semiconductor with unexpectedly high performance in organic devices. The strong intermolecular connection via hydrogen bonds is expected to promote good structural order. When deposited on a substrate, another relevant factor comes into play, namely the 2D-chirality of the quinacridone molecules adsorbed on a surface. Scanning tunneling microscopy (STM) images of monolayer quinacridone on Ag(111) deposited at room temperature reveal the formation of quasi-one-dimensional rows of parallel quinacridone molecules. These rows are segmented into short stacks of a few molecules in which adjacent, flat-lying molecules of a single handedness are linked via hydrogen bonds. After annealing to a temperature of T = 550–570 K, which is close to the sublimation temperature of bulk quinacridone, the structure changes into a stacking of heterochiral quinacridone dimers with a markedly different intermolecular arrangement. Electron diffraction (LEED) and photoelectron emission microscopy (PEEM) data corroborate the STM findings. These results illustrate how the effects of hydrogen bonding and chirality can compete and give rise to very different (meta)stable structures of quinacridone on surfaces.
doi:10.1021/jp502148x
PMCID: PMC4032182  PMID: 24883168
16.  Synthesis of a library of oligothiophenes and their utilization as fluorescent ligands for spectral assignment of protein aggregates 
Organic & biomolecular chemistry  2011;9(24):8356-8370.
Molecular probes for selective identification of protein aggregates are important to advance our understanding of the molecular pathogenesis underlying protein aggregation diseases. Here we report the chemical design of a library of anionic luminescent conjugated oligothiophenes (LCOs), which can be utilized as ligands for detection of protein aggregates. Certain molecular requirements were shown to be necessary for detecting: i) early non-thioflavinophilic protein assemblies of Aβ1-42 and insulin preceding the formation of amyloid fibrils and ii) for obtaining distinct spectral signatures of the two main pathological hallmarks observed in human Alzheimer’s diease brain tissue (Aβ plaques and neurofibrillary tangles). Our findings suggest that a superior anionic LCO based ligand should have a backbone consisting of five to seven thiophene units and carboxyl groups extending the conjugated thiophene backbone. Such LCOs will be highly useful for studying the underlying molecular events of protein aggregation diseases and could also be utilized for the development of novel diagnostic tools for these diseases.
doi:10.1039/c1ob05637a
PMCID: PMC3326384  PMID: 22051883
17.  Absolute cross section for loss of supercoiled topology induced by 10 eV electrons in highly uniform /DNA/1,3-diaminopropane films deposited on highly ordered pyrolitic graphite 
The Journal of chemical physics  2013;139(5):10.1063/1.4817323.
It was recently shown that the affinity of doubly charged, 1–3 diaminopropane (Dap2+) for DNA permits the growth on highly ordered pyrolitic graphite (HOPG) substrates, of plasmid DNA films, of known uniform thickness [O. Boulanouar, A. Khatyr, G. Herlem, F. Palmino, L. Sanche, and M. Fromm, J. Phys. Chem. C 115, 21291–21298 (2011)]. Post-irradiation analysis by electrophoresis of such targets confirms that electron impact at 10 eV produces a maximum in the yield of single strand breaks that can be associated with the formation of a DNA− transient anion. Using a well-adapted deterministic survival model for the variation of electron damage with fluence and film thickness, we have determined an absolute cross section for strand-break damage by 10 eV electrons and inelastic scattering attenuation length in DNA-Dap complex films.
doi:10.1063/1.4817323
PMCID: PMC3812120  PMID: 23927289 CAMSID: cams3599
18.  Computational Modeling of Poly(alkylthiophene) Conductive Polymer Insertion into Phospholipid Bilayers 
We have previously demonstrated that some poly(alkylthiophenes) (PATs) are able to increase the electrical conductance of unsupported phospholipid bilayers and have hypothesized that this effect is due to the ability of some PAT side chains to permit stable insertion into the bilayer. We have further proposed the development of long-term intracellular electrodes based on that phenomenon. In this article, we apply molecular dynamics techniques to study the insertion of two model PATs into a patch of a lipid bilayer. Steered molecular dynamics is used to obtain potential trajectories of insertion, followed by umbrella sampling to determine the free-energy change upon insertion. Our results indicate that both branched-side-chain poly(3-(2-ethylhexyl)thiophene) (EHPT) and straight-side-chain poly(3-hexylthiophene) (HPT) are able to enter the bilayer but only EHPT can cross the center of the membrane and establish an electrical bridge. HPT penetrates the head groups but is not able to enter the alkyl tail phase. These findings support the feasibility of our electrode concept and raise questions regarding the mechanisms by which branched side chains grant PATs greater solubility in a lipid bilayer environment. The parameters and methods used in this study establish a novel framework for studying these and similar systems, and the results hold promise for the use of EHPT in biosensing and neural interfacing.
doi:10.1021/la070214v
PMCID: PMC2872182  PMID: 17867709
19.  Polythiophenes Containing In-Chain Cobaltabisdicarbollide Centers 
New cobalt(III) bis(dicarbollide) complexes covalently linked to two 2-oligothienyl units have been synthesized and electropolymerized in acetonitrile electrolyte in order to produce the corresponding polythiophene films containing in-chain metallic centers. The polymer films electrogenerated from the bithienyl (4b) and terthienyl (4c) derivatives display redox processes attributed to the Co(III)/Co(II) couple at ca. −1.1 V vs SCE and to the p-doping/undoping of the expected quaterthienyl and sexithienyl segments at ca. 0.8 V vs SCE. In contrast, the anodic oxidation of the thienyl (4a) derivative leads to passivation of the electrode surface. As the length of the oligothiophene substituents increases, the metallic and dicarbollide cage carbon atoms contributions in the HOMO decrease dramatically so that the highest occupied frontier orbitals of 4b and 4c can be considered as almost purely oligothiophene-based. From further UV–vis spectroscopy analysis, it is demonstrated that the polymer incorporating the sexithienyl segments is more conjugated than that with the quaterthienyl segments as the absorption maximum for the interband π–π* transition was observed at 410 and 448 nm for poly(4b) and poly(4c) respectively. Furthermore, these polymers display a more extended degree of conjugation than the parent oligothiophenes. Such features indicate a significant electronic delocalization through the cobaltabisdicarbollide moiety. Their conducting probe atomic force microscopy characterization indicates that poly(4b) and poly(4c) behave like heavily doped semiconductors rather than pure semiconductors. Mean conductivity values extracted from the current–voltage profiles are 1.4 ×10−4 and 7.5 ×10−4 S cm−1 for poly(4b) and poly(4c), respectively. Such materials are found to be efficient for the electrocatalytic reduction of protons to dihydrogen, as exemplified for poly(4b). The overpotential for hydrogen evolution is significantly decreased by ca. 230 mV with respect to that obtained with the bare electrode (measured for a current density of 1.4 mA cm−2 in the presence of 20 mM HBF4).
doi:10.1021/am9007424
PMCID: PMC2919152  PMID: 20356270
conducting polymers; metallopolymers; polythiophenes; carboranes; electropolymerization
20.  Controlling Self-Assembly of Engineered Peptides on Graphite by Rational Mutation 
ACS Nano  2012;6(2):1648-1656.
Self-assembly of proteins on surfaces is utilized in many fields to integrate intricate biological structures and diverse functions with engineered materials. Controlling proteins at bio-solid interfaces relies on establishing key correlations between their primary sequences and resulting spatial organizations on substrates. Protein self-assembly, however, remains an engineering challenge. As a novel approach, we demonstrate here that short dodecapeptides selected by phage display are capable of self-assembly on graphite and form long-range ordered biomolecular nanostructures. Using atomic force microscopy and contact angle studies, we identify three amino-acid domains along the primary sequence that steer peptide ordering and lead to nanostructures with uniformly displayed residues. The peptides are further engineered via simple mutations to control fundamental interfacial processes, including initial binding, surface aggregation and growth kinetics, and intermolecular interactions. Tailoring short peptides via their primary sequence offers versatile control over molecular self-assembly, resulting in well-defined surface properties essential in building engineered, chemically rich, bio-solid interfaces.
doi:10.1021/nn204631x
PMCID: PMC3304023  PMID: 22233341
molecular self-assembly; inorganic binding peptides; nanotechnology; sequence mutation; atomic force microscopy; molecular recognition; liquid-solid interface
21.  Soft Lithographic Functionalization and Patterning Oxide-free Silicon and Germanium 
The development of hybrid electronic devices relies in large part on the integration of (bio)organic materials and inorganic semiconductors through a stable interface that permits efficient electron transport and protects underlying substrates from oxidative degradation. Group IV semiconductors can be effectively protected with highly-ordered self-assembled monolayers (SAMs) composed of simple alkyl chains that act as impervious barriers to both organic and aqueous solutions. Simple alkyl SAMs, however, are inert and not amenable to traditional patterning techniques. The motivation for immobilizing organic molecular systems on semiconductors is to impart new functionality to the surface that can provide optical, electronic, and mechanical function, as well as chemical and biological activity.
Microcontact printing (μCP) is a soft-lithographic technique for patterning SAMs on myriad surfaces.1-9 Despite its simplicity and versatility, the approach has been largely limited to noble metal surfaces and has not been well developed for pattern transfer to technologically important substrates such as oxide-free silicon and germanium. Furthermore, because this technique relies on the ink diffusion to transfer pattern from the elastomer to substrate, the resolution of such traditional printing is essentially limited to near 1 μm.10-16
In contrast to traditional printing, inkless μCP patterning relies on a specific reaction between a surface-immobilized substrate and a stamp-bound catalyst. Because the technique does not rely on diffusive SAM formation, it significantly expands the diversity of patternable surfaces. In addition, the inkless technique obviates the feature size limitations imposed by molecular diffusion, facilitating replication of very small (<200 nm) features.17-23 However, up till now, inkless μCP has been mainly used for patterning relatively disordered molecular systems, which do not protect underlying surfaces from degradation.
Here, we report a simple, reliable high-throughput method for patterning passivated silicon and germanium with reactive organic monolayers and demonstrate selective functionalization of the patterned substrates with both small molecules and proteins. The technique utilizes a preformed NHS-reactive bilayered system on oxide-free silicon and germanium. The NHS moiety is hydrolyzed in a pattern-specific manner with a sulfonic acid-modified acrylate stamp to produce chemically distinct patterns of NHS-activated and free carboxylic acids. A significant limitation to the resolution of many μCP techniques is the use of PDMS material which lacks the mechanical rigidity necessary for high fidelity transfer. To alleviate this limitation we utilized a polyurethane acrylate polymer, a relatively rigid material that can be easily functionalized with different organic moieties. Our patterning approach completely protects both silicon and germanium from chemical oxidation, provides precise control over the shape and size of the patterned features, and gives ready access to chemically discriminated patterns that can be further functionalized with both organic and biological molecules. The approach is general and applicable to other technologically-relevant surfaces.
doi:10.3791/3478
PMCID: PMC3369651  PMID: 22214997
Bioengineering;  Issue 58;  Soft lithography;  microcontact printing;  protein arrays;  catalytic printing;  oxide-free silicon
22.  Terthiophene on Au(111): A scanning tunneling microscopy and spectroscopy study 
Summary
Terthiophene (3T) molecules adsorbed on herringbone (HB) reconstructed Au(111) surfaces in the low coverage regime were investigated by means of low-temperature scanning tunneling microscopy (STM) and spectroscopy (STS) under ultra-high vacuum conditions. The 3T molecules adsorb preferentially in fcc regions of the HB reconstruction with their longer axis oriented perpendicular to the soliton walls of the HB and at maximum mutual separation. The latter observation points to a repulsive interaction between molecules probably due to parallel electrical dipoles formed during adsorption. Constant-separation (I-V) and constant-current (z-V) STS clearly reveal the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals, which are found at −1.2 eV and +2.3 eV, respectively. The HOMO–LUMO gap corresponds to that of a free molecule, indicating a rather weak interaction between 3T and Au(111). According to conductivity maps, the HOMO and LUMO are inhomogeneously distributed over the adsorbed 3T, with the HOMO being located at the ends of the linear molecule, and the LUMO symmetrically with respect to the longer axis of the molecule at the center of its flanks. Analysis of spectroscopic data reveals details of the contrast mechanism of 3T/Au(111) in STM. For that, the Shockley-like surface state of Au(111) plays an essential role and appears shifted outwards from the surface in the presence of the molecule. As a consequence, the molecule can be imaged even at a tunneling bias within its HOMO–LUMO gap. A more quantitative analysis of this detail resolves a previous discrepancy between the fairly small apparent STM height of 3T molecules (1.4–2.0 nm, depending on tunneling bias) and a corresponding larger value of 3.5 nm based on X-ray standing wave analysis. An additionally observed linear decrease of the differential tunneling barrier at positive bias when determined on top of a 3T molecule is compared to the bias independent barrier obtained on bare Au(111) surfaces. This striking difference of the barrier behavior with and without adsorbed molecules is interpreted as indicating an adsorption-induced dimensionality transition of the involved tunneling processes.
doi:10.3762/bjnano.2.60
PMCID: PMC3190626  PMID: 22003462
Au(111); electronic density of states; STM; STS; terthiophene
23.  Pure hydrogen low-temperature plasma exposure of HOPG and graphene: Graphane formation? 
Summary
Single- and multilayer graphene and highly ordered pyrolytic graphite (HOPG) were exposed to a pure hydrogen low-temperature plasma (LTP). Characterizations include various experimental techniques such as photoelectron spectroscopy, Raman spectroscopy and scanning probe microscopy. Our photoemission measurement shows that hydrogen LTP exposed HOPG has a diamond-like valence-band structure, which suggests double-sided hydrogenation. With the scanning tunneling microscopy technique, various atomic-scale charge-density patterns were observed, which may be associated with different C–H conformers. Hydrogen-LTP-exposed graphene on SiO2 has a Raman spectrum in which the D peak to G peak ratio is over 4, associated with hydrogenation on both sides. A very low defect density was observed in the scanning probe microscopy measurements, which enables a reverse transformation to graphene. Hydrogen-LTP-exposed HOPG possesses a high thermal stability, and therefore, this transformation requires annealing at over 1000 °C.
doi:10.3762/bjnano.3.96
PMCID: PMC3556725  PMID: 23365799
graphane; HOPG; hydrogenation; plasma
24.  Novel pentameric thiophene derivatives for in vitro and in vivo optical imaging of a plethora of protein aggregates in cerebral amyloidoses 
ACS chemical biology  2009;4(8):673-684.
Molecular probes for selective identification of protein aggregates are important to advance our understanding of the molecular pathogenesis underlying cerebral amyloidoses. Here we report the chemical design of pentameric thiophene derivatives, denoted luminescent conjugated oligothiophenes (LCOs), which could be used for real-time visualization of cerebral protein aggregates in transgenic mouse models of neurodegenerative diseases by multiphoton microscopy. One of the LCOs, p-FTAA, showed conformation-dependent optical properties and could be utilized for ex vivo spectral assignment of distinct prion deposits from two mouse-adapted prion strains. p-FTAA also revealed staining of transient soluble pre-fibrillar non-thioflavinophilic Aβ- assemblies during in vitro fibrillation of Aβ peptides. In brain tissue samples, Aβ deposits and neurofibrillary tangles (NFTs) were readily identified by a strong fluorescence from p-FTAA and the LCO staining showed complete co-localization with conventional antibodies (6E10 and AT8), indicating that p-FTAA detects all the immuno-positive aggregated proteinaceous species in Alzheimer disease, but with significantly shorter imaging time (100 fold) compared to immunofluorescence. In addition, a patchy islet-like staining of individual Aβ plaque was unveiled by the anti-oligomer A11 antibody during co-staining with p-FTAA, suggesting that pre-fibrillar species are likely an intrinsic component of Aβ plaques in human brain. The major hallmarks of Alzheimer’s disease, namely Aβ aggregates versus NFTs could also be distinguished due to distinct emission spectra from p-FTAA. Overall, we demonstrate that LCOs can be utilized as powerful practical research tools for studying protein aggregation diseases and facilitate the study of amyloid origin, evolution and maturation, Aβ−tau interactions and pathogenesis both ex vivo and in vivo.
doi:10.1021/cb900112v
PMCID: PMC2886514  PMID: 19624097
25.  Role of water in Protein Aggregation and Amyloid Polymorphism 
Accounts of Chemical Research  2011;45(1):83-92.
Conspectus
The link between oligomers and amyloid fibrils and a variety of neurodegenerative diseases raises the need to decipher the principles governing protein aggregation. Mechanisms of in vivo amyloid formation involve a number of coconspirators and complex interactions with membranes. Nevertheless, it is believed that understanding the biophysical basis of in vitro amyloid formation in well-defined systems is important in discovering ligands that preferentially bind to regions that harbor amyloidogenic tendencies. Determination of structures of fibrils of a variety of peptides has set the stage for probing the dynamics of oligomer formation and amyloid growth using computer simulations. Most experimental and simulation studies have been interpreted largely from the perspective of proteins without much consideration of the role of solvent in enabling or inhibiting oligomer formation and assembly to protofilaments and amyloid fibrils.
Here, we provide a perspective on how interactions with water affect folding landscapes of Aβ monomers, oligomer formation in Aβ16–22 fragment, protofilament formation in a peptide from yeast prion Sup35. Explicit molecular dynamics simulations of these systems illustrate how water controls the self-assembly of higher order structures and provide a structural basis for understanding the kinetics of oligomer and fibril growth. Simulations show that monomers of Aβ-peptides sample a number of compact conformations. Population of aggregation-prone structures (N*) with salt-bridge, which bear a striking similarity to the peptide structure in the fibril, requires overcoming a high desolvation barrier. In general, sequences for which N* structures are not significantly populated are unlikely to aggregate.
Generically oligomers and fibrils form in two steps. In the first stage water is expelled from the region between peptides rich in hydrophobic residues (for example Aβ16–22) resulting in the disordered oligomers. In the second stage, the peptides align along a preferred axis to form ordered structures with anti-parallel β-strand arrangement. The rate limiting step in the ordered assembly is the rearrangement of the peptides within a confining volume.
The mechanism of protofilament formation in a polar peptide fragment from the yeast prion in which the two sheets are packed against each other creating a dry interface illustrates that water dramatically slows down self-assembly. As the sheets approach each other two perfectly ordered one-dimensional water wires, which are stabilized by hydrogen bonds to the amide groups of the polar side chains, results in the formation of long-lived metastable structures. Release of the trapped water from the pore creates a helically-twisted protofilament with a dry interface. Similarly, the driving force for addition of a solvated monomer to a preformed fibril is the release of water whose entropy gain and favorable inter peptide hydrogen bond formation compensates for loss in entropy of the peptides.
We suggest that the two-step mechanism, a model also used in protein crystallization, must hold good for higher order amyloid structure formation. In the first step a liquid droplet rich in proteins containing N* structures form. Conformational rearrangement of the peptides leading to an ordered state occurs within the droplet by incorporation of monomers or collision with other droplets and ultimately results in β-amyloid formation. Because there is an ensemble of distinct N* structures with varying water content there must be a number of distinct water-laden polymorphic structures. Evidence for this proposal is presented.
Water plays multifarious roles, which in the case of predominantly hydrophobic sequences, accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow down fibril growth rates in hydrophilic sequences.
doi:10.1021/ar2000869
PMCID: PMC3218239  PMID: 21761818

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