Bingqian Xu

Carbon nanotube based artificial water channel protein: membrane perturbation and water transportation.

We functionalized double-walled carbon nanotubes (DWCNTs) as artificial water channel proteins. For the first time, molecular dynamics simulations show that the bilayer structure of DWCNTs is advantageous for carbon nanotube based transmembrane channels. The shielding of the amphiphilic outer layer could guarantee biocompatibility of the synthetic channel and protect the inner tube (functional part) from disturbance of the membrane environment. This novel design could promote more sophisticated nanobiodevices which could function in a bioenvironment with high biocompatibility.

Axonal Fiber Terminations Concentrate on Gyri

Convoluted cortical folding and neuronal wiring are 2 prominent attributes of the mammalian brain. However, the macroscale intrinsic relationship between these 2 general cross-species attributes, as well as the underlying principles that sculpt the architecture of the cerebral cortex, remains unclear. Here, we show that the axonal fibers connected to gyri are significantly denser than those connected to sulci. In human, chimpanzee, and macaque brains, a dominant fraction of axonal fibers were found to be connected to the gyri. This finding has been replicated in a range of mammalian brains via diffusion tensor imaging and high-angular resolution diffusion imaging. These results may have shed some lights on fundamental mechanisms for development and organization of the cerebral cortex, suggesting that axonal pushing is a mechanism of cortical folding.

From Ring-in-Ring to Sphere-in-Sphere: Self-Assembly of Discrete 2D and 3D Architectures with Increasing Stability

Directed by increasing the density of coordination sites (DOCS) to increase the stability of assemblies, discrete 2D ring-in-rings and 3D sphere-in-sphere were designed and self-assembled by one tetratopic pyridyl-based ligand with 180° diplatinum(II) acceptors and naked Pd(II), respectively. The high DOCS resulted by multitopic ligand provided more geometric constraints to form discrete structures with high stability. Compared to reported supramolecular hexagons and polyhedra by ditotpic ligands, the self-assembly of such giant architectures using multitopic ligands with all rigid backbone emphasized the structural integrity with precise preorganization of entire architecture, and required elaborate synthetic operations for ligand preparation. In-depth structural characterization was conducted to support desired structures, including multinuclear NMR ((1)H, (31)P, and (13)C) analysis, 2D NMR spectroscopy (COSY and NOESY), diffusion-ordered NMR spectroscopy (DOSY), multidimensional mass spectrometry, TEM and AFM. Furthermore, a quantitative definition of DOCS was proposed to compare 2D and 3D structures and correlate the DOCS and stability of assemblies in a quantitative manner. Finally, ring-in-rings in DMSO or DMF could undergo hierarchical self-assembly into the ordered nanostructures and generated translucent supramolecular metallogels.

Molecular rectifier composed of DNA with high rectification ratio enabled by intercalation

The predictability, diversity and programmability of DNA make it a leading candidate for the design of functional electronic devices that use single molecules, yet its electron transport properties have not been fully elucidated. This is primarily because of a poor understanding of how the structure of DNA determines its electron transport. Here, we demonstrate a DNA-based molecular rectifier constructed by site-specific intercalation of small molecules (coralyne) into a custom-designed 11-base-pair DNA duplex. Measured current-voltage curves of the DNA-coralyne molecular junction show unexpectedly large rectification with a rectification ratio of about 15 at 1.1 V, a counter-intuitive finding considering the seemingly symmetrical molecular structure of the junction. A non-equilibrium Greens function-based model-parameterized by density functional theory calculations-revealed that the coralyne-induced spatial asymmetry in the electron state distribution caused the observed rectification. This inherent asymmetry leads to changes in the coupling of the molecular HOMO-1 level to the electrodes when an external voltage is applied, resulting in an asymmetric change in transmission.

Electrochemical fabrication of atomically thin metallic wires and electrodes separated with molecular-scale gaps

This article summarizes our recent effort to fabricate electrochemically metallic nanowires and electrodes separated with molecular scale nanogaps. The nanowires were fabricated by etching a small portion of a micron-scale metallic wire supported on a solid substrate. The etching was controlled by continuously monitoring the conductance of the wire. When the thinnest portion of the wire reached the atomic scale, the conductance decreased in a stepwise fashion. By further etching away the last few atoms, a molecular-scale gap between two electrodes was created and the ballistic electron transport through the nanowire was replaced with quantum tunneling. By depositing atoms back, the above processes could be reversed, allowing us to achieve a desired nanowire or gap. The nanowires may be used for chemical sensor applications and the nanogaps may be used to wire small molecules to the outside world for molecular electronics applications.

Self-assembly of giant supramolecular cubes with terpyridine ligands as vertices and metals on edges

Self-assembly of three-dimensional (3-D) architecture using terpyridine (tpy)-based building blocks is challenging and seldom addressed due the fixed geometry (around 180°) of tpy-M(II)-tpy (M = Ru, Fe, Zn, and Cd) connectivity. Here we describe the self-assembly of 3-D giant metallo-supramolecular cubes using three-armed terpyridine ligands constructed on adamantane with molecular weight up to 18 k and edge length at ∼4.9 nm, which is significantly larger than the sizes of previous metallo-supramolecular cubes. Instead of using metal center as vertices in the commonly used synthetic strategy of 3-D molecular coordination ensembles, these cages [M12L8] bear 8 ligands as vertices with 12 metal ions on the edges. With a suitable edge length, the giant cubes appear to be the sole product after self-assembly from a variety of possible architectures. The 3-D metallo-supramolecules were characterized and supported by NMR, DOSY, ESI-MS, travelling wave ion mobility-MS and AFM.

Mapping out the structural changes of natural and pretreated plant cell wall surfaces by atomic force microscopy single molecular recognition imaging

BackgroundEnzymatic hydrolysis of lignocellulosic biomass (mainly plant cell walls) is a critical process for biofuel production. This process is greatly hindered by the natural complexity of plant cell walls and limited accessibility of surface cellulose by enzymes. Little is known about the plant cell wall structural and molecular level component changes after pretreatments, especially on the outer surface. Therefore, a more profound understanding of surface cellulose distributions before and after pretreatments at single-molecule level is in great need. In this study, we determined the structural changes, specifically on crystalline cellulose, of natural, dilute sulfuric acid pretreated and delignified cell wall surfaces of poplar, switchgrass, and corn stover using single molecular atomic force microscopy (AFM) recognition imaging.ResultsThe AFM tip was first functionalized by a family 3 carbohydrate-binding module (CBM3a) (Clostridium thermocellum Scaffoldin) which specifically recognizes crystalline cellulose by selectively binding to it. The surface structural changes were studied at single molecule level based on the recognition area percentage (RAP) of exposed crystalline cellulose over the imaged cell wall surface. Our results show that the cell wall surface crystalline cellulose coverage increased from 17-20% to 18-40% after dilute acid pretreatment at 135°C under different acid concentrations and reached to 40-70% after delignification. Pretreated with 0.5% sulfuric acid, the crystalline cellulose surface distributions of 23% on poplar, 28% on switchgrass and, 38% on corn stover were determined as an optimized result. Corn stover cell walls also show less recalcitrance due to more effective pretreatments and delignification compared to poplar and switchgrass.ConclusionsThe dilute acid pretreatment can effectively increase the cellulose accessibility on plant cell wall surfaces. The optimal acid concentration was determined to be 0.5% acid at 135°C, especially for corn stover. This study provides a better understanding of surface structural changes after pretreatment such as lignin relocation, re-precipitation, and crystalline cellulose distribution, and can lead to potential improvements of biomass pretreatment.

Direct Optical Detection of Viral Nucleoprotein Binding to an Anti-Influenza Aptamer

We have demonstrated label-free optical detection of viral nucleoprotein binding to a polyvalent anti-influenza aptamer by monitoring the surface-enhanced Raman (SERS) spectra of the aptamer-nucleoprotein complex. The SERS spectra demonstrated that selective binding of the aptamer-nucleoprotein complex could be differentiated from that of the aptamer alone based solely on the direct spectral signature for the aptamer-nucleoprotein complex. Multivariate statistical methods, including principal components analysis, hierarchical clustering, and partial least squares, were used to confirm statistically significant differences between the spectra of the aptamer-nucleoprotein complex and the spectra of the unbound aptamer. Two separate negative controls were used to evaluate the specificity of binding of the viral nucleoproteins to this aptamer. In both cases, no spectral changes were observed that showed protein binding to the control surfaces, indicating a high degree of specificity for the binding of influenza viral nucleoproteins only to the influenza-specific aptamer. Statistical analysis of the spectra supports this interpretation. AFM images demonstrate morphological changes consistent with formation of the influenza aptamer-nucleoprotein complex. These results provide the first evidence for the use of aptamer-modified SERS substrates as diagnostic tools for influenza virus detection in a complex biological matrix.

Self-Assembly of Concentric Hexagons and Hierarchical Self-Assembly of Supramolecular Metal–Organic Nanoribbons at the Solid/Liquid Interface

In an effort to exert more precise control over structural features of supramolecules, a series of giant concentric hexagons were assembled as discrete structures using tetratopic terpyridine (tpy) ligands. In preparation of tetratopic ligand, pyrylium and pyridinium salts chemistry significantly facilitated synthesis. The key compounds were obtained by condensation reactions of pyrylium salts with corresponding primary amine derivatives in good yields. These discrete metallo-supramolecular concentric hexagons were fully characterized by NMR, ESI-MS, TWIM-MS, and TEM, establishing their hexagon-in-hexagon architectures. The combination of different tetratopic ligands also assembled hybrid concentric hexagons with increasing diversity and complexity. Furthermore, these concentric hexagon supramolecules with precisely controlled shapes and sizes were utilized as building blocks to hierarchically self-assemble supramolecular metal-organic nanoribbons (SMON) at solid-liquid interfaces. Ambient STM imaging showed the formation of long 1D SMON rather than 2D assembly on the basal plane of highly oriented pyrolytic graphite (HOPG) surface after simple dropcasting of the solution of preassembled concentric hexagons onto a freshly cleaved surface of HOPG. This wet chemical method based on self-assembly may offer simple, economical, and scalable routes to deliver complex materials.

High-resolution single-molecule recognition imaging of the molecular details of ricin-aptamer interaction.

We studied the molecular details of DNA aptamer-ricin interactions. The toxic protein ricin molecules were immobilized on a Au(111) surface using a N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in situ using the AFM tip modified with an antiricin aptamer. Computer simulation was used to illustrate the protein and aptamer structures, the single-molecule ricin images on a Au(111) surface, and the binding conformations of ricin-aptamer and ricin-antibody complexes. The various ricin conformations on a Au(111) surface were caused by the different lysine residues reacting with the NHS ester. It was also observed that most of the binding sites for aptamer and antibody on the A chains of ricin molecules were not interfered by the immobilization reaction. The different locations of the ricin binding sites to aptamer and antibody were also distinguished by AFM recognition images and interpreted by simulations.