Probing the structure and dynamics of end-grafted flexible polymer chain layers by combined atomic force-electrochemical microscopy. Cyclic voltammetry within nanometer-thick macromolecular poly(ethylene glycol) layers

The combined atomic force-electrochemical microscopy (AFM-SECM) technique was used in aqueous solution to determine both the static and dynamical properties of nanometer-thick monolayers of poly(ethylene glycol) (PEG) chains end-grafted to a gold substrate surface. Approach of a microelectrode tip from a redox end-labeled PEG layer triggered a tip-to-substrate cycling motion of the chains' free ends as a result of the redox heads' oxidation at the tip and re-reduction at the substrate surface. As few as approximately 200 chains at a time could be addressed in such a way. Quantitative analysis of the data, in the light of a simple model of elastic bounded diffusion SECM positive feedback, gave access to the end-tethered polymer layer thickness and the end-to-end diffusion coefficient of the chains. The thickness of the grafted PEG layer was shown to increase with the chain surface coverage, while the end-to-end diffusion coefficient was found to be constant and close to the one predicted by Rouse dynamics. At close tip-substrate separation, slowing of the chains' motion, as a consequence of their vertical confinement within the tip-substrate gap, was observed and quantitatively modeled.     

Electron transport by molecular motion of redox-DNA strands: unexpectedly slow rotational dynamics of 20-mer ds-DNA chains end-grafted onto surfaces via C6 linkers

The dynamics of electron transport within molecular layers of 3'-ferrocenylated 20-mer oligonucleotide, 5'-thiol end-grafted onto gold electrode surfaces via a six-carbon (C6) linker, is studied by cyclic voltammetry. Single-stranded Fc-DNA layers are observed to behave as diffusionless systems reflecting the rapid dynamics of the ssDNA strand. Following hybridization, the Fc-dsDNA-C6 layers give rise to a characteristic cyclic voltammetry behavior evidencing that the Fc head is animated by a purely diffusional motion, which is ascribed to free rotation of the rigid DNA duplex around its C6 anchoring linker. A model, describing the motion of the Fc head as resulting from hinge motion of the DNA duplex, is developed allowing the motional dynamics of the Fc-dsDNA-C6 chains to be quantified in terms of an apparent rotational diffusion coefficient, Dr. The value found for Dr is approximately 3-4 orders of magnitude slower than expected for free rotation of dsDNA in solution, pointing to a drastic motion-slowing role of the anchoring surface. Accessibility of the Fc head for the electron transfer at the electrode is also shown to modulate the apparent dsDNA dynamics. The dynamics of Fc-dsDNA-C 6 is found to be insensitive to the presence of a single mismatch in the middle of the strand, confirming that charge transport by dsDNA conduction (DNA CT) is not present for the systems studied here. However, electron transport by free hinge motion of the dsDNA chain is shown to be fast enough to, a priori, compete favorably with DNA CT.     

A dual-electrode approach for highly selective detection of glucose based on diffusion layer theory: experiments and simulation

A dual-electrode configuration for the highly selective detection of glucose in the diffusion layer of the substrate electrode is presented. In this approach, a glassy carbon electrode (GCE, substrate) modified with a conductive layer of glucose oxidase/Nafion/graphite (GNG) was used to create an interference-free region in its diffusion layer by electrochemical depletion of interfering electroactive species. A Pt microelectrode (tip, 5 microm in radius) was located in the diffusion layer of the GNG-modified GCE (GNG-G) with the help of scanning electrochemical microscopy. Consequently, the tip of the electrode could sense glucose selectively by detecting the amount of hydrogen peroxide (H2O2) formed from the oxidization of glucose on the glucose oxidase layer. The influences of parameters, including tip-substrate distance, substrate potential, and electrolyzing time, on the interference-removing efficiency of this dual-electrode approach have been investigated systematically. When the electrolyzing time was 30 s, the tip-substrate distance was 1.8 a (9.0 microm) (where a is the radius of the tip electrode), the potentials of the tip and substrate electrodes were 0.7 V and 0.4 V, respectively, and a mixture of ascorbic acid (0.3 mM), uric acid (0.3 mM), and 4-acetaminophen (0.3 mM) had no influence on the glucose detection. In addition, the current-time responses of the tip electrode at different tip-substrate distances in a solution containing interfering species were numerically simulated. The results from the simulation are in good agreement with the experimental data. This research provides a concept of detection in the diffusion layer of a substrate electrode, as an interference-free region, for developing novel microelectrochemical devices.     

Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the parameters to greatly increase the simulation efficiency. The method is carefully validated against standard molecular dynamics (MD) simulations and available experimental structural and kinetic data on ligand diffusion in T-state deoxyHbA. The methodology provides a viable alternative approach to traditional MD simulations and/or potential of mean force calculations for: (i) characterizing kinetically accessible diffusion tunnels and escape routes for light ligands in porous proteins; (ii) very large systems when realistic simulations require the inclusion of multiple subunits of a protein; and (iii) proteins that access short-lived conformations relative to the simulation time. In the case of T-state deoxyHbA, we find distinct ligand diffusion tunnels consistent with the experimentally observed disparate Xe cavities in the α- and β-subunits. We identify two distal barriers including the distal histidine (E7) that control access to the heme. The multiple escape routes uncovered by our simulations call for a review of the current popular hypothesis on ligand escape from hemoglobin. Larger deviations from the crystal structure during simulated diffusion in isolated α- and β-subunits highlight the dampening effects of subunit interactions and the importance of including all subunits of multisubunit proteins to map realistic kinetically accessible diffusion tunnels and escape routes.     

Direct deposition and assembly of gold colloidal particles using a nanofountain probe

We report the direct delivery and assembly of negatively charged gold colloidal particles atop positively charged amino-terminated silicon oxide surfaces using a nanofountain atomic force microscopy probe. The experimental results and fluid simulations indicate that the flow of nanoparticles is confined to the core tip region of the probe. This leads to the assembly of high-resolution submicron patterns (200 nm) on the substrate with feature sizes dependent on the tip-substrate contact time. A diffusion mechanism for the patterning is proposed and discussed.     

Finite element simulations of tip-enhanced Raman and fluorescence spectroscopy

Finite element electromagnetic simulations of scanning probe microscopy tips and substrates are presented. The enhancement of the scattered light intensity is found to be as high as 10(12) for a 20 nm radius gold tip, and tip-substrate separation of 1 nm. Molecular resolution imaging (< 1 nm) is achievable, even with a relatively large radius tip (20 nm). We also make predictions for imaging in aqueous environments, noting a sizable red shift of the spectral peaks. Finally, we discuss signal levels, and predict that high-speed Raman mapping should be possible with gold substrates and a small tip-substrate separation (< 4 nm).     

Li-KCl熔融界面上离子扩散的分子动力学研究

采用分子动力学(MD)方法研究了熔融Li(电极)-KCl(电解质)界面上离子的扩散行为。熔融界面上离子的扩散动力学通过离子质心的均方位移(MSD)和速度自相关函数(VACF)进行研究,扩散系数由MSD(t)函数线性区间的斜率和VACF(t)函数积分得到。模拟结果表明,在熔融的Li-KCl界面上,Li+离子在浓度梯度的驱动下穿过界面发生定向迁移,导致双电层的形成和外电路上电流的输出。Li+离子的扩散系数比K+和Cl-离子的大7～8倍,说明在界面上Li+离子是主要的载荷子,热电池的电荷传输机制主要与Li+离子的扩散运动有关。由Nernst-Einstein公式对电导率进行估算,由扩散到KCl层中的Li+离子产生的电导率约为0.4 S.cm-2,对应的电流密度估算值为3.27×105A.cm-2。     

Mechanistic studies of Fc-PNA(⋅DNA) surface dynamics based on the kinetics of electron-transfer processes

N‐Terminally ferrocenylated and C‐terminally gold‐surface‐grafted peptide nucleic acid (PNA) strands were exploited as unique tools for the electrochemical investigation of the strand dynamics of short PNA(?DNA) duplexes. On the basis of the quantitative analysis of the kinetics and the diffusional characteristics of the electron‐transfer process, a nanoscopic view of the Fc‐PNA(?DNA) surface dynamics was obtained. Loosely packed, surface‐confined Fc‐PNA single strands were found to render the charge‐transfer process of the tethered Fc moiety diffusion‐limited, whereas surfaces modified with Fc‐PNA?DNA duplexes exhibited a charge‐transfer process with characteristics between the two extremes of diffusion and surface limitation. The interplay between the inherent strand elasticity and effects exerted by the electric field are supposed to dictate the probability of a sufficient approach of the Fc head group to the electrode surface, as reflected in the measured values of the electron‐transfer rate constant, k⁰. An in‐depth understanding of the dynamics of surface‐bound PNA and PNA?DNA strands is of utmost importance for the development of DNA biosensors using (Fc‐)PNA recognition layers.     

Poly(ethylene glycol)-conjugated phospholipids in aqueous micellar solutions: hydration, static structure, and interparticle interactions

By means of dielectric relaxation spectroscopy (DRS) and small-angle X-ray scattering (SAXS), we have investigated hydration behavior, solvent dynamics, and static structures of aqueous solutions of poly(ethylene glycol)-conjugated distearoyl phosphatidylethanolamine (DSPE-PEG) (molecular weight of PEG: M(PEG)= 2000, 5000, and 12,000 Da). A quantitative analysis of the bulk-water relaxation amplitude revealed the effective hydration number of a DSPE-PEG molecule per ethylene oxide monomer unit to be approximately 5.0-5.5, virtually independent of M(PEG). The overall hydration number of a DSPE-PEG molecule is ca. 20% higher than that of the corresponding normal PEG (without DSPE). This is attributed to both hydration of a charged head group of phosphoric acid in DSPE and a packing effect of PEG chains into micellar structures. The pair-distance distribution functions, p(r), extracted from the GIFT analysis of SAXS intensities show that the DSPE-PEGs form spherical-like micelles in water having the maximum diameter of approximately 16, 22, and 31 nm, respectively, for M(PEG) = 2000, 5000, and 12,000 Da and nearly identical aggregation numbers of 72 (+/-10%). The DSPE-PEG micelles behave as charged colloids whose interparticle interaction potential can be approximated by the screened Coulomb potential model. The extracted pair correlation function g(r) demonstrates that both electrostatic repulsion induced by the charged head group and excluded volume effects of the fully hydrated PEG layer contribute to repulsive interactions among the PEG-lipid micelles. This should be a key factor for the function of PEG lipids as a stabilizer of liposomes.     

二茂铁及其与DNA复合物的电化学行为

在Tris-NaCl(pH=7.2)缓冲溶液中, 应用循环伏安法、微分脉冲伏安法、旋转圆盘电极实验、电化学阻抗谱等技术研究了二茂铁在旋转碳纳米管(CNT)修饰电极上的电化学行为及其与小牛胸腺DNA的相互作用. 结果表明, 二茂铁及其与双链DNA的电活性产物在静止的CNT修饰电极上均呈现一对基本可逆的氧化还原峰；在旋转电极上呈现出明显的极限扩散电流, 电化学阻抗谱呈现一个压扁的半圆. 二茂铁与DNA的作用在扩散控制过程中表现为峰电流和极限扩散电流随DNA浓度增大而减小；电化学控制过程则表现为电化学反应电阻随DNA浓度增大而增大, 条件电位下的速度常数也有一定程度的减小.     

Langevin dynamics simulations of polymer translocation through nanopores

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of an external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time tau(e) required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that tau(e) scales with the chain length N as tau(e) approximately N(1+2nu), where nu is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficient xi, the driving force E, and the length of the chain N on the translocation time tau, which is defined as the time duration between the first monomer entering the pore and the last monomer leaving the pore. For strong driving forces, the distribution of translocation times is symmetric and narrow without a long tail and tau approximately E(-1). The influence of xi depends on the ratio between the driving and frictional forces. For intermediate xi, we find a crossover scaling for tau with N from tau approximately N(2nu) for relatively short chains to tau approximately N(1+nu) for longer chains. However, for higher xi, only tau approximately N(1+nu) is observed even for short chains, and there is no crossover behavior. This result can be explained by the fact that increasing xi increases the Rouse relaxation time of the chain, in which case even relatively short chains have no time to relax during translocation. Our results are in good agreement with previous simulations based on the fluctuating bond lattice model of polymers at intermediate friction values, but reveal additional features of dependency on friction.     

Quantification of grafted poly(ethylene glycol)-silanes on silicon by time-of-flight secondary ion mass spectrometry

Silicon grafted monodisperse poly(ethylene glycol) (PEG) silanes with various PEG chain lengths and mixtures of these were systematically analyzed with static time-of-flight secondary ion mass spectrometry (TOF-SIMS). The mass spectra show differences in the various relative signal intensities, an observation that was used to elucidate important aspects of the grafting process. The relationship between PEG-silane fragment ion abundances and Si(+) ion abundances were used to (i) qualitatively describe layer thicknesses of grafted mixtures of PEG-silanes on silicon, (ii) construct a calibration curve from which PEG chain length (or molecular mass) can be determined and (iii) quantitatively determine surface mixture compositions of grafted monodisperse PEG-silanes of different chain lengths (3, 7 and 11 PEG units). The results suggest that discrimination does take place in the adsorption process. The PEG-silane with the shorter PEG chain is discriminated for mixtures containing PEG3-silane, whereas the PEG-silane with the longer PEG chain is discriminated in PEG7/PEG11-silane mixtures. The origin of this difference in adsorption behavior is not well understood. Aspects of the grafting process and the TOF-SIMS analyses are discussed.     

Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide

Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within this layer, water molecules show marked orientations relative to a peptide surface. Using the two-particle contribution to entropy as a measure of structural ordering of water, we found that the first solvation shell contributes 95% or more to the total water ordering around the peptide molecule. In investigating the dynamic properties of water, diffusion coefficients and lifetime of the hydrogen bond, clear differences between solvation layer and the bulk water were observed. It was found that the translational diffusion coefficient, D(T), decreases by 30% or more compared to bulk water; also, the lifetime of the water-water hydrogen bond clearly increases. The rotational diffusion coefficient, however, decreases only slightly, no more than approximately 10%. These differences correspond to the slightly higher energy of the hydrogen bond, and to its slightly distorted geometry. Analyzing the translational dynamics of water in the vicinity of the peptide molecule, it was deduced that the structure of the first solvation shell becomes more rigid than the structure of the bulk water. Investigation of a "pure hydrophobic" form of the polypeptide shows that the structure and the properties of water within the solvation shell are predominantly determined by the hydrophobic effect. The specific interactions between water molecules and various charge groups of the peptide molecule modifies this effect only slightly.     

Intermolecular interactions in electron transfer through stretched helical peptides

The helical peptide Cys-Ala-Lys-(Glu-Ala-Ala-Ala-Lys)(2)-Ala-NH-(CH(2))(2)-SH has been organized forming a self-assembled monolayer on gold (0.602 peptides per nm(2)), its conductance behavior under stretching conditions being studied using scanning tunnelling microscopy and current sensing atomic force microscopy. The helical conformation of the peptide has been found to play a fundamental role in the conductance. Moreover, variation of the current upon molecular stretching indicates that peptides can be significantly elongated before the conductance drops to zero, the critical elongation being 1.22 ± 0.47 nm. Molecular dynamics simulations of a single peptide in the free state and of a variable number of peptides tethered to a gold surface (i.e. densities ranging from 0.026 to 1.295 peptides per nm(2)) have indicated that the helical conformation is intrinsically favored in solvated environments while in desolvated environments it is retained because of the fundamental role played by peptide-peptide intermolecular interactions. The structure obtained for the system with 24 tethered peptides, with a density of 0.634 peptides per nm(2) closest to the experimental one, is in excellent agreement with experimental observations. On the other hand, simulations in which a single molecule is submitted to different compression and stretching processes while the rest remain in the equilibrium have been used to mimic the variation of the tip-substrate distance in experimental measures. Results allowed us to identify the existence, and in some cases coexistence, of intermolecular and intramolecular ionic ladders, suggesting that peptide-mediated electron transfer occurs through the hopping mechanism. Finally, quantum mechanical calculations have been used to investigate the variation of the electronic structure upon compression and stretching deformations.     

Molecular dynamics simulations of the Li-ion diffusion in the amorphous solid electrolyte interphase

The solid electrolyte interphase (SEI), a passivation film covering the electrode surface, is crucial to the lifetime and efficiency of the lithium-ion (Li-ion) battery. Understanding the Li-ion diffusion mechanism within possible components in the mosaic-structured SEI is an essential step to improve the Li-ion conductivity and thus the battery performance. Here, we investigate the Li-ion diffusion mechanism within three amorphous SEI components (i.e., the inorganic inner layer, organic outer layer, and their mixture with 1:1 molar ratio) via ab initio molecular dynamic (AIMD) simulations. Our simulations show that the Li-ion diffusion coefficient in the inorganic layer is two orders of magnitude faster than that in the organic layer. Therefore, the inorganic layer makes a major contribution to the Li-ion diffusion. Furthermore, we find that the Li-ion diffusivity in the organic layer decreases slightly with the increase of the carbon chain from the methyl to ethyl owing to the steric hindrance induced by large groups. Overall, our current work unravels the Li-ion diffusion mechanism, and provides an atomic-scale insight for the understanding of the Li-ion transport in the SEI components.     

Polyelectrolyte Multilayer Films Containing Ferrocene: Effects of Polyelectrolyte Type and Ferrocene Contents in the Film on the Redox Properties

Electrochemical properties of Fc‐PEM films have been studied by changing the chemical structure of the polymer chains and the content of Fc moiety in the film systematically. We have prepared a series of PEM films by a layer‐by‐layer deposition of polycations, Fc‐modified poly(allylamine) (Fc‐PAA) and poly(ethyleneimine) (Fc‐PEI), and polyanionic poly(vinyl sulfate) (PVS) on the surface of a gold electrode. The redox properties of the Fc‐PAA/PVS and Fc‐PEI/PVS films depended significantly on the content of Fc moiety in the polymer chains and on the polymer type. Fc‐ PAA and Fc‐PEI polymer chains can penetrate 3 or 4 PAA/PVS bilayers inserted between the redox polymers and electrode. The Fc‐PAA film‐modified electrode can be used for electrocatalytic oxidation of ascorbic acid.     

循环伏安法研究超分子有机凝胶中二茂铁的扩散

4,4′-二(硬脂酰胺基)-二苯甲烷(BSAPM)在LiClO4/碳酸丙烯酯(PC)中能形成超分子有机凝胶。用循环伏安法研究了包埋在凝胶中的二茂铁的氧化还原行为。结果表明,有机凝胶内的二茂铁仍具有氧化还原活性,其氧化还原行为是受扩散控制的单电子可逆转移过程。与溶液相比,最低化凝胶浓度下凝胶中二茂铁和二茂铁离子的扩散系数分别从5.62×10-6cm2/s和6.47×10-6cm2/s下降为3.32×10-6cm2/s和4.41×10-6cm2/s,且随凝胶因子浓度的增加,凝胶中二茂铁和二茂铁离子的扩散系数降低。     

Diffusion on a self-assembled monolayer: molecular modeling of a bound + mobile lubricant

The diffusion of tricresyl phosphate molecules on an octadecyltrichlorosilane self-assembled monolayer (SAM) was characterized using molecular dynamics simulations. The simulations predict that when placed on the top of a close-packed SAM, the molecules remain mobile on the surface with an isotropic diffusion activation energy of approximately 9 kJ/mol. In contrast, an anisotropic barrier that results from chain tilt within the SAM is predicted for diffusion into a defect created by reducing the alkane chain length within a cylinderical region of the surface. Once in the defect, the molecules become trapped by embedding part of the molecule into the side of the SAM.     

Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method

Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed.     

Exercising spatiotemporal control of cell attachment with optically transparent microelectrodes

This paper describes a novel approach of controlling cell-surface interactions through an electrochemical "switching" of biointerfacial properties of optically transparent microelectrodes. The indium tin oxide (ITO) microelectrodes, fabricated on glass substrates, were modified with poly(ethylene glycol) (PEG) silane to make glass and ITO regions resistant to protein and cell adhesion. Cyclic voltammetry, with potassium ferricyanide serving as a redox reporter molecule, was used to monitor electron transfer across the electrolyte-ITO interface. PEG silane modification of ITO correlated with diminished electron transfer, judged by the disappearance of ferricyanide redox activity. Importantly, application of reductive potential (-1.4 V vs Ag/AgCl reference) corresponded with reappearance of typical ferricyanide redox peaks, thus pointing to desorption of an insulating PEG silane layer. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) characterization of the silanized ITO surfaces after electrical stimulation indicated complete removal of the silane layer. Significantly, electrical stimulation allowed to "switch" chosen electrodes from nonfouling to protein-adhesive while leaving other ITO and glass regions protected by a nonfouling PEG silane layer. The spatial and temporal control of biointerfacial properties afforded by our approach was utilized to micropattern proteins and cells and to construct micropatterned co-cultures. In the future, control of the biointerfacial properties afforded by this novel approach may allow the organization of multiple cell types into precise geometric configurations in order to create better in vitro mimics of cellular complexity of the native tissues.