Effects of Proline on Internal Friction in Simulated Folding Dynamics of Several Alanine-Based α-Helical Peptides

We have studied in silico the effect of proline, a model cosolvent, on local and global friction coefficients in (un)folding of several typical alanine-based α-helical peptides. Local friction is related to dwell times of a single, ensemble-averaged hydrogen bond (HB) within each peptide. Global friction is related to energy dissipated in a series of configurational changes of each peptide experienced by increasing the number of HBs during folding. Both of these approaches are important in relation to future atomic force microscopic-based measurements of internal friction via force-clamp single-molecule force spectroscopy. Molecular dynamics (MD) simulations for six peptides, namely, ALA5, ALA8, ALA15, ALA21, (AAQAA)3, and H2N-GN(AAQAA)2G-COONH2, have been conducted at 2 and 5 M proline solutions in water. Using previously obtained MD data for these peptides in pure water as well as upgraded theoretical models, we obtained variations of local and global internal friction coefficients as a function of solution viscosity. The results showed the substantial role of proline in stabilizing the folded state and slowing the overall folding dynamics. Consequently, larger friction coefficients were obtained at larger viscosities. The local and global internal friction, i.e., respective, friction coefficients approximated to zero viscosity, was also obtained. The evolution of friction coefficients with viscosity was weakly dependent on the number of concurrent folding pathways but was rather dominated by a stabilizing effect of proline on the folded states. Obtained values of local and global internal friction showed qualitatively similar results and a clear dependency on the structure of the studied peptide.

Plasma Processing and Treatment of 2D Transition Metal Dichalcogenides: Tuning Properties and Defect Engineering

Two-dimensional transition metal dichalcogenides (TMDs) offer fascinating opportunities for fundamental nanoscale science and various technological applications. They are a promising platform for next generation optoelectronics and energy harvesting devices due to their exceptional characteristics at the nanoscale, such as tunable bandgap and strong light-matter interactions. The performance of TMD-based devices is mainly governed by the structure, composition, size, defects, and the state of their interfaces. Many properties of TMDs are influenced by the method of synthesis so numerous studies have focused on processing high-quality TMDs with controlled physicochemical properties. Plasma-based methods are cost-effective, well controllable, and scalable techniques that have recently attracted researchers' interest in the synthesis and modification of 2D TMDs. TMDs' reactivity toward plasma offers numerous opportunities to modify the surface of TMDs, including functionalization, defect engineering, doping, oxidation, phase engineering, etching, healing, morphological changes, and altering the surface energy. Here we comprehensively review all roles of plasma in the realm of TMDs. The fundamental science behind plasma processing and modification of TMDs and their applications in different fields are presented and discussed. Future perspectives and challenges are highlighted to demonstrate the prominence of TMDs and the importance of surface engineering in next-generation optoelectronic applications.

A brief review on thermally induced oxidation and oxidative etching of thin MoS2 crystals

Thin and single MoS₂ flakes have already been employed in the world of flexible nanoelectronics, particularly in sensing, optoelectronics and energy harvesting. This review article briefly summarizes the recent advancements in the research on thermally induced oxidation and oxidative etching of such MoS₂ crystals. Various temperature regimes are discussed along with the proposed mechanistic insights into respective oxidation and etching processes. The methods utilized to detect any surface-remaining minute amounts of Mo oxides are also mentioned.

GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction

We have performed molecular dynamics (MD) and replica-exchange (REMD) simulations of folding of the GB1 hairpin peptide in aqueous solution. REMD results were consistent with a cooperative zipper folding model. 120 μ s MD trajectories at 320 K yielded relaxation times of 1.8 μ s and 100 ns, with the slower assigned to global folding. The MD folding/unfolding transitions also followed the cooperative zipper model, specifying nucleation at the central turn followed by consecutive hydrogen bond formation. Formation of hydrogen bonds and hydrophobic contacts were highly correlated. Coarse-grained kinetic models constructed with the Optimal Dimensionality Reduction (ODR) approach found a folding time of 3.3 μ s and unfolding time of 4.0 μ s . Additionally, relaxation times in the 130-170 ns range could be assigned to formation of the transition state and off-path intermediates. The unfolded state was the most highly populated and, significantly, most heterogenous, assembling the largest number of microstates, primarily composed of extended and turn structures. The folded state was also heterogenous, but a to a lesser degree, involving the fully folded and partially folded in-register hairpins at early stages of the zipper pathway. The transition state corresponded to the nucleated hairpin, with central turn and first beta-sheet hydrogen bond, while the off-path intermediates were off-register partial hairpins. Our simulation results were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. The new findings from this work suggest a highly cooperative zipper folding mechanism, nascent hairpin transition state and ∼100 ns relaxation related to intermediate formation.Communicated by Ramaswamy H. Sarma.

Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations

In this paper we derive analytically from molecular dynamics (MD) simulations the friction coefficients related to conformational transitions within several model peptides with α-helical structures. We study a series of alanine peptides with various length from ALA₅ to ALA₂₁ as well as their two derivatives, the (AAQAA)₃ peptide and a 13-residue KR1 peptide that is a derivative of the (AAQAA)₂ peptide with the formula GN(AAQAA)₂G. We use two kinds of approaches to derive their friction coefficients. In the local approach, friction associated with fluctuations of single hydrogen bonds are studied. In the second approach, friction coefficients associated with a folding transitions within the studied peptides are obtained. In both cases, the respective friction coefficients differentiated very well the subtle structural changes between studied peptides and compared favorably to experimentally available data.

MoS2 oxidative etching caught in the act: formation of single (MoO3) n molecules

We report the presence of sub-nm MoO x clusters formed on basal planes of the 2H MoS2 crystals during thermal oxidative etching in air at a temperature of 370 °C. Using high resolution non-contact atomic force microscopy (AFM) we provide a histogram of their preferred heights. The AFM results combined with density functional theory (DFT) simulations show remarkably well that the MoO x clusters are predominantly single MoO3 molecules and their dimers at the sulfur vacancies. Additional Raman spectroscopy, and energy and wavelength dispersive X-ray spectroscopies as well as Kelvin probe AFM investigations confirmed the presence of the MoO3/MoO x species covering the MoS2 surface only sparsely. The X-ray absorption near edge spectroscopy data confirm the MoO3 stoichiometry. Taken together, our results show that oxidative etching and removal of Mo atoms at the atomic level follow predominantly via formation of single MoO3 molecules. Such findings confirm the previously only proposed oxidative etching stoichiometry.

Local Interactions of Atmospheric Oxygen with MoS2 Crystals

Thin and single MoS2 flakes are envisioned to contribute to the flexible nanoelectronics, particularly in sensing, optoelectronics and energy harvesting. Thus, it is important to study their stability and local surface reactivity. Their most straightforward surface reactions in this context pertain to thermally induced interactions with atmospheric oxygen. This review focuses on local and thermally induced interactions of MoS2 crystals and single MoS2 flakes. First, experimentally observed data for oxygen-mediated thermally induced morphological and chemical changes of the MoS2 crystals and single MoS2 flakes are presented. Second, state-of-the-art mechanistic insight from computer simulations and arising open questions are discussed. Finally, the properties and fate of the Mo oxides arising from thermal oxidation are reviewed, and future directions into the research of the local MoS2/MoOx interface are provided.

Surface Characterization of MoS2 Atomic Layers Mechanically Exfoliated on a Si Substrate

Mo disulfide overlayers with the thickness exceeding 1.77 nm were obtained on Si substrates through mechanical exfoliation. The resulting Mo disulfide flakes were then analyzed ex situ using combination of Auger electron spectroscopy (AES), elastic-peak electron spectroscopy (EPES) and scanning electron microscopy (SEM) in order to characterize their surface chemical composition, electron transport phenomena and surface morphology. Prior to EPES measurements, the Mo disulfide surface was sputter-cleaned and amorphized by 3 kV argon ions, and the resulting S/Mo atomic ratio varied in the range 1.80-1.88, as found from AES measurements. The SEM images revealed single crystalline small-area (up to 15 μm in lateral size) Mo disulfide flakes having polygonal or near-triangular shapes. Such irregular-edged flakes exhibited high crystal quality and thickness uniformity. The inelastic mean free path (IMFP), characterizing electron transport, was evaluated from the relative EPES using Au reference material for electron energies E = 0.5-2 keV. Experimental IMFPs, λ, determined for the AES-measured surface compositions were approximated by the simple function λ = kEp, where k = 0.0289 and p = 0.946 were fitted parameters. Additionally, these IMFPs were compared with IMFPs resulting from the two methods: (i) present calculations based on the formalism of the Oswald et al. model; (ii) the predictive equation of Tanuma et al. (TPP-2M) for the measured Mo0.293S0.551C0.156 surface composition (S/Mo = 1.88), and also for stoichiometric MoS2 composition. The fitted function was found to be reasonably consistent with the measured, calculated and predicted IMFPs. We concluded that the measured IMFP value at 0.5 keV was only slightly affected by residual carbon contamination at the Mo disulfide surface.

Surface-Bound and Volatile Mo Oxides Produced During Oxidation of Single MoS2 Crystals in Air and High Relative Humidity

We report on the MoO₃ oxides and their derivatives on microscopic 2H MoS₂ flakes oxidized in air and high relative humidity at a moderate temperature range below 410 °C. We combine XPS and AFM measurements such as topography, friction, creation of nanoscale ripples and scratches on the MoS₂ flakes deposited on Si substrates. We detect MoO₃ oxides mostly by measuring selected nanomechanical properties of the MoO₃ layer, such as its compressive mechanical stress at the plastic yield. We discuss basal surface coverage of the single MoS₂ flakes by the MoO₃ oxides. We discuss conditions for appearance of all possible MoO₃ oxide derivatives, such as molybdenum(VI) hydroxyoxides and MoO₃ hydrates. Our findings agree with an expected mechanistic switch in thermal oxidation in water vapors vs. air.

Visualization of the internal structure of Didymosphenia geminata frustules using nano X-ray tomography

For the first time, the three-dimensional (3D) internal structure of naturally produced Didymosphenia geminata frustules were nondestructively visualized at sub-100 nm resolution. The well-optimized hierarchical structures of these natural organisms provide insight that is needed to design novel, environmentally friendly functional materials. Diatoms, which are widely distributed in freshwater, seawater and wet soils, are well known for their intricate, siliceous cell walls called ‘frustules’. Each type of diatom has a specific morphology with various pores, ribs, minute spines, marginal ridges and elevations. In this paper, the visualization is performed using nondestructive nano X-ray computed tomography (nano-XCT). Arbitrary cross-sections through the frustules, which can be extracted from the nano-XCT 3D data set for each direction, are validated via the destructive focused ion beam (FIB) cross-sectioning of regions of interest (ROIs) and subsequent observation by scanning electron microscopy (SEM). These 3D data are essential for understanding the functionality and potential applications of diatom cells.

Microstructure and nanomechanical properties of single stalks from diatom Didymosphenia geminata and their change due to adsorption of selected metal ions

We present topographical and nanomechanical characterization of single Didymosphenia geminata stalk. We compared the samples before and after adsorption of metal ions from freshwater samples. Transmission electron microscopy studies of single stalk cross-sections have shown three distinct layers and an additional thin extra coat on the external layer (called "EL"). Using scanning electron microscopy and atomic force microscopy (AFM), we found that topography of single stalks after ionic adsorption differed significantly from topography of pristine stalks. AFM nanoindentation studies in ambient conditions yielded elastic moduli of 214 ± 170 MPa for pristine stalks and 294 ± 108 MPa for stalks after ionic adsorption. Statistical tests showed that those results were significantly different. We conducted only preliminary comparisons between ionic adsorption of several stalks in air and in water. While the stalks with ions were on average stiffer than the pristine stalks in air, they became more compliant than the pristine stalks in water. We also heated the stalks and detected EL softening at 50°C ± 15°C. AFM nanoindentation in air on the softened samples yielded elastic moduli of 26 ± 9 MPa for pristine samples and 43 ± 22 MPa for stalks with absorbed metal ions. Substantial decrease of the EL elastic moduli after heating was expected. Significantly different elastic moduli for the samples after ionic adsorption in both cases (i.e., for heated and nonheated samples), as well as behavior of the stalks immersed in water, point to permanent structural EL changes due to ions.

Single molecule studies of force-induced S2 site exposure in the mammalian Notch negative regulatory domain

Notch signaling in metazoans is responsible for key cellular processes related to embryonic development and tissue homeostasis. Proteolitic cleavage of the S2 site within an extracellular NRR domain of Notch is a key early event in Notch signaling. We use single molecule force-extension (FX) atomic force microscopy (AFM) to study force-induced exposure of the S2 site in the NRR domain from mouse Notch 1. Our FX AFM measurements yield a histogram of N-to-C termini lengths, which we relate to conformational transitions within the NRR domain. We detect four classes of such conformational transitions. From our steered molecular dynamics (SMD) results, we associate first three classes of such events with the S2 site exposure. AFM experiments yield their mean unfolding forces as 69 ± 42, 79 ± 45, and 90 ± 50 pN, respectively, at 400 nm/s AFM pulling speeds. These forces are matched by the SMD results recalibrated to the AFM force loading rates. Next, we provide a conditional probability analysis of the AFM data to support the hypothesis that a whole sequence of conformational transitions within those three clases is the most probable pathway for the force-induced S2 site exposure. Our results support the hypothesis that force-induced Notch activation requires ligand binding to exert mechanical force not in random but in several strokes and over a substantial period of time.

Single-molecule studies of disulfide bond reduction pathways used by human thioredoxin

Disulfide bond reduction pathways used by human thioredoxin (hTrx) are studied at the single molecule level using a recombinant protein (I27SS)8. (I27SS)8 contains eight tandem repeats of identical immunoglobulin-like modules with one disulfide bond in each module. Single (I27SS)8 molecules are stretched at constant force applied by a cantilever in a force-clamp mode of atomic force microscopy (FC-AFM). Disulfide reduction events are accurately detected from stepwise increases in the end-to-end length of (I27SS)8. Earlier FC-AFM studies observed one disulfide reduction pathway used by hTrx and suggested an additional electron tunneling mechanism. Here, a very large set of unbiased FC-AFM data is collected in a range of clamping forces. By analyzing the data using exponential fits and dwell time histograms two disulfide reduction pathways used by hTrx are resolved. Based on previous studies one of these pathways is attributed to force-dependent Michaelis-Menten catalysis. The latter reduction pathway is weakly force-inhibited and occurs sporadically. Bimolecular nucleophilic substitutions (SN2) and electron tunneling (ET) mechanisms are discussed to explain the second pathway. Direct SN2 and ET mechanisms cannot be discounted, but a hypothetical E2-SN2 mechanism involving a hydride reducing a disulfide bond provides an interesting alternative, which needs to be verified in future experiments.

Local thermomechanical analysis of a microphase-separated thin lamellar PS-b-PEO film

We use atomic force microscopy (AFM) and hot tip AFM (HT-AFM) to thermophysically characterize a 30 nm thick film of poly(styrene-block-ethylene oxide), PS-b-PEO, and to modify its lamellar patterns having spacing of 39 ± 3 nm. AFM tip scans of the polymer film induce either abrasive surface patterns or nanoscale ripples, which depend upon the tip force, temperature, and number of scans. The evolution of the lamellar patterns is explained by the polymer film molecular structure and mode I crack propagation in the polymer combined with the stick-and-slip behavior of the AFM tip. The HT-AFM measurements at various tip-sample temperatures and scanning speeds yield several thermophysical quantities: the PEO melting temperature of 54 ± 12 °C, the PS glass transition temperature of 54 ± 12 °C, the PS-b-PEO specific heat of 3.6 ± 2.7 J g(-1) K(-1), the PEO melting enthalpy of 111 ± 88 J g(-1), and the free energy of Helmholtz for PEO unfolding (and melting) of 10(-20) J nm(-2). These quantities are obtained for PS-b-PEO volumes of 30,000 nm(3), which correspond to 30 ag of the polymer.

Complete noise analysis of a simple force spectroscopy AFM setup and its applications to study nanomechanics of mammalian Notch 1 protein

We describe a complete noise analysis and application of a custom made AFM force spectroscopy setup on pulling a recombinant protein with an NRR domain of mouse Notch 1. Our table top AFM setup is affordable, has an open architecture, and is easily transferable to other laboratories. Its calculated noise characteristics are dominated by the Brownian noise with 2% non-Brownian components integrated over the first thermally induced resonance of a typical cantilever. For a typical SiN cantilever with a force constant of ~15 pN nm(-1) and in water the force sensitivity and resolution are less than 10 pN, and the corresponding deflection sensitivities are less than 100 pm Hz(-1/2). Also, we obtain a sub-ms time resolution in detecting the protein length change, and only few ms cantilever response times as measured in the force clamp mode on a well-known protein standard. Using this setup we investigate force-induced conformational transitions in the NRR region of a mouse Notch 1. Notch is an important protein related to leukemia and breast cancers in humans. We demonstrate that it is feasible to develop AFM-based studies of the force-induced conformational transitions in Notch. Our results match recent steered molecular dynamics simulations of the NRR unfolding and constitute a first step towards a detailed study of Notch activation with AFM.

Comment on "Print your atomic force microscope" [Rev. Sci. Instrum. 78, 075105 (2007)]

The paper of Kühner et al. [Rev. Sci. Instrum. 78, 075105 (2007)], presents a sound realization of a very nice idea. Namely, to design and prepare (via rapid prototyping) a custom head for atomic force microscope (AFM). Custom AFM heads are essential for various applications, which include the AFM force spectroscopy modes and convenient AFM coupling with other techniques. Our comment concerns the deflection data for a thermally driven AFM cantilever obtained by Kühner et al. using their AFM setup (Figure 3 therein). The results of Kühner et al. imply that a thermally excited AFM cantilever vibrates with aberrantly large amplitudes. Namely, the deflection noise amplitudes for the MLCT-D cantilever are 60-100 times larger than what is typically observed in our lab and by others. As we argue, the author's mistake is likely attributed to an improper usage of the AFM bandwidth. We explain the necessary correction and discuss the issue of bandwidth for the AFM force spectroscopy measurements.

Dwell time analysis of a single-molecule mechanochemical reaction

Force-clamp spectroscopy is a novel technique for studying mechanochemistry at the single-bond level. Single disulfide bond reduction events are accurately detected as stepwise increases in the length of polyproteins that contain disulfide bonds and that are stretched at a constant force with the cantilever of an atomic force microscope (AFM). The kinetics of this reaction has been measured from single-exponential fits to ensemble averages of the reduction events. However, exponential fits are notoriously ambiguous to use in cases of kinetic data showing multiple reaction pathways. Here we introduce a dwell time analysis technique, of widespread use in the single ion channel field, that we apply to the examination of the kinetics of reduction of disulfide bonds measured from single-molecule force-clamp spectroscopy traces. In this technique, exponentially distributed dwell time data is plotted as a histogram with a logarithmic time scale and a square root ordinate. The advantage of logarithmic histograms is that exponentially distributed dwell times appear as well-defined peaks in the distribution, greatly enhancing our ability to detect multiple kinetic pathways. We apply this technique to examine the distribution of dwell times of 4488 single disulfide bond reduction events measured in the presence of two very different kinds of reducing agents: tris-(2-carboxyethyl)phosphine hydrochloride (TCEP) and the enzyme thioredoxin (TRX). A different clamping force is used for each reducing agent to obtain distributions of dwell times on a similar time scale. In the case of TCEP, the logarithmic histogram of dwell times showed a single peak, corresponding to a single reaction mechanism. By contrast, similar experiments done with TRX showed two well-separated peaks, marking two distinct modes of chemical reduction operating simultaneously. These experiments demonstrate that dwell time analysis techniques are a powerful approach to studying chemical reactions at the single-molecule level.

High-speed, sub-15 nm feature size thermochemical nanolithography

We report a nanolithography technique that allows simultaneous direct control of the local chemistry and topography of thin polymer films. Specifically, a heated atomic force microscope (AFM) tip can write sub-15 nm hydrophilic features onto a hydrophobic polymer at the rate of 1.4 mm per s. The thermally activated chemical reactions and topography changes depend on the chemical composition of the polymer, the raster speed, the temperature at the AFM tip/sample interface, and the normal load. This method is conceptually simple, direct, extremely rapid, achievable in a range of environments, and potentially adaptable to other materials systems.

Volume of a nanoscale water bridge

Water bridges formed through capillary condensation at nanoscale contacts first stretch and then break during contact rupture. Atomic force microscopy (AFM) pull-off experiments performed in air with hydrophilic tips and samples show that stretched nanoscopic water bridges are in mechanical equilibrium with the external pull-off force acting at the contact but not in thermodynamic equilibrium with the water vapor in air. The experimental findings are explained by a theoretical model that considers constant water volume and decrease of water meniscus curvature during meniscus stretching. The model predicts that the water bridge breakup distance will be roughly equal to the cubic root of the water bridge volume. A thermodynamic instability was noticed for large water bridges formed at the contact of a blunt AFM tip (curvature radius of 400 nm) with a flat sample. In this case, experiments showed rise and stabilization of the volume of the water at the contact in about 1 s. For sharp AFM tips (curvature radius below 50 nm), the experiments indicated that formation of stable water bridges occurs in a much shorter time (below 5 ms).

Nucleation time of nanoscale water bridges

Water capillaries bind together grains of sand. They also can bind an atomic force microscope tip to a substrate. The kinetics of capillary condensation at the nanoscale is studied here using friction force microscopy. At 40% relative humidity we find that the meniscus nucleation times increase from 0.7 to 4.2 ms when the temperature decreases from 332 to 299 K. The nucleation times grow exponentially with the inverse temperature 1/T obeying an Arrhenius law. We obtain a nucleation energy barrier of 7.8 x 10(-20) J and an attempt frequency ranging between 4 and 250 GHz, in excellent agreement with theoretical predictions. These results provide direct experimental evidence that capillary condensation is a thermally activated phenomenon.

Correlations between adhesion hysteresis and friction at molecular scales

Correlations between adhesion hysteresis and local friction are theoretically and experimentally investigated. The model is based on the classical theory of adhesional friction, contact mechanics, capillary hysteresis, and nanoscale roughness. Adhesion hysteresis was found to scale with friction through the scaling factor containing a varying ratio of adhesion energy over the reduced Young's modulus. Capillary forces can offset the relationship between adhesion hysteresis and friction. Measurements on a wide range of engineering samples with varying adhesive and elastic properties confirm the model. Adhesion hysteresis is investigated under controlled, low humidity atmosphere via ultrasonic force microscopy. Friction is measured by the friction force microscopy.

Quantitative measure of nanoscale adhesion hysteresis by ultrasonic force microscopy

Adhesion hysteresis is the difference between the work used on separating two surfaces and the work gained on bringing them back together. Although much effort has been invested into adhesion hysteresis investigations at macroscales and microscales, its measurements at the nanolengths or even molecular lengths are still not easy. In this paper we demonstrate how to obtain quantitative measures of local adhesion hysteresis from ultrasonic force microscopy investigations. We derive analytical models fitting all the experimental cases and apply them to experimental data.