We extend thermochemical nanolithography (TCNL) capabilities toward thermally induced modifications of thin MoS2 and CrSBr flakes in air. We perform atomic force microscopy studies and thermal TCNL calibration with Raman spectroscopy as well as analytic heat-flow models. While TCNL cannot provide a high enough temperature to thermally oxidize and etch the basal planes of such flakes, it can deform the underlying Si and SiO2 substrates and pattern the surfaces of 2D materials in some specific cases. In particular, TCNL enables thermally induced deposition of Cr oxides/hydroxides onto CrSBr basal planes in a new, reverse patterning scheme. It is also able to pattern already oxidized MoS2 layers. In addition, the microscopic oxidation of CrSBr crystals has been studied upon their hot-plate heating. Thick CrSBr flakes start to oxidize at around 330 °C, while thin ones etch above 350 °C. Their oxidation leads to the formation of surface-bound Cr(III) oxides and/or hydroxides, as well as some sulfates.

MoS2 has found many applications in optoelectronics, energy harvesting, and catalysis due to its unique properties and functionalities. It has been shown that its properties can be tuned by thermal oxidation and plasma treatment. Herein, we examined the capability of oxidation scanning probe lithography (o-SPL) for direct nitrogenation of the MoS2 crystals under ambient conditions. By utilizing Kelvin probe force microscopy together with Auger electron spectroscopy, we found out that the o-SPL method was able to simultaneously oxidize and nitrogenize MoS2 flakes when a relatively high input voltage was exerted. Under such harsh conditions, oxygen and nitrogen atoms were incorporated and replaced the sulfur atoms within MoS2. At the same time, large surface topographical changes were observed mostly due to sample delamination. On the contrary, low input voltage was able to produce large topographical changes associated only with desulfurization but without any oxidation/nitrogenation. Finally, high voltage o-SPL treatment of MoS2 samples pre-oxidized in air also produced their nitrogenation coupled with oxidation.

2D materials with intrinsic magnetic ordering opened new grounds in spintronics and quantum information processing. Out of these CrSBr has been suggested to be an air stable 2D magnet. Herein, we ponder into the mechanisms behind structural stability and thermal oxidation of bulk CrSBr crystals in air. Our XAS and XPS studies show that long-time storage of this material in air produces Br vacancies as well as near-surface defective S and Cr atoms. Experimental AFM, XAS and XPS studies supported by DFT calculations show that heating CrSBr crystals produces vacancies first and then some surface-bound oxides/hydroxides, which increase the surface micro-roughness. In particular, fifteen minutes heating at 270 °C leads to Br and S vacancies as well as presence of sulfates at the surface but without any Cr oxides. However, 15 min heating at 330 °C induces oxidation of Cr atoms into Cr2O3 and/or Cr(OH)3. Furthermore, defective CrSBr undergoes a unique thermal oxidative etching with formation of sub-surface square etch pits. This leads to occasional bursts of the top-most layers once a maximum strain within the CrSBr membrane has been met. The DFT calculations support favorable oxygen incorporation underneath the top-most layers through the Br vacancies and passivation of the S vacancies in the top-most layer.

We present a computational investigation to explore the influence of the protective osmolyte proline as a co-solvent on peptide structure and dynamics for a series of alanine-based peptides, (ALA)n of length n = 5, 8, 15, and 21 residues. Applying multi-microsecond molecular dynamics simulations in a 2 M proline solution, we evaluate peptide structure, solvation and helix folding dynamics and compare to behavior in pure water. Proline addition enhances helix content and significantly slows folding and unfolding times, correlating with a 1.9-fold increase in solvent viscosity. Notably, ALA15 helix content increases from 25% to 49% and relaxation time rises from 110 ns to 540 ns in proline relative to water. Microscopic solvation effects of proline include peptide compaction and dehydration, exclusion of proline from the backbone, formation of weak interactions with the ALA methyl sidechains, and strong interactions with water. The differences of these effects on the helix and coil states drive helix stabilization by proline. Low-dimensional kinetic modeling with Optimal Dimensionality Reduction predicts distinct folding mechanisms: shorter peptides (ALA5-ALA15) exhibit direct helix-coil transitions, and only the longest ALA21 follows a more complex folding pathway involving intermediates. Statistically, enhanced stability of hydrogen bonds in the peptide centers and strong correlation between transitions on neighboring residues are shared between water and proline solutions. However, there is a preference for helix initiation at the N-terminus under proline influence. Our analysis describes the molecular mechanisms of how proline modulates peptide behavior, offering atomistic insights into helix stabilization and folding mechanisms mediated by osmolytes.

We present an analysis of α-helix folding in the coarse-grained coordinate of number of formed helical hydrogen bonds (NHBs) for four alanine peptides (ALA)n, with n = 5, 8, 15, and 21 residues. Starting with multi-microsecond all-atom molecular dynamics trajectories in aqueous solution, we represent the system dynamics in a space of between four (for ALA5) and twenty (for ALA21) hydrogen-bonding microstates. In all cases, transitions changing the hydrogen bond count by 1–2 dominate and the coil formation, NHB 1 → 0, is the fastest process. The calculation of global maximum weight paths shows that, when analyzed at a sufficiently long lag time, folding in the NHB coordinate is consecutive, with direct folding, 0 → 3, for ALA5 and bottlenecks at transitions 4 → 6 for ALA8, 0 → 5 for ALA15, and 0 → 9 for ALA21. Further coarse-graining to 2–4 dimensions was performed with the optimal dimensionality reduction method, allowing the identification of crucial folding intermediates and time scales of their formation in ALA8, ALA15, and ALA21. The detailed analysis of hydrogen bonding patterns revealed that folding is initiated preferentially at both peptide termini. The kinetic model was also used to estimate diffusion and friction coefficients for helix propagation. The description of the helix formation process in the hydrogen bonding coordinate NHB was in good general agreement with the experimental data and qualitatively similar to previous kinetic models of higher dimensions based on structural clustering. Use of the low-dimensional hydrogen bonding picture thus provides a different, complementary way of describing the complex and fascinating mechanism of helix formation.

MoS2, its oxides and heterostructures are increasingly utilized in nanoscale opto-electronics and catalysis, where electrical properties such as work function (WF) affect their performance. Herein, a detailed study of the thickness-dependent work function in the case of thermally produced layered Mo oxides onto SiO2 and MoS2 substrates in air is presented. First, the effects of typical contaminants on the mechanically exfoliated MoS2 substrates are investigated. Then, high resolution structural characterization by atomic force microscopy supported by X-ray photoelectron spectroscopy shows that thermal MoS2 oxidation in humid air produces layered amorphous MoO3 with nano-crystallites. Kelvin-probe force microscopy analysis shows that the first MoO3 layer on both substrates is negatively charged and that the MoO3 work function depends on the oxide thickness. The thickness-dependent WF is explained by presence of screened electric field at the MoO3/substrate interface. The negative doping to MoO3 by the studied substrates is confirmed through density functional theory simulations. Moreover, an electrical device from amorphous MoO3 monolayer onto MoS2 is built and shows rectification behavior due to p-type doping of the MoS2 by the oxide layer. Overall, this study provides an insight to understand and manipulate electrical properties of MoO3 and MoO3/MoS2 heterostructures in various devices.

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 alpha-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)(2)G-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.

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.

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.

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 mu s MD trajectories at 320 K yielded relaxation times of 1.8 mu 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 mu s and unfolding time of 4.0 mu 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 similar to 100 ns relaxation related to intermediate formation.Communicated by Ramaswamy H. Sarma

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.

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.

Molybdenum Disulfide (MoS2) is a well-known transition metal dichalcogenide with a hexagonal structure arrangement analogous to graphene. Two dimensional (2D) MoS2 has attracted wide attention in various applications such as energy storage, catalysis, sensing, energy conversion and optoelectronics due to its unique properties including tunable bandgap, substantial carrier mobility, outstanding mechanical strength and dangling-bond free basal surface. Moreover, MoS2 has shown an excellent capability to be a host for foreign atoms which tune its physicochemical properties. Herein, currently known structural changes in the MoS2 crystals introduced by various single atom dopants coming from all over the chemical table of elements are reviewed. Accompanying electrical, optical and magnetic properties of such structures are discussed in detail. Potential applications of the doped MoS2 are introduced briefly as well. The review concentrates on the recent state-of-the-art results obtained mostly by the high resolution scanning transmission electron microscopy (STEM), such as high angle annular dark field (HAADF) imaging as well as scanning probe microscopy (SPM) such as scanning tunneling microscopy (STM). These techniques have been used to decipher dopant positions and other sub-atomic structural changes introduced to the MoS2 structure by isolated dopants.

The chemical presence of the MoO x species on single microscopic MoS 2 flakes is shown at two conditions, which are of interest for future MoS 2 ‐based devices and where their presence is not previously confirmed. First, the case of thick MoS 2 flakes oxidatively etched at 350–370 °C in air is treated. Atomic force microscopy (AFM), high resolution X‐ray photoelectron spectroscopy, and X‐ray absorption spectroscopy are combined to unambiguously confirm the chemical presence of the α‐MoO 3 species on such samples, mostly in the form of loose particles. Second, it is shown that MoS 2 flakes heated at temperatures of only 220 °C display a quite uniform ≈2 nm thick MoO x layer at already 10% relative humidity. The presence of such MoO x oxide layers is confirmed by scratching the sample with AFM tips and performing comparative Kelvin probe force microscopy and Auger photoelectron spectroscopy on scratched‐out and untouched parts of the flakes.

We present a computer simulation study of helix folding in alanine homopeptides (ALA)n of length n = 5, 8, 15, and 21 residues. Based on multi-microsecond molecular dynamics simulations at room temperature, we found helix populations and relaxation times increasing from about 6% and ~2 ns for ALA5 to about 60% and ~500 ns for ALA21, and folding free energies decreasing linearly with the increasing number of residues. The helix folding was analyzed with the Optimal Dimensionality Reduction method, yielding coarse-grained kinetic models that provided a detailed representation of the folding process. The shorter peptides, ALA5 and ALA8, tended to convert directly from coil to helix, while ALA15 and ALA21 traveled through several intermediates. Coarse-grained aggregate states representing the helix, coil, and intermediates were heterogeneous, encompassing multiple peptide conformations. The folding involved multiple pathways and interesting intermediate states were present on the folding paths, with partially formed helices, turns, and compact coils. Statistically, helix initiation was favored at both termini, and the helix was most stable in the central region. Importantly, we found the presence of underlying universal local dynamics in helical peptides with correlated transitions for neighboring hydrogen bonds. Overall, the structural and dynamical parameters extracted from the trajectories are in good agreement with experimental observables, providing microscopic insights into the complex helix folding kinetics.

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.

In article number 2100328, Maciej Rogala, Stanislaw Sokolowski, Robert Szoszkiewicz, and co-workers investigate chemical origins of the MoOx species appearing on single MoS2 flakes due to their oxidation in dry and humid air. MoOx species on the oxidatively etched MoS2 surface are shown to originate from loosely surface-bound (MoO3)n (n > 0) single clusters with an average height of 0.32 ± 0.05 nm. Their presence has been confirmed topographically and chemically via combined AFM, XPS, and XAS studies.

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.