Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities.

Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can nowadays be efficiently obtained via machine learning models trained on first-principles data. However, the transferability of the models trained on small molecules to larger structures is unclear, and direct training on large structures is prohibitively expensive. In this work, we first train two machine learning models to predict the polarizabilities of all 20 amino acids. Both models are carefully benchmarked and compared to density functional theory (DFT) calculations, with the neural network method being found to offer better transferability. By combination of machine learning models with classical force field molecular dynamics, Raman spectra of all amino acids are also obtained and investigated, showing good agreement with experiments. The models are further extended to small peptides. We find that adding structures containing peptide bonds to the training set greatly improves predictions, even for peptides not included in training sets.

Structural Phase Transitions to 2D and 3D Oxygen Vacancy Patterns in a Perovskite Film Induced by Electrical and Mechanical Nanoprobing.

Oxygen vacancy migration and ordering in perovskite oxides enable manipulation of material properties through changes in the cation oxidation state and the crystal lattice. In thin-films, oxygen vacancies conventionally order into equally spaced planes. Here, it is shown that the planar 2D symmetry is broken if a mechanical nanoprobe restricts the chemical lattice expansion that the vacancies generate. Using in situ scanning transmission electron microscopy, a transition from a perovskite structure to a 3D vacancy-ordered phase in an epitaxial La2/3 Sr1/3 MnO3- δ film during voltage pulsing under local mechanical straining is imaged. The never-before-seen ordering pattern consists of a complex network of distorted oxygen tetrahedra, pentahedra, and octahedra that, together, produce a corrugated atomic structure with lattice constants varying between 3.5 and 4.6 Å. The giant lattice distortions respond sensitively to strain variations, offering prospects for non-volatile nanoscale physical property control driven by voltage and gated by strain.

Which Transition Metal Atoms Can Be Embedded into Two-Dimensional Molybdenum Dichalcogenides and Add Magnetism?

As compared to bulk solids, large surface-to-volume ratio of two-dimensional (2D) materials may open new opportunities for postsynthesis introduction of impurities into these systems by, for example, vapor deposition. However, it does not work for graphene or h-BN, as the dopant atoms prefer clustering on the surface of the material instead of getting integrated into the atomic network. Using extensive first-principles calculations, we show that counterintuitively most transition metal (TM) atoms can be embedded into the atomic network of the pristine molybdenum dichalcogenides (MoDCs) upon atom deposition at moderate temperatures either as interstitials or substitutional impurities, especially in MoTe2, which has the largest spacing between the host atoms. We further demonstrate that many impurity configurations have localized magnetic moments. By analyzing the trends in energetics and values of the magnetic moments across the periodic table, we rationalize the results through the values of TM atomic radii and the number of (s + d) electrons available for bonding and suggest the most promising TMs for inducing magnetism in MoDCs. Our results are in line with the available experimental data and should further guide the experimental effort toward a simple postsynthesis doping of 2D MoDCs and adding new functionalities to these materials.

Hydrogen-assisted post-growth substitution of tellurium into molybdenum disulfide monolayers with tunable compositions.

Herein we report the successful doping of tellurium (Te) into molybdenum disulfide (MoS2) monolayers to form MoS2x Te2(1-x) alloy with variable compositions via a hydrogen-assisted post-growth chemical vapor deposition process. It is confirmed that H2 plays an indispensable role in the Te substitution into as-grown MoS2 monolayers. Atomic-resolution transmission electron microscopy allows us to determine the lattice sites and the concentration of introduced Te atoms. At a relatively low concentration, tellurium is only substituted in the sulfur sublattice to form monolayer MoS2(1-x)Te2x alloy, while with increasing Te concentration (up to ∼27.6% achieved in this study), local regions with enriched tellurium, large structural distortions, and obvious sulfur deficiency are observed. Statistical analysis of the Te distribution indicates the random substitution. Density functional theory calculations are used to investigate the stability of the alloy structures and their electronic properties. Comparison with experimental results indicate that the samples are unstrained and the Te atoms are predominantly substituted in the top S sublattice. Importantly, such ultimately thin Janus structure of MoS2(1-x)Te2x exhibits properties that are distinct from their constituents. We believe our results will inspire further exploration of the versatile properties of asymmetric 2D TMD alloys.

Structural Distortions and Charge Density Waves in Iodine Chains Encapsulated inside Carbon Nanotubes.

Atomic chains are perfect systems for getting fundamental insights into the electron dynamics and coupling between the electronic and ionic degrees of freedom in one-dimensional metals. Depending on the band filling, they can exhibit Peierls instabilities (or charge density waves), where equally spaced chain of atoms with partially filled band is inherently unstable, exhibiting spontaneous distortion of the lattice that further leads to metal-insulator transition in the system. Here, using high-resolution scanning transmission electron microscopy, we directly image the atomic structures of a chain of iodine atoms confined inside carbon nanotubes. In addition to long equidistant chains, the ones consisting of iodine dimers and trimers were also observed, as well as transitions between them. First-principles calculations reproduce the experimentally observed bond lengths and lattice constants, showing that the ionic movement is largely unconstrained in the longitudinal direction, while naturally confined by the nanotube in the lateral directions. Moreover, the trimerized chain bears the hallmarks of a charge density wave. The transition is driven by changes in the charge transfer between the chain and the nanotube and is enabled by the charge compensation and additional screening provided by the nanotube.

Atomic structure and dynamic behaviour of truly one-dimensional ionic chains inside carbon nanotubes.

Materials with reduced dimensionality have attracted much interest in various fields of fundamental and applied science. True one-dimensional (1D) crystals with single-atom thickness have been realized only for few elemental metals (Au, Ag) or carbon, all of which showed very short lifetimes under ambient conditions. We demonstrate here a successful synthesis of stable 1D ionic crystals in which two chemical elements, one being a cation and the other an anion, align alternately inside carbon nanotubes. Unusual dynamical behaviours for different atoms in the 1D lattice are experimentally corroborated and suggest substantial interactions of the atoms with the nanotube sheath. Our theoretical studies indicate that the 1D ionic crystals have optical properties distinct from those of their bulk counterparts and that the properties can be engineered by introducing atomic defects into the chains.

Finite-size supercell correction for charged defects at surfaces and interfaces.

A finite-size supercell correction scheme is introduced for the formation energy of charged defects at surfaces and interfaces. The scheme combines classical electrostatics with the dielectric profile and the electrostatic potential extracted from the electronic-structure calculation. Spurious electrostatic interactions are removed while retaining the dielectric and quantum-mechanical features of the system of interest, which may have no interface (bulk), a single interface or surface, or two interfaces. A pertinent extrapolation scheme validates the proposed corrections. Applications to the charged Cl vacancy at the surface of NaCl and to the dangling bond at the Si(100) surface show that the corrected formation energies are largely independent of the supercell dimensions and of the size of the vacuum region.

High-throughput computation of Raman spectra from first principles.

Raman spectroscopy is a widely-used non-destructive material characterization method, which provides information about the vibrational modes of the material and therefore of its atomic structure and chemical composition. Interpretation of the spectra requires comparison to known references and to this end, experimental databases of spectra have been collected. Reference Raman spectra could also be simulated using atomistic first-principles methods but these are computationally demanding and thus the existing databases of computational Raman spectra are fairly small. In this work, we developed an optimized workflow to calculate the Raman spectra efficiently and taking full advantage of the phonon properties found in existing material databases. The workflow was benchmarked and validated by comparison to experiments and previous computational methods for select technologically relevant material systems. Using the workflow, we performed high-throughput calculations for a large set of materials (5099) belonging to many different material classes, and collected the results to a database. Finally, the contents of database are analyzed and the calculated spectra are shown to agree well with the experimental ones.

Identification of Material Dimensionality Based on Force Constant Analysis.

Identification of low-dimensional structural units from the bulk atomic structure is a widely used approach for discovering new low-dimensional materials with new properties and applications. Such analysis is usually based solely on bond-length heuristics, whereas an analysis based on bond strengths would be physically more justified. Here, we study dimensionality classification based on the interatomic force constants of a structure with different approaches for selecting the bonded atoms. The implemented approaches are applied to the existing database of first-principles calculated force constants with a large variety of materials, and the results are analyzed by comparing them to those of several bond-length-based classification methods. Depending on the approach, they can either reproduce results from bond-length-based methods or provide complementary information. As an example of the latter, we managed to identify new non-van der Waals two-dimensional material candidates.

Lateral Integration of SnS and GeSe van der Waals Semiconductors: Interface Formation, Electronic Structure, and Nanoscale Optoelectronics.

The emergence of atomically thin crystals has allowed extending materials integration to lateral heterostructures where different 2D materials are covalently connected in the plane. The concept of lateral heterostructures can be generalized to thicker layered crystals, provided that a suitably faceted seed crystal presents edges to which a compatible second van der Waals material can be attached layer by layer. Here, we examine the possibility of integrating multilayer crystals of the group IV monochalcogenides SnS and GeSe, which have the same crystal structure, small lattice mismatch, and similar bandgaps. In a two-step growth process, lateral epitaxy of GeSe on the sidewalls of multilayer SnS flakes (obtained by vapor transport of a SnS2 precursor on graphite) yields heterostructures of laterally stitched crystalline GeSe and SnS without any detectable vertical overgrowth of the SnS seeds and with sharp lateral interfaces. Combined cathodoluminescence spectroscopy and ab initio calculations show the effects of small band offsets on carrier transport and radiative recombination near the interface. The results demonstrate the possibility of forming atomically connected lateral interfaces across many van der Waals layers, which is promising for manipulating optoelectronics, photonics, and for managing charge- and thermal transport.

Highly Selective H2S Gas Sensor Based on Ti3C2Tx MXene-Organic Composites.

Cost-effective and high-performance H2S sensors are required for human health and environmental monitoring. 2D transition-metal carbides and nitrides (MXenes) are appealing candidates for gas sensing due to good conductivity and abundant surface functional groups but have been studied primarily for detecting NH3 and VOCs, with generally positive responses that are not highly selective to the target gases. Here, we report on a negative response of pristine Ti3C2Tx thin films for H2S gas sensing (in contrast to the other tested gases) and further optimization of the sensor performance using a composite of Ti3C2Tx flakes and conjugated polymers (poly[3,6-diamino-10-methylacridinium chloride-co-3,6-diaminoacridine-squaraine], PDS-Cl) with polar charged nitrogen. The composite, preserving the high selectivity of pristine Ti3C2Tx, exhibits an H2S sensing response of 2% at 5 ppm (a thirtyfold sensing enhancement) and a low limit of detection of 500 ppb. In addition, our density functional theory calculations indicate that the mixture of MXene surface functional groups needs to be taken into account to describe the sensing mechanism and the selectivity of the sensor in agreement with the experimental results. Thus, this report extends the application range of MXene-based composites to H2S sensors and deepens the understanding of their gas sensing mechanisms.

Two-dimensional transition metal dichalcogenides under electron irradiation: defect production and doping.

Using first-principles atomistic simulations, we study the response of atomically thin layers of transition metal dichalcogenides (TMDs)--a new class of two-dimensional inorganic materials with unique electronic properties--to electron irradiation. We calculate displacement threshold energies for atoms in 21 different compounds and estimate the corresponding electron energies required to produce defects. For a representative structure of MoS2, we carry out high-resolution transmission electron microscopy experiments and validate our theoretical predictions via observations of vacancy formation under exposure to an 80 keV electron beam. We further show that TMDs can be doped by filling the vacancies created by the electron beam with impurity atoms. Thereby, our results not only shed light on the radiation response of a system with reduced dimensionality, but also suggest new ways for engineering the electronic structure of TMDs.

1D Germanium Sulfide van der Waals Bicrystals by Vapor-Liquid-Solid Growth.

Defects in two-dimensional and layered materials have attracted interest for realizing properties different from those of perfect crystals. Even stronger links between defect formation, fast growth, and emerging functionality can be found in nanostructures of van der Waals crystals, but only a few prevalent morphologies and defect-controlled synthesis processes have been identified. Here, we show that in vapor-liquid-solid growth of 1D van der Waals nanostructures, the catalyst controls the selection of the predominant (fast-growing) morphologies. Growth of layered GeS over Bi catalysts leads to two coexisting nanostructure types: chiral nanowires carrying axial screw dislocations and bicrystal nanoribbons where a central twin plane facilitates rapid growth. While Au catalysts produce exclusively dislocated nanowires, their modification with an additive triggers a switch to twinned bicrystal ribbons. Nanoscale spectroscopy shows that, while supporting fast growth, the twin defects in the distinctive layered bicrystals are electronically benign and free of nonradiative recombination centers.

Stacking Fault Induced Symmetry Breaking in van der Waals Nanowires.

While traditional ferroelectrics are based on polar crystals in bulk or thin film form, two-dimensional and layered materials can support mechanisms for symmetry breaking between centrosymmetric building blocks, e.g., by creating low-symmetry interfaces in van der Waals stacks. Here, we introduce an approach toward symmetry breaking in van der Waals crystals that relies on the spontaneous incorporation of stacking faults in a nonpolar bulk layer sequence. The concept is realized in nanowires consisting of Se-rich group IV monochalcogenide (GeSe1-xSx) alloys, obtained by vapor-liquid-solid growth. The single crystalline wires adopt a layered structure in which the nonpolar A-B bulk stacking along the nanowire axis is interrupted by single-layer stacking faults with local A-A' stacking. Density functional theory explains this behavior by a reduced stacking fault formation energy in GeSe (or Se-rich GeSe1-xSx alloys). Computations demonstrate that, similar to monochalcogenide monolayers, the inserted A-layers should show a spontaneous electric polarization with a switching barrier consistent with a Curie temperature above room temperature. Second-harmonic generation signals are consistent with a variable density of stacking faults along the wires. Our results point to possible routes for designing ferroelectrics via the layer stacking in van der Waals crystals.

First principles study of the stability of MXenes under an electron beam.

Interactions between two-dimensional MXene sheets and electron beams of a (scanning) transmission electron microscope are studied by first-principles calculations. We simulated the knock-on sputtering threshold for Ti3C2 MXene sheets via ab initio molecular dynamics simulations and for five other MXenes (Ti2C, Ti2N, Nb2C, Mo2TiC2, and Ti3CN) approximately from defect formation energies. We evaluated the sputtering cross section and sputtering rates and based on those evaluated the surface composition. We find that at the exit surface and for "low" TEM energies H and F sputter at equal rates, but at "high" TEM energies the F is sputtered most strongly. In the entry surface, H sputtering dominates. The results were found to be largely similar for all studied MXenes, and although the sputtering thresholds varied between the different metal atoms the thresholds were always too high to lead to significant sputtering of the metal atoms. We simulated electron microscope images at the successive stages of sputtering and found that while it is likely difficult to identify surface groups based on the spot intensities, the local contraction of the lattice around O groups should be observable. We also studied MXenes encapsulated with graphene and found them to provide efficient protection from knock-on damage for all surface group atoms except H.

Surface Functionalization of 2D MXenes: Trends in Distribution, Composition, and Electronic Properties.

Using a multiscale computational scheme, we study the trends in distribution and composition of the surface functional groups -O, -OH, and -F on two-dimensional (2D) transition metal carbides and nitrides (MXenes). We consider Ti2N, Ti4N3, Nb2C, Nb4C3, Ti2C, and Ti3C2 to explore MXenes with different chemistry and different number of atomic layers. Using a combination of cluster expansion, Monte Carlo, and density functional theory methods, we study the distribution and composition of functional groups at experimentally relevant conditions. We show that mixtures of functional groups are favorable on all studied MXene surfaces. The distribution of functional groups appears to be largely independent of the type of metal, carbon, or nitrogen species and/or number of atomic layers in the MXene. We further show that some properties (e.g., the work function) strongly depend on the surface composition, while others, for example, the electric conductivity, exhibit only a weak dependence.

C60Br24/SWCNT: A Highly Sensitive Medium to Detect H2S via Inhomogeneous Carrier Doping.

H2S is a toxic and corrosive gas, whose accurate detection at sub-ppm concentrations is of high practical importance in environmental, industrial, and health safety applications. Herein, we propose a chemiresistive sensor device that applies a composite of single-walled carbon nanotubes (SWCNTs) and brominated fullerene (C60Br24) as a sensing component, which is capable of detecting 50 ppb H2S even at room temperature with an excellent response of 1.75% in a selective manner. In contrast, a poor gas response of pristine C60-based composites was found in control measurements. The experimental results are complemented by density functional theory calculations showing that C60Br24 in contact with SWCNTs induces localized hole doping in the nanotubes, which is increased further when H2S adsorbs on C60Br24 but decreases in the regions, where direct adsorption of H2S on the nanotubes takes place due to electron doping from the analyte. Accordingly, the heterogeneous chemical environment in the composite results in spatial fluctuations of hole density upon gas adsorption, hence influencing carrier transport and thus giving rise to chemiresistive sensing.

Synthesis and Properties of Monolayer MnSe with Unusual Atomic Structure and Antiferromagnetic Ordering.

Transition metal chalcogenides (TMCs) are a large family of 2D materials that are currently attracting intense interest. TMCs with 3d transition metals provide opportunities for introducing magnetism and strong correlations into the material with manganese standing out as a particularly attractive option due to its large magnetic moment. Here we report on the successful synthesis of monolayer manganese selenide on a NbSe2 substrate. Using scanning tunneling microscopy and spectroscopy experiments and global structure prediction calculations at the density functional theory level, we identify the atomic structure and magnetic and electronic properties of the layered Mn2Se2 phase. The structure is similar to the layered bulk phase of CuI or a buckled bilayer of h-BN. Interestingly, our results suggest that the monolayer is antiferromagnetic, but with an unusual out-of-plane ordering that results in two ferromagnetic planes.

Formation of Highly Doped Nanostripes in 2D Transition Metal Dichalcogenides via a Dislocation Climb Mechanism.

Doping of materials beyond the dopant solubility limit remains a challenge, especially when spatially nonuniform doping is required. In 2D materials with a high surface-to-volume ratio, such as transition metal dichalcogenides, various post-synthesis approaches to doping have been demonstrated, but full control over spatial distribution of dopants remains a challenge. A post-growth doping of single layers of WSe2 is performed by adding transition metal (TM) atoms in a two-step process, which includes annealing followed by deposition of dopants together with Se or S. The Ti, V, Cr, and Fe impurities at W sites are identified by using transmission electron microscopy and electron energy loss spectroscopy. Remarkably, an extremely high density (6.4-15%) of various types of impurity atoms is achieved. The dopants are revealed to be largely confined within nanostripes embedded in the otherwise pristine WSe2 . Density functional theory calculations show that the dislocations assist the incorporation of the dopant during their climb and give rise to stripes of TM dopant atoms. This work demonstrates a possible spatially controllable doping strategy to achieve the desired local electronic, magnetic, and optical properties in 2D materials.

Band Bending and Valence Band Quantization at Line Defects in MoS2.

The variation of the electronic structure normal to 1D defects in quasi-freestanding MoS2, grown by molecular beam epitaxy, is investigated through high resolution scanning tunneling spectroscopy at 5 K. Strong upward bending of valence and conduction bands toward the line defects is found for the 4|4E mirror twin boundary and island edges but not for the 4|4P mirror twin boundary. Quantized energy levels in the valence band are observed wherever upward band bending takes place. Focusing on the common 4|4E mirror twin boundary, density functional theory calculations give an estimate of its charging, which agrees well with electrostatic modeling. We show that the line charge can also be assessed from the filling of the boundary-localized electronic band, whereby we provide a measurement of the theoretically predicted quantized polarization charge at MoS2 mirror twin boundaries. These calculations elucidate the origin of band bending and charging at these 1D defects in MoS2. The 4|4E mirror twin boundary not only impairs charge transport of electrons and holes due to band bending, but holes are additionally subject to a potential barrier, which is inferred from the independence of the quantized energy landscape on either side of the boundary.