Effect of Interlayer Bonding on Superlubric Sliding of Graphene Contacts: A Machine-Learning Potential Study.

Surface defects and their mutual interactions are anticipated to affect the superlubric sliding of incommensurate layered material interfaces. Atomistic understanding of this phenomenon is limited due to the high computational cost of ab initio simulations and the absence of reliable classical force-fields for molecular dynamics simulations of defected systems. To address this, we present a machine-learning potential (MLP) for bilayer defected graphene, utilizing state-of-the-art graph neural networks trained against many-body dispersion corrected density functional theory calculations under iterative configuration space exploration. The developed MLP is utilized to study the impact of interlayer bonding on the friction of bilayer defected graphene interfaces. While a mild effect on the sliding dynamics of aligned graphene interfaces is observed, the friction coefficients of incommensurate graphene interfaces are found to significantly increase due to interlayer bonding, nearly pushing the system out of the superlubric regime. The methodology utilized herein is of general nature and can be adapted to describe other homogeneous and heterogeneous defected layered material interfaces.

Proton-Transfer-Induced Fluorescence in Self-Assembled Short Peptides.

We employ molecular dynamics (MD) and time-dependent density functional theory (TDDFT) to explore the fluorescence of hydrogen-bonded dimer and trimer structures of cyclic FF (Phe-Phe) molecules. We show that in some of these configurations a photon can induce either an intra-molecular proton transfer, or an inter-molecular proton transfer that can occur in the excited S1 and S2 states. This proton transfer, taking place within the hydrogen bond, leads to a significant red-shift that can explain the experimentally observed visible fluorescence in biological and bioinspired peptide nanostructures with a ß-sheet biomolecular arrangement. Finally, we also show that such proton transfer is highly sensitive to the geometrical bonding of the dimers and trimers and that it occurs only in specific configurations allowed by the formation of hydrogen bonds.

The Structure and Composition Statistics of 6A Binary and Ternary Crystalline Materials.

The fundamental principles underlying the arrangement of elements into solid compounds with an enormous variety of crystal structures are still largely unknown. This study presents a general overview of the structure types appearing in an important subset of the solid compounds, i.e., binary and ternary compounds of the 6A column oxides, sulfides and selenides. It contains an analysis of these compounds, including the prevalence of various structure types, their symmetry properties, compositions, stoichiometries and unit cell sizes. It is found that these compound families include preferred stoichiometries and structure types that may reflect both their specific chemistry and research bias in the available empirical data. Identification of nonoverlapping gaps and missing stoichiometries in these structure populations may be used as guidance in the search for new materials.

Efficient Computation of the Hartree-Fock Exchange in Real-Space with Projection Operators.

We describe an efficient projection-based real-space implementation of the nonlocal single-determinant exchange operator. Through a matrix representation of the projected operator, we show that this scheme works equally well for both occupied and virtual states. Our scheme reaches a speedup of 2 orders of magnitude and has no significant loss of accuracy compared to an implementation of the full nonlocal single-determinant exchange operator. We find excellent agreement upon comparing Hartree-Fock eigenvalues, dipoles, and polarizabilities of selected molecules calculated using our method to values in the literature. To illustrate the efficiency of this scheme we perform calculations on systems with up to 240 carbon atoms.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures.

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

PFC and Triglyme for Li-Air Batteries: A Molecular Dynamics Study.

In this work, we present an all-atom molecular dynamics (MD) study of triglyme and perfluorinated carbons (PFCs) using classical atomistic force fields. Triglyme is a typical solvent used in nonaqueous Li-air battery cells. PFCs were recently reported to increase oxygen availability in such cells. We show that O2 diffusion in two specific PFC molecules (C6F14 and C8F18) is significantly faster than in triglyme. Furthermore, by starting with two very different initial configurations for our MD simulation, we demonstrate that C8F18 and triglyme do not mix. The mutual solubility of these molecules is evaluated both theoretically and experimentally, and a qualitative agreement is found. Finally, we show that the solubility of O2 in C8F18 is considerably higher than in triglyme. The significance of these results to Li-air batteries is discussed.

Asymptotic behavior and interpretation of virtual states: The effects of confinement and of basis sets.

A real-space high order finite difference method is used to analyze the effect of spherical domain size on the Hartree-Fock (and density functional theory) virtual eigenstates. We show the domain size dependence of both positive and negative virtual eigenvalues of the Hartree-Fock equations for small molecules. We demonstrate that positive states behave like a particle in spherical well and show how they approach zero. For the negative eigenstates, we show that large domains are needed to get the correct eigenvalues. We compare our results to those of Gaussian basis sets and draw some conclusions for real-space, basis-sets, and plane-waves calculations.

Reconstructive Phase Transition in Ultrashort Peptide Nanostructures and Induced Visible Photoluminescence.

A reconstructive phase transition has been found and studied in ultrashort di- and tripeptide nanostructures, self-assembled from biomolecules of different compositions and origin such as aromatic, aliphatic, linear, and cyclic (linear FF-diphenylalanine, linear LL-dileucine, FFF-triphenylalanine, and cyclic FF-diphenylalanine). The native linear aromatic FF, FFF and aliphatic LL peptide nanoensembles of various shapes (nanotubes and nanospheres) have asymmetric elementary structure and demonstrate nonlinear optical and piezoelectric effects. At elevated temperature, 140-180 °C, these native supramolecular structures (except for native Cyc-FF nanofibers) undergo an irreversible thermally induced transformation via reassembling into a completely new thermodynamically stable phase having nanowire morphology similar to those of amyloid fibrils. This reconstruction process is followed by deep and similar modification at all levels: macroscopic (morphology), molecular, peptide secondary, and electronic structures. However, original Cyc-FF nanofibers preserve their native physical properties. The self-fabricated supramolecular fibrillar ensembles exhibit the FTIR and CD signatures of new antiparallel ß-sheet secondary folding with intermolecular hydrogen bonds and centrosymmetric structure. In this phase, the ß-sheet nanofibers, irrespective of their native biomolecular origin, do not reveal nonlinear optical and piezoelectric effects, but do exhibit similar profound modification of optoelectronic properties followed by the appearance of visible (blue and green) photoluminescence (PL), which is not observed in the original peptides and their native nanostructures. The observed visible PL effect, ascribed to hydrogen bonds of thermally induced ß-sheet secondary structures, has the same physical origin as that of the fluorescence found recently in amyloid fibrils and can be considered to be an optical signature of ß-sheet structures in both biological and bioinspired materials. Such PL centers represent a new class of self-assembled dyes and can be used as intrinsic optical labels in biomedical microscopy as well as for a new generation of novel optoelectronic nanomaterials for emerging nanophotonic applications, such as biolasers, biocompatible markers, and integrated optics.

An auxilliary grid method for the calculation of electrostatic terms in density functional theory on a real-space grid.

In this work we show the implementation of a linear scaling algorithm for the calculation of the Poisson integral. We use domain decomposition and non-uniform auxiliary grids (NGs) to calculate the electrostatic interaction. We demonstrate the approach within the PARSEC density functional theory code and perform calculations of long 1D carbon chains and other long molecules. Finally, we discuss possible applications to additional problems and geometries.

Fock-exchange for periodic structures in the real-space formalism and the KLI approximation.

The calculation of Fock-exchange interaction is an important task in the computation of molecule and solid properties. In this work we describe how we implement the Fock exchange in the real-space formalism using the KLI approximation for the OEP equation for 3D periodic systems. The implementation is demonstrated within the PARSEC real-space pseudopotential code that uses a discrete uniform grid and norm conserving pseudopotentials for the ionic potentials.

Structural and optical properties of short peptides: nanotubes-to-nanofibers phase transformation.

Thermally induced phase transformation in bioorganic nanotubes, which self-assembled from two ultrashort dipeptides of different origin, aromatic diphenylalanine (FF) and aliphatic dileucine (LL), is studied. In both FF and LL nanotubes, irreversible phase transformation found at 120-180 °C is governed by linear-to-cyclic dipeptide molecular modification followed by formation of extended ß-sheet structure. As a result of this process, native open-end FF and LL nanotubes are transformed into ultrathin nanofibrils. Found deep reconstructions at all levels from macroscopic (morphology) and structural space symmetry to molecular give rise to new optical properties in both aromatic FF and aliphatic LL nanofibrils and generation of blue photoluminescence (PL) emission. It is shown that observed blue PL peak is similar in these supramolecular nanofibrillar structures and is excited by the network of non-covalent hydrogen bonds that link newly thermally induced neighboring cyclic dipeptide strands to final extended ß-sheet structure of amyloid-like nanofibrils. The observed blue PL peak in short dipeptide nanofibrils is similar to the blue PL peak that was recently found in amyloid fibrils and can be considered as the optical signature of ß-sheet structures. Nanotubular structures were characterized by environmental scanning electron microscope, ToF-secondary ion mass spectroscopy, CD and fluorescence spectroscopy.

Insights into graphene functionalization by single atom doping.

Chemical modification of graphene is a common approach to control its electronic properties and hence fabricate electronic devices with new or improved functionalities. In this work we analyze, with density functional based calculations, the effect of chemical adsorption of fluorine atoms at different coverage levels on the electronic structure of graphene. We suggest a simple and general model for the shift of the Fermi level with coverage level and show the trends of the band gap and the Fermi level shift with coverage. We then show that the same model can be applied to explain the Fermi level shift in a different system of nitrogen substitution in graphene. Finally, we analyze the resulting charge transfer patterns and show that they are consistent with the model for the Fermi level shift.

Dimensionality effects in the electronic structure of organic semiconductors consisting of polar repeat units.

In conjugated organic molecules, excitation gaps typically decrease reciprocally with increasing the number of repeat units, n. This usually holds for individual molecules as well as for the corresponding bulk materials. Here, we show using density-functional theory calculations that a qualitatively different evolution is found for layers built from molecules consisting of polar repeat units. Whereas a 1/n-dependence is still observed in the case of isolated polar molecules, the global gap decreases essentially linearly with n in the corresponding 2D-periodic systems and vanishes beyond a certain molecular length, with the frontier states being localized at opposite ends of the layer. The latter is accompanied by a saturation of the dipole moment per molecule, an effect not observed in the isolated polar molecules. Interestingly, in both cases the limit of the gap for long (but finite) molecules differs qualitatively from that of infinite length obtained in 1D-periodic and 3D-periodic calculations, the latter serving as models for polymers and the bulk. We rationalize these dimensionality effects as a consequence of the potential gradient within the finite-length layers. They arise from the collective action of intra-molecular dipoles in the 2D periodic layers and can be traced back to surface effects.

Collectively induced quantum-confined Stark effect in monolayers of molecules consisting of polar repeating units.

The electronic structure of terpyrimidinethiols is investigated by means of density-functional theory calculations for isolated molecules and monolayers. In the transition from molecule to self-assembled monolayer (SAM), we observe that the band gap is substantially reduced, frontier states increasingly localize on opposite sides of the SAM, and this polarization in several instances is in the direction opposite to the polarization of the overall charge density. This behavior can be analyzed by analogy to inorganic semiconductor quantum-wells, which, as the SAMs studied here, can be regarded as semiperiodic systems. There, similar observations are made under the influence of a, typically external, electric field and are known as the quantum-confined Stark effect. Without any external perturbation, in oligopyrimidine SAMs one encounters an energy gradient that is generated by the dipole moments of the pyrimidine repeat units. It is particularly strong, reaching values of about 1.6 eV/nm, which corresponds to a substantial electric field of 1.6 × 10(7) V/cm. Close-lying σ- and π-states turn out to be a particular complication for a reliable description of the present systems, as their order is influenced not only by the docking groups and bonding to the metal, but also by the chosen computational approach. In the latter context we demonstrate that deliberately picking a hybrid functional allows avoiding pitfalls due to the infamous self-interaction error. Our results show that when aiming to build a monolayer with a specific electronic structure one can not only resort to the traditional technique of modifying the molecular structure of the constituents, but also try to exploit collective electronic effects.

The molecularly controlled semiconductor resistor: how does it work?

We examine the current response of molecularly controlled semiconductor devices to the presence of weakly interacting analytes. We evaluate the response of two types of devices, a silicon oxide coated silicon device and a GaAs/AlGaAs device, both coated with aliphatic chains and exposed to the same set of analytes. By comparing the device electrical response with contact potential difference and surface photovoltage measurements, we show that there are two mechanisms that may affect the underlying substrate, namely, formation of layers with a net dipolar moment and molecular interaction with surface states. We find that whereas the Si device response is mostly correlated to the analyte dipole, the GaAs device response is mostly correlated to interactions with surface states. Existence of a silicon oxide layer, whether native on the Si or deliberately grown on the GaAs, eliminates analyte interaction with the surface states.

Electrostatic properties of adsorbed polar molecules: opposite behavior of a single molecule and a molecular monolayer.

We compare the electrostatic behavior of a single polar molecule adsorbed on a solid substrate with that of an adsorbed polar monolayer. This is accomplished by comparing first principles calculations obtained within a cluster model and a periodic slab model, using benzene derivatives on the Si(111) surface as a representative test case. We find that the two models offer diametrically opposite descriptions of the surface electrostatic phenomena. Slab electrostatics is dominated by dipole reduction due to intermolecular dipole-dipole interactions that partially depolarize the molecules, with charge migration to the substrate playing a negligible role due to electric field suppression outside the monolayer. Conversely, cluster electrostatics is dominated by dipole enhancement due to charge migration to/from the substrate, with only a small polarization of the molecule. This establishes the important role played by long-range interactions, in addition to local chemical properties, in tailoring surface chemistry via polar molecule adsorption.