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.

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 β-sheet biomolecular arrangement.

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.

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.

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.

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.

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.

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.

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.

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 β-sheet structure. As a result of this process, native open-end FF and LL nanotubes are transformed into ultrathin nanofibrils.

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.

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, . 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.

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.

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.

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.