Amir Natan

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 × 107 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.

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 β-sheet secondary folding with intermolecular hydrogen bonds and centrosymmetric structure. In this phase, the β-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 β-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 β-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.

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. 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 β‐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 β‐sheet structures. Nanotubular structures were characterized by environmental scanning electron microscope, ToF‐secondary ion mass spectroscopy, CD and fluorescence spectroscopy. Copyright

Electron effective mass in graphene

The particle effective mass in graphene is a challenging concept because the commonly used theoretical expression is mathematically divergent. In this paper, we use basic principles to present a simple theoretical expression for the effective mass that is suitable for both parabolic and non-parabolic isotropic materials. We demonstrate that this definition is consistent with the definition of the cyclotron effective mass, which is one of the common methods for effective mass measurement in solid state materials. We apply the proposed theoretical definition to graphene and demonstrate linear dependence of the effective mass on momentum, as confirmed by experimental cyclotron resonance measurements. Therefore, the proposed definition of the effective mass can be used for non-parabolic materials such as graphene.

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.

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.

Bioorganic nanodots for non-volatile memory devices

In recent years we are witnessing an intensive integration of bio-organic nanomaterials in electronic devices. Here we show that the diphenylalanine bio-molecule can self-assemble into tiny peptide nanodots (PNDs) of ∼2 nm size, and can be embedded into metal-oxide-semiconductor devices as charge storage nanounits in non-volatile memory. For that purpose, we first directly observe the crystallinity of a single PND by electron microscopy. We use these nanocrystalline PNDs units for the formation of a dense monolayer on SiO2 surface, and study the electron/hole trapping mechanisms and charge retention ability of the monolayer, followed by fabrication of PND-based memory cell device.

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.