IRA: A Shape Matching Approach for Recognition and Comparison of Generic Atomic Patterns.

We propose a versatile, parameter-less approach for solving the shape matching problem, specifically in the context of atomic structures when atomic assignments are not known a priori. The algorithm Iteratively suggests Rotated atom-centered reference frames and Assignments (iterative rotations and assignments (IRA)). The frame for which a permutationally invariant set-set distance, namely, the Hausdorff distance, returns a minimal value is chosen as the solution of the matching problem. IRA is able to find rigid rotations, reflections, translations, and permutations between structures with different numbers of atoms, for any atomic arrangement and pattern, periodic or not. When distortions are present between the structures, optimal rotation and translation are found by further applying a standard singular value decomposition-based method. To compute the atomic assignments under the one-to-one assignment constraint, we develop our own algorithm, constrained shortest distance assignments (CShDA). The overall approach is extensively tested on several structures, including distorted structural fragments. The efficiency of the proposed algorithm is shown as a benchmark comparison against two other shape matching algorithms. We discuss the use of our approach for the identification and comparison of structures and structural fragments through two examples: a replica-exchange trajectory of a cyanine molecule, in which we show how our approach could aid the exploration of relevant collective coordinates for clustering the data, and a SiO2 amorphous model, in which we compute distortion scores, and compare them with a classical strain-based potential. The source code and benchmark data are available at https://github.com/mammasmias/IterativeRotationsAssignments.

Structure-property relationships of curved aromatic materials from first principles.

CONSPECTUS: Considerable effort in the past decade has been extended toward achieving computationally affordable theoretical methods for accurate prediction of the structure and properties of materials. Theoretical predictions of solids began decades ago, but only recently have solid-state quantum techniques become sufficiently reliable to be routinely chosen for investigation of solids as quantum chemistry techniques are for isolated molecules. Of great interest are ab initio predictive theories for solids that can provide atomic scale insights into properties of bulk materials, interfaces, and nanostructures. Adaption of the quantum chemical framework is challenging in that no single theory exists that provides prediction of all observables for every material type. However, through a combination of interdisciplinary efforts, a richly textured and substantive portfolio of methods is developing, which promise quantitative predictions of materials and device properties as well as associated performance analysis. Particularly relevant for device applications are organic semiconductors (OSC), with electrical conductivity between that of insulators and that of metals. Semiconducting small molecules, such as aromatic hydrocarbons, tend to have high polarizabilities, small band-gaps, and delocalized π electrons that support mobile charge carriers. Most importantly, the special nature of optical excitations in the form of a bound electron-hole pairs (excitons) holds significant promise for use in devices, such as organic light emitting diodes (OLEDs), organic photovoltaics (OPVs), and molecular nanojunctions. Added morphological features, such as curvature in aromatic hydrocarbon structure, can further confine the electronic states in one or more directions leading to additional physical phenomena in materials. Such structures offer exploration of a wealth of phenomenology as a function of their environment, particularly due to the ability to tune their electronic character through functionalization. This Account offers discussion of current state-of-the-art electronic structure approaches for prediction of structural, electronic, optical, and transport properties of materials, with illustration of these capabilities from a series of investigations involving curved aromatic materials. The class of curved aromatic materials offers the ability to investigate methodology across a wide range of materials complexity, including (a) molecules, (b) molecular crystals, (c) molecular adsorbates on metal surfaces, and (d) molecular nanojunctions. A reliable pallet of theoretical tools for such a wide array relies on expertise spanning multiple fields. Working together with experimental experts, advancements in the fundamental understanding of structural and dynamical properties are enabling focused design of functional materials. Most importantly, these studies provide an opportunity to compare experimental and theoretical capabilities and open the way for continual improvement of these capabilities.

Deep Levels and Electron Paramagnetic Resonance Parameters of Substitutional Nitrogen in Silicon from First Principles.

Nitrogen is commonly implanted in silicon to suppress the diffusion of self-interstitials and the formation of voids through the creation of nitrogen-vacancy complexes and nitrogen-nitrogen pairs. Yet, identifying a specific N-related defect via spectroscopic means has proven to be non-trivial. Activation energies obtained from deep-level transient spectroscopy are often assigned to a subset of possible defects that include non-equivalent atomic structures, such as the substitutional nitrogen and the nitrogen-vacancy complex. Paramagnetic N-related defects were the object of several electron paramagnetic spectroscopy investigations which assigned the so-called SL5 signal to the presence of substitutional nitrogen (NSi). Nevertheless, its behaviour at finite temperatures has been imprecisely linked to the metastability of the NSi center. In this work, we build upon the robust identification of the SL5 signature and we establish a theoretical picture of the substitutional nitrogen. Through an understanding of its symmetry-breaking mechanism, we provide a model of its fundamental physical properties (e.g., its energy landscape) based on ab initio calculations. Moreover by including more refined density functional theory-based approaches, we calculate EPR parameters (↔g and ↔A tensors), elucidating the debate on the metastability of NSi. Finally, by computing thermodynamic charge transition levels within the GW method, we present reference values for the donor and acceptor levels of NSi.

The Influence of Catechols on the Magnetization of Iron Oxide Nanoparticles.

In this study, MNPs were functionalized with pyrocatechol (CAT), pyrogallol (GAL), caffeic acid (CAF), and nitrodopamine (NDA) at pH 8 and pH 11. The functionalization of the MNPs was successful, except in the case of NDA at pH 11. The thermogravimetric analyses indicated that the surface concentration of the catechols was between 1.5 and 3.6 molecules/nm2. The saturation magnetizations (Ms) of the functionalized MNPs were higher than the starting material. XPS analyses showed only the presence of Fe(III) ions on the surface, thus refuting the idea of the Fe being reduced and magnetite being formed on the surfaces of the MNPs. Density functional theory (DFT) calculations were performed for two modes of adsorption of CAT onto two model surfaces: plain and adsorption via condensation. The total magnetization of both adsorption modes remained the same, indicating that the adsorption of the catechols does not affect the Ms. The analyses of the size and the size distribution showed an increase in the average size of the MNPs during the functionalization process. This increase in the average size of the MNPs and the reduction in the fraction of the smallest (i.e., <10 nm) MNPs explained the increase in the Ms values.

Saturation magnetisation as an indicator of the disintegration of barium hexaferrite nanoplatelets during the surface functionalisation.

Barium hexaferrite nanoplatelets (BHF NPLs) are permanent nanomagnets with the magnetic easy axis aligned perpendicular to their basal plane. By combining this specific property with optimised surface chemistry, novel functional materials were developed, e.g., ferromagnetic ferrofluids and porous nanomagnets. We compared the interaction of chemically different phosphonic acids, hydrophobic and hydrophilic with 1-4 phosphonic groups, with BHF NPLs. A decrease in the saturation magnetisation after functionalising the BHF NPLs was correlated with the mass fraction of the nonmagnetic coating, whereas the saturation magnetisation of the NPLs coated with a tetraphosphonic acid at 80 °C was significantly lower than expected. We showed that such a substantial decrease in the saturation magnetisation originates from the disintegration of BHF NPLs, which was observed with atomic-resolution scanning transmission electron microscopy and confirmed by a computational study based on state-of-the-art first-principles calculations. Fe K-edge XANES (X-ray absorption near-edge structure) and EXAFS (Extended X-ray absorption fine structure) combined with Fourier-transformed infrared (FTIR) spectroscopy confirmed the formation of an Fe-phosphonate complex on the partly decomposed NPLs. Comparing our results with other functionalised magnetic nanoparticles confirmed that saturation magnetisation can be exploited to identify the disintegration of magnetic nanoparticles when insoluble disintegration products are formed.

Effect of molecular packing on corannulene-based materials electroluminescence.

The present investigation reports for the first time a detailed theoretical analysis of the optical absorption spectra of corannulene-based materials using state-of-the-art first-principles many-body GW-BSE theory. The study specifically addresses the nature of optical excitations for predictions regarding suitability for device fabrication. The well-defined structure-correlation relationship in functionalized corannulenes is used in a focused investigation of the predicted optoelectronic properties in both the isolated state and bulk crystals. The findings suggest that the excitonic properties are strongly dependent on the specific substituent group as well as the crystalline arrangement. Arylethynyl-substituted corannulene derivatives are shown to be the most suitable for device purposes.

Finding Reaction Pathways and Transition States: r-ARTn and d-ARTn as an Efficient and Versatile Alternative to String Approaches.

Finding transition states and diffusion pathways is essential to understand the evolution of materials and chemical reactions. Such characterization is hampered by the heavy computation costs associated with exploring energy landscapes at ab initio accuracy. Here, we revisit the activation-relaxation technique (ARTn) to considerably reduce its costs when used with the density functional theory and propose three adapted versions of the algorithm to efficiently (i) explore the energy landscape of complex materials with the knowledge of a single minimum (ARTn); (ii) identify a transition state when two minima or a guess transition state is given (refining ART or r-ART); and (iii) reconstruct complex pathways between two given states (directed ART or d-ART). We show the application of these three variants on benchmark examples and on various complex defects in silicon. For the latter, the presented improvements to ART lead to much more precise transition states while being 2 to 6 times faster than the commonly used string methods such as the climbing image nudged elastic band method (CI-NEB).

Study of silica-based intrinsically emitting nanoparticles produced by an excimer laser.

We report an experimental study demonstrating the feasibility to produce both pure and Ge-doped silica nanoparticles (size ranging from tens up to hundreds of nanometers) using nanosecond pulsed KrF laser ablation of bulk glass. In particular, pure silica nanoparticles were produced using a laser pulse energy of 400 mJ on pure silica, whereas Ge-doped nanoparticles were obtained using 33 and 165 mJ per pulse on germanosilicate glass. The difference in the required energy is attributed to the Ge doping, which modifies the optical properties of the silica by facilitating energy absorption processes such as multiphoton absorption or by introducing absorbing point defects. Defect generation in bulk pure silica before nanoparticle production starts is also suggested by our results. Regarding the Ge-doped samples, scanning electron microscopy (SEM) and cathodoluminescence (CL) investigations revealed a good correspondence between the morphology of the generated particles and their emission signal due to the germanium lone pair center (GLPC), regardless of the energy per pulse used for their production. This suggests a reasonable homogeneity of the emission features of the samples. Similarly, energy dispersive X-ray spectroscopy (EDX) data showed that the O, Ge and Si signals qualitatively correspond to the particle morphology, suggesting a generally uniform chemical composition of the Ge-doped samples. No significant CL signal could be detected in pure silica nanoparticles, evidencing the positive impact of Ge for the development of intrinsically emitting nanoparticles. Transmission electron microscope (TEM) data suggested that the Ge-doped silica nanoparticles are amorphous. SEM and TEM data evidenced that the produced nanoparticles tend to be slightly more spherical in shape for a higher energy per pulse. Scanning transmission electron microscope (STEM) data have shown that, regardless of size and applied energy per pulse, in each nanoparticle, some inhomogeneity is present in the form of brighter (i.e., more dense) features of a few nanometers.

Optical Properties of Saturated and Unsaturated Carbonyl Defects in Polyethylene.

Polyethylene (PE), one of the simplest and most used aliphatic polymers, is generally provided with a number of additives, in particular antioxidants, because of its tendency to get oxidized. Carbonyl defects, a product of the oxidation of PE, are occurring in various forms, in particular saturated ones, known as ketones, where a C═O double bond substitutes a CH2 group, and various unsaturated ones, i.e., with further missing hydrogens. Many experimental investigations of the optical properties in the visible/UV range mainly attribute the photoluminescence of PE to one specific kind of unsaturated carbonyls, following analogies to the emission spectra of similar small molecules. However, the reason why saturated carbonyls should not be optically detected is not clear. We investigated the optical properties of PE with and without carbonyl defects using perturbative GW and the Bethe-Salpeter equation in order to take into account excitonic effects. We discuss the calculated excitonic states in comparison with experimental absorption/emission energies and the stability of both saturated and unsaturated carbonyl defects. We conclude that the unsaturated defects are indeed the best candidate for the luminescence of oxidized PE, and the reason is mainly due to oscillator strengths.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.