From Local Atomic Environments to Molecular Information Entropy.

The similarity of local atomic environments is an important concept in many machine learning techniques, which find applications in computational chemistry and material science. Here, we present and discuss a connection between the information entropy and the similarity matrix of a molecule. The resulting entropy can be used as a measure of the complexity of a molecule. Exemplarily, we introduce and evaluate two specific choices for defining the similarity: one is based on a SMILES representation of local substructures, and the other is based on the SOAP kernel. By tuning the sensitivity of the latter, we can achieve good agreement between the respective entropies. Finally, we consider the entropy of two molecules in a mixture. The gain of entropy due to the mixing can be used as a similarity measure of the molecules. We compare this measure to the average and best-match kernel. The results indicate a connection between the different approaches and demonstrate the usefulness and broad applicability of the similarity-based entropy approach.

Enhancing the Carrier Transport in Monolayer MoS2 through Interlayer Coupling with 2D Covalent Organic Frameworks.

The coupling of different 2D materials (2DMs) to form van der Waals heterostructures (vdWHs) is a powerful strategy for adjusting the electronic properties of 2D semiconductors, for applications in opto-electronics and quantum computing. 2D molybdenum disulfide (MoS2 ) represents an archetypical semiconducting, monolayer thick versatile platform for the generation of hybrid vdWH with tunable charge transport characteristics through its interfacing with molecules and assemblies thereof. However, the physisorption of (macro)molecules on 2D MoS2 yields hybrids possessing a limited thermal stability, thereby jeopardizing their technological applications. Herein, the rational design and optimized synthesis of 2D covalent organic frameworks (2D-COFs) for the generation of MoS2 /2D-COF vdWHs exhibiting strong interlayer coupling effects are reported. The high crystallinity of the 2D-COF films makes it possible to engineer an ultrastable periodic doping effect on MoS2 , boosting devices' field-effect mobility at room temperature. Such a performance increase can be attributed to the synergistic effect of the efficient interfacial electron transfer process and the pronounced suppression of MoS2 's lattice vibration. This proof-of-concept work validates an unprecedented approach for the efficient modulation of the electronic properties of 2D transition metal dichalcogenides toward high-performance (opto)electronics for CMOS digital circuits.

Facial disgust in response to touches, smells, and tastes.

Disgust serves to defend the body from the entry of toxins and disease. Central to this function is a strong relationship with the proximate senses of smell, taste, and touch. Theory suggests that distinct and reflexive facial movements should be evoked by gustatory and olfactory disgusts, serving to impede bodily entry. While this hypothesis has received some support from facial recognition studies, whether smell and taste disgusts actually produce distinct facial responses, is unknown. Moreover, there has been no assessment of the facial response evoked by contact with disgusting objects. To address these issues, this study compared facial responses to touch, smell, and taste disgusts. Sixty-four participants were asked to touch, smell, and taste disgust-evoking and neutral control stimuli, and rate them on disgust, on two occasions-first, while they were video recorded and second, with facial electromyography (EMG) applied (measuring levator labii and corrugator supercilii activity). Videos were coded for facial expressions by humans and for facial action units (FAUs) by machines. Self-report data confirmed the disgust stimuli as highly disgusting. Comparison of the overall pattern of FAUs evoked by touch, smell, and taste disgusts, indicated two distinct facial disgusts for the proximate senses-a chemosensory and a tactile-disgust face. The nose wrinkle and upper lip raise were central to all facial disgusts, indicating their centrality to the disgust face. Several facial disgusts appear to exist, each with different functional goals. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

An olfactory perceptual fingerprint in people with olfactory dysfunction due to COVID-19.

The sense of smell is based on sensory detection of the molecule(s), which is then further perceptually interpreted. A possible measure of olfactory perception is an odor-independent olfactory perceptual fingerprint (OPF) defined by Snitz et al. We aimed to investigate whether OPF can distinguish patients with olfactory dysfunction (OD) due to coronavirus disease (COVID-19) from controls and which perceptual descriptors are important for that separation. Our study included 99 healthy controls and 41 patients. They rated 10 odors using 8 descriptors such as "pleasant," "intense," "familiar," "warm," "cold," "irritating," "edible," and "disgusting." An unsupervised machine learning method, hierarchical cluster analysis, showed that OPF can distinguish patients from controls with an accuracy of 83%, a sensitivity of 51%, and a specificity of 96%. Furthermore, a supervised machine learning method, random forest classifier, showed that OPF can distinguish patients and controls in the testing dataset with an accuracy of 86%, a sensitivity of 64%, and a specificity of 96%. Principal component analysis and random forest classifier showed that familiarity and intensity were the key qualities to explain the variance of the data. In conclusion, people with COVID-19-related OD have a fundamentally different olfactory perception.

Site-selective chemical reactions by on-water surface sequential assembly.

Controlling site-selectivity and reactivity in chemical reactions continues to be a key challenge in modern synthetic chemistry. Here, we demonstrate the discovery of site-selective chemical reactions on the water surface via a sequential assembly approach. A negatively charged surfactant monolayer on the water surface guides the electrostatically driven, epitaxial, and aligned assembly of reagent amino-substituted porphyrin molecules, resulting in a well-defined J-aggregated structure. This constrained geometry of the porphyrin molecules prompts the subsequent directional alignment of the perylenetetracarboxylic dianhydride reagent, enabling the selective formation of a one-sided imide bond between porphyrin and reagent. Surface-specific in-situ spectroscopies reveal the underlying mechanism of the dynamic interface that promotes multilayer growth of the site-selective imide product. The site-selective reaction on the water surface is further demonstrated by three reversible and irreversible chemical reactions, such as imide-, imine-, and 1, 3-diazole (imidazole)- bonds involving porphyrin molecules. This unique sequential assembly approach enables site-selective chemical reactions that can bring on-water surface synthesis to the forefront of modern organic chemistry.

Bond formation insights into the Diels-Alder reaction: A bond perception and self-interaction perspective.

The behavior of electrons during bond formation and breaking cannot commonly be accessed from experiments. Thus, bond perception is often based on chemical intuition or rule-based algorithms. Utilizing computational chemistry methods, we present intrinsic bond descriptors for the Diels-Alder reaction, allowing for an automatic bond perception. We show that these bond descriptors are available from localized orbitals and self-interaction correction calculations, e.g., from Fermi-orbital descriptors. The proposed descriptors allow a sparse, simple, and educational inspection of the Diels-Alder reaction from an electronic perspective. We demonstrate that bond descriptors deliver a simple visual representation of the concerted bond formation and bond breaking, which agrees with Lewis' theory of bonding.

Exploring the similarity of single-layer covalent organic frameworks using electronic structure calculations.

Two-dimensional Covalent Organic Frameworks (2D COFs) have attracted considerable interest because of their potential for a broad range of applications. Different combinations of the monomeric units can lead to potentially novel materials with varying physico-chemical properties. In this study, we investigate the electronic properties of various 2D COFs with square lattice topology based on a tight-binding density functional theory approach. We first classify the 2D COFs into different classes according to the degree of π-conjugation. Interestingly, this classification is recovered by using a similarity measure based on specific features of the electronic band-structure of the COFs. Further, we study the effect of aromaticity on the electronic structure of fully-conjugated COFs. Our results show that the conjugation and aromaticity are keys in the electronic band-structure of COFs.

Control of Crystallinity of Vinylene-Linked Two-Dimensional Conjugated Polymers by Rational Monomer Design.

The interest in two-dimensional conjugated polymers (2D CPs) has increased significantly in recent years. In particular, vinylene-linked 2D CPs with fully in-plane sp2 -carbon-conjugated structures, high thermal and chemical stability, have become the focus of attention. Although the Horner-Wadsworth-Emmons (HWE) reaction has been recently demonstrated in synthesizing vinylene-linked 2D CPs, it remains largely unexplored due to the challenge in synthesis. In this work, we reveal the control of crystallinity of 2D CPs during the solvothermal synthesis of 2D-poly(phenylene-quinoxaline-vinylene)s (2D-PPQVs) and 2D-poly(phenylene-vinylene)s through the HWE polycondensation. The employment of fluorinated phosphonates and rigid aldehyde building blocks is demonstrated as crucial factors in enhancing the crystallinity of the obtained 2D CPs. Density functional theory (DFT) calculations reveal the critical role of the fluorinated phosphonate in enhancing the reversibility of the (semi)reversible C-C single bond formation.

Effect of lubricants on the rotational transmission between solid-state gears.

Lubricants are widely used in macroscopic mechanical systems to reduce friction and wear. However, on the microscopic scale, it is not clear to what extent lubricants are beneficial. Therefore, in this study, we consider two diamond solid-state gears at the nanoscale immersed in different lubricant molecules and perform classical MD simulations to investigate the rotational transmission of motion. We find that lubricants can help to synchronize the rotational transmission between gears regardless of the molecular species and the center-of-mass distance. Moreover, the influence of the angular velocity of the driving gear is investigated and shown to be related to the bond formation process between gears.

Multiscale Modeling Strategy of 2D Covalent Organic Frameworks Confined at an Air-Water Interface.

Two-dimensional covalent organic frameworks (2D COFs) have attracted attention as versatile active materials in many applications. Recent advances have demonstrated the synthesis of monolayer 2D COF via an air-water interface. However, the interfacial 2D polymerization mechanism has been elusive. In this work, we have used a multiscale modeling strategy to study dimethylmethylene-bridged triphenylamine building blocks confined at the air-water interface to form a 2D COF via Schiff-base reaction. A synergy between the computational investigations and experiments allowed the synthesis of a 2D-COF with one of the linkers considered. Our simulations complement the experimental characterization and show the preference of the building blocks to be at the interface with a favorable orientation for the polymerization. The air-water interface is shown to be a key factor to stabilize a flat conformation when a dimer molecule is considered. The structural and electronic properties of the monolayer COFs based on the two monomers are calculated and show a semiconducting nature with direct bandgaps. Our strategy provides a first step toward the in silico polymerization of 2D COFs at air-water interfaces capturing the initial steps of the synthesis up to the prediction of electronic properties of the 2D material.

Olfactory Perception in Relation to the Physicochemical Odor Space.

A growing body of research aims at solving what is often referred to as the stimulus-percept problem in olfactory perception. Although computational efforts have made it possible to predict perceptual impressions from the physicochemical space of odors, studies with large psychophysical datasets from non-experts remain scarce. Following previous approaches, we developed a physicochemical odor space using 4094 molecular descriptors of 1389 odor molecules. For 20 of these odors, we examined associations with perceived pleasantness, intensity, odor quality and detection threshold, obtained from a dataset of 2000 naïve participants. Our results show significant differences in perceptual ratings, and we were able to replicate previous findings on the association between perceptual ratings and the first dimensions of the physicochemical odor space. However, the present analyses also revealed striking interindividual variations in perceived pleasantness and intensity. Additionally, interactions between pleasantness, intensity, and olfactory and trigeminal qualitative dimensions were found. To conclude, our results support previous findings on the relation between structure and perception on the group level in our sample of non-expert raters. In the challenging task to relate olfactory stimulus and percept, the physicochemical odor space can serve as a reliable and helpful tool to structure the high-dimensional space of olfactory stimuli. Nevertheless, human olfactory perception in the individual is not an analytic process of molecule detection alone, but is part of a holistic integration of multisensory inputs, context and experience.

Predicting the bulk modulus of single-layer covalent organic frameworks with square-lattice topology from molecular building-block properties.

Two-dimensional Covalent Organic Frameworks (2D COFs) have attracted a lot of interest because of their potential for a broad range of applications. Different combinations of their molecular building blocks can lead to new materials with different physical and chemical properties. In this study, the elasticity of different single-layer tetrabenzoporphyrin (H2-TBPor) and phthalocyanine (H2-Pc) based 2D COFs is numerically investigated using a density-functional based tight-binding approach. Specifically, we calculate the 2D bulk modulus and the equivalent spring constants of the respective molecular building-blocks. Using a spring network model we are able to predict the 2D bulk modulus based on the properties of the isolated molecules. This provides a path to optimize elastic properties of 2D COFs.

Stabilization of aqueous graphene dispersions utilizing a biocompatible dispersant: a molecular dynamics study.

Flavin mononucleotide sodium (FMNS) was recently reported as a highly efficient dispersant for the exfoliation of defect-free, few-layer, stabilized aqueous graphene dispersions. Most importantly, FMNS is innocuous and eco-friendly and can facilitate biomedical applications of graphene. Complementing those experimental studies, the influence of FMNS molecules on the aggregation behavior of graphene flakes in solution is investigated via all-atom molecular dynamics simulations. The stabilizing role of FMNS is demonstrated by the potential of mean force calculations for pairs of graphene flakes covered by FMNS molecules. These results indicate that the optimal amount ratio between FMNS molecules and carbon atoms in monolayer graphene is about 0.026 leading to a surface coverage of 0.34 FMNS molecules per nm2 on the graphene flakes. Overall the simulations support the high efficiency of FMNS as a surfactant compared to other surfactants.

Influence of Mesityl and Thiophene Peripheral Substituents on Surface Attachment, Redox Chemistry, and ORR Activity of Molecular Iron Porphyrin Catalysts on Electrodes.

Two iron porphyrin complexes with either mesityl (FeTMP) or thiophene (FeT3ThP) peripheral substituents were attached to basal pyrolytic graphite and Ag electrodes via different immobilization methods. By combining cyclic voltammetry and in-operando surface-enhanced Raman spectroscopy along with MD simulations and DFT calculations, their respective surface attachment, redox chemistry and activity toward electrocatalytic oxygen reduction was investigated. For both porphyrin complexes, it could be shown that catalytic activity is restricted to the first (few) molecular layer(s), although electrodes covered with thiophene-substituted complexes showed a better capability to consume the oxygen at a given overpotential even in thicker films. The spectroscopic data and simulations suggest that both porphyrin complexes attach to a Ag electrode surface in a way that maximum planarity and minimum distance between the catalytic iron site and the electrode is achieved. However, due to the distinctive design of the FeT3ThP complex, the thiophene rings are capable of occupying a conformation, via rotation around the bonding axis to the porphyrin, in which all four sulfur atoms can coordinate to the Ag surface. This effect creates a dense and planar surface coverage of the porphyrin on the electrode facilitating a fast (multi) electron transfer via several covalent Ag-S bonds. In contrast, bulky mesityl groups as peripheral substituents, which have been initially introduced to prevent aggregation and improve catalytic behavior in solution, exert a negative effect on the overall electrocatalytic performance in the immobilized state as a less dense coverage and less stable interactions with the surface are formed. Our results underline the importance of rationally designed heterogenized molecular catalysts to achieve optimal turnover, which not only strictly applies to the here discussed oxygen reduction reaction but eventually holds also true for other energy conversion reactions such as carbon dioxide reduction.

Quantum Phonon Transport in Nanomaterials: Combining Atomistic with Non-Equilibrium Green's Function Techniques.

A crucial goal for increasing thermal energy harvesting will be to progress towards atomistic design strategies for smart nanodevices and nanomaterials. This requires the combination of computationally efficient atomistic methodologies with quantum transport based approaches. Here, we review our recent work on this problem, by presenting selected applications of the PHONON tool to the description of phonon transport in nanostructured materials. The PHONON tool is a module developed as part of the Density-Functional Tight-Binding (DFTB) software platform. We discuss the anisotropic phonon band structure of selected puckered two-dimensional materials, helical and horizontal doping effects in the phonon thermal conductivity of boron nitride-carbon heteronanotubes, phonon filtering in molecular junctions, and a novel computational methodology to investigate time-dependent phonon transport at the atomistic level. These examples illustrate the versatility of our implementation of phonon transport in combination with density functional-based methods to address specific nanoscale functionalities, thus potentially allowing for designing novel thermal devices.

Corrigendum:(2013 Nanotechnology {\bf 24} 395702)]{Corrigendum: Frequency tuning, nonlinearities and mode coupling in circular mechanical graphene resonators (2013 Nanotechnology {\bf 24} 395702).

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Multi-scale approach for strain-engineering of phosphorene.

A multi-scale approach for the theoretical description of deformed phosphorene is presented. This approach combines a valence-force model to relate macroscopic strain to microscopic displacements of atoms and a tight-binding model with distance-dependent hopping parameters to obtain electronic properties. The resulting self-consistent electromechanical model is suitable for large-scale modeling of phosphorene devices. We demonstrate this for the case of inhomogeneously deformed phosphorene drum, which may be used as an exciton funnel.

Valence-force model and nanomechanics of single-layer phosphorene.

In order to understand the relation of strain and material properties, both a microscopic model connecting a given strain to the displacement of atoms, and a macroscopic model relating applied stress to induced strain, are required. Starting from a valence-force model for black phosphorous [Kaneta et al., Solid State Communications, 1982, 44, 613] we use recent experimental and computational results to obtain an improved set of valence-force parameters for phosphorene. From the model we calculate the phonon dispersion and the elastic properties of single-layer phosphorene. Finally, we use these results to derive a complete continuum model, including the bending rigidities, valid for long-wavelength deformations of phosphorene. This continuum model is then used to study the properties of pressurized suspended phosphorene sheets.

Comment on 'Parametrization of Stillinger-Weber potential based on a valence force field model: application to single-layer MoS2 and black phosphorus'.

We compare the simplified valence-force model for single-layer black phosphorus with the original model and recent ab initio results. Using an analytic approach and numerical calculations we find that the simplified model yields Young's moduli that are smaller compared to the original model and are almost a factor of two smaller than ab initio results. Moreover, the Poisson ratios are an order of magnitude smaller than values found in the literature.

Strain-tuning of vacancy-induced magnetism in graphene nanoribbons.

Vacancies in graphene lead to the appearance of localized electronic states with non-vanishing spin moments. Using a mean-field Hubbard model and an effective double-quantum dot description we investigate the influence of strain on localization and magnetic properties of the vacancy-induced states in semiconducting armchair nanoribbons. We find that the exchange splitting of a single vacancy and the singlet-triplet splitting for two vacancies can be widely tuned by applying uniaxial strain, which is crucial for spintronic applications.