Neighboring Atoms Research Articles

A parametric approach for molecular encodings using multilevel atomic neighborhoods applied to peptide classification.

Exploring new ways to represent and discover organic molecules is critical to the development of new therapies. Fingerprinting algorithms are used to encode or machine-read organic molecules. Molecular encodings facilitate the computation of distance and similarity measurements to support tasks such as similarity search or virtual screening. Motivated by the ubiquity of carbon and the emerging structured patterns, we propose a parametric approach for molecular encodings using carbon-based multilevel atomic neighborhoods. It implements a walk along the carbon chain of a molecule to compute different representations of the neighborhoods in the form of a binary or numerical array that can later be exported into an image. Applied to the task of binary peptide classification, the evaluation was performed by using forty-nine encodings of twenty-nine data sets from various biomedical fields, resulting in well over 1421 machine learning models. By design, the parametric approach is domain- and task-agnostic and scopes all organic molecules including unnatural and exotic amino acids as well as cyclic peptides. Applied to peptide classification, our results point to a number of promising applications and extensions. The parametric approach was developed as a Python package (cmangoes), the source code and documentation of which can be found at https://github.com/ghattab/cmangoes and https://doi.org/10.5281/zenodo.7483771.

N-doped carbon–iron heterointerfaces for boosted electrocatalytic active and selective ammonia production

The electrochemical conversion of waste nitrate (NO3-) to valuable ammonia (NH3) is an economical and environmentally friendly technology for sustainable NH3 production. It is beneficial for environmental nitrogen pollution management and is also an appealing alternative to the current Haber-Bosch process for NH3 production. However, owing to the competing hydrogen evolution reaction, it is necessary to design highly efficient and stable electrocatalysts with high selectivity. Herein, we report a rational design of Fe nanoparticles wrapped in N-doped carbon (Fe@N10-C) as a high NH3 selective and efficient electrocatalyst using a metal-organic framework precursor. We constructed a catalyst with new active sites by doping with nitrogen, which activated neighboring carbon atoms and enhanced metal-to-carbon electron transfer, resulting in high catalytic activity. These doped N sites play a key role in the NO3- electroreduction. As a result, the Fe@N10-C nanoparticles with optimal doping of N demonstrated remarkable performance, with a record-high NO3- removal capacity of 125.8 ± 0.5 mg N gcat-1 h-1 and nearly 100 % (99.7 ± 0.1%) selectivity. The catalyst also delivers an impressive NH3 production rate of 2647.7 μg h-1 cm-2 and high faradaic efficiency of 91.8 ± 0.1%. This work provides a new route for N-doped carbon-iron catalysis application and paves the way for addressing energy and environmental issues.

GPU-accelerated artificial neural network potential for molecular dynamics simulation

Artificial neural network potential (ANNP), obtained by training a large database by the first-principles calculations, has become popular in molecular dynamics (MD) simulation since it can capture accurate physical and chemical properties. However, the complex procedure and heavy data dependence during implementation make the performance of CPU-only runs worse, which further limits its application. In this contribution, we report a flexible computation method for ANNP in LAMMPS, in which the simulation box is divided into several parts in accordance with the resource on the accelerator such as the size of global memory and the number of work items (cores). The number of dividing parts has little influence on the performance when the number of calculated atoms per loop is larger than the number of work items on the device. In this approach, the forces of neighbor atoms are updated using hierarchical memory without atomic operation. Typical dynamic and static tests are performed to validate the implementation. The results show that our approach is 12 or 13 times faster when using one graphics processing unit (GPU) compared with 8-MPI tasks CPU-only runs. Additionally, this implementation is supported for CUDA- and OpenCL-enabled GPU cards.

Same effect of biquadratic exchange interaction and Heisenberg linear interaction in a spin spiral.

Monolayer (ML) NiCl2 exhibits a strong biquadratic exchange interaction between the first neighboring magnetic atoms (B1), as demonstrated by the spin spiral model in J. Ni et al., Phys. Rev. Lett., 2021, 127, 247204. This interaction is crucial for stabilizing the ferromagnetic collinear order within the ML NiCl2. However, they neither point out the role of B1 nor discuss the dispersion relation from spin orbit coupling (SOC) in the spin spiral. As we have done in this work, these parameters might theoretically potentially be derived directly by fitting the calculated spin spiral dispersion relation. Here, we draw attention to the fact that B1 is equivalent to half of J3 in Heisenberg linear interactions and that the positive B1 partially counteracts the negative J3's impact on the spin spiral to make the ML NiCl2 ferromagnetic. The comparatively small J3 + 1/2B1 from the spin spiral led us to believe that J3 could be substituted by B1, yet it still exists and plays a crucial function in magnetic semiconductors or insulators. The dispersion relation, which we also obtain from SOC, displays weak antiferromagnetic behavior in the spin spiral.

Molecular modelling framework of metal-organic clusters for conserving surfaces: Langmuir sorption through the TD-DFT/ONIOM approach

ABSTRACT The Langmuir adsorption model of some organic inhibitors containing benzotriazole (BTA), 8- hydroxyquinoline (8-HQ), and 2-mercaptobenzothiazole (2-MBT) onto the Al-X (X=Mg, Ga, Si) alloy surface.The ONIOM method has been accomplished with a three-layered step of high level of DFT method using EPR-III, 6-31+G (d,p) and LANL2DZ basis sets. NMR spectroscopy has indeed concentrated on the Al shielding in the intra-atomic interaction with Mg, Ga and Si and meanwhile interatomic interaction with other atoms in BTA, 8-HQ, and 2-MBT compounds. Aluminum-silicon binary alloy with highest changes in the shielding tensors of NMR spectrum produced by intra-atomic interaction directs us to the most penetration in the neighbor atoms created by interatomic reaction. IR computations based on comparing the amounts has exhibited that 2-MBT with high stability based on its active zone of sulfur atoms and high molecular size shows high corrosive inhibition as 2-MBT →Al-Ga>Al-Mg ≈ Al-Si. Furthermore, BTA with nitrogen atom and 8-HQ with oxygen atom can coat the Al-X (X=Mg/Ga/Si) alloys surface through Langmuir adsorption as BTA →Al-Ga>Al-Mg ≈ Al-Si, and 8-HQ →Al-Ga>Al-Mg ≈ Al-Si, respectively. Moreover, it has been observed that the inhibition yield is ordered as: Al-Ga> Al-Mg ≈ Al-Si.

Electron Density Analysis of Metal–Metal Bonding in a Ni4 Cluster Featuring Ferromagnetic Exchange

We present a combined experimental and theoretical study of the nature of the proposed metal-metal bonding in the tetranuclear cluster Ni4(NPtBu3)4, which features four nickel(I) centers engaged in strong ferromagnetic coupling. High-resolution single-crystal synchrotron X-ray diffraction data collected at 25 K provide an accurate geometrical structure and a multipole model electron density description. Topological analysis of the electron density in the Ni4N4 core using the quantum theory of atoms in molecules clearly identifies the bonding as an eight-membered ring of type [Ni-N-]4 without direct Ni-Ni bonding, and this result is generally corroborated by an analysis of the energy density distribution. In contrast, the calculated bond delocalization index of ∼0.6 between neighboring Ni atoms is larger than what has been found for other bridged metal-metal bonds and implies direct Ni-Ni bonding. Similar support for the presence of direct Ni-Ni bonding is found in the interacting quantum atom approach, an energy decomposition scheme, which suggests the presence of stabilizing Ni-Ni bonding interactions with an exchange-correlation energy contribution approximately 50% of that of the Ni-N interactions. Altogether, while the direct interactions between neighboring Ni centers are too weak and sterically constrained to bear the signature of a topological bond critical point, other continuous measures clearly indicate significant Ni-Ni bonding. These metal-metal bonding interactions likely mediate direct ferromagnetic exchange, giving rise to the high-spin ground state of the molecule.

Investigating the Diversity of Coordination Environments around Pt Atoms

AbstractModulating the local coordination environment of catalysts is of overriding importance to control reactivity, but systematic investigation of catalytic active sites with different coordination environments remains elusive. Here, a new strategy is provided to investigate the coordination environment of the catalytic center. Pt atoms, a known catalytic center, were selected to examine the effect of the coordination environment on the electro‐catalytic hydrogen evolution reaction (HER), a well‐studied system. Rather than alter the catalytic metal center as reported in previous work, “surrounding atoms” were tuned to modify the coordination environment around the Pt active center. A clear trend between HER activity and coordination environments with different neighboring atoms, was observed in this work. Based on experimental results, DFT calculations analyzed all coordinated patterns with respect to electronic structures and geometric transformations, giving a full “map” of the relationship between the coordination environments around Pt atoms and their catalytic performances. Such coordination environment engineering could be widely used to screen new catalysts for other conversions, and also provide a novel method for investigating the fundamental chemistry of active sites in catalysis.

Computational Nanomaterials Design: Towards The Realization of Nanoparticle Use in Radiotherapy - Case Study 1: Adsorption States of I on Au(111) Surface

Abstract Radioactive iodine (e.g. I-125, I-131) have been used for decades in the medical community for cancer treatment and imaging. Using gold nanoparticles as a carrier for iodine opens possibilities of new treatments for cancer and also for tracking cancerous cells. To design an optimized version of gold nanoparticle for such purpose, we need to understand the bonding mechanism and gauge the strength of such bonding. To this end we performed theoretical calculations on the adsorption state of iodine on gold (111) surface. The results show good adsorption of iodine to gold, most stably on the hollow sites. The bonding mechanism is via the hybridization of the 5p orbital of the iodine with the 6s and 5d orbitals of the neighboring gold atoms. These results act as a first step to designing an optimized gold nanoparticle that can be used in future radiotherapy treatments

A theoretical analysis for the normal impact fracture in thin brittle plates based on the principle of minimum external work

This paper presents a theoretical methodology for predicting the fracture pattern of a thin brittle plate subjected to normal impact loads. The approach is based on the principle of minimum external work, which is obtained directly from the principle of least action. Global scaling laws of the number of radial cracks, the maximum radial crack speed, and the critical impact velocity when radial cracks appear are established. It is found that the fracture pattern is controlled by two dimensionless parameters: one is the ratio of the striking velocity to the longitudinal wave speed, and the other is the ratio of the surface energy to Young's modulus (bridging the material length to the macroscopic geometrical size). The physical meaning of this material length is further investigated by assuming that a body's internal energy should simultaneously consider the surface and the volumetric parts. On the one hand, this length represents the competition of the internal energy between the surface and the volumetric parts. On the other hand, this material length is consistent with the distance of neighbor atoms in equilibrium.

Structural stability and the low-lying singlet and triplet states of BN-n-acenes, n=1-7.

The chemical stability and the low-lying singlet and triplet excited states of BN-n-acenes (n=1-7) were studied using single reference and multireference methodologies. From the calculations, descriptors such as the singlet-triplet splitting, the natural orbital (NO) occupations and aromaticity indexes are used to provide structural and energetic analysis. The boron and nitrogen atoms form an isoelectronic pair of two carbon atoms, which was used for the complete substitution of these units in the acene series. The structural analysis confirms the effects originated from the insertion of a uniform pattern of electronegativity difference within the molecular systems. The covalent bonds tend to be strongly polarized which does not happen in the case of a carbon-only framework. This effect leads to a charge transfer between neighbor atoms resulting in a more strengthened structure, keeping the aromaticity roughly constant along the chain. The singlet-triplet splitting also agrees with this stability trend, maintaining a consistent gap value for all molecules. The BN-n-acenes molecules possess a ground state with monoconfigurational character indicating their electronic stability. The low-lying singlet excited states have charge transfer character, which proceeds from nitrogen to boron.

Atomic mechanisms of self-diffusion in amorphous silicon

Based on recent calculations of the self-diffusion (SD) coefficient in amorphous silicon (a-Si) by classical Molecular Dynamics simulation [Posselt et al., J. Appl. Phys. 131, 035102 (2022)], detailed investigations on atomic mechanisms are performed. For this purpose, two Stillinger–Weber-type potentials are used, one strongly overestimates the SD coefficient, while the other leads to values much closer to the experimental data. By taking into account the individual squared displacements (or diffusion lengths) of atoms, the diffusional and vibrational contributions to the total mean squared displacement can be determined separately. It is shown that the diffusional part is not directly correlated with the concentration of coordination defects. The time-dependent distribution of squared displacements of atoms indicates that in a-Si, a well-defined elemental diffusion length does not exist, in contrast to SD in the crystalline Si. The analysis of atoms with large squared displacements reveals that the mechanisms of SD in a-Si are characterized by complex rearrangements of bonds or exchanges of neighbors. These are mono- and bi-directional exchanges of neighbors and neighbor replacements. Exchanges or replacements may concern up to three neighbors and may occur in relatively short periods of some ps. Bi- or mono-directional exchange or replacement of one neighbor atom happens more frequently than processes including more neighbors. A comparison of results for the two interatomic potentials shows that an increased three-body parameter only slows down the migration but does not change the migration mechanisms fundamentally.

Dynamic lattice distortion in metallic nanocrystals

Advanced design of metallic nanocrystals (NCs) for plasmonic applications requires control of the dynamic lattice distortion. Here we apply atomistic simulations coupled with total scattering to study the lattice vibrations induced by the thermal motion of atoms in Pd NCs. Quantitative analysis of the dynamic-relative displacement of neighbor atoms details the correlation of the lattice vibrations fading with the increase of atom-pair distance. Negative correlations are revealed from displacements of far-neighbor atoms with pair direction normal to the crystal surface, which we explain as breathing vibration modes. We propose a phenomenological dynamical model to predict the influence of material structure and NCs shape on the dynamic lattice distortion. Lattice vibrations show a marked dependence on the atom-pair direction, which enhances with decreasing size and cubic shape of crystals. Our work demonstrates that, if proper distortion models are used, the thermal motion of atoms near the surface of metallic NCs can be observed from total scattering data. Further simulations and experiments will support the future extension to compositionally and architecturally complex nanoparticles of the anisotropic lattice distortion model (ALDi) that is here introduced.

Spin regulation for efficient electrocatalytic N2 reduction over diatomic Fe-Mo catalyst

Electrocatalytic nitrogen reduction reaction (eNRR) is a promising method for the sustainable production of ammonia as an alternative to the traditional energy-intensive Haber-Bosch process. In this work, an efficient strategy by atomic spin regulation to promote NRR through Fe-transition metal (TM) hybrid heteronuclear dual-atom catalysts has been studied. By means of DFT computations, the stability, activity, and selectivity of 30 kinds of Fe-based dual-atoms anchored on N-doped porous graphene are systematically investigated to evaluate their catalytic performance. Fe/MoNC is screened as an excellent NRR catalyst with the limiting potentials of 0.63 V, and also suppresses HER. In the Fe/MoNC, the neighboring Fe atom regulates the spin state of the Mo center in MoN4 from high-spin state (2.63 μB) to medium-spin state (0.74 μB), which can effectively relieve the strong overlapping between Mo 4d orbital with the NxHy intermediates, promote the desorption of reaction product, and eventually achieve a lower limiting potential. Interestingly, the archetype of the active center of nitrogenase is also a FeMo-cofactor, which is consistent with our screening results. The work may provide new insight into the mechanism of nitrogenase, and promote the rational design of efficient NRR catalysts by atomic spin regulation.

Atomically dispersed single ruthenium sites anchored on bismuth tungstate with synergistic geometric and electronic effects for epoxidation of trans-stilbene

The feasibility of elegantly tuned geometric structures and electronic environments of metal active sites in single atom catalysts (SACs) is crucial for developing highly robust and efficient catalytic materials. Here we report a straightforward and efficient approach to accessing single ruthenium (Ru) atoms over a Bi2WO6 assemblage, with each Ru atom coordinated with four neighboring oxygen atoms. This Ru catalyst, exhibits synergistic geometric and electronic effects, resulting in a significantly enhanced catalytic performance for epoxidation of trans-stilbene to give trans-stilbene oxide. The reaction takes place under mild conditions, with high conversion (>99 %) and selectivity (>99 %) within a mere 2 h and a high turnover frequency (TOF) of 558 h−1. The theoretical calculations demonstrate that the high catalytic activity originates from the strong electronic metal-support interaction and the charge state of ruthenium sites in Bi2WO6. This work opens an avenue to engineer SACs on Aurivillius (perovskite) phase materials at the atomic level and serves as a promising platform for further studies of many other organic transformations.

Revision and Extension of a Generally Applicable Group Additivity Method for the Calculation of the Refractivity and Polarizability of Organic Molecules at 298.15 K

In a continuation and extension of an earlier publication, the calculation of the refractivity and polarizability of organic molecules at standard conditions is presented, applying a commonly applicable computer algorithm based on an atom group additivity method, where the molecules are broken down into their constituting atoms, these again being further characterized by their immediate neighbor atoms. The calculation of their group contributions, carried out by means of a fast Gauss–Seidel fitting calculus, used the experimental data of 5988 molecules from literature. An immediate subsequent ten-fold cross-validation test confirmed the extraordinary accuracy of the prediction of the molar refractivity, indicated by a correlation coefficient R2 and a cross-validated analog Q2 of 0.9997, a standard deviation σ of 0.38, a cross-validated analog S of 0.41, and a mean absolute deviation of 0.76%. The high reliability of the predictions was exemplified with three classes of molecules: ionic liquids and silicon- and boron-containing compounds. The corresponding molecular polarizabilities were calculated indirectly from the refractivity using the inverse Lorentz–Lorenz relation. In addition, it could be shown that there is a close relationship between the “true” volume and the refractivity of a molecule, revealing an excellent correlation coefficient R2 of 0.9645 and a mean absolute deviation of 7.53%.

Selective Formation of Unsymmetric Multidentate Azine-Based Ligands in Nickel(II) Complexes.

A mixture of 2-pyridine carboxaldehyde, 4-formylimidazole (or 2-methyl-4-formylimidazole), and NiCl2·6H2O in a molar ratio of 2:2:1 was reacted with two equivalents of hydrazine monohydrate in methanol, followed by the addition of aqueous NH4PF6 solution, afforded a NiII complex with two unsymmetric azine-based ligands, [Ni(HLH)2](PF6)2 (1) or [Ni(HLMe)2](PF6)2 (2), in a high yield, where HLH denotes 2-pyridylmethylidenehydrazono-(4-imidazolyl)methane and HLMe is its 2-methyl-4-imidazolyl derivative. The spectroscopic measurements and elemental analysis confirmed the phase purity of the bulk products, and the single-crystal X-ray analysis revealed the molecular and crystal structures of the NiII complexes bearing an unsymmetric HLH or HLMe azines in a tridentate κ3 N, N’, N” coordination mode. The HLH complex with a methanol solvent, 1·MeOH, crystallizes in the orthorhombic non-centrosymmetric space group P212121 with Z = 4, affording conglomerate crystals, while the HLMe complex, 2·H2O·Et2O, crystallizes in the monoclinic and centrosymmetric space group P21/n with Z = 4. In the crystal of 2·H2O·Et2O, there is intermolecular hydrogen-bonding interaction between the imidazole N–H and the neighboring uncoordinated azine-N atom, forming a one-dimensional polymeric structure, but there is no obvious magnetic interaction among the intra- and interchain paramagnetic NiII ions.

Effect of Interstitial Oxygen in Stainless Steel 316L Formed Via Laser Powder Bed Fusion on Corrosion Properties

Laser powder bed fusion (PBF) has been used to create structures of many different alloys including stainless steels (SS). In contrast to SS prepared via conventional approaches, PBF-produced SS often contains a high concentration of oxygen. It is generally believed that the oxygen primarily exists as oxide inclusions with diameters ranging from tens of nanometers to several microns. Thermodynamic calculations also show that the solubility of the oxygen is extremely low in the liquid, face center cubic (FCC), or body center cubic phases that are relevant to the composition of the SS investigated in this study. Additionally, these calculations predict that majority of oxygen stays in the metastable MnSiO3 phase. In this study, we perform multi-scale, quantitative electron microscopic analysis on the as-printed SS 316L and find that a large amount of oxygen actually exists in the interstitial sites of the alloy lattice, suggesting that oxygen might have been trapped in the alloy substrate during the rapid cooling process of PBF. The observations from the atomic-scale-resolution characterization are supported by the first principles simulations through density functional theory calculations, which reveal that oxygen can stay energetically stable in the octahedral site of the FCC structure. Additionally, these interstitial oxygen atoms can form ionic bonds with the neighboring metal atoms, with a particularly high affinity towards Cr atoms. The presence of interstitial oxygen in the SS substrate appears to assist the surface passivation processes and lead to the exceptionally high pitting potential. The identification of a large amount of interstitial oxygen in the alloy may have a profound impact on the design of strong, tough, and corrosion resistant alloys.

Electrolyte Deprotonation Stimulates Phase Transition of Ni-Rich Cathodes in Na-Ion Batteries

Sodium-ion batteries (SIBs) are considered as a promising alternative to lithium-ion batteries (LIBs), Since they are composed of naturally abundant elements, cheaper and larger scale battery modules can be assembled. However, due to their similar electrochemical mechanisms, their practical utilization is hindered by high reactivity of conventional carbonate electrolytes with electrode materials leading to the capacity fading over repeated charging cycles. To overcome this obstacle, localized high concentration electrolytes (LHCEs) are used as an effective approach to maintain localized solvation structure of active electrolyte salts by using hydrofluoroether as diluents. Earlier studies are mainly focusing on the interactions between electrolytes with anode materials. Little was known about the electrochemical reactions of LHCEs on SIB cathode. In this work, we examined the reactivities of carbonate electrolytes and LHCEs on NaNiO2 surfaces. Ab initio molecular dynamics simulations showed that carbonate electrolytes involve more dehydrogenation reactions than LHCEs. The proton-transfer reactions between electrolyte molecules and cathode surface oxygens cause the formation of hydroxyl (-OH) groups, which leads to reduction of neighboring surface nickel atoms from Ni3+ to Ni2+. As cathode surface gets desodiated, more proton-transfer reactions were observed and Ni migrations from transition metal layer to Na layer were also identified. Consequently, it results in the oxygen loss of NaNiO2 which accelerates the layered-rock salt phase transition of bulk cathodes.

New properties of boron-oxygen dimer defect in boron-doped Czochralski silicon

Silicon doped with boron is the most widely used material in modern microelectronic devices based on p-Si. Therefore, it is important to thoroughly understand boron’s role in the processes of defect-impurity interaction in Si both on growing the material and during operation of devices. In this work, interactions of boron with oxygen in Si are investigated by studying boron absorption intracenter transitions, which are known to be highly sensitive to the local environment. In boron-doped Si, two lines with maxima at 228 and 261.3 cm−1 were detected. The linear dependence of lines intensity on boron concentration and the quadratic on oxygen content testifies that the defect responsible for the lines can be identified as BsO2i. The observed absorption lines correspond to the transitions from the ground to the excited states of boron, which are shifted toward lower frequencies relative to the main transitions due to a deformation perturbation from neighboring oxygen atoms. The activation energy of annealing and ionization energy of defect are determined. The properties of the registered ВsO2i defect differ from the known ВsO2 associated with the light-induced degradation of solar cells by local configuration. The data obtained testify that the ВsO2i defects with different properties can be formed in Si and must be taken into account when developing Si:B-based devices because they can play an important role in charge carrier transfer and affect the electrical and optical parameters of the material.

WSe2 Monolayer: A Stable Two-Dimensional Heterostructure Material from First-Principles of Simulation Calculations

P-N junctions or heterostructures are commonly used in the fabrication of self-driven photodetectors because they serve critical roles in influencing the electrical characteristics of two-dimensional (2D) materials. For stable 2D heterostructures, planar WSe2 monolayers have attracted a lot of interest. Using first-principles energetic and dynamic calculations, we find that the transition from the indirect band gap of WSe2 bulk phase to the direct band gap of a two-dimensional plane is caused by the formation of p-n hetero junctions. Furthermore, it affects the carrier concentration transport mode and results in a significant orbital spin coupling. There is no virtual frequency in the phonon dispersion curve across the Brillouin zone at zero pressure. The interaction of the nearest neighbour atoms causes the frequency of the two acoustic modes of the G-point to be zero, as well as the frequency of the two optical films to merge. The theoretical analysis can provide support for the transport of two-dimensional planar carriers in electronics and photonics.