Ground-state Structure Research Articles

Infrared and Raman vibrational modelling of β-C2S and C3S compounds

Density Functional Theory was applied to obtain a refined IR and Raman theoretical vibrational spectra of the major silicate phases of Portland cement, i.e. dicalcium silicate (β-C2S) and tricalcium silicate (C3S). We investigate the crystal structure and vibrational frequency values in the electronic ground state using a plane wave density functional method with new norm-conserving pseudopotentials. The calculated results show that the optimized geometry can reproduce the crystal structure well, and the theoretical vibrational frequency values show good agreement with the experimental values and allow us to describe some uncertainties in the experimental assignments previously described. The assignment performed for 100–1200 cm−1 region shows that the vibrations of C2S and C3S are presented in the IR spectra, while the vibrations with a minor contribution from the silica groups are observed in the Raman spectra. Satellite bands from C3S are observed in the experimental spectra but there not in the calculated one.

Concentration effects on the microstructures and electronic features of Nd[formula omitted]Y[formula omitted]AlO3 crystals: A first-principles study

Nd3＋ doped YAP has attracted considerable attention because it shows promise for use in solid-state lasers and medical care. However, the microstructures underlying the electronic features with various dopant concentrations are still unclear. In this study, we carried out first-principles calculations on the microstructures of NdxY1−xAlO3 crystals (x = 0.25, 0.125, 0.0625 and 0.03125). Based on density functional theory and the particle swarm optimization algorithm, the four ground state structures for each concentration of NdxY1−xAlO3 were shown to adopt monoclinic phases. The peak values of the diffraction angles showed distinct shifts, and the subshell orbitals that most affected the lower bands varied as the dopant concentration changed. The validities of these structures were confirmed by the good agreement between the calculated X-ray diffraction (XRD) patterns and the experimental patterns. Moreover, the electronic band structures of NdxY1−xAlO3 were meticulously analysed. The conduction bands of the four structures all broke through the Fermi levels, suggesting that the doped systems were all conductors. By calculating the crystal structure electron localization function (ELF), we determined that both the Nd-O and Y-O bonds in NdxY1−xAlO3 are ionic. These results fill the small gaps in microstructure research and reveal the commonalities and individualities of the physical features formed in NdxY1−xAlO3 with different dopant concentrations, which will provide inspiration for designing luminescent materials in the future.

Reaction mechanism between Gen (n = 2–5) clusters and single water molecule based on density functional theory

AbstractThe ground state structures of Gen (n = 2–5) clusters and their adsorption energy values with single water molecule were calculated using density functional theory. We also investigated the reaction pathways between Gen (n = 2–5) clusters and single water molecule. Based on molecular orbital and natural population analysis (NPA) figures, it was found that the O atom in H2O binds to the Gen (n = 2–5) clusters to form GenO (n = 2–5) and releases hydrogen. Notably, the Ge2 cluster exhibited the most efficient interaction with single water molecule based on the comparison of the energy values during the reaction of hydrogen generation. Furthermore, NPA and density of states analyses indicate that the Ge atoms in the products did not reach their highest oxidation state, suggesting that GenO (n = 2–5) may continue to react with more water molecules to generate hydrogen. Our results provide a deeper understanding of the chemical reaction properties.

Regulating the photophysical properties of ESIPT-based fluorescent probes by functional group substitution: a DFT/TDDFT study.

In recent years, fluorescent probe technology has received more and more attention. However, the photophysical and photochemical properties of probe molecules still need to be further explored. This paper presents the excited state intramolecular proton transfer (ESIPT) processes and photophysical properties of the probe molecule 4-bromo-2-((E)-((Z)-((5-bromo-1H-indol-2-yl) methylene) hydrazono) methyl) phenol (BHPL) and its four derivatives (BHPL2, BHPL3, BHPL4, and BHPL5). Infrared spectra and geometric structure analyses revealed that introducing the -NH2 group on the benzene ring with the hydroxyl group will enhance the intramolecular hydrogen bond, which benefits the ESIPT process. Combining their absorption and fluorescence spectra, it can be concluded that BHPL2 and BHPL4 are both excellent probe candidates due to their large Stokes shift. The hole and electron and root mean square displacement analyses manifest that the fluorescence quenching of BHPL4 may be due to the intramolecular charge transfer process. Potential energy curves of BHPL and its four derivatives noted that ESIPT process of the BHPL2 is the most favorable to occur. The frontier molecular orbital and NBO analyses indicated that besides introducing electron-donating groups to reduce the energy gap and enhance fluorescence emission, introducing double electron-withdrawing groups can also achieve this effect, explaining why the energy barrier of ESIPT process for BHPL2 is lower than BHPL5. This work would provide the theoretical basis for designing novel fluorescence probes with more prominent properties. The ground (S0) and excited (S1) state structures of all compounds were optimized by density functional theory (DFT) and time-dependent (TDDFT) method, with B3LYP/6-311+G(d,p) level, respectively. The infrared spectra and potential energy curves were simulated at the same theoretical level. The reduced density gradient scatter plots and interaction region indicator isosurfaces were drawn using Multiwfn and VMD programs. The absorption and fluorescence spectra were simulated by the TDDFT/B3PW91/6-311+G(d,p) method. All the calculations in this work are carried out in Gaussian 16 program package.

Room-temperature synthesis of lead-free copper(I)-antimony(III)-based double perovskite nanocrystals

In the field of perovskite solar cells, explorations of new lead-free all-inorganic perovskite materials are of great interest to address the instability and toxicity issues of lead-based hybrid perovskites. Recently, copper-antimony-based double perovskite materials have been reported with ideal band gaps, which possess great potential as absorbers for photovoltaic applications. Here, we synthesize Cs2CuSbCl6 double perovskite nanocrystals (DPNCs) at ambient conditions by a facile and fast synthesis method, namely, a modified ligand-assisted reprecipitation method. We choose methanol as a solvent for precursor salts as it is less toxic and easily removed in contrast to widely used dimethylformamide. Our computational structure search shows that the Cs2CuSbCl6 structure containing alternating [CuCl6]5− and [SbCl6]3− octahedral units is a metastable phase that is 30 meV/atom higher in energy compared to the ground state structure with [CuCl3]2− and [SbCl6]3− polyhedra. However, this metastable Cs2CuSbCl6 double perovskite structure can be stabilized through solution-based nanocrystal synthesis. Using an anion-exchange method, Cs2CuSbBr6 DPNCs are obtained for the first time, featuring a narrow bandgap of 0.9 eV. Finally, taking advantage of the solution processability of DPNCs, smooth and dense Cs2CuSbCl6 and Cs2CuSbBr6 DPNC films are successfully fabricated.

Ab Initio Prediction of Ultra‐Wide Band Gap BxAl1−xN Materials

AbstractUltra‐wide bandgap (UWBG) materials are poised to play an important role in the future of power electronics. Devices made from UWBG materials are expected to operate at higher voltages, frequencies, and temperatures than current silicon and silicon‐carbide‐based devices and can even lead to significant miniaturization of such devices. In the UWBG field, aluminum nitride and boron nitride have attracted great interest; however, the BxAl1−xN alloys are much less studied. In this work, using first‐principles simulations combining density‐functional theory and the cluster expansion method, the crystal structure of BxAl1−xN alloys is predicted. Seventeen ground state structures of BxAl1−xN with formation energies between 0.11 and 0.25 eV atom‐1 are found. All of these structures are found to be dynamically stable. The BxAl1−xN structures are found to have predominantly a tetrahedral bonding environment; however, some structures exhibit sp2 bonds similar to hexagonal BN. This work expands knowledge of the structures, energies, and bonding in BxAl1−xN which aids their synthesis, the innovation of lateral or vertical devices, and discovery of compatible dielectric and Ohmic contact materials.

First-Principles Study of the Magnetic and Electronic Structure of NdB4

Due to their magnetic and physical properties, rare earth magnetic borides have been applied to a variety of critical technologies. In particular, rare earth tetraborides are more abundant as frustrated antiferromagnets. Here, the atomic structures, magnetic structures, and electronic structures of NdB4 have been studied by first-principle calculations. The ground state magnetic structure of NdB4 is determined. Moreover, the small energy difference between different magnetic structures means that there may be more than one magnetic structure that coexist. One can glean from the electronic structure of the magnetic ground state that the d orbital of Nd is strongly hybridized with the p orbital of B, and the f electron of Nd is highly localized. The computational results reveal the complexity of the magnetic structure and provide a theoretical basis for studying the magnetic ground state of NdB4.

Thermodynamics of phase stability and disorder in Inter-Lanthanide ternary ABO3 oxides from first principles

Inter-lanthanide ternary oxides (IL-ABO3) find application in various technological fields due to their diverse properties and flexible chemistries that are readily synthesizable in multiple crystal structures. Here, we investigate the chemistry-dependent thermodynamic formability and the tendency to disorder for IL-ABO3 (A, B = La–Lu) compounds having different structures using density functional theory. We reproduce the previously observed relationship between the IL-ABO3 crystal structure and difference in the A and B ionic radii. We investigate the formation of metastable phases, finding a region of IL-ABO3 chemistries with rich metastability in a small energy interval. We analyze the influence of disordering on the stability of the ground state structures, correlating the propensity for disorder with the energy difference between different cation orderings. Our results provide fundamental insights into the phase stability of IL-ABO3, the energetics of their metastable structures, and their tendency to disorder, paving the way towards their broader technological applicability.

Structural evolution, electronic and magnetic properties investigation of V3Sin− (n = 14–18) clusters based on photoelectron spectroscopy and density functional theory calculations

Silicon clusters doped with a transition metal (TM) atom have been intensively studied due to their novel properties and superior stability for possible usage as building blocks of future nanoelectronics. Besides the selection of the doped element, introducing the number of dopant atoms as another dimension adds versatility to tuning the cluster properties. However, there are few studies of silicon clusters doped with multiple TM atoms. Here, we present a study of V3Sin− (n = 14–18) by combining high-resolution photoelectron spectroscopy (PES) measurements with a search of their global minimum energy structures based on a homemade genetic algorithm coupled with density functional theory (DFT) for energy calculations. The simulated photoelectron spectra of the putative global minimum structures are in fair agreement with the experimental ones, which gives evidence for their authenticity as the ground-state structures. In these clusters the three V atoms always bond with each other and form an acute triangle, which can be seen as a nanoscale analogue of phase segregation in the bulk. For the size range n = 14–17, each of the ground-state structures has a silicon basket-like structure with the vanadium triangle inside, while V3Si18− has a baseball-mitt-like structure almost completely encapsulating the V3 triangle. The average binding energy of TMSin− (TM = V1, V2, V3) indicates that the more V atoms are doped the more stable the clusters are. Among these clusters, only V3Si14− have a total magnetic moment of 2 μB, making it a potential structural unit for magnetic storage devices. Mulliken population analysis and the electron spin density show that V atoms at different positions have different contributions to the total magnetic moments, and d electrons in V atoms contribute the most.

Targeting high symmetry in structure predictions by biasing the potential energy surface

Ground-state structures found in nature are, in many cases, of high symmetry. But structure prediction methods typically render only a small fraction of high-symmetry structures. Especially for large crystalline unit cells, there are many low-energy defect structures. For this reason, methods have been developed where either preferentially high-symmetry structures are used as input or where the whole structural search is done within a certain symmetry group. In both cases, it is necessary to specify the correct symmetry group beforehand. However, it can in general not be predicted which symmetry group is the correct one leading to the ground state. For this reason, we introduce a potential energy biasing scheme that favors symmetry and where it is not necessary to specify any symmetry group beforehand. On this biased potential energy surface, high-symmetry structures will be found much faster than on an unbiased surface and independently of the symmetry group to which they belong. For our two test cases, i.e., a ${C}_{60}$ fullerene and bulk silicon carbide, we get speedups of 25 and 63. In our data, we also find a clear correlation between the similarity of the atomic environments and the energy. In low-energy structures, all the atoms of a species tend to have similar environments.

Deciphering the Impact of Helium Tagging on Flexible Molecules: Probing Microsolvation Effects of Protonated Acetylene by Quantum Configurational Entropy

Helium, the lightest and most weakly interacting noble gas, is well-known for its unsurpassed chemical inertness. In many applications of helium in experimental techniques, such as tagging, messenger, or nanodroplet isolation action spectroscopy of molecules or complexes, it is assumed that the interaction of helium with the respective species, and thus the resulting interaction-induced perturbation, is small enough not to affect their structure and dynamics. Here, we probe the impact of one up to many attached helium atoms on protonated acetylene─an important nonclassical carbocation subject to three-center two-electron bonding in its ground state structure─using highly accurate interaction potentials in conjunction with entropy-based higher-order nonlinear correlation analysis. In particular, using neural network potentials at CCSD(T) accuracy, we disclose the specific structural perturbations due to the tagging of C2H3+ with up to 20 He atoms at a temperature of 1 K. Analysis reveals that microsolvation by helium influences the structure of C2H3+ noticeably, while our investigation of the quantum configurational information entropy additionally shows that correlations between individual orientational degrees of freedom are affected as a function of cluster size. In particular, it is found that the most probable bridge-like structure of the ro-vibrational quantum ground state of C2H3+, which is nonplanar and trans-bent in contrast to the perfectly planar equilibrium structure, becomes increasingly more localized upon adding helium atoms. The remarkably nonlinear behavior of the angular correlations as a function of cluster size is traced back to the buildup of the quantum microsolvation shell that enhances anisotropy up to NHe = 6 while more and more isotropic solvation takes over beyond six. Our approach is general and thus sets the stage to investigate the salient effects on the structure of flexible molecules due to tagging beyond the specific case.

Profiling the off-center atomic displacements in CuCl at finite temperatures with a deep-learning potential

Cuprous halides ($\mathrm{Cu}X$, $X=\mathrm{Cl}$, Br, or I) have been extensively investigated in the literature, but there still exist debates on whether the ground-state structures of $\mathrm{Cu}X$ are zinc blende. By performing molecular dynamics simulations at finite temperatures with a newly developed accurate deep-learning potential for CuCl, we find that, in the absence of accurate exchange interactions, there exist collective off-center displacements of Cu, leading to the formation of large complex Cu cluster structures. However, these cluster structures are unstable once exchange interactions are properly included. Nevertheless, due to strong anharmonicity, thermal fluctuations could also lead to sizable off-center Cu displacements, resulting in instantaneous small Cu clusters. Still, these cluster configurations are not stable or metastable in the ground state. We thus unambiguously demonstrate that, although anharmonic off-center displacements of Cu are present in CuCl at finite temperatures, zinc blende is still the thermodynamically most favorable phase. These insights are critical to the understanding of liquidlike anharmonic behavior of Cu atoms in various Cu-containing compounds, which impacts a number of important properties such as thermal conductivity, ferroelectricity, and superconductivity.

Ground states and magnonics in orthogonally coupled symmetric all-antiferromagnetic junctions

In this paper, the rich ground-state structure of orthogonally coupled symmetric all-antiferromagnetic junctions with easy-plane anisotropy is reported. A spin reorientation process rather than the traditional spin flop (SF) occurs, resulting in a phase in which N\'eel vectors preserve the mirror-reflection symmetry (termed MRS phase). The phase transitions in the ground state between SF and MRS phases can be either first or second order. After disturbed by external stimuli, magnons with different parities emerge. For in-plane dc fields, no couplings between magnons occur. When dc fields become oblique, coherent couplings between magnons with opposite parity emerge, leading to anticrossings in resonance frequencies. However, self-hybridization among magnons with the same parity never happens. More interestingly, spin waves based on MRS phases are linearly polarized and their polarization directions can be fine controlled.

Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network

Cryptic pockets expand the scope of drug discovery by enabling targeting of proteins currently considered undruggable because they lack pockets in their ground state structures. However, identifying cryptic pockets is labor-intensive and slow. The ability to accurately and rapidly predict if and where cryptic pockets are likely to form from a structure would greatly accelerate the search for druggable pockets. Here, we present PocketMiner, a graph neural network trained to predict where pockets are likely to open in molecular dynamics simulations. Applying PocketMiner to single structures from a newly curated dataset of 39 experimentally confirmed cryptic pockets demonstrates that it accurately identifies cryptic pockets (ROC-AUC: 0.87) >1,000-fold faster than existing methods. We apply PocketMiner across the human proteome and show that predicted pockets open in simulations, suggesting that over half of proteins thought to lack pockets based on available structures likely contain cryptic pockets, vastly expanding the potentially druggable proteome.

Algebraic Graph-Based Machine Learning Model for Li-Cluster Prediction.

In cluster research, determining the ground-state structure of medium-sized clusters is hindered by a large number of local minimum on potential energy surfaces. The global optimization heuristic algorithm is time-consuming due to the use of DFT to determine the relative size of the cluster energy. Although machine learning (ML) is proved to be a promising way to reduce the DFT computational costs, a suitable method to represent clusters as input vectors is one of the bottlenecks in the application of ML to cluster research. In this work, we proposed a multiscale weighted spectral subgraph (MWSS) as an effective low-dimension representation of clusters and build an MWSS-based ML model to discover the structure-energy relationships in lithium clusters. We combine this model with the particle swarm optimization algorithm and DFT calculations to search for globally stable structures of clusters. We have successfully predicted the ground-state structure of Li20.

Investigating the structural and electronic properties of anionic calcium-doped magnesium clusters

In recent years, the structure and properties of alkaline earth metal-doped Mg clusters have attracted much attention. Here, we investigated the structural properties, stability analysis, chemical bonding properties and charge transfer properties of Ca2Mgnˉ (n=1-15) nanoclusters by using the efficient CALYPSO structure search software and the DFT full domain search method based on B3PW91 level calculation. It is found that most of their ground state structures can inherit pure Mgn+2ˉ (n=1-15) clusters with high symmetry. We further compare the experimental and theoretical PES spectral data using pure Mgn+2ˉ (n=1-15) and find a high agreement, which also indicating the validity of my calculated all-domain most stable structure. We found the outstanding stability of the pentagonal Ca2Mg7ˉ by stability analysis. Charge transfer occurred in all Ca2Mgnˉ clusters, and this transfer was from Ca to Mg. The chemical bonding properties and molecular orbital revealed that the contribution of Mg-s and Mg-p to the molecular orbitals led to the formation of strong Mg-Mg bonds in the Ca2Mg7ˉ cluster, the s-p hybridization between Ca and Mg atoms and between Mg and Mg atoms also led to more powerful Mg-Mg bonds and Ca-Mg bonds, which is strong evidence for the stability of the Ca2Mg7ˉ clusters.

Identifying the ground state structures of point defects in solids

Point defects are a universal feature of crystals. Their identification is addressed by combining experimental measurements with theoretical models. The standard modelling approach is, however, prone to missing the ground state atomic configurations associated with energy-lowering reconstructions from the idealised crystallographic environment. Missed ground states compromise the accuracy of calculated properties. To address this issue, we report an approach to navigate the defect configurational landscape using targeted bond distortions and rattling. Application of our workflow to eight materials (CdTe, GaAs, Sb2S3, Sb2Se3, CeO2, In2O3, ZnO, anatase-TiO2) reveals symmetry breaking in each host crystal that is not found via conventional local minimisation techniques. The point defect distortions are classified by the associated physico-chemical factors. We demonstrate the impact of these defect distortions on derived properties, including formation energies, concentrations and charge transition levels. Our work presents a step forward for quantitative modelling of imperfect solids.

Structural phase stability and thermodynamical properties of transition metal complex hydrides Na2MgTMH7 (TM=Sc−Cu) for hydrogen storage applications

In order to predict ground state structure as well as thermodynamical properties of transition metal-based complex hydrides (TMCHs) and identify potential hydrogen storage materials for energy storage applications, we have performed first-principles density functional spin polarized total energy calculations for Na2MgTMH7 where TM ​= ​Sc, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu. To investigate the thermodynamical properties of transition metal-based complex hydrides (TMCHs) and to find potential hydrogen storage materials for energy storage applications. Our spin-polarized calculations show that all these materials are having a finite magnetic moment at the transition metal site with ferromagnetic or anti−ferromagnetic ordering as ground state configuration except the cases where TM ​= ​Sc, Co, Ni, and Cu. Our calculated enthalpy of formation and hydrogen site energy of TMCHs suggest that these systems are stable and the hydrogen is expected to release at a relatively low temperature compared to that of pure binary hydrides. We have performed the chemical bonding analyses between the constituents of TMCHs through density of states, charge density, electron localization function, Born effective charge, Bader effective charge, Mulliken charge, and COHP and these analyses suggest that there is an ionic bonding between hydrogen with Na, Mg, and transition metal with noticeable covalent bonding between hydrogen and Mg/TM.

Do-It-Yourself 5-Color 3D Printing of Molecular Orbitals and Electron Density Surfaces

This report outlines an approach for preparing 5-color 3D printed plastic models of molecular orbitals and electron density surfaces using a hobby-grade 3D printer. Instructions are provided for preparing 3D orbital and electron density surface (EDS) models using solid or mesh representations in ground state and transition state structures. We show that the information content of 3D orbital and surface models can be enhanced with text annotation, bisection, strut and dashed bond placement, and composite orbital-EDS model constructions. Example prints illustrate orbital concepts in organic and inorganic chemistry, such as the ethyl cation (σ–p hyperconjugation), methane (hybridization and C–H bonding), ethane (σ–σ* hyperconjugation in the staggered and eclipsed conformations), 2-hydroxytetrahydropyran (the anomeric effect/n−σ* hyperconjugation), the water dimer (hydrogen bonding/n−σ* overlap), ethylene, 1,3-butadiene, and benzene (π molecular orbitals), Re2Cl82–, and U2(COT)2 (metal–metal quadruple bonds). Transition state models illustrate orbital interactions in the SN2 reaction of cyanide with methyl, ethyl, and isopropyl chloride and in a hydroboration reaction of BH3 with propene. Composite EDS models of methyl and isopropyl chloride (for exploring their relative reactivities as SN2 electrophiles) and methylcyclohexane (visualizing 1,3-diaxial interactions) are described. Student perceptions of a multicolor 3D orbital print used in an introductory organic chemistry laboratory course are reported.

Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network.

Cryptic pockets expand the scope of drug discovery by enabling targeting of proteins currently considered undruggable because they lack pockets in their ground state structures. However, identifying cryptic pockets is labor-intensive and slow. The ability to accurately and rapidly predict if and where cryptic pockets are likely to form from a protein structure would greatly accelerate the search for druggable pockets. Here, we present PocketMiner, a graph neural network trained to predict where pockets are likely to open in molecular dynamics simulations. Applying PocketMiner to single structures from a newly-curated dataset of 39 experimentally confirmed cryptic pockets demonstrates that it accurately identifies cryptic pockets (ROC-AUC: 0.87) >1,000-fold faster than existing methods. We apply PocketMiner across the human proteome and show that predicted pockets open in simulations, suggesting that over half of proteins thought to lack pockets based on available structures are likely to contain cryptic pockets, vastly expanding the druggable proteome.