Low-energy Structures Research Articles

An Investigation of the Structures of [(Glycine)(1-Methyluracil)]M+ Complexes (M = H, Li, Na, K) in the Gas Phase by IRMPD Spectroscopy and Theoretical Methods.

The presence of ions in the complexation of molecules can profoundly affect the structure, resulting in changes to functionality and stability. These non-covalent interactions drive many biological processes both necessary and inimical and require extensive research to understand and predict their effects. Protonated and alkali metalated complexes of glycine (Gly) and 1-methyluracil (1-mUra) were studied using infrared multiphoton dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. The experimental and simulated vibrational spectra were compared to help elucidate the structure of each complex. The lowest energy structure for [(Gly)(1-mUra)]H+ consists of amine protonated Gly bound to O4 of canonical 1-mUra through a single ionic hydrogen bond with another, intraglycine ionic hydrogen bond between the protonated amine group and the carbonyl oxygen. For [(Gly)(1-mUra)]Li+, [(Gly)(1-mUra)]Na+ and [(Gly)(1-mUra)]K+, the experimental spectra are most consistent with the metal cations binding in a trigonal planar geometry with 1-mUra bound to the metal cation via the O4 carbonyl. In [(Gly)(1-mUra)]Li+ and [(Gly)(1-mUra)]Na+, the metal cation is bound to canonical Gly via the carbonyl oxygen and amine nitrogen, but in [(Gly)(1-mUra)]K+, Gly is bound through both oxygens and contains an intraglycine hydrogen bond from the hydroxyl to the amine nitrogen.

Prediction of the lowest energy structure of Sn(BH4)2 and its electronic properties

Prediction of the lowest energy structure of Sn(BH4)2 and its electronic properties

Two-Band Electronic Reconstruction Induced via Correlation and CDW Order Effects

The emergence of a charge density wave (CDW) in transition-metal dichalcogenides opens up a route to charge order, followed by superconductivity at low temperatures. A key question here concerns how many particle electron–electron interations govern the low-energy electronic structure in the normal and CDW states. Using dynamical mean-field theory, we explore the many-body properties of an extended, two-band Hubbard model applicable to 2H-TaSe2. We reveal the electronic structure reconstruction in the normal and CDW states driven by two-band dynamical correlations. Our results demonstrate a remarkable renormalization of the Ta-5d bands crossing the Fermi level, showing a continuous reduction in the CDW gap up to an incomplete gapping, followed by a CDW to a CDW–Mott phase transition pertinent to strongly correlated transition-metal dichalcogenides.

Disassembling one-dimensional chains in molybdenum oxides

Abstract The dimensionality of quantum materials strongly affects their physical properties. Although many emergent phenomena, such as charge-density wave and Luttinger liquid behavior, are well understood in one-dimensional (1D) systems, the generalization to explore them in higher dimensional systems is still a challenging task. In this study, we aim to bridge this gap by systematically investigating the crystal and electronic structures of molybdenum-oxide family compounds, where the contexture of 1D chains facilitates rich emergent properties. While the quasi-1D chains in these materials share general similarities, such as the motifs made up of MoO6 octahedrons, they exhibit vast complexity and remarkable tunability. We disassemble the 1D chains in molybdenum oxides with different dimensions and construct effective models to excellently fit their low-energy electronic structures obtained by ab initio calculations. Furthermore, we discuss the implications of such chains on other physical properties of the materials and the practical significance of the effective models. Our work establishes the molybdenum oxides as simple and tunable model systems for studying and manipulating the dimensionality in quantum systems.

Solvent-Free in Situ Synthesis of a CsPbBr3 Nanocrystal/ZrO2 Hybrid Phosphor with Excellent Thermal Stability for White Light-Emitting Diodes.

All-inorganic cesium lead halide perovskite CsPbX3 (X = Cl, Br, I, or mixed) nanocrystals (NCs) are emerging as promising candidates in light-emitting diodes (LEDs) owing to their excellent luminescent properties. However, CsPbX3 NCs are extremely susceptible to the elevated temperature associated with prolonged LED operation due to their low formation energy and soft ionic crystal structure. Here, CsPbBr3 NCs hybridized with ZrO2 were in situ synthesized by a rapid solvent-free method under an ambient environment for the first time, which was also suitable for large-scale production. The as-prepared CsPbBr3/ZrO2 hybrid phosphor not only presented enhanced photoluminescence (PL) properties but also exhibited improved thermal stability. For example, the PL intensity of the CsPbBr3/ZrO2 hybrid phosphor could retain 70% of the initial value at 130 °C, obviously higher than that of 34% for pure CsPbBr3. The exceptional thermal stability of the CsPbBr3/ZrO2 hybrid phosphor could be attributed to the introduction of ZrO2, which effectively preserved the initial perovskite structure of CsPbBr3 during heat treatment, as confirmed by XRD results. The as-prepared CsPbBr3/ZrO2 hybrid phosphor had great practical applications verified by the construction of white LEDs (WLEDs) with a luminance degradation of only 9% after continuous operation for 24 h at the initial luminance of 2000 cd m-2, which was significantly better than that of 63% for control WLEDs. The proposed thermally stable hybrid phosphor is expected to greatly contribute to the industrialization process of perovskites.

Structure and Bonding of Titanium Alanate

AbstractTitanium alanate Ti(AlH4)4 is a candidate material for high‐density hydrogen storage that thus far has been scarcely investigated. This study determines the low energy structures of Ti(AlH4)4 by adopting a global optimization algorithm combined with density functional theories, and systematically compares their stabilities, electronic structures, and bonding properties with Mg(AlH4)2 and Ca(AlH4)2. Compared to other compounds, Ti(AlH4)4 is less stable and the Ti−H bond is of covalent nature with strong polarities. The covalent Ti−H interaction can weaken the Al−H bonds. Because both the ionic and covalent interactions of the Al−H bonds are the weakest in Ti(AlH4)4, it is favorable for the desorption of hydrogen.

Insights into the gas-phase structure and internal dynamics of diphenylsilane: A broadband rotational spectroscopy study.

The rotational spectrum of diphenylsilane was investigated using chirped-pulse Fourier transform microwave spectroscopy in the frequency range of 2-8 GHz. The lowest energy structure of diphenylsilane has C2 point group symmetry with the C2 symmetry axis coinciding with the binertial axis of the molecule. Through the assignment of the main isotopologue as well as singly substituted heavy-atom isotopologues, including 13C, 29Si, and 30Si, we were able to obtain a comprehensive gas-phase structure of diphenylsilane. The structure of diphenylsilane was compared with its oxygen analogue, diphenylether, including a discussion of the barrier height to the large-amplitude motion of the phenyl rings. Furthermore, the structural comparison was extended to include a range of C-Si bond lengths and bond angles from other organosilicon molecules where the silicon atom is bonded to aliphatic and/or aromatic moieties.

The aromatic amino acid phenylalanine: a versatile tool for binding transition metal ions.

The human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn2+, Cu2+, Fe2+, and Mn2+ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn2+ is combined with two C's of the benzene ring, Cu2+ with four C's of the benzene ring, and Fe2+ and Mn2+ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu2+(-294.9kcal/mol) > Zn2+(-261.3kcal/mol) > Fe2+(-247.5kcal/mol) > Mn2+(-220.2kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O. Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe.

Static or dynamic pear shapes in radioactive nucleus 224Rn?

We report a comprehensive study on low-lying parity doublet states of 224Rn by mixing both quadrupole- and octupole-shaped configurations in multireference covariant density functional theory, in which broken symmetries in configurations are restored using projection techniques. The low-lying energy spectrum is reasonably reproduced when the shape fluctuations in both the quadrupole and octupole shapes are considered. Electric octupole transition strength in 224Rn is found to be B(E3;31-→01+)=43\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$B(E3; 3^-_1 \\rightarrow 0^+_1)=43$$\\end{document} W.u., comparable to that in 224Ra, whose data are 42(3) W.u.. Our results indicate that 224Rn shares similar low-energy structure with 224Ra despite the excitation energy of first 3-\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$3^-$$\\end{document} state of the former nucleus is higher than that of the latter. This study suggests 224Rn is a candidate for the search for permanent electric dipole moment.

Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions.

Exploring potential energy surfaces (PES) is fundamental in computational chemistry, as it provides insights into the relationship between molecular energy, geometry, and chemical reactivity. We introduce Kick-MEP, a hybrid method for exploring the PES of atomic and molecular clusters, particularly those dominated by non-covalent interactions. Kick-MEP computes the Coulomb integral between the maximum and minimum electrostatic potential values on a 0.001 a.u. electron density isosurface for two interacting fragments. This approach efficiently estimates interaction energies and selects low-energy configurations at reduced computational cost. Kick-MEP was evaluated on silicon-lithium clusters, water clusters, and thymol encapsulated within Cucurbit[7]uril, consistently identifying the lowest energy structures, including global minima and relevant local minima. Kick-MEP generates an initial population of molecular structures using the stochastic Kick algorithm, which combines two molecular fragments (A and B). The molecular electrostatic potential (MEP) values on a 0.001 a.u. electron density isosurface for each fragment are used to compute the Coulomb integral between them. Structures with the lowest Coulomb integral are selected and refined through gradient-based optimization and DFT calculations at the PBE0-D3/Def2-TZVP level. Molecular docking simulations for the thymol-Cucurbit[7]uril complex using AutoDock Vina were performed for benchmarking. Kick-MEP was validated across different molecular systems, demonstrating its effectiveness in identifying the lowest energy structures, including global minima and relevant local minima, while maintaining a low computational cost.

Acceleration of grain boundary diffusion during ultra-fast firing (UHS) of alumina powder compacts

The sintering rate of a ceramic at a given temperature and relative density is often higher if the heating to that sintering temperature is more rapid. This has previous been explained in terms of microstructural coarsening during slow heating, which degrades the sinterability of the body before it reaches the sintering temperature. In this work the sintering of pure alumina with conventional heating rates (CS, 100-900 °C/hour) was compared with ultra-fast firing, using the method known as ultrafast high-temperature sintering (UHS, 120-140 °C/s). Despite the wide difference in heating rate, the SEM microstructures for a given density were similar and a modified Master Sintering Curve analysis of the results showed that the small pore size reduction observed was not sufficient to account for the acceleration in sintering of UHS samples compared with CS. There remained an additional acceleration by a factor of up to ∼20 that was attributed to a higher grain boundary diffusion coefficient in UHS. It is suggested that this is the result of the boundaries forming between powder particles not having time to relax to their lowest energy, most compact structures during UHS, i.e. non-equilibrium grain boundaries. In support of this hypothesis, it is shown that powder compacts that were first partially pre-sintered with conventional heating rates and then subjected to UHS did not show the same acceleration of sintering displayed by UHS of green bodies. The implication is that the slow pre-sintering allowed relaxation of the grain boundaries to low energy structures with low diffusion coefficients.

Molecular Dynamics Insights into Mechanical Stability, Elastic Properties, and Fracture Behavior of PHOTH-Graphene.

PHOTH-graphene is a newly predicted 2D carbon material with a low-energy structure. However, its mechanical stability and fracture properties are still elusive. The mechanical stability, elastic, and fracture properties of PHOTH-graphene were investigated using classical molecular dynamics (MD) simulations equipped with REBO potential in this study. The influence of orientation and temperature on mechanical properties was evaluated. Specifically, the Young's modulus, toughness, and ultimate stress and strain varied by -26.14%, 36.46%, 29.04%, and 25.12%, respectively, when comparing the armchair direction to the zigzag direction. The percentage reduction in ultimate stress, ultimate strain, and toughness of the material in both directions after a temperature increase of 1000 K (from 200 K to 1200 K) ranged from 56.69% to 91.80%, and the Young's modulus was reduced by 13.63% and 7.25% in both directions, respectively, with Young's modulus showing lower sensitivity. Defects usually weaken the material's strength, but adding random point defects in the range of 3% to 5% significantly increases the ultimate strain of the material. Furthermore, hydrogen atom adsorption induces crack expansion to occur earlier, and the crack tip without hydrogen atom adsorption just began to expand when the strain was 0.135, while the crack tip with hydrogen atom adsorption had already undergone significant expansion. This study provides a reference for the possible future practical application of PHOTH-graphene in terms of mechanical properties and fracture failure.

What is the true ground state of intermetallic compound Fe3Al?

We discuss recent doubts about the true ground-state (GS) structure of the intermetallic compound Fe3Al. It seems that it should be the D03 structure (observed experimentally), but there are some considerations that, perhaps, D03 might be a high-temperature (>400 K) structure and the GS at 0 K might be the L12 structure because there might be a high energy barrier between both structures and, when the temperature is lowered, the system is not able to transform into the (perhaps) lower-energy L12 structure. To elucidate this problem, we re-interpret our recent extended ab initio electronic structure calculations for Fe3Al performed with the help of the VASP code and using various exchange-correlation energies within the generalized gradient approximation (GGA). Regrettably, some calculations provide the L12 and some of them D03 as the GS structure.To resolve this question, we performed further calculations testing 9 frequently applied metaGGAs, such as TPSS, revTPSS, M06-L, SCAN(-L), rSCAN(-L) and r2SCAN(-L) representing a higher rung of the Jacob's ladder. It turns out that also here some meta-GGAs lead to L12 and some others to D03 GS structure and, again, we cannot decide.In this way, the present results represent the very first step on the way to understand the energetics of the Fe3Al compound and its ground state. We hope they may motivate future theoretical and experimental work in this direction.

Ab Initio Molecular Dynamics Simulations of Phosphocholine Interactions with a Calcium Oxalate Dihydrate (110) Surface.

We use ab initio modeling (CASTEP) to help elucidate the crystallization phenomena and chemistry behind kidney stone composition and formation. To explore the stone formation process, we have constructed a surface model of calcium oxalate dihydrate-the mineral most commonly found in patients with hypercalciuria and modeled stone growth, by simulating further calcium oxalate adsorption onto the surface (-7.446 eV, -0.065 eV/atom). Furthermore, urine analysis of kidney stone patients has previously revealed that their urine contains higher concentrations of phospholipids compared to healthy individuals. Therefore, to investigate the interactions between urinary macromolecules and the growing crystal surfaces at an atomic level, we have performed ab initio molecular dynamics simulations of phosphocholine adsorption on calcium oxalate surfaces. We have shown that the phosphocholine headgroups become entrapped within the growing crystal and the lowest energy structures (-18.008 eV, -0.0396 eV/atom) are those where the calcium oxalate dihydrate surfaces have become disrupted, with reorganization of their crystallographic structure. Urinary calculi (kidney stones) are a common ailment affecting around 10% of the world's population and resulting in nearly 90,000 finished consultant episodes (FCE) each year in the United Kingdom [Hospital Episode Statistics, Admitted Patient Care-England, 2011-12 NHS Digital, 2021-2022. https://digital.nhs.uk/data-and-information/publications/statistical/hospital-admitted-patient-care-activity/hospital-episode-statistics-admitted-patient-care-england-2011-12].

Extracting the crystal electric field levels of Ce-4f1 states in CeB6 by atomic multiplet simulations

The crystal electric field (CEF) is vital in defining the low-energy electronic structure of lanthanide compound, and thus very essential in understanding the many-body physics of the strongly correlated 4 f electrons. Many efforts have been made to determine the low-energy electronic structure of the intrinsically correlated material CeB6 and its derived compounds. In this paper, we performed atomic multiplet (AM) simulations on the Ce-4f1 states in CeB6 and directly fitted them with previously reported resonant inelastic x-ray scattering spectroscopy (RIXS). The simulation results suggest that the discrepancy of excitations energies extracted from Raman spectroscopy and RIXS is a result of intrinsic varied crystal electric field strength, which can be reconciled by considering the enhanced CEF by eliminating the insulating scenario.

The ferrite/perovskite interface and helium partition in nano-structured ferritic alloys from the first-principles

Nano-oxides are largely responsible for the excellent mechanical properties and irradiation tolerance of nano-structured ferritic alloys (NFAs) for nuclear reactor applications. In this work, the roles of perovskite YTiO3 and its interface in trapping helium in NFAs were investigated from the first-principles. Similarly as other two Y-Ti-oxide phases (Y2TiO5 and Y2Ti2O7), bulk YTiO3 can trap insoluble helium at its interstitial sites, but with a lower trapping ability that is only comparable to matrix vacancies. The ferrite/YTiO3 interface phase diagram was constructed based on the experimental orientation relationship and the calculated interface formation energy, and the lowest-energy interface structure was predicted as the ns-Ti or the stoichiometric. Helium always prefers to consume individual interfacial vacancies and interstitial sites to the extent possible, before forming higher-order helium-vacancy clusters at the interface. Similarly as Y2Ti2O7, YTiO3 preferably traps helium at its interface, followed by its bulk interior and the ferritic matrix. However, in view of all the bulk and interface results, perovskite YTiO3 cannot compete with pyrochlore Y2Ti2O7 in trapping helium in NFAs.

MB38(M=Be and Zn): A Quasi-Planar Structure Rather Than a Core-Shell Octahedral Borospherene Structure.

In a recent paper (ChemPhysChem, 2023, 24, e202200947), based on the results computed using DFT method, the perfect core-shell octahedral configuration Be@B38 and Zn@B38 was reported to be the global minima of the MB38(M=Be and Zn) clusters. However, this paper presents the lower energy structures of MB38(M=Be and Zn) clusters as a quasi-planar configuration, the Be atom is found to reside on the convex surface of the quasi-planar B38 isomer, while the Zn atom tends to be attached to the top three B atoms of the quasi-planar B38 isomer. Our results show that quasi-planar MB38(M=Be and Zn) at DFT method have lower energy than core-shell octahedral configuration M@B38(M=Be and Zn). Natural atomic charges, valence electron density, electron localization function (ELF) analyses identify the MB38(M=Be and Zn) to be charge transfer complexes (Be2+B38 2-and Zn1+B38 1-) and suggest primarily the electrostatic interactions between doped atom and B38 fragment. The photoelectron spectra of the corresponding anionic structures were simulated, providing theoretical basis for future structural identification.

Structures and stabilities Ru-doped Agn (n = 1–13) clusters: Ag10Ru a 18-ve cluster superatom

The geometrical and stability properties of Ru-doped silver clusters (AgnRu with n = 1–13) are investigated by density functional theory (DFT) calculations. The results show that the Ru dopant adopts central positions in the lowest-energy structures of AgnRu clusters. The most stable structures found are planar and curved for n = 3–6, while for n = 6 onward the structures follow a pentagonal growth pattern. Interestingly for n = 10, we found a cage structure with fulfills the 18 electron rule. The relative stability of the clusters is further evaluated through energetic parameters such as ionization energy, electron affinity, second order energy difference and HOMO–LUMO gap. The results show that the most stable structures in this series are Ag3Ru, Ag6Ru and Ag10Ru, as supported by electronic structure analyses. The plausible formation of the Ag10Ru cluster as a superatomic species is rationalized with 1.64 eV of HOMO–LUMO gap and 6.23 eV of adiabatic ionization energy.

Trinuclear and Tetranuclear Ruthenium Carbonyl Nitrosyls: Oxidation of a Carbonyl Ligand by an Adjacent Nitrosyl Ligand.

Trinuclear and tetranuclear ruthenium carbonyls of the types Ru3(CO)n(NO)2, Ru3(N)(CO)n(NO), Ru3(N)2(CO)n, Ru3(N)(CO)n(NCO), Ru3(CO)n(NCO)(NO), Ru4(N)(CO)n(NO), Ru4(N)(CO)n(NCO), and Ru4(N)2(CO)n related to species observed experimentally in the chemistry of Ru3(CO)10(µ-NO)2 have been investigated using density functional theory. In all cases, the experimentally observed structures have been found to be low-energy structures. The low-energy trinuclear structures typically have a central strongly bent Ru-Ru-Ru chain with terminal CO groups and bridging nitrosyl, isocyanate, and/or nitride ligands across the end of the chain. The low-energy tetranuclear structures typically have a central Ru4N unit with terminal CO groups and a non-bonded pair of ruthenium atoms bridged by a nitrosyl or isocyanate group.

LoGAN: local generative adversarial network for novel structure prediction

Abstract The efficient generation and filtering of candidate structures for new materials is becoming increasingly important as starting points for computational studies. In this work, we introduce an approach to Wasserstein generative adversarial networks for predicting unique crystal and molecular structures. Leveraging translation- and rotation-invariant atom-centered local descriptors addresses some of the major challenges faced by similar methods. Our models require only small sets of known structures as training data. Furthermore, the approach is able to generate both non-periodic and periodic structures based on local coordination. We showcase the data efficiency and versatility of the approach by recovering all stable C5H12O isomers using only 39 C4H10O and C6H14O training examples, as well as a few randomly selected known low-energy SiO2 crystal structures utilizing only 167 training examples of other SiO2 crystal structures. We also introduce a filtration technique to reduce the computational cost of subsequent characterization steps by selecting samples from unique basins on the potential energy surface, which allows to minimize the number of geometry relaxations needed after structure generation. The present method thus represents a new, versatile approach to generative modeling of crystal and molecular structures in the low-data regime, and is available as open-source.