Ground-state Structure Research Articles

Ground-State Structure of Quaternary Alloys (SiC)1−x (AlN)x and (SiC)1−x (GaN)x

Despite III-nitride and silicon carbide being the materials of choice for a wide range of applications, theoretical studies on their quaternary alloys are limited. Here, we report a systematic computational study on the electronic structural properties of (SiC)x (AlN)1-x and (SiC)x (AlN)1-x quaternary alloys, based on state-of-the-art first-principles evolutionary algorithms. Trigonal (SiCAlN, space group P3m1) and orthorhombic (SiCGaN, space group Pmn21) crystal phases were as predicted for x = 0.5. SiCAlN showed relatively weak thermodynamic instability, while that of SiCGaN was slightly elevated, rendering them both dynamically and mechanically stable at ambient pressure. Our calculations revealed that the Pm31 crystal has high elastic constants, (C11~458 GPa and C33~447 GPa), a large bulk modulus (B0~210 GPa), and large Young's modulus (E~364 GPa), and our results suggest that SiCAlN is potentially a hard material, with a Vickers hardness of 21 GPa. Accurate electronic structures of SiCAlN and SiCGaN were calculated using the Tran-Blaha modified Becke-Johnson semi-local exchange potential. Specifically, we found evidence that SiCGaN has a very wide direct bandgap of 3.80 eV, while that of SiCAlN was indirect at 4.6 eV. Finally, for the quaternary alloys, a relatively large optical bandgap bowing of ~3 eV was found for SiCGaN, and a strong optical bandgap bowing of 0.9 eV was found for SiCAlN.

Novel Ultrahard Extended Hexagonal C10, C14 and C18 Allotropes with Mixed sp2/sp3 Hybridizations: Crystal Chemistry and Ab Initio Investigations

Based on 4H, 6H and 8H diamond polytypes, novel extended lattice allotropes C10, C14 and C18 characterized by mixed sp3/sp2 carbon hybridizations were devised based on crystal chemistry rationale and first-principles calculations of the ground state structures and energy derived properties: mechanical, dynamic (phonons), and electronic band structure. The novel allotropes were found increasingly cohesive along the series, with cohesive energy values approaching those of diamond polytypes. Regarding mechanical properties, C10, C14, and C18 were found ultrahard with Vickers hardness slightly below that of diamond. All of them are dynamically stable, with positive phonon frequencies reaching maxima higher than in diamond due to the stretching modes of C=C=C linear units. The electronic band structures expectedly reveal the insulating character of all three diamond polytypes and the conductive character of the hybrid allotropes. From the analysis of the bands crossing the Fermi level, a nesting Fermi surface was identified, allowing us to predict potential superconductive properties.

Structure optimization with stochastic density functional theory.

Linear-scaling techniques for Kohn-Sham density functional theory are essential to describe the ground state properties of extended systems. Still, these techniques often rely on the localization of the density matrix or accurate embedding approaches, limiting their applicability. In contrast, stochastic density functional theory (sDFT) achieves linear- and sub-linear scaling by statistically sampling the ground state density without relying on embedding or imposing localization. In return, ground state observables, such as the forces on the nuclei, fluctuate in sDFT, making optimizing the nuclear structure a highly non-trivial problem. In this work, we combine the most recent noise-reduction schemes for sDFT with stochastic optimization algorithms to perform structure optimization within sDFT. We compare the performance of the stochastic gradient descent approach and its variations (stochastic gradient descent with momentum) with stochastic optimization techniques that rely on the Hessian, such as the stochastic Broyden-Fletcher-Goldfarb-Shanno algorithm. We further provide a detailed assessment of the computational efficiency and its dependence on the optimization parameters of each method for determining the ground state structure of bulk silicon with varying supercell dimensions.

Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding

Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with FoF1 ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of FoF1, where the overall structure of the F1 domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway.

The influence of double lanthanide metal atoms on the stability of germanium-based clusters

The influence of double lanthanide metal atoms on the stability of germanium-based clusters was conducted by means of density functional theory calculations. The consistency and accuracy of structure optimization are tested with three exchange correlation functionals (PBE, BPW91 and B3LYP). Unlike the pentagonal bipyramid derivatives of LnGe7- and pure germanium, the ground state structures of Ln2Ge6- (Ln = La, Ce and Lu) clusters are preference to tetragonal bipyramid with two capped atoms. The enhancement effect on clusters stability is Ce/ La > Lu > Yb. Total density of states diagram represents the extremely inconspicuous spin polarization of Ln2Ge6- clusters. In fact, the value of the magnetic moment is also very small, which is 1 μB.

The largest fullerene.

Fullerenes are lowest energy structures for gas phase all-carbon particles for a range of sizes, but graphite remains the lowest energy allotrope of bulk carbon. This implies that the lowest energy structure changes nature from fullerenes to graphite or graphene at some size and therefore, in turn, implies a limit on the size of free fullerenes as ground state structures. We calculate this largest stable single shell fullerene to be of size N = 1 × 104, using the AIREBO effective potential. Above this size fullerene onions are more stable, with an energy per atom that approaches graphite structures. Onions and graphite have very similar ground state energies, raising the intriguing possibility that fullerene onions could be the lowest free energy states of large carbon particles in some temperature range.

Synthesis of and theoretical research on some azine derivatives and investigation of their antimicrobial activities

This study includes experimental, theoretical, and antimicrobial investigations on 1-(diphenylmethylene)-2-(4-methoxybenzylidene)hydrazine (5), 1-(3,5-dimethoxybenzylidene)-2-(diphenylmethylene)hydrazine (6) and 1- (diphenylmethylene)-2-(2,3,4-trimethoxybenzylidene)hydrazine (7). The structures of the compounds synthesized by microwave method were determined by spectroscopic methods and elemental analysis. Conformational analysis, ground state structure, fourier transform infrared spectra (FT-IR), and nuclear magnetic resonance (NMR) spectra of the compounds were computed using density functional theory (DFT) calculations in the theoretical research. Based on the B3LYP/6-31G(d,p) level, the conformers from the torsional barrier scanning were optimized. The B3LYP/6-311++G .(d,p) was used to determine the harmonic vibrational frequencies, potential energy distribution (PED), infrared intensities, and NMR chemical shifts of the most stable conformers. The experimental findings were compared with theoretically expected spectral data. The antibacterial activity of the prepared compounds was tested in vitro against nine bacteria and one yeast species. The antimicrobial activity of the compounds was tested by minimum inhibitory concentration (MIC) and agar well diffusion method. Compound 7 showed good activity against the bacteria and yeast, while 5 and 6 showed no antimicrobial activity. Compound 7 showed zone of inhibition values in the range of 10-15 mm against Klebsiella pneumonia, Pseudomonas aeruginosa and Salmonella typhimurium The results indicated that compound 7 was effective against bacteria.

Structural evolution, charge transfer and bonding properties of medium-sized atomic rubidium-doped boron clusters

In this work, the bonding properties of B8Rb2 cluster were characterized by molecular orbitals and bonding order. The electrostatic potentials of the clusters were also analyzed, and the interaction of particles between the alkali metal orbitals and the boron backbone was found.

Phosphorus nanoclusters and insight into the formation of phosphorus allotropes.

Elemental phosphorus has a striking variety of allotropes, which we analyze by looking at stable phosphorus clusters. We determine the ground-state structures of Pn clusters in a wide range of compositions (n = 2-50) using density functional calculations and global optimization techniques. We explain why the high-energy white phosphorus is so easily formed, compared to the much more stable allotropes - the tetrahedral P4 cluster is so much more stable than nearby compositions that only by increasing the size to P10 one can get a more stable non-P4-based structure. Starting from 17 atoms, phosphorus clusters have a single-stranded structure, consisting of a set of well-resolved structural units connected by P2 linking fragments. The investigation of relative stability has revealed even-odd alternations and structural magic numbers. The former are caused by the higher stability of clusters with even numbers of atoms due to closed electronic shells. The structural magic numbers are associated with the presence of particular stable structural units and lead to enhanced stability of P18+12k (k = 0, 1, 2) clusters. We also compare the energies of the obtained ground-state structures with clusters of different phosphorus allotropes. Clusters of fibrous phosphorus are energetically the closest to the ground states, white phosphorus clusters are found to be less stable, and the least stable allotrope at the nanocluster scale is black phosphorene.

Electron affinities and lowest triplet and singlet state properties of para-oligophenylenes (n = 3-5): theory and experiment.

We apply photodetachment-photoelectron spectroscopy to measure the electron affinities and the energetics of the lowest excited electronic states of the neutral molecules para-terphenyl (p3P), para-quaterphenyl (p4P) and para-quinquephenyl (p5P), including especially the triplet states below S1. The interpretation of the experimental data is based on the comparison to calculated 0-0 energies and Dyson norms, using density functional theory and multireference configuration interaction methods, as well as Franck-Condon patterns. The comparison between calculated and experimental vibrational fine-structures reveals a twisted benzoid-like molecular structure of the S0 ground state and nearly planar quinoid-like nuclear arrangements in the S1 and T1 excited states as well as in the D0 anion ground state. For all para-oligophenylenes (ppPs) in this series, at least two triplet states have been identified in the energy regime below the S1 state. The large optical S0-S1 cross sections of the ppPs are rationalised by the nodal structure of the molecular orbitals involved in the transition. The measured electron affinities range from 380 meV (p3P) over 620 meV (p4P) to 805 meV (p5P). A saturation of the electron binding energy with the increasing number of phenyl units is thus not yet in sight.

Theoretical study of the absorption and emission spectrum and non‐adiabatic excited state dynamics of gas‐phase xanthone

AbstractThe ground, singlet, and triplet excited state structures (S1, S2, T1, and T2) of xanthone have been calculated and characterized in the adiabatic representation by using time‐dependent density functional theory (TDDFT). However, the fast intramolecular transition mechanisms of xanthone are still under debate, and so we perform non‐adiabatic excited state dynamics of the photochemistry of xanthone gas phase and find that it follows El‐Sayed's rule. Electronic transition mechanism of xanthone is sequential from the S2 state: the singlet internal conversion (IC) time from S2 (1ππ*) to S1 (1nπ*) is 3.85 ps, the intersystem crossing (ISC) from S1 (1nπ*) to T2 (3ππ*) takes 4.76 ps, and the triplet internal conversion from T2 (3ππ*) to T1 (3nπ*) takes 472 fs. The displaced oscillator, Franck–Condon approximation, and one‐photon excitation equations were used to simulate the absorption spectra of S0 → S2 transition, with v55 being most crucial for S0 structure; the fluorescence spectra of S1 → S0 transition with v47 for S1; and the phosphorescence spectra of T1 → S0 transition with v4 for T1. Our method can reproduce the experimental absorption, fluorescence, and phosphorescence spectra of gas‐phase xanthone.

Photophysics of the red-form Kaede chromophore.

The green fluorescent protein (GFP) drove revolutionary progress in bioimaging. Photoconvertible fluorescent proteins (PCFPs) are an important branch of the FP family, of which Kaede is the prototype. Uniquely, PCFPs can be permanently switched from green to red emitting forms on UV irradiation, facilitating applications in site-specific photolabelling and protein tracking. Optimisation and exploitation of FPs requires understanding of the photophysical and photochemical behaviour of the chromophore. Accordingly, the principal GFP chromophore has been the subject of intense experimental and theoretical investigation. In contrast, the photophysics of the red emitting PCFP chromophore are largely unstudied. Here we present a detailed investigation of the excited-state properties of the Kaede chromophore in solution, utilising steady state measurements, ultrafast time-resolved electronic and vibrational spectroscopies, and electronic structure theory. Its excited state dynamics are very different to those of the parent GFP. Most remarkably, the PCFP chromophore has highly complex wavelength-dependent fluorescence decays and a mean lifetime an order of magnitude longer than the GFP chromophore. Transient electronic and vibrational spectroscopies suggest that these dynamics arise from a range of excited-state conformers that are spectrally and kinetically distinct but chemically similar. These conformers are populated directly by excitation of a broad thermal distribution of ground state structures about a single conformer, suggesting an excited-state potential surface with several minima. Temperature-dependence confirms the existence of barriers on the excited-state surface and reveals the radiationless decay mechanism to be internal conversion. These experimental observations are consistent with a model assuming a simple ground state potential energy surface accessing a complex excited state possessing multiple minima.

Photoluminescence and energy transfer mechanisms of Tm3+ doped Y2O3 laser crystals: experimental and theoretical insights.

Rare-earth thulium (Tm3+) doped yttrium oxide (Y2O3) host single crystals are promising "eye-safe" laser materials. However, the mechanisms of photoluminescence and energy transfer in Tm3+ doped Y2O3 crystals are not yet understood at the fundamental level. Here, we synthetize a series of Y2O3:Tm3+ samples by the sol-gel method. Our experimental results show that the most intensive absorption line of the 3H6 → 1D2 transition occurs at 358 nm, and the strongest emission line of the 1D2 → 3F4 transition is located at 453 nm, which are in good agreement with the calculations of 363 nm and 458 nm, respectively. By using the CALYPSO structural search method, the ground state structure of Y2O3:Tm3+ with P2 space group symmetry is uncovered. The complete energy levels, including free-ion LS terms and crystal-field LSJ multiplet manifolds, of Y2O3:Tm3+ are obtained based on our developed WEPMD method. The present findings show that our WEPMD method can be used in experiments to elucidate the underlying mechanisms of photoluminescence and energy transfer in Tm3+ doped Y2O3 crystals, which offer insights for further understanding of other rare-earth doped laser materials.

Phase stability and magnetic properties of B2 and L10 PtMn1-XFeX alloys: a cluster expansion and ab initio approach

MnPt-based alloys are promising new materials for magnetic recording and spintronic applications due to their interesting magnetic properties. The underlying thermodynamic properties are still unclear, despite numerous efforts to improve ferromagnetic stability through alloying. In this work, the phase stability of B2 and L10 PtMn1-xFex alloys is investigated using a combination of density functional theory (DFT) and Cluster Expansion (CE). CE model accuracy is evaluated against DFT data, where cross-validation scores were found to be reasonable. The CE generated 16 and 27 new structures on B2 and L10 PtMn1-xFex, respectively. The ground state line predicted 6 stable structures with negative formation energies for both B2 and L10 PtMn1-xFex alloys, suggesting thermodynamic stability. Furthermore, the magnetic strength of the ground state structures is evaluated using DFT.

Structural and photoelectron spectroscopic study on the heterotrinuclear nickel-titanium dioxide carbonyl complexes Ni2TiO2(CO) n - (n = 2-4).

Herein, the configurations and intrinsic electronic properties of heteronuclear transition metal dioxide carbonyl anions Ni2TiO2(CO) n - (n = 2-4) in the gas phase were investigated using mass spectrometry coupled anionic photoelectron spectroscopy, ab initio calculations, and simulated density-of-state (DOS) spectra. The results clearly show that the binding of electrons is enhanced by the addition of CO. The ground state structures of Ni2TiO2(CO) n - (n = 2-4) are characterized to show that three transition metal atoms (one Ti atom and two Ni atoms) forming a quasi-line is favored. The interaction between Ni and C becomes weaker as the cluster size increases. The natural electron configuration shows that the extra electron is enriched on O atoms attached to Ti, and there is strong interaction between Ti and O atoms. This work gives significant insight into the configuration and electronic structures of nickel-titanium dioxide carbonyl anions, which has potential application in adsorption of carbon monoxide on the surfaces/interfaces of alloys.

Structural evolution and electronic properties of neutral and anionic TiASil (A = Sc, Ti; l ≤ 12): relatively stable TiASi4 as a structural unit.

Simulated photoelectron spectroscopy was conducted to investigate the structural evolution and electronic properties of TiASil (A = Sc, Ti; l ≤ 12) clusters and their anions via the Perdew-Burke-Enzerhof scheme and extensive cluster search using the ABCluster software. The results revealed that the ground-state structures of the TiASil (A = Sc, Ti) clusters generally exhibited similar configurations except for the Ti2Si3, ScTiSi3, and TiScSi10 clusters. Furthermore, the TiASil clusters exhibited an adsorptive evolution pattern, and the TiASi4 unit was considered the basic constituent framework of the structure, excluding several distortions and minor changes. With the increase in the cluster size, the lowest-energy structures varied from the exohedral to the cage structures of the single-metal atom at the center. Regarding the second energy difference data, the neutral TiASi4 clusters exhibited better stability among the neutral and anionic TiASil (A = Sc, Ti; l ≤ 12) clusters. Furthermore, the chemical bonding in the TiASi4 clusters was analyzed by molecular orbitals (MOs), highest occupied MO-lowest unoccupied MO gaps, and adaptive natural density partitioning analyses for the best Ti2Si4 cluster especially, and the results were combined with the natural population analysis data. The hybridization of the spd orbital of the metal atoms, eight localized bonds, and four delocalized bonds may primarily account for the relative stabilities of the neutral, square bipyramidal structure of Ti2Si4. Thus, the TiASi4 clusters may be assembled as the basic units of silicon-based semiconductor clusters of large-size neutral and anionic TiASil.

Synthesis, Biological Activity and DFT Studies of 1,3,4-oxadiazole Ring in Combination with Pyridinium Salt

Aims: In this study, the synthesis and biological activity of new 1,3,4-oxadiazole derivatives will be discussed. Background: Microbial contagion via different bacterial strains discomposes the healthcare system globally. In 2019 E. coli, S. aureus, K. pneumoniae, and S. pneumoniae were reported as the most bacteremia deaths causes. Over time, bacteria develop different ways to overcome antibiotic activity, causing multidrug resistant bacteria (MDR). The MDR is considered one of the biggest concerns to scientists worldwide due to its direct effect on patients' lives. As a result, developing new drugs has become imperative for scientists to protect human life. Objective: Developing new water soluble antibacterial drugs from cheap and commercially available materials. Methods: Microdilution Assay Antimicrobial potential was performed based on the reported experimental procedure with slight modifications. Briefly, chemical preparations were serially diluted (2-fold) ten times with Muller Hinton broth. Well number eleven was considered a negative control of bacterial growth, while well number twelve contained nutrient broth only and was used as a positive control for bacterial growth. The achieved ten concentrations of the chemical solutions were from 10 mg/mL to 9 μg/mL. A serial two-fold dilution of DMSO with Muller Hinton broth was prepared to ensure that the antimicrobial potential was not from DMSO. Moreover, the blank or the background was a two-fold dilution for each chemical with broth. The final bacterial concentration in each well (except positive control) was adjusted to 0.75 × 106 CFU/ml. After the inoculation of bacteria, the plates were covered and incubated overnight at 37oC for 24 hours. The plates were then scanned with an enzyme-linked immunosorbent assay (ELISA) reader at 600 Nano moles to examine the bacterial density. The lowest concentration of the chemical that did not allow any visible microbial growth in the test broth was considered the minimal inhibitory concentration (MIC), which was then further confirmed by culturing each (MIC) well on Muller Henton agar and incubating overnight at 37oC for twenty-four hours. The molecular geometries of compounds 4a, 4e, 4j, and 4p were optimized at the B3LYP/6-311+G(d,p) level of theory using DFT calculations. Results: The antimicrobial examination results show that compound 4j has an interesting activity against E. faecium with MIC value of 9 μg/mL. However, it was found to have low activity against E.coli and K. pneumoniae with an MIC value of 625 μg/mL. On the other hand, compound 4e showed very good activity against E.coli with an MIC value of 78 μg/mL and good activity against K. pneumoniae with an MIC value of 312 μg/mL. The structural properties were further investigated by density functional theory (DFT) calculations. The most biologically active compounds 4e and 4j were optimized in the gas phase using B3LYP method and 6-31+G(d,p) as a bases set. The resulting ground-state structures take a V shape as the two conjugated system are connected by methylene group. The molecular electrostatic potential map (MEP) of 4e and 4j was calculated and the results indicate that, the most intense blue region with the largest positive potential is distributed over the pyridinium ring, which indicates its binding with the chloride ion.

Ground state of Rydberg-dressed Bose gas confined in periodic moiré lattices

The experimental realization of Rydberg dressing and spin-orbit coupling greatly broadens the research field of ultracold atoms as a quantum simulation platform. Very recently, moiré lattices have attracted intensive study, ranging from condensed matter to ultracold physics. In this paper, the ground-state structure of Rydberg-dressed Bose gas with spin-orbit coupling and confined in moiré lattices is studied, and the effects of nonlocal Rydberg interaction and spin-orbit coupling on the ground state of the system are explored. Our results show that the system has no translational symmetry due to the presence of nonlocal Rydberg interaction, and more and more regular periodic structures present with the increases of the strength of nonlocal Rydberg interaction. In the presence of spin-orbit coupling, the Hamiltonian of the system has an imaginary part, and the phase of the system is not uniformly distributed. It is found that the ground state of the system with spin-orbit coupling present more abundant internal structure base on these periodic structures. The results pave the way for future study of moiré physics in ultracold atom system.

Accessible chemical space for metal nitride perovskites.

Building on the extensive exploration of metal oxide and metal halide perovskites, metal nitride perovskites represent a largely unexplored class of materials. We report a multi-tier computational screening of this chemical space. From a pool of 3660 ABN3 compositions covering I-VIII, II-VII, III-VI and IV-V oxidation state combinations, 279 are predicted to be chemically feasible. The ground-state structures of the 25 most promising candidate compositions were explored through enumeration over octahedral tilt systems and global optimisation. We predict 12 dynamically and thermodynamically stable nitride perovskite materials, including YMoN3, YWN3, ZrTaN3, and LaMoN3. These feature significant electric polarisation and low predicted switching electric field, showing similarities with metal oxide perovskites and making them attractive for ferroelectric memory devices.

Double-bond delocalization in non-alternant hydrocarbons induces inverted singlet-triplet gaps.

Molecules where the first excited singlet state is lower in energy than the first excited triplet state have the potential to revolutionize OLEDs. This inverted singlet-triplet gap violates Hund's rule and currently there are only a few molecules which are known to have this property. Here, we screen the complete set of non-alternant hydrocarbons consisting of 5-, 6-, 7-membered rings fused into two-, three- and four-ring polycyclic systems. We identify several molecules where the symmetry of the ground-state structure is broken due to bond-length alternation. Through symmetry-constrained optimizations we identify several molecular cores where the singlet-triplet gap is inverted when the structure is in a higher symmetry, pentalene being a known example. We uncover a strategy to stabilize the molecular cores into their higher-symmetry structures with electron donors or acceptors. We design several substituted pentalenes, s-indacenes, and indeno[1,2,3-ef]heptalenes with inverted gaps, among which there are several synthetically known examples. In contrast to known inverted gap emitters, we identify the double-bond delocalized structure of their conjugated cores as the necessary condition to achieve the inverted gap. This strategy enables chemical tuning and paves the way for the rational design of polycyclic hydrocarbons with inverted singlet-triplet gaps. These molecules are prospective emitters if their properties can be optimized for use in OLEDs.