Relative Structural Stability Research Articles

Competing Phases of Iron at Earth's Core Conditions From Deep‐Learning‐Aided ab‐initio Simulations

AbstractThe properties and relative stability of different structures of iron at the extreme conditions of pressure and temperature of relevance for the Earth's core were determined with ab‐initio atomistic simulations aided by a machine‐learning force‐field. We find that the body‐centered cubic (bcc) structure is mechanically stable at core temperatures, but its free energy is marginally higher than those of the hexagonal close‐packed and face‐centered cubic structures. The bcc structure is the only structure whose shear sound velocity matches seismic data. The small free‐energy difference between competing structures suggests that the role of impurities could be crucial in stabilizing the bcc structure in the inner core.

Controlled Synthesis and Phase Transition Mechanisms of Palladium Selenide: A First-Principles Study.

Using density functional theory, we carefully calculated the relative stability of monolayer, few-layer, and cluster structures with Penta PdSe2, T-phase PdSe2, and Pd2Se3-phase. We found that the stability of Penta PdSe2 increases with the number of layers. The Penta PdSe2, T-phase PdSe2, and Pd2Se3 monolayers are all semiconducting, with band gaps of 1.77, 0.81, and 0.65 eV, respectively. The formation energy of palladium selenide clusters with different phase structures is calculated, considering the cluster size, stoichiometry, and chemical environment. Under typical experimental conditions, Pd2Se3 phase clusters are found to be dominant, having the lowest formation energy among all of the phases considered, with this dominance increasing as cluster size grows. Adjusting the Pd-Se ratio in the environment allows for controlled synthesis of specific palladium selenide phases, providing theoretical insights into the nucleation mechanisms of PdSe2 and other transition metal chalcogenides.

Structures, simulated photoelectron spectroscopy, and electronic properties of CuASix(A = Sc, Cu, x ≤ 13) clusters: Relatively stable neutral pentagonal bipyramid structures of CuASi5

Structural design and optimization, simulated photoelectron spectroscopy, electronic properties and chemical bond analysis of CuASix(A = Sc, Cu, x ≤ 13) clusters were systematically studied using the PBE scheme to integrate with global search program of ABCluster. Firstly, neutral MS (the most stable structures) of CuASi5 of the basic 1 + 5 + 1 structures (1 metal + 5 silicons + 1 metal atoms) can be found as the basic units for assembling more lager clusters under the condition of neglecting distortions and minor changes. If the Cu atoms in Cu2Six(x ≤ 13) systems was replaced by one Sc atom, the geometries of MS will be reconstructed. Compared with the wheel geometries of Cu2Si12 and Cu2Si13, CuScSi12 and CuScSi13 clusters belong to near-wheel geometries with peripheral metal atoms. The neutral CuScSi5 and Cu2Si5 clusters possess relatively higher stability in all of cluster sizes. A combination of NPA analysis of CuASi5, sp of the Cu atom and spd of the Sc atom hybridizations were crucial to the chemical bonds of A–Si in the neutral CuASi5 clusters. In view of the higher SED value of the Cu2Si5 molecule, chemical bond analysis was carried out using MO, HLg and AdNDP analysis. 18 localized bonds and four delocalized bonds can play a positive role for the relative stabilities of neutral pentagonal bipyramid structures of Cu2Si5. Thus, the Cu2Si5 cluster with a lager HLg(1.80 eV) may be a good candidate for the basic unit of silicon-based semiconductor material assembly.

Effects of coffee pericarp and litter mulsching on soil microbiomes diversity and functions in a tropical coffee plantation, South China.

In recent decades, ecological cyclic cultivation models have attracted increasing attention, primarily because the decomposition of crop residues and litter enhances soil organic matter content, thereby altering the soil microenvironment and regulating the diversity and functions of soil microbial communities. However, the effects of different coffee waste mulching on the diversity of soil microbial communities and their functions are still unclear. Therefore, this study set up four kinds of covering treatments: uncovered coffee waste (C), covered coffee litter (L), covered coffee pericarp (P), and both covered coffee litter and pericarp (PL). The results showed that compared to the control, coffee pericarp mulching significantly increased the soil available potassium (SAK) content by 18.45% and alkali hydrolyzed N (SAN) content by 17.29%. Furthermore, coffee pericarp mulching significantly increased bacterial richness and diversity by 7.75 and 2.79%, respectively, while litter mulching had little effect on bacterial abundance and diversity was smaller. The pericarp mulching significantly increased the abundance of Proteus by 22.35% and the abundance of Chlamydomonas by 80.04%, but significantly decreased the abundance of Cyanobacteria by 68.38%, while the coffee litter mulching significantly increased the abundance of Chlamydomonas by 48.28%, but significantly decreased the abundance of Cyanobacteria by 73.98%. The increase in soil SAK promoted bacterial Anoxygenic_photoautotrophy, Nitrogen_respiration, Nitrate_respiration, Nitrite_respiration, and Denitrification functions. The above results indicate that the increase in available soil potassium and alkali hydrolyzed N content under coffee pericarp cover is the main reason for promoting the diversity and richness of bacterial community and promoting the changes in bacterial community structure and function. The use of coffee pericarps in coffee plantations for ecological recycling helps to improve the diversity of the soil microbial community and maintain the relative stability of the microbial community structure and function, promoting soil health conservation and the sustainable development of related industries.

Rationalizing polymorphism with local correlation-based methods: a case study of pnictogen molecular crystals.

A computational workflow is proposed to quantify and rationalize the relative stability of different structures of molecular crystals using cluster models and quantum chemical methods. The Hartree-Fock plus London Dispersion (HFLD) scheme is used to estimate the lattice energy of molecular crystals in various structural arrangements. The fragment-pairwise Local Energy Decomposition (fp-LED) scheme is then employed to quantify the key intermolecular interactions responsible for the relative stability of different crystal structures. The fp-LED scheme provides also in-depth chemical insights by decomposing each interaction into energy components such as dispersion, electrostatics, and exchange. Notably, this analysis requires only a single interaction energy computation per structure on a suitable cluster model. As a case study, two polymorphs of each of the following are considered: naphthyl-substituted dipnictanes (with As, Sb, and Bi as the pnictogen atom) and tris(thiophen-2-yl)bismuthane. The approach outlined offers high accuracy as well as valuable insights for developing design principles to engineer crystal structures with tailored properties, opening up new avenues in the study of molecular aggregates, potentially impacting diverse fields in materials science and beyond.

Role of explicit hydrogen bonding in solvation calculation on the photophysics of 2-(2′-Hydroxyphenyl)oxazolo[4,5-b]pyridine

The photophysics of 2-(2′-hydroxyphenyl)oxazolo[4,5-b]pyridine (HPOP) was theoretically examined by employing the integral equation formalism variant of polarizable continuum model (PCM) at the level of density functional theory with M06 functional. Polar protic methanol and water and aprotic acetonitrile and tetrahydrofuran, which have varied dielectric constants, were considered to study the role of polarity on the photophysics of HPOP and was compared with the results obtained in vacuum. Six different structural forms of HPOP were observed: cis and trans-closed enol, cis and trans-open enol, and cis and trans-keto. cis-closed enol is the most stable and trans-keto the least in the ground state. In the S1 state, cis-keto is the most stable and cis-open enol the most unstable. The relative stabilities of the different structures increase with the polarity of the solvent. The calculations were extended to vacuum and methanol environments by adding two methanol molecules, and similarly done with two water molecules in vacuum and water environments which are explicitly hydrogen bonded to HPOP at different hydrogen bonding centres of HPOP to study the role of solute–solvent hydrogen bond on its photophysics and the changes in results obtained under the PCM formalism. The hydrogen bond between the solute and solvent molecules further increases the relative stabilities of the different hydrogen bonded clusters. The calculations show that the intramolecular proton transfer (IPT) between cis-closed enol and cis-keto is a barrierless process with the transition state displaying a submerged barrier both in S0 and S1 states where the IPT occurs within a single OH stretching vibration. The IPT trajectory is shorter in the S1 state.

Interdecadal changes in ichthyofauna in a tropical bay with high anthropogenic influences: functional stability despite turnover predominance.

Functional characteristics of species are of great importance for understanding their roles in ecosystems and can be used to detect long-term chances in the environment. We evaluated temporal changes (1983-1985 and 2017-2019) in taxonomic and functional indices of the fish fauna in shallow areas of a tropical bay heavily impacted by anthropogenic activities in recent decades. The hypothesis that functional indices change over time as a result of environmental degradation was tested. Our results showed a significant decrease in species richness and abundance over time, and in functional richness, while others functional diversity indices (divergency, evenness, and originality) remained stable. Thirteen functional groups were detected, some of which contained only one species, raising concerns about the loss of ecosystem functions due to ongoing changes. We also observed an increase in beta diversity over time, which may be the result of a decrease in local richness without leading to regional extinctions. Turnover was the most important process in structuring the fish fauna at the evaluated time scale. The relative stability of the functional structure and the higher levels of turnover seem to be related to the dominance of functional groups, within which species replace each other according to their responses to environmental filters that select for specific functional traits. Incorporating functional diversity indices and beta diversity variations in the fish community helped to enhance the existing information about this coastal system by offering improved estimates of biological diversity through diverse approaches. The predominance of turnover identified in the preset study suggests a dynamic and fluctuating species composition within the habitat. In this sense, habitat preservation should prioritize the protection of diverse habitats to accommodate a broad spectrum of species.

Ab initio calculations of structural stability, thermodynamic and elastic properties of Ni, Pd, Rh, and Ir at high pressures

This paper presents results of a comprehensive study from first principles into the properties of Ni, Pd, Rh, and Ir crystals under pressure. We calculated elastic constants, phonon spectra, isotherms, Hugoniots, sound velocities, relative structural stability, and phase diagrams. It is shown that in nickel and palladium under high pressures (>0.14 TPa) and temperatures (>4 kK), the body-centered cubic structure is thermodynamically most stable than of the face-centered cubic one. Calculated results suggest that nickel under Earth-core conditions (P∼0.3 TPa, T∼6 kK) have a bcc structure. No structural changes were found to occur in Rh and Ir under pressures to 1 TPa at least. This paper also provides estimations for the pressure and temperature at which the metals of interest begin to melt under shock compression.

Computational exploration of Cu(II)-en chelate-catalyzed hydrolysis of O-isopropyl methylphosphonofluoridate

In contrast to un-catalyzed hydrolysis of organophosphorus (OP) compounds, metal ions or/and their complexes with chelating ligands show catalytic effects in several ways depending upon the nature of the metal, ligand, substrate, and medium. It is known that Cu(II)-en chelate containing copper complexes accelerate the hydrolysis of OP compounds. However, the mechanism for this rate enhancement in the Cu(II)-en chelate catalytic hydrolysis reaction of sarin remains unexplored. We have examined possible mechanisms involving a Cu(II)-en with hydroxide nucleophile for the reaction pathway of the hydrolysis of O-isopropyl methylphosphonofluoridate (sarin) computationally. The density functional (B3LYP) employed in this study has reproduced the experimental Gibb’s free energy of activation value 15.5 kcal/mol for alkaline hydrolysis of sarin. Earlier proposal of push–pull mechanism for metal ion chelate-catalyzed hydrolysis of OP compounds has been found to be unfavorable in the present study. The role of water molecules in catalyzing the hydrolysis of sarin with Cu(II)-en chelate is crucial. The catalytic process involving Cu(II)-en chelate with one water molecule is the more plausible pathway to achieve the hydrolysis of sarin with Cu(II)-en chelate complexes. The most popular B3LYP method was used for optimization of given geometries. Except LANL2DZ for Cu atom, all the atoms are described using the 6–31 + G(d) basis set. The stability test has been performed for the wave functions as we are dealing with the open-shell molecules in order to ensure stable electronic configuration form, and the stable wavefunction is used as the initial configuration for the subsequent optimization. Harmonic frequency calculations and thermodynamic corrections were performed at the same level of theory. PCM method has been used for solvation effects. In order to ensure that each saddle point is linked to a minimum, IRC calculations were performed in forward and reverse directions to ensure the eigenvectors associated with the unique negative eigenvalues of the Hessian matrix. All energies discussed are solvated Gibbs free energies corrected to 298.15 K for the relative stability of the chemical structure. All calculations were performed using the Gaussian 09 code.

Entropic stabilization and descriptors of structural transformation in high entropy alloys

With first-principles theoretical analysis of the local structure using Bond-Orientational Order parameters and Voronoi partitioning, we establish (a) HCP→BCC structural transformation in high-entropy alloys (HEAs) Nbx(HfZrTi)y at 16% Nb-concentration, and (b) that the internal lattice distortions (ILDs) peak at the transition. We demonstrate that the relative stability of HCP and BCC structures is driven by energetics, while the overall stability is achieved with contribution from the vibrational entropy that exceeds the configurational entropy of mixing. We show that along with atomic size mismatch, low average number (<5) of valence electrons and disparity in the crystal structures of constituent elements are responsible for larger ILDs in Nbx(HfZrTi)y than in HEAs like NbaMobWcTad.

First principles investigation of voltage, structure, ionic and electronic conduction of olivine and maricite NaMnPO4

Mn2+/Mn3+ redox couple is expected to provide high operating voltage, but the Mn-based orthophosphate is difficult to achieve stable and reversible (de)intercalation of alkali-metal ions. Using first principles calculations, we investigated the structure, voltage, ionic and electronic transport properties of olivine and maricite NaMnPO4, trying to unveil the factors affecting the electrochemical performance. Our calculations show that the energetically favored structure transforms from the electrochemically active olivine to the inactive maricite with the decrease of sodium. This is likely to cause Mn to occupy Na site, blocking the diffusion channel along b axis. Lattice strain was found to have significantly influence on the relative structural stability. Both compressive and tensile ac biaxial strains induce the olivine MnPO4 to be in an energetically stable state. The enhanced structural stability of desodiated phase may prevent the irreversible structural transformation, contributing to the stable and reversible (de)intercalation of sodium ions.

Single point mutations at the S129 residue of α-synuclein and their effect on structure, aggregation, and neurotoxicity.

Parkinson's disease is an age-related neurological disorder, and the pathology of the disease is linked to different types of aggregates of α-synuclein or alpha-synuclein (aS), which is an intrinsically disordered protein. The C-terminal domain (residues 96-140) of the protein is highly fluctuating and possesses random/disordered coil conformation. Thus, the region plays a significant role in the protein's solubility and stability by an interaction with other parts of the protein. In the current investigation, we examined the structure and aggregation behavior of two artificial single point mutations at a C-terminal residue at position 129 that represent a serine residue in the wild-type human aS (wt aS). Circular Dichroism (CD) and Raman spectroscopy were performed to analyse the secondary structure of the mutated proteins and compare it to the wt aS. Thioflavin T assay and atomic force microscopy imaging helped in understanding the aggregation kinetics and type of aggregates formed. Finally, the cytotoxicity assay gave an idea about the toxicity of the aggregates formed at different stages of incubation due to mutations. Compared to wt aS, the mutants S129A and S129W imparted structural stability and showed enhanced propensity toward the α-helical secondary structure. CD analysis showed proclivity of the mutant proteins toward α-helical conformation. The enhancement of α-helical propensity lengthened the lag phase of fibril formation. The growth rate of β-sheet-rich fibrillation was also reduced. Cytotoxicity tests on SH-SY5Y neuronal cell lines established that the S129A and S129W mutants and their aggregates were potentially less toxic than wt aS. The average survivability rate was ∼40% for cells treated with oligomers (presumably formed after 24h of incubation of the freshly prepared monomeric protein solution) produced from wt aS and ∼80% for cells treated with oligomers obtained from mutant proteins. The relative structural stability with α-helical propensity of the mutants could be a plausible reason for their slow rate of oligomerization and fibrillation, and this was also the possible reason for reduced toxicity to neuronal cells.

Dissipative Systems: Relative Roughness, Nonroughness of Various Degrees, and Integrability

This paper is devoted to the study of the relative structural stability (the relative roughness) of dynamical systems considered not on the whole space of dynamical systems, but only on a certain subspace of it. Moreover, the space of deformations of dynamical systems also does not coincide with the whole space of admissible deformations. In particular, we consider dissipative systems of differential equations that arise in the rigid-body dynamics and the theory of oscillations; dissipation in such systems may by positive or negative. We examine the relative roughness of such systems and, under certain conditions, their relative nonroughness of various degrees. We also discuss problems of integrability of these systems in finite combinations of elementary functions.

Implementation of a Core-Shell Design Approach for Constructing MOFs for CO2 Capture.

Adsorption-based capture of CO2 from flue gas and from air requires materials that have a high affinity for CO2 and can resist water molecules that competitively bind to adsorption sites. Here, we present a core-shell metal-organic framework (MOF) design strategy where the core MOF is designed to selectively adsorb CO2, and the shell MOF is designed to block H2O diffusion into the core. To implement and test this strategy, we used the zirconium (Zr)-based UiO MOF platform because of its relative structural rigidity and chemical stability. Previously reported computational screening results were used to select optimal core and shell MOF compositions from a basis set of possible building blocks, and the target core-shell MOFs were prepared. Their compositions and structures were characterized using scanning electron microscopy, transmission electron microscopy, and powder X-ray diffraction. Multigas (CO2, N2, and H2O) sorption data were collected both for the core-shell MOFs and for the core and shell MOFs individually. These data were compared to determine whether the core-shell MOF architecture improved the CO2 capture performance under humid conditions. The combination of experimental and computational results demonstrated that adding a shell layer with high CO2/H2O diffusion selectivity can significantly reduce the effect of water on CO2 uptake.

In silico investigation of the structural stability as the origin of the pathogenicity of α-synuclein protofibrils

α-Synuclein is a presynaptic neuronal protein. The fibril form of α-synuclein is a major constituent of the intraneuronal inclusion called Lewy body, a characteristic hallmark of Parkinson’s disease. Recent ssNMR and cryo-EM experiments of wild-type α-synuclein fibrils have shown polymorphism and observed two major polymorphs, rod and twister. To associate the cytotoxicity of α-synuclein fibrils with their structural features, it is essential to understand the origins of their structural stability. In this study, we performed molecular dynamics simulations of the two major polymorphs of wild-type α-synuclein fibrils. The predominance of specific fibril polymorphs was rationalized in terms of relative structural stability in aqueous environments, which was attributed to the cooperative contributions of various stabilizing features. The results of the simulations indicated that highly stable structures in aqueous environments could be maintained by the cooperation of compact sidechain packing in the hydrophobic core, backbone geometry of the maximal β-sheet content wrapping the hydrophobic core, and solvent-exposed sidechains with large fluctuations maximizing the solvation entropy. The paired structure of the two protofilaments provides additional stability, especially at the interface region, by forming steric zipper interactions and hiding the hydrophobic residues from exposure to water. The sidechain interaction analyses and pulling simulations showed that the rod polymorph has stronger sidechain interactions and exhibits higher dissociation energy than the twister polymorph. It is expected that our study will provide a basis for understanding the pathogenic behaviors of diverse amyloid strains in terms of their structural properties.Communicated by Ramaswamy H. Sarma

Optimizing the structure of acene clusters.

We present a study of the potential energy surface of anthracene, tetracene, and pentacene clusters with up to 30 molecules. We have applied the basin-hopping Monte Carlo algorithm to clusters of acene molecules in order to find their lowest energy states. The acene molecules are described by the polymer-consistent force field-interface force field. We present the structures with the lowest observed energy, and we discuss the relative stability and accessibility of structures corresponding to local energy minima.

Three-dimensional S-scheme heterojunction by integration of purple tungsten oxide nanowires and cadmium sulfide nanospheres for effective photocatalytic hydrogen generation

The practical photocatalytic application of cadmium sulfide (CdS) has been significantly constrained by fast carrier recombination and significant photocorrosion. Therefore, we developed a three-dimensional (3D) step-by-step (S-scheme) heterojunction using the coupling interface between purple tungsten oxide (W18O49) nanowires and CdS nanospheres. The photocatalytic hydrogen evolution rate of optimized W18O49/CdS 3D S-scheme heterojunction can reach 9.7 mmol·h−1·g−1, 7.5 and 16.2 times greater than pure CdS (1.3 mmol·h−1·g−1) and 10 wt%-W18O49/CdS (mechanical mixing, 0.6 mmol·h−1·g−1), proving that the tight S-scheme heterojunction constructed by the hydrothermal method can efficiently enhance the carrier separation. Notably, the apparent quantum efficiency (AQE) of W18O49/CdS 3D S-scheme heterojunction approaches 7.5% and 3.5% at 370 nm and 456 nm, respectively, which is 7.5 and 8.8 times than pure CdS (1.0% and 0.4%). The produced W18O49/CdS catalyst also has relative stability of structure and hydrogen production. Additionally, the H2 evolution rate of W18O49/CdS 3D S-scheme heterojunction is 1.2 times greater than 1 wt%-platinum (Pt)/CdS (8.2 mmol·h−1·g−1), which indicates that the W18O49 can effectively replace the precious metal for boosting the hydrogen production rate.

Conformational preferences of aza-proline residues and their impact on the relative stability of polyproline structures

The collagen model peptide Ac-(Hyp-Gly-Pro)2-NMe2 with the replacement of Pro3 by azPro in the middle of the sequence well adopted polyproline II structures with RMSD = 0.6 Å in water.

Extending interstitial tetrelides into carbides: synthesis and crystal and electronic structures- of RE2Co2AlC (RE = La, Pr, Nd).

New quaternary compounds RE2Co2AlC (RE = La, Pr, Nd) of the filled W2CoB2 structure type were synthesized by the reaction of samples with the nominal composition RE40Co40Al20 (RE = La, Pr, Nd) and carbon. Single crystal X-ray diffraction data show that the RE2Co2AlC compounds crystallize in a body-centered orthorhombic space group Immm (oI12) with Z = 2 and a = 4.1841(11) Å, b = 6.1161(15) Å, c = 9.091(2) Å (La2Co2AlC); a = 4.1290(9) Å, b = 6.1152(18) Å, c = 8.844(3) Å (Pr2Co2AlC); a = 4.1168(15) Å, b = 6.1131(17) Å, c = 8.792(5) Å (Nd2Co2AlC) and are isotypic to the recently reported Nd2Co2SiC. The structures can be described as interstitial carbides of the W2CoB2 structure type with carbon atoms fully occupying the octahedral voids, which leads to the anisotropic expansion of the unit cell, more pronounced along the b-axis. Electronic structure calculations predict the RE2Co2AlC (RE = La, Pr, Nd) compounds to be metallic. The relative stability of the La2Co2AlX structures where X = C, O, Si, or a vacancy was investigated based on the bonding analysis, which emphasizes the important role that carbon plays in stabilizing the structural motif.

Fabrication of Fe-doped lithium-aluminum-layered hydroxide chloride with enhanced reusable stability inspired by computational theory and its application in lithium extraction

Lithium-aluminum-layered double hydroxide chloride (Li-Al-Cl LDH) is one of the most promising adsorbents for lithium extraction from low-grade salt lake brine, but achieving its high reusable stability with high adsorption performance is still a huge challenge. Here, a novel strategy combining simulation with a “one-pot” reaction was proposed to prepare Fe-doped lithium-aluminum-layered double hydroxide chloride (Li-Al-Fe-Cl LDH). More specifically, the geometric parameters and binding energy of aluminum-based adsorbent clusters have been investigated to predict the relative structural stability of adsorbents by density functional theory (DFT). The simulation results showed that Fe-doping increases the binding energy of the host layers, thus enhancing the structural stability of the adsorbent. Inspired by the computational theory result, Li-Al-Fe-Cl LDH was synthesized by a facile “one-pot” reaction method with excellent reusable stability and adsorption performance. The Li-Al-Fe-Cl LDH was characterized by XRD, FTIR, SEM, EDS, BET-BJH, and pHZPC. The Li+ adsorption capacity of Li-Al-Fe-Cl LDH was up to 11.3 mg/g, about 13% higher than Li-Al-Cl LDH. After 30 cycles, the decrease in lithium adsorption capacity of Li-Al-Fe-Cl LDH was 2.5%, far lower than 28.5% of Li-Al-Cl LDH. The Li-Al-Fe-Cl LDH had an excellent adsorption selectivity to Li+ with the ion-selective sequence of Li+>>Mg2+> Na+>K+>Ca2+, and the separation factor between Li+ and Mg2+ reached up to 35.83. The pseudo-second-order and the Langmuir model adequately described the adsorption kinetics and isotherms of Li-Al-Fe-Cl LDH for Li+ adsorption, respectively. The thermodynamic study proved that the Li+ adsorption of Li-Al-Fe-Cl LDH was an endothermic process. Moreover, the adsorption selectivity mechanism of Li-Al-Fe-Cl LDH is the interfacial effects of limited geometric pores and the dehydration of hydrated ions.