Relative Structural Stability Research Articles

Machine-Learned Fragment-Based Energies for Crystal Structure Prediction.

Crystal structure prediction involves a search of a complex configurational space for local minima corresponding to stable crystal structures, which can be performed efficiently using atom-atom force fields for the assessment of intermolecular interactions. However, for challenging systems, the limitations in the accuracy of force fields prevent a reliable assessment of the relative thermodynamic stability of potential structures, while the cost of fully quantum mechanical approaches can limit applications of the methods. We present a method to rapidly improve force field lattice energies by correcting two-body interactions with a higher level of theory in a fragment-based approach and predicting these corrections with machine learning. Corrected lattice energies with commonly used density functionals and second order perturbation theory (MP2) all significantly improve the ranking of experimentally known polymorphs where the rigid molecule model is applicable. The relative lattice energies of known polymorphs are also found to systematically improve with the fragment corrections. Predicting two-body interactions with atom-centered symmetry functions in a Gaussian process is found to give highly accurate results using as little as 10-20% of the data for training, reducing the cost of the energy correction by up to an order of magnitude. The machine learning approach opens up the possibility of more widespread use of fragment-based methods in crystal structure prediction, whose increased accuracy at a low computational cost will benefit applications in areas such as polymorph screening and computer-guided materials discovery.

The diagnostic value of circulating microRNAs in heart failure.

Heart failure (HF) is a complex clinical syndrome, characterized by inadequate blood perfusion of tissues and organs caused by decreased heart ejection capacity resulting from structural or functional cardiac disorders. HF is the most severe heart condition and it severely compromises human health; thus, its early diagnosis and effective management are crucial. However, given the lack of satisfactory sensitivity and specificity of the currently available biomarkers, the majority of patients with HF are not diagnosed early and do not receive timely treatment. A number of studies have demonstrated that peripheral blood circulating nucleic acids [such as microRNAs (miRs), mRNA and DNA] are important for the diagnosis and monitoring of treatment response in HF. miRs have been attracting increasing attention as promising biomarkers, given their presence in body fluids and relative structural stability under diverse conditions of sampling. The aim of the present review was to analyze the associations between the mechanisms underlying the development of HF and the expression of miRs, and discuss the value of using circulating miRs as diagnostic biomarkers in HF management. In particular, miR-155, miR-22 and miR-133 appear to be promising for the diagnosis, prognosis and management of HF patients.

First-Principles Study of the Structural Stability and Dynamic Properties of Li2MSiO4 (M = Mn, Co, Ni) Polymorphs

In recent years, the scientific community has shown an increasing interest in regards to the investigation of novel materials for the intercalation of lithium atoms, suitable for application as cathodes in the new generations of Li-ion batteries. Within this framework, we have computed the relative structural stability, the electronic structure, the elastic and dynamic properties of Li2MSiO4 compounds (M = Mn, Co, Ni) by means of first-principles calculations based on density functional theory. The so-obtained structural parameters of the examined phases are in agreement with previous reports. The energy differences between different polymorphs are found to be small, and most of these structures are dynamically stable. The band structures and density of states are computed to analyse the electronic properties and characterise the chemical bonding. The single crystal elastic constants are calculated for all the examined modifications, proving their mechanical stability. These Li2MSiO4 materials are found to present a ductile behaviour upon deformation. The diffusion coefficients of Li ions, calculated at room temperature for all the examined modifications, reveal a poor conductivity for this class of materials.

Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations.

A method for evaluating binding free energy differences of protein-protein complex structures generated by protein docking was recently developed by some of us. The method, termed evERdock, combined short (2 ns) molecular dynamics (MD) simulations in explicit water and solution theory in the energy representation (ER) and succeeded in selecting the near-native complex structures from a set of decoys. In the current work, we performed longer (up to 100 ns) MD simulations before employing ER analysis in order to further refine the structures of the decoy set with improved binding free energies. Moreover, we estimated the binding free energies for each complex structure based on an average value from five individual MD snapshots. After MD simulations, all decoys exhibit a decrease in binding free energy, suggesting that proper equilibration in explicit solvent resulted in more favourably bound complexes. During the MD simulations, non-native structures tend to become unstable and in some cases dissociate, while near-native structures maintain a stable interface. The energies after the MD simulations show an improved correlation between similarity criteria (such as interface root-mean-square distance) to the native (crystal) structure and the binding free energy. In addition, calculated binding free energies show sensitivity to the number of contacts, which was demonstrated to reflect the relative stability of structures at earlier stages of the MD simulation. We therefore conclude that the additional equilibration step along with the use of multiple conformations can make the evERdock scheme more versatile under low computational cost.

Computational investigation of inverse Heusler compounds for spintronics applications

First-principles calculations of the electronic structure, magnetism and structural stability of inverse-Heusler compounds with the chemical formula \textit{X$_2$YZ} are presented and discussed with a goal of identifying compounds of interest for spintronics. Compounds for which the number of electrons per atom for \textit{Y} exceed that for \textit{X} and for which \textit{X} is one of Sc, Ti, V, Cr, Mn, Fe, Co, Ni, or Cu; \textit{Y} is one of Ti, V, Cr, Mn, Fe, Co, Ni, Cu, or Zn; and \textit{Z} is one of Al, Ga, In, Si, Ge, Sn, P, As or Sb were considered. The formation energy per atom of each compound was calculated. By comparing our calculated formation energies to those calculated for phases in the Inorganic Crystal Structure Database (ICSD) of observed phases, we estimate that inverse-Heuslers with formation energies within 0.052 eV/atom of the calculated convex hull are reasonably likely to be synthesizable in equilibrium. The observed trends in the formation energy and relative structural stability as the \textit{X}, \textit{Y} and \textit{Z} elements vary are described. In addition to the Slater-Pauling gap after 12 states per formula unit in one of the spin channels, inverse-Heusler phases often have gaps after 9 states or 14 states. We describe the origin and occurrence of these gaps. We identify 14 inverse-Heusler semiconductors, 51 half-metals and 50 near half-metals with negative formation energy. In addition, our calculations predict 4 half-metals and 6 near half-metals to lie close to the respective convex hull of stable phases, and thus may be experimentally realized under suitable synthesis conditions, resulting in potential candidates for future spintronics applications.

Control and prediction of the organic solid state: a challenge to theory and experiment†.

The ability of theoretical chemists to quantitatively model the weak forces between organic molecules is being exploited to predict their crystal structures and estimate their physical properties. Evolving crystal structure prediction methods are increasingly being used to aid the design of organic functional materials and provide information about thermodynamically plausible polymorphs of speciality organic materials to aid, for example, pharmaceutical development. However, the increasingly sophisticated experimental studies for detecting the range of organic solid-state behaviours provide many challenges for improving quantitative theories that form the basis for the computer modelling. It is challenging to calculate the relative thermodynamic stability of different organic crystal structures, let alone understand the kinetic effects that determine which polymorphs can be observed and are practically important. However, collaborations between experiment and theory are reaching the stage of devising experiments to target the first crystallization of new polymorphs or create novel organic molecular materials.

One-Dimensional Arsenic Allotropes: Polymerization of Yellow Arsenic Inside Single-Wall Carbon Nanotubes.

The pnictogen nanomaterials, including phosphorene and arsenene, display remarkable electronic and chemical properties. Yet, the structural diversity of these main group elements is still poorly explored. Here we fill single-wall carbon nanotubes with elemental arsenic from the vapor phase. Using electron microscopy, we find chains of highly reactive As4 molecules as well as two new one-dimensional allotropes of arsenic: a single-stranded zig-zag chain and a double-stranded zig-zag ladder. These linear structures are important intermediates between the gas-phase clusters of arsenic and the extended sheets of arsenene. Raman spectroscopy indicates weak electronic interaction between the arsenic and the nanotubes which implies that the formation of the new allotropes is driven primarily by the geometry of the confinement. The relative stabilities of the new arsenic structures are estimated computationally. Band-gap calculations predict that the insulating As4 chains become semiconducting, once converted to the zig-zag ladder, and form a fully metallic allotrope of arsenic as the zig-zag chain.

One‐Dimensional Arsenic Allotropes: Polymerization of Yellow Arsenic Inside Single‐Wall Carbon Nanotubes

AbstractThe pnictogen nanomaterials, including phosphorene and arsenene, display remarkable electronic and chemical properties. Yet, the structural diversity of these main group elements is still poorly explored. Here we fill single‐wall carbon nanotubes with elemental arsenic from the vapor phase. Using electron microscopy, we find chains of highly reactive As4 molecules as well as two new one‐dimensional allotropes of arsenic: a single‐stranded zig‐zag chain and a double‐stranded zig‐zag ladder. These linear structures are important intermediates between the gas‐phase clusters of arsenic and the extended sheets of arsenene. Raman spectroscopy indicates weak electronic interaction between the arsenic and the nanotubes which implies that the formation of the new allotropes is driven primarily by the geometry of the confinement. The relative stabilities of the new arsenic structures are estimated computationally. Band‐gap calculations predict that the insulating As4 chains become semiconducting, once converted to the zig‐zag ladder, and form a fully metallic allotrope of arsenic as the zig‐zag chain.

Revealing carbocations in highly asynchronous concerted reactions: The ene-type reaction between dithiocarboxylic acids and alkenes

The ene-type reaction between (dithio)carboxylic acids and alkenes has been studied computationally by DFT and topological (analysis of the electron localization function, ELF) methods. The reaction proceeds under kinetic control and the observed differences in regioselectivity are well-explained by the relative stability of the different transition structures. In agreement with experimental observations, electron-rich alkenes lead to Markownikoff adducts while electron-poor alkenes lead to Michael adducts. In all cases the reaction proceeds through an only transition structure (one kinetic step) although a different synchronicity was observed depending on the alkene electronics. The ELF analysis of the reactions corroborates the existence of a transient carbocation (hidden intermediate) in the reactions with electron-rich alkenes. On the other hand, electron-poor alkenes proceed through a more synchronous concerted mechanism. It can be predicted that with electron-rich alkenes bearing highly donating the transient carbocations might be captured by a nucleophile.

Effect of spin-orbit interactions on the structural stability, thermodynamic properties, and transport properties of lead under pressure

The paper investigates the role of spin-orbit interaction in the prediction of structural stability, lattice dynamics, elasticity, thermodynamic and transport properties (electrical resistivity and thermal conductivity) of lead under pressure with the FP-LMTO (full-potential linear-muffin-tin orbital) method for the first-principles band structure calculations. Our calculations were carried out for three polymorphous lead modifications (fcc, hcp, and bcc) in generalized gradient approximation with the exchange-correlation functional PBEsol. They suggest that compared to the scalar-relativistic calculation, the account for the SO effects insignificantly influences the compressibility of Pb. At the same time, in the calculation of phonon spectra and transport properties, the role of SO interaction is important, at least, for $P\ensuremath{\lesssim}150$ GPa. At higher pressures, the contribution from SO interaction reduces but not vanishes. As for the relative structural stability, our studies show that SO effects influence weakly the pressure of the $\mathrm{fcc}\ensuremath{\rightarrow}\mathrm{hcp}$ transition and much higher the pressure of the $\mathrm{hcp}\ensuremath{\rightarrow}\mathrm{bcc}$ transition.

Rocksalt or cesium chloride: Investigating the relative stability of the cesium halide structures with random phase approximation based methods

The ground state structural and energetic properties for rocksalt and cesium chloride phases of the cesium halides were explored using the random phase approximation (RPA) and beyond-RPA methods to benchmark the nonempirical SCAN meta-GGA and its empirical dispersion corrections. The importance of nonadditivity and higher-order multipole moments of dispersion in these systems is discussed. RPA generally predicts the equilibrium volume for these halides within 2.4% of the experimental value, while beyond-RPA methods utilizing the renormalized adiabatic LDA (rALDA) exchange-correlation kernel are typically within 1.8%. The zero-point vibrational energy is small and shows that the stability of these halides is purely due to electronic correlation effects. The rAPBE kernel as a correction to RPA overestimates the equilibrium volume and could not predict the correct phase ordering in the case of cesium chloride, while the rALDA kernel consistently predicted results in agreement with the experiment for all of the halides. However, due to its reasonable accuracy with lower computational cost, SCAN+rVV10 proved to be a good alternative to the RPA-like methods for describing the properties of these ionic solids.

Investigation of the Water Adsorption Properties and Structural Stability of MIL-100(Fe) with Different Anions.

Investigating metal-organic frameworks (MOFs) as water adsorbents has drawn increasing attention for their potential in energy-related applications such as water production and heat transformation. A specific MOF, MIL-100(Fe), is of particular interest for its large adsorption capacity with the occurrence of water condensation at a relatively low partial pressure. In the synthesis of MIL-100(Fe), depending on the reactants, structures with varying anion terminals (e.g., F-, Cl-, or OH-) on the metal trimer have been reported. In this study, we employed molecular simulations and density functional theory calculations for investigating the water adsorption behaviors and the relative structural stability of MIL-100(Fe) with different anions. We also proposed a possible defective structure and explored its water adsorption properties. The results of this study are in good agreement with the experimental measurements and are in support of the observations reported in the literature. Understanding the spatial configurations and energetics of water molecules in these materials has also shed light on their adsorption mechanism at the atomic level.

Non-canonical DNA structures: Comparative quantum mechanical study

A study of relative thermodynamic stability of non-canonical DNA structures (triplexes, G-quadruplexes, i-motifs) for the first time was conducted on the basis of quantum chemical DFT/B3LYP/6-31++G (d) calculations. Results of the calculations completely reproduce the experimental data on stability of G-quadruplexes comparatively Watson-Crick B-DNA. It was discovered that combinations of non-canonical DNA structures were energetically more favorable than separated nitrogenous bases. Supramolecular complexes of the non-canonical DNA structures (NSs) can be considered as a biological drug targets in gene regulation (for example in tumor therapy), in contrast to previous works, where NSs were studied independently.

First principles study of the structural phase stability and magnetic order in various structural phases of Mn2FeGa

We investigate the structural and magnetic properties of Mn2FeGa for different phases (cubic, hexagonal and tetragonal) reported experimentally using density functional theory. The relative structural stabilities, and the possible phase transformation mechanisms are discussed using results for total energy, electronic structure and elastic constants. We find that the phase transformation form hexagonal to ground state tetragonal structure would take place through a Heusler-like phase which has a pronounced electronic instability. The electronic structures, the elastic constants and the supplementary phonon dispersions indicate that the transition from the Heusler-like to the tetragonal phase is of pure Jahn-Teller origin. We also describe the ground state magnetic structures in each phase by computations of the exchange interactions. For Heusler-like and tetragonal phases, the ferromagnetic exchange interactions associated with the Fe atoms balance the dominating antiferromagnetic interactions between the Mn atoms leading to collinear magnetic structures. In the hexagonal phase, the directions of atomic moments are completely in the planes with a collinear like structure, in stark contrast to the well known non-collinear magnetic structure in the hexagonal phase of Mn3Ga, another material with similar structural properties. The overwhelmingly large exchange interactions of Fe with other magnetic atoms destroy the possibility of magnetic frustration in the hexagonal phase of Mn2FeGa. This comprehensive study provides significant insights into the microscopic physics associated with the structural and magnetic orders in this compound.

Effect of Fe and Co substitution on the martensitic stability and the elastic, electronic, and magnetic properties ofMn2NiGa: Insights fromab initiocalculations

We investigate the effects of Fe and Co substitutions on the phase stability of the martensitic phase, mechanical, electronic and magnetic properties of magnetic shape memory system Mn$_{2}$NiGa by first-principles Density functional theory(DFT) calculations. The evolution of these aspects upon substitution of Fe and Co at different crystallographic sites are investigated by computing the electronic structure, mechanical properties and magnetic exchange parameters. We find that the martensitic phase of Mn$_{2}$NiGa gradually de-stabilises with increase in concentration of Fe/Co due to the weakening of the minority spin hybridisation of Ni and Mn atoms occupying crystallographically equivalent sites. The interplay between relative structural stability and the compositional changes are understood from the variations in the elastic modulii and electronic structures. We find that the elastic shear modulus C$^{\prime}$ can be considered as a predictor of composition dependence of martensitic transformation temperature in substituted Mn$_{2}$NiGa. The magnetic properties of Mn$_{2}$NiGa are found to be greatly improved by the substitutions due to stronger ferromagnetic interactions in the compounds. The gradually weaker(stronger) Jahn-Teller distortion (covalent bonding) in the minority spin densities of states due to substitutions lead to a half-metallic like gap in these compounds resulting in materials with high spin-polarisation when the substitutions are complete. The substitutions at the Ga site result in two new compounds Mn$_{2}$NiFe and Mn$_{2}$NiCo with very high magnetic moments and Curie temperatures. Thus, our work indicates that although the substitutions de-stabilise the martensitic phase in Mn$_{2}$NiGa, new magnetic materials with very good magnetic parameters and potentially useful for novel magnetic applications can be obtained.

Clarifying Anionic Redox Chemistry in LiCoO2 By Direct Detection of O-O Bond Length and First-Principle Investigations

Developing high energy density lithium ion battery cathode materials requires exploring novel chemistries that go beyond the conventional redox couple which is solely based on transition metal. Anionic redox reaction that activates lattice oxygen anions during charging and discharging can almost double the capacity of conventional cathode and thereby significantly increases the energy density. The nature of chemical bonding, in particular whether or not oxygen anions can bond in forming dimers or peroxo-like species, is critical to the reversibility of anionic redox couple and consequent cyclability of the material. Unfortunately, because oxygen scatters X-ray weakly and dimers may form locally rather than globally, it is very challenging to characterize the oxygen-oxygen bond unambiguously using conventional structural study tools like XRD. Here it is shown that neutron pair distribution function (NPDF) analysis is an effective tool in probing the existence of oxygen dimers without limitation to long range order. This technique is applied to LiCoO2 which still attracts lots of attention due to its high packing density and potential high energy density (delivers around 220 mAh/g when charged to 4.6 V). Through combining experimental results with theoretical calculations, the nature of anionic redox reaction is unraveled and it is shown that the structure of LiCoO2 can be fairly robust against oxygen release, suggesting the relative stability of the bulk structure and the possibility of fulfilling its potential of high energy density. Acknowledgement The work done at Brookhaven National Laboratory were supported by the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Vehicle Technologies of the U.S. Department of Energy through the Advanced Battery Materials Research (BMR) Program, including Battery500 Consortium under contract DE-SC0012704. Research conducted at ORNL's Spallation Neutron Source was sponsored by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.

Modeling Durability of PGM-Free Active Site Structures at the Atomic Scale

The replacement of Pt group metal (PGM) electrocatalysts with earth-abundant PGM-free materials in polymer electrolyte fuel cell (PEFC) cathodes faces several technological hurdles, including the need for improved long-term durability. In PGM systems, catalyst durability is achieved by maintaining Pt catalyst surface area that is in electrical contact with the electrode (electrochemical surface area, ESA).1,2 This ESA can be probed directly by electrochemical methods. Loss of electrical contact (via carbon corrosion or Pt particle detachment) as well as Pt surface area loss (via Pt dissolution into ionomer, particle agglomeration, surface blocking, or Ostwald ripening) lead to a loss in oxygen reduction reaction (ORR) activity in aged PGM cathodes. State-of-the-art PGM-free catalysts are highly heterogeneous systems due to pyrolysis processing and contain a great diversity of atom-scale structures. As such, there is still much debate regarding the atomic scale structure of the ORR active site. It has been proposed that a number of sites in the materials are ORR active, with varying degrees of activity and durability, further complicating study. Unlike their PGM counterparts, PGM-free materials do not have an easily electrochemically probed property such as ESA that can be determined and correlated to measured activity loss. These complexities necessitate different approaches to identifying and predicting durability properties and degradation mechanisms in PGM-free systems. One proposed approach for understanding PGM-free catalyst durability3 is combining quantum chemical modeling with a TEM beam-damage model4 to identify how local atomic structure affects the kinetics of atom removal. Calculation of the knock-on displacement threshold energy (KODTE) could serve as a durability descriptor for a given atomic structure, similar to how thermodynamic limiting potential serves as a computationally-accessible activity descriptor of ORR active site structures. This descriptor would go beyond relative thermodynamic stability of active site structures and actively probe the kinetics of bond breaking in the system. As part of the DOE Electrocatalysis Consortium (ElectroCat), an automated workflow for calculating the KODTE for a given atomic scale structure using ab initio molecular dynamics has been developed and applied to a variety of possible PGM-free ORR active site structures as well as C-host materials. These methods have identified that N are most susceptible to removal and that edge-hosted structures are more susceptible than bulk-hosted structures. Utilized methodology, as well as identified trends from these calculations and comparisons to available experiments will be discussed.

DFT Studies of Ru-Catalyzed C–O versus C–H Bond Functionalization of Aryl Ethers with Organoboronates

Density functional theory calculations have been performed to investigate how different nucleophiles and directing groups affect the preference of C–H versus C–O bond functionalization in the ruthenium-catalyzed coupling reactions of aryl ethers with organoboronates. Our results indicate that the preference depends on the relative stability of the transition state structures for the C–O bond activation in the C–O bond functionalization pathway and the transmetalation with boronate to form a Ru–C bond in the C–H bond functionalization pathway. When the transition state structure for the transmetalation with boronate lies lower in energy than that for the C–O bond activation, C–H bond functionalization is preferred, and vice versa. How different nucleophiles and directing groups affect the relative stability of the transition structures has been discussed in detail.

Effect of Noncovalent Interactions on Vibronic Transitions: An Experimental and Theoretical Study of the C2H⋅⋅⋅CO2 Complex

We report on the experimental and theoretical infrared spectrum of the C2 H⋅⋅⋅CO2 complex. This complex was prepared by UV photolysis of propiolic acid (HC3 OOH) in argon and krypton matrices. The experimental bands of C2 H in the C2 H⋅⋅⋅CO2 complex are blue-shifted from those of the C2 H monomer. The calculations on the C2 H⋅⋅⋅CO2 structures were performed at the RMP2/aug-cc-pVTZ level. The relative stability of the complex structures was evaluated by using the RCCSD(T)/aug-cc-pVQZ level. To simulate the spectrum of the C2 H⋅⋅⋅CO2 complex, we developed the theoretical approach used earlier for the C2 H monomer. Based on the calculations, the main experimental bands of the C2 H⋅⋅⋅CO2 complex are assigned to the most stable parallel structure. Almost all the strong bands predicted by theory (with intensities >30 km mol-1 ) are observed in the experiment. To our knowledge, it is the first study of the effect of noncovalent interactions on vibronic transitions and the first report on an intermolecular complex of the C2 H radical.

Ab initio calculations of the elastic and thermodynamic properties of gold under pressure

The paper presents first-principles FP-LMTO calculations on the relative stability of fcc, bcc, hcp and dhcp gold under pressure. They were done in local density approximation (LDA), as well as in generalized gradient approximation (GGA) with and without spin–orbit interaction. Phonon spectra for the considered gold structures were obtained from LDA calculations within linear response theory and the contribution of lattice vibrations to the free energy of the system was determined in quasiharmonic approximation. Our thorough adjustment of FP-LMTO internal parameters (linearization and tail energies, the MT-sphere radius) helped us to obtain results that agree well with the available experimental phase relation Dubrovinsky et al (2007 Phys. Rev. Lett. 98 045503) between fcc and hcp structures of gold under pressure. The calculations suggest that gold compressed at room temperature successively undergoes the following structural changes: . The paper also presents the calculated elastic constants of fcc, bcc and hcp Au, the principal Hugoniot and the melting curve. Calculated results were used to construct the PT-diagram which describes the relative stability of the gold structures under study up to 500 GPa.