Integrating Data Mining and Natural Language Processing to Construct a Melting Point Database for Organometallic Compounds.

As semiconductor devices are miniaturized, the importance of atomic layer deposition (ALD) technology is growing. When designing ALD precursors, it is important to consider the melting point, because the precursors should have melting points lower than the process temperature. However, obtaining melting point data is challenging due to experimental sensitivity and high computational costs. As a result, a comprehensive and well-organized database for the melting point of the OMCs has not been fully reported yet. Therefore, in this study, we constructed a database of melting points for 1,845 OMCs, including 58 metal and 6 metalloid elements. The database contains CAS numbers, molecular formulas, and structural information and was constructed through automatic extraction and systematic curation. The melting point information was extracted using two methods: 1) 1,434 materials from 11 chemical vendor databases and 2) 411 materials identified through natural language processing (NLP) techniques with an accuracy of 86.3%, based on 2,096 scientific papers published over the past 29 years. In our database, the OMCs contain up to around 250 atoms and have melting points that range from -170 to 1610 °C. The main source is the Chemsrc database, accounting for 607 materials (32.9%), and Fe is the most common central metal or metalloid element (15.0%), followed by Si (11.6%) and B (6.7%). To validate the utilization of the constructed database, a multimodal neural network model was developed integrating graph-based and feature-based information as descriptors to predict the melting points of the OMCs but moderate performance. We believe the current approach reduces the time and cost associated with hand-operated data collection and processing, contributing to effective screening of potentially promising ALD precursors and providing crucial information for the advancement of the semiconductor industry.

Exploring the large chemical space in search of thermodynamically stable and mechanically robust MXenes via machine learning.

To effectively utilize MXenes, a family of two-dimensional materials, in various applications that include thermoelectric devices, semiconductors, and transistors, their thermodynamic and mechanical properties, which are closely related to their stability, must be understood. However, exploring the large chemical space of MXenes and verifying their stability using first-principles calculations are computationally expensive and inefficient. Therefore, this study proposes a machine learning (ML)-based high-throughput MXene screening framework to identify thermodynamically stable MXenes and determine their mechanical properties. A dataset of 23 857 MXenes with various compositions was used to validate this framework, and 48 MXenes were predicted to be stable by ML models in terms of heat of formation and energy above the convex hull. Among them, 45 MXenes were validated using density functional theory calculations, of which 23 MXenes, including Ti2CClBr and Zr2NCl2, have not been previously known for their stability, confirming the effectiveness of this framework. The in-plane stiffness, shear moduli, and Poisson's ratio of the 45 MXenes were observed to vary widely according to their constituent elements, ranging from 90.11 to 198.02 N m-1, 64.00 to 163.40 N m-1, and 0.19 to 0.58, respectively. MXenes with Group-4 transition metals and halogen surface terminations were shown to be both thermodynamically stable and mechanically robust, highlighting the importance of electronegativity difference between constituent elements. Structurally, a smaller volume per atom and minimum bond length were determined to be preferable for obtaining mechanically robust MXenes. The proposed framework, along with an analysis of these two properties of MXenes, demonstrates immense potential for expediting the discovery of stable and robust MXenes.

AmorProt: Amino Acid Molecular Fingerprints Repurposing-Based Protein Fingerprint.

As protein therapeutics play an important role in almost all medical fields, numerous studies have been conducted on proteins using artificial intelligence. Artificial intelligence has enabled data-driven predictions without the need for expensive experiments. Nevertheless, unlike the various molecular fingerprint algorithms that have been developed, protein fingerprint algorithms have rarely been studied. In this study, we proposed the amino acid molecular fingerprints repurposing-based protein (AmorProt) fingerprint, a protein sequence representation method that effectively uses the molecular fingerprints corresponding to 20 amino acids. Subsequently, the performances of the tree-based machine learning and artificial neural network models were compared using (1) amyloid classification and (2) isoelectric point regression. Finally, the applicability and advantages of the developed platform were demonstrated through a case study and the following experiments: (3) comparison of dataset dependence with feature-based methods, (4) feature importance analysis, and (5) protein space analysis. Consequently, the significantly improved model performance and data-set-independent versatility of the AmorProt fingerprint were verified. The results revealed that the current protein representation method can be applied to various fields related to proteins, such as predicting their fundamental properties or interaction with ligands.

MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder.

The ultimate goal of various fields is to directly generate molecules with desired properties, such as water-soluble molecules in drug development and molecules suitable for organic light-emitting diodes or photosensitizers in the field of development of new organic materials. This study proposes a molecular graph generative model based on an autoencoder for the de novo design. The performance of the molecular graph conditional variational autoencoder (MGCVAE) for generating molecules with specific desired properties was investigated by comparing it to a molecular graph variational autoencoder (MGVAE). Furthermore, multi-objective optimization for MGCVAE was applied to satisfy the two selected properties simultaneously. In this study, two physical properties, calculated logP and molar refractivity, were used as optimization targets for designing de novo molecules. Consequently, it was confirmed that among the generated molecules, 25.89% of the optimized molecules were generated in MGCVAE compared to 0.66% in MGVAE. This demonstrates that MGCVAE effectively produced drug-like molecules with two target properties. The results of this study suggest that these graph-based data-driven models are an effective method for designing new molecules that fulfill various physical properties.

Dual doping with cations and anions for enhancing the structural stability of the sodium-ion layered cathode.

First-principles-based calculations were implemented to explore the ideal combination of cations and anions as dual dopants for enhancing the structural stability of the sodium-ion layered cathode for application in sodium ion batteries (SIBs), leading to improved electrochemical properties. Cation-doped NaNi0.42Mn0.5D0.08O2 was chosen as the reference structure, where D represents twelve cation dopants (Ga, Ge, Hf, In, Pt, Rh, Ru, Sb, Te, Ti, Y, and Zr), which have been proven to have excellent performance. Fluoride was selected as the anion dopant to give the general formula NaNi0.42Mn0.5D0.08O1.96F0.04, leading to a total of twelve different combinations of cation and anion co-doped structures. The screening criteria include the formation energy, which was used to confirm the thermodynamically favored locations of the dopants; the phase stability; and the volume change accompanying the transformation from the O3- to P3-phase after 50% desodiation. The calculations show that Te-, Sb-, Hf-, Y-, and Ti-F are the five most effective dual dopants for potentially enhancing the structural stability of the sodium-ion layered oxide during cycling. The present study provides an essential design map for developing an ideal dual doping strategy for SIBs.

Optimal machine learning feature selection for assessing the mechanical properties of a zeolite framework.

In this study, 45 and 249 critical features were discovered among 896 zeolite descriptors generated by the matminer package for estimating the shear and bulk moduli of zeolites, respectively. A database containing the mechanical properties of 873 zeolite structures, calculated using density functional theory, was used to train the machine learning regression model. The results of using these critical features with the LightGBM algorithm were rigorously compared with those from other regressors as well as with different sets of features. The comparison results indicate that the surrogate model with critical features increases the prediction accuracy of the bulk and shear moduli of zeolites by 17.3% and 10.6%, respectively, and reduces the prediction uncertainty by one-third of that achieved using previously available features. The suggested features originating from several physical and chemical groups highlight the unveiled relationships between the features and mechanical properties of zeolites. The robustness of the constructed model with 356 features was confirmed by applying a set of different training-test set ratios. We believe that the suggested critical features of zeolites can help to understand the mechanical behavior of a half million unlabeled hypothetical zeolite structures and accelerate the discovery of novel zeolites with unprecedented mechanical properties.

Prediction of dielectric constants of ABO3-type perovskites using machine learning and first-principles calculations.

In this study, the machine-learning method, combined with density functional perturbation theory (DFPT) calculations, was implemented to predict and validate the dielectric constants of ABO3-type perovskites. For the construction of the training database, the dielectric constants of 7113 inorganic materials were extracted from the Materials Project. The chemical, structural, and physical descriptors were generated and trained using the gradient-boosting-based regressor after feature engineering. The prediction accuracies were 0.83 and 0.67 (R2) and 0.12 and 0.26 (root mean square error) for the electronic and ionic contributions to the dielectric constant, respectively. The constructed surrogate model was then employed to predict the dielectric constants of the ABO3-type perovskites (216 structures), whose thermodynamic stabilities were satisfactory. The predicted values were validated using DFPT calculations. The constructed database was further used to develop a surrogate model for the prediction of dielectric constants. The final R2 prediction accuracies reached 0.79 (electronic) and 0.67 (ionic).

Revealing the role of dopants in mitigating degradation phenomena in sodium-ion layered cathodes.

Prevention of the degradation of sodium-based layered cathode materials is the key to developing high-performance and high-stability sodium-ion batteries. In this study, the working mechanism of Mg and Ti dopants in mitigating degradation was investigated through the use of first-principles calculations. More specifically, the effects of each dopant in suppressing the phase transition, lattice expansion and shrinkage, and possible oxygen generation during repeated charging and discharging processes were validated. The results showed that the pristine structure exhibits irreversible O3-P3 phase transition after 75% desodiation, while doping with Mg or Ti effectively delays this transition. In addition, the change in lattice parameters as well as in the volume during desodiation was investigated. It was found that both dopants reduce the magnitude of structural change, which potentially improves the structural stability. Furthermore, introducing the dopants increases the thickness of the Na diffusion channel, possibly leading to an enhanced rate capability. Finally, the oxygen atomic charge variation during charging indicated that doping can enhance the oxygen stability by reducing the initial charge of oxygen as well as its increase during desodiation.

Adaptive Learning Framework in Prediction and Validation of Gibbs Free Energy for Inorganic Crystalline Solids.

Gibbs free energy is a fundamental physical property for understanding the stability and synthesizability of materials under various thermodynamic conditions, but its accessibility and availability are still limited. In this study, we used 9880 phonon databases to construct a machine learning model to predict approximately 40 000 Inorganic Crystalline Solid Database (ICSD) materials, whose free energy information has not been fully explored. To improve the prediction accuracy, a sampling strategy was implemented by including structures with low accuracy metrics, leading to R2 and mean absolute error values of 0.99 and 18.7 kJ/mol, respectively, in the testing set. Uncertainty analysis was followed for unexplored ICSD materials by obtaining the standard deviation in predictions from 10 surrogate models with different samplings in the training set. Based on this, an optimization process was conducted: density functional calculations were performed for 50 structures with high uncertainty and the training database was updated; this loop was repeated 15 times. This demonstrates the reduction and saturation in the uncertainty, confirming that the constructed model can provide a comprehensive map of the Gibbs free energy for inorganic solid materials. This can accelerate the material screening process by providing information on thermodynamic stability.

Constructing surface models of silicate glasses using molecular dynamics to understand the effect of pH on the hydration properties.

In this work, we use realistic silicate glass surface models, with molecular dynamics simulations, and present an algorithm for proper atomic partial charge assignment, consistent with measurable internal dipoles. The immersion energy is calculated for different silicate glass compositions in solutions of varying pH. We use molecular dynamics to elucidate the differences in the structure of water between mono- and divalent cations. The immersion energy of the glass surface is found to increase with an increase in ionic surface density and pH. This can be attributed to the stronger interaction between water and cations, as opposed to the interactions between water and silanol groups. The developed models and methods provide new insights into the structure of glass-solution interfaces and the effect of cation surface density in common nanoscale environments.

Mechanistic understanding of intergranular cracking in NCM cathode material: mesoscale simulation with three-dimensional microstructure.

Intergranular cracking in the agglomerated form of secondary particles has been regarded as a major cause for mechanical degradation in layered oxide cathode materials for Li-ion batteries, but its detailed mechanistic origin linked to the mechanical properties of these materials is still unknown. In this study, a mesoscale simulation based on the description of the interaction between primary particles is established by combining the model of the shifted-force Lennard-Jones potential and granular Hertzian model to construct the microstructure of secondary particles of cathode materials. The optimized parameters for each model are developed to compute the mechanical properties based on the response from nano-indentation and uniaxial tensile tests. Furthermore, the adhesion between the primary particles is modified to examine their sensitivity to different modes of deformations. The results show that under tension, an increase in adhesion can significantly strengthen the structure along with increase in brittleness, whereas the response from the localized compression (nano-indentation) is shown to be much less sensitive. In addition, the structural changes during repeated volume expansion/contraction induced from electrochemical cycling are investigated. The results indicate that enhancing particle adhesion can prevent the propagation of intergranular cracking.

Intrinsic origin of intra-granular cracking in Ni-rich layered oxide cathode materials.

Mechanical degradation phenomena in layered oxide cathode materials during electrochemical cycling have limited their long-term usage because they deteriorate the structural stability and result in a poor capacity retention rate. Among them, intra-granular cracking inside primary particles progressively degrades the performance of the cathode but comprehensive understanding of its intrinsic origin is still lacking. In this study, the mechanical properties of the primary particle in a Ni-rich layered oxide cathode material (LiNi0.8Co0.1Mn0.1O2) are investigated under tensile and compressive deformation towards both in-plane and out-of-plane directions within the density functional theory framework. The Young's modulus and maximum strength values indicate that the pristine structure is more vulnerable to tensile deformation than compression. In addition, delithiation significantly deteriorates the mechanical properties regardless of the direction of deformation. In particular, a substantial degree of anisotropy is observed, indicating that the mechanical properties in the out-of-plane direction are much weaker than those in the in-plane direction. Particular weakness in that direction is further confirmed using heterogeneously delithiated structures as well as by calculating the accumulated mechanical stress values inside during delithiation. A comparison of the mechanical properties of the structure with a lower Ni content (Ni = 33%) demonstrates that the Ni-rich material is slightly weaker and hence its intra-granular cracking could become accelerated during cycling.

A first-principles study of the preventive effects of Al and Mg doping on the degradation in LiNi0.8Co0.1Mn0.1O2 cathode materials.

First-principles calculations have been used to investigate the effects of Al and Mg doping on the prevention of degradation phenomena in Li(Ni0.8Co0.1Mn0.1)O2 cathode materials. Specifically, we have examined the effects of dopants on the suppression of oxygen evolution and cation disordering, as well as their correlation. It is found that Al doping can suppress the formation of oxygen vacancies effectively, while Mg doping prevents the cation disordering behaviors, i.e., excess Ni and Li/Ni exchange, and Ni migration. This study also demonstrates that formation of oxygen vacancies can facilitate the construction of the cation disordering, and vice versa. Delithiation can increase the probabilities of formation of all defect types, especially oxygen vacancies. When oxygen vacancies are present, Ni can migrate to the Li site during delithiation. However, Al and Mg doping can inhibit Ni migration, even in structures with preformed oxygen defects. The analysis of atomic charge variations during delithiation demonstrates that the degree of oxidation behavior in oxygen atoms is alleviated in the case of Al doping, indicating the enhanced oxygen stability in this structure. In addition, changes in the lattice parameters during delithiation are suppressed in the Mg-doped structure, which suggests that Mg doping may improve the lattice stability.

Enhancement in the electrochemical performance of zirconium/phosphate bi-functional coatings on LiNi0.8Co0.15Mn0.05O2 by the removal of Li residuals.

The effect of bi-functional coatings consisting of Zr and phosphate (P) on the electrochemical performance of Li1.0Ni0.8Co0.15Mn0.05O2 (NCM) has been investigated. The presence of various types of Zr and P compounds such as oxides (ZrO2 and Li2ZrO3) and phosphates (Zr2P2O9, ZrP2O7 and LiZr2(PO4)3) in the coating was confirmed by experiments as well as density functional theory (DFT) calculations. When the NCM samples were coated with the Zr/P hybrid material, the cycle retention and the amount of removed Li residuals (LiOH, Li2CO3) were enhanced by the synergistic effect from Zr and P. The NCM sample coated with a Zr/P layer with a Zr/P ratio of 1 : 1 exhibited an increase in the initial capacity (209.3 mA h g-1) compared to the pristine sample (207.4 mA h g-1) at 0.1C, owing to the formation of the coating layer. The capacity retention of the Zr/P coated sample (92.4% at the 50th cycle) was also improved compared to that of the pristine NCM sample (90.6% at the 50th cycle). Moreover, the amount of Li residuals in the Zr/P coated NCM sample was greatly reduced from 3693 ppm (pristine NCM) to 2525 ppm (Zr/P = 5 : 5).

Machine-Learning-Driven High-Throughput Screening for High-Energy Density and Stable NASICON Cathodes.

The Na super ionic conductor (NASICON), which has outstanding structural stability and a high operating voltage, is an appealing material for overcoming the limits of low specific energy and larger volume distortion of sodium-ion batteries. In this study, to discover ideal NASICON cathode materials, a screening platform based on density functional theory (DFT) calculations and machine learning (ML) is developed. A training database was generated utilizing the previous 124 545 electrode databases, and a test set of 3126 potential NASICON structures [NaxMyM'1-y(PO4)3] with 27 dopants at the metal site and 6 dopants at the polyanion central site was constructed. The developed ML surrogate model identifies 796 materials that satisfy the following criteria: formation energy of <0.0 eV/atom, energy above hull of ≤0.025 eV/atom, volume change of ≤4%, and theoretical capacity of ≥50 mAh/g. The thermodynamically stable configurations of doped NASICON structures were then selected using machine learning interatomic potential (MLIP), enabling rapid consideration of various dopant site configurations. DFT calculations are followed on 796 screened materials to obtain energy density, average voltage, and volume change. Finally, 50 candidates with an average voltage of ≥3.5 V are identified. The suggested platform accelerates the exploration for optimal NASICON materials by narrowing the focus on materials with desired properties, saving considerable resources.

Active Learning Framework for Expediting the Search of Thermodynamically Stable MXenes in the Extensive Chemical Space.

MXenes possess a wide range of materials properties owing to their compositional and stoichiometric diversities, facilitating their utilization in various technological applications such as electrodes, catalysts, and supercapacitors. To explore their applicability, identification of thermodynamically stable and synthesizable MXenes should precede. The energy above the convex hull (Ehull) calculated using the density functional theory (DFT) is a powerful scale to probe the thermodynamic stability. However, the high calculation cost of DFT limits the search space of unknown chemistry. To address this challenge, this study proposes an active learning (AL) framework consisting of a surrogate model and utility function for expeditious identification of thermodynamically stable MXenes in the extensive chemical space of 23,857 MXenes with compositional and stoichiometric diversity. Exploiting the fast inference speed and the capability of the AL framework to accurately identify stable MXenes, only 480 DFT calculations were required to identify 126 thermodynamically stable MXenes; among these, the stabilities of 89 MXenes have not been previously reported. In contrast, only two stable MXenes were identified among randomly selected 1693 MXenes, demonstrating the inefficiency of using only DFT calculations in exploring a large chemical space. The AL framework successfully minimized the number of DFT calculations while maximizing that of thermodynamically stable MXenes identified and can contribute to future studies in finding stable MXenes expeditiously.

Enhancing protein aggregation prediction: a unified analysis leveraging graph convolutional networks and active learning.

Protein aggregation (PA) is a critical phenomenon associated with Alzheimer's and Parkinson's disease. Recent studies have suggested that factors like aggregation-prone regions (APRs) and ß-strand interactions are crucial in understanding such behavior. While experimental methods have provided valuable insights, there has been a shift towards computational strategies, particularly machine learning, for their efficacy and speed. The challenge, however, lies in effectively incorporating structural information into these models. This study constructs a Graph Convolutional Network (GCN) to predict PA scores with the expanded and refined Protein Data Bank (PDB) and AlphaFold2.0 dataset. We employed AGGRESCAN3D 2.0 to calculate PA propensity and to enhance the dataset, we systematically separated multi polypeptide chains within PDB data into single polypeptide chains, removing redundancy. This effort resulted in a dataset comprising 302 032 unique PDB entries. Subsequently, we compared sequence similarity and obtained 22 774 Homo sapiens data from AlphaFold2.0. Using this expanded and refined dataset, the trained GCN model for PA prediction achieves a remarkable coefficient of determination (R 2) score of 0.9849 and a low mean absolute error (MAE) of 0.0381. Furthermore, the efficacy of the active learning process was demonstrated through its rapid identification of proteins with high PA propensity. Consequently, the active learning approach achieved an MAE of 0.0291 in expected improvement, surpassing other methods. It identified 99% of the target proteins by exploring merely 29% of the entire search space. This improved GCN model demonstrates promise in selecting proteins susceptible to PA, advancing protein science. This work contributes to the development of efficient computational tools for PA prediction, with potential applications in disease diagnosis and therapy.

Uncovering the Relationship between Metal Elements and Mechanical Stability for Metal-Organic Frameworks.

Assessing the mechanical robustness of metal-organic frameworks (MOFs) is crucial to enhance their applicability in various fields. Although considerable research has been conducted on the relationship between the mechanical properties of MOFs and their structural features (such as pore size, surface area, and topology), the insufficient exploration of metal elements has prevented researchers from fully understanding their mechanical behavior. To plug this knowledge gap, we constructed a database of mechanical properties for 20,342 MOFs included in the QMOF database using molecular simulations to investigate the impact of metal elements on mechanical stability. Through Shapley additive explanations (SHAP) analysis, we found that Co and Ln could enhance the structural stability of MOFs. We validated these findings using newly generated hypothetical MOFs. Notably, we adopted an interpretable machine learning technique to analyze the contribution of remarkably diverse metal elements in the 20,342 MOFs to the mechanical properties of each MOF. We anticipate that this research will serve as a valuable tool for future studies on identifying mechanically robust MOFs suitable for various industrial applications.

Screening Platform for Promising Na Superionic Conductors for Na-Ion Solid-State Electrolytes.

Na-ion batteries are considered a promising alternative to the analogous Li-ion batteries because of their low manufacturing cost, large abundance, and similar chemical/electrochemical properties. In particular, research on Na-ion solid electrolytes, which resolve the flammability issues associated with liquid electrolytes and increase the energy density obtained using a particular metal anode, is rapidly growing. However, the ionic conductivities of these materials are lower than those of liquids. We present a novel classification approach based on machine learning for identifying Na superionic conductor (NASICON) materials with outstanding ionic conductivities. We obtained new features based on chemical descriptors such as Na content, elemental radii, and electronegativity. We then classified 3573 NASICON structures by implementing the ensemble model of gradient boosting algorithms, with an average prediction accuracy of 84.2%. We further validated the thermodynamic stability and ionic conductivity values of the materials classified as superionic materials by employing density functional theory calculations and ab initio molecular dynamics simulations. Na3YTaSi2PO12, Na3HfZrSi2PO12, Na3LaTaSi2PO12, and Na3ScTaSi2PO12 were confirmed as promising NASICON structures that fulfill the requirements of solid-state electrolytes.

Extracting Chemical Information from Scientific Literature Using Text Mining: Building an Ionic Conductivity Database for Solid-State Electrolytes.

Recently, as the demand for electric vehicles has rapidly grown, concerns regarding the safety of liquid electrolytes used as battery materials have increased. Rechargeable batteries made of liquid electrolytes pose a risk of fire and may explode due to the decomposition reaction of the electrolyte. Accordingly, interest in solid-state electrolytes (SSEs), which have greater stability than liquid electrolytes, is increasing, and research into finding stable SSEs with high ionic conductivity is actively being conducted. Consequently, it is essential to obtain a large amount of material data to explore new SSEs. However, the data collection process is highly repetitive and time-consuming. Therefore, the goal of this study is to automatically extract the ionic conductivities of SSEs from published literature using text-mining algorithms and use this information to construct a materials database. The extraction procedure includes document processing, natural language preprocessing, phase parsing, relation extraction, and data post-processing. For performance verification, the ionic conductivities are extracted from 38 studies, and the accuracy of the proposed model is confirmed by comparing extracted conductivities with the actual ones. In previous research, 93% of battery-related records were unable to distinguish between ionic and electrical conductivities. However, by applying the proposed model, the proportion of undistinguished records was successfully reduced from 93 to 24.3%. Finally, the ionic conductivity database was constructed by extracting the ionic conductivity from 3258 papers, and the battery database was reconstructed by adding eight pieces of representative structural information.