Processing have resulted in immense progress on downstream tasks.

Developing machine learning protocols for molecular simulations requires comprehensive and efficient datasets. Here we introduce the QMe14S dataset, comprising 186,102 small organic molecules featuring 14 elements (H, B, C, N, O, F, Al, Si, P, S, Cl, As, Se, Br) and 47 functional groups. Using density functional theory at the B3LYP/TZVP level, we optimized the geometries and calculated properties including energy, atomic charge, atomic force, dipole moment, quadrupole moment, polarizability, octupole moment, first hyperpolarizability, and Hessian. At the same level, we obtained the harmonic IR, Raman and NMR spectra. Furthermore, we conducted ab initio molecular dynamics simulations to generate dynamic configurations and extract nonequilibrium properties, including energy, forces, and Hessians. By leveraging our E(3)-equivariant message-passing neural network (DetaNet), we demonstrated that models trained on QMe14S outperform those trained on the previously developed QM9S dataset in simulating molecular spectra. The QMe14S dataset thus serves as a comprehensive benchmark for molecular simulations, offering valuable insights into structure-property relationships.

Recent advances in diffusion models have shown remarkable potential in the conditional generation of novel molecules. These models can be guided in two ways: (i) explicitly, through additional features representing the condition, or (ii) implicitly, using a property predictor. However, training property predictors or conditional diffusion models requires an abundance of labeled data and is inherently challenging in real-world applications. We propose a novel approach that attenuates the limitations of acquiring large labeled datasets by leveraging domain knowledge from quantum chemistry as a non-differentiable oracle to guide an unconditional diffusion model. Instead of relying on neural networks, the oracle provides accurate guidance in the form of estimated gradients, allowing the diffusion process to sample from a conditional distribution specified by quantum chemistry. We show that this results in more precise conditional generation of novel and stable molecular structures. Our experiments demonstrate that our method: (1) significantly reduces atomic forces, enhancing the validity of generated molecules when used for stability optimization; (2) is compatible with both explicit and implicit guidance in diffusion models, enabling joint optimization of molecular properties and stability; and (3) generalizes effectively to molecular optimization tasks beyond stability optimization.

We propose a framework to learn the time-dependent Hartree-Fock (TDHF) inter-electronic potential of a molecule from its electron density dynamics. Though the entire TDHF Hamiltonian, including the inter-electronic potential, can be computed from first principles, we use this problem as a testbed to develop strategies that can be applied to learn \emph{a priori} unknown terms that arise in other methods/approaches to quantum dynamics, e.g., emerging problems such as learning exchange-correlation potentials for time-dependent density functional theory. We develop, train, and test three models of the TDHF inter-electronic potential, each parameterized by a four-index tensor of size up to $60 \times 60 \times 60 \times 60$. Two of the models preserve Hermitian symmetry, while one model preserves an eight-fold permutation symmetry that implies Hermitian symmetry. Across seven different molecular systems, we find that accounting for the deeper eight-fold symmetry leads to the best-performing model across three metrics: training efficiency, test set predictive power, and direct comparison of true and learned inter-electronic potentials. All three models, when trained on ensembles of field-free trajectories, generate accurate electron dynamics predictions even in a field-on regime that lies outside the training set. To enable our models to scale to large molecular systems, we derive expressions for Jacobian-vector products that enable iterative, matrix-free training.

Advancements in lithium battery technology heavily rely on the design and engineering of electrolytes. However, current schemes for molecular design and recipe optimization of electrolytes lack an effective computational-experimental closed loop and often fall short in accurately predicting diverse electrolyte formulation properties. In this work, we introduce Uni-ELF, a novel multi-level representation learning framework to advance electrolyte design. Our approach involves two-stage pretraining: reconstructing three-dimensional molecular structures at the molecular level using the Uni-Mol model, and predicting statistical structural properties (e.g., radial distribution functions) from molecular dynamics simulations at the mixture level. Through this comprehensive pretraining, Uni-ELF is able to capture intricate molecular and mixture-level information, which significantly enhances its predictive capability. As a result, Uni-ELF substantially outperforms state-of-the-art methods in predicting both molecular properties (e.g., melting point, boiling point, synthesizability) and formulation properties (e.g., conductivity, Coulombic efficiency). Moreover, Uni-ELF can be seamlessly integrated into an automatic experimental design workflow. We believe this innovative framework will pave the way for automated AI-based electrolyte design and engineering.

Breast cancer, the second most prevalent cancer among women worldwide, necessitates the exploration of novel therapeutic approaches. To target the four subgroups of breast cancer "hormone receptor-positive and HER2-negative, hormone receptor-positive and HER2-positive, hormone receptor-negative and HER2-positive, and hormone receptor-negative and HER2-negative" it is crucial to inhibit specific targets such as EGFR, HER2, ER, NF-kB, and PR. In this study, we evaluated various methods for binary and multiclass classification. Among them, the GA-SVM-SVM:GA-SVM-SVM model was selected with an accuracy of 0.74, an F1-score of 0.73, and an AUC of 0.94 for virtual screening of ligands from the BindingDB database. This model successfully identified 4454, 803, 438, and 378 ligands with over 90% precision in both active/inactive and target prediction for the classes of EGFR+HER2, ER, NF-kB, and PR, respectively, from the BindingDB database. Based on to the selected ligands, we created a dendrogram that categorizes different ligands based on their targets. This dendrogram aims to facilitate the exploration of chemical space for various therapeutic targets. Ligands that surpassed a 90% threshold in the product of activity probability and correct target selection probability were chosen for further investigation using molecular docking. The binding energy range for these ligands against their respective targets was calculated to be between -15 and -5 kcal/mol. Finally, based on general and common rules in medicinal chemistry, we selected 2, 3, 3, and 8 new ligands with high priority for further studies in the EGFR+HER2, ER, NF-kB, and PR classes, respectively.

Quantum chemical simulations can be greatly accelerated by constructing machine learning potentials, which is often done using active learning (AL). The usefulness of the constructed potentials is often limited by the high effort required and their insufficient robustness in the simulations. Here we introduce the end-to-end AL for constructing robust data-efficient potentials with affordable investment of time and resources and minimum human interference. Our AL protocol is based on the physics-informed sampling of training points, automatic selection of initial data, uncertainty quantification, and convergence monitoring. The versatility of this protocol is shown in our implementation of quasi-classical molecular dynamics for simulating vibrational spectra, conformer search of a key biochemical molecule, and timeresolved mechanism of the Diels-Alder reactions. These investigations took us days instead of weeks of pure quantum chemical calculations on a high-performance computing cluster. Introduction The introduction of machine learning potentials (MLPs) pushed the boundaries of what was previously possible in molecular dynamics (MD). MLPs enable simulations of longer time scales and larger systems with higher accuracy.

Tropospheric ozone, known as a concerning air pollutant, has been associated with health issues including asthma, bronchitis, and impaired lung function. The rates at which peroxy radicals react with NO play a critical role in the overall formation and depletion of tropospheric ozone. However, obtaining comprehensive kinetic data for these reactions remains challenging. Traditional approaches to determine rate constants are costly and technically intricate. Fortunately, the emergence of machine learning-based models offers a less resource and time-intensive alternative for acquiring kinetics information. In this study, we leveraged deep reinforcement learning to predict ranges of rate constants (\textit{k}) with exceptional accuracy, achieving a testing set accuracy of 100%. To analyze reactivity trends based on the molecular structure of peroxy radicals, we employed 51 global descriptors as input parameters. These descriptors were derived from optimized minimum energy geometries of peroxy radicals using the quantum composite G3B3 method. Through the application of Integrated Gradients (IGs), we gained valuable insights into the significance of the various descriptors in relation to reaction rates. We successfully validated and contextualized our findings by conducting cross-comparisons with established trends in the existing literature. These results establish a solid foundation for pioneering advancements in chemistry, where computer analysis serves as an inspirational source driving innovation.

Although there is not an ideal biotype for all production systems, the adequate biotype should be determined according to the objectives that have been established for the herd, along with the production system being practiced [9]. This is not without consequences. For instance, larger animals usually have higher nutritional and general maintenance requirements [7]. Among the methods used to evaluate beef cattle, the EPMURAS methodology synthesized by Koury Filho [11], Koury Filho et al. [13] is one of the most utilized in Brazil. It consists in a visual assessment of body structure, precocity, muscularity, sheath, racial aspects, angulation and sexuality.