physics.chem-ph

arXiv:2406.00047v3 Announce Type: replace-cross Abstract: A central problem in quantum mechanics involves solving the Electronic Schrodinger Equation for a molecule or material. The Variational Monte Carlo approach to this problem approximates a particular variational objective via sampling, and then optimizes this approximated objective over a chosen parameterized family of wavefunctions, known as the ansatz. Recently neural networks have been used as the ansatz, with accompanying success. However, sampling from such wavefunctions has required the use of a Markov Chain Monte Carlo approach, which is inherently inefficient. In this work, we propose a solution to this problem via an ansatz which is cheap to sample from, yet satisfies the requisite quantum mechanical properties. We prove that a normalizing flow using the following two essential ingredients satisfies our requirements: (a) a base distribution which is constructed from Determinantal Point Processes; (b) flow layers which are equivariant to a particular subgroup of the permutation group. We then show how to construct both continuous and discrete normalizing flows which satisfy the requisite equivariance. We further demonstrate the manner in which the non-smooth nature ("cusps") of the wavefunction may be captured, and how the framework may be generalized to provide induction across multiple molecules. The resulting theoretical framework entails an efficient approach to solving the Electronic Schrodinger Equation.

arXiv:2311.02798v3 Announce Type: replace Abstract: Reliable molecular property prediction is essential for various scientific endeavors and industrial applications, such as drug discovery. However, the data scarcity, combined with the highly non-linear causal relationships between physicochemical and biological properties and conventional molecular featurization schemes, complicates the development of robust molecular machine learning models. Self-supervised learning (SSL) has emerged as a popular solution, utilizing large-scale, unannotated molecular data to learn a foundational representation of chemical space that might be advantageous for downstream tasks. Yet, existing molecular SSL methods largely overlook chemical knowledge, including molecular structure similarity, scaffold composition, and the context-dependent aspects of molecular properties when operating over the chemical space. They also struggle to learn the subtle variations in structure-activity relationship. This paper introduces a novel pre-training framework that learns robust and generalizable chemical knowledge. It leverages the structural hierarchy within the molecule, embeds them through distinct pre-training tasks across channels, and aggregates channel information in a task-specific manner during fine-tuning. Our approach demonstrates competitive performance across various molecular property benchmarks and offers strong advantages in particularly challenging yet ubiquitous scenarios like activity cliffs.

arXiv:2501.07077v1 Announce Type: new Abstract: Understanding and predicting the diverse conformational states of molecules is crucial for advancing fields such as chemistry, material science, and drug development. Despite significant progress in generative models, accurately generating complex and biologically or material-relevant molecular structures remains a major challenge. In this work, we introduce a diffusion model for three-dimensional (3D) molecule generation that combines a classifiable diffusion model, Diffusion Transformer, with multihead equivariant self-attention. This method addresses two key challenges: correctly attaching hydrogen atoms in generated molecules through learning representations of molecules after hydrogen atoms are removed; and overcoming the limitations of existing models that cannot generate molecules across multiple classes simultaneously. The experimental results demonstrate that our model not only achieves state-of-the-art performance across several key metrics but also exhibits robustness and versatility, making it highly suitable for early-stage large-scale generation processes in molecular design, followed by validation and further screening to obtain molecules with specific properties.

arXiv:2501.06669v1 Announce Type: new Abstract: Deep learning models for anticipating the products of organic reactions have found many use cases, including validating retrosynthetic pathways and constraining synthesis-based molecular design tools. Despite compelling performance on popular benchmark tasks, strange and erroneous predictions sometimes ensue when using these models in practice. The core issue is that common benchmarks test models in an in-distribution setting, whereas many real-world uses for these models are in out-of-distribution settings and require a greater degree of extrapolation. To better understand how current reaction predictors work in out-of-distribution domains, we report a series of more challenging evaluations of a prototypical SMILES-based deep learning model. First, we illustrate how performance on randomly sampled datasets is overly optimistic compared to performance when generalizing to new patents or new authors. Second, we conduct time splits that evaluate how models perform when tested on reactions published in years after those in their training set, mimicking real-world deployment. Finally, we consider extrapolation across reaction classes to reflect what would be required for the discovery of novel reaction types. This panel of tasks can reveal the capabilities and limitations of today's reaction predictors, acting as a crucial first step in the development of tomorrow's next-generation models capable of reaction discovery.

arXiv:2501.01576v1 Announce Type: cross Abstract: The integration of machine learning (ML) into chemistry offers transformative potential in the design of molecules. However, the focus has often been on creating highly efficient predictive models, sometimes at the expense of interpretability. We leverage explainable AI techniques to explore the design of boron-based Lewis acids, which play a pivotal role in organic reactions. Using Fluoride Ion Affinity as a proxy for Lewis acidity, we developed interpretable ML models based on chemically meaningful descriptors, including ab initio features and substituent-based parameters. By constraining the chemical space to well-defined molecular scaffolds, we achieved highly accurate predictions, surpassing conventional black-box deep learning models in low-data regime. Interpretability analyses of the models unraveled the origin of Lewis acidity in these compounds and identified actionable levers to modulate it. This work bridges ML and chemist's way of thinking, demonstrating how explainable models can inspire molecular design and enhance scientific understanding of chemical reactivity.

arXiv:2501.01811v1 Announce Type: cross Abstract: Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we validate relative binding free energy (RBFE) accuracy using neural network potentials (NNPs) for the ligands. We utilize a novel NNP model, AceForce 1.0, based on the TensorNet architecture for small molecules that broadens the applicability to diverse drug-like compounds, including all important chemical elements and supporting charged molecules. Using established benchmarks, we show overall improved accuracy and correlation in binding affinity predictions compared with GAFF2 for molecular mechanics and ANI2-x for NNPs. Slightly less accuracy but comparable correlations with OPLS4. We also show that we can run the NNP simulations at 2 fs timestep, at least two times larger than previous NNP models, providing significant speed gains. The results show promise for further evolutions of free energy calculations using NNPs while demonstrating its practical use already with the current generation. The code and NNP model are publicly available for research use.

arXiv:2407.20294v2 Announce Type: replace Abstract: In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

arXiv:2411.15221v2 Announce Type: replace Abstract: Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

arXiv:2409.19838v2 Announce Type: replace Abstract: Identifying informative low-dimensional features that characterize dynamics in molecular simulations remains a challenge, often requiring extensive manual tuning and system-specific knowledge. Here, we introduce geom2vec, in which pretrained graph neural networks (GNNs) are used as universal geometric featurizers. By pretraining equivariant GNNs on a large dataset of molecular conformations with a self-supervised denoising objective, we obtain transferable structural representations that are useful for learning conformational dynamics without further fine-tuning. We show how the learned GNN representations can capture interpretable relationships between structural units (tokens) by combining them with expressive token mixers. Importantly, decoupling training the GNNs from training for downstream tasks enables analysis of larger molecular graphs (such as small proteins at all-atom resolution) with limited computational resources. In these ways, geom2vec eliminates the need for manual feature selection and increases the robustness of simulation analyses.

arXiv:2501.00001v1 Announce Type: new Abstract: In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and multiple-component cases are considered with constant or variable velocity. Non-dimensionalisation indicates the small effect of diffusion. The system where diffusion is neglected is analysed using Laplace transforms. In the multiple-component case, it is demonstrated that the competition between the compounds is negligible and the equations may be decoupled. This reduces the problem to solving a single integral equation to determine the concentration profile for all components (since they are scaled versions of each other). For a given analyte, we then only two parameters need to be fitted to the data. To verify this approach, the full governing equations are also solved numerically using the finite difference method and a global adaptive quadrature method to integrate the Laplace transformation. Comparison with the Laplace solution verifies the high degree of accuracy of the simpler Laplace form. The Laplace solution is then verified against experimental data from BTEX chromatography. This novel method, which involves solving a single equation and fitting parameters in pairs for individual components, is highly efficient. It is significantly faster and simpler than the full numerical solution and avoids the computationally expensive methods that would normally be used to fit all curves at the same time.

arXiv:2412.18263v1 Announce Type: new Abstract: Irreducible Cartesian tensors (ICTs) play a crucial role in the design of equivariant graph neural networks, as well as in theoretical chemistry and chemical physics. Meanwhile, the design space of available linear operations on tensors that preserve symmetry presents a significant challenge. The ICT decomposition and a basis of this equivariant space are difficult to obtain for high-order tensors. After decades of research, we recently achieve an explicit ICT decomposition for $n=5$ \citep{bonvicini2024irreducible} with factorial time/space complexity. This work, for the first time, obtains decomposition matrices for ICTs up to rank $n=9$ with reduced and affordable complexity, by constructing what we call path matrices. The path matrices are obtained via performing chain-like contraction with Clebsch-Gordan matrices following the parentage scheme. We prove and leverage that the concatenation of path matrices is an orthonormal change-of-basis matrix between the Cartesian tensor product space and the spherical direct sum spaces. Furthermore, we identify a complete orthogonal basis for the equivariant space, rather than a spanning set \citep{pearce2023brauer}, through this path matrices technique. We further extend our result to the arbitrary tensor product and direct sum spaces, enabling free design between different spaces while keeping symmetry. The Python code is available in the appendix where the $n=6,\dots,9$ ICT decomposition matrices are obtained in <0.1s, 0.5s, 1s, 3s, 11s, and 4m32s, respectively.

arXiv:2412.18414v1 Announce Type: cross Abstract: Generative model for 2D materials has shown significant promise in accelerating the material discovery process. The stability and performance of these materials are strongly influenced by their underlying symmetry. However, existing generative models for 2D materials often neglect symmetry constraints, which limits both the diversity and quality of the generated structures. Here, we introduce a symmetry-constrained diffusion model (SCDM) that integrates space group symmetry into the generative process. By incorporating Wyckoff positions, the model ensures adherence to symmetry principles, leading to the generation of 2,000 candidate structures. DFT calculations were conducted to evaluate the convex hull energies of these structures after structural relaxation. From the generated samples, 843 materials that met the energy stability criteria (Ehull < 0.6 eV/atom) were identified. Among these, six candidates were selected for further stability analysis, including phonon band structure evaluations and electronic properties investigations, all of which exhibited phonon spectrum stability. To benchmark the performance of SCDM, a symmetry-unconstrained diffusion model was also evaluated via crystal structure prediction model. The results highlight that incorporating symmetry constraints enhances the effectiveness of generated 2D materials, making a contribution to the discovery of 2D materials through generative modeling.

arXiv:2412.16483v1 Announce Type: new Abstract: Molecular representation learning plays a crucial role in various downstream tasks, such as molecular property prediction and drug design. To accurately represent molecules, Graph Neural Networks (GNNs) and Graph Transformers (GTs) have shown potential in the realm of self-supervised pretraining. However, existing approaches often overlook the relationship between molecular structure and electronic information, as well as the internal semantic reasoning within molecules. This omission of fundamental chemical knowledge in graph semantics leads to incomplete molecular representations, missing the integration of structural and electronic data. To address these issues, we introduce MOL-Mamba, a framework that enhances molecular representation by combining structural and electronic insights. MOL-Mamba consists of an Atom & Fragment Mamba-Graph (MG) for hierarchical structural reasoning and a Mamba-Transformer (MT) fuser for integrating molecular structure and electronic correlation learning. Additionally, we propose a Structural Distribution Collaborative Training and E-semantic Fusion Training framework to further enhance molecular representation learning. Extensive experiments demonstrate that MOL-Mamba outperforms state-of-the-art baselines across eleven chemical-biological molecular datasets. Code is available at https://github.com/xian-sh/MOL-Mamba.

arXiv:2411.15722v2 Announce Type: replace Abstract: We investigate the convergence of a backward Euler finite element discretization applied to a multi-domain and multi-scale elliptic-parabolic system, derived from the Doyle-Fuller-Newman model for lithium-ion batteries. We establish optimal-order error estimates for the solution in the norms $l^2(H^1)$ and $l^2(L^2(H^q_r))$, $q=0,1$. To improve computational efficiency, we propose a novel solver that accelerates the solution process and controls memory usage. Numerical experiments with realistic battery parameters validate the theoretical error rates and demonstrate the significantly superior performance of the proposed solver over existing solvers.

arXiv:2405.06659v2 Announce Type: replace-cross Abstract: Due to the vast design space of molecules, generating molecules conditioned on a specific sub-structure relevant to a particular function or therapeutic target is a crucial task in computer-aided drug design. Existing works mainly focus on specific tasks, such as linker design or scaffold hopping, each task requires training a model from scratch, and many well-pretrained De Novo molecule generation model parameters are not effectively utilized. To this end, we propose a two-stage training approach, consisting of condition learning and condition optimization. In the condition learning stage, we adopt the idea of ControlNet and design some meaningful adjustments to make the unconditional generative model learn sub-structure conditioned generation. In the condition optimization stage, by using human preference learning, we further enhance the stability and robustness of sub-structure control. In our experiments, only trained on randomly partitioned sub-structure data, the proposed method outperforms previous techniques by generating more valid and diverse molecules. Our method is easy to implement and can be quickly applied to various pre-trained molecule generation models.

arXiv:2403.09549v3 Announce Type: replace Abstract: Understanding the interactions of atoms such as forces in 3D atomistic systems is fundamental to many applications like molecular dynamics and catalyst design. However, simulating these interactions requires compute-intensive ab initio calculations and thus results in limited data for training neural networks. In this paper, we propose to use denoising non-equilibrium structures (DeNS) as an auxiliary task to better leverage training data and improve performance. For training with DeNS, we first corrupt a 3D structure by adding noise to its 3D coordinates and then predict the noise. Different from previous works on denoising, which are limited to equilibrium structures, the proposed method generalizes denoising to a much larger set of non-equilibrium structures. The main difference is that a non-equilibrium structure does not correspond to local energy minima and has non-zero forces, and therefore it can have many possible atomic positions compared to an equilibrium structure. This makes denoising non-equilibrium structures an ill-posed problem since the target of denoising is not uniquely defined. Our key insight is to additionally encode the forces of the original non-equilibrium structure to specify which non-equilibrium structure we are denoising. Concretely, given a corrupted non-equilibrium structure and the forces of the original one, we predict the non-equilibrium structure satisfying the input forces instead of any arbitrary structures. Since DeNS requires encoding forces, DeNS favors equivariant networks, which can easily incorporate forces and other higher-order tensors in node embeddings. We study the effectiveness of training equivariant networks with DeNS on OC20, OC22 and MD17 datasets and demonstrate that DeNS can achieve new state-of-the-art results on OC20 and OC22 and significantly improve training efficiency on MD17.