arXiv subjects

Luis Itza Vazquez-Salazar

Publications and source records attributed to Luis Itza Vazquez-Salazar.

11 recordsLinked to original sources

arXiv2026

Recovering molecules from coarse-grained beads: free-energy-conditioned generative backmapping across chemical space

Transferable coarse-grained (CG) force fields compress chemical space: by aggregating atoms into a reduced set of interaction beads, models such as MARTINI reduce the number of distinguishable compounds by roughly three orders of magnitude, making high-throughput screening of thermodynamic properties tractable across soft matter, with drug--membrane permeability as a well-developed example. The compression is lossy and, so far, one-way: a screen returns a combination of beads, with no established route back to the compounds it stands for. Recovering those compounds--compositional backmapping--is a one-to-many inverse map, distinct from the better-studied conformational problem of rebuilding atomic coordinates from a known mapping. Here we formulate compositional backmapping as conditional graph generation by introducing juniper, a discrete denoising diffusion model over molecular graphs conditioned on the octanol--water partition free energy $ΔG_{\mathrm{W} \mapsto \mathrm{O}}$, the principal driver of MARTINI bead type assignment and hence a proxy for bead identity. Trained on molecules of up to 9 heavy atoms mapped onto one or two beads, juniper generates molecules that are 93\% valid and 92\% unique for two-bead targets, and whose $ΔG_{\mathrm{W} \mapsto \mathrm{O}}$ distributions track the target $ΔG^{\mathrm{CG}}_{\mathrm{W} \mapsto \mathrm{O}}$ linearly ($r^{2} \geq 0.96$), departing only in the hydrophobic and hydrophilic tails. Although the model receives no chemical information beyond a single scalar, the functional groups shift systematically with the imposed free energy, from branched hydrocarbons at the apolar end to amides, imides, and isocyanates at the polar end. A bead combination flagged by a CG screen can therefore be turned into candidate molecules for atomistic study or synthesis.

physics.chem-ph↗

arXiv2025

Design, Assessment, and Application of Machine Learning Potential Energy Surfaces

Potential Energy Surfaces (PESs) are an indispensable tool to investigate, characterise and understand chemical and biological systems in the gas and condensed phases. Advances in Machine Learning (ML) methodologies have led to the development of Machine Learned Potential Energy Surfaces (ML-PES) which are now widely used to simulate such systems. The present work provides an overview of concepts, methodologies and recommendations for constructing and using ML-PESs. The choice of topics is focused on practical and recurrent issues to conceive and use such model. Application of the principles discussed are illustrated through two different systems of biomolecular importance: the non-reactive dynamics of the Alanine-Lysine-Alanine tripeptide in gas and solution phases, and double proton transfer reactions in DNA base pairs.

physics.chem-ph↗

arXiv2025

Augmenting chemical databases for atomistic machine learning by sampling conformational space

Machine learning (ML) has become a standard tool for the exploration of chemical space. Much of the performance of such models depends on the chosen database for a given task. Here, this aspect is investigated for "chemical tasks" including the prediction of hybridization, oxidation, substituent effects, and aromaticity, starting from an initial "restricted" database (iRD). Choosing molecules for augmenting this iRD, including increasing numbers of conformations generated at different temperatures, and retraining the models can improve predictions of the models on the selected "tasks". Addition of a small percentage of conformers (1 % ) obtained at 300 K improves the performance in almost all cases. On the other hand, and in line with previous studies, redundancy and highly deformed structures in the augmentation set compromise prediction quality. Energy and bond distributions were evaluated by means of Kullback-Leibler ($D_{\rm KL}$) and Jensen-Shannon ($D_{\rm JS}$) divergence and Wasserstein distance ($W_{1}$). The findings of this work provide a baseline for the rational augmentation of chemical databases or the creation of synthetic databases.

physics.chem-ph↗

arXiv2024

${\it Asparagus}$: A Toolkit for Autonomous, User-Guided Construction of Machine-Learned Potential Energy Surfaces

With the establishment of machine learning (ML) techniques in the scientific community, the construction of ML potential energy surfaces (ML-PES) has become a standard process in physics and chemistry. So far, improvements in the construction of ML-PES models have been conducted independently, creating an initial hurdle for new users to overcome and complicating the reproducibility of results. Aiming to reduce the bar for the extensive use of ML-PES, we introduce ${\it Asparagus}$, a software package encompassing the different parts into one coherent implementation that allows an autonomous, user-guided construction of ML-PES models. ${\it Asparagus}$ combines capabilities of initial data sampling with interfaces to ${\it ab initio}$ calculation programs, ML model training, as well as model evaluation and its application within other codes such as ASE or CHARMM. The functionalities of the code are illustrated in different examples, including the dynamics of small molecules, the representation of reactive potentials in organometallic compounds, and atom diffusion on periodic surface structures. The modular framework of ${\it Asparagus}$ is designed to allow simple implementations of further ML-related methods and models to provide constant user-friendly access to state-of-the-art ML techniques.

physics.chem-ph↗

arXiv2024

Outlier-Detection for Reactive Machine Learned Potential Energy Surfaces

Uncertainty quantification (UQ) to detect samples with large expected errors (outliers) is applied to reactive molecular potential energy surfaces (PESs). Three methods - Ensembles, Deep Evidential Regression (DER), and Gaussian Mixture Models (GMM) - were applied to the H-transfer reaction between ${\it syn-}$Criegee and vinyl hydroxyperoxide. The results indicate that ensemble models provide the best results for detecting outliers, followed by GMM. For example, from a pool of 1000 structures with the largest uncertainty, the detection quality for outliers is $\sim 90$ \% and $\sim 50$ \%, respectively, if 25 or 1000 structures with large errors are sought. On the contrary, the limitations of the statistical assumptions of DER greatly impacted its prediction capabilities. Finally, a structure-based indicator was found to be correlated with large average error, which may help to rapidly classify new structures into those that provide an advantage for refining the neural network.

physics.chem-ph↗

arXiv2023

Improving Potential Energy Surfaces Using Experimental Feshbach Resonance Tomography

The structure and dynamics of a molecular system is governed by its potential energy surface (PES), representing the total energy as a function of the nuclear coordinates. Obtaining accurate potential energy surfaces is limited by the exponential scaling of Hilbert space, restricting quantitative predictions of experimental observables from first principles to small molecules with just a few electrons. Here, we present an explicitly physics-informed approach for improving and assessing the quality of families of PESs by modifying them through linear coordinate transformations based on experimental data. We demonstrate this "morphing" of the PES for the He-H$_{2}^{+}$ complex for reference surfaces at three different levels of quantum chemistry and using recent comprehensive Feshbach resonance(FR) measurements. In all cases, the positions and intensities of peaks in the collision cross-section are improved. We find these observables to be mainly sensitive to the long-range part of the PES.

physics.chem-ph↗

arXiv2023

PhysNet Meets CHARMM: A Framework for Routine Machine Learning / Molecular Mechanics Simulations

Full dimensional potential energy surfaces (PESs) based on machine learning (ML) techniques provide means for accurate and efficient molecular simulations in the gas- and condensed-phase for various experimental observables ranging from spectroscopy to reaction dynamics. Here, the MLpot extension with PhysNet as the ML-based model for a PES is introduced into the newly developed pyCHARMM API. To illustrate conceiving, validating, refining and using a typical workflow, para-chloro-phenol is considered as an example. The main focus is on how to approach a concrete problem from a practical perspective and applications to spectroscopic observables and the free energy for the -OH torsion in solution are discussed in detail. For the computed IR spectra in the fingerprint region the computations for para-chloro-phenol in water are in good qualitative agreement with experiment carried out in CCl$_4$. Also, relative intensities are largely consistent with experimental findings. The barrier for rotation of the -OH group increases from $\sim 3.5$ kcal/mol in the gas phase to $\sim 4.1$ kcal/mol from simulations in water due to favourable H-bonding interactions of the -OH group with surrounding water molecules.

physics.chem-ph↗

arXiv2022

Neural Network Potentials for Chemistry: Concepts, Applications and Prospects

Artificial Neural Networks (ANN) are already heavily involved in methods and applications for frequent tasks in the field of computational chemistry such as representation of potential energy surfaces (PES) and spectroscopic predictions. This perspective provides an overview of the foundations of neural network-based full-dimensional potential energy surfaces, their architectures, underlying concepts, their representation and applications to chemical systems. Methods for data generation and training procedures for PES construction are discussed and means for error assessment and refinement through transfer learning are presented. A selection of recent results illustrates the latest improvements regarding accuracy of PES representations and system size limitations in dynamics simulations, but also NN application enabling direct prediction of physical results without dynamics simulations. The aim is to provide an overview for the current state-of-the-art NN approaches in computational chemistry and also to point out the current challenges in enhancing reliability and applicability of NN methods on larger scale.

physics.chem-ph↗

arXiv2022

Uncertainty quantification for predictions of atomistic neural networks

The value of uncertainty quantification on predictions for trained neural networks (NNs) on quantum chemical reference data is quantitatively explored. For this, the architecture of the PhysNet NN was suitably modified and the resulting model was evaluated with different metrics to quantify calibration, quality of predictions, and whether prediction error and the predicted uncertainty can be correlated. The results from training on the QM9 database and evaluating data from the test set within and outside the distribution indicate that error and uncertainty are not linearly related. The results clarify that noise and redundancy complicate property prediction for molecules even in cases for which changes - e.g. double bond migration in two otherwise identical molecules - are small. The model was then applied to a real database of tautomerization reactions. Analysis of the distance between members in feature space combined with other parameters shows that redundant information in the training dataset can lead to large variances and small errors whereas the presence of similar but unspecific information returns large errors but small variances. This was, e.g., observed for nitro-containing aliphatic chains for which predictions were difficult although the training set contained several examples for nitro groups bound to aromatic molecules. This underlines the importance of the composition of the training data and provides chemical insight into how this affects the prediction capabilities of a ML model. Finally, the approach put forward can be used for information-based improvement of chemical databases for target applications through active learning optimization.

physics.chem-ph↗

arXiv2022

Structure, Organization and Heterogeneity of Water-Containing Deep Eutectic Solvents

The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SCN$^-$ anions as the reporter) and THz spectroscopy. Molecular dynamics simulations correctly describe the non-trivial dependence of both spectroscopic signatures depending on water content. For the 2D IR spectra, the MD simulations relate the steep increase in the cross relaxation rate at high water content to parallel alignment of packed SCN$^-$ anions. Conversely, the non-linear increase of the THz absorption with increasing water content is mainly attributed to the formation of larger water clusters. The results demonstrate that a combination of structure sensitive spectroscopies and molecular dynamics simulations provides molecular-level insights into emergence of heterogeneity of such mixtures by modulating their composition.

physics.chem-ph↗

arXiv2021

Impact of the characteristics of quantum chemical databases on machine learning predictions of tautomerization energies

An essential aspect for adequate predictions of chemical properties by machine learning models is the database used for training them. However, studies that analyze how the content and structure of the databases used for training impact the prediction quality are scarce. In this work, we analyze and quantify the relationships learned by a machine learning model (Neural Network) trained on five different reference databases (QM9, PC9, ANI-1E, ANI-1 and ANI-1x) to predict tautomerization energies from molecules in Tautobase. For this, characteristics such as the number of heavy atoms in a molecule, number of atoms of a given element, bond composition, or initial geometry on the quality of the predictions are considered. The results indicate that training on a chemically diverse database is crucial for obtaining good results but also that conformational sampling can partly compensate for limited coverage of chemical diversity. We explicitly demonstrate that when certain types of bonds need to be covered in the target database (Tautobase) but are undersampled in the reference databases the resulting predictions are poor. A quantitative measure for these deficiencies is the Kullback-Leibler divergence between reference and target distributions. Analysis of the results with a TreeMAP algorithm provides deeper understanding of specific deficiencies in the reference data sets. Capitalizing on this information can be used to either improve existing databases or to generate new databases of sufficient diversity for a range of ML applications in chemistry.

physics.chem-ph↗