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AI Chemistry

AI Chemistry is an international, peer-reviewed, scholarly, open access journal on the intersection of artificial intelligence and chemistry published quarterly online by MDPI.
  • Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
  • Rapid Publication: first decisions in 18 days; acceptance to publication in 7 days (median values for MDPI journals in the first half of 2026).
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All Articles (19)

  • Article
  • Open Access

The sperm chromatin dispersion (SCD) test is widely used to assess sperm DNA fragmentation by observing the halo structure around the sperm head. However, manual halo interpretation is labor-intensive and subjective, which limits its consistency and throughput in clinical practice. To address these limitations, we propose SHIELD-Net, an image-level single-sperm halo morphology classification framework for four halo categories: large halo, medium halo, small halo, and without halo. SHIELD-Net includes two modules, i.e., a hybrid ROI extraction (HyREx) module and dual-view learning with ROI-guided gate fusion (RGF). The HyREx module converts the traditional direct classification pipeline into a segmentation-classification pipeline. It uses the cell segmentation foundation model, i.e., Cellpose, to segment halo-centered regions of interest (ROIs) and proposes a fallback mechanism to ensure segmentation effectiveness. In this way, HyREx can construct a head–halo-centered ROI and reduce interference from tail and background regions. Based on the original image and the extracted ROI, SHIELD-Net performs dual-view ConvNeXt encoding. RGF further uses the ROI representation to generate a spatial gate that recalibrates the original-view feature map toward halo-morphology-related responses. Experiments were conducted on a public expert-annotated sperm microscopy dataset containing 403 individual sperm halo images using stratified five-fold cross-validation. SHIELD-Net achieved a Macro F1 of 0.9290 ± 0.0161. Compared with the original-image ConvNeXt-Small baseline, SHIELD-Net improved Macro F1 by 0.1755. These results indicate that combining head–halo-centered ROI construction with ROI-guided feature recalibration improves image-level sperm halo morphology classification.

AI Chem.

2 November 2026

Motivation for automated single-sperm halo classification. (a) In the SCD test, halo morphology around the sperm head provides visual evidence for DNA fragmentation assessment. (b) Traditional visual inspection is labor-intensive and subjective. (c) Image-level halo classification assigns each sperm image to one of four categories: large halo, medium halo, small halo, and without halo. (d) Full-view classification can be affected by tail, debris, and background interference, whereas ROI-guided dual-view learning focuses the model on head–halo evidence.
  • Article
  • Open Access

Data-Driven FTIR–PLS Modeling of Ethanol in Agave Distillates: Chemometric Design Factors and Matrix Sensitivity

  • Deyani Nocedo-Mena,
  • Melanie Sarahí Mateo González and
  • Eduardo Gerardo Pérez-Tijerina
  • + 1 author

Agave distillates are chemically heterogeneous matrices whose composition may affect the performance and transferability of spectroscopic calibration models. Accurate determination of their ethanol content is therefore essential for quality control and regulatory compliance. This study established a comparative ATR-FTIR chemometric framework for ethanol prediction using 46 agave-distillate samples measured in triplicate. Thirty-five samples were assigned to calibration and 11 to a validation set. Eighteen principal PLS configurations were developed by varying spectral-data strategy, spectral-region combination, and number of factors. Replicate dispersion, first- and second-derivative preprocessing, and model dimensionality were also evaluated, and PLS was benchmarked against PCR and PCA–SVR. Models based on averaged spectra produced lower RMSEP and higher rPred values than their corresponding individual-replicate configurations in all nine pairwise comparisons. The best averaged-spectrum PLS model achieved an RMSEP of 0.96% v/v and an rPred of 0.9897, whereas the best individual-replicate configuration yielded an RMSEP of 2.37% v/v. The benchmark showed that model performance depended on dimensionality and validation criterion; consequently, no regression approach was universally superior. Application of representative PLS, PCR, and PCA–SVR models to three additional samples produced similar descriptive mean absolute errors of 2.16 to 2.32% v/v. Overall, ATR-FTIR combined with multivariate regression provides a promising proof-of-concept strategy for the rapid estimation of ethanol in agave distillates. These findings support the future development of accessible and reliable quality-control protocols for agave spirits and other complex distilled beverages.

AI Chem.

26 October 2026

Unprocessed FTIR spectra of pure ethanol and the 138 individual replicate spectra acquired from the 46 agave-derived samples included in the study. The colored solid lines represent the FTIR spectra of the agave distillates, with different colors used solely to distinguish the spectra. The black dashed line represents pure ethanol.
  • Article
  • Open Access

Transition-metal-catalyzed direct C-3 arylation of imidazo[1,2-a]pyridines has witnessed significant advances in recent years. However, identifying optimal reaction conditions for this transformation relies heavily on labor-intensive trial-and-error experiments, which consume significant time and costs. To address this challenge, 275 valid reaction data entries conforming to the reaction mechanism were collected as training data, including substrates, catalysts, additives, solvents, reaction temperature, and experimental yield. Three mainstream tree-based ensemble regression models, including GradientBoosting, Random Forest and ExtraTrees, were constructed after strict data cleaning and advanced feature engineering for systematic benchmark comparison. The GradientBoosting model, which delivered the best fitting and generalization performance among all candidates, was selected as the objective function for subsequent constrained Bayesian optimization. A constrained Bayesian optimization algorithm (with predicted yield bounded within 0–100%) was adopted to globally screen high-dimensional reaction parameters for maximum yield. Comprehensive cross-model evaluation indicated the test-set determination coefficients followed the order GradientBoosting (R2 = 0.4416) > Random Forest (R2 = 0.3864) > ExtraTrees (R2 = 0.3544), while the root mean square error (RMSE) of GradientBoosting was 15.3144, outperforming the other two models in prediction stability. Under the optimal parameter set recommended by GradientBoosting (catalyst Pd(acac)2BuAd2P, reactants ref-5-1d and ref-9-2d, additive CsOAc, solvent DMA, 150 °C), the model predicted a theoretical maximum yield of 100%, whereas Random Forest and ExtraTrees only reached predicted peak yields of 83.63% and 80.80%, respectively. This multi-model benchmarking workflow eliminates the bias risk from single-model prediction, provides an efficient tool for optimizing metal-catalyzed C-3 arylation of imidazo[1,2-a]pyridines, and can be generalized to other complex transition-metal catalytic systems.

AI Chem.

12 October 2026

(a) General introduction of imidazo[1,2-a]pyridine; (b) Drug and bioactive compounds containing imidazo[1,2-a]pyridine; (c) Machine learning for C-3 arylation of imidazo[1,2-a]pyridines.
  • Article
  • Open Access

Somatostatin receptor subtype 2 (SSTR2), encoded at chromosome 17q25.1, is overexpressed in high-risk stage 4 neuroblastoma with a 17q gain, yet no non-peptide small-molecule ligand exists for this indication. From the agonist L-054,522, BROOD generated 5766 analogues, of which 292 were docked to SSTR2 (PDB 7XN9) with FRED, HYBRID, and POSIT; no physicochemical filter was applied. The query achieved an ROC AUC of 0.798 against known ligands and decoys. Eight compounds reaching GREAT pose confidence were re-docked with AutoDock Vina Extended, FITTED, Flare, and DiffDock and then assessed across five ADMET and two retrosynthesis platforms. Redocking the crystallographic ligand recovered the experimental pose with four site-directed programs (RMSD 0.85–1.79 Å), but none run blind or as ensembles, indicating that pose recovery depends on the search protocol rather than the scoring function. Docking scores were not reproducible across repeat runs, so candidates are not ranked. Compound 8 reproduced the Asp122, Gln126, and Thr194 contacts, alone received a Spaya RScore of 1.0 indicating a fully precedented route, and it held its pose over three 100 ns molecular dynamic simulations in a POPC bilayer (ligand RMSD 1.70 ± 0.12 Å). Because docking cannot distinguish agonism from antagonism, this work delivers a synthesisable hypothesis set, not a characterised pharmacological agent.

AI Chem.

10 October 2026

Representative of a section of BROOD output from round 6, showing analogues and associated Tanimoto scores.

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AI Chem. - ISSN 3042-6723