Behavior of counterpoise correction in many-body molecular clusters of organic compounds: Hartree-Fock interaction energy perspective

Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method

An auxiliary polarization formulation of the fragment molecular orbital (FMO) method is developed, combining a basis set correction computed for capped isolated fragments with a polarization obtained from uncapped fragments. For a set of organic and inorganic test systems, it is shown that the total energy and atomic charges are accurately reproduced with respect to full unfragmented calculations. It is demonstrated that the method is accurate for computing electronic excited states. The developed approach is applied to rank the isomers of chignolin from experimental NMR data (PDB: 1UAO) according to their relative energy. Contributions of polarization and basis set effects to pair interactions between fragments are elucidated.

Cluster energy prediction based on multiple strategy fusion whale optimization algorithm and light gradient boosting machine

BACKGROUND

Clusters, a novel hierarchical material structure that emerges from atoms or molecules, possess unique reactivity and catalytic properties, crucial in catalysis, biomedicine, and optoelectronics. Predicting cluster energy provides insights into electronic structure, magnetism, and stability. However, the structure of clusters and their potential energy surface is exceptionally intricate. Searching for the global optimal structure (the lowest energy) among these isomers poses a significant challenge. Currently, modelling cluster energy predictions with traditional machine learning methods has several issues, including reliance on manual expertise, slow computation, heavy computational resource demands, and less efficient parameter tuning.

RESULTS

This paper introduces a predictive model for the energy of a gold cluster comprising twenty atoms (referred to as Au20 cluster). The model integrates the Multiple Strategy Fusion Whale Optimization Algorithm (MSFWOA) with the Light Gradient Boosting Machine (LightGBM), resulting in the MSFWOA-LightGBM model. This model employs the Coulomb matrix representation and eigenvalue solution methods for feature extraction. Additionally, it incorporates the Tent chaotic mapping, cosine convergence factor, and inertia weight updating strategy to optimize the Whale Optimization Algorithm (WOA), leading to the development of MSFWOA. Subsequently, MSFWOA is employed to optimize the parameters of LightGBM for supporting the energy prediction of Au20 cluster.

CONCLUSIONS

The experimental results show that the most stable Au20 cluster structure is a regular tetrahedron with the lowest energy, displaying tight and uniform atom distribution, high geometric symmetry. Compared to other models, the MSFWOA-LightGBM model excels in accuracy and correlation, with MSE, RMSE, and R2 values of 0.897, 0.947, and 0.879, respectively. Additionally, the MSFWOA-LightGBM model possesses outstanding scalability, offering valuable insights for material design, energy storage, sensing technology, and biomedical imaging, with the potential to drive research and development in these areas.

Optimized solubility and bioavailability of genistein based on cocrystal engineering

With various potential health-promoting bioactivities, genistein has great prospects in treatment of a series of complex diseases and metabolic syndromes such as cancer, diabetes, cardiovascular diseases, menopausal symptoms and so on. However, poor solubility and unsatisfactory bioavailability seriously limits its clinical application and market development. To optimize the solubility and bioavailability of genistein, the cocrystal of genistein and piperazine was prepared by grinding assisted with solvent based on the concept of cocrystal engineering. Using a series of analytical techniques including single-crystal X-ray diffraction, powder X-ray diffraction, Fourier transform infrared spectroscopy, differential scanning calorimetry and thermogravimetric analysis, the cocrystal was characterized and confirmed. Then, structure analysis on the basis of theoretical calculation and a series of evaluation on the stability, dissolution and bioavailability were carried out. The results indicated that the cocrystal of genistein and piperazine improved the solubility and bioavailability of genistein. Compared with the previous studies on the cocrystal of genistein, this is a systematic and comprehensive investigation from the aspects of preparation, characterization, structural analysis, stability, solubility and bioavailability evaluation. As a simple, efficient and green approach, cocrystal engineering can pave a new path to optimize the pharmaceutical properties of natural products for successful drug formulation and delivery.

Two Novel Co-Crystals of Naproxen: Comparison of Stability, Solubility and Intermolecular Interaction

Two novel co-crystals of naproxen (NPX) were designed and prepared at a stoichiometric ratio of 1:1, namely, naproxen–caprolactam (NPX–CPL) and naproxen–oxymatrine (NPX–OMT). The characteristics of the co-crystals were evaluated in terms of stability and solubility studies. In terms of solubility, in four kinds of solvent systems with different pH, the solubility of NPX–OMT was significantly improved compared with that of NPX, whereas the NPX–CPL showed advantages in acidic solvent systems, indicating that the co-crystals can be applied to concoct preparations depending on therapeutic purposes. Furthermore, the experimental results of the thermal analysis showed that the co-crystal NPX–OMT had better thermal stability than the co-crystal NPX–CPL. Finally, as a complement to the single crystal X-ray diffraction (SC XRD) method, the theoretical calculation based on density functional theory (DFT) was also used to reveal the intermolecular interaction of the co-crystals at the molecular level and visually display the difference between them.