Electron density-based implicit solvation models are a class of techniques for quantifying solvation effects and calculating free energies of solvation without an explicit representation of solvent molecules. Integral to the accuracy of solvation modeling is the proper definition of the solvation shell separating the solute molecule from the solvent environment, allowing for a physical partitioning of the free energies of solvation. Unlike state-of-the-art implicit solvation models for molecular quantum chemistry calculations, .., the solvation model based on solute electron density (SMD), solvation models for systems under periodic boundary conditions with plane-wave (PW) basis sets have been limited in their accuracy. Furthermore, a unified implicit solvation model with both homogeneous solution-phase and heterogeneous interfacial structures treated on equal footing is needed. In order to address this challenge, we developed a high-accuracy solvation model for periodic PW calculations that is applicable to molecular, ionic, interfacial, and bulk-phase chemistry. Our model, PW-SMD, is an extension of the SMD molecular solvation model to periodic systems in water. The free energy of solvation is partitioned into the electrostatic and cavity-dispersion-solvent structure (CDS) contributions. The electrostatic contributions of the solvation shell surrounding solute structures are parametrized based on their geometric and physical properties. In addition, the nonelectrostatic contribution to the solvation energy is accounted for by extending the CDS formalism of SMD to incorporate periodic boundary conditions. We validate the accuracy and robustness of our solvation model by comparing predicted solvation free energies against experimental data for molecular and ionic systems, carved-cluster composite energetic models of solvated reaction energies and barriers on surface systems, and deep-learning-accelerated molecular dynamics (AIMD). Our developed periodic implicit solvation model shows significantly improved accuracy compared to previous work (namely, solvation models in aqueous solution) and can be applied to simulate solvent effects in a wide range of surface and crystalline materials.
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http://dx.doi.org/10.1021/acs.jctc.4c00594 | DOI Listing |
J Mol Model
December 2024
Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Avenida Ferrocarril San Rafael Atlixco, Número 186, Colonia Leyes de Reforma 1A Sección, Alcaldía Iztapalapa, Código Postal 09310, Ciudad de Mexico, Mexico.
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View Article and Find Full Text PDFJ Comput Chem
January 2025
Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas, USA.
Multi-copper oxidases (MCOs) are enzymes of significant interest in biotechnology due to their efficient catalysis of oxygen reduction to water, making them valuable in sustainable energy production and bio-electrochemical applications. This study employs time-dependent density functional theory (TDDFT) to investigate the electronic structure and spectroscopic properties of the Type 1 (T1) copper site in Azurin, which serves as a model for similar sites in MCOs. Four model complexes of varying complexity were derived from the T1 site, including 3 three-coordinate models and 1 four-coordinate model with axial methionine ligation, to explore the impact of molecular branches and axial coordination.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA.
Voltage-dependent anion channel (VDAC) is the primary conduit for regulated passage of ions and metabolites into and out of a mitochondrion. Calculating the solvation free energy for VDAC is crucial for understanding its stability, function, and interactions within the cellular environment. In this article, numerical schemes for computing the total solvation free energy for VDAC-comprising electrostatic, ideal gas, and excess free energies plus the nonpolar energy-are developed based on a nonuniform size modified Poisson-Boltzmann ion channel (nuSMPBIC) finite element solver along with tetrahedral meshes for VDAC proteins.
View Article and Find Full Text PDFIn Silico Pharmacol
December 2024
Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russian Federation.
Unlabelled: Urinary tract infections (UTIs), largely caused by uropathogenic (UPEC), are increasingly resistant to antibiotics and frequently recur. Using immunoinformatics, we designed a multiepitope peptide vaccine targeting UPEC virulence factors, including iron acquisition systems and adhesins. The construct features 12 cytotoxic T lymphocyte epitopes, six helper T lymphocyte epitopes, and six B-cell epitopes,and isoptimized for high antigenicity, immunogenicity, nontoxic, and low allergenic potential.
View Article and Find Full Text PDFLangmuir
December 2024
Department of Architectural Engineering, Hanyang University ERICA, 55 Hanyangdaehak-ro, Sangrok-gu, Ansan-si 15588, Gyeonggi-do, Republic of Korea.
Reliable corrosion inhibition systems are crucial for extending the lifespan of industrial metal structures. Quinolines, with their high adsorption capacity and protective efficiency, are promising next-generation inhibitors. However, the impact of substitutions on their coordination with iron surfaces requires deeper understanding.
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