A new hybrid discrete-continuum approach named the cluster-continuum static approximation (CCSA) has been proposed for acetonitrile solvent. The continuum part uses the conductor-like polarizable continuum model for electrostatic and a surface area-dependent term for nonelectrostatic solvation. The CCSA includes only one explicit acetonitrile solvent molecule and a damping function, which makes the CCSA method reduce to pure continuum solvation in the case of weaker potential of mean force for solute-solvent interaction. The performance of the model was tested for 22 anions and 22 cations, including challenge species that cannot be adequately described by pure continuum solvation. A comparison was done with the widely used solvent model density (SMD) model. For anions, the CCSA reduces to pure continuum solvation and the method has the same performance as the SMD model, with a standard deviation of the mean signed error (SD-MSE) of 2.7 kcal mol for both models. However, the CCSA method for cations considerably outperforms the SMD model, with an SD-MSE of 3.3 kcal mol for the former and 8.4 kcal mol for the latter. The method can be automated, and the present study suggests that continuum solvation models could be parameterized taking into account the explicit solvation as proposed in this work.
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http://dx.doi.org/10.1021/acs.jpca.4c03593 | DOI Listing |
J Chem Inf Model
January 2025
Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada.
The near neutral p of histidine is commonly exploited to engineer pH-sensitive biomolecules. For example, histidine mutations introduced in the complementarity-determining region (CDR) of therapeutic antibodies can enhance selectivity for antigens in the acidic microenvironment of solid tumors or increase dissociation rates in the acidic early endosomes of cells. While solvent-exposed histidines typically have a p near 6.
View Article and Find Full Text PDFJ Phys Chem A
January 2025
Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China.
The fundamental hydrolysis behavior of tetravalent actinide cations (An) with a high charge is crucial for understanding their solution chemistry, particularly in nuclear fuel reprocessing and environmental behavior. Using Th as a reference of the An series, this work employed both the periodic model and the cluster model to calculate the first hydrolysis reaction constant (p) of the Th aqua ion and conducted a detailed evaluation of these approaches. In the periodic model, molecular dynamics (AIMD) simulations of Th in the explicit solvation environment are conducted, using metadynamics and constrained molecular dynamics to calculate p values.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
The complete active space second-order perturbation theory (CASPT2) is valuable for accurately predicting electronic structures and transition energies. However, optimizing molecular geometries in the solution phase has proven challenging. In this study, we develop analytic first-order derivatives of CASPT2 using an implicit solvation model, specifically the polarizable continuum model, within the open-source package OpenMolcas.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Barcelona, Spain.
Continuum solvation models such as the polarizable continuum model and the conductor-like screening model are widely used in quantum chemistry, but their application to large biosystems is hampered by their computational cost. Here, we report the parametrization of the Miertus-Scrocco-Tomasi (MST) model for the prediction of hydration free energies of neutral and ionic molecules based on the domain decomposition formulation of COSMO (ddCOSMO), which allows a drastic reduction of the computational cost by several orders of magnitude. We also introduce several novelties in MST, like a new definition of atom types based on hybridization and an automatic setup of the cavity for charged regions.
View Article and Find Full Text PDFMolecules
December 2024
Institute of Earth Sciences, Faculty of Natural Sciences, University of Silesia in Katowice, 60, Będzińska, 41-200 Sosnowiec, Poland.
Cathinone and its synthetic derivatives belong to organic compounds with narcotic properties. Their structural diversity and massive illegal use create the need to develop new analytical methods for their identification in different matrices. NMR spectroscopy is one of the most versatile methods for identifying the structure of organic substances.
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