We investigate the suitability of subsystem time-dependent density-functional theory (sTDDFT) for describing chiroptical properties with a focus on optical rotation parameters. Our starting point is a new implementation of the recently proposed projection-based, coupled frozen-density embedding (FDEc) framework. We adapt the generalized, non-Hermitian formulation of TDDFT and derive corresponding expressions for regular and damped response properties from subsystem TDDFT. We verify that our implementation of this "exact" formulation allows to reproduce supermolecular results of electronic circular dichroism (ECD) spectra, of optical rotatory dispersion, and of polarizabilities. We present a systematic test of the main approximations typically introduced in practical frozen-density embedding (FDE) calculations of response properties: (i) the use of approximate nonadditive kinetic-energy (NAKE) functionals, which can be avoided through projection techniques, (ii) the use of monomer (subsystem) basis sets rather than supersystem basis sets, and (iii) the neglect of intersubsystem response coupling within the so-called uncoupled FDE (or FDEu) approximation. While approximation (i) is known to generally lead to large errors for covalently bound subsystems, we present cases in which either the basis set or the coupling step are similarly or even (much) more important. In particular, we explicitly demonstrate by comparison to a fully coupled calculation that missing intersubsystem response couplings are responsible for the failure of FDE reported in a previous study [ 2015, 11, 5305-5315]. We show that good agreement with reference results can be obtained in this case even with standard NAKE approximations for the FDE potentials and efficient monomer basis sets, making calculations for larger systems well accessible.
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http://dx.doi.org/10.1021/acs.jctc.0c00125 | DOI Listing |
Unlabelled: The reflexive translation of symbols in one chemical language to another defined genetics. Yet, the co-linearity of codons and amino acids is so commonplace an idea that few even ask how it arose. Readout is done by two distinct sets of proteins, called aminoacyl-tRNA synthetases (AARS).
View Article and Find Full Text PDFJ Mol Model
January 2025
Department of Chemistry, Military Institute of Engineering, Praça General Tibúrcio 80, Rio de Janeiro, Brazil.
Context: Nitrocellulose, widely used in energetic materials, is prone to thermal and chemical degradation, compromising safety and performance. Stabilizers are molecules used in the composition of nitrocellulose-based propellants to inhibit the autocatalytic degradation process that produces nitrous gases and free nitric acids. Curcumin, (1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione, known for its antioxidant properties and a potential green stabilizer, was investigated using Density Functional Theory (DFT) focusing on its interaction with nitrogen dioxide.
View Article and Find Full Text PDFBiochem Biophys Rep
March 2025
Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Kunming Medical University, No.374 Yunnan-Burma Road, Kunming, Yunnan, 650101, China.
Background: Hepatocellular carcinoma (HCC) is a globally prevalent disease. Our article evaluates risk models based on autophagy- and HCC-related genes and their prognostic value by bioinformatics analytical methods to provide a scientific basis for clinical treatment.
Methods: Prognostic genes were identified by univariate and multivariate Cox analyses, and risk scores were calculated.
Med Chem
January 2025
Graduate School of NanoBio Sciences, Yokohama City University, 22-2, Seto, Kanazawa-Ku, Yokohama 236-0027, Japan.
Aim: There is an urgent need for new antimicrobial compounds with alternative modes of action for the treatment of drug-resistant bacterial and fungal pathogens.
Background: Carbohydrates and their derivatives are essential for biochemical and medicinal research because of their efficacy in the synthesis of biologically active drugs.
Objective: In the present study, a series of methyl α-D-mannopyranoside (MMP) derivatives (2-6) were prepared via direct acylation, and their biological properties were characterized.
J Immunother Cancer
January 2025
National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, China
Background: Clear cell renal cell carcinoma (ccRCC) is the most common histologic type of RCC. However, the spatial and functional heterogeneity of immunosuppressive cells and the mechanisms by which their interactions promote immunosuppression in the ccRCC have not been thoroughly investigated.
Methods: To further investigate the cellular and regional heterogeneity of ccRCC, we analyzed single-cell and spatial transcriptome RNA sequencing data from four patients, which were obtained from samples from multiple regions, including the tumor core, tumor-normal interface, and distal normal tissue.
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