A new approach is presented to improve the performance of semiempirical quantum mechanical (SQM) methods in the description of noncovalent interactions. To show the strategy, the PM6 Hamiltonian was selected, although, in general, the procedure can be applied to other semiempirical Hamiltonians and to different methodologies. A set of small molecules were selected as representative of various functional groups, and intermolecular potential energy curves (IPECs) were evaluated for the most relevant orientations of interacting molecular pairs. Then, analytical corrections to PM6 were derived from fits to B3LYP-D3/def2-TZVP reference-PM6 interaction energy differences. IPECs provided by the B3LYP-D3/def2-TZVP combination of the electronic structure method and basis set were chosen as the reference because they are in excellent agreement with CCSD(T)/aug-cc-pVTZ curves for the studied systems. The resulting method, called PM6-FGC (from functional group corrections), significantly improves the performance of PM6 and shows the importance of including a sufficient number of orientations of the interacting molecules in the reference data set in order to obtain well-balanced descriptions.
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http://dx.doi.org/10.1021/acs.jctc.1c00365 | DOI Listing |
Acta Crystallogr C Struct Chem
January 2025
College of Chemistry and Materials Science, Anhui Normal University, Wuhu, Anhui 241000, People's Republic of China.
A new twofold interpenetrated 3D metal-organic framework (MOF), namely, poly[[μ-aqua-diaqua{μ-2,2'-[terephthaloylbis(azanediyl)]diacetato}barium(II)] dihydrate], {[Ba(CHNO)(HO)]·2HO}, (I), has been assembled through a combination of the reaction of 2,2'-[terephthaloylbis(azanediyl)]diacetic acid (TPBA, HL) with barium hydroxide and crystallization at low temperature. In the crystal structure of (I), the nine-coordinated Ba ions are bridged by two μ-aqua ligands and two carboxylate μ-O atoms to form a 1D loop-like Ba-O chain, which, together with the other two coordinated water molecules and μ-carboxylate groups, produces a rod-like secondary building unit (SBU). The resultant 1D polynuclear SBUs are further extended into a 3D MOF via the terephthalamide moiety of the ligand as a spacer.
View Article and Find Full Text PDFTalanta
December 2024
Department of Pathology, College of Medicine, King Khalid University, Asir, 61421, Saudi Arabia; Forensic Medicine and Clinical Toxicology Department, Mansoura University, Egypt. Electronic address:
Complexing medications with cyclodextrins can enhance their solubility and stability. In this study, we investigated the host-guest complexation between Tetrahydrocurcumin (THC) and Hydroxypropyl-β-Cyclodextrin (HP-β-CD) using density functional theory (DFT) at the B3LYP-D3/TPZ level of theory in two possible orientations. To determine the reactive sites in both complexes for electrophilic and nucleophilic attacks, we calculated and interpreted the binding energy, HOMO and LUMO orbitals, global chemical reactivity descriptors, natural bond orbital (NBO) analysis, and Fukui indices.
View Article and Find Full Text PDFJ Mol Model
January 2025
Laboratorio de Química Teórica Computacional (QTC), Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, 7820436, Santiago de Chile, Chile.
Context: Dopamine -monooxygenase (D M) is an essential enzyme in the organism that regioselectively converts dopamine into R-norepinephrine, the key step of the reaction, studied in this paper, is a hydrogen atom transfer (HAT) from dopamine to a superoxo complex on D M, forming a hydroperoxo intermediate and dopamine radical. It was found that the formation of a hydrogen bond between dopamine and the D M catalyst strengthens the substrate-enzyme interaction and facilitates the HAT which takes place selectively to give the desired enantiomeric form of the product. Six reactions leading to the hydroperoxo intermediate were analyzed in detail using theoretical and computational tools in order to identify the most probable reaction mechanism.
View Article and Find Full Text PDFChem Commun (Camb)
January 2025
Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain.
Discrimination of enantiomeric substrate molecules is one of the fundamental properties of biological hosts. Replicating enantioselective molecular recognition with synthetic receptors is a topic of interest with implications in diverse applications such as bioinspired enantioselective catalysis, enantiomer separation, or sensing. In this review, five different systems reported in the literature are discussed, and their performance and versatility are analyzed.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Chemistry, Columbia University, New York, NY, USA.
Variants of SARS-CoV-2 have continued to emerge across the world and cause hundreds of deaths each week. Due to the limited efficacy of vaccines against SARS-CoV-2 and resistance to current therapies, additional anti-viral therapeutics with pan-coronavirus activity are of high interest. Here, we screen 2.
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