Density functionals fail to provide a consistent description of weak intra- (i.e., short-range) and inter- (i.e., long-range) molecular interactions arising from nonoverlapping electron densities. An efficient way to correct the long-range errors is to add an empirical atom pair wise interaction-correction, inspired by the Lennard-Jones potential (R(-6) dependence). We show that the universal damping function of Tang and Toennies (TT) that includes higher-order correction terms (R(-8) and R(-10) dependent) reduces the intramolecular errors more efficiently, without altering the long-range correction. For general applicability, the TT damping function is augmented by a Fermi damping to prevent corrections at covalent distances. The performance of the new dD10 correction was tested in combination with three nonempirical GGAs (PBE, PBEsol, RGE2) on 64 illustrative reaction energies featuring both intra- and intermolecular interactions. With only two empirical parameters, PBE-dD10 outperforms the computationally more demanding and most recent functionals such as M06-2X or B2PLYP-D (MAD = 3.78 and 1.95 kcal mol(-1), respectively). At the cc-pVTZ level, PBE-dD10 (MAD = 1.24 kcal mol(-1)) considerably reduces common DFT errors successfully balancing intra- (short-range) and inter- (long-range) molecular interactions. While REG2-dD10 performs closely to PBE-dD10 (MAD = 1.48 kcal mol(-1)), the overall MAD of PBEsol-dD10 is again slightly higher (MAD = 1.76 kcal mol(-1)).
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R Soc Open Sci
January 2025
Department of Chemistry, Jagannath University, Dhaka 1100, Bangladesh.
In this study, three pyridine- and four thiophene-containing chalcone derivatives were synthesized via Claisen-Schmidt condensation reaction, where five derivatives were new. Different spectral analyses (IR, H NMR, HRMS) clarified the structures and these proposed compounds were screened for antimicrobial activity by the agar disc diffusion technique. Compound was conspicuously active against most of the bacterial and fungal strains.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar-470003, India.
In a recent communication (A. Shivhare, B. Dehariya, S.
View Article and Find Full Text PDFRSC Adv
January 2025
Department of Chemistry, Debre Tabor University Ethiopia.
DFT calculations were performed to investigate the possible reaction mechanisms underlying catalyst-free chloroboration reactions of carbonyl compounds with BCl. The interaction between BCl and the C[double bond, length as m-dash]O moiety of carbonyl compounds is a two-step reaction. In the first step, B of BCl forms a bond with the O of the C[double bond, length as m-dash]O moiety, followed by the 1,3-Cl migration process from BCl to the C of the carbonyl group.
View Article and Find Full Text PDFMolecules
January 2025
Department of Chemistry, Hunter College, The City University of New York, 695 Park Ave., New York, NY 10065, USA.
Using methods of DFT, we investigated the effect of electron withdrawing and electron donating groups on the relative stability of tentative glycosyl donor reaction intermediates. The calculation shows that by changing the stereoelectronic properties of the protecting group, we can influence the stability of the dioxolenium type of intermediates by up to 10 kcal mol, and that by increasing nucleophillicity of the 4--Bz group, the dioxolenium intermediate becomes more stable than a triflate-donor pair. We exploited this mechanism to design galactosyl donors with custom protecting groups on O2 and O4, and investigated the outcome of the reaction with cyclohexanol.
View Article and Find Full Text PDFPredicting reaction barriers for arbitrary configurations based on only a limited set of density functional theory (DFT) calculations would render the design of catalysts or the simulation of reactions within complex materials highly efficient. We here propose Gaussian process regression (GPR) as a method of choice if DFT calculations are limited to hundreds or thousands of barrier calculations. For the case of hydrogen atom transfer in proteins, an important reaction in chemistry and biology, we obtain a mean absolute error of 3.
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