Following the full realization of the importance of noncovalent interactions, finding and characterizing stationary points (SP), of various order, for weakly bound oligomers have become important tasks for computational chemists. An efficient algorithm and an associated computer code, called oligoCGO, are described, facilitating constrained geometry optimization of oligomers of arbitrary structure and complexity and normal-mode vibrational analysis at nonstationary geometries. To minimize the adverse effects of nonzero forces on harmonic vibrational analyses at constrained stationary points (cSP), two residual gradient correction (RGC) schemes are proposed. RGC, for which a rigorous justification is given, is based on ignoring the remaining forces in internal-coordinate space. RGC modifies the geometry of the cSP in a single Newton step and recalculates the Cartesian Hessian at this updated geometry. As demonstrated by 10 examples related to the water-water, water-methane, and methane-methane dimers as well as the methane trimer, without RGC the harmonic analysis of cSPs may result in even qualitatively incorrect results when compared to reference values obtained at the nearby unconstrained SPs (uSP). Both RGC protocols work exceedingly well, and the corrected harmonic wavenumbers of the cSPs are very close to their uSP counterparts.
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http://dx.doi.org/10.1021/acs.jctc.1c01148 | DOI Listing |
J Phys Chem A
January 2025
Institute of Modern Physics, Shaanxi Key Laboratory for Theoretical Physics Frontiers, Northwest University, Xi'an, Shaanxi 710127, China.
The full-dimensional potential energy surface (PES) for the photodissociation of HNCS in the S(″) electronic state has been built up by the neural network method based on more than 48,000 points, which were calculated at the multireference configuration interaction level with Davidson correction using the augmented correlation consistent polarized valence triple-ζ basis set. It was found that two minima, namely, and isomers of HNCS, and seven stationary points exist on the S PES for the three dissociation pathways: HNCS(S) → H + NCS/HNC + S(D)/HN(Δ) + CS(Σ). The dissociation energies of two lowest product channels H + NCS and HNC + S(D) calculated on the PES are in good agreement with experimental results, validating the high accuracy of the PES.
View Article and Find Full Text PDFChaos
January 2025
IGCE-Physics Department, São Paulo State University (UNESP), 13506-900 Rio Claro, SP, Brazil.
The dynamics of the convergence for the stationary state considering a Duffing-like equation are investigated. The driven potential for these dynamics is supplied by a damped forced oscillator that has a piecewise linear function. Fixed points and their basins of attraction were identified and measured.
View Article and Find Full Text PDFJ Mol Model
January 2025
Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland.
Context: The analysis of the changes in the electronic structure along intrinsic reaction coordinate (IRC) paths for model reactions: (i) ethylene + butadiene cycloaddition, (ii) prototype SN2 reaction Cl + CH3Cl, (iii) HCN/CNH isomerization assisted by water, (iv) CO + HF → C(O)HF was performed, in terms of changes in the deformation density (Δr) and the deformation of MEP (ΔMEP). The main goal was to further examine the utility of the ΔMEP as a descriptor of chemical bonding, and to compare the pictures resulting from Δr and ΔMEP. Both approaches clearly show that the main changes in the electronic structure occur in the TS region.
View Article and Find Full Text PDFNeural Netw
December 2024
College of Life Science, Hunan Normal University, Changsha, PR China. Electronic address:
Sci Rep
December 2024
Department of Biophysics, Faculty of Environmental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
We present a comprehensive spectroscopic study supported by theoretical quantum chemical calculations conducted on a molecular system (4-(5-methyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (C1) and the antibiotic Amphotericin B (AmB)) that exhibits highly synergistic properties. We previously reported the strong synergism of this molecular system and now wish to present related stationary measurements of UV-Vis absorption, fluorescence, and fluorescence anisotropy in a polar, aprotic solvent (DMSO and a PBS buffer), followed by time-resolved fluorescence intensity and anisotropy decay studies using different ratios of the selected 1,3,4-thiadiazole derivative to Amphotericin B. Absorption spectra measured for the system revealed discrepancies in terms of the shapes of absorption bands, particularly in PBS.
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