We present an investigation of the excited-state structural parameters determined for a large set of small compounds with the dual goals of defining reference values for further works and assessing the quality of the geometries obtained with relatively cheap computational approaches. In the first stage, we compare the excited-state geometries obtained with ADC(2), CC2, CCSD, CCSDR(3), CC3, and CASPT2 and large atomic basis sets. It is found that CASPT2 and CC3 results are generally in very good agreement with one another (typical differences of ca. 3 × 10 Å) when all electrons are correlated and when the aug-cc-pVTZ atomic basis set is employed with both methods. In a second stage, a statistical analysis reveals that, on the one hand, the excited-state (ES) bond lengths are much more sensitive to the selected level of theory than their ground-state (GS) counterparts and, on the other hand, that CCSDR(3) is probably the most cost-effective method delivering accurate structures. Indeed, CCSD tends to provide too compact multiple bond lengths on an almost systematic basis, whereas both CC2 and ADC(2) tend to exaggerate these bond distances, with more erratic error patterns, especially for the latter method. The deviations are particularly marked for the polarized CO and CN bonds, as well as for the puckering angle in formaldehyde homologues. In the last part of this contribution, we provide a series of CCSDR(3) GS and ES geometries of medium-sized molecules to be used as references in further investigations.
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http://dx.doi.org/10.1021/acs.jctc.7b00921 | DOI Listing |
J Phys Chem Lett
January 2025
Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway.
Minimum energy conical intersections can be used to rationalize photochemical processes. In this Letter, we examine an algorithm to locate these structures that does not require the evaluation of nonadiabatic coupling vectors, showing that it minimizes the energy on hypersurfaces that envelop the intersection seam. By constraining the states to be separated by a small non-zero energy difference, the algorithm ensures that numerical artifacts and convergence problems of coupled cluster theory at conical intersections are not encountered during the optimization.
View Article and Find Full Text PDFMolecules
December 2024
Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677, USA.
Molecular dyes containing carbazole-based π bridges and/or julolidine-based donors should be promising molecules for intense SWIR emission with potential application to molecular bioimaging. This study stochastically analyzes the combinations of more than 250 organic dyes constructed within the D-π-D (or equivalently D-B-D) motif. These dyes are built from 22 donors (D) and 14 π bridges (B) and are computationally examined using density functional theory (DFT).
View Article and Find Full Text PDFMolecules
December 2024
High & New Technology Research Center of Henan Academy of Sciences, No. 56 Hongzhuan Road, Zhengzhou 450002, China.
A series of colorful binuclear Schiff bases derived from the different diamine bridges including 1,2- ethylenediamine (bis-Et-SA, bis-Et-4-NEt, bis-Et-5-NO, bis-Et-Naph), 1,2-phenylenediamine (bis-Ph-SA, bis-Ph-4-NEt, bis-Ph-5-NO, bis-Ph-Naph), dicyano-1,2-ethenediamine (bis-CN-SA, bis-CN-4-NEt, bis-CN-5-NO, bis-CN-Naph) have been designed and prepared. The optical properties of these binuclear Schiff base ligands were fully determined by UV-Vis absorption spectroscopy, fluorescence emission spectroscopy, and time-dependent-density functional theory (TD-DFT) calculations. The inclusion of D-A systems and/or π-extended systems in these binuclear Schiff base ligands not only enables adjustable RGB light absorption and emission spectra (300~700 nm) but also yields high fluorescence quantum efficiencies of up to 0.
View Article and Find Full Text PDFBiomolecules
December 2024
Institut de Chimie Physique, CNRS-UMR8000, Université Paris-Saclay, 91405 Orsay, France.
There is compelling evidence that the absorption of low-energy UV radiation directly by DNA in solution generates guanine radicals with quantum yields that are strongly dependent on the secondary structure. Key players in this unexpected phenomenon are the photo-induced charge transfer () states, in which an electric charge has been transferred from one nucleobase to another. The present work examines the factors affecting the population of these states during electronic relaxation.
View Article and Find Full Text PDFProtein Sci
January 2025
Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.
Cyclooxygenase-2 (COX-2) plays a crucial role in inflammation and has been implicated in cancer development. Understanding the behavior of COX-2 in different cellular contexts is essential for developing targeted therapeutic strategies. In this study, we investigate the fluorescence spectrum of a fluorogenic probe, NANQ-IMC6, when bound to the active site of human COX-2 in both its monomeric and homodimeric forms.
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