Interpretation of Nucleophilic α- and their relative β-, γ- and δ-Effects from Recognition of Tetrel Bonding Interaction: An Experimental Validation in Solution through Fluorometry

Published: 20 October 2023| Version 1 | DOI: 10.17632/vw5n227z7k.1
Angel Romero, Gustavo Cabrera,


The data consists of NMR spectra and output for all calculations performed in the corresponding article. Theoretical Calculation. Herein we reported a simple and rapid strategy to validate the nucleophilicity and nucleophilic α-effect from simple steady state fluorescence measurements at room temperature with minimal sample and time requirements using a convenient fluorophore featuring an σ-hole region. The key point was the occurrence of a tetrel bond (TtB) between σ/π-hole region (A-acceptor) of the fluorophore with nucleophilic side of nucleophile. That TtB promoted a selective quenching that was dependent on the nucleophilicity of the nucleophile. Other key point was the existence of an ICT mechanism into fluorophore upon excitation, which enhanced the selectivity and strength of the quenching response. A broad number of nucleophiles from anionic species to neutral nucleophiles was analyzed. The occurrence of the TtB was theoretically and experimentally supported. Also, we introduced the concept of “nucleophilic β, γ- and δ-effects” for interpreting the over-nucleophilicity of some “β-, γ- and δ-nucleophiles”. A general interpretation of the origin of the anomalous nucleophilic effects based on the extra stabilization of transition-state and the high magnitude of HOMO energies was provided. Our strategy opens new perspective for quantifying the nucleophilicity and their anomalous effects based on the recognition of non-covalent interaction and using the fluorometry as key technique for detection. The data consisted of experimental NMR for supporting tetrel bond adduct between probe and iodide. Output documents with all details are available from calculation derived from tetrel bond between probe 3k with different nucleophiles as well as simple .log document from optimization and HOMO/LUMO output for all studied nucleophiles at different theoretical approach. Also, simulation transition state between probe and nucleophile adduct, their optimization output as .log document are found.


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All DFT calculations were carried out at the Copernico Cluster of the computational center at Science Faculty (Universidad Central Venezuela, Caracas, Venezuela). All theoretical calculations, in gas phase, were performed by using density functional theory (DFT) with the Gaussian 09 quantum chemistry software.8 To achieve a balance between the computational cost and accuracy of the calculations, two combined DFT based approaches were employed: (i) CAM-B3LYP functional9 and (ii) B3LYP functional10 in combination with 6-31G(d,p) basis set11. Optimization of geometry of N1-(4-aryl)-2-(trifluoromethyl)-8-methoxybenzo[b][1,8]naphthyridin-4(1H)-ones 3k (Chart 1S) and their adduct with nucleophiles were performed. Previously, we found that the B3LYP/6-31G(d,p) gave good estimations for structural parameters of the N1-aryl-2-(trifluoromethyl)benzo[b][1,8]naphthyridin-4(1H)-ones (Figure 1 and S1), being a convenient approach for providing reasonably results for intermolecular interactions.11-13 All structures were optimized in ground state without restrictions, using tight optimization criteria and ultrafine grid in the computation of two-electron integrals and their derivatives. Optimization calculations were performed using Berny algorithm and, they were successfully completed under the following parameters: maximum force 0.000450, RMS force of 0.000300, maximum displacement 0.001800, RMS displacement 0.001200 and predicted change in energy of -1.488276x10-8 Hartree for most of studied cases. The vibrational frequencies of the stationary-point geometries of the molecules and Natural Bond Orbitals (NBO) were calculated at the same computational level. Vibration frequency calculations were performed to obtain vibrational zero-point energies and to validate that the located structures corresponded to the energy minima. The structures should have only positive harmonic vibrations. Further analysis to identify the occurrence of non-covalent interaction was performed on Multiwfn software,14 version 3.8. NCI plots, RDG isosurfaces and ELF analysis were obtained for the 3k-(I2)n adducts (Figures 2-5 and Figure S2). EPS maps were obtained for the different studied 3k-(I2)n adducts (Table 1). A detailed HOMO-LUMO analysis based on the nucleophile was analyzed in Section 4 of Supporting Information Material. Data is summarized and illustrated in Table S3 and Figures S12-S14. All calculation outputs can be found at the Section 5 of the Supporting Information. NMR-experiments for dye 3g-iodide binding. To a solution of 3g in DMSO-d6, iodide anion was added and, their 1H-NMR (Figure S3) and 19F-NMR (Figure S4) spectra were collected at room temperature and compared with its spectrum in absence of molecular iodide anion. For the experiment, probe 3g (8 mg/mL, 23.5 mM, 1.0 equiv.) and iodide potassium (16 mg/mL, 96.4 mM) were used.


Universidad de la Republica Uruguay


Physical Organic Chemistry


Agencia Nacional de Investigación e Innovación


Universidad de la República Uruguay