Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione

Etsè, Koffi Sénam; Lamela, Laura Comeron; Zaragoza, Guillermo; Pirotte, Bernard

doi:10.5155/eurjchem.11.2.91-99.1973

Cited by 13 publications

(5 citation statements)

References 24 publications

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“…For a best description and measure the weight of the different contacts, the molecular fingerprint is generally used. Indeed, the de and di are combined to generate a 2D histogram named molecular fingerprint (FP) plot [38,39]. Due the molecular diversity in the immediate environment, the fingerprint of a selected molecule is unique.…”

Section: Resultsmentioning

confidence: 99%

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

Etsè

Quashie

2022

Eur J Chem

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This work reports for the first time, the analysis of intermolecular interactions in crystal structures of auxin (Indole-3-acetic acid) crystallized as pure sample (Aux-A) or co-crystallized with transport inhibitor response 1 (Aux-B). Using crystal packing of pure auxin and a cluster of residues in a radius of 6 Å around this ligand in the transport inhibitor response 1 binding domain, various properties were calculated and mapped on the Hirshfeld surface (HS). The HSs of the two molecules are characterized by close parameters of volume, area, globularity, and asphericity revealing the efficiency of the considered cluster. The HS mapped over descriptors like de, di and dnorm showed red spots corresponding to hydrogen bonds contacts. In addition to the shape index and curvedness descriptors, the results highlight weak interactions stabilizing the auxin structures. The analyses of electrostatic potential, electron density, and deformation density maps confirm the slightly change in the electron donor and acceptor groups localization. Furthermore, the molecular fingerprint analyses revealed a notable discrepancy in the shape and percentage value of the various contacts. Decomposition of the fingerprint shows that the contributions of important contacts (H···H, H···O, and O···O) are higher in Aux-B than in Aux-A. Finally, the quantitative approach by the determination of the molecular interaction energies of the two structures in their respective crystallographic environment revealed that Aux-A is slightly more stabilized than Aux-B.

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Section: Resultsmentioning

confidence: 99%

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

Etsè

Quashie

2022

Eur J Chem

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“…The computation of energy frames was developed to better understand the topology of the overall interaction energies between the components of a crystal. Total intermolecular interaction energy (E tot) using scale factors of 1.057, 0.740, 0.871 and 0.618, respectively, using four energy terms (electrostatic (E ele ), polarization (E pol ), dispersion (E disp ) and exchangerepulsion (E rep ) ) are added together (Etse et al, 2020;Mackenzie et al, 2017;Madan Kumar, 2019). The closeness of the total energy values calculated in all four isostructural complexes is shown in Table 2.…”

Section: Interactions Energy Analysismentioning

confidence: 98%

Determination of Intermolecular Interactions of Nicotinamide Liganded Complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-Formilbenzoates by Hirshfeld Surface Analysis and Investigation of Interaction Energies.

Sertçelik

2022

Caucasian Journal of Science

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CrystalExplorer program is a program that has been used frequently in the field of theoretical chemistry in recent years and its popularity has increased. First of all, Hirshfeld surface analysis of molecules can be done in this program. Thanks to Hirshfeld surface analysis, intermolecular interactions and their contributions to the crystal surface can be determined. In this study, Hirshfeld surface analyzes and energy frameworks of nicotinamide complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-formylbenzoate were investigated. Dnorm index, shape index, curvature index and 2D fingerprint graphs were examined for all complexes. In addition, the intermolecular interaction energies of the complexes were calculated using the CE-B3LYP/6-31G (d,p) and CEHF/3-21G energy models. As a result of all these, it was seen that the most important interaction in the four isostructured complexes was H...H interactions. According to Hirshfeld surface analysis and energy frameworks, O-H...O and N-H...O hydrogen bonds and π•••π stacking and C−H••π interaction energies are seen as the most important interaction types in the crystal structure.

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“…Hirshfeld surface analysis was obtained utilizing the CIF file from single-crystal XRD analysis to quantify and depict multiple intermolecular contacts, and they were used to explore intermolecular interactions and their quantitative contributions [29]. The region on the surface where atoms make intermolecular interactions that are closer together than the sum of their Van der Waals radii is depicted by the color red.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

Synthesis, crystal structure, DFT and Hirshfeld surface analysis of 4-fluoro-N-(1,3-dioxoisoindolin-2-yl)benzamide

et al. 2023

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The 4-fluoro-N-(1,3-dioxoisoindolin-2-yl)benzamide was synthesized by the reaction of 4-fluorobenzohydrazide with phthalic anhydride in acetic acid. The compound was characterized by analytical instruments like FT-IR and NMR. The three-dimensional structure of the title compound was further confirmed by single-crystal X-ray diffraction study. In addition to the experimental study, theoretical calculations were performed to explore the molecular structure in order to analyze experimental and theoretical findings. The title compound crystallizes in the monoclinic space group P21/n as determined by the X-ray diffraction investigation, crystal data for C15H9FN2O3·H2O: a = 14.094(6) Å, b = 7.248(3) Å, c = 14.517(6) Å, β = 105.116(14)°, V = 1431.6(10) Å3, Z = 4, T = 298(2) K, μ(MoKα) = 0.112 mm-1, Dcalc = 1.402 g/cm3, 37521 reflections measured (4.684° ≤ 2Θ ≤ 60.6°), 4225 unique (Rint = 0.0517, Rsigma = 0.0311) that were used in all calculations. The final R1 was 0.0537 (I > 2σ(I)) and wR2 was 0.1501 (all data). The N-H···O and O-H···O hydrogen bonds linking molecules in the crystal form a three-dimensional framework structure. The electronic states and molecular properties of the title compound were determined using computational studies, like density functional theory and Hirshfeld surface analysis.

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Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione

Cited by 13 publications

References 24 publications

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal

Determination of Intermolecular Interactions of Nicotinamide Liganded Complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-Formilbenzoates by Hirshfeld Surface Analysis and Investigation of Interaction Energies.

Synthesis, crystal structure, DFT and Hirshfeld surface analysis of 4-fluoro-N-(1,3-dioxoisoindolin-2-yl)benzamide

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