The study of interactions with a halogen atom: influence of NH2group insertion on the crystal structures ofmeta-bromonitrobenzene derivatives

2018 ◽  
Vol 74 (11) ◽  
pp. 1509-1517 ◽  
Author(s):  
Paulina H. Marek ◽  
Mateusz Urban ◽  
Izabela D. Madura
Keyword(s):  
Crystal Structures ◽  
Molecular Crystals ◽  
Noncovalent Interaction ◽  
Hirshfeld Surface ◽  
Potential Surfaces ◽  
Acta Cryst ◽  
Reduced Density Gradient ◽  
Reduced Density ◽  
Structure Stabilization ◽  
Electron Donating Groups

Halogen atoms in molecular crystals may be involved in various interactions, often playing a very important role in structure stabilization. By introducing electron-donating groups, such as NH2, the electron density of the molecule is changed and thus interactions with the bromine substituent may alter. Herein, the crystal structures ofmeta-bromonitrobenzene and its NH2-substituted derivatives are analyzed. In all four described structures, namelym-bromonitrobenzene [Charlton & Trotter (1963).Acta Cryst.16, 313], 4-bromo-2-nitroaniline (C6H5BrN2O2,1), 2-bromo-6-nitroaniline (2) and 2-bromo-4-nitroaniline [Arshadet al.(2009).Acta Cryst.E65, o480], the Br atom is engaged in different interactions (Br...π, Br...O, Br...Br and C—H...Br, respectively). The Hirshfeld surface analysis (HS) and Reduced Density Gradient NonCovalent Interaction (RDG NCI) plots are used to prove the relevance, directionality and stabilizing nature of these interactions. Their modifications have been associated with the position of the amino group in the molecular structure and its influence on charge distribution analyzed with electrostatic potential surfaces (EPS). The diversification of the interactions has been correlated with a σ-hole potential value that enables a switching of the Br-atom character from electrophilic to nucleophilic.

scholarly journals Crystal structures and Hirshfeld surface analyses of (E)-N′-benzylidene-2-oxo-2H-chromene-3-carbohydrazide and the disordered hemi-DMSO solvate of (E)-2-oxo-N′-(3,4,5-trimethoxybenzylidene)-2H-chromene-3-carbohydrazide: lattice energy and intermolecular interaction energy calculations for the former. Corrigendum

2019 ◽  
Vol 75 (12) ◽  
pp. 1952-1952
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
James L. Wardell ◽  
Camila Capelini ◽  
José Daniel Figueroa Villar ◽  
...  
Keyword(s):  
Interaction Energy ◽  
Crystal Structures ◽  
Intermolecular Interaction ◽  
Lattice Energy ◽  
Hirshfeld Surface ◽  
Intermolecular Interaction Energy ◽  
Acta Cryst ◽  
Energy Calculations

In the paper by Gomes et al. [Acta Cryst. (2019), E75, 1403–1410], there was an error and omission in the author and affiliation list.

scholarly journals Vibrational Spectral Studies, Quantum Mechanical Properties, and Biological Activity Prediction and Inclusion Molecular Self-Assembly Formation of N-N’-Dimethylethylene Urea

2021 ◽  
Vol 12 (3) ◽  
pp. 3996-4017
Keyword(s):  
Self Assembly ◽  
Interaction Analysis ◽  
Noncovalent Interaction ◽  
Potential Energy Distribution ◽  
Spectral Studies ◽  
Quantum Mechanical ◽  
Ft Ir ◽  
Reduced Density Gradient ◽  
Localized Orbital ◽  
Reduced Density

A cyclic urea analog, N-N'-dimethylethylene urea, was studied using different spectral methods like FT-IR, FT-Raman, and UV-VIS methods followed by computational simulations. The experimental and simulated spectra are compared, and a detailed assignment of vibrations and potential energy distribution is made. It was followed by various quantum mechanical studies like frontier orbital analysis, energy descriptors, average local ionization energies, and nonlinear optical properties. The NBO gave an insight into the various intramolecular stabilizing electron delocalization by hyperconjugation. Noncovalent interaction analysis provided various types of interactions present in the molecule. We also studied ALIE, local information entropy, electron localized function, reduced density gradient studies, localized orbital locator studies, and other analyses. Molecular docking results indicated that this urea derivative acted as an ATP-hydrolysing inhibitor, and the drug delivery ability of cyclodextrin on NND was tested by forming an inclusion complex with both compounds with dispersion and without dispersion interaction.

scholarly journals Utilizing Hirshfeld surface calculations, non-covalent interaction (NCI) plots and the calculation of interaction energies in the analysis of molecular packing

2019 ◽  
Vol 75 (3) ◽  
pp. 308-318 ◽  
Author(s):  
Sang Loon Tan ◽  
Mukesh M. Jotani ◽  
Edward R. T. Tiekink
Keyword(s):  
Molecular Crystals ◽  
Molecular Packing ◽  
Hirshfeld Surface ◽  
Complete Picture ◽  
Interaction Energies ◽  
Acta Cryst ◽  
Covalent Interaction ◽  
Residue Contacts

The analysis of atom-to-atom and/or residue-to-residue contacts remains a favoured mode of analysing the molecular packing in crystals. In this contribution, additional tools are highlighted as methods for analysis in order to complement the `crystallographer's tool', PLATON [Spek (2009). Acta Cryst. D65, 148–155]. Thus, a brief outline of the procedures and what can be learned by using Crystal Explorer [Spackman & Jayatilaka (2009). CrystEngComm 11, 19–23] is presented. Attention is then directed towards evaluating the nature, i.e. attractive/weakly attractive/repulsive, of specific contacts employing NCIPLOT [Johnson et al. (2010). J. Am. Chem. Soc. 132, 6498–6506]. This is complemented by a discussion of the calculation of energy frameworks utilizing the latest version of Crystal Explorer. All the mentioned programs are free of charge and straightforward to use. More importantly, they complement each other to give a more complete picture of how molecules assemble in molecular crystals.

scholarly journals Crystal Structure and Computational Study on Methyl-3-Aminothiophene-2-Carboxylate

Crystals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 19 ◽  
Author(s):  
Yaping Tao ◽  
Ligang Han ◽  
Andong Sun ◽  
Kexi Sun ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Computational Study ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Dispersion Energy ◽  
Monoclinic Crystal ◽  
Hydrogen Bond Interactions ◽  
Calculation Results ◽  
Reduced Density Gradient ◽  
Reduced Density

Methyl-3-aminothiophene-2-carboxylate (matc) is a key intermediate in organic synthesis, medicine, dyes, and pesticides. Single crystal X-ray diffraction analysis reveals that matc crystallizes in the monoclinic crystal system P21/c space group. Three matc molecules in the symmetric unit are crystallographically different and further linked through the N–H⋯O and N–H⋯N hydrogen bond interactions along with weak C–H⋯S and C–H⋯Cg interactions, which is verified by the three-dimensional Hirshfeld surface, two-dimensional fingerprint plot, and reduced density gradient (RDG) analysis. The interaction energies within crystal packing are visualized through dispersion, electrostatic, and total energies using three-dimensional energy-framework analyses. The dispersion energy dominates in crystal packing. To better understand the properties of matc, electrostatic potential (ESP) and frontier molecular orbitals (FMO) were also calculated and discussed. Experimental and calculation results suggested that amino and carboxyl groups can participate in various inter- and intra-interactions.

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