Synthesis, crystal structure, Hirshfeld surface analysis and frontier molecular orbital analysis of 2-((2-hydroxynaphthalen-1-yl)methylene)hydrazinecarbothioamide

The molecule of the title Schiff base compound, C14H13N3O3·H2O, displays a trans configuration with respect to the C=N bond. The dihedral angle between the benzene and pyridine rings is 29.63 (7)°. The crystal structure features intermolecular N—H...O, C—H...O, O—H...O and O—H...N hydrogen-bonding interactions, leading to the formation of a supramolecular framework. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (37.0%), O...H/H...O (23.7%)), C...H/H...C (17.6%) and N...H/H...N (11.9%) interactions. The title compound has also been characterized by frontier molecular orbital analysis.

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Density functional theory calculations and Hirshfeld surface analysis of propyl-para-hydroxybenzoate (PHB) for optoelectronic application

Materials Science-Poland ◽

10.2478/msp-2020-0046 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

V. Mohankumar ◽

N. Karunagaran ◽

M. Senthil Pandian ◽

P. Ramasamy

Keyword(s):

Charge Transfer ◽

Surface Analysis ◽

Density Functional ◽

Hirshfeld Surface ◽

Basis Set ◽

Hirshfeld Surface Analysis ◽

Frontier Molecular Orbital ◽

Mulliken Charge ◽

Charge Analysis ◽

Orbital Analysis

AbstractThe geometries, electrostatic potential, Mulliken charge analysis, Natural Bond Orbital analysis and polarizabilities of propyl-para-hydroxybenzoate were calculated using B3LYP functional with 6-311++G(d,p) basis set. The calculated geometries are well matched with the experimental values. The Mullliken atomic charge analysis shows that the eventual charges are contained in the molecule. The NBO analysis explains the intramolecular charge transfer in the PHB molecule. The bonding features of the molecule were analyzed with the aid of Hirshfeld surface analysis. The frontier molecular orbital analysis showed the charge transfer obtained within the molecule. The calculated hyperpolarizability of the PHB molecule was 6.977E−30 esu and it was 8.9 times that of standard urea molecule.

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Synthesis, Single Crystal X-Ray Structure, Hirshfeld Surface Analysis, DFT Computations, Docking Studies on Aurora Kinases and an Anticancer Property of 3-(2,3-Dihydrobenzo[b][1,4]dioxin-6-yl)-6-methoxy-4H-chromen-4-one

Crystals ◽

10.3390/cryst10050413 ◽

2020 ◽

Vol 10 (5) ◽

pp. 413 ◽

Cited By ~ 2

Author(s):

Seunghyun Ahn ◽

Jiha Sung ◽

Ji Hye Lee ◽

Miri Yoo ◽

Yoongho Lim ◽

...

Keyword(s):

Molecular Orbital ◽

Surface Analysis ◽

Active Sites ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Frontier Molecular Orbital ◽

Monoclinic Space Group ◽

Term Survival ◽

X Ray ◽

Anti Cancer

The isoflavone compound 3-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-6-methoxy-4H-chromen-4-one (6) was prepared and structurally characterized using NMR, mass spectrum and X-ray crystallography. Compound 6, C18H14O5, was crystallized in the monoclinic space group P21/n with the cell parameters; a = 7.1869(4) Å, b = 10.2764(6) Å, c = 19.6771(10) Å, β = 99.442(2)°, V = 1433.57(14) Å3, Z = 4. In the title compound, the chromenone ring system is slightly twisted from planarity and the dihedral angle formed between the plane of the chromenone ring and benzene ring is 47.75°. Several intermolecular hydrogen bonds make the crystal stabilized in the three-dimensional structure, which was confirmed by Hirshfeld surface analysis. Density functional theory (DFT) calculations at the B3LYP/6-311++G(d,p) level were carried out and the calculated geometric parameters were compared with the experimental results. A frontier molecular orbital calculation was performed to reveal that the energy values of highest occupied molecular orbital (HOMO) and lowest un-occupied molecular orbital (LUMO) were −5.8223 eV and −1.8447 eV, and the HOMO–LUMO energy gap was 3.9783 eV. A clonogenic long-term survival assay of compound 6 against HCT116 human colon cancer cells showed an anti-cancer ability, with GI50 value of 24.9 μM. Docking experiments within the active sites of aurora kinase A and B were carried out to explain the anti-cancer property of compound 6.

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Crystal structure, Hirshfeld surface analysis and DFT studies of 5-(adamantan-1-yl)-3-[(4-chlorobenzyl)sulfanyl]-4-methyl-4H-1,2,4-triazole, a potential 11β-HSD1 inhibitor

Scientific Reports ◽

10.1038/s41598-019-56331-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 5

Author(s):

Lamya H. Al-Wahaibi ◽

Jacques Joubert ◽

Olivier Blacque ◽

Nora H. Al-Shaalan ◽

Ali A. El-Emam

Keyword(s):

Crystal Structure ◽

Surface Analysis ◽

Density Functional ◽

Crystal Packing ◽

3D Structure ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Frontier Molecular Orbital ◽

Absolute Minimum ◽

Hydrogen Bond Interactions

Abstract5-(Adamantan-1-yl)-3-[(4-chlorobenzyl)sulfanyl]-4-methyl-4H-1,2,4-triazole (4) was identified as a potential 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) inhibitor and this paper describes the in-depth structural analysis thereof. Compound 4 was synthesized in a 92% yield and its 3D-structure confirmed by single-crystal X-ray diffraction. Hirshfeld surface analysis indicated that H…H, C-H…C, C-H…Cl and especially C-H…N hydrogen bond interactions are the primary contributors to the intermolecular stabilisation in the crystal. In order to explore the properties of 4, free from the influence of the crystal field, density functional theory (DFT) calculations were conducted. Results indicated that the DFT optimized geometry of 4 produced a conformer (4a) that is significantly different from the crystal structure. Further experiments confirmed that the crystal structure is not the absolute minimum conformation. This indicated that the crystal packing forces has significantly influenced the conformation thereof. Frontier molecular orbital energies and net atomic charges were also calculated to elucidate the electronic properties of 4a. These results provided insight into areas of the molecule that may present with the ability to form binding interactions at the 11β-HSD1 active site. Molecular docking experiments revealed important intermolecular interactions between 4a and 11β-HSD1. These results indicate that 4 may be considered for further drug design endeavors.

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An insight into the synthesis, crystal structure, geometrical modelling of crystal morphology, Hirshfeld surface analysis and characterization ofN-(4-methylbenzyl)benzamide single crystals

Journal of Applied Crystallography ◽

10.1107/s1600576717012316 ◽

2017 ◽

Vol 50 (5) ◽

pp. 1498-1511 ◽

Cited By ~ 16

Author(s):

Sahil Goel ◽

Harsh Yadav ◽

Nidhi Sinha ◽

Budhendra Singh ◽

Igor Bdikin ◽

...

Keyword(s):

Crystal Structure ◽

Single Crystals ◽

Molecular Orbital ◽

Surface Analysis ◽

Title Compound ◽

Crystal Morphology ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Orbital Energy ◽

Solution Technique

A versatile approach for the synthesis ofN-(4-methylbenzyl)benzamide, C15H15NO, using CuI as catalyst has been reported. Single crystals of the synthesized compound were grown using the slow evaporation solution technique. The crystal structure of theN-(4-methylbenzyl)benzamide crystals has been determined by single-crystal X-ray diffraction. The compound crystallizes in an orthorhombic lattice, noncentrosymmetric space groupPna21. The crystal structure is stabilized by intermolecular N—H...O hydrogen bonds and weak C—H...π interactions to form layers parallel to theaaxis. A user-friendly approach based on centre of mass propagation vector theory was used to predict the crystal morphology. The framework developed here utilizes the concept of intermolecular bond strength to discern the crystal morphology. Fourier transform IR, NMR and high-resolution mass spectrometry analytical techniques were used for the identification of functional groups and confirmation of the structure of the title compound. All of the intermolecular interactions present in the crystal structure, including the C—H...π, C—H...O and N—H...O interactions, were investigated and confirmed by molecular Hirshfeld surface analysis. From linear optical spectroscopy, the transmittance, optical band gap and UV cutoff wavelength were determined. The photoluminescence emission spectrum was recorded for a grown crystal. Dielectric measurements were performed at room temperature for various frequencies. The mechanical strength of the (001) plane of the title compound was measured using the Vickers micro-hardness technique. A piezo-coefficient of 15 pC N−1was found along the (001) plane of the title crystals. The thermal stability and melting point were also investigated. In addition, density functional theory simulations were used to calculate the optimized molecular geometry and the UV–vis spectrum, and to determine the highest occupied molecular orbital/lowest unoccupied molecular orbital energy gap. The results show thatN-(4-methylbenzyl)benzamide is a potential candidate for multifunctional optical and piezoelectric crystals.

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Crystal structure, Hirshfeld surface analysis and HOMO–LUMO analysis of (E)-4-bromo-N′-(4-methoxybenzylidene)benzohydrazide

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989018013373 ◽

2018 ◽

Vol 74 (10) ◽

pp. 1500-1503 ◽

Cited By ~ 3

Author(s):

Kasthuri Balasubramani ◽

Ganesan Premkumar ◽

Palaniyappan Sivajeyanthi ◽

Muthaiah Jeevaraj ◽

Bellarmin Edison ◽

...

Keyword(s):

Surface Analysis ◽

Crystal Packing ◽

Three Dimensional ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Frontier Molecular Orbital ◽

Compound C ◽

Dimensional Network ◽

Molecular Orbital Analysis ◽

Homo Lumo

The title Schiff base compound, C15H13BrN2O2, displays an E configuration with respect to the C=N double bond, which forms a dihedral angle of 58.06 (9)° with the benzene ring. In the crystal, the molecules are linked into chains parallel to the b axis by N—H...O and C—H...O hydrogen bonds, giving rise to rings with an R 2 1(6) graph-set motif. The chains are further linked into a three-dimensional network by C—H...π interactions. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from C...H (33.2%), H...H (27.7%), Br...H/H...Br (14.2%) and O...H/H...O (13.6%) interactions. The title compound has also been characterized by frontier molecular orbital analysis.

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The influence of Chloride Shift Position on hydroxychlorochalcone

10.21826/viiiseedmol202037 ◽

2020 ◽

Author(s):

Rogério F. Costa ◽

Antônio S. N. Aguiar ◽

Igor D. Borges ◽

Ricardo Ternavisk ◽

Clodoaldo Valverde ◽

...

Keyword(s):

Charge Transfer ◽

Organic Compound ◽

Aromatic Ring ◽

Molecular Orbital ◽

Surface Analysis ◽

Hirshfeld Surface ◽

Molecular Structures ◽

Hirshfeld Surface Analysis ◽

Frontier Molecular Orbital

This work describes molecular structures of chalcones 2'-Hydroxy-4',6'-dimethyl-2-chlorochalcone and 2'-Hydroxy-4',6'-dimethyl-4-chlorochalcone and overlap of these structures in order to detect the change in planarity. The Hirshfeld Surface analysis to investigate when the position of the atom the chlorine in the aromatic ring is changed and how does this change influence in the properties of the organic compound. The geometric molecular were obtained through the DFT/M06-2X/6-311++G(2d, 2p) theory level. Frontier Molecular Orbital, NBO and MEP map were determined, in order to observe the information related to charge transfer in the molecule. The interactions between the molecules were verified with the aid of QTAIM.

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Crystal structure, characterization, Hirshfeld surface analysis and DFT studies of two [propane 3-bromo-1-(triphenyl phosphonium)] cations containing bromide (I) and tribromide (II) anions: The anion (II) as a new brominating agent for unsaturated compounds

Journal of Molecular Structure ◽

10.1016/j.molstruc.2019.05.127 ◽

2019 ◽

Vol 1195 ◽

pp. 542-554 ◽

Cited By ~ 1

Author(s):

Seyed Reza Nokhbeh ◽

Mostafa Gholizadeh ◽

Alireza Salimi ◽

Hazel A. Sparkes

Keyword(s):

Crystal Structure ◽

Surface Analysis ◽

Hirshfeld Surface ◽

Structure Characterization ◽

Hirshfeld Surface Analysis ◽

Dft Studies ◽

Unsaturated Compounds ◽

Triphenyl Phosphonium ◽

Phosphonium Cations

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2,4-Diamino-6-phenyl-1,3,5-triazin-1-ium nitrate: intriguing crystal structure with high Z′/Z′′ and hydrogen bond numbers and Hirshfeld surface analysis of intermolecular interactions

CrystEngComm ◽

10.1039/d1ce00313e ◽

2021 ◽

Author(s):

Nicoleta Caimac ◽

Elena Melnic ◽

Diana Chisca ◽

Marina S. Fonari

Keyword(s):

Crystal Structure ◽

Hydrogen Bond ◽

Surface Analysis ◽

Intermolecular Interactions ◽

Title Compound ◽

Ionic Species ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Asymmetric Unit ◽

Space Group

The title compound crystallises in the triclinic centrosymmetric space group P1̄ with an intriguing high number of crystallographically unique binary salt-like adducts (Z′ = 8) and a total number of ionic species (Z′′ = 16) in the asymmetric unit.

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