Crystallographic and Theoretical Exploration of Weak Hydrogen Bonds in Arylmethyl <i>N</i>′-(adamantan-1-yl)piperidine-1-carbothioimidates and Molecular Docking Analysis

Al-Mutairi, Aamal A.; Alagappan, Kowsalya; Blacque, Olivier; Al-Alshaikh, Monirah A.; El-Emam, Ali A.; Percino, M. Judith; Thamotharan, Subbiah

doi:10.1021/acsomega.1c03559

Cited by 7 publications

(5 citation statements)

References 64 publications

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“…Hirshfeld surface, 2D fingerprinting, and intermolecular interaction analysis of donepezil polymorphs were performed using the CrystalExplorer program. − The closest distances from a point on the Hirshfeld surface to the inner and outer atoms of the surface are defined as d i and d e , respectively, and the standard distance d norm can be calculated using the following equation (eq ): …”

Section: Resultsmentioning

confidence: 99%

Quantitative Analysis the Weak Non-Covalent Interactions of the Polymorphs of Donepezil

Xing

Zhang

et al. 2022

ACS Omega

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Donepezil has polymorphism. Different crystalline forms can exhibit different physicochemical properties and biological activities. Exploration of intermolecular interactions is essential to reveal the formation mechanism and differences in properties of polymorphs. This study explores the weak non-covalent intermolecular interactions of donepezil polymorphs through fully ab initio quantum mechanical methods, semi-empirical methods, and Hirshfeld surface analysis. The results show that the Hirshfeld surface analysis method can clearly and intuitively reveal the intermolecular interactions. Theoretical calculations using the atom–atom Coulomb–London–Pauli (AA-CLP) method were also performed to understand the interaction energies toward the total lattice energy. The value of the lattice energy was in accordance with the melting points of the donepezil polymorphs and brought to light the nature of thermal stability. In the specific energy distribution, the contribution of the dispersion force is the most prominent. Further interaction energy analysis found that within a distance of 3.8 Å from the center of the donepezil molecule, different crystalline forms of donepezil molecules have different interaction energies with surrounding molecules. The different interaction energies between polymorphs may lead to polymorphs with different physical–chemical properties.

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Section: Resultsmentioning

confidence: 99%

Quantitative Analysis the Weak Non-Covalent Interactions of the Polymorphs of Donepezil

Xing

Zhang

et al. 2022

ACS Omega

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“…HS analysis has become an invaluable tool for understanding the nature of intermolecular interactions within a crystal structure using a fingerprint plot . This allows for easy identification of characteristic interactions throughout the structures or as a surface around the molecule .…”

Section: Resultsmentioning

confidence: 99%

“…HS analysis has become an invaluable tool for understanding the nature of intermolecular interactions within a crystal structure using a fingerprint plot. 67 This allows for easy identification of characteristic interactions throughout the structures 68 or as a surface around the molecule. 69 A d norm surface allows for easy comparison of intermolecular contacts relative to van der Waals radii by way of a simple red−white−blue color scheme.…”

Section: Materials Inorganic Salts (Cusomentioning

confidence: 99%

Pyromellitate Ligand as Building Blocks in the Synthesis of Metal–Organic Frameworks with Hydroxyalkylamines

Kondratenko

Zav’yalova

Arsent’ev

et al. 2022

Crystal Growth & Design

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Metal−organic frameworks (MOFs) are an extremely promising and rapidly growing class of coordination compounds. Pyromellitic acid (H 4 Prm) containing four carboxyl groups is a popular ligand for building MOFs. In this study, a twostep approach was used to synthesize MOFs containing polydentate pyromellitate and hydroxyalkylamine ligands. In the first stage, Cu(II), Co(II), and Ni(II) pyromellitates were synthesized by the reaction of sodium pyromellitate with inorganic Cu(II), Co(II), and Ni(II) salts in water. X-ray diffraction showed that the interaction of cobalt nitrate with Na 4 Prm leads to the formation of MOFs based on a heteronuclear polymer complex [Co 3 (μ-ONa) 6 (Prm) 3 (H 2 O) 18 ] n . In the second stage, the interaction of the synthesized pyromellitates with tris(2hydroxypropyl)amine (TPA), tris(hydroxymethyl)aminomethane (TRIS), and bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-TRIS) was studied. We describe the synthesis and spectroscopic and thermal properties of nine new complexes. The structure of the complexes [Co 2 (PRM)(BIS-TRIS) 2 ](H 2 O) 5 ( 6) and [Ni 2 (PRM)(BIS-TRIS) 2 ](H 2 O) 3 (9) was studied by X-ray diffraction supplemented by the Hirshfeld surface analysis and density functional theory (DFT) methods. The potential of using the complexes as adsorbents for lead ions has been demonstrated.

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“…The result shows five molecular dimers with intermolecular interaction energies for these dimers (M1 to M5) ranging from −24.4 to −4.0 kcal mol −1 . A quantum chemical calculation with the B97D3/def2-TZVP level of theory was used to obtain accurate interaction energies for these dimers as previously reported [ 53 , 54 , 55 ]. The complexation energies calculated by the PIXEL and DFT methods are comparable for the most of the dimers ( Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

X-ray Structures and Computational Studies of Two Bioactive 2-(Adamantane-1-carbonyl)-N-substituted Hydrazine-1-carbothioamides

et al. 2022

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Two biologically active adamantane-linked hydrazine-1-carbothioamide derivatives, namely 2-(adamantane-1-carbonyl)-N-(tert-butyl)hydrazine-1-carbothioamide) 1 and 2-(adamantane-1-carbonyl)-N-cyclohexylhydrazine-1-carbothioamide 2, have been synthesized. X-ray analysis was conducted to study the effect of the t-butyl and cyclohexyl moieties on the intermolecular interactions and conformation of the molecules in the solid state. X-ray analysis reveals that compound 1 exhibits folded conformation, whereas compound 2 adopts extended conformation. The Hirshfeld surface analysis indicates that the contributions of the major intercontacts involved in the stabilization of the crystal structures do not change much as a result of the t-butyl and cyclohexyl moieties. However, the presence and absence of these contacts is revealed by the 2D-fingerprint plots. The CLP–Pixel method was used to identify the energetically significant molecular dimers. These dimers are stabilized by different types of intermolecular interactions such as N–H···S, N–H···O, C–H···S, C–H···O, H–H bonding and C–H···π interactions. The strength of these interactions was quantified by using the QTAIM approach. The results suggest that N–H···O interaction is found to be stronger among other interactions. The in vitro assay suggests that both compounds 1 and 2 exhibit urease inhibition potential, and these compounds also display moderate antiproliferative activities. Molecular docking analysis shows the key interaction between urease enzyme and title compounds.

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Crystallographic and Theoretical Exploration of Weak Hydrogen Bonds in Arylmethyl N′-(adamantan-1-yl)piperidine-1-carbothioimidates and Molecular Docking Analysis

Cited by 7 publications

References 64 publications

Quantitative Analysis the Weak Non-Covalent Interactions of the Polymorphs of Donepezil

Quantitative Analysis the Weak Non-Covalent Interactions of the Polymorphs of Donepezil

Pyromellitate Ligand as Building Blocks in the Synthesis of Metal–Organic Frameworks with Hydroxyalkylamines

X-ray Structures and Computational Studies of Two Bioactive 2-(Adamantane-1-carbonyl)-N-substituted Hydrazine-1-carbothioamides

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