Pub Date : 2024-11-12DOI: 10.1016/j.molstruc.2024.140693
Febee R. Louka , Lily G. Ortte , Madison R. Maier , Nahed M.H. Salem , Ana Torvisco , Roland C. Fischer , Franz A. Mautner , Salah S. Massoud
The oxazines bearing piperazinyl moieties namely 2-(tert-butyl)-6-((4-(2-(8-(tert-butyl)-6-methyl-2H-benzo[e][1,3]oxazin-3(4H)-yl)ethyl)piperazin-1-yl)methyl)-4-methylphenol (1) and its corresponding 2,4-di-tert-butyl-6-((4-(2-(6,8-di-tert-butyl-2H-benzo[e]-[1,3]oxazin-3(4H)-yl)ethyl)piperazin-1-yl)methyl)phenol (2), which was previously isolated were described. The transformation of the piperazinyl tri-tert-butyl-phenol derivatives 6,6′-(((2-(4-(3-(tert-butyl)-2-hydroxy-5-methylbenzyl)piperazin-1-yl)ethyl)-azanediyl)bis-(methylene))bis-(2-(tert-butyl)-4-methylphenol) 3 and 6,6′-(((2-(4-(3,5-di-tert-butyl-2-hydroxybenzyl)piperazin-1-yl)ethyl)-azanediyl)-bis(methylene))bis(2,4-di-tert-butyl-phenol) 4 into 1 and 2, respectively was achieved in high yield by heating and stirring a methanolic solution containing Et3N and Ga(NO3)3·6H2O in the stochiometric ratio 1:3:1 for 30 min. The novel oxazine-piperazine 1 together with its triphenol-piperazine 3 (H3L4) were structurally characterized by spectroscopic and single crystal X-ray crystallography.
{"title":"Synthesis of 1,3-oxazines based on piperazine","authors":"Febee R. Louka , Lily G. Ortte , Madison R. Maier , Nahed M.H. Salem , Ana Torvisco , Roland C. Fischer , Franz A. Mautner , Salah S. Massoud","doi":"10.1016/j.molstruc.2024.140693","DOIUrl":"10.1016/j.molstruc.2024.140693","url":null,"abstract":"<div><div>The oxazines bearing piperazinyl moieties namely 2-(<em>tert-</em>butyl)-6-((4-(2-(8-(<em>tert</em>-butyl)-6-methyl-<em>2H</em>-benzo[<em>e</em>][1,3]oxazin-3(<em>4H</em>)-yl)ethyl)piperazin-1-yl)methyl)-4-methylphenol (1) and its corresponding 2,4-di-<em>tert</em>-butyl-6-((4-(2-(6,8-di-<em>tert</em>-butyl-<em>2H</em>-benzo[<em>e</em>]-[1,3]oxazin-3(<em>4H</em>)-yl)ethyl)piperazin-1-yl)methyl)phenol (2), which was previously isolated were described. The transformation of the piperazinyl tri-<em>tert</em>-butyl-phenol derivatives 6,6′-(((2-(4-(3-(<em>tert</em>-butyl)-2-hydroxy-5-methylbenzyl)piperazin-1-yl)ethyl)-azanediyl)bis-(methylene))bis-(2-(<em>tert-</em>butyl)-4-methylphenol) 3 and 6,6′-(((2-(4-(3,5-di-<em>tert</em>-butyl-2-hydroxybenzyl)piperazin-1-yl)ethyl)-azanediyl)-bis(methylene))bis(2,4-di-<em>tert</em>-butyl-phenol) 4 into 1 and 2, respectively was achieved in high yield by heating and stirring a methanolic solution containing Et<sub>3</sub>N and Ga(NO<sub>3</sub>)<sub>3</sub>·6H<sub>2</sub>O in the stochiometric ratio 1:3:1 for 30 min. The novel oxazine-piperazine 1 together with its triphenol-piperazine 3 (H<sub>3</sub>L<sup>4</sup>) were structurally characterized by spectroscopic and single crystal X-ray crystallography.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140693"},"PeriodicalIF":4.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-12DOI: 10.1016/j.molstruc.2024.140704
Anat Ram Sidar , Musheer Ahmad , Nazrul Haq , Kafeel Ahmad Siddiqui
Two Co(II)coordination polymers namely, [Co(mal)(4,4`-bpy)0.5 (H2O)]n(1) and [Co(mal)(4,4`-bpy)0.5 (H2O)]n(2)are synthesized at ambient temperature, both complexes are based on {Co(RCOO)2}unitserving as 3D network along with sqc and fes topology and corroborated by many analytical techniques. CPs(1) crystallized in a 2D manner and then constructed a 3D hydrogen bonding network which was demonstrated monoclinic crystal system while(2)is a 3D supramolecular network that possesses a tetrahedral crystal system, according to topological analysis CPs(1) shows 5-C net and CPs(2) elaborates a 3-C net which proves both are completely different. A luminescence investigation was performed using both coordination polymers (CPs), which demonstrated effective colorimetric detection of acetone, Cr₂O₇²⁻, and Fe³⁺, with corresponding detection limits of 1.91, 2.57, and 0.29 ppm, respectively, in an ethanolic medium. Additionally, the catalytic degradation of Naproxen was evaluated for both catalysts, revealing significant degradation efficiencies of 90 % for catalyst (1) and 38 % for catalyst (2).
{"title":"Topological Co(II)-malonate polymorph: Degradation properties of Naproxen and colorimetric recognition of acetone, Cr2O72−, and Fe3+","authors":"Anat Ram Sidar , Musheer Ahmad , Nazrul Haq , Kafeel Ahmad Siddiqui","doi":"10.1016/j.molstruc.2024.140704","DOIUrl":"10.1016/j.molstruc.2024.140704","url":null,"abstract":"<div><div>Two Co(II)coordination polymers namely, <em>[Co(mal)(4,</em>4`-bpy)<sub>0.5</sub> (<em>H<sub>2</sub>O)]<sub>n</sub></em>(1) and <em>[Co(mal)(4,</em>4`-bpy)<sub>0.5</sub> (<em>H<sub>2</sub>O)]<sub>n</sub></em>(2)are synthesized at ambient temperature, both complexes are based on {Co(RCOO)<sub>2</sub>}unitserving as 3D network along with <em>sqc</em> and <em>fes</em> topology and corroborated by many analytical techniques. CPs(1) crystallized in a 2D manner and then constructed a 3D hydrogen bonding network which was demonstrated monoclinic crystal system while(2)is a 3D supramolecular network that possesses a tetrahedral crystal system, according to topological analysis CPs(1) shows 5-C net and CPs(2) elaborates a 3-C net which proves both are completely different. A luminescence investigation was performed using both coordination polymers (CPs), which demonstrated effective colorimetric detection of acetone, Cr₂O₇²⁻, and Fe³⁺, with corresponding detection limits of 1.91, 2.57, and 0.29 ppm, respectively, in an ethanolic medium. Additionally, the catalytic degradation of Naproxen was evaluated for both catalysts, revealing significant degradation efficiencies of 90 % for catalyst (1) and 38 % for catalyst (2).</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140704"},"PeriodicalIF":4.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-10DOI: 10.1016/j.molstruc.2024.140700
Qing-Ge Li, Wei Li, Zhen-Zhu Li, Jun-Jie Cai, Kun Gao, Yu Nie, Hui-Jie Lun, Yan Bai, Ya-Min Li
Three heterometallic metal-organic frameworks, namely, {RE2Co3L6(H2O)6}n (RE = Gd (1), Dy (2), Y(3)), have been hydrothermally synthesized based on rare-earth (RE) and transition metal ions and the organic ligand of 3-hydroxyisonicotinic acid (H2L). Single-crystal X-ray diffraction reveals that compounds 1‒3 are isomorphic and features three-dimensional (3D) porous structure. In compound 1, the Gd3+ ion is located in the C3 axis, and every two propeller-like {GdCo3} units are capped up and down to a {Gd6Co6} ring through twelve L2‒ ligands, giving rise to the formation of the cavities. Notably, three compounds display high thermal stability determined by thermogravimetric analysis (TGA), and good water stability proved by the well-matched of PXRD curves before and after soaked three samples in water for three days. AC impedance measurements exhibit the proton conductivities of compounds 1‒3 with powder samples are distinctly temperature and humidity dependent, and the values can reach 3.38×10‒5, 1.91×10‒5, and 2.23×10‒5 S cm‒1 at 98% RH and 338 K, respectively. Moreover, compounds 1‒3 display antiferromagnetic behaviours, and the magnetocaloric effect (MCE) study indicates that the entropy change (−ΔSm) of compound 1 is 7.1 J kg−1 K−1 at 7 K and 7 T. Compound 2 exhibits the slow magnetic relaxation behaviour.
{"title":"RECo-containing metal-organic frameworks based on 3-hydroxyisonicotinic acid: Proton conduction and magnetism","authors":"Qing-Ge Li, Wei Li, Zhen-Zhu Li, Jun-Jie Cai, Kun Gao, Yu Nie, Hui-Jie Lun, Yan Bai, Ya-Min Li","doi":"10.1016/j.molstruc.2024.140700","DOIUrl":"10.1016/j.molstruc.2024.140700","url":null,"abstract":"<div><div>Three heterometallic metal-organic frameworks, namely, {RE<sub>2</sub>Co<sub>3</sub>L<sub>6</sub>(H<sub>2</sub>O)<sub>6</sub>}<sub>n</sub> (RE = Gd (<strong>1</strong>), Dy (<strong>2</strong>), Y(<strong>3</strong>)), have been hydrothermally synthesized based on rare-earth (RE) and transition metal ions and the organic ligand of 3-hydroxyisonicotinic acid (H<sub>2</sub>L). Single-crystal X-ray diffraction reveals that compounds <strong>1</strong>‒<strong>3</strong> are isomorphic and features three-dimensional (3D) porous structure. In compound <strong>1</strong>, the Gd<sup>3+</sup> ion is located in the <em>C</em><sub>3</sub> axis, and every two propeller-like {GdCo<sub>3</sub>} units are capped up and down to a {Gd<sub>6</sub>Co<sub>6</sub>} ring through twelve L<sup>2‒</sup> ligands, giving rise to the formation of the cavities. Notably, three compounds display high thermal stability determined by thermogravimetric analysis (TGA), and good water stability proved by the well-matched of PXRD curves before and after soaked three samples in water for three days. AC impedance measurements exhibit the proton conductivities of compounds <strong>1</strong>‒<strong>3</strong> with powder samples are distinctly temperature and humidity dependent, and the values can reach 3.38×10<sup>‒5</sup>, 1.91×10<sup>‒5</sup>, and 2.23×10<sup>‒5</sup> S cm<sup>‒1</sup> at 98% RH and 338 K, respectively. Moreover, compounds <strong>1</strong>‒<strong>3</strong> display antiferromagnetic behaviours, and the magnetocaloric effect (MCE) study indicates that the entropy change (−Δ<em>S</em><sub>m</sub>) of compound <strong>1</strong> is 7.1 J kg<sup>−1</sup> K<sup>−1</sup> at 7 K and 7 T. Compound <strong>2</strong> exhibits the slow magnetic relaxation behaviour.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140700"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-10DOI: 10.1016/j.molstruc.2024.140708
A. Ram Kumar , S. Selvaraj , A.S. Vickram , M. Thirunavukkarasu , Mohammad Shahzad Samdani , Priya SD , Ranjith Balu
In this study, computational methods were employed to analyze the molecular structure of (2E)-3-[4-(Dimethylamino)phenyl]-1-(3-nitrophenyl)prop-2-en-1-one (DMAPNP), investigating its structural and spectroscopic properties along with its biological activity. In particular, the Frontier Molecular Orbital (FMO) and Molecular Electrostatic Potential (MEP) surfaces in alkanolic solvents (ethanediol, ethanol, and methanol) and non-alkanolic solvents (DMSO, toluene, and water) were generated to analyze the solvent-solute interactions. The H→L transition shows low oscillator strengths (0.0002 in toluene to 0.0013 in ethanediol, DMSO, and water), indicating limited significance in the absorption spectrum. In contrast, the H→L+1 transition has much higher oscillator strengths, around 0.9412 for ethanediol and 0.9385 for DMSO and toluene, suggesting a greater likelihood of absorption at these wavelengths. The simulated vibrational wavenumbers revealed the presence of CH, NO2, CN, CC, CH3, and C=O groups in DMAPNP. The calculated chemical shifts confirmed the molecular structure of DMAPNP and aligned with standard values. In Hirshfeld surface analysis, the crystal packing of DMAPNP was primarily stabilized by H…H interactions, contributing 41.3%, followed by O…H / H…O interactions at 30.9%. In Natural Bond Orbital (NBO) analysis, the interaction between C20-H38 and C15-H33 shows a stabilization energy of 1102.89 kJ/mol, highlighting σ-σ* transitions. In contrast, the C12-C16 and C15-H33 interactions exhibit a stabilization energy of 2542.16 kJ/mol, indicating substantial π-σ* contributions. In the Mulliken charge distribution, the carbon atoms C18 (-1.33704e) and C13 (1.776064e), located in the para and meta positions concerning the nitro group (NO2), exhibit the highest positive and negative potentials, respectively. Molecular docking assessed DMAPNP as a potential anti-tumor agent by inhibiting the key regulatory enzyme fructose-2,6-bisphosphatase, with a binding energy of -8.13 kcal/mol.
{"title":"A theoretical investigation into the impact of solvents (alkanolic and non-alkanolic), structural and spectroscopic properties, donor-acceptor insights, Hirshfeld surface, and molecular docking of the anti-tumor compound (2E)-3-[4-(dimethylamino)phenyl]-1-(3-nitrophenyl)prop‑2-en-1-one","authors":"A. Ram Kumar , S. Selvaraj , A.S. Vickram , M. Thirunavukkarasu , Mohammad Shahzad Samdani , Priya SD , Ranjith Balu","doi":"10.1016/j.molstruc.2024.140708","DOIUrl":"10.1016/j.molstruc.2024.140708","url":null,"abstract":"<div><div>In this study, computational methods were employed to analyze the molecular structure of (2E)-3-[4-(Dimethylamino)phenyl]-1-(3-nitrophenyl)prop-2-en-1-one (DMAPNP), investigating its structural and spectroscopic properties along with its biological activity. In particular, the Frontier Molecular Orbital (FMO) and Molecular Electrostatic Potential (MEP) surfaces in alkanolic solvents (ethanediol, ethanol, and methanol) and non-alkanolic solvents (DMSO, toluene, and water) were generated to analyze the solvent-solute interactions. The <em>H</em>→<em>L</em> transition shows low oscillator strengths (0.0002 in toluene to 0.0013 in ethanediol, DMSO, and water), indicating limited significance in the absorption spectrum. In contrast, the <em>H</em>→<em>L</em>+1 transition has much higher oscillator strengths, around 0.9412 for ethanediol and 0.9385 for DMSO and toluene, suggesting a greater likelihood of absorption at these wavelengths. The simulated vibrational wavenumbers revealed the presence of CH, NO<sub>2</sub>, CN, CC, CH<sub>3</sub>, and C=O groups in DMAPNP. The calculated chemical shifts confirmed the molecular structure of DMAPNP and aligned with standard values. In Hirshfeld surface analysis, the crystal packing of DMAPNP was primarily stabilized by H…H interactions, contributing 41.3%, followed by O…H / H…O interactions at 30.9%. In Natural Bond Orbital (NBO) analysis, the interaction between C<sub>20</sub>-H<sub>38</sub> and C<sub>15</sub>-H<sub>33</sub> shows a stabilization energy of 1102.89 kJ/mol, highlighting σ-σ* transitions. In contrast, the C<sub>12</sub>-C<sub>16</sub> and C<sub>15</sub>-H<sub>33</sub> interactions exhibit a stabilization energy of 2542.16 kJ/mol, indicating substantial π-σ* contributions. In the Mulliken charge distribution, the carbon atoms C<sub>18</sub> (-1.33704e) and C<sub>13</sub> (1.776064e), located in the <em>para</em> and <em>meta</em> positions concerning the nitro group (NO<sub>2</sub>), exhibit the highest positive and negative potentials, respectively. Molecular docking assessed DMAPNP as a potential anti-tumor agent by inhibiting the key regulatory enzyme fructose-2,6-bisphosphatase, with a binding energy of -8.13 kcal/mol.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140708"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-10DOI: 10.1016/j.molstruc.2024.140588
Shruti P. Dhale , Nilesh S. Ugemuge , Vartika S. Singh , I.M. Nagpure , R.A. Nafdey , S.V. Moharil
Near Infra–red (NIR) emitting NaCaYF6:Nd3+and co–doped with Yb3+phosphor has been prepared by hydrothermal synthesis. The formation of Gagarinite structure of the host matrix with space group P63/m was confirmed by XRD and Rietveld analysis. FESEM analysis confirms the spherical morphology along with the homogeneity, and mapping of elemental composition by EDS analysis. NIR emission at 1065 nm due to 4F3/2→4I11/2 electronic transition of Nd3+ ion upon the exposure to 577 nm light. The prominent PL emission at 994 nm from NaCaYF6:Nd3+,Yb3+ phosphor was obtained due to 2F5/2→2F7/2 electronic transition of Yb3+ion. Yb3+ emission was sensitized by Nd3+ activator. The intensity of Yb3+emission increases at the cost of the Nd3+ luminescence. The results are ascribed to the energy transfer from Nd3+to Yb3+. The theoretical Judd-Ofelt (J-O) analysis was also reported to confirm the obtained luminescence behaviour and energy transfer (ET) mechanism of the phosphor. The obtained results specify that the phosphor has a potential application such as in–vivo, in−vitro imaging and NIR laser applications.
{"title":"Synthesis and spectroscopic analysis of NaCaYF6:Nd3+, Yb3+NIR emitting phosphor","authors":"Shruti P. Dhale , Nilesh S. Ugemuge , Vartika S. Singh , I.M. Nagpure , R.A. Nafdey , S.V. Moharil","doi":"10.1016/j.molstruc.2024.140588","DOIUrl":"10.1016/j.molstruc.2024.140588","url":null,"abstract":"<div><div>Near Infra–red (NIR) emitting NaCaYF<sub>6</sub>:Nd<sup>3+</sup>and co–doped with Yb<sup>3+</sup>phosphor has been prepared by hydrothermal synthesis. The formation of Gagarinite structure of the host matrix with space group P6<sub>3</sub>/m was confirmed by XRD and Rietveld analysis. FESEM analysis confirms the spherical morphology along with the homogeneity, and mapping of elemental composition by EDS analysis. NIR emission at 1065 nm due to <sup>4</sup>F<sub>3/2</sub>→<sup>4</sup>I<sub>11/2</sub> electronic transition of Nd<sup>3+</sup> ion upon the exposure to 577 nm light. The prominent PL emission at 994 nm from NaCaYF<sub>6</sub>:Nd<sup>3+</sup>,Yb<sup>3+</sup> phosphor was obtained due to <sup>2</sup>F<sub>5/2</sub>→<sup>2</sup>F<sub>7/2</sub> electronic transition of Yb<sup>3+</sup>ion. Yb<sup>3+</sup> emission was sensitized by Nd<sup>3+</sup> activator. The intensity of Yb<sup>3+</sup>emission increases at the cost of the Nd<sup>3+</sup> luminescence. The results are ascribed to the energy transfer from Nd<sup>3+</sup>to Yb<sup>3+</sup>. The theoretical Judd-Ofelt (J-O) analysis was also reported to confirm the obtained luminescence behaviour and energy transfer (ET) mechanism of the phosphor. The obtained results specify that the phosphor has a potential application such as in–vivo, in−vitro imaging and NIR laser applications.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140588"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-10DOI: 10.1016/j.molstruc.2024.140706
Shun-Qin Zeng , Ying-Hong Ma , Juan Lu , Dan-Dan Kong , Zi-Xuan Zhao , Xiang-Yuan Li , Na Li , Jing Xue , Chin-Ho Chen , Zi-Jian Zhao , Xian-Jin Wu , Gang Zhang , Yuan-Xiang Li , Qiong-Yu Zou , Yi-Min Li , Hai-Feng Wu
Structurally diverse triterpenoids have shown potential as pharmaceutical precursors for HIV treatment. Our previous research led to the discovery of a potent antiviral cycloartane triterpenoid derivative, (20S,24S)-15β,16β-diacetoxy-18,24;20,24-diepoxy-9,19-cyclolanostane-3β,25-diol 3-O-3′,3′-dimethyl succinate (DSC) derived from the triterpene glycoside beesioside I, exhibiting high-affinity interactions with the Capsid (CA) and spacer peptide 1 (SP1) domain (CA-SP1) region of the HIV Gag polyprotein. To discover new antiviral agents from natural resources, the methanolic extracts of Actaea vaginata were qualitatively analyzed using UPLC-QTOF-MS/MS. Based on characteristic ESIMS/MS fragmentations of cycloartane triterpenoids obtained from A. vaginata and relevant literature, twenty-one compounds including an unknown triterpenoid (1) were identified. Guided by LC-MS analysis, compound 1 was isolated and determined as (20S,24S)-15β,16β-diacetoxy-18,24;20,24-diepoxy-9,19-cyclanostane-3β,25-diol-3-O-β-d-xylopyranosyl-25-O-β-d-glucopyranoside by spectroscopic methods, showing moderate antiviral activity with an EC50 value of 8.6 µM against HIV-1NL-43 in MT4 cells. The structural data and electronic properties of compound 1 were determined using the B3LYP density functional method with the basis set 6–311+G(d,p). To further understand the compound's antiviral quality, molecular docking and molecular dynamics studies were conducted. The results indicated that compound 1 could be a potential candidate for anti-HIV treatment.
{"title":"Identification of anti-HIV cycloartane triterpenoids from Actaea vaginata using UPLC‐QTOF‐MS/MS, DFT calculations, docking, and molecular dynamics studies","authors":"Shun-Qin Zeng , Ying-Hong Ma , Juan Lu , Dan-Dan Kong , Zi-Xuan Zhao , Xiang-Yuan Li , Na Li , Jing Xue , Chin-Ho Chen , Zi-Jian Zhao , Xian-Jin Wu , Gang Zhang , Yuan-Xiang Li , Qiong-Yu Zou , Yi-Min Li , Hai-Feng Wu","doi":"10.1016/j.molstruc.2024.140706","DOIUrl":"10.1016/j.molstruc.2024.140706","url":null,"abstract":"<div><div>Structurally diverse triterpenoids have shown potential as pharmaceutical precursors for HIV treatment. Our previous research led to the discovery of a potent antiviral cycloartane triterpenoid derivative, (20<em>S</em>,24<em>S</em>)-15<em>β</em>,16<em>β</em>-diacetoxy-18,24;20,24-diepoxy-9,19-cyclolanostane-3<em>β</em>,25-diol 3-<em>O</em>-3′,3′-dimethyl succinate (DSC) derived from the triterpene glycoside beesioside I, exhibiting high-affinity interactions with the Capsid (CA) and spacer peptide 1 (SP1) domain (CA-SP1) region of the HIV Gag polyprotein. To discover new antiviral agents from natural resources, the methanolic extracts of <em>Actaea vaginata</em> were qualitatively analyzed using UPLC-QTOF-MS/MS. Based on characteristic ESIMS/MS fragmentations of cycloartane triterpenoids obtained from <em>A. vaginata</em> and relevant literature, twenty-one compounds including an unknown triterpenoid (<strong>1</strong>) were identified. Guided by LC-MS analysis, compound <strong>1</strong> was isolated and determined as (20<em>S</em>,24<em>S</em>)-15<em>β,</em>16<em>β</em>-diacetoxy-18,24;20,24-diepoxy-9,19-cyclanostane-3<em>β</em>,25-diol-3-<em>O</em>-<em>β</em>-<span>d</span>-xylopyranosyl-25-<em>O</em>-<em>β</em>-<span>d</span>-glucopyranoside by spectroscopic methods, showing moderate antiviral activity with an EC<sub>50</sub> value of 8.6 µM against HIV-1<sub>NL-43</sub> in MT4 cells. The structural data and electronic properties of compound <strong>1</strong> were determined using the B3LYP density functional method with the basis set 6–311+<em>G</em>(d,p). To further understand the compound's antiviral quality, molecular docking and molecular dynamics studies were conducted. The results indicated that compound <strong>1</strong> could be a potential candidate for anti-HIV treatment.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140706"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142660102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Overuse and misuse of antibiotics create superbugs as drug-resistant bacteria. The vital strategy is developing new antibiotics, and one of the vital compounds that proved activity as antimicrobials is imidazoles. So, we designed and synthesized a series of imidazolones via microwave radiation in excellent yield and evaluated them as antimicrobial agents with docking studies to promote and boost their activity. The results obtained from spectroscopic analyses approved the chemical structures of new compounds. The biological antimicrobial activity results was found that these compounds exert an excellent broad spectrum antimicrobial activity against many Gram-positive and Gram-negative bacteria, as well as different fungal strain including some highly human pathogenic microorganisms.
Compounds 5a-5c are active against Gram-positive bacteria and compounds 5d-5f against Gram-negative bacteria, together with Candida albicans as fungi. Molecular Docking study on the active compounds 5e, 5f showed ring-stacking interactions between them as ligands and related proteins, which are compatible with other results. Gaussian 09 program is used as computational chemistry software to confirm the obtained experimental results.
{"title":"Design, microwave synthesis, characterization and antimicrobial activity of imidazolone derivatives","authors":"Zainab Rabeea Banoon , Rasha Shaker Mahmood , Amenah Radhi Hamad , Zahraa Abed Hussein","doi":"10.1016/j.molstruc.2024.140701","DOIUrl":"10.1016/j.molstruc.2024.140701","url":null,"abstract":"<div><div>Overuse and misuse of antibiotics create superbugs as drug-resistant bacteria. The vital strategy is developing new antibiotics, and one of the vital compounds that proved activity as antimicrobials is imidazoles. So, we designed and synthesized a series of imidazolones via microwave radiation in excellent yield and evaluated them as antimicrobial agents with docking studies to promote and boost their activity. The results obtained from spectroscopic analyses approved the chemical structures of new compounds. The biological antimicrobial activity results was found that these compounds exert an excellent broad spectrum antimicrobial activity against many Gram-positive and Gram-negative bacteria, as well as different fungal strain including some highly human pathogenic microorganisms.</div><div>Compounds <strong>5a-5c</strong> are active against Gram-positive bacteria and compounds <strong>5d-5f</strong> against Gram-negative bacteria, together with <em>Candida albicans</em> as fungi. Molecular Docking study on the active compounds <strong>5e, 5f</strong> showed ring-stacking interactions between them as ligands and related proteins, which are compatible with other results. Gaussian 09 program is used as computational chemistry software to confirm the obtained experimental results.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140701"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this study, ten novel halogenated arylidenehydrazide derivatives were synthesized and characterized through ¹H, ¹³C APT, ¹⁹F NMR, HSQC, HMBC, HRMS, and FT-IR techniques. Cytotoxic evaluations against PC3 prostate cancer and HUVEC cell lines identified compounds 8 and 14 as lead candidates, achieving IC₅₀ values of 4.49 µM and 4.78 µM, respectively, with notable selectivity indexes of 12.15 and 11.78, underscoring their specificity against PC3 cells. Molecular docking studies targeting AR, VEGFR1, EGFR, and VEGFR2 suggested potential inhibitory mechanisms, with compounds 8 and 14 displaying substantial binding affinities for AR and VEGFR1. Compound 8 achieved IFD scores of -12.900 kcal/mol for AR and -10.895 kcal/mol for VEGFR1, while compound 14 recorded scores of -10.323 kcal/mol and -10.379 kcal/mol, respectively. Complementary MM-GBSA analyses revealed favorable binding energies, with compound 8 yielding ΔG values of -76.60 kcal/mol (AR) and -78.08 kcal/mol (VEGFR1) and compound 14 showing -80.67 kcal/mol (AR) and -78.61 kcal/mol (VEGFR1). MD simulations confirmed complex stability over 50 ns, indicating that compound 14 exhibited enhanced binding stability with key residues in AR and VEGFR1. ADME predictions highlighted drug-like properties, particularly for compounds 8 and 14, with high lipophilicity and favorable absorption characteristics, despite low aqueous solubility. SAR analysis emphasized the beneficial impact of halogen substitutions on potency and selectivity, establishing compounds 8 and 14 as promising candidates for further therapeutic development.
{"title":"Novel 4-((3-fluorobenzyl)oxy)benzohydrazide derivatives as promising anti-prostate cancer agents: Synthesis, characterization and in vitro & in silico biological activity studies","authors":"Furkan Çakır , Şeyma Ateşoğlu , Aytekin Köse , Mansour Ghaffari-Moghaddam , Fahri Akbaş , Habib Kınay , Ebru Didem Kuran , Nuray Ulusoy-Güzeldemirci , Namık Kılınç , Feyzi Sinan Tokalı , Halil Şenol","doi":"10.1016/j.molstruc.2024.140702","DOIUrl":"10.1016/j.molstruc.2024.140702","url":null,"abstract":"<div><div>In this study, ten novel halogenated arylidenehydrazide derivatives were synthesized and characterized through ¹H, ¹³C APT, ¹⁹F NMR, HSQC, HMBC, HRMS, and FT-IR techniques. Cytotoxic evaluations against PC3 prostate cancer and HUVEC cell lines identified compounds <strong>8</strong> and <strong>14</strong> as lead candidates, achieving IC₅₀ values of 4.49 µM and 4.78 µM, respectively, with notable selectivity indexes of 12.15 and 11.78, underscoring their specificity against PC3 cells. Molecular docking studies targeting AR, VEGFR1, EGFR, and VEGFR2 suggested potential inhibitory mechanisms, with compounds <strong>8</strong> and <strong>14</strong> displaying substantial binding affinities for AR and VEGFR1. Compound <strong>8</strong> achieved IFD scores of -12.900 kcal/mol for AR and -10.895 kcal/mol for VEGFR1, while compound <strong>14</strong> recorded scores of -10.323 kcal/mol and -10.379 kcal/mol, respectively. Complementary MM-GBSA analyses revealed favorable binding energies, with compound <strong>8</strong> yielding ΔG values of -76.60 kcal/mol (AR) and -78.08 kcal/mol (VEGFR1) and compound <strong>14</strong> showing -80.67 kcal/mol (AR) and -78.61 kcal/mol (VEGFR1). MD simulations confirmed complex stability over 50 ns, indicating that compound <strong>14</strong> exhibited enhanced binding stability with key residues in AR and VEGFR1. ADME predictions highlighted drug-like properties, particularly for compounds <strong>8</strong> and <strong>14</strong>, with high lipophilicity and favorable absorption characteristics, despite low aqueous solubility. SAR analysis emphasized the beneficial impact of halogen substitutions on potency and selectivity, establishing compounds <strong>8</strong> and <strong>14</strong> as promising candidates for further therapeutic development.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140702"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-10DOI: 10.1016/j.molstruc.2024.140710
Xiaoxu Dong , Baoxi Li , Ziheng Zhou , Chengshuo Hou , Chuan-Zeng Wang , Hui Yan , Zhiming Wang , Tian Zhang
Pyrene-based luminogens have attracted wide attention due to their promising applications in organic electronics, chemical sensing, and bioimaging. In this study, a cyanoethylene-functionalized pyrene-based luminogen CNPyCH3 was designed and synthesized. Experimental results show that CNPyCH3 exhibits distinct photophysical properties in dilute solution and various solid states. The mechano-fluorochromic (MFC) property is more attractive and interesting, as a red shift with enhanced emission was observed upon mechanical stimulation. The intriguing MFC enhancement behavior was further investigated by in-depth theoretical calculations combining Monte Carlo simulations, quantum mechanics/molecular mechanics calculations, and time-dependent density functional theory. It was found that the calculated emission wavelengths for both pristine and ground CNPyCH3 are in good agreement with the experimental values, and that the ground CNPyCH3 has a greater oscillator strength. From the perspective of intermolecular interactions, the weakened π-π interactions induced by the half-switched “face-to-edge” packing modes are beneficial for achieving brighter emission upon grinding. In terms of intramolecular structures, the ground CNPyCH3 has a more planar conformation around the cyanoethylene moiety in the excited-state equilibrium geometry than the pristine CNPyCH3, resulting in the grinding-induced red-shifted emission. Our study provides a unique insight into the MFC enhancement behavior of the pyrene-based luminogens.
{"title":"Understanding the mechano-fluorochromic enhancement in a cyanoethylene-functionalized pyrene-based luminogen: An experimental and theoretical study","authors":"Xiaoxu Dong , Baoxi Li , Ziheng Zhou , Chengshuo Hou , Chuan-Zeng Wang , Hui Yan , Zhiming Wang , Tian Zhang","doi":"10.1016/j.molstruc.2024.140710","DOIUrl":"10.1016/j.molstruc.2024.140710","url":null,"abstract":"<div><div>Pyrene-based luminogens have attracted wide attention due to their promising applications in organic electronics, chemical sensing, and bioimaging. In this study, a cyanoethylene-functionalized pyrene-based luminogen <strong>CNPyCH<sub>3</sub></strong> was designed and synthesized. Experimental results show that <strong>CNPyCH<sub>3</sub></strong> exhibits distinct photophysical properties in dilute solution and various solid states. The mechano-fluorochromic (MFC) property is more attractive and interesting, as a red shift with enhanced emission was observed upon mechanical stimulation. The intriguing MFC enhancement behavior was further investigated by in-depth theoretical calculations combining Monte Carlo simulations, quantum mechanics/molecular mechanics calculations, and time-dependent density functional theory. It was found that the calculated emission wavelengths for both pristine and ground <strong>CNPyCH<sub>3</sub></strong> are in good agreement with the experimental values, and that the ground <strong>CNPyCH<sub>3</sub></strong> has a greater oscillator strength. From the perspective of intermolecular interactions, the weakened π-π interactions induced by the half-switched “face-to-edge” packing modes are beneficial for achieving brighter emission upon grinding. In terms of intramolecular structures, the ground <strong>CNPyCH<sub>3</sub></strong> has a more planar conformation around the cyanoethylene moiety in the excited-state equilibrium geometry than the pristine <strong>CNPyCH<sub>3</sub></strong>, resulting in the grinding-induced red-shifted emission. Our study provides a unique insight into the MFC enhancement behavior of the pyrene-based luminogens.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140710"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-10DOI: 10.1016/j.molstruc.2024.140707
Abdelali Chihab , Nabil El Brahmi , Abdelmoula El Abbouchi , Abdelaziz El Alaoui , Mostapha Bousmina , Elmostafa El Fahime , Saïd El Kazzouli
Both the main protease (Mpro) and papain protease (PLpro) are fundamental enzymes in SARS-CoV-2 life cycle. In this study, we have targeted these two enzymes using novel indole derivatives as antiviral agents. The synthesized compounds were thoroughly characterized by Fourier-transform infrared spectroscopy (FT-IR), UV–vis, 1H, 13C, and 2D nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HRMS), and melting point (m.p.). The optimized structure, reactivity, and stability of the synthesized compounds were calculated using Density Functional Theory (DFT) at the B3LYP/6–31G(d,p) level. Using in silico ADMET prediction along with molecular docking, we found that the synthesized compounds presented good docking scores and very low predicted inhibition constants (Pki) from low micromolar to nanomolar ranges. In particular, compounds 10 and 11 with respective Pki values of 1.68 μM and 387.71 nM for Mpro and 402.50 nM and 27.10 nM for PLpro. These two compounds are engaged in vast range of interactions with the active sites of both enzymes. Further in vitro investigations using fluorescence resonance energy transfer (FRET) assays demonstrated that compounds 10 and 11 inhibited Mpro proteolytic activity with approximate IC50 values of 20 µM and 10 µM, respectively. These findings suggest that these new indole derivatives could serve as promising candidates for the development of drugs against SARS-CoV-2 and potentially other future coronaviruses.
{"title":"Synthesis, characterization, proteolytic activity inhibition, ADMET prediction, and molecular docking studies of novel indole derivatives as potential SARS-CoV-2 protease inhibitors","authors":"Abdelali Chihab , Nabil El Brahmi , Abdelmoula El Abbouchi , Abdelaziz El Alaoui , Mostapha Bousmina , Elmostafa El Fahime , Saïd El Kazzouli","doi":"10.1016/j.molstruc.2024.140707","DOIUrl":"10.1016/j.molstruc.2024.140707","url":null,"abstract":"<div><div>Both the main protease (M<sup>pro</sup>) and papain protease (PL<sup>pro</sup>) are fundamental enzymes in SARS-CoV-2 life cycle. In this study, we have targeted these two enzymes using novel indole derivatives as antiviral agents. The synthesized compounds were thoroughly characterized by Fourier-transform infrared spectroscopy (FT-IR), UV–vis, <sup>1</sup>H, <sup>13</sup>C, and 2D nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HRMS), and melting point (m.p.). The optimized structure, reactivity, and stability of the synthesized compounds were calculated using Density Functional Theory (DFT) at the B3LYP/6–31G(d,p) level. Using <em>in silico</em> ADMET prediction along with molecular docking, we found that the synthesized compounds presented good docking scores and very low predicted inhibition constants (Pki) from low micromolar to nanomolar ranges. In particular, compounds <strong>10</strong> and <strong>11</strong> with respective Pki values of 1.68 μM and 387.71 nM for M<sup>pro</sup> and 402.50 nM and 27.10 nM for PL<sup>pro</sup>. These two compounds are engaged in vast range of interactions with the active sites of both enzymes. Further in vitro investigations using fluorescence resonance energy transfer (FRET) assays demonstrated that compounds <strong>10</strong> and <strong>11</strong> inhibited M<sup>pro</sup> proteolytic activity with approximate IC<sub>50</sub> values of 20 µM and 10 µM, respectively. These findings suggest that these new indole derivatives could serve as promising candidates for the development of drugs against SARS-CoV-2 and potentially other future coronaviruses.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140707"},"PeriodicalIF":4.0,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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