Pub Date : 2024-11-15DOI: 10.1016/j.molstruc.2024.140714
Jia-Yu Li , Xin Hu , Si-Yuan Hu, Ai-Min Bai, Xin Ding, Miao-Miao Yin, Yan-Jun Hu
Bisphenol A is a hormone that contributes to the normal development of organisms. In this study, the structure-affinity relationship between bisphenol A and DNA was analyzed using calf thymus DNA as a biomacromolecule model. The influence of space volume and substituent effects on the interactions were investigated by fluorescence spectroscopy, viscosity measurements, circular dichroism spectroscopy, electrochemical tests and molecular simulations. The experimental findings demonstrated that adding electron-withdrawing groups increased the space volume on both sides of bisphenol A, limiting its insertion in DNA base pairs. Circular dichroism studies revealed that electron-withdrawing derivatives did not affect the base accumulation ability of DNA. The electrochemical measurements described a positive correlation between the substituents’ electron-withdrawing and the enhancement in interactions between bisphenol A and calf thymus DNA. Experimental results were further validated through molecular simulations. These findings provide crucial information for the structural modification of bisphenol A through space volume and substituent effects.
双酚 A 是一种有助于生物体正常发育的激素。本研究以小牛胸腺 DNA 为生物大分子模型，分析了双酚 A 与 DNA 之间的结构亲和力关系。通过荧光光谱、粘度测量、圆二色光谱、电化学测试和分子模拟，研究了空间体积和取代基效应对相互作用的影响。实验结果表明，加入抽电子基团会增加双酚 A 两侧的空间体积，从而限制其插入 DNA 碱基对。环二色性研究表明，吸电子衍生物不会影响 DNA 的碱基累积能力。电化学测量结果表明，取代基的吸电子性与双酚 A 和小牛胸腺 DNA 之间相互作用的增强呈正相关。分子模拟进一步验证了实验结果。这些发现为通过空间体积和取代基效应改变双酚 A 的结构提供了重要信息。
{"title":"The effect of electron-withdrawing groups on the binding properties of bisphenol A to DNA: Insights from multi-spectral, electrochemical, and molecular docking","authors":"Jia-Yu Li , Xin Hu , Si-Yuan Hu, Ai-Min Bai, Xin Ding, Miao-Miao Yin, Yan-Jun Hu","doi":"10.1016/j.molstruc.2024.140714","DOIUrl":"10.1016/j.molstruc.2024.140714","url":null,"abstract":"<div><div>Bisphenol A is a hormone that contributes to the normal development of organisms. In this study, the structure-affinity relationship between bisphenol A and DNA was analyzed using calf thymus DNA as a biomacromolecule model. The influence of space volume and substituent effects on the interactions were investigated by fluorescence spectroscopy, viscosity measurements, circular dichroism spectroscopy, electrochemical tests and molecular simulations. The experimental findings demonstrated that adding electron-withdrawing groups increased the space volume on both sides of bisphenol A, limiting its insertion in DNA base pairs. Circular dichroism studies revealed that electron-withdrawing derivatives did not affect the base accumulation ability of DNA. The electrochemical measurements described a positive correlation between the substituents’ electron-withdrawing and the enhancement in interactions between bisphenol A and calf thymus DNA. Experimental results were further validated through molecular simulations. These findings provide crucial information for the structural modification of bisphenol A through space volume and substituent effects.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140714"},"PeriodicalIF":4.0,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659574","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 : 2024-11-14DOI: 10.1016/j.molstruc.2024.140709
Theertha Nair A, D Antony Xavier, Eddith Sarah Varghese, Annmaria Baby, Akhila S
This study presents a comprehensive structural analysis of Iridium-cored dendrimers, denoted by , with an emphasis on degree and distance based metrics to elucidate their structure-property relationships. Dendrimers, known for their highly branched architectures, are versatile macromolecules with applications across various scientific fields. In this work, molecular descriptors serve as essential numerical indicators, capturing bonding characteristics and aiding in the prediction of material properties. Leveraging a novel quotient graph approach, we compute a range of distance based indices, including the Wiener (W), Szeged (Sz and ), Mostar (Mo and ), and Padmakar-Ivan (PI) indices. We further derive generalized expressions for entropy measures associated with degree based indices, such as Shannon's entropy, providing a robust framework for assessing the structural complexity of these compounds. Additionally, we examine various degree based descriptors with entropy measures—including the Zagreb (, , and HM), Harmonic (H), Forgotten (F), Randic (R and RR), ABC, GA, SC, σ, and Irregularity indices (irr). A linear regression analysis is conducted to model dendrimer properties and forecast attributes for subsequent generations, potentially minimizing the need for extensive laboratory experimentation. Our findings provide valuable insights into the molecular intricacies of Iridium-cored dendrimers, bridging theoretical chemistry with practical applications and contributing to future advancements in materials science and engineering.
{"title":"Topological characterization, entropy measures and prediction of properties of Iridium cored dendrimer","authors":"Theertha Nair A, D Antony Xavier, Eddith Sarah Varghese, Annmaria Baby, Akhila S","doi":"10.1016/j.molstruc.2024.140709","DOIUrl":"10.1016/j.molstruc.2024.140709","url":null,"abstract":"<div><div>This study presents a comprehensive structural analysis of Iridium-cored dendrimers, denoted by <span><math><mrow><msub><mrow><mi>I</mi></mrow><mrow><mi>n</mi></mrow></msub><mi>mlr</mi></mrow><mo>;</mo><mi>n</mi><mo>≥</mo><mn>1</mn></math></span>, with an emphasis on degree and distance based metrics to elucidate their structure-property relationships. Dendrimers, known for their highly branched architectures, are versatile macromolecules with applications across various scientific fields. In this work, molecular descriptors serve as essential numerical indicators, capturing bonding characteristics and aiding in the prediction of material properties. Leveraging a novel quotient graph approach, we compute a range of distance based indices, including the Wiener (<em>W</em>), Szeged (<em>Sz</em> and <span><math><mi>S</mi><msub><mrow><mi>z</mi></mrow><mrow><mi>e</mi></mrow></msub></math></span>), Mostar (<em>Mo</em> and <span><math><mi>M</mi><msub><mrow><mi>o</mi></mrow><mrow><mi>e</mi></mrow></msub></math></span>), and Padmakar-Ivan (<em>PI</em>) indices. We further derive generalized expressions for entropy measures associated with degree based indices, such as Shannon's entropy, providing a robust framework for assessing the structural complexity of these compounds. Additionally, we examine various degree based descriptors with entropy measures—including the Zagreb (<span><math><msub><mrow><mi>M</mi></mrow><mrow><mn>1</mn></mrow></msub></math></span>, <span><math><msub><mrow><mi>M</mi></mrow><mrow><mn>2</mn></mrow></msub></math></span>, and <em>HM</em>), Harmonic (<em>H</em>), Forgotten (<em>F</em>), Randic (<em>R</em> and <em>RR</em>), ABC, GA, SC, <em>σ</em>, and Irregularity indices (<em>irr</em>). A linear regression analysis is conducted to model dendrimer properties and forecast attributes for subsequent generations, potentially minimizing the need for extensive laboratory experimentation. Our findings provide valuable insights into the molecular intricacies of Iridium-cored dendrimers, bridging theoretical chemistry with practical applications and contributing to future advancements in materials science and engineering.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140709"},"PeriodicalIF":4.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659741","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 : 2024-11-14DOI: 10.1016/j.molstruc.2024.140667
R. Soria-Martínez , S. García-Granda
X-ray diffraction analysis, combined with the Quantum Theory of Atoms in Molecules (QTAIM), serves as a powerful tool for describing chemical bonding in real space for solids. By integrating theoretical and experimental data, a more accurate representation of atomic interactions including Van der Waals forces, hydrogen bonds, covalent, ionic, and metallic bonds is achieved. The analysis of noncovalent interactions through electronic density enables the identification of Lewis acid and base sites, while also revealing the directional ‘key-lock’ interactions that correspond to molecular recognition. The examination of critical points in the electron density and its derivatives allows for the characterization of the types of interactions present in crystal packing. This study focuses on the experimental and theoretical investigation of noncovalent interactions within a molecular crystal of a newly synthesized carbohydrazide derivative. The crystal structure was determined using X-ray single-crystal diffraction, and the crystallographic asymmetric unit was optimized via DFT, with the results compared to experimental data. Noncovalent interactions in real space such as Van der Waals forces, hydrogen bonds, and inter- and intramolecular steric repulsions were analyzed in terms of electron density and its derivatives. The QTAIM framework was applied to quantify the strength of these interactions, employing Voronoi deformation density and electron localization and delocalization indices for solids. The results presented in this work, using crystal engineering, reveal that derivatives of diurea compounds crystallize following a characteristic pattern that forms a synthon configuration. The strength of this interaction, quantified through QTAIM analysis of the electronic density, provides a deeper understanding of the chemistry of these compounds, both in terms of biological activity and coordination chemistry.
X 射线衍射分析与分子中原子的量子理论（QTAIM）相结合，是描述固体真实空间中化学键的有力工具。通过整合理论和实验数据，可以更准确地表示原子间的相互作用，包括范德华力、氢键、共价键、离子键和金属键。通过电子密度对非共价相互作用的分析，可以确定路易斯酸和碱的位点，同时还揭示了与分子识别相对应的定向 "键锁 "相互作用。通过对电子密度临界点及其衍生物的研究，可以确定晶体堆积中存在的相互作用类型。本研究的重点是对一种新合成的羧酰肼衍生物分子晶体中的非共价相互作用进行实验和理论研究。利用 X 射线单晶衍射确定了晶体结构，并通过 DFT 优化了晶体不对称单元，将结果与实验数据进行了比较。通过电子密度及其衍生物分析了实际空间中的非共价相互作用，如范德华力、氢键以及分子间和分子内的立体排斥。采用 QTAIM 框架，利用 Voronoi 变形密度和固体电子局域化和脱局域化指数来量化这些相互作用的强度。这项研究利用晶体工程学得出的结果表明，二脲化合物的衍生物结晶时遵循一种形成合子构型的特征模式。通过对电子密度进行 QTAIM 分析，量化了这种相互作用的强度，从而加深了对这些化合物在生物活性和配位化学方面的理解。
{"title":"Unraveling the noncovalent interactions in a organic crystal using Quantum theory of atoms in molecules","authors":"R. Soria-Martínez , S. García-Granda","doi":"10.1016/j.molstruc.2024.140667","DOIUrl":"10.1016/j.molstruc.2024.140667","url":null,"abstract":"<div><div>X-ray diffraction analysis, combined with the Quantum Theory of Atoms in Molecules (QTAIM), serves as a powerful tool for describing chemical bonding in real space for solids. By integrating theoretical and experimental data, a more accurate representation of atomic interactions including Van der Waals forces, hydrogen bonds, covalent, ionic, and metallic bonds is achieved. The analysis of noncovalent interactions through electronic density enables the identification of Lewis acid and base sites, while also revealing the directional ‘key-lock’ interactions that correspond to molecular recognition. The examination of critical points in the electron density and its derivatives allows for the characterization of the types of interactions present in crystal packing. This study focuses on the experimental and theoretical investigation of noncovalent interactions within a molecular crystal of a newly synthesized carbohydrazide derivative. The crystal structure was determined using X-ray single-crystal diffraction, and the crystallographic asymmetric unit was optimized via DFT, with the results compared to experimental data. Noncovalent interactions in real space such as Van der Waals forces, hydrogen bonds, and inter- and intramolecular steric repulsions were analyzed in terms of electron density and its derivatives. The QTAIM framework was applied to quantify the strength of these interactions, employing Voronoi deformation density and electron localization and delocalization indices for solids. The results presented in this work, using crystal engineering, reveal that derivatives of diurea compounds crystallize following a characteristic pattern that forms a synthon configuration. The strength of this interaction, quantified through QTAIM analysis of the electronic density, provides a deeper understanding of the chemistry of these compounds, both in terms of biological activity and coordination chemistry.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140667"},"PeriodicalIF":4.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659578","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}
Three novel series of cyanostyrene-based derivatives containing pyridine, cyanostyrene and terminal phenyl, naphthyl and anthryl as π-conjugated aromatic unit were synthesized by Suzuki coupling and Knoevenagel reactions. A slight modification in chemical structures induced significant differences in self-assembly property in bulk state, emissive properties in both solution and aggregated states, mechanochromic properties and acidochromism properties. The terminal phenyl cyanostyrene-based derivatives exhibited a mesophase transition from nematic phase to smectic A phase upon elongation of the terminal chain and decreasing temperature, whereas the other terminal naphthyl and anthryl cyanostyrene-based derivatives were non-mesogen, which might be attributed to the increased twisted molecular configuration and geometric anisotropy. All the compounds displayed positive solvatochromic behaviors and the redshift in emission spectra gradually increased from terminal naphthyl compound via phenyl compound to anthryl compound attributing to the enhancement in intramolecular charge transfer. All the compounds displayed emission in both solution and aggregated states due to the twisted molecular configurations or/and distinct intramolecular charge transfer. The terminal phenyl and naphthyl compounds displayed extremely weak mechanochromism, whereas the terminal anthryl compound displayed distinct mechanochromism due to the highly twisted molecular configuration of the anthryl compound. Reversible high-contrast acidochromism was realized for all the compounds due to the reversible protonation and deprotonation process of pyridine. In addition, the good applications in security paper, encrypted ink and bioimaging were also demonstrated. This investigation elucidates that a slight change in chemical structures could induce big differences in characteristics in different states, which afforded effective ways for the construction of multifunctional materials.
通过铃木偶联和克诺文纳格尔反应，合成了三个新系列的氰苯乙烯基衍生物，这些衍生物含有吡啶、氰苯乙烯和末端苯基、萘基和蒽基作为 π-共轭芳香单元。化学结构的细微改变会导致体态自组装特性、溶液和聚集态发射特性、机械变色特性和酸变色特性的显著差异。当端链拉长和温度降低时，端苯基氰基苯乙烯衍生物表现出从向列相到共晶 A 相的介相转变，而其他端萘基和蒽基氰基苯乙烯衍生物则没有介相，这可能是由于扭曲的分子构型和几何各向异性增加所致。所有化合物都显示出正溶解变色行为，并且发射光谱的红移从末端萘基化合物经苯基化合物到蒽基化合物逐渐增加，这归因于分子内电荷转移的增强。由于扭曲的分子构型或/和明显的分子内电荷转移，所有化合物在溶液和聚集状态下都显示出发射光谱。末端苯基和萘基化合物显示出极弱的机械致色性，而末端蒽基化合物则显示出明显的机械致色性，这是因为蒽基化合物的分子构型高度扭曲。由于吡啶可逆的质子化和去质子化过程，所有化合物都实现了可逆的高对比度酸致变色。此外，该化合物在防伪纸张、加密油墨和生物成像方面的良好应用也得到了证实。这项研究揭示了化学结构的细微变化可导致不同状态下特性的巨大差异，为构建多功能材料提供了有效途径。
{"title":"Insight into the effect of terminal aromatic group on the mesomorphic, emissive and stimuli-responsive properties of cyanostyrene-based derivatives with multiple applications","authors":"Xiaotong Liu , Baoyu Shen , Yurun Liang , Tianzhi Gao , Yulong Xiao","doi":"10.1016/j.molstruc.2024.140724","DOIUrl":"10.1016/j.molstruc.2024.140724","url":null,"abstract":"<div><div>Three novel series of cyanostyrene-based derivatives containing pyridine, cyanostyrene and terminal phenyl, naphthyl and anthryl as π-conjugated aromatic unit were synthesized by Suzuki coupling and Knoevenagel reactions. A slight modification in chemical structures induced significant differences in self-assembly property in bulk state, emissive properties in both solution and aggregated states, mechanochromic properties and acidochromism properties. The terminal phenyl cyanostyrene-based derivatives exhibited a mesophase transition from nematic phase to smectic A phase upon elongation of the terminal chain and decreasing temperature, whereas the other terminal naphthyl and anthryl cyanostyrene-based derivatives were non-mesogen, which might be attributed to the increased twisted molecular configuration and geometric anisotropy. All the compounds displayed positive solvatochromic behaviors and the redshift in emission spectra gradually increased from terminal naphthyl compound <em>via</em> phenyl compound to anthryl compound attributing to the enhancement in intramolecular charge transfer. All the compounds displayed emission in both solution and aggregated states due to the twisted molecular configurations or/and distinct intramolecular charge transfer. The terminal phenyl and naphthyl compounds displayed extremely weak mechanochromism, whereas the terminal anthryl compound displayed distinct mechanochromism due to the highly twisted molecular configuration of the anthryl compound. Reversible high-contrast acidochromism was realized for all the compounds due to the reversible protonation and deprotonation process of pyridine. In addition, the good applications in security paper, encrypted ink and bioimaging were also demonstrated. This investigation elucidates that a slight change in chemical structures could induce big differences in characteristics in different states, which afforded effective ways for the construction of multifunctional materials.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140724"},"PeriodicalIF":4.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651791","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 : 2024-11-13DOI: 10.1016/j.molstruc.2024.140582
Afshan Khurshid , Muhammad Nawaz Tahir , Tilo Söhnel , Ehsan Ullah Mughal , Ryan J. Trovitch , M. Naveed Zafar
A new class of donor flexible nitrogen ligands, namely pyridylidene sulfonamides (PYSAs; N-(1-benzylpyridin-4(1H)-ylidene)benzene-sulfonamide, N-(1-benzylpyridin-4(1H)-ylidene)thiophene-2-sulfonamide, N-(1-benzylpyridin-4(1H)-ylidene)pyridine-2-sulfonamide and N-(1-benzylpyridin-4(1H)-ylidene)-8-quinoline-sulfonamide), were prepared from 4-amino-1-benzylpyridin-1-ium chloride and various aromatic sulfonyl chlorides. The treatment of PYSAs with [(CH3CN)2PdCl2] afforded the corresponding Pd(II) complexes. The newly synthesized compounds were characterized by multinuclear 1H and 13C NMR spectroscopy, IR spectroscopy, elemental analysis, and single-crystal X-ray diffraction. Their redox chemistry was then evaluated under an inert atmosphere of nitrogen and carbon dioxide, both in the presence and absence of protons. An apparent interaction of CO2 with each Pd(II) catalyst was inferred by the collection of cyclic voltammograms and the enhancement of peak currents at respective peak potentials. All catalysts were robust under bulk electrolysis conditions over 3600 s.
{"title":"Palladium (II) pyridylidene sulfonamides (PYSAs) for electrocatalytic reduction of CO2","authors":"Afshan Khurshid , Muhammad Nawaz Tahir , Tilo Söhnel , Ehsan Ullah Mughal , Ryan J. Trovitch , M. Naveed Zafar","doi":"10.1016/j.molstruc.2024.140582","DOIUrl":"10.1016/j.molstruc.2024.140582","url":null,"abstract":"<div><div>A new class of donor flexible nitrogen ligands, namely pyridylidene sulfonamides (PYSAs; <em>N</em>-(1-benzylpyridin-4(1<em>H</em>)-ylidene)benzene-sulfonamide, <em>N</em>-(1-benzylpyridin-4(1<em>H</em>)-ylidene)thiophene-2-sulfonamide, <em>N</em>-(1-benzylpyridin-4(1<em>H</em>)-ylidene)pyridine-2-sulfonamide and <em>N</em>-(1-benzylpyridin-4(1<em>H</em>)-ylidene)-8-quinoline-sulfonamide), were prepared from 4-amino-1-benzylpyridin-1-ium chloride and various aromatic sulfonyl chlorides. The treatment of PYSAs with [(CH<sub>3</sub>CN)<sub>2</sub>PdCl<sub>2</sub>] afforded the corresponding Pd(II) complexes. The newly synthesized compounds were characterized by multinuclear <sup>1</sup>H and <sup>13</sup>C NMR spectroscopy, IR spectroscopy, elemental analysis, and single-crystal X-ray diffraction. Their redox chemistry was then evaluated under an inert atmosphere of nitrogen and carbon dioxide, both in the presence and absence of protons. An apparent interaction of CO<sub>2</sub> with each Pd(II) catalyst was inferred by the collection of cyclic voltammograms and the enhancement of peak currents at respective peak potentials. All catalysts were robust under bulk electrolysis conditions over 3600 s.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140582"},"PeriodicalIF":4.0,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659605","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 : 2024-11-13DOI: 10.1016/j.molstruc.2024.140730
Sana Malik , Faiza Akram , Muhammad Ali , Mohsin Javed , Rana Muhammad Mateen , Ammar Zidan , Ali Bahadur , Shahid Iqbal , Sajid Mahmood , Abd-ElAziem Farouk , Salman Aloufi
The bacterial cell-to-cell communication mechanism known as quorum sensing (QS) uses chemical cues called autoinducers (AIs) to control several processes, including pathogenicity, antibiotic resistance, and biofilm formation. This study investigates the QS receptor-ligand interactions and QS compatibility within and between bacterial species using computational molecular docking. Receptor proteins including LuxS, LuxP, AgrC, LuxN, SdiA, LasR, esaR, YenR, LamC, PlcR, and TraR were docked with their respective AIs (AHL, AI-1, AI-2, AIP1, LamD, PapR7) in both biofilm and non-biofilm producing bacteria. Our findings indicate that QS receptors exhibit high affinity for their cognate ligands, with binding affinities ≥ -4.5 Kcal/mol. Additionally, Zinc Pharmar-derived similar chemical structures demonstrated binding affinities ≥ -5.3 Kcal/mol. Density Functional Theory (DFT) analysis revealed AI-2 as the most reactive autoinducer. Molecular Dynamics (MD) simulations confirmed the stability of LasR-AHL and LuxP-AI-2 complexes. These insights pave the way for further in vitro and in vivo investigations of QS mechanisms.
{"title":"Unveiling quorum sensing mechanisms: Computational docking and dynamics of bacterial receptors and ligands","authors":"Sana Malik , Faiza Akram , Muhammad Ali , Mohsin Javed , Rana Muhammad Mateen , Ammar Zidan , Ali Bahadur , Shahid Iqbal , Sajid Mahmood , Abd-ElAziem Farouk , Salman Aloufi","doi":"10.1016/j.molstruc.2024.140730","DOIUrl":"10.1016/j.molstruc.2024.140730","url":null,"abstract":"<div><div>The bacterial cell-to-cell communication mechanism known as quorum sensing (QS) uses chemical cues called autoinducers (AIs) to control several processes, including pathogenicity, antibiotic resistance, and biofilm formation. This study investigates the QS receptor-ligand interactions and QS compatibility within and between bacterial species using computational molecular docking. Receptor proteins including LuxS, LuxP, AgrC, LuxN, SdiA, LasR, esaR, YenR, LamC, PlcR, and TraR were docked with their respective AIs (AHL, AI-1, AI-2, AIP1, LamD, PapR7) in both biofilm and non-biofilm producing bacteria. Our findings indicate that QS receptors exhibit high affinity for their cognate ligands, with binding affinities ≥ -4.5 Kcal/mol. Additionally, Zinc Pharmar-derived similar chemical structures demonstrated binding affinities ≥ -5.3 Kcal/mol. Density Functional Theory (DFT) analysis revealed AI-2 as the most reactive autoinducer. Molecular Dynamics (MD) simulations confirmed the stability of LasR-AHL and LuxP-AI-2 complexes. These insights pave the way for further <em>in vitro</em> and <em>in vivo</em> investigations of QS mechanisms.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140730"},"PeriodicalIF":4.0,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651624","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}
Development of bioactive candidates for cancer and bacterial infections are ever demanding challenges due to the resistance shown by these cancer and bacterial cells for already exposed drug molecules. Methyl carbazate derivatized phenanthroline compound 6-[2-(methoxycarbonyl)diazen-1-yl]-1,10-phenanthroline-5-one (MCDPO) is synthesized in a three step reaction from 1,10-phenanthroline. The spectroscopic features of MCDPO are studied by HRMS, IR, 1H NMR and 13C NMR, UV-visible spectroscopy. The three-dimensional molecular structure of the MCDPO is confirmed by single crystal XRD study. The MCDPO crystallized in a triclinic system P-1 space group with the following unit cell parameter: a = 5.0347(2) Å, b = 10.3509(4) Å, c = 11.8816(4) Å, α = 84.431(3)°, β = 84.172(3)°, γ = 81.380(4)°, and V = 606.92(4) Å3 at T = 133 K. The MCDPO is containing aromatic rings, hydrogen bonding donors as well as hydrogen bonding acceptor groups forming supramolecular molecular arrangements through C-H⋯O, CH⋯N, C-O⋯C, π-π and π⋯C non-covalent interactions. Electrochemical redox and electrochromic features of MCDPO are studied through cyclic voltammetry and UV-vis based spectroelectrochemistry. This compound shows good anticancer activity with IC50 values 1.438, 6.576 and 2.901 µM against 4T1, MCF-7 and PC-3 cancer cell lines respectively. The flow cytometry study on 4T1 cells suggests that the MCDPO promoted cancer cell death by inducing apoptosis, and cell cycle arrest in the G0/G1 phase. It also induces nuclear fragmentation and reactive oxygen species (ROS) generation, which was studied by DAPI, AO, and DCFH-DA based cellular staining studies by fluorescence confocal imaging. The MCDPO also studied for antibacterial activity against Escherichia Coil bacteria and Mycobacterium tuberculosis (Mtb). The MCDPO shows minimum inhibitory concentration (MIC) of 0.39 µg/mL against Mtb which is slightly better than the one of the clinically used drug candidates Ethambutol.
{"title":"Synthesis, characterisation, single crystal structure and evaluation of a redox innocent carbazate functionalized phenanthroline for antimycobacterial and anticancer activity","authors":"Ravallika Aluri , Aishwarya Natarajan , Tarun Patel , Darakhshan Begum , Jyothi Kumari , Dharmarajan Sriram , Balaram Ghosh , Krishnan Rangan","doi":"10.1016/j.molstruc.2024.140729","DOIUrl":"10.1016/j.molstruc.2024.140729","url":null,"abstract":"<div><div>Development of bioactive candidates for cancer and bacterial infections are ever demanding challenges due to the resistance shown by these cancer and bacterial cells for already exposed drug molecules. Methyl carbazate derivatized phenanthroline compound 6-[2-(methoxycarbonyl)diazen-1-yl]-1,10-phenanthroline-5-one (MCDPO) is synthesized in a three step reaction from 1,10-phenanthroline. The spectroscopic features of MCDPO are studied by HRMS, IR, <sup>1</sup>H NMR and <sup>13</sup>C NMR, UV-visible spectroscopy. The three-dimensional molecular structure of the MCDPO is confirmed by single crystal XRD study. The MCDPO crystallized in a triclinic system <em>P-</em>1 space group with the following unit cell parameter: a = 5.0347(2) Å, b = 10.3509(4) Å, c = 11.8816(4) Å, α = 84.431(3)°, β = 84.172(3)°, γ = 81.380(4)°, and V = 606.92(4) Å<sup>3</sup> at T = 133 K. The MCDPO is containing aromatic rings, hydrogen bonding donors as well as hydrogen bonding acceptor groups forming supramolecular molecular arrangements through C-H⋯O, C<img>H⋯N, C-O⋯C, π-π and π⋯C non-covalent interactions. Electrochemical redox and electrochromic features of MCDPO are studied through cyclic voltammetry and UV-vis based spectroelectrochemistry. This compound shows good anticancer activity with IC<sub>50</sub> values 1.438, 6.576 and 2.901 µM against 4T1, MCF-7 and PC-3 cancer cell lines respectively. The flow cytometry study on 4T1 cells suggests that the MCDPO promoted cancer cell death by inducing apoptosis, and cell cycle arrest in the G0/G1 phase. It also induces nuclear fragmentation and reactive oxygen species (ROS) generation, which was studied by DAPI, AO, and DCFH-DA based cellular staining studies by fluorescence confocal imaging. The MCDPO also studied for antibacterial activity against <em>Escherichia Coil</em> bacteria and <em>Mycobacterium tuberculosis (Mtb).</em> The MCDPO shows minimum inhibitory concentration (MIC) of 0.39 µg/mL against <em>Mtb</em> which is slightly better than the one of the clinically used drug candidates Ethambutol.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140729"},"PeriodicalIF":4.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651705","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.2024.140731
V. Lamprou , C. Kouderis , A. Tryfon , T.A. Kabanos , A.G. Kalampounias
In this work, we report on a concentration and temperature dependent study of the 1,2-Bis(4-pyridyl)ethylene (BPE) – ethanol solutions by means of ultrasonic relaxation spectroscopy. The results revealed two distinct relaxation processes that follow Debye-type frequency dependence. Despite the presence of both processes in the full concentration range studied, the low-frequency relaxation process, related to conformational change between the trans- and gauche-BPE conformers, dominates the acoustic spectra in the low-concentration range, while diminishes at higher concentrations with a parallel enhancement of the high-frequency relaxation process, which is attributed to the self-association of BPE molecules. Quantum mechanical calculations were performed to investigate the energetics of the trans- and gauche-conformers. The trans-species was found more thermodynamically stable than the gauche-conformer. By applying the Synchronous Transit-Guided Quasi-Newton (STQN) methodology, we confirmed the presence of a single transition structure. From the temperature dependence of the acoustic properties, we estimated the activation enthalpy and the enthalpy difference between the two conformers. Density Functional Theory (DFT) calculations have been applied to attain the corresponding enthalpies that were found close to the experimental values. Molecular docking calculations established the self-aggregation mechanism between BPE monomers forming three types of dimeric units, namely the trans-trans, the gauche-gauche and the trans-gauche dimer species with the latter found to be the most thermodynamically favorable. The concentration dependence of the sound velocity, mass density and shear viscosity evidenced the formation of BPE aggregates. From the temperature dependence of the acoustic spectra, the thermodynamic properties of the self-aggregation mechanism of BPE were also determined. Based on the vibrational spectroscopic data, the population of the gauche conformers was found to increase with concentration at the expense of the population of the trans conformers. From the study of the vibrational properties of the system in the short-rage order, we cannot exclude the presence of a specific dimer type in the overall structure. Nevertheless, regarding to the binding score of the trans-gauche dimer (-1.25 kcal/mol), this species is the most thermodynamically stable and most likely its population is higher in dense solutions relative to the other two dimer species.
{"title":"Evidence of conformational changes and self-aggregation of 1,2-Bis(4-pyridyl)ethylene in solutions with ethanol","authors":"V. Lamprou , C. Kouderis , A. Tryfon , T.A. Kabanos , A.G. Kalampounias","doi":"10.1016/j.molstruc.2024.140731","DOIUrl":"10.1016/j.molstruc.2024.140731","url":null,"abstract":"<div><div>In this work, we report on a concentration and temperature dependent study of the 1,2-Bis(4-pyridyl)ethylene (BPE) – ethanol solutions by means of ultrasonic relaxation spectroscopy. The results revealed two distinct relaxation processes that follow Debye-type frequency dependence. Despite the presence of both processes in the full concentration range studied, the low-frequency relaxation process, related to conformational change between the trans- and gauche-BPE conformers, dominates the acoustic spectra in the low-concentration range, while diminishes at higher concentrations with a parallel enhancement of the high-frequency relaxation process, which is attributed to the self-association of BPE molecules. Quantum mechanical calculations were performed to investigate the energetics of the trans- and gauche-conformers. The trans-species was found more thermodynamically stable than the gauche-conformer. By applying the Synchronous Transit-Guided Quasi-Newton (STQN) methodology, we confirmed the presence of a single transition structure. From the temperature dependence of the acoustic properties, we estimated the activation enthalpy and the enthalpy difference between the two conformers. Density Functional Theory (DFT) calculations have been applied to attain the corresponding enthalpies that were found close to the experimental values. Molecular docking calculations established the self-aggregation mechanism between BPE monomers forming three types of dimeric units, namely the trans-trans, the gauche-gauche and the trans-gauche dimer species with the latter found to be the most thermodynamically favorable. The concentration dependence of the sound velocity, mass density and shear viscosity evidenced the formation of BPE aggregates. From the temperature dependence of the acoustic spectra, the thermodynamic properties of the self-aggregation mechanism of BPE were also determined. Based on the vibrational spectroscopic data, the population of the gauche conformers was found to increase with concentration at the expense of the population of the trans conformers. From the study of the vibrational properties of the system in the short-rage order, we cannot exclude the presence of a specific dimer type in the overall structure. Nevertheless, regarding to the binding score of the trans-gauche dimer (-1.25 kcal/mol), this species is the most thermodynamically stable and most likely its population is higher in dense solutions relative to the other two dimer species.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140731"},"PeriodicalIF":4.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651623","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.2024.140612
Faustino Wahaia , Irmantas Kašalynas , Daniil Pashnev , Gintaras Valušis , Andrzej Urbanowicz , Mindaugas Karaliunas , Dinesh Pratap Singh , Sascha Wallentowitz , Birger Seifert
Metal-organic frameworks (MOFs) crystals are promising emerging materials for terahertz (THz) photonics i.e., for THz wave generation through difference frequency or optical rectification and electrooptic detection, including optical components for THz beam steering. The present work reports optical properties of three different non-centrosymmetric single MOF crystals, grown by an innovative solvo-thermal technique with tunable morphology, termed MOF [Zn(3-ptz)2]n (MIRO-101). THz time-domain spectroscopy (TTDS) in the range of 0.25 – 1.5 THz has been used for the measurement of the transfer function, of these MOF crystals. Through this experimental function , optical parameters such as refractive index, and absorption coefficient have been calculated for the analysis of the optical properties of this crystal. The results indicate that this MOF crystal offers opportunities for long-term exploration of properties toward the creation of novel nonlinear THz photonics materials, as a THz radiation emitter via Different Frequency Generation (DFG) or Optical Rectification (OR) and Electro-optic (EO) detection via optical sampling, including for its use in optoelectronics, and materials science.
{"title":"Optical properties of millimeter-size metal-organic framework single crystals using THz techniques","authors":"Faustino Wahaia , Irmantas Kašalynas , Daniil Pashnev , Gintaras Valušis , Andrzej Urbanowicz , Mindaugas Karaliunas , Dinesh Pratap Singh , Sascha Wallentowitz , Birger Seifert","doi":"10.1016/j.molstruc.2024.140612","DOIUrl":"10.1016/j.molstruc.2024.140612","url":null,"abstract":"<div><div>Metal-organic frameworks (MOFs) crystals are promising emerging materials for terahertz (THz) photonics i.e., for THz wave generation through difference frequency or optical rectification and electrooptic detection, including optical components for THz beam steering. The present work reports optical properties of three different non-centrosymmetric single MOF crystals, grown by an innovative solvo-thermal technique with tunable morphology, termed MOF [Zn(3-ptz)2]n (MIRO-101). THz time-domain spectroscopy (TTDS) in the range of 0.25 – 1.5 THz has been used for the measurement of the transfer function, <span><math><mrow><mi>H</mi><mo>(</mo><mi>ω</mi><mo>)</mo></mrow></math></span> of these MOF crystals. Through this experimental function <span><math><mrow><msub><mi>H</mi><mrow><mi>e</mi><mi>x</mi><mi>p</mi></mrow></msub><mrow><mo>(</mo><mi>ω</mi><mo>)</mo></mrow></mrow></math></span>, optical parameters such as refractive index, <span><math><mrow><msub><mi>n</mi><mrow><mi>M</mi><mi>O</mi><mi>F</mi></mrow></msub><mrow><mo>(</mo><mi>ω</mi><mo>)</mo></mrow></mrow></math></span> and absorption coefficient<span><math><mrow><mo>,</mo><mspace></mspace><msub><mi>α</mi><mrow><mi>M</mi><mi>O</mi><mi>F</mi></mrow></msub><mrow><mo>(</mo><mi>ω</mi><mo>)</mo></mrow></mrow></math></span> have been calculated for the analysis of the optical properties of this crystal. The results indicate that this MOF crystal offers opportunities for long-term exploration of properties toward the creation of novel nonlinear THz photonics materials, as a THz radiation emitter via Different Frequency Generation (DFG) or Optical Rectification (OR) and Electro-optic (EO) detection via optical sampling, including for its use in optoelectronics, and materials science.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1322 ","pages":"Article 140612"},"PeriodicalIF":4.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142659577","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.2024.140698
Muhammad Shahid Nadeem , Shawkat Hayat , Mustafa A. Zeyadi , Imran Kazmi , Hayat Ullah
A new series of isatin derivatives were synthesized, characterized by 1HNMR, 13CNMR and HREI-MS, and screened for α-glucosidase and alpha amylase inhibition. All the analogues were found to be dual inhibitors and showed good inhibitory potentials with IC50 values ranging from 5.28 ± 0.10 to 38.66 ± 0.30 µM (against alpha-amylase), and 5.45 ± 0.10 to 39.25 ± 0.50 µM (against alpha-glucosidase), as compared to the standard drug acarbose (IC50 = 11.12 ± 0.15 and 11.29 ± 0.07 µM, respectively). The most potent inhibitor among the series was analogue 24 (IC50 = 5.28 ± 0.10 for alpha-amylase and IC50 = 5.46 ± 0.10 µM for alpha-glucosidase), which has a nitro group attached at the meta-position of the phenyl ring A and the para position of phenyl ring B. Structure-activity relationship has been established mainly based on the position, nature and number of the substituent(s) attached to the phenyl ring. To investigate the binding interaction of the potent analog with the active site of an enzyme, molecular docking studies were carried out. To study the drug-likeness properties, the ADME study was also carried out. The most active compounds engage most of the amino acids composing the active site and display maximum interactions. These interactions majorly include formation of strong hydrogen bonds, which might be due to the presence of highly electronegative heteroatoms on aromatic rings. All the analogues were also tested for in vivo anti-nematodal activity against C. elegans to assess their cytotoxicity in comparison to the reference Levamisole. The cytotoxicity profile demonstrated that analogues 2, 7, 20 and 22 displayed minimum cytotoxicity at every concentration.
{"title":"Design, synthesis, biological and computational analysis of isatin-based bis-thiourea analogues as anti-diabetic and anti-nematode agents","authors":"Muhammad Shahid Nadeem , Shawkat Hayat , Mustafa A. Zeyadi , Imran Kazmi , Hayat Ullah","doi":"10.1016/j.molstruc.2024.140698","DOIUrl":"10.1016/j.molstruc.2024.140698","url":null,"abstract":"<div><div>A new series of isatin derivatives were synthesized, characterized by <sup>1</sup>HNMR, <sup>13</sup>CNMR and HREI-MS, and screened for α-glucosidase and alpha amylase inhibition. All the analogues were found to be dual inhibitors and showed good inhibitory potentials with IC<sub>50</sub> values ranging from 5.28 ± 0.10 to 38.66 ± 0.30 <em>µM</em> (against alpha-amylase), and 5.45 ± 0.10 to 39.25 ± 0.50 <em>µ</em>M (against alpha-glucosidase), as compared to the standard drug acarbose (IC<sub>50</sub> = 11.12 ± 0.15 and 11.29 ± 0.07 <em>µ</em>M, respectively). The most potent inhibitor among the series was analogue <strong>24</strong> (IC<sub>50</sub> = 5.28 ± 0.10 for alpha-amylase and IC<sub>50</sub> = 5.46 ± 0.10 <em>µM</em> for alpha-glucosidase), which has a nitro group attached at the meta-position of the phenyl ring A and the para position of phenyl ring B. Structure-activity relationship has been established mainly based on the position, nature and number of the substituent(s) attached to the phenyl ring. To investigate the binding interaction of the potent analog with the active site of an enzyme, molecular docking studies were carried out. To study the drug-likeness properties, the ADME study was also carried out. The most active compounds engage most of the amino acids composing the active site and display maximum interactions. These interactions majorly include formation of strong hydrogen bonds, which might be due to the presence of highly electronegative heteroatoms on aromatic rings. All the analogues were also tested for in vivo anti-nematodal activity against <em>C. elegans</em> to assess their cytotoxicity in comparison to the reference Levamisole. The cytotoxicity profile demonstrated that analogues <strong>2, 7, 20</strong> and <strong>22</strong> displayed minimum cytotoxicity at every concentration.</div></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":"1323 ","pages":"Article 140698"},"PeriodicalIF":4.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651679","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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