Milad Rayka, Ali Mohammad Latifi, Morteza Mirzaei, Gholamreza Farnoosh, Zeinab Khosravi
{"title":"ADDZYME: A software to predict effect of additives on enzyme activity","authors":"Milad Rayka, Ali Mohammad Latifi, Morteza Mirzaei, Gholamreza Farnoosh, Zeinab Khosravi","doi":"10.1007/s12039-024-02272-8","DOIUrl":"10.1007/s12039-024-02272-8","url":null,"abstract":"<div><p>Enzymes are biological catalysts that accelerate chemical reactions by reducing their activation energy. Enzymes specific environmental conditions to function optimally. Additive molecules and compounds, such as organic solvents, ionic liquids, and deep eutectic solvents, have crucial effects on enzyme behavior by changing activity and stability. However, finding and testing different additives is an expensive process that requires specialists, laboratory equipment, and chemical compounds. Machine learning, which has been present in all fields of science and technology in recent years, is one of the ways to find a suitable additive for our desired enzyme without doing a time-consuming experimental process. In this manuscript, we introduce ADDZYME, a machine learning-based software, to predict the effect of additives on enzyme activity. ADDZYME utilizes an ensemble of extremely randomized trees models alongside physicochemical descriptors to make a prediction. To ease usage, ADDZYME is accompanied by a graphical user interface. ADDZYME is freely available on www.github.com/miladrayka/addzyme for further experiments.</p><h3>Graphical abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div><div><p>SYNOPSIS: ADDZYME software applies a machine-learning algorithm to predict the effect of an additive on an enzyme activity. ADDZYME utilizes an ensemble of extremely randomized trees models alongside physicochemical descriptors to make a prediction.</p></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 3","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141338426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"High-resolution spectroscopic probing of allowed and forbidden ortho- and para-nuclear spin-isomers of NH3","authors":"Indrayani Patra, Soumyadipta Chakraborty, Ardhendu Pal, Biswajit Panda, Manik Pradhan","doi":"10.1007/s12039-024-02281-7","DOIUrl":"10.1007/s12039-024-02281-7","url":null,"abstract":"<div><p>Ammonia (NH<sub>3</sub>) is a pyramidal symmetric top molecule with inversion motion and it exists in two distinct nuclear spin isomeric forms, <i>ortho</i>-NH<sub>3</sub> (<i>K</i> = 3n) and <i>para</i>-NH<sub>3</sub> (<i>K</i> ≠ 3n). Here, a pair of electric dipole-allowed [<sup>R</sup>Q(4,3) and <sup>P</sup>P(2,2)] and weak forbidden [<sup>O</sup>P(3,3) and <sup>S</sup>Q(8,1)] transitions of gas-phase NH<sub>3</sub> were probed in the ν<sub>4</sub> fundamental vibrational band occurring at 6.2 <i>µ</i>m mid-IR interference-free spectral region using an external-cavity quantum cascade laser coupled cavity ring-down spectrometer. We have experimentally achieved the ortho-to-para ratio (OPR) of (1.03 ± 0.24) and (1.08 ± 0.14) at room temperature (296 K) for the allowed and forbidden transitions of NH<sub>3</sub>, respectively. Furthermore, our experimental findings confirm that the nuclear spin-symmetry is conserved under the nonreactive perturber-induced collisional processes. This study paves the way to directly probe the nuclear spin-isomers of gas-phase NH<sub>3</sub> and thus may lead to an in-depth understanding of nuclear spin-isomerism associated with various physical and chemical processes.</p><h3>Graphical Abstract</h3><p>This work shows the high-resolution probing of <i>ortho-</i> and <i>para-</i>nuclear spin-isomers of NH<sub>3</sub> in the gas phase at room temperature using quantum cascade laser coupled cavity ring-down spectroscopy at 6.2 <i>µ</i>m mid-IR spectral region.\u0000</p><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 3","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141347938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"An oxidative expansion mechanism of isatin-derived imines","authors":"Mariana Umba-Erazo, Rodolfo Quevedo","doi":"10.1007/s12039-024-02283-5","DOIUrl":"10.1007/s12039-024-02283-5","url":null,"abstract":"<div><p>Sodium borohydride induces the oxidative expansion of the imine derived from isatin and phenylethylamine to form 3-phenethylquinazoline-2,4(1<i>H</i>,3<i>H</i>)-dione. It has been proposed that this transformation occurs by <i>in situ</i> formation of hydroperoxyl anions by a reaction between sodium borohydride and atmospheric oxygen. To contribute to understanding this oxidative expansion, the reaction between the imine derived from isatin and phenylethylamine with hydrogen peroxide was studied in this work. From this reaction, 3-phenethylquinazoline-2,4(1<i>H</i>,3<i>H</i>)-dione was isolated and two by-products were identified: <i>N</i>-phenethyl-2-(3-phenethyl-ureido)-benzamide and methyl(2-(phenethylcarbamoyl)phenyl)carbamate. This article analyses the structure of these by-products and proposes a mechanism that explains the reaction.</p><h3>Graphical abstract</h3><p>It was established that the reaction of the imine derived from isatin and phenylethylamine with hydrogen peroxide produces a mixture of three compounds: 3-phenethylquinazoline-2,4(1<i>H</i>,3<i>H</i>)-dione, <i>N</i>-phenethyl-2-(3-phenethyl-ureido)-benzamide and methyl(2-(phenethylcarbamoyl)phenyl)carbamate. A reaction mechanism is proposed that explains this behaviour\u0000</p><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 3","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141375128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Parimal J Maliekal, Arati S Gavali, Priyanka Patel, Purav M. Badani
{"title":"Switching the regio-, stereo- and enantioselectivity in L-proline catalyzed asymmetric Mannich reaction: A case study of H-acceptor and H-donor solvents","authors":"Parimal J Maliekal, Arati S Gavali, Priyanka Patel, Purav M. Badani","doi":"10.1007/s12039-024-02279-1","DOIUrl":"10.1007/s12039-024-02279-1","url":null,"abstract":"<p>We report the detailed mechanistic insights of L-proline catalyzed, solvent-controlled, regioselective Mannich reaction. Different solvation models were employed to understand the formation of critical intermediates. The seminal difference in the nature of H-acceptor solvents and H-donor solvents leads to variation in the attachment site on the reactant molecule. Our calculations suggest that the H-acceptor solvent exhibits selective non-covalent interaction with <i>α</i>-hydrogen atoms of the iminium group, facilitating the reactivity at the more hindered site, which results in the formation of a branched isomer. On the other hand, the H-donor solvent preferentially binds to the carboxylate group, thus enabling the reactivity to proceed from the less hindered carbon chain, leading to a linear isomer. The above distinct interactions force a regioselective generation of enamines. Thus, the iminium ion's site-specific solvent interaction has been observed to cause a switch in the regioselectivity. These enamines subsequently react with cyclic ketone to produce Mannich base with excellent enantioselectivity (>99%ee).</p>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 3","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141376847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A nano-molar sensitive fluorescence sensor for cucurbit[7]uril","authors":"Karuppasamy Karpagalakshmi, Ramesh Prakash, Govindaraj Usha, Pavitra Rajendran, Lakshminarayanan Piramuthu, Narayanan Selvapalam","doi":"10.1007/s12039-024-02285-3","DOIUrl":"10.1007/s12039-024-02285-3","url":null,"abstract":"<div><p>Cucurbit[<i>n</i>]urils (CB[<i>n</i>], <i>n</i> = 5–8) are the most important class of host molecules that are widely applied in various important applications. Until now, no sensitive sensor has been developed exclusively for detecting cucurbiturils. Here, we have utilized the supramolecular assembly of acriflavine and graphene oxide (ACF-GO) as a fluorescence sensor for the detection of cucurbituril family members such as CB[5], CB[6] and CB[7] with the discrimination of fluorescence intensities. Among them, CB[7] displayed the highest sensitivity, which can be detected as low as nano-molar concentration, and that allowed us to make a facile fluorescence method of detection for CB[7] and other CBs.</p><h3>Graphical abstract</h3><p>Supramolecular assembly of acriflavine on the graphene oxide turn-off the fluorescence of acriflavine and upon interaction with cucurbit[7]uril, that released the acriflavine to the solution and turn-on the fluorescence, which allowed to detect the CB[7] to the lowest of nano-molar concentration.</p><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141170533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fatemeh Doraghi, Mehdi Ghanbarlou, Amir Mohammad Mahdavian, Bahareh Bari, Bagher Larijani, Mohammad Mahdavi
{"title":"Coumarin-3-carboxylic acid: C3/C4-functionalizations and cyclization reactions","authors":"Fatemeh Doraghi, Mehdi Ghanbarlou, Amir Mohammad Mahdavian, Bahareh Bari, Bagher Larijani, Mohammad Mahdavi","doi":"10.1007/s12039-024-02267-5","DOIUrl":"10.1007/s12039-024-02267-5","url":null,"abstract":"<p>Due to the presence of a carboxyl group, coumarin-3-carboxylic acid can easily participate in C3-, and C4-functionalization, as well as cyclization reactions. The carboxyl moiety as a directing group enhances the reactivity of coumarins as dienophiles, which facilitates the participation of these scaffolds in the synthesis of various heterocycles. Hence, this review highlights the reports since 2010 on the contribution of coumarin-3-carboxylic acids in decarboxylative and cyclization reactions and discusses interesting reaction mechanisms.</p><p> Coumarins are privileged <i>O</i>-heterocycles and appear in biologically active natural and medicinal products. The presence of carboxyl as a directing group allowed coumarin-3-carboxylic acid to participate in C3-, or C4-functionalization, and annulations. This compound has attracted extensive attention from chemists in the field of cross-coupling methodologies to provide functionalized structures.</p>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141167568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ashok Kumar Maurya, Ashish Kumar Pandey, Piyali Deb Barman
{"title":"Chromite ore: X-ray fluorescence spectral analysis of Kβ and L-lines by WD-XRF","authors":"Ashok Kumar Maurya, Ashish Kumar Pandey, Piyali Deb Barman","doi":"10.1007/s12039-024-02280-8","DOIUrl":"10.1007/s12039-024-02280-8","url":null,"abstract":"<div><p>This work delves into the utility of chromium’s X-ray fluorescence (XRF) lines for the analysis of chromite ores, employing a wavelength-dispersive XRF spectrometer. The CrL<i>α</i><sub>1,2</sub> and CrL<i>β</i><sub>1</sub> fluorescence lines, despite not involving electronic transitions from valence to K-core shell, offer substantial insights into the valence state of chromium. This study examines these relatively unexplored but potentially valuable lines and compares them with the CrK<i>β</i> series fluorescence lines. Intriguingly, our investigation reveals striking differences in the L-line fluorescence spectra between metallic chromium (Cr(0)), chromite ores (Fe, Mg)Cr<sub>2</sub>O<sub>4</sub>, and K<sub>2</sub>Cr<sub>2</sub>O<sub>7</sub>. Chemical shifts and peak shapes emerge as key discriminators, surpassing the sensitivity of the CrK<i>β</i><sub>1,3</sub> lines. Notably, the chemical shifts of L-lines are amplified, showcasing a clear trend: Cr(III) exhibits a larger shift than Cr(VI), mirroring the pattern observed in the K<i>β</i>-lines. The fluorescence peak shapes of L<i>α</i><sub>1,2</sub> and L<i>β</i><sub>1</sub> for metallic chromium and chromite ores (both have unpaired 3d-electrons) are similar, whereas those of K<sub>2</sub>Cr<sub>2</sub>O<sub>7</sub> differ considerably in peak shape, indicating that unpaired 3d-electrons influence these peaks. A linear relationship was found between the area under the curve ratio for L<i>α</i><sub>1,2</sub> and L<i>β</i><sub>1</sub> and the valence state of chromium.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12039-024-02280-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141167572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Padmakar A Kulkarni, Sandeep S Kahandal, Ashok G Awale, Jagdish C Bhangoji, Suresh S Shendage
{"title":"Synthesis of Au–Pd@CeO2 nanocomposite as a potential catalyst for the Buchwald–Hartwig cross-coupling and amination of benzyl alcohol reactions","authors":"Padmakar A Kulkarni, Sandeep S Kahandal, Ashok G Awale, Jagdish C Bhangoji, Suresh S Shendage","doi":"10.1007/s12039-024-02271-9","DOIUrl":"10.1007/s12039-024-02271-9","url":null,"abstract":"<div><p>Herein, we report the novel protocol for synthesizing bimetallic gold and palladium nanoparticles decorated on rigid and stable cerium oxide support using aloe vera extract. The Au–Pd@CeO<sub>2</sub> catalyst was found to be effective for the Buchwald–Hartwig C–N cross-coupling reaction and amination of benzyl alcohol due to the synergistic influence generated by Au and Pd metals. The prepared catalyst was characterized by using XRD, TEM, SEM, and EDS. The catalyst can be efficiently used for a diverse range of substrates in the Buchwald–Hartwig C–N cross-coupling and amination of benzyl alcohol reactions compared to previously described protocols. The catalyst retains its catalytic activity even after seven cycles.</p><h3>Graphical abstract</h3><p>The synthesis of bimetallic gold and palladium nanoparticles decorated on cerium oxide support using aloe vera extract. The Au-Pd@CeO<sub>2</sub> catalyst was found to be effective for Buchwald–Hartwig C-N cross-coupling and amination of benzyl alcohol reactions due to the synergistic effect generated by Au and Pd metals.\u0000</p><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141102351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Potassium tert-butoxide promoted a direct one-pot synthesis of nitriles from aldehydes at room temperature","authors":"Saurav Kumar, Ritika Kubba, Nityananda Agasti, Anitha Selvaraj, Anil Kumar","doi":"10.1007/s12039-024-02282-6","DOIUrl":"10.1007/s12039-024-02282-6","url":null,"abstract":"<div><p>Potassium <i>tert</i>-butoxide mediated a direct one-pot synthesis of diversely substituted nitriles from aldehydes <i>via</i> the sequential addition of hydroxylamine and benzoyl chloride is reported. A wide range of aromatic, heteroaromatic, and vinyl aldehydes were converted into corresponding nitriles in good to excellent yields. Room temperature reactions, transition metal-free conditions, wide functional group tolerance, simple operation, and short reaction time are the salient features of the developed methodology.</p><h3>Graphical abstract</h3><p>An efficient base-mediated a direct synthesis of aromatic and heteroaromatic nitriles from corresponding aldehydes was reported. As the starting ingredients for the synthesis, aldehyde, and hydroxylamine were combined with benzoyl chloride in a series of reactions. Notably, this process may be carried out at room temperature without the need for transition metal catalysts, making it a practical and effective process. A wide variety of aromatic and heteroaromatic aldehydes gave the products in good to excellent yields. Broad substrate scope, easy operation, quick reactions, tolerance of different functional groups, and room temperature reactions are the important features of the developed methodology.</p>\u0000<div><figure><div><div><picture><img></picture></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141107015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
N Nagappan, Ganapathi Rao Kandregula, Kothandaraman Ramanujam
{"title":"Selection of solid-state electrolytes for lithium-ion batteries using clustering technique","authors":"N Nagappan, Ganapathi Rao Kandregula, Kothandaraman Ramanujam","doi":"10.1007/s12039-024-02263-9","DOIUrl":"10.1007/s12039-024-02263-9","url":null,"abstract":"<div><p>In the context of solid-state electrolytes for batteries, ambient temperature ionic conductivity stands as a pivotal attribute. This investigation presents a compilation of potential candidates for solid-state electrolytes in lithium-ion batteries, employing clustering—an unsupervised machine-learning technique. To achieve this, a fusion of data from two distinct datasets was undertaken: a smaller dataset consisting of 51 compounds endowed with experimental lithium-ion conductivity data and a substantially larger dataset of 15,530 compounds devoid of such information. The compounds in our dataset were divided into various groups based on several characteristics that influence the conductivity of lithium-ion batteries. Then, the location of the compounds known to have high lithium-ion conductivity (>10<sup>−4</sup> S cm<sup>−1</sup>) at room temperature was observed. The 427 compounds (i.e., unique material project IDs) found in the same cluster as most of these high-conducting compounds are then further examined. This paper concludes by offering a catalog of solid-state compounds that can be utilized to choose compounds for solid-state electrolytes in batteries.</p><h3>Graphical Abstract</h3><p><b>Synopsis:</b> The above plot shows the 15530 lithium-based compounds clustered into 7 clusters based on several factors that were identified to affect lithium-ion conductivity. We observe the location of the already known good lithium-ion conductors (represented by the golden stars) to identify other similar compounds.</p>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":616,"journal":{"name":"Journal of Chemical Sciences","volume":"136 2","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141119516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}