Compounds最新文献_第4页

Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues 赖氨酸、半胱氨酸肽和蛋白质残基生物偶联反应的热力学综述

Compounds Pub Date : 2023-08-30 DOI: 10.3390/compounds3030035

Maja Lopandic, Fatima Merza, J. Honek

{"title":"Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues","authors":"Maja Lopandic, Fatima Merza, J. Honek","doi":"10.3390/compounds3030035","DOIUrl":"https://doi.org/10.3390/compounds3030035","url":null,"abstract":"Bioconjugation reactions are critical to the modification of peptides and proteins, permitting the introduction of biophysical probes onto proteins as well as drugs for use in antibody-targeted medicines. A diverse set of chemical reagents can be employed in these circumstances to covalently label protein side chains, such as the amine moiety in the side chain of lysine and the thiol functionality in cysteine residues, two of the more frequently employed sites for modification. To provide researchers with a thermodynamic survey of the reaction of these residues with frequently employed chemical modification reagents as well as reactive cellular intermediates also known to modify proteins non-enzymatically, a theoretical investigation of the overall thermodynamics of models of these reactions was undertaken at the T1 and G3(MP2) thermochemical recipe levels (gas phase), the M06-2X/6-311+G(2df,2p)/B3LYP/6-31G(d) (gas and water phase), and the M06-2X/cc-PVTZ(-f)++ density functional levels of theory (water phase). Discussions of the relationship between the reagent structure and the overall thermodynamics of amine or thiol modification are presented. Of additional interest are the observations that routine cellular intermediates such as certain thioesters, acyl phosphates, and acetyl-L-carnitine can contribute to non-enzymatic protein modifications. These reactions and representative click chemistry reactions were also investigated. The computational survey presented herein (>320 reaction computations were undertaken) should serve as a valuable resource for researchers undertaking protein bioconjugation. A concluding section addresses the ability of computation to provide predictions as to the potential for protein modification by new chemical entities, with a cautionary note on protein modification side reactions that may occur when employing synthetic substrates to measure enzyme kinetic activities.","PeriodicalId":10621,"journal":{"name":"Compounds","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91262242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computer Modeling and Machine Learning in Chemistry and Materials Science: From Properties and Reactions of Small Organic and Inorganic Molecules to the Smart Design of Polymers and Composites 化学和材料科学中的计算机建模和机器学习:从有机和无机小分子的性质和反应到聚合物和复合材料的智能设计

Compounds Pub Date : 2023-08-24 DOI: 10.3390/compounds3030034

Alexander S. Novikov

引用次数: 0

Combined Analysis by GC(RI), GC-MS and 13C NMR of Leaf and Wood Essential Oils from Vietnamese Glyptostrobus pensilis (Staunton ex D. Don) K. Koch GC(RI)、GC- ms和13C NMR联合分析越南Glyptostrobus pensilis (Staunton ex D. Don) K. Koch

Compounds Pub Date : 2023-08-11 DOI: 10.3390/compounds3030033

Tran Huy Thai, M. Paoli, Nguyen Thi Hien, Nguyen Quang Hung, A. Bighelli, J. Casanova, F. Tomi

引用次数: 0

Thiazolidine-Based Fluorescent Chiral Ionic Liquids for Trace Copper(II) Ion Sensing 噻唑烷基荧光手性离子液体用于痕量铜(II)离子传感

Compounds Pub Date : 2023-08-11 DOI: 10.3390/compounds3030032

C. H. Griebeler, Mariana F. Bach, Henrique C. Silva, F. Rodembusch, Felipe L. Coelho, P. Schneider

{"title":"Thiazolidine-Based Fluorescent Chiral Ionic Liquids for Trace Copper(II) Ion Sensing","authors":"C. H. Griebeler, Mariana F. Bach, Henrique C. Silva, F. Rodembusch, Felipe L. Coelho, P. Schneider","doi":"10.3390/compounds3030032","DOIUrl":"https://doi.org/10.3390/compounds3030032","url":null,"abstract":"This study presents a comprehensive analysis of the synthesis and photophysical properties of thiazolidine-functionalized chiral ionic liquids (CILs) derived from L-cysteine. The synthesis involves a four-step route, encompassing N-protection, coupling reactions with bromoalcohols, and ionic liquid formation. The optical properties of the compounds were evaluated using UV–Vis absorption and fluorescence emission spectroscopies, revealing distinct behavior for different heterocycles and counter-ions. Notably, the investigation reveals that thiazolidine-based CILs exhibit unconventional intrinsic luminescence characteristics. Building upon these photophysical properties, an interaction study was conducted between copper (II) and the CILs. The findings exhibit a robust linear relationship between the optical response and the concentration of the metal ion. Through the calculation of the Stern–Volmer quenching constant, it was determined that the 1:1 binding model is applicable. This research underscores the potential of UV–Vis absorption spectroscopy as a highly sensitive method for detecting metal ions. By elucidating the synthesis, photophysical behavior, and metal ion interaction of thiazolidine-based CILs, this study contributes valuable insights into the field of functionalized ionic liquids and their potential applications in various areas.","PeriodicalId":10621,"journal":{"name":"Compounds","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80776322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst 利用咖啡研磨油(阿拉比卡咖啡)的脂质组成生产酯:Eversa®转化2.0脂肪酶作为酶促生物催化剂的理论研究

Compounds Pub Date : 2023-07-28 DOI: 10.3390/compounds3030031

Millena M.R. Nobre, Ananias Freire da Silva, Amanda Maria Menezes, Francisco Lennon Barbosa da Silva, Iesa Matos Lima, R. P. Colares, M. C. M. Souza, E. S. Marinho, R. Melo, J. C. D. Santos, Aluísio Marques da Fonseca

{"title":"Ester Production Using the Lipid Composition of Coffee Ground Oil (Coffea arabica): A Theoretical Study of Eversa® Transform 2.0 Lipase as an Enzymatic Biocatalyst","authors":"Millena M.R. Nobre, Ananias Freire da Silva, Amanda Maria Menezes, Francisco Lennon Barbosa da Silva, Iesa Matos Lima, R. P. Colares, M. C. M. Souza, E. S. Marinho, R. Melo, J. C. D. Santos, Aluísio Marques da Fonseca","doi":"10.3390/compounds3030031","DOIUrl":"https://doi.org/10.3390/compounds3030031","url":null,"abstract":"The scientific community recognizes coffee grounds (Coffea arabica) as an important biological residue, which led to using the Eversa® Transform 2.0 lipase as an in silico enzymatic catalyst for coffee grounds’ free fatty acids (FFA). Molecular modeling studies, including molecular docking, were performed, which revealed the structures of the lipase and showed the primary interactions between the ligands and the amino acid residues in the active site of the enzyme. Of the ligands tested, 6,9-methyl octadienoate had the best free energy of −6.1 kcal/mol, while methyl octadecenoate and methyl eicosanoate had energies of −5.7 kcal/mol. Molecular dynamics confirmed the stability of the bonds with low Root Mean Square Deviation (RMSD) values. The MMGBSA study showed that methyl octadecenoate had the best free energy estimate, and CASTp identified key active sites for potential enzyme immobilization in experimental studies. Overall, this study provides efficient and promising results for future experimental investigations, showing a classification of oils present in coffee grounds and their binding affinity with Eversa.","PeriodicalId":10621,"journal":{"name":"Compounds","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85949421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Electrospun Nanofibrous Membranes for Air Filtration: A Critical Review 电纺丝纳米纤维膜用于空气过滤:综述

Compounds Pub Date : 2023-07-14 DOI: 10.3390/compounds3030030

M. F. De Riccardis

引用次数: 1

First Report on Several NO-Donor Sets and Bidentate Schiff Base and Its Metal Complexes: Characterization and Antimicrobial Investigation 几种无供体和双齿希夫碱及其金属配合物的首次报道:表征和抗菌研究

Compounds Pub Date : 2023-07-05 DOI: 10.3390/compounds3030029

A. A. Mohamed, Abeer A. Nassr, S. Sadeek, N. Rashid, S. M. Abd El‐Hamid

{"title":"First Report on Several NO-Donor Sets and Bidentate Schiff Base and Its Metal Complexes: Characterization and Antimicrobial Investigation","authors":"A. A. Mohamed, Abeer A. Nassr, S. Sadeek, N. Rashid, S. M. Abd El‐Hamid","doi":"10.3390/compounds3030029","DOIUrl":"https://doi.org/10.3390/compounds3030029","url":null,"abstract":"The condensation product of the reaction between aniline and salicylaldehyde was a 2-(2-hydroxybenzylidinemine)—aniline Schiff base bidentate ligand (L). L was used to generate complexes by interacting with the metal ions lanthanum(III), zirconium(IV), yttrium(III), and copper(II), in addition to cobalt(II). Various physicochemical techniques were utilized to analyze the synthesized L and its metal chelates, including elemental analysis (CHN), conductimetry (Λ), magnetic susceptibility investigations (μeff), Fourier-transform infrared spectroscopy (FT-IR), proton nuclear magnetic resonance (1H NMR) spectroscopy, ultraviolet–visible (UV-Vis.) spectrophotometry, and thermal studies (TG/DTG). FT-IR revealed that the L molecule acted as a bidentate ligand by binding to metal ions via both the oxygen atom of the phenolic group in addition to the nitrogen atom of the azomethine group. Additionally, 1H NMR data indicated the formation of complexes via the oxygen atom of the phenolic group. An octahedral geometrical structure for all of the chelates was proposed according to the UV-Vis. spectra and magnetic moment investigations. Thermal analysis provided insight into the pattern of L in addition to its chelates’ breakdown. In addition, the investigation furnished details on the chelates’ potential chemical formulas, the characteristics of adsorbed or lattice H2O molecules, and the water that is coordinated but separated from the structure at temperatures exceeding 120 °C. The thermodynamic parameters utilizing Coats–Redfern in addition to Horowitz–Metzger equations were studied. The antimicrobial effectiveness of L and its chelates against distinct species of bacteria and fungi was studied using the disc diffusion method. Cu(II) and Y(III) chelates had significant antimicrobial activity against Staphylococcus aureus and Micrococcus luteus.","PeriodicalId":10621,"journal":{"name":"Compounds","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81248180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated Analysis by GC/MS and 13C NMR of Moroccan Cladanthus mixtus Essential Oil; Identification of Uncommon Epoxyfarnesanes 气相色谱/质谱及13C核磁共振综合分析摩洛哥石竹挥发油罕见环氧法内酯的鉴定

Compounds Pub Date : 2023-05-17 DOI: 10.3390/compounds3020028

Souad El Hafidi, K. Bakhy, M. Ouhssine, A. Benzakour, J. Casanova, M. Paoli, F. Tomi

{"title":"Integrated Analysis by GC/MS and 13C NMR of Moroccan Cladanthus mixtus Essential Oil; Identification of Uncommon Epoxyfarnesanes","authors":"Souad El Hafidi, K. Bakhy, M. Ouhssine, A. Benzakour, J. Casanova, M. Paoli, F. Tomi","doi":"10.3390/compounds3020028","DOIUrl":"https://doi.org/10.3390/compounds3020028","url":null,"abstract":"Cladanthus mixtus (L.) Chevall., Asteraceae, also known as Moroccan chamomile, is a spontaneous, annual plant growing wild in North-Western Morocco. Economically, the essential oil of C. mixtus is of high interest, Morocco being the only supplier on the international market. Two essential oil samples (EO) were isolated from aerial parts of Cladanthus mixtus (L.) Chevall., and analyzed by a combination of chromatographic and spectroscopic techniques (gas chromatography (GC) in combination with retention indices (RI), gas chromatography-mass spectrometry (GC/MS), and 13C NMR spectroscopy). Computer matching against the in-house 13C NMR library allowed the identification of the eight components at appreciable contents, namely 3,6,6,9-bis-epoxy-farnesa-1,7(14),10-triene, and its 3-epi, 9-epi, and 3,9-diepi epimers, and 6,9-epoxy-farnesa-1,7(14),10-trien-3-ol and its 3-epi, 6-epi, and 3,6-diepi epimers. Our results confirm the tremendous chemical variability of Moroccan C. mixtus essential oil and the usefulness of 13C NMR analysis, in combination with GC(RI), for the identification of uncommon oxygenated sesquiterpenes that induce an original composition.","PeriodicalId":10621,"journal":{"name":"Compounds","volume":"36 8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80176695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interplay between Fe(II) and Fe(III) and Its Impact on Thermoelectric Properties of Iron-Substituted Colusites Cu26−xFexV2Sn6S32 Fe(II)和Fe(III)相互作用及其对铁取代共渗体Cu26−xFexV2Sn6S32热电性能的影响

Compounds Pub Date : 2023-05-15 DOI: 10.3390/compounds3020027

Alexey O. Polevik, A. Sobolev, I. Glazkova, I. Presniakov, V. Verchenko, J. Link, Raivo Stern, A. Shevelkov

{"title":"Interplay between Fe(II) and Fe(III) and Its Impact on Thermoelectric Properties of Iron-Substituted Colusites Cu26−xFexV2Sn6S32","authors":"Alexey O. Polevik, A. Sobolev, I. Glazkova, I. Presniakov, V. Verchenko, J. Link, Raivo Stern, A. Shevelkov","doi":"10.3390/compounds3020027","DOIUrl":"https://doi.org/10.3390/compounds3020027","url":null,"abstract":"Following the trend of finding better thermoelectric materials among synthetic analogs of copper–chalcogenide minerals, we have synthesized iron-bearing colusites of a general formula Cu26−xFexV2Sn6S32. They crystallize in the cubic space group P-43n with the unit cell parameter increasing linearly with the iron content. At a low iron concentration, the crystal structure features disorder manifested by an anti-site effect and a shift of a part of the tin atoms from their ideal positions, which is absent for higher iron contents. The magnetization and 57Fe/119Sn Mössbauer studies showed that, for x = 1, iron is present as Fe3+, whereas for x > 1, Fe2+ and Fe3+ coexist. Additionally, weak antiferromagnetic interactions between iron atoms and fast on the 57Fe Mössbauer time scale (107–109 s−1) electron transfer between adjacent Fe2+ and Fe3+ centers were revealed. Thermoelectric studies showed that iron-bearing colusites are p-type semiconductors with low thermal conductivity stemming from their complex crystal structure and structural disorder. The highest ZT of 0.78 at 700 K was found for the x = 1 iron content, where iron is present as Fe3+ only.","PeriodicalId":10621,"journal":{"name":"Compounds","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83786912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enzymatic Screening of β-Amyloid Precursor Protein-Based Substrates β-淀粉样前体蛋白基底物的酶促筛选

Compounds Pub Date : 2023-05-10 DOI: 10.3390/compounds3020026

Reo Yamada, Masaki Midorikawa, Ayu Asai, Norimasa Takasu, Ren Fujii, Taeko Kakizawa

引用次数: 0