化学•材料最新文献

{"title":"G-Quadruplex Recognition by Tetraalkylammonium Ions: A New Paradigm for Discrimination between Parallel and Antiparallel G-Quadruplexes.","authors":"Xuan Li, David N Dubins, Jens Völker, Tigran V Chalikian","doi":"10.1021/acs.jpcb.4c06355","DOIUrl":"10.1021/acs.jpcb.4c06355","url":null,"abstract":"<p><p>G-quadruplexes are an important class of noncanonical secondary structures of DNA that exist in the cell and are involved in the regulation of principal genomic events. Any regulatory role of a G-quadruplex in the genome is coupled with the attendant interconversions between the G-quadruplex and duplex states. Much effort has been invested in the quest for agents that can recognize individual G-quadruplexes and shift the associated duplex-G-quadruplex equilibria toward the G-quadruplex state. In this communication, we demonstrate that, notwithstanding their simplicity, tetraalkylammonium ions, [H(CH₂)_<i>n</i>]₄N⁺, recognize and strongly stabilize the parallel c-MYC G-quadruplex, while not binding to the antiparallel human telomeric G-quadruplex or duplex DNA. The affinity of TAA⁺ ions for the c-MYC G-quadruplex correlates with the length of the aliphatic side chains. Our CD spectral data suggest that the binding of tetraalkylammonium ions is external, not resulting in structural changes in the host G-quadruplex. The observed discriminatory power identifies tetraalkylammonium salts as a starting point for developing topology-selective G-quadruplex-binding agents.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556667","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}

{"title":"Atmospheric Degradation of CH₂═C(CH₃)C(O)O[CH₂]₄CH₃ by ^•OH Radicals: Reactivity, POCP, and Carbonyl Formation.","authors":"Vianni Giovanna Straccia Cepeda, María B Blanco, Mariano Teruel","doi":"10.1021/acs.jpca.4c04393","DOIUrl":"10.1021/acs.jpca.4c04393","url":null,"abstract":"<p><p>Relative rate studies of the gas-phase reaction of amyl methacrylate, CH₂═C(CH₃)C(O)O[CH₂]₄CH₃, with ^•OH radicals were performed at (298 ± 2) K and 1000 mbar. The experiments were conducted in an atmospheric Pyrex chamber coupled to <i>in situ</i> Fourier transform infrared spectroscopy (FTIR). The rate coefficient obtained from the average of several experiments was <i>k</i>_AMMA+•OH = (8.10 ± 1.98) × 10^-11 cm³ molecule^-1 s^-1. Additionally, product studies were conducted under conditions similar to those of the kinetic experiments by using <i>in situ</i> FTIR spectroscopy. Pentanal, butanal, and hydroxyacetone were identified as the main reaction products. The initial pathway for the degradation of amyl methacrylate with ^•OH radicals occurs via addition of ^•OH to the >C═C< bond or hydrogen abstraction from the alkyl chain of the ester. The likelihood of hydrogen atom abstraction is 25%, while the addition of hydroxyl radicals to the double bond occurs with a probability of 75%. Based on these outcomes, a degradation mechanism is postulated. Furthermore, the atmospheric implications of the studied reaction were evaluated by estimating the tropospheric lifetime of amyl methacrylate toward ^•OH radicals as τ_OH = 3.43 h. Additionally, the Photochemical Ozone Creation Potential (POCP) of 84 was calculated for the reaction studied. Carbonyl compounds found as reaction products can exert a substantial influence on both air quality and public health.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142562397","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}

{"title":"Ab Initio Structure and Dynamics of Beryllium Monofluoride and Its Anion.","authors":"Jacek Koput","doi":"10.1021/acs.jpca.4c06334","DOIUrl":"10.1021/acs.jpca.4c06334","url":null,"abstract":"<p><p>The accurate potential energy functions of beryllium monofluoride, BeF, and its anion, BeF^-, have been determined from ab initio calculations using the coupled-cluster approach, up to the CCSDTQP level of approximation, in conjunction with the augmented correlation-consistent core-valence basis sets, aug-cc-pCV<i>n</i>Z, up to septuple-zeta quality. The vibration-rotation energy levels of the two species were predicted to near the \"spectroscopic\" accuracy. Changes in the electron density distribution upon formation of the Be-F chemical bond are discussed.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575439","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}

{"title":"Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational Changes in Acidic pH.","authors":"Shadi A Badiee, Vivek Govind Kumar, Mahmoud Moradi","doi":"10.1021/acs.jpcb.4c04607","DOIUrl":"10.1021/acs.jpcb.4c04607","url":null,"abstract":"<p><p>The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational state is pH-sensitive, impacting its receptor-binding ability and evasion of the host immune response. In this study, we conducted extensive equilibrium microsecond-level all-atom molecular dynamics (MD) simulations of the HA protein to explore the influence of low pH on its conformational dynamics. Specifically, we investigated the impact of protonation on conserved histidine residues (H106₂) located in the hinge region of HA2. Our analysis encompassed comparisons between nonprotonated (NP), partially protonated (1P, 2P), and fully protonated (3P) conditions. Our findings reveal substantial pH-dependent conformational alterations in the HA protein, affecting its receptor-binding capability and immune evasion potential. Notably, the nonprotonated form exhibits greater stability compared to protonated states. Conformational shifts in the central helices of HA2 involve outward movement, counterclockwise rotation of protonated helices, and fusion peptide release in protonated systems. Disruption of hydrogen bonds between the fusion peptide and central helices of HA2 drives this release. Moreover, HA1 separation is more likely in the fully protonated system (3P) compared to nonprotonated systems (NP), underscoring the influence of protonation. These insights shed light on influenza virus infection mechanisms and may inform the development of novel antiviral drugs targeting HA protein and pH-responsive drug delivery systems for influenza.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142575460","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}

{"title":"Photooxidation of Nonanoic Acid by Molecular and Complex Environmental Photosensitizers.","authors":"Grace Freeman-Gallant, Emily J Davis, Elizabeth Scholer, Onita Alija, Juan G Navea","doi":"10.1021/acs.jpca.4c05608","DOIUrl":"10.1021/acs.jpca.4c05608","url":null,"abstract":"<p><p>Photochemical aging and photooxidation of atmospheric particles play a crucial role in both the chemical and physical processes occurring in the troposphere. In particular, the presence of organic chromophores within atmospheric aerosols can trigger photosensitized oxidation that drives the atmospheric processes in these interfaces. However, the light-induced oxidation of the surface of atmospheric aerosols, especially those enriched with organic components, remains poorly understood. Herein, we present a gravimetric and vibrational spectroscopy study aimed to investigate the photosensitized oxidation of nonanoic acid (NA), a model system of fatty acids within organic aerosols, in the presence of complex organic photosensitizers and molecular proxies. Specifically, this study shows a comparative analysis of the photosensitized reactions of thin films containing nonanoic acid and four different organic photosensitizers, namely marine dissolved organic matter (m-DOM) and humic acids (HA) as environmental photosensitizers, and 4-imidazolecarboxaldehyde (4IC) and 4-benzoylbenzoic acid (4BBA) as molecular proxies. All reactions show predominant photooxidation of nonanoic acid, with important differences in the rate and yield of product formation depending on the photosensitizer. Limited changes were observed in the organic photosensitizer itself. Results show that, among the photosensitizers examined, 4BBA is the most effective in photooxidizing nonanoic acid. Overall, this work underscores the role of chromophores in the photooxidation of organic thin films and the relevance of such reactions on the surface of aerosols in the marine environment.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580931","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}

{"title":"Synthesis of Pyrrolidine-2-ylidenes from Isoxazolines and Allenes","authors":"Dylan C. Keane, Guanqun Zhang, Abdullah S. Alshreimi, Donald J. Wink, Laura L. Anderson","doi":"10.1021/acs.joc.4c01976","DOIUrl":"https://doi.org/10.1021/acs.joc.4c01976","url":null,"abstract":"A diastereoselective addition and rearrangement reaction has been developed for the synthesis of pyrrolidine-2-ylidenes from N<i>H</i>-isoxazolines and electron-deficient allenes. This method proceeds via the rearrangement of a proposed <i>N</i>-alkenylisoxazoline intermediate to generate densely functionalized pyrrolidine-2-ylidenes under simple catalyst-free conditions that tolerate ketone substituents and install relative stereochemistry at positions 3 and 4 of the heterocycle. Reaction optimization and the substrate scope are described in addition to studies evaluating the reactivity of the <i>gem</i>-dione and enaminone groups of the products.","PeriodicalId":57,"journal":{"name":"The Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":4.354,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610390","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}

{"title":"Regio- and Stereoselective Construction of 1,3,5-Triaroylcyclohexanes via KOtBu-Mediated Cyclotrimerization of Aryl Vinyl Ketones","authors":"Sachin D. Mahale, Vinita Yadav, Rajesh G. Gonnade, Santosh B. Mhaske","doi":"10.1021/acs.joc.4c01695","DOIUrl":"https://doi.org/10.1021/acs.joc.4c01695","url":null,"abstract":"Herein, we disclose a simple one-pot method for an efficient regio- and stereoselective synthesis of 1,3,5-triaroylcyclohexanes from aryl vinyl ketones using potassium <i>tert</i>-butoxide. The developed protocol allows the construction of various symmetrically substituted cyclohexanes in good to excellent yields. The major product <b>2</b> also can be converted to the product <b>3</b> (all equatorial) conveniently by acid catalysis. This protocol features a good substrate scope and functional group compatibility.","PeriodicalId":57,"journal":{"name":"The Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":4.354,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142601881","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}

{"title":"Cascade Cyclization/Annulation of β-Enamino Diketones and o-Phenylenediamine: A Strategy to Access Pyrrole-fused 1,5-Benzodiazepines","authors":"Julia Poletto, Julia C. M. Willig, Jeniffer N. A. Camargo, Helio G. Bonacorso, Michael J. V. Silva, Fernanda A. Rosa","doi":"10.1021/acs.joc.4c02483","DOIUrl":"https://doi.org/10.1021/acs.joc.4c02483","url":null,"abstract":"Herein, we introduce an unprecedented cascade reaction for the assembly of pyrrole-fused 1,5-benzodiazepine frameworks. These diverse privileged scaffolds were controllably constructed by intramolecular cyclization of β-enamino diketone, followed by annulation with <i>o</i>-phenylenediamine. The protocol features efficient one-pot cascade cyclization/annulation, performed under simple and mild reaction conditions. The products are obtained in a metal-free manner, in good to excellent yields (65–91%), and represent a fused heterocyclic scaffold that is not yet found in nature.","PeriodicalId":57,"journal":{"name":"The Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":4.354,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609843","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}

{"title":"Topological Crystalline Insulator Phases in Magnetic van der Waals Crystal MnBi4Te7 and Mn2Bi2Te5 Families","authors":"Jia-Yi Lin, Zhipeng Cao, Zhong-Jia Chen, Wenxin He, Jiarui Zeng, Xiao-Bao Yang, Yichen Hua, Ji-Hai Liao, Yu-Jun Zhao","doi":"10.1021/acs.jpcc.4c05870","DOIUrl":"https://doi.org/10.1021/acs.jpcc.4c05870","url":null,"abstract":"In the past several years, the discoveries of multiple magnetic topological phases in MnBi₂Te₄ and its analogues have highlighted the research in modern condensed matter physics. The topological crystalline insulator (TCI) phase protected by space group symmetry is a valuable platform to understand the profound relation of crystalline symmetry and band topology in materials. Via first-principles calculations, we predict that the MnBi₂Te₄ analogues, MnBi₄Te₇, MnSb₄Te₇, Mn₂Bi₂Te₅, and Eu₂Bi₂Te₅, are all mirror-symmetry-protected TCI candidates when magnetized along the in-plane <i>x</i> orientation. Gapless surface states are expected for the van der Waals terminations in this phase. Particularly, the magnetic easy axis of Eu₂Bi₂Te₅ is along the in-plane direction in our calculations. These findings open opportunities for research and application of magnetic TCIs and magnetically controllable topological quantum phase transitions.","PeriodicalId":61,"journal":{"name":"The Journal of Physical Chemistry C","volume":null,"pages":null},"PeriodicalIF":4.126,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142601513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Manipulating Interface Magnetism in Manganite Thin Film Membranes by Substrate Surface Chemistry","authors":"Purnima P. Balakrishnan, Qinwen Lu, Qing Wang, Shin Muramoto, Paige Quarterman, Michael R. Fitzsimmons, Timothy R. Charlton, Xiaofang Zhai, Alexander J. Grutter","doi":"10.1021/acs.jpcc.4c05014","DOIUrl":"https://doi.org/10.1021/acs.jpcc.4c05014","url":null,"abstract":"We demonstrate an unexpected substrate dependence of the magnetic properties of complex oxide thin film membranes. While the tunable magnetism of complex oxides is attractive for many applications, device integration has long been limited by the strict substrate requirements necessary for high-quality film growth. Recently, water-soluble sacrificial layers have been used to separate oxide thin films from the substrate after growth, decoupling the structural and chemical degrees of freedom at the interface. This approach is hoped to enable integration with previously incompatible material platforms, but interface studies of transferred films remain limited. In this work, we use polarized neutron reflectometry and secondary ion mass spectroscopy to provide a detailed understanding of depth-dependent chemistry and magnetization of LaMnO₃ membranes. We find that the final substrate plays a key role in either incorporating or excluding hydrogen species at the surfaces of transferred LaMnO₃ thin films, modifying the magnetism in these interfacial regions. Despite elimination of the epitaxial relationship, the choice of substrate influences the magnetism within the transferred membranes to an unexpected degree, with important implications for integration into existing silicon-based technologies.","PeriodicalId":61,"journal":{"name":"The Journal of Physical Chemistry C","volume":null,"pages":null},"PeriodicalIF":4.126,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}