Mikhail Rumyantsev, Ivan Yu Kalagaev, Sergey Rumyantsev
{"title":"Catalytic Effect of Potassium Xanthates and Related Compounds on Disulfide Bond Enrichment of Polyalkylene Sulfides Synthesized in the Course of Episulfide Polymerization.","authors":"Mikhail Rumyantsev, Ivan Yu Kalagaev, Sergey Rumyantsev","doi":"10.1021/acs.jpcb.4c05474","DOIUrl":"10.1021/acs.jpcb.4c05474","url":null,"abstract":"<p><p>The original method for the preparation of high-molecular-weight polyalkylene sulfides was reported. Assuming anomalous peculiarities of the reaction (high polymerization rates, high degrees of polymerization, and huge discrepancy between the expected <i>M</i><sub>n</sub> values and the experimentally obtained values), the priority task was set to study the mechanism underlying the observed new type of polymerization. Thus, it was demonstrated that xanthate and related molecules could act as pure catalysts, facilitating both the chain-growth polymerization (ring-opening of episulfides) realized via an anionic route and the direct attack of the sulfur atom of one episulfide molecule on the methylene carbon atom of the second (neighbor) episulfide molecule, accompanied by the subsequent formation of a stable thiiranium-based zwitterionic adduct. The role of xanthate and related compounds as catalysts and stabilizing particles was further supplemented by modeling the attack of thiolate on the sulfur atom of a thiiranium-based adduct. The xanthate molecule acting as a catalyst was found to be involved in all stages of the process discussed by sharing the potassium atom with the sulfur atoms of active components of the system (the initial episulfide molecule, thiolate, and the zwitterionic intermediate). The subsequent analysis revealed the exceptional transparency of the materials obtained, which was found to exceed 99%. The pronounced self-healing ability was also found to be a distinctive feature of the synthesized high-molecular-weight polyalkylene sulfides enriched with disulfide bonds.</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":"142566429","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":"Prediction of Redox Potentials for Ac, Th, and Pa in Aqueous Solution.","authors":"Felipe R Dutra, João G F Romeu, David A Dixon","doi":"10.1021/acs.jpca.4c05693","DOIUrl":"10.1021/acs.jpca.4c05693","url":null,"abstract":"<p><p>Density functional theory in conjunction with small core pseudopotentials and the associated basis sets was used to calculate potentials for multiple redox couples, covering a range of oxidation states for Ac (0 to III), Th (0 to IV), and Pa (0 to V) in aqueous solution. Solvation effects were incorporated using a supermolecule-continuum approach, with 30 water molecules representing two solvation shells, and the COSMO and SMD implicit solvation models. The calculated geometries for Ac(III), Th(IV), and Pa(V) were in reasonable agreement with the available experimental data. Using the COSMO model with the B3LYP functional, the calculated redox potentials were within ±0.2 V from experiment for most redox couples. Several pathways were explored for the Pa(V/IV) redox couple for different forms of Pa(V) and Pa(IV). Most Pa(V/IV) redox couples have very similar potentials, ranging from 0 to -0.4 V up to a pH of 1.4. At pH = 1.4, the potentials shift to values that are more negative than -0.7 V, reflecting the growing unfavorable nature of the redox process at higher pH levels. The calculated values for An(III/II) potentials were consistent with prior estimates and the available experimental data. The predicted redox potentials for An(II/I) were highly negative, as expected. For An(I/0) potentials, Th and Pa exhibited positive values, contrasting with the negative values calculated for Ac. The An<sup>+m</sup>/An(0) potentials agreed better with the experimental data when using the COSMO solvation model as compared to the SMD model.</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":"142542918","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}
Nader M Boshta, Michael Lewash, Meryem Köse, Vigneshwaran Namasivayam, Soumya Sarkar, Jan H Voss, Andy J Liedtke, Anna Junker, Maoqun Tian, Anne Stößel, Mahmoud Rashed, Ahmed Mahal, Nicole Merten, Cécile Pegurier, Jörg Hockemeyer, Evi Kostenis, Christa E Müller
{"title":"Discovery of Anthranilic Acid Derivatives as Antagonists of the Pro-Inflammatory Orphan G Protein-Coupled Receptor GPR17.","authors":"Nader M Boshta, Michael Lewash, Meryem Köse, Vigneshwaran Namasivayam, Soumya Sarkar, Jan H Voss, Andy J Liedtke, Anna Junker, Maoqun Tian, Anne Stößel, Mahmoud Rashed, Ahmed Mahal, Nicole Merten, Cécile Pegurier, Jörg Hockemeyer, Evi Kostenis, Christa E Müller","doi":"10.1021/acs.jmedchem.4c01755","DOIUrl":"10.1021/acs.jmedchem.4c01755","url":null,"abstract":"<p><p>The G protein-coupled receptor 17 (GPR17) is an orphan receptor involved in inflammatory diseases. GPR17 antagonists have been proposed for the treatment of multiple sclerosis due to their potential to induce remyelination. Potent, selective antagonists are required to enable target validation. In the present study, we describe the discovery of a novel class of GPR17 antagonists based on an anthranilic acid scaffold. The compounds' potencies were evaluated in calcium mobilization and radioligand binding assays, and structure-activity relationships were analyzed. Selected antagonists were additionally studied in cAMP and G protein activation assays. The most potent antagonists were 5-methoxy-2-(5-(3'-methoxy-[1,1'-biphenyl]-2-yl)furan-2-carboxamido)benzoic acid (<b>52</b>, PSB-22269, K<sub>i</sub> 8.91 nM) and its 3'-trifluoromethyl analog (<b>54</b>, PSB-24040, K<sub>i</sub> 83.2 nM). Receptor-ligand docking studies revealed that the compounds' binding site is characterized by positively charged arginine residues and a lipophilic pocket. These findings yield valuable insights into this poorly characterized receptor providing a basis for future drug development.</p>","PeriodicalId":46,"journal":{"name":"Journal of Medicinal Chemistry","volume":null,"pages":null},"PeriodicalIF":6.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Na Liu, Yifei Zhang, Xi Wang, Kangwei Niu, Faming Lu, Jie Chen, Dongping Zhong
{"title":"Optical Quantum Control of the Electron Transfer Reactions in Protein Flavodoxin.","authors":"Na Liu, Yifei Zhang, Xi Wang, Kangwei Niu, Faming Lu, Jie Chen, Dongping Zhong","doi":"10.1021/acs.jpcb.4c04254","DOIUrl":"10.1021/acs.jpcb.4c04254","url":null,"abstract":"<p><p>The optical quantum control has been successfully applied in modulating biological processes such as energy transfer and bond isomerization. Among the reactions in realizing biological functions, the electron transfer (ET) process is fundamental; hence, the quantum control over such an ET reaction is of far-reaching significance. Here, we realized optical quantum control over ultrafast ET processes in a protein, flavodoxin, by applying various chirped excitation pulses. We observed the wavepacket dynamics within a dephasing time of less than 1 ps. Within this time window, we found that the ultrafast photoinduced ET reaction can be controlled by different chirped excitations with a rate change by a factor of about 2. Furthermore, the control effect is propagated into the subsequent ultrafast back ET reaction, showing a variation of the BET dynamics with different excitation chirps. The underlying mechanism is the initial wavepacket dynamics; the differently prepared wavepackets with chirped excitation evolve along various pathways, resulting in the changes of ET rates. The successful demonstration of optical quantum control of ultrafast biological ET is significant and opens a new avenue to explore the quantum control of real biological ET reactions.</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":"142556670","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":"Transferable and Interpretable Prediction of Site-Specific Dehydrogenation Reaction Rate Constants with NMR Spectra.","authors":"Yanbo Li, Fenfen Ma, Zhandong Wang, Xin Chen","doi":"10.1021/acs.jpclett.4c02647","DOIUrl":"10.1021/acs.jpclett.4c02647","url":null,"abstract":"<p><p>Accurate and efficient determination of site-specific reaction rate constants over a wide temperature range remains challenging, both experimentally and theoretically. Taking the dehydrogenation reaction as an example, our study addresses this issue by an innovative combination of machine learning techniques and cost-effective NMR spectra. Through descriptor screening, we identified a minimal set of NMR chemical shifts that can effectively determine reaction rate constants. The constructed model performs exceptionally well on theoretical data sets and demonstrates impressive generalization capabilities, extending from small molecules to larger ones. Furthermore, this model shows outstanding performance when applied to limited experimental data sets, highlighting its robust applicability and transferability. Utilizing the Sure Independence Screening and Sparsifying Operator (SISSO) algorithm, we also present an interpretable rate constant-temperature-NMR (k-T-NMR) relationship with a mathematical formula. This study reveals the great potential of combining machine learning with easily accessible spectroscopic descriptors in the study of reaction kinetics, enabling the rapid determination of reaction rate constants and promoting our understanding of reactivity.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566369","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":"<i>In Silico</i> Structural Comparison of Aromatic and Aliphatic Chiral Peptoid Oligomers.","authors":"Rakshit Kumar Jain, Carol K Hall, Erik E Santiso","doi":"10.1021/acs.jpcb.4c06577","DOIUrl":"10.1021/acs.jpcb.4c06577","url":null,"abstract":"<p><p>Atomistic simulations of peptoids have the capability to predict structure-property relationships, depending on the accuracy of the associated force field. This work presents an addendum to the CGenFF-NTOID peptoid force field for aliphatic side chains. We develop parameters for two aliphatic side chains, R<sub><i>N</i></sub>1-tertiary butylethyl glycine (<i>r1tbe</i>) and S<sub><i>N</i></sub>1-tertiary butylethyl glycine (<i>s1tbe</i>). Enhanced sampled (well-tempered metadynamics) atomistic simulations are performed using CGenFF-NTOID to determine the monomer structural preferences for these side chains. The free energy minima attained through these simulations are compared with structural observations obtained from experiments. We also compare the structural preferences of aliphatic <i>s1tbe</i> and aromatic S<sub><i>N</i></sub>1-naphthylethyl glycine (<i>s1ne</i>). This is done through parallel bias metadynamics on monomers and pentamers of <i>s1tbe</i> and <i>s1ne</i>. The structural observations through simulations are also compared with available experimental metrics of the dihedral angles and pitch. The pentamer minima structures are also compared with <i>ab initio</i> optimized structures, which show excellent agreement. This comparison illustrates alternatives to aromatic side chains that can be used to stabilize peptoid secondary structures. The developed parameters help to increase the diversity of peptoid side chains available for materials discovery through computational studies.</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":"142566428","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}
Isabelle Weber, Prasad Ramesh Joshi, David T Anderson, Yuan-Pern Lee
{"title":"Unique Applications of <i>para</i>-Hydrogen Matrix Isolation to Spectroscopy and Astrochemistry.","authors":"Isabelle Weber, Prasad Ramesh Joshi, David T Anderson, Yuan-Pern Lee","doi":"10.1021/acs.jpclett.4c02733","DOIUrl":"10.1021/acs.jpclett.4c02733","url":null,"abstract":"<p><p>Cryogenic solid <i>para</i>-hydrogen (<i>p</i>-H<sub>2</sub>) exhibits pronounced quantum effects, enabling unique experiments that are typically not possible in noble-gas matrices. The diminished cage effect facilitates the production of free radicals via <i>in situ</i> photolysis or photoinduced reactions. Electron bombardment during deposition readily produces protonated and hydrogenated species, such as polycyclic aromatic hydrocarbons, that are important in astrochemistry. In addition, quantum diffusion delocalizes hydrogen atoms in solid <i>p</i>-H<sub>2</sub>, allowing efficient H atom reactions with astrochemical species and introducing new concepts in astrochemical models. Some H atom reactions display anomalous temperature behaviors, highlighting the rich chemistry in <i>p</i>-H<sub>2</sub>. The investigation on quantum diffusion of heavier atoms and molecules is also important for our understanding of the chemistry in interstellar ice. Additionally, matrix shifts of electronic transitions of polycyclic aromatic hydrocarbons in <i>p</i>-H<sub>2</sub> are less divergent than those in solid Ne such that systematic measurements in <i>p</i>-H<sub>2</sub> might help in the assignment of diffuse interstellar bands.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581035","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}
Mayank Saraswat, Adrian Portela-Gonzalez, Enrique Mendez-Vega, Wolfram Sander, Patrick Hemberger
{"title":"<i>N</i>-Carbazolyl π-Radical and Its Antiaromatic Nitrenium Ion: A Threshold Photoelectron Spectroscopic Study.","authors":"Mayank Saraswat, Adrian Portela-Gonzalez, Enrique Mendez-Vega, Wolfram Sander, Patrick Hemberger","doi":"10.1021/acs.jpca.4c05855","DOIUrl":"10.1021/acs.jpca.4c05855","url":null,"abstract":"<p><p>Understanding the structure and properties of heterocyclic radicals and their cations is crucial for elucidating reaction mechanisms as they serve as versatile synthetic intermediates. In this work, the <i>N</i>-carbazolyl radical <b>1</b> was generated via pyrolysis and characterized using photoion mass-selected threshold photoelectron spectroscopy coupled with tunable vacuum-ultraviolet synchrotron radiation. The <i>N</i>-centered radical <b>1</b> is classified as a π-radical (<sup>2</sup>B<sub>1</sub>), with the unpaired electron found to be delocalized over the central five-membered ring of the carbazole. Adiabatic ionization energies corresponding to the transition from radical <b>1</b> to its singlet <b>1</b><sup>+</sup>(<sup>1</sup>A<sub>1</sub>) and triplet <b>1</b><sup>+</sup>(<sup>3</sup>B<sub>2</sub>) cations were determined to be 7.70 ± 0.03 and 8.14 ± 0.03 eV, respectively. The antiaromatic nitrenium ion <b>1</b><sup><b>+</b></sup> exhibits a singlet ground state with an experimental singlet-triplet energy gap (Δ<i>E</i><sub>S-T</sub>) of -0.44 eV (10.1 kcal/mol), in very good agreement with theory. <i>N</i>-centered radicals are found to have a higher ionization energy than their <i>C</i>-centered analogues due to stabilization of the singly occupied molecular orbital.</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":"142491175","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}
Yingxia Gao, Yanfang Dong, Xuran Wang, Wenyue Su, Pierre Cloutier, Yi Zheng, Léon Sanche
{"title":"Comparisons between the Direct and Indirect Effect of 1.5 keV X-rays and 0-30 eV Electrons on DNA: Base Lesions, Stand Breaks, Cross-Links, and Cluster Damages.","authors":"Yingxia Gao, Yanfang Dong, Xuran Wang, Wenyue Su, Pierre Cloutier, Yi Zheng, Léon Sanche","doi":"10.1021/acs.jpcb.4c02799","DOIUrl":"10.1021/acs.jpcb.4c02799","url":null,"abstract":"<p><p>The interaction of low energy electrons (LEEs; 1-30 eV) with genomic material can induce multiple types of damage that may cause the loss of genetic information, mutations, genome instability, and cell death. For all damages measurable by electrophoresis, we provide the first complete set of <i>G</i>-values (yield of a specific product per energy deposited) induced in plasmid DNA by the direct and indirect effects of LEEs (<i>G</i><sub>LEE</sub>) and 1.5 keV X-rays (<i>G</i><sub>X</sub>) under identical conditions. Low energy photoelectrons are produced via X-rays incident on a tantalum (Ta) substrate covered with DNA and placed in a chamber filled with nitrogen at atmospheric pressure, under four different humidity levels, ranging from dry conditions to full hydration (Γ = 2.5 to Γ = 33, where Γ is the number of water molecules/nucleotide). Damage yields are measured as a function of X-ray fluence and humidity. <i>G</i><sub>LEE</sub> values are between 2 and 27 times larger than those for X-rays. At Γ = 2.5 and 33, <i>G</i><sub>LEE</sub> values for double strand breaks are 27 and 16 times larger than <i>G</i><sub>X</sub>, respectively. The indirect effect contributes ∼50% to the total damage. These <i>G</i>-values allow quantification of potentially lethal lesions composed of strand breaks and/or base damages in the presence of varying amounts of water, i.e., closer to cellular conditions.</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":"142491191","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":"Synaptic Properties of an Interfacial Memristor Based on a Ga<sub>2</sub>O<sub>3</sub>/Nb:SrTiO<sub>3</sub> Heterojunction.","authors":"Youhong Wang, Wei Hu, Kaijin Kang, Caili Dong, Xiaosheng Tang","doi":"10.1021/acs.jpclett.4c02548","DOIUrl":"10.1021/acs.jpclett.4c02548","url":null,"abstract":"<p><p>Memristors have been extensively studied for tremendous potential for future neuromorphic computing hardware applications because of their ability to imitate biological synaptic processes. Herein, we report an interfacial memristor based on a Ga<sub>2</sub>O<sub>3</sub>/Nb:SrTiO<sub>3</sub> heterojunction that shows stable bipolar resistive switching behavior, long retention time, and high switching ratio. The conductance of the Au/Ga<sub>2</sub>O<sub>3</sub>/Nb:SrTiO<sub>3</sub>/In memristor can be gradually modulated under the voltage sweep mode as well as positive and negative pulse voltage stimulations, respectively, thus realizing the long-term potentiation/depression characteristics of the simulated biological synapse. A neural network based on the prepared memristor was built to recognize the handwritten picture data set with a recognition accuracy of 92.78% by using the NeuroSimV3.0 platform. Our work indicates that the Ga<sub>2</sub>O<sub>3</sub>/Nb:SrTiO<sub>3</sub> heterojunction memristor has significant potential in a neuromorphic computing system.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542933","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}