Carlos Augusto Augusto Campos Roldán, Raphael Chattot, Pierre-Yves Blanchard, Deborah J. Jones, Sara Cavaliere
Platinum-based nanoalloys are considered as efficient electrocatalysts for the oxygen reduction reaction (ORR). However, in situ/operando measurements have revealed that key properties (e.g. induced strain, chemical composition, coordination environment, etc.) evolve significally during operation, hampering their effective implementation in fuel cells. In fact, recent studies have indicated that the impact of the early surface activation steps of Pt-based nanoalloys has been hitherto underestimated and are an important factor contributing to the loss of their electroactivity. In this short perspective, we highlight the need for in situ/operando characterization of Pt-based electrocatalysts during the initial operation steps in the ORR by discussing recent insights into their early degradation and evolution of their key properties during electrochemical characterization.
{"title":"Platinum-Based Nanoalloys for the Oxygen Reduction Reaction: Exposing the True Active Phase via In Situ/Operando Techniques","authors":"Carlos Augusto Augusto Campos Roldán, Raphael Chattot, Pierre-Yves Blanchard, Deborah J. Jones, Sara Cavaliere","doi":"10.1039/d4cp03665d","DOIUrl":"https://doi.org/10.1039/d4cp03665d","url":null,"abstract":"Platinum-based nanoalloys are considered as efficient electrocatalysts for the oxygen reduction reaction (ORR). However, in situ/operando measurements have revealed that key properties (e.g. induced strain, chemical composition, coordination environment, etc.) evolve significally during operation, hampering their effective implementation in fuel cells. In fact, recent studies have indicated that the impact of the early surface activation steps of Pt-based nanoalloys has been hitherto underestimated and are an important factor contributing to the loss of their electroactivity. In this short perspective, we highlight the need for in situ/operando characterization of Pt-based electrocatalysts during the initial operation steps in the ORR by discussing recent insights into their early degradation and evolution of their key properties during electrochemical characterization.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"30 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546653","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}
This study investigates the spin-dependent transport properties of two different magnetic tunnel junctions (MTJs) with a slab with three Ni atomic layers: Ni(111)/Vacuum/Ni(111) and Ni(111)-{it h}-BN/{it h}-BN/Ni(111)-{it h}-BN. By density functional calculations combined with nonequilibrium Green’s function technique, we found that the Ni/Vacuum/Ni MTJ has a low TMR ratio of only 3.4%. However, when monolayer of {it h}-BN is epitaxially grown on the Ni(111) surface, the TMR ratio can be increased to 136.07% at equilibrium state. When a bias of [0, 100] mV is applied, the TMR ratios are greater than 100% in a wide voltage range. Furthermore, the MTJ exhibits a spin injection efficiency of 88.53% in the parallel magnetic configuration, which remains stable above 80% throughout the entire bias range. All these results indicate that the TMR and spin injection of the MTJs with freestanding Ni as the leads and vacuum as the tunneling barrier can be dramatically improved by epitaxially growing monolayer {it h}-BN on the surface of Ni(111). The length of the pure {it h}-BN region can affect the TMR performance of the device. Specifically, TMR tends to decrease with the length of central barrier, but it can still be greater than 100% within a certain bias range. Meanwhile, the spin injection of the MTJs is hardly affected and can be maintained above 80%, indicating high spin injection efficiency. The findings of this study have significant implications in the understanding TMR and spin injection mechanisms in MTJs and the design of TMR devices.
{"title":"Ab initio study on enhancement of tunneling magnetoresistance and spin injection in Ni/Vacuum/Ni magnetic tunnel junctions by h-BN stacking","authors":"Ziqi Han, Chun-sheng Liu, Xiaohong Zheng, Dayong Liu, Weiyang Wang, Yushen Liu","doi":"10.1039/d4cp04428b","DOIUrl":"https://doi.org/10.1039/d4cp04428b","url":null,"abstract":"This study investigates the spin-dependent transport properties of two different magnetic tunnel junctions (MTJs) with a slab with three Ni atomic layers: Ni(111)/Vacuum/Ni(111) and Ni(111)-{it h}-BN/{it h}-BN/Ni(111)-{it h}-BN. By density functional calculations combined with nonequilibrium Green’s function technique, we found that the Ni/Vacuum/Ni MTJ has a low TMR ratio of only 3.4%. However, when monolayer of {it h}-BN is epitaxially grown on the Ni(111) surface, the TMR ratio can be increased to 136.07% at equilibrium state. When a bias of [0, 100] mV is applied, the TMR ratios are greater than 100% in a wide voltage range. Furthermore, the MTJ exhibits a spin injection efficiency of 88.53% in the parallel magnetic configuration, which remains stable above 80% throughout the entire bias range. All these results indicate that the TMR and spin injection of the MTJs with freestanding Ni as the leads and vacuum as the tunneling barrier can be dramatically improved by epitaxially growing monolayer {it h}-BN on the surface of Ni(111). The length of the pure {it h}-BN region can affect the TMR performance of the device. Specifically, TMR tends to decrease with the length of central barrier, but it can still be greater than 100% within a certain bias range. Meanwhile, the spin injection of the MTJs is hardly affected and can be maintained above 80%, indicating high spin injection efficiency. The findings of this study have significant implications in the understanding TMR and spin injection mechanisms in MTJs and the design of TMR devices.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"83 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538691","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}
To investigate the radical-site-dependence of the exchange coupling in bisnitroxides, we have synthesized novel three acridan-based diradicals, tert-butyl nitroxide groups at the 2,7-, 2,6- and 3,6-positions of 10-benzyl-10’-methyl-9,9’(10H,10’H)spirobiacridine (1-pp, 1-mp and 1-mm, respectively). Theoretical and experimental magnetic studies indicate that 1-pp and 1-mm exhibit a singlet ground state, while 1-mp exhibits a triplet ground state. These spin states can be explained by the spin polarization mechanism. Quantitative analysis revealed a difference in the magnitude of the exchange coupling constants between 1-pp and 1-mm owing to their local spin structures corresponding to 1,4- and 1,3-phenylene diradical motifs (Kekulé and non-Kekulé structures, respectively).
{"title":"Radical-Site-Dependent Exchange Interactions in Acridane-Based Bisnitroxides","authors":"Yuta Takenouchi, Takuya Kanetomo, Masaya Enomoto","doi":"10.1039/d4cp04393f","DOIUrl":"https://doi.org/10.1039/d4cp04393f","url":null,"abstract":"To investigate the radical-site-dependence of the exchange coupling in bisnitroxides, we have synthesized novel three acridan-based diradicals, tert-butyl nitroxide groups at the 2,7-, 2,6- and 3,6-positions of 10-benzyl-10’-methyl-9,9’(10<em>H</em>,10’<em>H</em>)spirobiacridine (<strong>1-pp</strong>, <strong>1-mp</strong> and <strong>1-mm</strong>, respectively). Theoretical and experimental magnetic studies indicate that <strong>1-pp</strong> and <strong>1-mm</strong> exhibit a singlet ground state, while <strong>1-mp</strong> exhibits a triplet ground state. These spin states can be explained by the spin polarization mechanism. Quantitative analysis revealed a difference in the magnitude of the exchange coupling constants between <strong>1-pp</strong> and <strong>1-mm</strong> owing to their local spin structures corresponding to 1,4- and 1,3-phenylene diradical motifs (Kekulé and non-Kekulé structures, respectively).","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"211 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538685","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}
Bagrat Shainyan, Alexey Eroshin, Sergey A. Shlykov
A gas-phase electron diffraction analysis combined with mass-spectrometry (GED/MS) of (2R,9S)-trans-2,9-diiodo-13-(triflyl)-13-azabicyclo[8.2.1]tridec-5-ene 5 was performed and the results compared with the earlier studied by GED/MS and X-ray analysis triflamide derivatives, that is 3,7,9-tris(triflyl)-3,7,9-triazabicyclo[3.3.1]nonane 2, 6-iodo-3-(triflamidomethyl)-4-triflyl-1,4,2,7-oxazadisilepane 3, and2,2,4,4-tetramethyl-6,8-bis(triflyl)-3-oxa-6,8-diaza-2,4-disilabicyclo[3.2.2]nonane 4. In addition, the first GED study was performed for triflamide CF3SO2NH2, 6, for which the X-ray structure has also been studied. Two conformers of 5 with the oppositely distorted dihedral angles in the five-membered ring were proved in gas phase, and, after careful analysis, also in the crystal. Very low barrier to interconversion (1.7 kcal/mol) and energy difference (0.6 kcal/mol) were calculated. In gas, the S–N and S–C bonds are longer than in the crystal, clearly indicating tightening due to crystal packing effects.
{"title":"Heterocyclic products of oxidative triflamidation of unsaturated compounds: gas-phase vs. crystal structure","authors":"Bagrat Shainyan, Alexey Eroshin, Sergey A. Shlykov","doi":"10.1039/d4cp04855e","DOIUrl":"https://doi.org/10.1039/d4cp04855e","url":null,"abstract":"A gas-phase electron diffraction analysis combined with mass-spectrometry (GED/MS) of (2R,9S)-trans-2,9-diiodo-13-(triflyl)-13-azabicyclo[8.2.1]tridec-5-ene 5 was performed and the results compared with the earlier studied by GED/MS and X-ray analysis triflamide derivatives, that is 3,7,9-tris(triflyl)-3,7,9-triazabicyclo[3.3.1]nonane 2, 6-iodo-3-(triflamidomethyl)-4-triflyl-1,4,2,7-oxazadisilepane 3, and2,2,4,4-tetramethyl-6,8-bis(triflyl)-3-oxa-6,8-diaza-2,4-disilabicyclo[3.2.2]nonane 4. In addition, the first GED study was performed for triflamide CF3SO2NH2, 6, for which the X-ray structure has also been studied. Two conformers of 5 with the oppositely distorted dihedral angles in the five-membered ring were proved in gas phase, and, after careful analysis, also in the crystal. Very low barrier to interconversion (1.7 kcal/mol) and energy difference (0.6 kcal/mol) were calculated. In gas, the S–N and S–C bonds are longer than in the crystal, clearly indicating tightening due to crystal packing effects.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"29 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532843","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}
Marco Marino, Gonzalo Rivero Carracedo, Andrey Rybakov, José J. Baldoví, Guido Fratesi
Magnonics is a rapidly growing field that is nowadays broadly recognized as a paradigm shift for information and communication technologies. In this context, antiferromagnetic materials are particularly relevant due to the lack of stray fields and their faster dynamics, with frequencies in the THz range and longer spin relaxation times. Herein, we investigate the chemical tuning of magnons in a prototypical antiferromagnetic transition metal oxide through the creation of a hybrid heterostructure formed by an Fe-phthalocyanine layer over a NiO(001) substrate. Our first-principles calculations for the hybrid material allow us to evaluate the effect of the adsorbed molecules on the electronic structure, charge transfer and magnetic exchange couplings of NiO. In particular, we observe an electron density flow from the O towards the Ni atoms in the substrate, and from the O atoms towards the molecule at the interface. As a result, the magnetic couplings are enhanced by 7.7% at the surface, accompanied by a decrease by 19.1% in the layer below the surface. Interestingly, our results predict a shift of the magnon frequencies by ~10 meV in the optical branch. This work provides a new step towards the design of molecular controlled magnetic materials for magnonic applications.
{"title":"Chemical Tuning of Magnons in NiO(001) by Fe-Phthalocyanine Adsorption","authors":"Marco Marino, Gonzalo Rivero Carracedo, Andrey Rybakov, José J. Baldoví, Guido Fratesi","doi":"10.1039/d4cp04547e","DOIUrl":"https://doi.org/10.1039/d4cp04547e","url":null,"abstract":"Magnonics is a rapidly growing field that is nowadays broadly recognized as a paradigm shift for information and communication technologies. In this context, antiferromagnetic materials are particularly relevant due to the lack of stray fields and their faster dynamics, with frequencies in the THz range and longer spin relaxation times. Herein, we investigate the chemical tuning of magnons in a prototypical antiferromagnetic transition metal oxide through the creation of a hybrid heterostructure formed by an Fe-phthalocyanine layer over a NiO(001) substrate. Our first-principles calculations for the hybrid material allow us to evaluate the effect of the adsorbed molecules on the electronic structure, charge transfer and magnetic exchange couplings of NiO. In particular, we observe an electron density flow from the O towards the Ni atoms in the substrate, and from the O atoms towards the molecule at the interface. As a result, the magnetic couplings are enhanced by 7.7% at the surface, accompanied by a decrease by 19.1% in the layer below the surface. Interestingly, our results predict a shift of the magnon frequencies by ~10 meV in the optical branch. This work provides a new step towards the design of molecular controlled magnetic materials for magnonic applications.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532841","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}
Ke Xiao, Xiaohui Shi, Xingyuan Zhang, Qingming Ping, Lulu Du
Fe4N with the high curie temperature, large saturation magnetization and good stability has been widely used in spintronic devices. However, the in-plane magnetic anisotropy of Fe4N limits its further developments in the next-generation spintronic devices. Element substitution is an effective method to improve the magnetic properties of Fe4N. Here, the electronic structures and magnetic properties of ternary iron nitrides MxFe4-xN (x = 1 and 3, M = paramagnetic, antiferromagnetic, ferromagnetic, or heavy metal element) are investigated by first-principles calculations. The magnetic moments of Gd3FefN (21.22 μB) are 2.14 times larger than that of Fe4N (9.89 μB). Due to the antiferromagnetic coupling or low spin state, the total magnetic moments of 0 μB occur in Cr3FefN, YcFe3N, and Y3FefN. The spin polarization in Cu3FecN (76.1%), PtfFe3N (68.4%), and PtcFe3N (65.5%) are 1.59 and 1.42, and 1.37 times larger than that of Fe4N (47.9%). In addition, the tendence from perpendicular magnetic anisotropy (PMA) to in-plane magnetic anisotropy (IMA) in MfFe3N and from IMA to PMA in M3FefN is dependent to the increase the number of M. These novel magnetic properties provide a new avenue for Fe4N in next-generation spintronic devices with high density, low energy consumption, and high speed.
{"title":"Emergence of the novel magnetic properties in ternary iron nitrides toward spintronics: first-principles calculations","authors":"Ke Xiao, Xiaohui Shi, Xingyuan Zhang, Qingming Ping, Lulu Du","doi":"10.1039/d5cp00405e","DOIUrl":"https://doi.org/10.1039/d5cp00405e","url":null,"abstract":"Fe4N with the high curie temperature, large saturation magnetization and good stability has been widely used in spintronic devices. However, the in-plane magnetic anisotropy of Fe4N limits its further developments in the next-generation spintronic devices. Element substitution is an effective method to improve the magnetic properties of Fe4N. Here, the electronic structures and magnetic properties of ternary iron nitrides MxFe4-xN (x = 1 and 3, M = paramagnetic, antiferromagnetic, ferromagnetic, or heavy metal element) are investigated by first-principles calculations. The magnetic moments of Gd3FefN (21.22 μB) are 2.14 times larger than that of Fe4N (9.89 μB). Due to the antiferromagnetic coupling or low spin state, the total magnetic moments of 0 μB occur in Cr3FefN, YcFe3N, and Y3FefN. The spin polarization in Cu3FecN (76.1%), PtfFe3N (68.4%), and PtcFe3N (65.5%) are 1.59 and 1.42, and 1.37 times larger than that of Fe4N (47.9%). In addition, the tendence from perpendicular magnetic anisotropy (PMA) to in-plane magnetic anisotropy (IMA) in MfFe3N and from IMA to PMA in M3FefN is dependent to the increase the number of M. These novel magnetic properties provide a new avenue for Fe4N in next-generation spintronic devices with high density, low energy consumption, and high speed.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"49 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532844","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}
Jin Zou, Daoyun Zhu, Zhongfei Mu, Song Xu, Nurahmat· Wali, Fugen Wu, Huafeng Dong, Xin Zhang, Yifei Luo, Yuchun Zhan
Near-infrared phosphor-converted light-emitting diodes (NIR pc-led) have wide applications in fields of biological imaging and food detection. However, developing an efficient, inexpensive, and broadband near-infrared fluorescent phosphor with sufficient spectral coverage remains a huge challenge. Herein, we report the synthesis of a series of broadband near-infrared phosphors, LiTi2(PO4)3:xCr3+ (LTP), and analyze their crystal structure, luminescent properties, and thermal quenching mechanism. The experimental results indicated that at x = 0.07, the luminescence intensity of the LTP:0.07Cr3+ sample reached its maximum value, followed by the concentration quenching phenomenon, which resulted from the energy transfer between the adjacent Cr3+–Cr3+. Under 455 nm excitation, LTP:0.07Cr3+ exhibited a broadband emission spectrum in the range of 700–1250 nm, with a peak centered at 890 nm and a full width at half maximum (FWHM) of 210 nm. The analyses of the crystal structure and PL spectra as well as the calculation of Cr3+ crystal field intensity indicated that the realization of a broadband near-infrared emission was attributed to the occupancy of Cr3+ at multiple sites of Li+ and Ti4+ in a weak crystal field (Dq/B = 1.92). At a high temperature of 373 K, the luminescence intensity of LTP:0.07Cr3+ was 41% of that observed at room temperature, indicating that the thermal stability of the fluorescent phosphor needed further improvement. Finally, NIR pc-LED devices were prepared using the fluorescent phosphor and blue LED chips, confirming the potential application value of the fluorescent phosphor in biomedical imaging, night vision, and food detection.
{"title":"Broadband near-infrared phosphor LiTi2(PO4)3:xCr3+ realized via multi-site occupation","authors":"Jin Zou, Daoyun Zhu, Zhongfei Mu, Song Xu, Nurahmat· Wali, Fugen Wu, Huafeng Dong, Xin Zhang, Yifei Luo, Yuchun Zhan","doi":"10.1039/d4cp03561e","DOIUrl":"https://doi.org/10.1039/d4cp03561e","url":null,"abstract":"Near-infrared phosphor-converted light-emitting diodes (NIR pc-led) have wide applications in fields of biological imaging and food detection. However, developing an efficient, inexpensive, and broadband near-infrared fluorescent phosphor with sufficient spectral coverage remains a huge challenge. Herein, we report the synthesis of a series of broadband near-infrared phosphors, LiTi<small><sub>2</sub></small>(PO<small><sub>4</sub></small>)<small><sub>3</sub></small>:<em>x</em>Cr<small><sup>3+</sup></small> (LTP), and analyze their crystal structure, luminescent properties, and thermal quenching mechanism. The experimental results indicated that at <em>x</em> = 0.07, the luminescence intensity of the LTP:0.07Cr<small><sup>3+</sup></small> sample reached its maximum value, followed by the concentration quenching phenomenon, which resulted from the energy transfer between the adjacent Cr<small><sup>3+</sup></small>–Cr<small><sup>3+</sup></small>. Under 455 nm excitation, LTP:0.07Cr<small><sup>3+</sup></small> exhibited a broadband emission spectrum in the range of 700–1250 nm, with a peak centered at 890 nm and a full width at half maximum (FWHM) of 210 nm. The analyses of the crystal structure and PL spectra as well as the calculation of Cr<small><sup>3+</sup></small> crystal field intensity indicated that the realization of a broadband near-infrared emission was attributed to the occupancy of Cr<small><sup>3+</sup></small> at multiple sites of Li<small><sup>+</sup></small> and Ti<small><sup>4+</sup></small> in a weak crystal field (<em>Dq</em>/<em>B</em> = 1.92). At a high temperature of 373 K, the luminescence intensity of LTP:0.07Cr<small><sup>3+</sup></small> was 41% of that observed at room temperature, indicating that the thermal stability of the fluorescent phosphor needed further improvement. Finally, NIR pc-LED devices were prepared using the fluorescent phosphor and blue LED chips, confirming the potential application value of the fluorescent phosphor in biomedical imaging, night vision, and food detection.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"39 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532839","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}
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) to explore molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of CDK6. The DL finds that the β-sheets, αC helix as well as the T-loop are involved in obvious differences of conformation contacts and suggests that T-loop plays a key role in the function of CDK6. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of T177 leads to alterations of the T-loop conformation and the results from principal component analysis (PCA) indicate that the phosphorylation affects the fluctuation behavior of the β-sheets and the T-loop in CDK6. Interaction networks of inhibitors with CDK6 were analyzed and the information reveals that 6ZV contributes more hydrogen binding interactions (HBIs) and hot interaction spots with CDK6. Our MM-GBSA calculations suggest that the binding ability of 6ZV to CDK6 is stronger than 6ZZ and 0RS. We anticipate that this work could provide useful information for further understanding of CDK6 function and developing new promising inhibitors targeting CDK6.
{"title":"Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning","authors":"Lu Zhao, Jian Wang, Wanchun Yang, Canqing Zhang, Weiwei Zhang, Jianzhong Chen","doi":"10.1039/d4cp04579c","DOIUrl":"https://doi.org/10.1039/d4cp04579c","url":null,"abstract":"The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) to explore molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of CDK6. The DL finds that the β-sheets, αC helix as well as the T-loop are involved in obvious differences of conformation contacts and suggests that T-loop plays a key role in the function of CDK6. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of T177 leads to alterations of the T-loop conformation and the results from principal component analysis (PCA) indicate that the phosphorylation affects the fluctuation behavior of the β-sheets and the T-loop in CDK6. Interaction networks of inhibitors with CDK6 were analyzed and the information reveals that 6ZV contributes more hydrogen binding interactions (HBIs) and hot interaction spots with CDK6. Our MM-GBSA calculations suggest that the binding ability of 6ZV to CDK6 is stronger than 6ZZ and 0RS. We anticipate that this work could provide useful information for further understanding of CDK6 function and developing new promising inhibitors targeting CDK6.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"86 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532845","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}
Single-atom catalysts revolutionize catalysis by maximizing atomic efficiency and enhancing reaction specificity, offering high activity and selectivity with minimal material usage, which is crucial for sustainable processes. However, the unique properties that distinguish single-atom catalysts from other forms, including bulk and nanoparticle catalysts, as well as the physical mechanisms behind their high activity and selectivity, remain unclear, limiting their broader application. Here, through first-principles calculations, we have identified an environmentally adaptive gold single-atom catalyst on a CeO2(111) surface capable of adjusting its valence state in response to different environmental conditions. This adaptability enables the catalyst to simultaneously maintain high stability and activity. In a CO gas atmosphere, numerous oxygen vacancies form on the CeO2(111) surface, where Au single atoms stably adsorb, exhibiting a negative oxidation state that deactivates the catalyst. In an O2 atmosphere, these vacancies are filled, causing the Au single atoms to adsorb onto lattice oxygen and become oxidized to a positive oxidation state, thereby reactivating the catalyst. During CO oxidation reaction conditions, the Au single atoms oscillate between these positive and negative oxidation states, effectively facilitating the CO oxidation process. These findings provide new insights into the unique properties and high performance of single-atom catalysts, contributing to a better understanding and utilization of these catalysts in various applications.
{"title":"Environmentally Adaptive Gold Single-Atom Catalyst with Variable Valence States","authors":"Meiliang Ma, Wen Liu, Xiaojuan Hu, Ying Jiang, Wentao Yuan, Zhongkang Han, Yong Wang","doi":"10.1039/d5cp00468c","DOIUrl":"https://doi.org/10.1039/d5cp00468c","url":null,"abstract":"Single-atom catalysts revolutionize catalysis by maximizing atomic efficiency and enhancing reaction specificity, offering high activity and selectivity with minimal material usage, which is crucial for sustainable processes. However, the unique properties that distinguish single-atom catalysts from other forms, including bulk and nanoparticle catalysts, as well as the physical mechanisms behind their high activity and selectivity, remain unclear, limiting their broader application. Here, through first-principles calculations, we have identified an environmentally adaptive gold single-atom catalyst on a CeO2(111) surface capable of adjusting its valence state in response to different environmental conditions. This adaptability enables the catalyst to simultaneously maintain high stability and activity. In a CO gas atmosphere, numerous oxygen vacancies form on the CeO2(111) surface, where Au single atoms stably adsorb, exhibiting a negative oxidation state that deactivates the catalyst. In an O2 atmosphere, these vacancies are filled, causing the Au single atoms to adsorb onto lattice oxygen and become oxidized to a positive oxidation state, thereby reactivating the catalyst. During CO oxidation reaction conditions, the Au single atoms oscillate between these positive and negative oxidation states, effectively facilitating the CO oxidation process. These findings provide new insights into the unique properties and high performance of single-atom catalysts, contributing to a better understanding and utilization of these catalysts in various applications.","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"9 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532943","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}
Concerted Proton Electron Transfer (CPET) and Hydrogen Atom Transfer (HAT) are two important mechanisms in many fields of chemistry, which are characterized by the transfer of one proton and one electron. The distinction between these mechanisms may be challenging in several reactions; thus, different computational methods have been developed for this purpose. In this work, we present a computational strategy to distinguish the two mechanisms, rationalizing the factors controlling the reactivity in four different model reactions. Fist, the transition state SOMO (Singly Occupied Molecular Orbital) is visualized, presenting all the limits and ambiguities of this analysis. Then, the electron flow along the reaction path is evaluated through the Intrinsic Bond Orbitals (IBOs); this analysis allows to describe correctly the mechanism of each reaction in agreement with previous studies. Furthermore, some structural modifications are applied to the transition state of each system and the energetic differences are rationalized in the framework of the Activation Strain Analysis to understand the geometrical and electronic factors governing the reactivity and the selection of CPET or HAT mechanism. Lastly, the effect of the donor-acceptor distance is evaluated. It emerges that a combined computational analysis is crucial to understand not only the distinction between the two mechanisms, but also the molecular reasons why one mechanism is operative in a specific reaction,
{"title":"Concerted Proton Electron Transfer or Hydrogen Atom Transfer? An Unequivocal Strategy to Discriminate these Mechanisms in Model Systems","authors":"DAVIDE ZEPPILLI, Laura Orian","doi":"10.1039/d5cp00690b","DOIUrl":"https://doi.org/10.1039/d5cp00690b","url":null,"abstract":"Concerted Proton Electron Transfer (CPET) and Hydrogen Atom Transfer (HAT) are two important mechanisms in many fields of chemistry, which are characterized by the transfer of one proton and one electron. The distinction between these mechanisms may be challenging in several reactions; thus, different computational methods have been developed for this purpose. In this work, we present a computational strategy to distinguish the two mechanisms, rationalizing the factors controlling the reactivity in four different model reactions. Fist, the transition state SOMO (Singly Occupied Molecular Orbital) is visualized, presenting all the limits and ambiguities of this analysis. Then, the electron flow along the reaction path is evaluated through the Intrinsic Bond Orbitals (IBOs); this analysis allows to describe correctly the mechanism of each reaction in agreement with previous studies. Furthermore, some structural modifications are applied to the transition state of each system and the energetic differences are rationalized in the framework of the Activation Strain Analysis to understand the geometrical and electronic factors governing the reactivity and the selection of CPET or HAT mechanism. Lastly, the effect of the donor-acceptor distance is evaluated. It emerges that a combined computational analysis is crucial to understand not only the distinction between the two mechanisms, but also the molecular reasons why one mechanism is operative in a specific reaction,","PeriodicalId":99,"journal":{"name":"Physical Chemistry Chemical Physics","volume":"23 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538486","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}
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