化学•材料最新文献

{"title":"The Heat Capacity of Al(OH)₃ Revisited.","authors":"Charles W Bauschlicher, Nathan S Jacobson","doi":"10.1021/acs.jpca.4c07024","DOIUrl":"10.1021/acs.jpca.4c07024","url":null,"abstract":"<p><p>We consider different approximations to compute the heat capacity for Al(OH)₃ and compare the computed results to the experiment. We find that the calculation of anharmonic effects for this molecule is not currently practical, and scaled harmonics, using the scaling factor for H₂O(g), offer the best approach to including anharmonic effects. The Pitzer-Gwinn approach for hindered rotations is recommended.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"1952-1959"},"PeriodicalIF":2.7,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412414","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":"Using Conformational Sampling to Model Spectral and Structural Changes of Molecules at Elevated Pressures.","authors":"Felix Zeller, Philipp Pracht, Tim Neudecker","doi":"10.1021/acs.jpca.4c08065","DOIUrl":"10.1021/acs.jpca.4c08065","url":null,"abstract":"<p><p>Conformational sampling is nowadays a standard routine in computational chemistry. Within this work, we present a method to perform conformational sampling for systems exposed to elevated pressures within the CREST program, allowing us to model pressure-induced changes of molecular ensembles and structural parameters. For this purpose, we extend the molecular Hamiltonian with the PV (pressure times volume) term, using the solvent-accessible volume. The volume computation is performed within the new standalone library libpvol. A first application shows good agreement with experimental data and provides a reasonable explanation for severe pressure-induced structural and spectroscopic changes of the molecules dichloroethane and tetra(4-methoxyphenyl)ethylene.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2108-2116"},"PeriodicalIF":2.7,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397614","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":"Release of Neutrals in Electron-Induced Ligand Separation from MeCpPtMe₃: Theory Meets Experiment.","authors":"Hlib Lyshchuk, Alexey V Verkhovtsev, Jaroslav Kočišek, Juraj Fedor, Andrey V Solov'yov","doi":"10.1021/acs.jpca.4c08259","DOIUrl":"10.1021/acs.jpca.4c08259","url":null,"abstract":"<p><p>The interest in the electron impact-induced ligand release from MeCpPtMe₃ [trimethyl(methylcyclopentadienyl)platinum(IV)] is motivated by its widespread use as a precursor in focused electron and ion beam nanofabrication. By experimentally studying the electron impact dissociative ionization of MeCpPtMe₃ under single-collision conditions, we have found that the removal of two methyl radicals is energetically more favorable than the removal of one radical and even energetically comparable to the nondissociative ionization of MeCpPtMe₃. This observation is explained by the structural rearrangement of the MeCpPtMe₃⁺ ion prior to dissociation, resulting in the removal of ethane instead of two methyl groups. This fragmentation pathway is computationally confirmed and studied by irradiation-driven molecular dynamics (IDMD) simulations. The formation of complex molecules in irradiation-induced molecular dissociation is a general phenomenon that can occur in various molecular systems. This study explains the puzzling results of previous experiments with MeCpPtMe₃ molecules and highlights the use of the IDMD approach to describe radiation-induced chemical transformations in molecular systems.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"2016-2023"},"PeriodicalIF":2.7,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412412","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":"Test of the Orbital-Based LI3 Index as a Predictor of the Height of the ³MLCT →³MC Transition-State Barrier for [Ru(N^∧N)₃]²⁺ Polypyridine Complexes in CH₃CN.","authors":"Ala Aldin M H M Darghouth, Denis Magero, Mark E Casida","doi":"10.1021/acs.jpca.4c07424","DOIUrl":"10.1021/acs.jpca.4c07424","url":null,"abstract":"<p><p>Ruthenium(II) polypyridine compounds often have a relatively long-lived triplet metal-ligand charge transfer (³MLCT) state, making these complexes useful as chromophores for photoactivated electron transfer in photomolecular devices (PMDs). As different PMDs typically require different ligands and as the luminescence lifetime of the ³MLCT is sensitive to the structure of the ligand, it is important to understand this state and what types of photoprocesses can lead to its quenching. Recent work has increasingly emphasized that there are likely multiple competing pathways involved, which should be explored in order to fully comprehend the ³MLCT state. However, the lowest barrier that needs to be crossed to pass over to the nonluminescent triplet metal-centered (³MC) state has been repeatedly found to be a <i>trans</i> dissociation of the complex, at least in the simpler cases studied. This is the fourth in a series of articles investigating the possibility of an orbital-based luminescence index (LI3, because it was the most successful of three) for predicting luminescence lifetimes. In an earlier study of bidentate (N^∧N) ligands, we showed that the gas-phase ³MLCT → ³MC mechanism proceeded via an initial charge transfer to a single N^∧N ligand, which moves symmetrically away from the central ruthenium atom, followed by a bifurcation pathway to one of two ³MC enantiomers. The actual transition state barrier was quite small and independent, to within the limits of our calculations, of the choice of ligand studied. Here, we investigate the same reaction in acetonitrile, CH₃CN, solution and find that the mechanism differs from that in the gas phase in that the reaction passes directly via a <i>trans</i> mechanism. This has implications for the interpretation of LI3 via the Bell-Evans-Polanyi principle.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":" ","pages":"1960-1971"},"PeriodicalIF":2.7,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439397","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":"Deep Learning Protocol for Predicting Full-Spectrum Infrared and Raman Spectra of Polypeptides and Proteins Using All-Atom Models.","authors":"Xiaochen Yang, Xun Zhang, Yujin Zhang, Jun Jiang, Wei Hu","doi":"10.1021/acs.jpclett.5c00169","DOIUrl":"10.1021/acs.jpclett.5c00169","url":null,"abstract":"<p><p>Infrared (IR) spectroscopy and Raman spectroscopy are powerful tools for probing protein and peptide structures due to their capability to provide molecular fingerprints. As a popular spectral simulation method, the quantum chemistry (QC) calculation is usually hampered by the high computational cost and low efficiency. In this study, we developed a comprehensive data set of IR and Raman spectra for amino acids, dipeptides, and tripeptides. Using this data set, we applied transfer learning with DetaNet (a deep equivariant tensor attention network) to simulate full-spectrum IR and Raman spectra for large polypeptides and proteins. We have demonstrated that the transfer-learned DetaNet (TL-DetaNet) model successfully simulated the vibrational spectra of proteins with thousands of atoms, far exceeding traditional QC limitations. Additionally, TL-DetaNet achieved an efficiency that was 10³-10⁵ times greater than that of QC methods. This work highlights the importance of data sets in machine learning and positions transfer learning as a transformative tool for large-scale biomolecular simulations, marking a substantial advancement in protein vibrational spectroscopy.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"2023-2028"},"PeriodicalIF":4.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447517","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":"Crystallite Size Effects on the Heat of Water Intrusion/Extrusion into/from Metal-Organic Frameworks.","authors":"Liam J W Johnson, Alexander R Lowe, Andrea Le Donne, Emre Arkan, Sebastiano Merchiori, Luis Bartolomé, Eder Amayuelas, Diego Mirani, Gabriel A López, Giulia Grancini, Mirosław Chora Żewski, Simone Meloni, Yaroslav Grosu","doi":"10.1021/acs.jpclett.4c02639","DOIUrl":"10.1021/acs.jpclett.4c02639","url":null,"abstract":"<p><p>The wettability of nanoporous materials is a key property for a diverse range of applications. However, the heat generated in this process remains largely unexplored. Herein, the heats of intrusion/extrusion into/from ZIF-8 + water systems of various ZIF-8 crystallite sizes were measured at different temperatures. We found that decreasing crystallite size to the nanoscale resulted in a reduction of the magnitude of the heats of intrusion/extrusion. These results were mirrored in simulations, where the reduction of intrusion heat by reducing the characteristics dependent on crystallite size was comparable to the values obtained experimentally. We related this to the reduction in filling at lower pressures. We recorded the inversion of the sign of the heats of intrusion/extrusion measured at high temperatures. In addition, the heat/work ratio of the intrusion/extrusion processes was dependent on temperature while independent of crystallite size, decoupling the two parameters and making them tunable <i>exogenously</i>.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":" ","pages":"2089-2096"},"PeriodicalIF":4.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456298","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":"Macroscopic Fracture Properties of Glassy Nanocomposites from Molecular Dynamics Simulations and Empirical Force Fields.","authors":"I Delasoudas, S V Kallivokas, V Kostopoulos","doi":"10.1021/acs.jpcb.4c08381","DOIUrl":"10.1021/acs.jpcb.4c08381","url":null,"abstract":"<p><p>In this study, we extend a previously developed methodology for calculating macroscopic fracture properties in glassy polymers using molecular dynamics (MD) and empirical force fields to glassy nanocomposites. We apply this approach to epoxy nanocomposites with randomly dispersed carbon nanotubes (CNTs), modeling four system types: two with pristine CNTs (1 and 2% by weight) and two with hydroxyl (OH)-functionalized CNTs at similar concentrations. Using a macroscopic analytical model, we calculate the fracture energy and the stress intensity factor for each system and examine how interfacial adhesion influences load transfer and failure mechanisms. Moreover, the cohesive energies and the mean squared displacements for the different systems are calculated, to further analyze the load transfer mechanisms between CNTs and the matrix. Our results demonstrate that functionalized CNTs significantly enhance fracture properties compared to pristine CNTs due to improved interfacial adhesion, enabling better load transfer and delaying crack propagation. This study offers a computationally efficient approach for exploring fracture characteristics in CNT-epoxy nanocomposites. Using empirical force fields, we get faster calculations enabling us to model bigger and more complex systems.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2318-2327"},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432047","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":"Coupled Heterogeneity to Dimeric Site-Specific Binding by the POU-Family Transcription Factor OCT2.","authors":"J Ross Terrell, Gregory M K Poon","doi":"10.1021/acs.jpcb.4c07071","DOIUrl":"10.1021/acs.jpcb.4c07071","url":null,"abstract":"<p><p>POU-family transcription factors regulate metazoan gene expression via a bipartite DNA-binding domain consisting of two covalently linked helix-turn-helix subdomains, POU_S and POU_H. POU factors bind as dimers to DNA half-sites to form complexes with a variable quaternary structure. To enhance the knowledge of the physical chemistry of dimeric POU/DNA recognition, we carried out a crystallographic and titration analysis of the cooperative homodimer formed by the POU factor OCT2 and an optimized palindromic DNA site known as MORE. The data evidence strong heterogeneity in the binding and formation of secondary complexes in site-specific DNA recognition by OCT2 at thermodynamic equilibrium. These secondary complexes are strictly contingent to the site-specific complex, detectable at subsaturating OCT2 concentrations, and cooperate with nonspecific binding to guide the affinity of the site-specific complex. Modulation with salt and poly[d(I-C)] unmasks the compensation between nonspecific DNA depleting unbound OCT2 on the one hand while driving specific binding by intermolecular transfer of OCT2 via secondary complexes on the other. Molecular dynamics simulations extend a mechanism, previously proposed for POU monomers, in which the two subdomains dynamically cross-link DNA strands to form supramolecular dimeric POU/DNA complexes at equilibrium.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2138-2148"},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439401","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":"Coupled Nuclear and Electron Dynamics in Chlorophyll Unraveled by XMS-CASPT2 X-ray Absorption Spectra.","authors":"Lena Bäuml, Regina de Vivie-Riedle","doi":"10.1021/acs.jpcb.4c07787","DOIUrl":"10.1021/acs.jpcb.4c07787","url":null,"abstract":"<p><p>Attosecond spectroscopy, especially time-resolved X-ray absorption spectra (XAS), enables direct observation of ultrafast molecular dynamics. The complementary and even preceding development of theoretical simulations can offer the necessary guidance and stimulate new experiments. In this work, we simulated high-level XAS for the magnesium and nitrogen K-edge of chlorophyll <i>a</i>. In our previous work on the ultrafast relaxation process in the Q-band, our quantum dynamics simulations found the <i>Q</i>_<i>x</i> and <i>Q</i>_<i>y</i> states to be energetically close and therefore strongly coupled. Here, we analyze the strong coupling between <i>Q</i>_<i>x</i> and <i>Q</i>_<i>y</i> via XAS, indicating promising possibilities for experimental observation. The excited-state energies, potential energy surfaces, and XAS are computed at the XMS-CASPT2 level of theory to capture the complex multireference character of chlorophyll excitations. In our simulated spectra, we could follow the ultrafast population transfer between <i>Q</i>_<i>x</i> and <i>Q</i>_<i>y</i> and thus draw conclusions about the strong vibrational coupling between them.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":"2159-2167"},"PeriodicalIF":2.8,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439402","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":"Minisci C-H Alkylation of Heterocycles with Unactivated Alkyl Iodides Enabled by Visible Light Photocatalysis.","authors":"Girish Suresh Yedase, Ruveen Murgeshan, Veera Reddy Yatham","doi":"10.1021/acs.joc.4c03151","DOIUrl":"https://doi.org/10.1021/acs.joc.4c03151","url":null,"abstract":"<p><p>In this work, we developed a general catalytic strategy that allows Minisci C-H alkylation of a variety of heterocycles using unactivated alkyl halide as an alkyl radical source under visible light photocatalysis. Mild reaction conditions, employing 4CzIPN as an organophotocatalyst and aerial oxygen as a green terminal oxidant, a broad scope, good functional group tolerance, and late-stage C-H alkylation of bioactive and pharmaceutically relevant molecules are advantages of the protocol. Preliminary mechanistic studies indicate the involvement of the α-amino alkyl radical and the alkyl radical and further involvement of aerial oxygen under our reaction conditions.</p>","PeriodicalId":57,"journal":{"name":"Journal of Organic Chemistry","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514045","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}