ACS Physical Chemistry Au最新文献

{"title":"The Structure of the Density-Potential Mapping. Part II: Including Magnetic Fields","authors":"Markus Penz,&nbsp;Erik I. Tellgren,&nbsp;Mihály A. Csirik,&nbsp;Michael Ruggenthaler and Andre Laestadius*,&nbsp;","doi":"10.1021/acsphyschemau.3c00006","DOIUrl":"10.1021/acsphyschemau.3c00006","url":null,"abstract":"<p >The Hohenberg–Kohn theorem of density-functional theory (DFT) is broadly considered the conceptual basis for a full characterization of an electronic system in its ground state by just one-body particle density. In this Part II of a series of two articles, we aim at clarifying the status of this theorem within different extensions of DFT including magnetic fields. We will in particular discuss current-density-functional theory (CDFT) and review the different formulations known in the literature, including the conventional paramagnetic CDFT and some nonstandard alternatives. For the former, it is known that the Hohenberg–Kohn theorem is no longer valid due to counterexamples. Nonetheless, paramagnetic CDFT has the mathematical framework closest to standard DFT and, just like in standard DFT, nondifferentiability of the density functional can be mitigated through Moreau–Yosida regularization. Interesting insights can be drawn from both Maxwell–Schrödinger DFT and quantum-electrodynamic DFT, which are also discussed here.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 6","pages":"492–511"},"PeriodicalIF":0.0,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45925626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Situ Optical Microspectroscopy Study of Isothermal Bleaching of γ-Irradiated International Simple Glass","authors":"Mariana Sendova,&nbsp;José A. Jiménez* and Charles L. Crawford,&nbsp;","doi":"10.1021/acsphyschemau.3c00020","DOIUrl":"10.1021/acsphyschemau.3c00020","url":null,"abstract":"<p >The isothermal bleaching of γ-irradiated glass was studied at elevated temperatures (280–340 °C) by real-time <i>in situ</i> optical microspectroscopy for the first time. The study was performed on γ-irradiated (0.83 and 1.99 MGy) International Simple Glass (ISG) borosilicate nuclear waste simulant made by Mo-SCI Corporation (Rolla, MO, USA). The current investigation proposes real-time optical transmission methodology for the activation energy assessment of isothermal bleaching of γ-irradiated glass. The method is based on robust quantification of the Urbach energy decay rates and yields similar activation energies for both doses within ∼0.24–0.26 eV.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 6","pages":"515–520"},"PeriodicalIF":0.0,"publicationDate":"2023-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43061607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disrupting Dimeric β-Amyloid by Electric Fields","authors":"Pablo Andrés Vargas-Rosales,&nbsp;Alessio D’Addio,&nbsp;Yang Zhang and Amedeo Caflisch*,&nbsp;","doi":"10.1021/acsphyschemau.3c00021","DOIUrl":"10.1021/acsphyschemau.3c00021","url":null,"abstract":"<p >The early oligomers of the amyloid Aβ peptide are implicated in Alzheimer’s disease, but their transient nature complicates the characterization of their structure and toxicity. Here, we investigate the stability of the minimal toxic species, i.e., β-amyloid dimers, in the presence of an oscillating electric field. We first use deep learning (AlphaFold-multimer) for generating initial models of Aβ42 dimers. The flexibility and secondary structure content of the models are then analyzed by multiple runs of molecular dynamics (MD). Structurally stable models are similar to ensemble representatives from microsecond-long MD sampling. Finally, we employ the validated model as the starting structure of MD simulations in the presence of an external oscillating electric field and observe a fast decay of β-sheet content at high field strengths. Control simulations using the helical dimer of the 42-residue leucine zipper peptide show higher structural stability than the Aβ42 dimer. The simulation results provide evidence that an external electric field (oscillating at 1 GHz) can disrupt amyloid oligomers which should be further investigated by experiments with brain organoids <i>in vitro</i> and eventually <i>in vivo</i>.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 5","pages":"456–466"},"PeriodicalIF":0.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41168151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temperature-Dependent Intensity Modulated Two-Photon Excited Fluorescence Microscopy for High Resolution Mapping of Charge Carrier Dynamics","authors":"Qi Shi,&nbsp;Pushpendra Kumar and Tönu Pullerits*,&nbsp;","doi":"10.1021/acsphyschemau.3c00013","DOIUrl":"10.1021/acsphyschemau.3c00013","url":null,"abstract":"<p >We present a temperature-dependent intensity modulated two-photon excited fluorescence microscopy technique that enables high-resolution quantitative mapping of charge carrier dynamics in perovskite microcrystal film. By disentangling the emission into harmonics of the excitation modulation frequency, we analyze the first and second order charge carrier recombination processes, including potential accumulation effects. Our approach allows for a quantitative comparison of different emission channels at a micrometer resolution. To demonstrate the effectiveness of the method, we applied it to a methylammonium lead bromide perovskite microcrystal film. We investigated the temperature-dependent modulated imaging, encompassing the exciton dissociation-association and charge carrier trapping-detrapping equilibrium. Additionally, we explored the potential freezing out of traps and the phase transition occurring at low temperatures.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 5","pages":"467–476"},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41117320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure Determination and Refinement of Paramagnetic Materials by Solid-State NMR","authors":"Jonas Koppe,&nbsp; and ,&nbsp;Andrew J. Pell*,&nbsp;","doi":"10.1021/acsphyschemau.3c00019","DOIUrl":"10.1021/acsphyschemau.3c00019","url":null,"abstract":"<p >Paramagnetism in solid-state materials has long been considered an additional challenge for structural investigations by using solid-state nuclear magnetic resonance spectroscopy (ssNMR). The strong interactions between unpaired electrons and the surrounding atomic nuclei, on the one hand, are complex to describe, and on the other hand can cause fast decaying signals and extremely broad resonances. However, significant progress has been made over the recent years in developing both theoretical models to understand and calculate the frequency shifts due to paramagnetism and also more sophisticated experimental protocols for obtaining high-resolution ssNMR spectra. While the field is continuously moving forward, to date, the combination of state-of-the-art numerical and experimental techniques enables us to obtain high-quality data for a variety of systems. This involves the determination of several ssNMR parameters that represent different contributions to the frequency shift in paramagnetic solids. These contributions encode structural information on the studied material on various length scales, ranging from crystal morphologies, to the mid- and long-range order, down to the local atomic bonding environment. In this perspective, the different ssNMR parameters characteristic for paramagnetic materials are discussed with a focus on their interpretation in terms of structure. This includes a summary of studies that have explored the information content of these ssNMR parameters, mostly to complement experimental data from other methods, e.g., X-ray diffraction. The presented overview aims to demonstrate how far ssNMR has hitherto been able to determine and refine the structures of materials and to discuss where it currently falls short of its full potential. We attempt to highlight how much further ssNMR can be pushed to determine and refine structure to deliver a comprehensive structural characterization of paramagnetic materials comparable to what is to date achieved by the combined effort of electron microscopy, diffraction, and spectroscopy.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 5","pages":"419–433"},"PeriodicalIF":0.0,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41151784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical Insights into the Dynamics of Gas-Phase Bimolecular Reactions with Submerged Barriers","authors":"Hongwei Song*,&nbsp; and ,&nbsp;Hua Guo*,&nbsp;","doi":"10.1021/acsphyschemau.3c00009","DOIUrl":"10.1021/acsphyschemau.3c00009","url":null,"abstract":"<p >Much attention has been paid to the dynamics of both activated gas-phase bimolecular reactions, which feature monotonically increasing integral cross sections and Arrhenius kinetics, and their barrierless capture counterparts, which manifest monotonically decreasing integral cross sections and negative temperature dependence of the rate coefficients. In this Perspective, we focus on the dynamics of gas-phase bimolecular reactions with submerged barriers, which often involve radicals or ions and are prevalent in combustion, atmospheric chemistry, astrochemistry, and plasma chemistry. The temperature dependence of the rate coefficients for such reactions is often non-Arrhenius and complex, and the corresponding dynamics may also be quite different from those with significant barriers or those completely dominated by capture. Recent experimental and theoretical studies of such reactions, particularly at relatively low temperatures or collision energies, have revealed interesting dynamical behaviors, which are discussed here. The new knowledge enriches our understanding of the dynamics of these unusual reactions.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 5","pages":"406–418"},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2f/72/pg3c00009.PMC10540288.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41136123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-Range Conductivity in Proteins Mediated by Aromatic Residues","authors":"Siddharth Krishnan,&nbsp;Aleksei Aksimentiev*,&nbsp;Stuart Lindsay* and Dmitry Matyushov*,&nbsp;","doi":"10.1021/acsphyschemau.3c00017","DOIUrl":"10.1021/acsphyschemau.3c00017","url":null,"abstract":"Single-molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen over 10 nm distances, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1 V. This is puzzling because, for fast transport (i.e., a free energy barrier of zero), the hopping rate is determined by the reorganization energy of approximately 0.8 eV, and this sets the time scale of a single hop to at least 1 μs. Furthermore, the Fermi energies of typical metal electrodes are far removed from the energies required for sequential oxidation and reduction of the aromatic residues of the protein, which should further reduce the hopping current. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox-active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transport. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the non-ergodic sampling of molecular configurations by the protein results in reaction-reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ∼0.2 eV, which is small enough to enable long-range conductivity, without invoking quantum coherent transport. Using the MD values of the reorganization energies, we calculate a current decay with distance that is in agreement with experiment.","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 5","pages":"444–455"},"PeriodicalIF":0.0,"publicationDate":"2023-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4c/9d/pg3c00017.PMC10540285.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41138577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Delta SARS-CoV-2 s2m Structure, Dynamics, and Entropy: Consequences of the G15U Mutation","authors":"Joseph A. Makowski,&nbsp;Adam H. Kensinger,&nbsp;Caylee L. Cunningham,&nbsp;Caleb J. Frye,&nbsp;Morgan Shine,&nbsp;Patrick E. Lackey,&nbsp;Mihaela Rita Mihailescu and Jeffrey D. Evanseck*,&nbsp;","doi":"10.1021/acsphyschemau.3c00008","DOIUrl":"10.1021/acsphyschemau.3c00008","url":null,"abstract":"<p >Bioinformatic analysis of the Delta SARS-CoV-2 genome reveals a single nucleotide mutation (G15U) in the stem-loop II motif (s2m) relative to ancestral SARS-CoV-2. Despite sequence similarity, unexpected differences between SARS-CoV-2 and Delta SARS-CoV-2 s2m homodimerization experiments require the discovery of unknown structural and thermodynamic changes necessary to rationalize the data. Using our reported SARS-CoV-2 s2m model, we induced the G15U substitution and performed 3.5 microseconds of unbiased molecular dynamics simulation at 283 and 310 K. The resultant Delta s2m adopted a secondary structure consistent with our reported NMR data, resulting in significant deviations in the tertiary structure and dynamics from our SARS-CoV-2 s2m model. First, we find differences in the overall three-dimensional structure, where the characteristic 90° L-shaped kink of the SARS-CoV-2 s2m did not form in the Delta s2m resulting in a “linear” hairpin with limited bending dynamics. Delta s2m helical parameters are calculated to align closely with A-form RNA, effectively eliminating a hinge point to form the L-shape kink by correcting an upper stem defect in SARS-CoV-2 induced by a noncanonical and dynamic G:A base pair. Ultimately, the shape difference rationalizes the migration differences in reported electrophoresis experiments. Second, increased fluctuation of the Delta s2m palindromic sequence, within the terminal loop, compared to SARS-CoV-2 s2m results in an estimated increase of entropy of 6.8 kcal/mol at 310 K relative to the SARS-CoV-2 s2m. The entropic difference offers a unique perspective on why the Delta s2m homodimerizes less spontaneously, forming fewer kissing dimers and extended duplexes compared to SARS-CoV-2. In this work, both the L-shape reduction and palindromic entropic penalty provides an explanation of our reported in vitro electrophoresis homodimerization results. Ultimately, the structural, dynamical, and entropic differences between the SARS-CoV-2 s2m and Delta s2m serve to establish a foundation for future studies of the s2m function in the viral lifecycle.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 5","pages":"434–443"},"PeriodicalIF":0.0,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41172110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of Interlayer Na-Ions in Ga-Substituted Na2Zn2TeO6 (NZTO) Studied by Variable-Temperature Solid-State 23Na NMR Spectroscopy and DFT Modeling","authors":"Frida Sveen Hempel,&nbsp;Charlotte Martineau-Corcos,&nbsp;Federico Bianchini,&nbsp;Helmer Fjellvåg and Bjørnar Arstad*,&nbsp;","doi":"10.1021/acsphyschemau.3c00012","DOIUrl":"https://doi.org/10.1021/acsphyschemau.3c00012","url":null,"abstract":"<p >Local Na-coordination and dynamics of Na_2–<i>x</i>Zn_2–<i>x</i>Ga<i>_x</i>TeO₆; <i>x</i> = 0.00 (NZTO), 0.05, 0.10, 0.15, 0.20, were studied by variable-temperature, ²³Na NMR methods and DFT AIMD simulations. Structure and dynamics were probed by NMR in the temperature ranges of 100–293 K in a magnetic field of 18.8 T and from 293 up to 500 K in a magnetic field of 11.7 T. Line shapes and <i>T</i>₁ relaxation constants were analyzed. At 100 K, the otherwise dynamic Na-ions are frozen out on the NMR time scale, and a local structure characterization was performed for Na-ions at three interlayer sites. On increasing the temperature, complex peak shape coalescences occurred, and at 293 K, the Na NMR spectra showed some averaging due to Na-ion dynamics. A further increase to 500 K did not reveal any new peak shape variations until the highest temperatures, where an apparent peak splitting was observed, similar to what was observed in the 18.8 T experiments at lower temperatures. A three-site exchange model coupled with reduced quadrupolar couplings due to dynamics appear to explain these peak shape observations. The Ga substitution increases the Na-jumping rate, as proved by relaxation measurements and by a decrease in temperature for peak coalescence. The estimated activation energy for Na dynamics in the NZTO sample, from relaxation measurements, corresponds well to results from DFT AIMD simulations. Upon Ga substitution, measured activation energies are reduced, which is supported, in part, by DFT calculations. Addressing the correlated motion of Na-ions appears important for solid-state ion conductors since benefits can be gained from the decrease in activation energy upon Ga substitution, for example.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 4","pages":"394–405"},"PeriodicalIF":0.0,"publicationDate":"2023-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsphyschemau.3c00012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49768800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway","authors":"Xin Meng,&nbsp;Srividya Ganapathy*,&nbsp;Lars van Roemburg,&nbsp;Marco Post and Daan Brinks*,&nbsp;","doi":"10.1021/acsphyschemau.3c00003","DOIUrl":"10.1021/acsphyschemau.3c00003","url":null,"abstract":"<p >Voltage imaging using genetically encoded voltage indicators (GEVIs) has taken the field of neuroscience by storm in the past decade. Its ability to create subcellular and network level readouts of electrical dynamics depends critically on the kinetics of the response to voltage of the indicator used. Engineered microbial rhodopsins form a GEVI subclass known for their high voltage sensitivity and fast response kinetics. Here we review the essential aspects of microbial rhodopsin photocycles that are critical to understanding the mechanisms of voltage sensitivity in these proteins and link them to insights from efforts to create faster, brighter and more sensitive microbial rhodopsin-based GEVIs.</p>","PeriodicalId":29796,"journal":{"name":"ACS Physical Chemistry Au","volume":"3 4","pages":"320–333"},"PeriodicalIF":0.0,"publicationDate":"2023-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a1/0f/pg3c00003.PMC10375888.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9921994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}