Structural Dynamics-Us最新文献

{"title":"Artificial intelligence in structural biology: Preface.","authors":"George N Phillips, Charles W Carter","doi":"10.1063/4.0001198","DOIUrl":"10.1063/4.0001198","url":null,"abstract":"","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 6","pages":"060401"},"PeriodicalIF":2.3,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12640247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Happy 100th, structural biology.","authors":"George N Phillips, Eaton Edward Lattman","doi":"10.1063/4.0000788","DOIUrl":"10.1063/4.0000788","url":null,"abstract":"<p><p>About 100 years ago, the field of structural biology was born, led by James B. Sumner who recognized that enzymes were molecules with specific functions. In its contemporary form structural biology is used to interpret and understand molecular and cellular function, to design drugs, and to advance biotechnology in general.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 6","pages":"061001"},"PeriodicalIF":2.9,"publicationDate":"2025-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12629662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145565975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The hydrogen sublattice in hydrated molybdenum trioxides: Insight from multi-energy neutron scattering.","authors":"Kacper Drużbicki, Erwin Lalik, Robert Kosydar, Matthias Gutmann, Ivan da Silva, Svemir Rudić, Fabio Orlandi, Dmitry Khalyavin, Pascal Manuel, Matthew Krzystyniak","doi":"10.1063/4.0000785","DOIUrl":"10.1063/4.0000785","url":null,"abstract":"<p><p>Molybdenum oxides have attracted considerable attention in heterogeneous catalysis and energy storage applications owing to the unusual chemical flexibility of the Mo center. Unlike many transition metals, molybdenum can shift between several oxidation states without losing structural integrity, largely due to the stabilizing role of oxo-bridged linkages. This versatility gives rise to an extraordinary diversity of structural motifs that can be tailored for specific catalytic and electrochemical functions. In this study, we investigate the elusive structure and nuclear dynamics of the monohydrate (MoO₃ <math><mo>·</mo></math> H₂O) and dihydrate (MoO₃ <math><mo>·</mo></math>  2H₂O) phases of <math><mi>β</mi></math> -MoO₃, an important family of precursors for molybdenum oxide-based hybrid materials. We employ a combined experimental and computational approach to explore the local environment and nuclear dynamics of protons in water confined within the interlamellar space of the <math><mi>β</mi></math> -MoO₃ layers. High-resolution neutron diffraction confirms the established structure of the dihydrate phase while revealing hydrogen-sublattice disorder in the metastable monohydrate. Complementary computational analysis, including harmonic lattice dynamics and <i>ab initio</i> Born-Oppenheimer molecular dynamics simulations, provides deeper insight into proton confinement in these systems, yielding plausible models of their local structure. These findings further validated through temperature-dependent inelastic neutron scattering and neutron Compton scattering, which probe the vibrational response and proton momentum distributions, respectively. The joint analysis of experimental data and molecular dynamics simulations identifies rotationally bound, orientationally disordered water molecules as the mechanism underlying proton disorder in <math><mi>β</mi></math> -MoO₃ <math><mo>·</mo></math> H₂O. Overall, the results reveal pronounced differences in water ordering and proton dynamics between the mono- and dihydrate forms, offering a detailed quantum-mechanical description of the hydrogen behavior in hydrated molybdenum trioxides and highlighting the interplay between the thermal effect and the confinement-induced local proton dynamics.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 6","pages":"064501"},"PeriodicalIF":2.9,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12611397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145514830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conformer-selective photoelectron circular dichroism: Experimental development and application to nitrogen chirality.","authors":"Etienne Rouquet, Julien Vincent, Valéria Lepère, Lionel Poisson, Anne Zehnacker","doi":"10.1063/4.0000776","DOIUrl":"10.1063/4.0000776","url":null,"abstract":"<p><p>Here, we describe recently developed upgrades to our experimental scheme for obtaining the photoelectron spectrum, the anisotropy parameter, and the photoelectron circular dichroism (PECD) of jet-cooled flexible molecules with conformer selectivity. The one-color resonance-enhanced multiphoton ionization process used allows ionizing selectively the different conformers present in the supersonic expansion by selecting their S₀-S₁ transition. We first describe the experimental setup with emphasis on the data acquisition and processing. Then, we apply this ionization scheme to a flexible molecule, 1,2,3,4-tetrahydro-3-isoquinoline methanol (THIQM). This molecule shows two stereogenic centers, namely, an asymmetric carbon and a nitrogen atom. It exists in two conformers, THIQM_I and THIQM_II, which differ by the direction of the intramolecular hydrogen bond and the absolute configuration of the nitrogen atom. Therefore, these two conformers are also diastereomers, endowed with slightly different ionization energies. The ionization energy of THIQM_I, which shows an OH…N hydrogen bond, is slightly higher than that of THIQM_II. Their PECD spectra, although of identical signs, differ in shape and magnitude. Surprisingly, the anisotropy parameter is more sensitive than the PECD to the conformational isomerism at play in this system.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 6","pages":"064301"},"PeriodicalIF":2.3,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12596092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145483167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.","authors":"Sriram Srinivasa Raghavan, Keiko Shinoda, Eriko Nango, Florence Tama, Osamu Miyashita","doi":"10.1063/4.0000779","DOIUrl":"10.1063/4.0000779","url":null,"abstract":"<p><p>Time-resolved serial femtosecond crystallography (TR-SFX) is a technique designed to reveal the molecular dynamics underlying chemical reactions, thereby providing insights into the relationship between structure and function. By capturing a series of conformational changes in intermediate states, TR-SFX enables the visualization of dynamic structural transitions. In this study, we have presented a new approach for modeling reaction state conformations using molecular dynamics (MD) simulations. In this approach, MD simulations were first performed to generate a large number of conformational samples, which were then used as initial models for refinement against diffraction data from the triggered states, thereby facilitating the construction of accurate dynamic structure models. The derived models were evaluated using tools such as Edstats and MolProbity to identify models with high-quality geometries and local electron density metrics. This procedure provides a semi-automated approach for building dynamic structural models from TR-SFX data, ensuring their robustness for further exploration and understanding of macromolecular dynamics.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054701"},"PeriodicalIF":2.9,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12579552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145432900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anharmonic phonons in the high-temperature phase of KNiCl₃.","authors":"M J Gutmann, Kang Wang, Sun-Woo Kim, Bartomeu Monserrat, G L Pascut","doi":"10.1063/4.0000786","DOIUrl":"10.1063/4.0000786","url":null,"abstract":"<p><p>The high-temperature phase of the hexagonal halide perovskite KNiCl₃ is investigated using time-of-flight single crystal neutron diffraction at 633 K (360 °C). Phonons are captured through thermal diffuse scattering, integrated in energy but resolved in momentum. Harmonic phonon calculations based on density functional theory yield imaginary phonon frequencies for this phase, indicating the presence of structural instabilities at this level of theory. It is shown that the inclusion of anharmonic phonon-phonon interactions removes these instabilities, leading to good qualitative agreement with the experimental diffuse scattering. These results demonstrate that the high-temperature phase of KNiCl₃ is stabilized by anharmonic phonon-phonon interactions.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054103"},"PeriodicalIF":2.3,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12543366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SISYPHOS: An automatic procedure for the serial refinement of single-crystal diffraction data in Olex2.","authors":"Florian Meurer, Florian Kleemiss, Birgit Hischa, Daniel Brüx, Ann-Cathrin Koch, Michael Bodensteiner","doi":"10.1063/4.0000784","DOIUrl":"10.1063/4.0000784","url":null,"abstract":"<p><p>A program for serial handling of crystallographic data is presented within Olex2. Especially for small molecule electron and x-ray diffraction, the handling of several datasets of the same structure can be tedious and prone to errors, which can affect comparability. The program SISYPHOS allows for the individual refinement of a starting model against several recorded datasets (in \".hkl\" format) with adaptation to changes in the unit cell, wavelength, among other parameters. The program was tested for resonant diffraction (also known as anomalous dispersion), investigations on radiation damage, the benchmarking of different configurations for quantum crystallographic modeling, electron diffraction data, and for testing several datasets from the same measurement using various settings to identify the most suitable dataset.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054102"},"PeriodicalIF":2.3,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145233834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of 3D cryoEM single-particle reconstruction correctness and handedness with Ewald's sphere correction.","authors":"R Bromberg, Y Guo, D Borek, Z Otwinowski","doi":"10.1063/4.0000777","DOIUrl":"10.1063/4.0000777","url":null,"abstract":"<p><p>The correct description of quantum scattering places the observed scattering contributions on the Ewald's sphere and its Friedel mate copy. In electron microscopy, due to the large radius of the Ewald's sphere, these scattering contributions are typically merged during data analysis. We present an approach that separates and factorizes those contributions into real and imaginary components of the image. When an inverted solution is calculated, the map derived from the real component of the image generates an inverted solution, while the map derived from the imaginary component of the image generates an inverted and sign-flipped solution. Therefore, the sign of correlation between reconstructions derived from the real and imaginary components provides the automatic determination of handedness and additional validation for the quality of 3D reconstructions. The factorization and its implementation are robust enough to be routinely used in single-particle reconstructions, even at resolutions below the limit where the curvature of the Ewald's sphere affects the overall signal-to-noise ratio.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054301"},"PeriodicalIF":2.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12488216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spin dynamics in elemental Ni and Ni₈₅Co₁₅ thin films probed by high harmonic generated photons around the <i>M</i> _2,3 edges.","authors":"Juliette Dubois, Emmanuelle Jal, Carlos Rodriguez Cortez, Marcel Hennes, Renaud Delaunay, Guillaume Lambert, Boris Vodungbo","doi":"10.1063/4.0000769","DOIUrl":"10.1063/4.0000769","url":null,"abstract":"<p><p>We compared ultrafast spin dynamics in laser-excited Ni₈₅Co₁₅ alloy and pure Ni thin films exhibiting magnetic weak stripe domains using x-ray resonant magnetic scattering. By relying on extreme ultraviolet pulses obtained via high-harmonic generation, we simultaneously probed our samples using four energies around the Co and Ni <math> <mrow> <mrow> <msub><mrow><mi>M</mi></mrow> <mrow><mn>2</mn> <mo>,</mo> <mn>3</mn></mrow> </msub> </mrow> </mrow> </math> edges. Our results show a significant laser-induced reduction of the intensity of the magnetic scattering peaks on fs timescales and clearly highlight that this effect depends sensitively on the probing wavelength: different quenching amplitudes and characteristic timescales are found when changing the probing energy. More particularly, in our alloyed thin film, we observe a delay of about 17 fs in the scattered intensity dynamics between probing energies close to the Ni and Co edges, respectively. This delay is not observed in the pure Ni sample and is therefore most likely induced by the presence of Co in the thin film, reflecting the different ultrafast magnetic responses of the two 3<i>d</i> metals in these alloys.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054501"},"PeriodicalIF":2.9,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12440127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145082033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benchmarking crystal structure refinement: A systematic study on Hirshfeld atom refinement.","authors":"Daniel Brüx, Florian Meurer, Florian Kleemiss","doi":"10.1063/4.0000774","DOIUrl":"10.1063/4.0000774","url":null,"abstract":"<p><p>This study systematically investigates the influence of various parameters of the wavefunction calculation during Hirshfeld atom refinement (HAR). We aim to address the lack of consensus in the literature and conflicting information on a generally recommended procedure. A set of amino acid test structures, known for their immense biochemical importance and unimpeachable experimental data quality, was employed to ensure reliable results, unbiased by the question of insufficient diffraction data quality. A comprehensive permutation of refinement parameters was conducted to avoid overlooking potential influences, resulting in 2496 structure refinements per amino acid. Applying a solvent model systematically improved refinement results compared to gas-phase calculations. Additionally, it was observed that the pure Hartree-Fock method outperforms all tested density functional theory methods across all structures in this test set of polar-organic molecules. These findings underscore the importance of carefully considering the level of theory applied in HAR and offer an overview of the performance of various methods and parameters.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"12 5","pages":"054101"},"PeriodicalIF":2.3,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12422757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145041940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}