Structural Dynamics-Us最新文献

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Study of trioleoylglycerol two-layer and adiposome cross-section mimicking four-layer systems through atomic-level simulations. 通过原子级模拟研究三油酰甘油两层和脂肪体横截面模拟四层系统。
IF 2.3 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-12-05 eCollection Date: 2022-11-01 DOI: 10.1063/4.0000168
Ahmed Hammad Mirza
{"title":"Study of trioleoylglycerol two-layer and adiposome cross-section mimicking four-layer systems through atomic-level simulations.","authors":"Ahmed Hammad Mirza","doi":"10.1063/4.0000168","DOIUrl":"10.1063/4.0000168","url":null,"abstract":"<p><p>Adiposomes are artificially prepared lipid droplet (LD)-mimetic structures, which, unlike LDs, do not harbor proteins. The dynamics of interaction between triacylglycerols (TAGs), drug molecule, and phospholipids in adiposomes is currently not well-established. Trioleoylglycerol (TOG) molecule was divided into three parts: two oleoyl tails and one 2-monooleoylglycerol (MOG). Forcefield parameters for two oleoyl tails were adopted from the AMBER18 repository while that of the MOG forcefield was taken from the literature. Charge correction was performed on the MOG forcefield before its utilization. After charge correction, the resulting TOG molecule had zero charge. TOG bilayer (2L) and tetralayer (4L) systems were prepared and simulated. TOG bilayer (2L) systems-modeled from two different initial conformations, the TOG3 conformation and the TOG2:1 conformation-showed that TOG2:1 conformation was more prevailing irrespective of the starting conformation and was subsequently used in further simulations. The hydrated TOG 2L system showed TOG-water solution solubility of 0.051 mol L<sup>-1</sup> which is near experimental values. This validated the correct parameterization of the TOG molecule. The simulations of 4L systems showed stable membrane behaviors toward the end of simulations. It was also observed that in the 4L system, the TOG molecules showed the formation of micelles with the drug molecule. Almost six TOGs remained continuously in contact with the drug molecule throughout the simulation. The availability of charge-corrected TOG parameterization is expected to equip future studies with a framework for molecular dynamics simulations of adiposomes and/or LDs at the atomic level.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9726221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10372174","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}
引用次数: 0
Accurate quantification of lattice temperature dynamics from ultrafast electron diffraction of single-crystal films using dynamical scattering simulations. 利用动态散射模拟从单晶薄膜的超快电子衍射中精确量化晶格温度动态。
IF 2.3 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-12-05 eCollection Date: 2022-11-01 DOI: 10.1063/4.0000170
Daniel B Durham, Colin Ophus, Khalid M Siddiqui, Andrew M Minor, Daniele Filippetto
{"title":"Accurate quantification of lattice temperature dynamics from ultrafast electron diffraction of single-crystal films using dynamical scattering simulations.","authors":"Daniel B Durham, Colin Ophus, Khalid M Siddiqui, Andrew M Minor, Daniele Filippetto","doi":"10.1063/4.0000170","DOIUrl":"10.1063/4.0000170","url":null,"abstract":"<p><p>In ultrafast electron diffraction (UED) experiments, accurate retrieval of time-resolved structural parameters, such as atomic coordinates and thermal displacement parameters, requires an accurate scattering model. Unfortunately, kinematical models are often inaccurate even for relativistic electron probes, especially for dense, oriented single crystals where strong channeling and multiple scattering effects are present. This article introduces and demonstrates dynamical scattering models tailored for quantitative analysis of UED experiments performed on single-crystal films. As a case study, we examine ultrafast laser heating of single-crystal gold films. Comparison of kinematical and dynamical models reveals the strong effects of dynamical scattering within nm-scale films and their dependence on sample topography and probe kinetic energy. Applying to UED experiments on an 11 nm thick film using 750 keV electron probe pulses, the dynamical models provide a tenfold improvement over a comparable kinematical model in matching the measured UED patterns. Also, the retrieved lattice temperature rise is in very good agreement with predictions based on previously measured optical constants of gold, whereas fitting the Debye-Waller factor retrieves values that are more than three times lower. Altogether, these results show the importance of a dynamical scattering theory for quantitative analysis of UED and demonstrate models that can be practically applied to single-crystal materials and heterostructures.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9726223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10439320","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}
引用次数: 0
Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties. x射线自由电子激光单粒子成像对真实光源和探测器性能的预期分辨率限制。
IF 2.8 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-11-16 eCollection Date: 2022-11-01 DOI: 10.1063/4.0000169
Juncheng E, Y Kim, J Bielecki, M Sikorski, R de Wijn, C Fortmann-Grote, J Sztuk-Dambietz, J C P Koliyadu, R Letrun, H J Kirkwood, T Sato, R Bean, A P Mancuso, C Kim
{"title":"Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties.","authors":"Juncheng E,&nbsp;Y Kim,&nbsp;J Bielecki,&nbsp;M Sikorski,&nbsp;R de Wijn,&nbsp;C Fortmann-Grote,&nbsp;J Sztuk-Dambietz,&nbsp;J C P Koliyadu,&nbsp;R Letrun,&nbsp;H J Kirkwood,&nbsp;T Sato,&nbsp;R Bean,&nbsp;A P Mancuso,&nbsp;C Kim","doi":"10.1063/4.0000169","DOIUrl":"https://doi.org/10.1063/4.0000169","url":null,"abstract":"<p><p>The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions with this technique. The currently achievable resolution of SPI is limited to the sub-10 nanometer range, mainly due to background effects, such as instrumental noise and parasitic scattering from the carrier gas used for sample delivery. Recent theoretical studies have quantified the effects of x-ray pulse parameters, as well as the required number of diffraction patterns to achieve a certain resolution, in a 3D reconstruction, although the effects of detector noise and the random particle orientation in each diffraction snapshot were not taken into account. In this work, we show these shortcomings and address limitations on achievable image resolution imposed by the adaptive gain integrating pixel detector noise.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9675053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40480826","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}
引用次数: 4
Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy. 用时间分辨俄歇电子能谱探测甘氨酸中的电荷诱导化学动力学。
IF 2.8 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-11-08 eCollection Date: 2022-11-01 DOI: 10.1063/4.0000165
David Schwickert, Marco Ruberti, Přemysl Kolorenč, Andreas Przystawik, Slawomir Skruszewicz, Malte Sumfleth, Markus Braune, Lars Bocklage, Luis Carretero, Marie Kristin Czwalinna, Dian Diaman, Stefan Düsterer, Marion Kuhlmann, Steffen Palutke, Ralf Röhlsberger, Juliane Rönsch-Schulenburg, Sven Toleikis, Sergey Usenko, Jens Viefhaus, Anton Vorobiov, Michael Martins, Detlef Kip, Vitali Averbukh, Jon P Marangos, Tim Laarmann
{"title":"Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy.","authors":"David Schwickert,&nbsp;Marco Ruberti,&nbsp;Přemysl Kolorenč,&nbsp;Andreas Przystawik,&nbsp;Slawomir Skruszewicz,&nbsp;Malte Sumfleth,&nbsp;Markus Braune,&nbsp;Lars Bocklage,&nbsp;Luis Carretero,&nbsp;Marie Kristin Czwalinna,&nbsp;Dian Diaman,&nbsp;Stefan Düsterer,&nbsp;Marion Kuhlmann,&nbsp;Steffen Palutke,&nbsp;Ralf Röhlsberger,&nbsp;Juliane Rönsch-Schulenburg,&nbsp;Sven Toleikis,&nbsp;Sergey Usenko,&nbsp;Jens Viefhaus,&nbsp;Anton Vorobiov,&nbsp;Michael Martins,&nbsp;Detlef Kip,&nbsp;Vitali Averbukh,&nbsp;Jon P Marangos,&nbsp;Tim Laarmann","doi":"10.1063/4.0000165","DOIUrl":"https://doi.org/10.1063/4.0000165","url":null,"abstract":"<p><p>In the present contribution, we use x-rays to monitor charge-induced chemical dynamics in the photoionized amino acid glycine with femtosecond time resolution. The outgoing photoelectron leaves behind the cation in a coherent superposition of quantum mechanical eigenstates. Delayed x-ray pulses track the induced coherence through resonant x-ray absorption that induces Auger decay. Temporal modulation of the Auger electron signal correlated with specific ions is observed, which is governed by the initial electronic coherence and subsequent vibronic coupling to nuclear degrees of freedom. In the time-resolved x-ray absorption measurement, we monitor the time-frequency spectra of the resulting many-body quantum wave packets for a period of 175 fs along different reaction coordinates. Our experiment proves that by measuring specific fragments associated with the glycine dication as a function of the pump-probe delay, one can selectively probe electronic coherences at early times associated with a few distinguishable components of the broad electronic wave packet created initially by the pump pulse in the cation. The corresponding coherent superpositions formed by subsets of electronic eigenstates and evolving along parallel dynamical pathways show different phases and time periods in the range of <math><mrow><mo>(</mo> <mo>-</mo> <mn>0.3</mn> <mo>±</mo> <mn>0.1</mn> <mo>)</mo> <mi>π</mi> <mo>≤</mo> <mi>ϕ</mi> <mo>≤</mo> <mo>(</mo> <mn>0.1</mn> <mo>±</mo> <mn>0.2</mn> <mo>)</mo> <mi>π</mi></mrow> </math> and <math> <mrow> <msubsup><mrow><mn>18.2</mn></mrow> <mrow><mo>-</mo> <mn>1.4</mn></mrow> <mrow><mo>+</mo> <mn>1.7</mn></mrow> </msubsup> <mo>≤</mo> <mi>T</mi> <mo>≤</mo> <msubsup><mrow><mn>23.9</mn></mrow> <mrow><mo>-</mo> <mn>1.1</mn></mrow> <mrow><mo>+</mo> <mn>1.2</mn></mrow> </msubsup> </mrow> </math> fs. Furthermore, for long delays, the data allow us to pinpoint the driving vibrational modes of chemical dynamics mediating charge-induced bond cleavage along different reaction coordinates.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2022-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9646253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40481439","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}
引用次数: 1
Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle. 对洗涤剂胶束中的整体膜蛋白进行差异 X 射线散射观测的建模。
IF 2.3 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-10-31 eCollection Date: 2022-09-01 DOI: 10.1063/4.0000157
Daniel Sarabi, Lucija Ostojić, Robert Bosman, Adams Vallejos, Johanna-Barbara Linse, Michael Wulff, Matteo Levantino, Richard Neutze
{"title":"Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle.","authors":"Daniel Sarabi, Lucija Ostojić, Robert Bosman, Adams Vallejos, Johanna-Barbara Linse, Michael Wulff, Matteo Levantino, Richard Neutze","doi":"10.1063/4.0000157","DOIUrl":"10.1063/4.0000157","url":null,"abstract":"<p><p>Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9625836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40465526","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}
引用次数: 0
Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays. 高强度x射线照射下有机分子动力学的化学效应。
IF 2.8 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-10-31 eCollection Date: 2022-09-01 DOI: 10.1063/4.0000166
Sourav Banerjee, Zoltan Jurek, Malik Muhammad Abdullah, Robin Santra
{"title":"Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays.","authors":"Sourav Banerjee,&nbsp;Zoltan Jurek,&nbsp;Malik Muhammad Abdullah,&nbsp;Robin Santra","doi":"10.1063/4.0000166","DOIUrl":"https://doi.org/10.1063/4.0000166","url":null,"abstract":"<p><p>The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years. The present study aims for extending the XMDYN toolkit to treat chemical bonds using the reactive force field. In order to study its impact, a highly intense x-ray pulse was made to interact with the simplest amino acid, glycine. Different model variants were used to highlight the consequences of charge rearrangement and chemical bonds on the time evolution. The charge-rearrangement-enhanced x-ray ionization of molecules effect is also discussed to address the capability of a classical MD based approach, i.e., XMDYN, to capture such a molecular phenomenon.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2022-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9625838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40465527","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}
引用次数: 0
A machine learning photon detection algorithm for coherent x-ray ultrafast fluctuation analysis. 用于相干 X 射线超快波动分析的机器学习光子检测算法。
IF 2.3 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-10-17 eCollection Date: 2022-09-01 DOI: 10.1063/4.0000161
Sathya R Chitturi, Nicolas G Burdet, Youssef Nashed, Daniel Ratner, Aashwin Mishra, T J Lane, Matthew Seaberg, Vincent Esposito, Chun Hong Yoon, Mike Dunne, Joshua J Turner
{"title":"A machine learning photon detection algorithm for coherent x-ray ultrafast fluctuation analysis.","authors":"Sathya R Chitturi, Nicolas G Burdet, Youssef Nashed, Daniel Ratner, Aashwin Mishra, T J Lane, Matthew Seaberg, Vincent Esposito, Chun Hong Yoon, Mike Dunne, Joshua J Turner","doi":"10.1063/4.0000161","DOIUrl":"10.1063/4.0000161","url":null,"abstract":"<p><p>X-ray free electron laser experiments have brought unique capabilities and opened new directions in research, such as creating new states of matter or directly measuring atomic motion. One such area is the ability to use finely spaced sets of coherent x-ray pulses to be compared after scattering from a dynamic system at different times. This enables the study of fluctuations in many-body quantum systems at the level of the ultrafast pulse durations, but this method has been limited to a select number of examples and required complex and advanced analytical tools. By applying a new methodology to this problem, we have made qualitative advances in three separate areas that will likely also find application to new fields. As compared to the \"droplet-type\" models, which typically are used to estimate the photon distributions on pixelated detectors to obtain the coherent x-ray speckle patterns, our algorithm achieves an order of magnitude speedup on CPU hardware and two orders of magnitude improvement on GPU hardware. We also find that it retains accuracy in low-contrast conditions, which is the typical regime for many experiments in structural dynamics. Finally, it can predict photon distributions in high average-intensity applications, a regime which up until now has not been accessible. Our artificial intelligence-assisted algorithm will enable a wider adoption of x-ray coherence spectroscopies, by both automating previously challenging analyses and enabling new experiments that were not otherwise feasible without the developments described in this work.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2022-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9583189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40664775","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}
引用次数: 0
Ultrafast electron diffraction from transiently aligned asymmetric top molecules: Rotational dynamics and structure retrieval. 瞬时排列的不对称顶分子的超快电子衍射:旋转动力学和结构检索。
IF 2.3 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-10-17 eCollection Date: 2022-09-01 DOI: 10.1063/4.0000163
Kyle J Wilkin, Yanwei Xiong, Haoran Zhao, Sri Bhavya Muvva, Sajib Kumar Saha, Martin Centurion
{"title":"Ultrafast electron diffraction from transiently aligned asymmetric top molecules: Rotational dynamics and structure retrieval.","authors":"Kyle J Wilkin, Yanwei Xiong, Haoran Zhao, Sri Bhavya Muvva, Sajib Kumar Saha, Martin Centurion","doi":"10.1063/4.0000163","DOIUrl":"10.1063/4.0000163","url":null,"abstract":"<p><p>Ultrafast electron diffraction (UED) from aligned molecules in the gas phase has successfully retrieved structures of both linear and symmetric top molecules. Alignment of asymmetric tops has been recorded with UED but no structural information was retrieved. We present here the extraction of two-dimensional structural information from simple transformations of experimental diffraction patterns of aligned molecules as a proof-of-principle for the recovery of the full structure. We align 4-fluorobenzotrifluoride with a linearly polarized laser and show that we can distinguish between atomic pairs with equal distances that are parallel and perpendicular to the aligned axis. We additionally show with numerical simulations that by cooling the molecules to a rotational temperature of 1 K, more distances and angles can be resolved through direct transformations.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2022-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9578756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40660384","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}
引用次数: 0
Picosecond infrared laser driven sample delivery for simultaneous liquid-phase and gas-phase electron diffraction studies. 皮秒红外激光驱动样品同时输送液相和气相电子衍射研究。
IF 2.8 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-09-16 eCollection Date: 2022-09-01 DOI: 10.1063/4.0000159
Zhipeng Huang, Meghanad Kayanattil, Stuart A Hayes, R J Dwayne Miller
{"title":"Picosecond infrared laser driven sample delivery for simultaneous liquid-phase and gas-phase electron diffraction studies.","authors":"Zhipeng Huang,&nbsp;Meghanad Kayanattil,&nbsp;Stuart A Hayes,&nbsp;R J Dwayne Miller","doi":"10.1063/4.0000159","DOIUrl":"https://doi.org/10.1063/4.0000159","url":null,"abstract":"<p><p>Here, we report on a new approach based on laser driven molecular beams that provides simultaneously nanoscale liquid droplets and gas-phase sample delivery for femtosecond electron diffraction studies. The method relies on Picosecond InfraRed Laser (PIRL) excitation of vibrational modes to strongly drive phase transitions under energy confinement by a mechanism referred to as Desorption by Impulsive Vibrational Excitation (DIVE). This approach is demonstrated using glycerol as the medium with selective excitation of the OH stretch region for energy deposition. The resulting plume was imaged with both an ultrafast electron gun and a pulsed bright-field optical microscope to characterize the sample source simultaneously under the same conditions with time synchronization equivalent to sub-micrometer spatial resolution in imaging the plume dynamics. The ablation front gives the expected isolated gas phase, whereas the trailing edge of the plume is found to consist of nanoscale liquid droplets to thin films depending on the excitation conditions. Thus, it is possible by adjusting the timing to go continuously from probing gas phase to solution phase dynamics in a single experiment with 100% hit rates and very low sample consumption (<100 nl per diffraction image). This approach will be particularly interesting for biomolecules that are susceptible to denaturation in turbulent flow, whereas PIRL-DIVE has been shown to inject molecules as large as proteins into the gas phase fully intact. This method opens the door as a general approach to atomically resolving solution phase chemistry as well as conformational dynamics of large molecular systems and allow separation of the solvent coordinate on the dynamics of interest.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9482465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40370767","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}
引用次数: 0
Structure and dynamics of supercooled water in the hydration layer of poly(ethylene glycol). 聚乙二醇水化层中过冷水的结构与动力学。
IF 2.8 2区 物理与天体物理
Structural Dynamics-Us Pub Date : 2022-09-08 eCollection Date: 2022-09-01 DOI: 10.1063/4.0000158
Yuqing Li, Zehua Han, Changli Ma, Liang Hong, Yanwei Ding, Ye Chen, Junpeng Zhao, Dong Liu, Guangai Sun, Taisen Zuo, He Cheng, Charles C Han
{"title":"Structure and dynamics of supercooled water in the hydration layer of poly(ethylene glycol).","authors":"Yuqing Li,&nbsp;Zehua Han,&nbsp;Changli Ma,&nbsp;Liang Hong,&nbsp;Yanwei Ding,&nbsp;Ye Chen,&nbsp;Junpeng Zhao,&nbsp;Dong Liu,&nbsp;Guangai Sun,&nbsp;Taisen Zuo,&nbsp;He Cheng,&nbsp;Charles C Han","doi":"10.1063/4.0000158","DOIUrl":"https://doi.org/10.1063/4.0000158","url":null,"abstract":"<p><p>The statics and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) (PEG) were studied by a combination of quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. Two samples, that is, hydrogenated PEG/deuterated water (h-PEG/D<sub>2</sub>O) and fully deuterated PEG/hydrogenated water (d-PEG/H<sub>2</sub>O) with the same molar ratio of ethylene glycol (EG) monomer to water, 1:1, are compared. The QENS data of h-PEG/D<sub>2</sub>O show the dynamics of PEG, and that of d-PEG/H<sub>2</sub>O reveals the motion of water. The temperature-dependent elastic scattering intensity of both samples has shown transitions at supercooled temperature, and these transition temperatures depend on the energy resolution of the instruments. Therefore, neither one is a phase transition, but undergoes dynamic process. The dynamic of water can be described as an Arrhenius to super-Arrhenius transition, and it reveals the hydrogen bonding network relaxation of hydration water around PEG at supercooled temperature. Since the PEG-water hydrogen bond structural relaxation time from MD is in good agreement with the average relaxation time from QENS (d-PEG/H<sub>2</sub>O), MD may further reveal the atomic pictures of the supercooled hydration water. It shows that hydration water molecules form a series of pools around the hydrophilic oxygen atom of PEG. At supercooled temperature, they have a more bond ordered structure than bulk water, proceed a trapping sites diffusion on the PEG surface, and facilitate the structural relaxation of PEG backbone.</p>","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9462885/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33459684","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}
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