Structural Dynamics-Us最新文献

英文中文

A versatile experimental system for tracking ultrafast chemical reactions with X-ray free-electron lasers 用X射线自由电子激光器跟踪超快化学反应的通用实验系统

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-09-01 DOI: 10.1063/1.5111795

T. Katayama, S. Nozawa, Y. Umena, Sung-Hak Lee, T. Togashi, S. Owada, M. Yabashi

An experimental system, SPINETT (SACLA Pump-probe INstrumEnt for Tracking Transient dynamics), dedicated for ultrafast pump-probe experiments using X-ray free-electron lasers has been developed. SPINETT consists of a chamber operated under 1 atm helium pressure, two Von Hamos spectrometers, and a large two-dimensional detector having a short work distance. This platform covers complementary X-ray techniques; one can perform time-resolved X-ray absorption spectroscopy, time-resolved X-ray emission spectroscopy, and time-resolved X-ray diffuse scattering. Two types of liquid injectors have been prepared for low-viscosity chemical solutions and for protein microcrystals embedded in a matrix. We performed a test experiment at SPring-8 Angstrom Compact free-electron LAser and demonstrated the capability of SPINETT to obtain the local electronic structure and geometrical information simultaneously.

已经开发了一个实验系统SPINETT（SACLA泵浦探针INstrumEnt用于跟踪瞬态动力学），专门用于使用X射线自由电子激光器的超快泵浦探针实验。SPINETT由一个在1 大气压氦气、两个Von Hamos光谱仪和一个工作距离短的大型二维探测器。该平台涵盖补充X射线技术；可以执行时间分辨的X射线吸收光谱、时间分辨的X-射线发射光谱和时间分辨的X-射线扩散散射。已经为低粘度化学溶液和嵌入基质中的蛋白质微晶制备了两种类型的液体注射器。我们在SPring-8 Angstrom Compact自由电子激光器上进行了测试实验，证明了SPINETT同时获得局部电子结构和几何信息的能力。

引用次数: 12

New insights and innovation from a million crystal structures in the Cambridge Structural Database. 剑桥结构数据库中一百万个晶体结构的新见解和创新。

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-08-28 eCollection Date: 2019-09-01 DOI: 10.1063/1.5116878

Jason C Cole, Seth Wiggin, Francesca Stanzione

The Cambridge Structural Database (CSD) is the world's largest and most comprehensive collection of organic, organometallic, and metal-organic crystal structure information. Analyses using the data have wide impact across the chemical sciences in allowing understanding of structural preferences. In this short review, we illustrate the more common methods by which CSD data influence molecular design. We show how more data could lead to more refined insights into the future using a simple example of trifluoromethylphenyl fragments, highlighting how with sufficient data one can build a reasonable model of geometric change in a chemical fragment with torsional rotation, and show some recent examples where the CSD has been used in conjunction with other methods to provide design ideas and more computationally tractable workflows for derivation of useful insights into structural design.

剑桥结构数据库（CSD）是世界上最大、最全面的有机、有机金属和金属有机晶体结构信息集合。使用这些数据进行的分析在理解结构偏好方面对整个化学科学产生了广泛的影响。在这篇简短的综述中，我们展示了CSD数据影响分子设计的更常见方法。我们用一个三氟甲基苯基片段的简单例子展示了更多的数据如何能够对未来产生更精细的见解，强调了如何在有足够数据的情况下，建立一个合理的扭转旋转化学片段几何变化模型，并展示了一些最近的例子，其中CSD已与其他方法结合使用，以提供设计思想和更易于计算的工作流程，从而导出对结构设计的有用见解。

引用次数: 12

Structure determination of the tetracene dimer in helium nanodroplets using femtosecond strong-field ionization. 飞秒强场电离法测定氦纳米液滴中丁烯二聚体的结构。

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-08-27 eCollection Date: 2019-07-01 DOI: 10.1063/1.5118005

Constant Schouder, Adam S Chatterley, Florent Calvo, Lars Christiansen, Henrik Stapelfeldt

Dimers of tetracene molecules are formed inside helium nanodroplets and identified through covariance analysis of the emission directions of kinetic tetracene cations stemming from femtosecond laser-induced Coulomb explosion. Next, the dimers are aligned in either one or three dimensions under field-free conditions by a nonresonant, moderately intense laser pulse. The experimental angular covariance maps of the tetracene ions are compared to calculated covariance maps for seven different dimer conformations and found to be consistent with four of these. Additional measurements of the alignment-dependent strong-field ionization yield of the dimer narrow the possible conformations down to either a slipped-parallel or parallel-slightly rotated structure. According to our quantum chemistry calculations, these are the two most stable gas-phase conformations of the dimer and one of them is favorable for singlet fission.

丁烯分子的二聚体在氦纳米液滴内形成，并通过对飞秒激光诱导的库仑爆炸产生的动力学丁烯阳离子发射方向的协方差分析进行识别。接下来，在无场条件下，通过非共振、中等强度的激光脉冲，在一维或三维上排列二聚体。将丁烯离子的实验角协方差图与七种不同二聚体构象的计算协方差图进行比较，发现与其中四种构象一致。二聚体的取向依赖性强场电离产率的额外测量将可能的构象缩小到滑动平行或平行轻微旋转的结构。根据我们的量子化学计算，这是二聚体最稳定的两种气相构象，其中一种有利于单线态裂变。

引用次数: 16

Exploring the multiparameter nature of EUV-visible wave mixing at the FERMI FEL. 探索FERMI FEL中EUV可见波混合的多参数性质。

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-07-29 eCollection Date: 2019-07-01 DOI: 10.1063/1.5111501

L Foglia, F Capotondi, H Höppner, A Gessini, L Giannessi, G Kurdi, I Lopez Quintas, C Masciovecchio, M Kiskinova, R Mincigrucci, D Naumenko, I P Nikolov, E Pedersoli, G M Rossi, A Simoncig, F Bencivenga

The rapid development of extreme ultraviolet (EUV) and x-ray ultrafast coherent light sources such as free electron lasers (FELs) has triggered the extension of wave-mixing techniques to short wavelengths. This class of experiments, based on the interaction of matter with multiple light pulses through the Nth order susceptibility, holds the promise of combining intrinsic ultrafast time resolution and background-free signal detection with nanometer spatial resolution and chemical specificity. A successful approach in this direction has been the combination of the unique characteristics of the seeded FEL FERMI with dedicated four-wave-mixing (FWM) setups, which leads to the demonstration of EUV-based transient grating (TG) spectroscopy. In this perspective paper, we discuss how the TG approach can be extended toward more general FWM spectroscopies by exploring the intrinsic multiparameter nature of nonlinear processes, which derives from the ability of controlling the properties of each field independently.

极紫外（EUV）和x射线超快相干光源（如自由电子激光器）的快速发展引发了波混频技术向短波长的扩展。这类实验基于物质与多个光脉冲通过N阶磁化率的相互作用，有望将固有的超快时间分辨率和无背景信号检测与纳米空间分辨率和化学特异性相结合。这方面的一个成功方法是将种子FEL FERMI的独特特性与专用的四波混频（FWM）装置相结合，从而展示了基于EUV的瞬态光栅（TG）光谱。在这篇前瞻性的论文中，我们讨论了如何通过探索非线性过程的内在多参数性质，将TG方法扩展到更通用的FWM光谱，这源于独立控制每个场的性质的能力。

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引用次数: 3

FACT and FAIR with Big Data allows objectivity in science: The view of crystallography 大数据的事实和公平使得科学客观:晶体学的观点

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-07-20 DOI: 10.1063/1.5124439

J. Helliwell

A publication is an important narrative of the work done and interpretations made by researchers securing a scientific discovery. As The Royal Society neatly states though, “Nullius in verba” (“Take nobody's word for it”), whereby the role of the underpinning data is paramount. Therefore, the objectivity that preserving that data within the article provides is due to readers being able to check the calculation decisions of the authors. But how to achieve full data archiving? This is the raw data archiving challenge, in size and need for correct metadata. Processed diffraction data and final derived molecular coordinates archiving in crystallography have achieved an exemplary state of the art relative to most fields. One can credit IUCr with developing exemplary peer review procedures, of narrative, underpinning structure factors and coordinate data and validation report, through its checkcif development and submission system introduced for Acta Cryst. C and subsequently developed for its other chemistry journals. The crystallographic databases likewise have achieved amazing success and sustainability these last 50 years or so. The wider science data scene is celebrating the FAIR data accord, namely, that data be Findable, Accessible, Interoperable, and Reusable [Wilkinson et al., “Comment: The FAIR guiding principles for scientific data management and stewardship,” Sci. Data 3, 160018 (2016)]. Some social scientists also emphasize more than FAIR being needed, the data should be “FACT,” which is an acronym meaning Fair, Accurate, Confidential, and Transparent [van der Aalst et al., “Responsible data science,” Bus Inf. Syst. Eng. 59(5), 311–313 (2017)], this being the issue of ensuring reproducibility not just reusability. (Confidentiality of data not likely being relevant to our data obviously.) Acta Cryst. B, C, E, and IUCrData are the closest I know to being both FACT and FAIR where I repeat for due emphasis: the narrative, the automatic “general” validation checks, and the underpinning data are checked thoroughly by subject specialists (i.e., the specialist referees). IUCr Journals are also the best that I know of for encouraging and then expediting the citation of the DOI for a raw diffraction dataset in a publication; examples can be found in IUCrJ, Acta Cryst D, and Acta Cryst F. The wish for a checkcif for raw diffraction data has been championed by the IUCr Diffraction Data Deposition Working Group and its successor, the IUCr Committee on Data.

出版物是对研究人员为确保科学发现所做工作和所做解释的重要叙述。然而，正如英国皇家学会巧妙地指出的那样，“Nullius in verba”（“不相信任何人的话”），即基础数据的作用至关重要。因此，在文章中保留这些数据所提供的客观性是因为读者能够检查作者的计算决策。但是如何实现完整的数据归档呢？这是原始数据归档的难题，在大小和对正确元数据的需求方面都是如此。晶体学中经过处理的衍射数据和最终导出的分子坐标存档已经实现了相对于大多数领域的示例性技术状态。通过为Acta Cryst引入的checkcif开发和提交系统，IUCr开发了示例性的同行评审程序，包括叙述、基础结构因素以及协调数据和验证报告。C，随后为其其他化学期刊开发。在过去的50年里，晶体学数据库同样取得了惊人的成功和可持续性更广泛的科学数据领域正在庆祝FAIR数据协议，即数据是可查找、可访问、可互操作和可重复使用的[Wilkinson等人，“评论：科学数据管理和管理的FAIR指导原则”，《科学数据》316018（2016）]。一些社会科学家还强调，除了需要FAIR之外，数据还应该是“FACT”，这是一个缩写词，意思是公平、准确、机密和透明[van der Aalst et al.，“负责任的数据科学”，Bus Inf.Syst.Eng.59（5），311-313（2017）]，这是确保再现性而不仅仅是可重用性的问题。（数据的保密性显然与我们的数据无关。）《晶体报》。B、 C、E和IUCrData是我所知道的最接近FACT和FAIR的数据，我在这里重复强调：叙述、自动“一般”验证检查和基础数据由主题专家（即专家裁判）彻底检查。IUCr期刊也是我所知道的最好的期刊，它鼓励并加快了出版物中原始衍射数据集的DOI引用；实例可在IUCrJ、Acta Cryst D和Acta Crystal F中找到。IUCr衍射数据沉积工作组及其继任者IUCr数据委员会一直支持对原始衍射数据进行核对。

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引用次数: 7

Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization 同步加速器自然偏振的时间分辨瞬态圆二色光谱

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-07-02 DOI: 10.1063/1.5120346

François Auvray, D. Dennetiere, A. Giuliani, F. Jamme, F. Wien, B. Nay, S. Zirah, F. Polack, C. Menneglier, B. Lagarde, J. Hirst, M. Réfrégiers

Ultraviolet (UV) synchrotron radiation circular dichroism (SRCD) spectroscopy has made an important contribution to the determination and understanding of the structure of bio-molecules. In this paper, we report an innovative approach that we term time-resolved SRCD (tr-SRCD), which overcomes the limitations of current broadband UV SRCD setups. This technique allows accessing ultrafast time scales (down to nanoseconds), previously measurable only by other methods, such as infrared (IR), nuclear magnetic resonance (NMR), fluorescence and absorbance spectroscopies, and small angle X-ray scattering (SAXS). The tr-SRCD setup takes advantage of the natural polarization of the synchrotron radiation emitted by a bending magnet to record broadband UV CD faster than any current SRCD setup, improving the acquisition speed from 10 mHz to 130 Hz and the accessible temporal resolution by several orders of magnitude. We illustrate the new approach by following the isomer concentration changes of an azopeptide after a photoisomerization. This breakthrough in SRCD spectroscopy opens up a wide range of potential applications to the detailed characterization of biological processes, such as protein folding and protein-ligand binding.

紫外（UV）同步辐射圆二色性（SRCD）光谱对生物分子结构的测定和理解做出了重要贡献。在本文中，我们报告了一种创新的方法，我们称之为时间分辨SRCD（tr SRCD），它克服了当前宽带UV SRCD设置的局限性。这项技术允许访问超快的时间尺度（低至纳秒），以前只能通过其他方法测量，如红外（IR）、核磁共振（NMR）、荧光和吸收光谱以及小角度X射线散射（SAXS）。tr SRCD装置利用弯曲磁体发射的同步辐射的自然偏振，以比任何当前SRCD装置更快的速度记录宽带UV CD，将采集速度从10mHz提高到130 Hz和几个数量级的可访问时间分辨率。我们通过跟踪偶氮肽在光异构化后的异构体浓度变化来说明新方法。SRCD光谱的这一突破为生物过程的详细表征开辟了广泛的潜在应用，如蛋白质折叠和蛋白质配体结合。

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引用次数: 15

Hole dynamics in a photovoltaic donor-acceptor couple revealed by simulated time-resolved X-ray absorption spectroscopy 用模拟时间分辨X射线吸收光谱揭示光伏施主-受主对中的空穴动力学

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-07-01 DOI: 10.1063/1.5097653

Khadijeh Khalili, L. Inhester, C. Arnold, R. Welsch, J. W. Andreasen, R. Santra

Theoretical and experimental methodologies that can characterize electronic and nuclear dynamics, and the coupling between the two, are needed to understand photoinduced charge transfer in molecular building blocks used in organic photovoltaics. Ongoing developments in ultrafast pump-probe techniques such as time-resolved X-ray absorption spectroscopy, using an X-ray free electron laser in combination with an ultraviolet femtosecond laser, present desirable probes of coupled electronic and nuclear dynamics. In this work, we investigate the charge transfer dynamics of a donor-acceptor pair, which is widely used as a building block in low bandgap block copolymers for organic photovoltaics. We simulate the dynamics of the benzothiadiazole-thiophene molecule upon photoionization with a vacuum ultraviolet (VUV) pulse and study the potential of probing the subsequent charge dynamics using time-resolved X-ray absorption spectroscopy. The photoinduced dynamics are calculated using on-the-fly nonadiabatic molecular dynamics simulations based on Tully's Fewest Switches Surface Hopping approach. We calculate the X-ray absorption spectrum as a function of time after ionization at the Hartree-Fock level. The changes in the time-resolved X-ray absorption spectrum at the sulfur K-edge reveal the ultrafast charge carrier dynamics in the molecule occurring on a femtosecond time scale. These theoretical findings anticipate that ultrafast time-resolved X-ray absorption spectroscopy using an X-ray probe in combination with a VUV pump offers a new approach to investigate the detailed dynamics of organic photovoltaic materials.

要理解用于有机光伏发电的分子构件中的光诱导电荷转移，需要能够表征电子和核动力学以及两者之间耦合的理论和实验方法。超快泵浦探测技术的持续发展，如时间分辨x射线吸收光谱，使用x射线自由电子激光器与紫外飞秒激光器相结合，提供了理想的耦合电子和核动力学探针。在这项工作中，我们研究了一个供体-受体对的电荷转移动力学，它被广泛用于有机光伏电池的低带隙嵌段共聚物。我们模拟了苯并噻唑-噻吩分子在真空紫外(VUV)脉冲光电离时的动力学，并研究了利用时间分辨x射线吸收光谱探测后续电荷动力学的潜力。利用基于Tully最小开关表面跳变方法的动态非绝热分子动力学模拟计算了光致动力学。我们计算了电离后在Hartree-Fock能级的x射线吸收光谱作为时间的函数。硫k边的时间分辨x射线吸收谱的变化揭示了分子中发生在飞秒时间尺度上的超快载流子动力学。这些理论发现预示着使用x射线探针与VUV泵相结合的超快时间分辨x射线吸收光谱为研究有机光伏材料的详细动力学提供了一种新的方法。

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引用次数: 10

Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers? 辐射损伤是x射线自由电子激光高分辨率单粒子成像的限制因素吗?

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-07-01 DOI: 10.1063/1.5098309

C. Östlin, N. Tîmneanu, C. Caleman, A. V. Martin

The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors for achieving subnanometer X-ray imaging of single particles and that X-ray pulses need to be as short as possible. Based on the molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs, and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of high-resolution single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.

原子分辨率单粒子成像的前景是X射线自由电子激光器发展的科学驱动因素之一。从一开始就认为，强X射线脉冲对样品造成的损伤是实现单粒子亚纳米X射线成像的限制因素之一，并且X射线脉冲需要尽可能短。基于蛋白质在不同持续时间（5fs、25fs和50fs）的X射线场中的分子动力学模拟，我们表明，由辐射损伤引起的衍射信号中的噪声小于其他来源的预期，例如样品的不均匀性和X射线发射到发射的变化。这些发现显示了使用自由电子激光器进行高分辨率单粒子成像的可行性的另一个方面，其中使用更长持续时间的X射线脉冲仍然可以提供高于库仑爆炸噪声的有用衍射信号。

引用次数: 11

Condensation of ground state from a supercooled phase in the Si(111)-(4 × 1) → (8 × 2)-indium atomic wire system Si(111)-(4 × 1)→(8 × 2)-铟原子线体系中过冷相的基态冷凝

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-07-01 DOI: 10.1063/1.5111636

B. Hafke, T. Witte, D. Janoschka, P. Dreher, F. Meyer Zu Heringdorf, M. Horn-von Hoegen

Strong optical irradiation of indium atomic wires on a Si(111) surface causes the nonthermal structural transition from the (8 × 2) reconstructed ground state to an excited (4 × 1) state. The immediate recovery of the system to the ground state is hindered by an energy barrier for the collective motion of the indium atoms along the reaction coordinate from the (4 × 1) to the (8 × 2) state. This metastable, supercooled state can only recover through nucleation of the ground state at defects like adsorbates or step edges. Subsequently, a recovery front propagates with constant velocity across the surface and the (8 × 2) ground state is reinstated. In a combined femtosecond electron diffraction and photoelectron emission microscopy study, we determined—based on the step morphology—a velocity of this recovery front of ∼100 m/s.

铟原子线在Si（111）表面上的强光辐照导致从（8） × 2）重建基态到激发态（4 × 1）州。系统立即恢复到基态受到铟原子沿着反应坐标从（4）集体运动的能垒的阻碍 × 1）至（8 × 2）州。这种亚稳的过冷状态只能通过吸附质或台阶边缘等缺陷处基态的成核来恢复。随后，恢复锋以恒定速度在地表和（8 × 2）地面状态恢复。在飞秒电子衍射和光电子发射显微镜的联合研究中，我们根据台阶形态确定了这种恢复前沿的速度为～100 m/s。

引用次数: 2

Establishment of the Structural Equation of Motion 结构运动方程的建立

IF 2.8 2区物理与天体物理 Q3 CHEMISTRY, PHYSICAL

Structural Dynamics-Us

Pub Date : 2019-06-28 DOI: 10.1002/9781119605775.ch2

引用次数: 0

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