Structural Dynamics最新文献_第3页

BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules BioCARS：用于探测生物大分子结构动力学的同步加速器设施

Structural Dynamics Pub Date : 2024-01-31 DOI: 10.1063/4.0000238

Robert W. Henning, Irina Kosheleva, Vukica Šrajer, In-Sik Kim, Eric Zoellner, Rama Ranganathan

{"title":"BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules","authors":"Robert W. Henning, Irina Kosheleva, Vukica Šrajer, In-Sik Kim, Eric Zoellner, Rama Ranganathan","doi":"10.1063/4.0000238","DOIUrl":"https://doi.org/10.1063/4.0000238","url":null,"abstract":"A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139658481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthesis technique and electron beam damage study of nanometer-thin single-crystalline thymine 纳米薄单晶胸腺嘧啶的合成技术和电子束损伤研究

Structural Dynamics Pub Date : 2024-01-31 DOI: 10.1063/4.0000221

Hazem Daoud, Sreelaja Pulleri Vadhyar, Ehsan Nikbin, Cheng Lu, R. J. Dwayne Miller

{"title":"Synthesis technique and electron beam damage study of nanometer-thin single-crystalline thymine","authors":"Hazem Daoud, Sreelaja Pulleri Vadhyar, Ehsan Nikbin, Cheng Lu, R. J. Dwayne Miller","doi":"10.1063/4.0000221","DOIUrl":"https://doi.org/10.1063/4.0000221","url":null,"abstract":"Samples suitable for electron diffraction studies must satisfy certain characteristics such as having a thickness in the range of 10–100 nm. We report, to our knowledge, the first successful synthesis technique of nanometer-thin sheets of single-crystalline thymine suitable for electron diffraction and spectroscopy studies. This development provides a well-defined system to explore issues related to UV photochemistry of DNA and high intrinsic stability essential to maintaining integrity of genetic information. The crystals are grown using the evaporation technique, and the nanometer-thin sheets are obtained via microtoming. The sample is characterized via x-ray diffraction and is subsequently studied using electron diffraction via a transmission electron microscope. Thymine is found to be more radiation resistant than similar molecular moieties (e.g., carbamazepine) by a factor of 5. This raises interesting questions about the role of the fast relaxation processes of electron scattering-induced excited states, extending the concept of radiation hardening beyond photoexcited states. The high stability of thymine in particular opens the door for further studies of these ultrafast relaxation processes giving rise to the high stability of DNA to UV radiation.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139658476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Toward ultrafast soft x-ray spectroscopy of organic photovoltaic devices 实现有机光伏设备的超快软 X 射线光谱学

Structural Dynamics Pub Date : 2024-01-19 DOI: 10.1063/4.0000214

Douglas Garratt, Mary Matthews, Jon Marangos

引用次数: 0

Angle-resolved photoelectron spectroscopy in a low-energy electron microscope 低能电子显微镜中的角度分辨光电子能谱学

Structural Dynamics Pub Date : 2023-12-29 DOI: 10.1063/4.0000216

Alexander Neuhaus, Pascal Dreher, Florian Schütz, Helder Marchetto, Torsten Franz, Frank Meyer zu Heringdorf

引用次数: 0

Few-femtosecond electronic and structural rearrangements of CH4+ driven by the Jahn–Teller effect 由贾恩-泰勒效应驱动的 CH4+ 几飞秒电子和结构重排

Structural Dynamics Pub Date : 2023-12-15 DOI: 10.1063/4.0000217

Kristina S. Zinchenko, Fernando Ardana-Lamas, Valentina Utrio Lanfaloni, Nicholas Monahan, Issaka Seidu, Michael S. Schuurman, Simon P. Neville, Hans Jakob Wörner

{"title":"Few-femtosecond electronic and structural rearrangements of CH4+ driven by the Jahn–Teller effect","authors":"Kristina S. Zinchenko, Fernando Ardana-Lamas, Valentina Utrio Lanfaloni, Nicholas Monahan, Issaka Seidu, Michael S. Schuurman, Simon P. Neville, Hans Jakob Wörner","doi":"10.1063/4.0000217","DOIUrl":"https://doi.org/10.1063/4.0000217","url":null,"abstract":"The Jahn–Teller effect (JTE) is central to the understanding of the physical and chemical properties of a broad variety of molecules and materials. Whereas the manifestations of the JTE in stationary properties of matter are relatively well studied, the study of JTE-induced dynamics is still in its infancy, largely owing to its ultrafast and non-adiabatic nature. For example, the time scales reported for the distortion of CH4+ from the initial Td geometry to a nominal C2v relaxed structure range from 1.85 fs over 10 ± 2 fs to 20 ± 7 fs. Here, by combining element-specific attosecond transient-absorption spectroscopy and quantum-dynamics simulations, we show that the initial electronic relaxation occurs within 5 fs and that the subsequent nuclear dynamics are dominated by the Q2 scissoring and Q1 symmetric stretching modes, which dephase in 41 ± 10 fs and 13 ± 3 fs, respectively. Significant structural relaxation is found to take place only along the e-symmetry Q2 mode. These results demonstrate that CH4+ created by ionization of CH4 is best thought of as a highly fluxional species that possesses a long-time-averaged vibrational distribution centered around a D2d structure. The methods demonstrated in our work provide guidelines for the understanding of Jahn–Teller driven non-adiabatic dynamics in other more complex systems.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Observations on Laue diffraction within synchrotron radiation and neutron macromolecular crystallography research and developments 同步辐射和中子大分子晶体学研究与发展中的 Laue 衍射观察

Structural Dynamics Pub Date : 2023-12-15 DOI: 10.1063/4.0000225

John R. Helliwell

引用次数: 0

Theoretical study of time-resolved photoelectron circular dichroism in the photodissociation of a chiral molecule 手性分子光解过程中时间分辨光电子圆二色性的理论研究

Structural Dynamics Pub Date : 2023-12-15 DOI: 10.1063/4.0000213

Marit R. Fiechter, Vít Svoboda, Hans Jakob Wörner

{"title":"Theoretical study of time-resolved photoelectron circular dichroism in the photodissociation of a chiral molecule","authors":"Marit R. Fiechter, Vít Svoboda, Hans Jakob Wörner","doi":"10.1063/4.0000213","DOIUrl":"https://doi.org/10.1063/4.0000213","url":null,"abstract":"Photoelectron circular dichroism (PECD), the forward–backward asymmetry of the photoelectron angular distribution when ionizing randomly oriented chiral molecules with circularly polarized light, is an established method to investigate chiral properties of molecules in their electronic ground state. Here, we develop a computational strategy for predicting time-resolved PECD (TRPECD) of chemical reactions and demonstrate the method on the photodissociation of 1-iodo-2-methylbutane. Our approach combines multi-configurational quantum-chemical calculations of the relevant potential-energy surfaces of the neutral and singly ionized molecule with ab initio molecular-dynamics (AIMD) calculations. The PECD parameters along the AIMD trajectories are calculated with the aid of electron-molecule scattering calculations based on the Schwinger variational principle implemented in ePolyScat. Our calculations have been performed for two probe wavelengths (133 and 160 nm) accessible through low-order harmonic generation in gases. Our results show that the TRPECD is a highly sensitive probe of photochemical reaction dynamics. Most interestingly, the TRPECD is found to change sign multiple times along the photodissociation coordinate, in agreement with recent experiments on CHBrFI [Svoboda et al., “Femtosecond photoelectron circular dichroism of chemical reactions,” Sci. Adv. 8, eabq2811 (2022)]. The computational protocol introduced in the present work is general and readily applicable to other chiral photochemical processes.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Simulation of ultrafast electron diffraction intensity under coherent acoustic phonons 相干声子下超快电子衍射强度的模拟

Structural Dynamics Pub Date : 2023-11-01 DOI: 10.1063/4.0000199

Yongzhao Zhang, Jun Li, Wentao Wang, Huanfang Tian, Wenli Gao, Jianqi Li, Shuaishuai Sun, Huaixin Yang

{"title":"Simulation of ultrafast electron diffraction intensity under coherent acoustic phonons","authors":"Yongzhao Zhang, Jun Li, Wentao Wang, Huanfang Tian, Wenli Gao, Jianqi Li, Shuaishuai Sun, Huaixin Yang","doi":"10.1063/4.0000199","DOIUrl":"https://doi.org/10.1063/4.0000199","url":null,"abstract":"Ultrafast electron diffraction has been proven to be a powerful tool for the study of coherent acoustic phonons owing to its high sensitivity to crystal structures. However, this sensitivity leads to complicated behavior of the diffraction intensity, which complicates the analysis process of phonons, especially higher harmonics. Here, we theoretically analyze the effects of photoinduced coherent transverse and longitudinal acoustic phonons on electron diffraction to provide a guide for the exploitation and modulation of coherent phonons. The simulation of the electron diffraction was performed in 30-nm films with different optical penetration depths based on the atomic displacements obtained by solving the wave equation. The simulation results exhibit a complex relationship between the frequencies of the phonons and diffraction signals, which highly depends on the laser penetration depth, sample thickness, and temporal stress distribution. In addition, an intensity decomposition method is proposed to account for the in-phase oscillation and high harmonics caused by inhomogeneous excitation. These results can provide new perspectives and insights for a comprehensive and accurate understanding of the lattice response under coherent phonons.","PeriodicalId":21992,"journal":{"name":"Structural Dynamics","volume":"57 1-2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135715084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0