Structural Dynamics-Us最新文献_第6页

Fragment screening for a protein-protein interaction inhibitor to WDR5 WDR5蛋白相互作用抑制剂的片段筛选

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-11-01 DOI: 10.1063/1.5122849

M. Dennis, B. J. Morrow, O. Dolezal, A. Cuzzupe, Alexandra E Stupple, J. Newman, J. Bentley, M. Hattarki, S. Nuttall, R. Foitzik, I. Street, P. Stupple, B. Monahan, T. Peat

{"title":"Fragment screening for a protein-protein interaction inhibitor to WDR5","authors":"M. Dennis, B. J. Morrow, O. Dolezal, A. Cuzzupe, Alexandra E Stupple, J. Newman, J. Bentley, M. Hattarki, S. Nuttall, R. Foitzik, I. Street, P. Stupple, B. Monahan, T. Peat","doi":"10.1063/1.5122849","DOIUrl":"https://doi.org/10.1063/1.5122849","url":null,"abstract":"The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and antagonism of the WDR5-MLL1 interaction by small molecules has been proposed as a therapeutic strategy for MLL-rearranged cancers. Small molecule binders of the “WIN” site of WDR5 that cause displacement from chromatin have been additionally implicated to be of broader use in cancer treatment. In this study, a fragment screen with Surface Plasmon Resonance (SPR) was used to identify a highly ligand-efficient imidazole-containing compound that is bound in the WIN site. The subsequent medicinal chemistry campaign—guided by a suite of high-resolution cocrystal structures with WDR5—progressed the initial hit to a low micromolar binder. One outcome from this study is a moiety that substitutes well for the side chain of arginine; a tripeptide containing one such substitution was resolved in a high resolution structure (1.5 Å) with a binding mode analogous to the native tripeptide. SPR furthermore indicates a similar residence time (kd = ∼0.06 s−1) for these two analogs. This novel scaffold therefore represents a possible means to overcome the potential permeability issues of WDR5 ligands that possess highly basic groups like guanidine. The series reported here furthers the understanding of the WDR5 WIN site and functions as a starting point for the development of more potent WDR5 inhibitors that may serve as cancer therapeutics.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5122849","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44703840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years 大分子晶体学再现性的综合资源：前四年的经验

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-11-01 DOI: 10.1063/1.5128672

M. Grabowski, M. Cymborowski, P. Porebski, T. Osinski, I. Shabalin, D. Cooper, W. Minor

{"title":"The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years","authors":"M. Grabowski, M. Cymborowski, P. Porebski, T. Osinski, I. Shabalin, D. Cooper, W. Minor","doi":"10.1063/1.5128672","DOIUrl":"https://doi.org/10.1063/1.5128672","url":null,"abstract":"It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5128672","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44236757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 21

Femtosecond gas-phase mega-electron-volt ultrafast electron diffraction. 飞秒气相兆电子伏特超快电子衍射。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-10-15 eCollection Date: 2019-09-01 DOI: 10.1063/1.5120864

X Shen, J P F Nunes, J Yang, R K Jobe, R K Li, Ming-Fu Lin, B Moore, M Niebuhr, S P Weathersby, T J A Wolf, C Yoneda, Markus Guehr, Martin Centurion, X J Wang

{"title":"Femtosecond gas-phase mega-electron-volt ultrafast electron diffraction.","authors":"X Shen, J P F Nunes, J Yang, R K Jobe, R K Li, Ming-Fu Lin, B Moore, M Niebuhr, S P Weathersby, T J A Wolf, C Yoneda, Markus Guehr, Martin Centurion, X J Wang","doi":"10.1063/1.5120864","DOIUrl":"10.1063/1.5120864","url":null,"abstract":"The development of ultrafast gas electron diffraction with nonrelativistic electrons has enabled the determination of molecular structures with atomic spatial resolution. It has, however, been challenging to break the picosecond temporal resolution barrier and achieve the goal that has long been envisioned-making space- and-time resolved molecular movies of chemical reaction in the gas-phase. Recently, an ultrafast electron diffraction (UED) apparatus using mega-electron-volt (MeV) electrons was developed at the SLAC National Accelerator Laboratory for imaging ultrafast structural dynamics of molecules in the gas phase. The SLAC gas-phase MeV UED has achieved 65 fs root mean square temporal resolution, 0.63 Å spatial resolution, and 0.22 Å-1 reciprocal-space resolution. Such high spatial-temporal resolution has enabled the capturing of real-time molecular movies of fundamental photochemical mechanisms, such as chemical bond breaking, ring opening, and a nuclear wave packet crossing a conical intersection. In this paper, the design that enables the high spatial-temporal resolution of the SLAC gas phase MeV UED is presented. The compact design of the differential pump section of the SLAC gas phase MeV UED realized five orders-of-magnitude vacuum isolation between the electron source and gas sample chamber. The spatial resolution, temporal resolution, and long-term stability of the apparatus are systematically characterized.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"6 5","pages":"054305"},"PeriodicalIF":2.3,"publicationDate":"2019-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41216713","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

Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics. 核和电子蛋白质动力学的超快X射线晶体学和超快结构光学晶体学的进展和机遇。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-09-24 eCollection Date: 2019-09-01 DOI: 10.1063/1.5110685

Jasper J van Thor

{"title":"Advances and opportunities in ultrafast X-ray crystallography and ultrafast structural optical crystallography of nuclear and electronic protein dynamics.","authors":"Jasper J van Thor","doi":"10.1063/1.5110685","DOIUrl":"https://doi.org/10.1063/1.5110685","url":null,"abstract":"Both nuclear and electronic dynamics contribute to protein function and need multiple and complementary techniques to reveal their ultrafast structural dynamics response. Real-space information obtained from the measurement of electron density dynamics by X-ray crystallography provides aspects of both, while the molecular physics of coherence parameters and frequency-frequency correlation needs spectroscopy methods. Ultrafast pump-probe applications of protein dynamics in crystals provide real-space information through direct X-ray crystallographic structure analysis or through structural optical crystallographic analysis. A discussion of methods of analysis using ultrafast macromolecular X-ray crystallography and ultrafast nonlinear structural optical crystallography is presented. The current and future high repetition rate capabilities provided by X-ray free electron lasers for ultrafast diffraction studies provide opportunities for optical control and optical selection of nuclear coherence which may develop to access higher frequency dynamics through improvements of sensitivity and time resolution to reveal coherence directly. Specific selection of electronic coherence requires optical probes, which can provide real-space structural information through photoselection of oriented samples and specifically in birefringent crystals. Ultrafast structural optical crystallography of photosynthetic energy transfer has been demonstrated, and the theory of two-dimensional structural optical crystallography has shown a method for accessing the structural selection of electronic coherence.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"6 5","pages":"050901"},"PeriodicalIF":2.8,"publicationDate":"2019-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5110685","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41216711","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

Electrostatic subframing and compressive-sensing video in transmission electron microscopy. 透射电子显微镜中的静电亚分支和压缩传感视频。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-09-23 eCollection Date: 2019-09-01 DOI: 10.1063/1.5115162

B W Reed, A A Moghadam, R S Bloom, S T Park, A M Monterrosa, P M Price, C M Barr, S A Briggs, K Hattar, J T McKeown, D J Masiel

{"title":"Electrostatic subframing and compressive-sensing video in transmission electron microscopy.","authors":"B W Reed, A A Moghadam, R S Bloom, S T Park, A M Monterrosa, P M Price, C M Barr, S A Briggs, K Hattar, J T McKeown, D J Masiel","doi":"10.1063/1.5115162","DOIUrl":"https://doi.org/10.1063/1.5115162","url":null,"abstract":"We present kilohertz-scale video capture rates in a transmission electron microscope, using a camera normally limited to hertz-scale acquisition. An electrostatic deflector rasters a discrete array of images over a large camera, decoupling the acquisition time per subframe from the camera readout time. Total-variation regularization allows features in overlapping subframes to be correctly placed in each frame. Moreover, the system can be operated in a compressive-sensing video mode, whereby the deflections are performed in a known pseudorandom sequence. Compressive sensing in effect performs data compression before the readout, such that the video resulting from the reconstruction can have substantially more total pixels than that were read from the camera. This allows, for example, 100 frames of video to be encoded and reconstructed using only 15 captured subframes in a single camera exposure. We demonstrate experimental tests including laser-driven melting/dewetting, sintering, and grain coarsening of nanostructured gold, with reconstructed video rates up to 10 kHz. The results exemplify the power of the technique by showing that it can be used to study the fundamentally different temporal behavior for the three different physical processes. Both sintering and coarsening exhibited self-limiting behavior, whereby the process essentially stopped even while the heating laser continued to strike the material. We attribute this to changes in laser absorption and to processes inherent to thin-film coarsening. In contrast, the dewetting proceeded at a relatively uniform rate after an initial incubation time consistent with the establishment of a steady-state temperature profile.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"6 5","pages":"054303"},"PeriodicalIF":2.8,"publicationDate":"2019-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5115162","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41216712","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: 11

High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures. 粘细菌光敏色素在低温和室温下的高分辨率晶体结构。

IF 2.3 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-09-17 eCollection Date: 2019-09-01 DOI: 10.1063/1.5120527

Juan C Sanchez, Melissa Carrillo, Suraj Pandey, Moraima Noda, Luis Aldama, Denisse Feliz, Elin Claesson, Weixiao Yuan Wahlgren, Gregory Tracy, Phu Duong, Angela C Nugent, Andrew Field, Vukica Šrajer, Christopher Kupitz, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Marius Schmidt, Emina A Stojković

{"title":"High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures.","authors":"Juan C Sanchez, Melissa Carrillo, Suraj Pandey, Moraima Noda, Luis Aldama, Denisse Feliz, Elin Claesson, Weixiao Yuan Wahlgren, Gregory Tracy, Phu Duong, Angela C Nugent, Andrew Field, Vukica Šrajer, Christopher Kupitz, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Marius Schmidt, Emina A Stojković","doi":"10.1063/1.5120527","DOIUrl":"10.1063/1.5120527","url":null,"abstract":"Phytochromes (PHYs) are photoreceptor proteins first discovered in plants, where they control a variety of photomorphogenesis events. PHYs as photochromic proteins can reversibly switch between two distinct states: a red light (Pr) and a far-red light (Pfr) absorbing form. The discovery of Bacteriophytochromes (BphPs) in nonphotosynthetic bacteria has opened new frontiers in our understanding of the mechanisms by which these natural photoswitches can control single cell development, although the role of BphPs in vivo remains largely unknown. BphPs are dimeric proteins that consist of a photosensory core module (PCM) and an enzymatic domain, often a histidine kinase. The PCM is composed of three domains (PAS, GAF, and PHY). It holds a covalently bound open-chain tetrapyrrole (biliverdin, BV) chromophore. Upon absorption of light, the double bond between BV rings C and D isomerizes and reversibly switches the protein between Pr and Pfr states. We report crystal structures of the wild-type and mutant (His275Thr) forms of the canonical BphP from the nonphotosynthetic myxobacterium Stigmatella aurantiaca (SaBphP2) in the Pr state. Structures were determined at 1.65 Å and 2.2 Å (respectively), the highest resolution of any PCM construct to date. We also report the room temperature wild-type structure of the same protein determined at 2.1 Å at the SPring-8 Angstrom Compact free electron LAser (SACLA), Japan. Our results not only highlight and confirm important amino acids near the chromophore that play a role in Pr-Pfr photoconversion but also describe the signal transduction into the PHY domain which moves across tens of angstroms after the light stimulus.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"6 5","pages":"054701"},"PeriodicalIF":2.3,"publicationDate":"2019-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41216715","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

Full-dimensional theoretical description of vibrationally resolved valence-shell photoionization of H₂O. H2O振动分辨价壳层光电离的全维理论描述。

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-09-11 eCollection Date: 2019-09-01 DOI: 10.1063/1.5106431

Selma Engin, Jesús González-Vázquez, Gianluigi Grimaldi Maliyar, Aleksandar R Milosavljević, Taishi Ono, Saikat Nandi, Denys Iablonskyi, Kuno Kooser, John D Bozek, Piero Decleva, Edwin Kukk, Kiyoshi Ueda, Fernando Martín

{"title":"Full-dimensional theoretical description of vibrationally resolved valence-shell photoionization of H2O.","authors":"Selma Engin, Jesús González-Vázquez, Gianluigi Grimaldi Maliyar, Aleksandar R Milosavljević, Taishi Ono, Saikat Nandi, Denys Iablonskyi, Kuno Kooser, John D Bozek, Piero Decleva, Edwin Kukk, Kiyoshi Ueda, Fernando Martín","doi":"10.1063/1.5106431","DOIUrl":"https://doi.org/10.1063/1.5106431","url":null,"abstract":"We have performed a full-dimensional theoretical study of vibrationally resolved photoelectron emission from the valence shell of the water molecule by using an extension of the static-exchange density functional theory that accounts for ionization as well as for vibrational motion in the symmetric stretching, antisymmetric stretching, and bending modes. At variance with previous studies performed in centrosymmetric molecules, where vibrationally resolved spectra are mostly dominated by the symmetric stretching mode, in the present case, all three modes contribute to the calculated spectra, including intermode couplings. We have found that diffraction of the ejected electron by the various atomic centers is barely visible in the ratios between vibrationally resolved photoelectron spectra corresponding to different vibrational states of the remaining H2O+ cation (the so-called v-ratios), in contrast to the prominent oscillations observed in K-shell ionization of centrosymmetric molecules, including those that only contain hydrogen atoms around the central atoms, e.g., CH4. To validate the conclusions of our work, we have carried out synchrotron radiation experiments at the SOLEIL synchrotron and determined photoelectron spectra and v-ratios for H2O in a wide range of photon energies, from threshold up to 150 eV. The agreement with the theoretical predictions is good.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"6 5","pages":"054101"},"PeriodicalIF":2.8,"publicationDate":"2019-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5106431","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41216714","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

Photoemission sources and beam blankers for ultrafast electron microscopy 用于超快电子显微镜的光发射源和光束消光器

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-09-01 DOI: 10.1063/1.5117058

Lixin Zhang, J. Hoogenboom, B. Cook, P. Kruit

{"title":"Photoemission sources and beam blankers for ultrafast electron microscopy","authors":"Lixin Zhang, J. Hoogenboom, B. Cook, P. Kruit","doi":"10.1063/1.5117058","DOIUrl":"https://doi.org/10.1063/1.5117058","url":null,"abstract":"Observing atomic motions as they occur is the dream goal of ultrafast electron microscopy (UEM). Great progress has been made so far thanks to the efforts of many scientists in developing the photoemission sources and beam blankers needed to create short pulses of electrons for the UEM experiments. While details on these setups have typically been reported, a systematic overview of methods used to obtain a pulsed beam and a comparison of relevant source parameters have not yet been conducted. In this report, we outline the basic requirements and parameters that are important for UEM. Different types of imaging modes in UEM are analyzed and summarized. After reviewing and analyzing the different kinds of photoemission sources and beam blankers that have been reported in the literature, we estimate the reduced brightness for all the photoemission sources reviewed and compare this to the brightness in the continuous and blanked beams. As for the problem of pulse broadening caused by the repulsive forces between electrons, four main methods available to mitigate the dispersion are summarized. We anticipate that the analysis and conclusions provided in this manuscript will be instructive for designing an UEM setup and could thus push the further development of UEM.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5117058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41487329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

The role of transition dipole phase in atomic attosecond transient absorption from the multi-level model 跃迁偶极相在原子阿秒瞬态吸收中的作用

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-09-01 DOI: 10.1063/1.5124441

Guanglu Yuan, Shicheng Jiang, Zi-wei Wang, Weijie Hua, Chao Yu, C. Jin, R. Lu

引用次数: 6

Probing ultrafast C–Br bond fission in the UV photochemistry of bromoform with core-to-valence transient absorption spectroscopy 用核价瞬态吸收光谱探测溴仿紫外光化学中超快C-Br键裂变

IF 2.8 2区物理与天体物理

Structural Dynamics-Us Pub Date : 2019-09-01 DOI: 10.1063/1.5113798

Benjamin W. Toulson, M. Borgwardt, Han Wang, F. Lackner, A. Chatterley, C. D. Pemmaraju, D. Neumark, S. Leone, D. Prendergast, O. Gessner

{"title":"Probing ultrafast C–Br bond fission in the UV photochemistry of bromoform with core-to-valence transient absorption spectroscopy","authors":"Benjamin W. Toulson, M. Borgwardt, Han Wang, F. Lackner, A. Chatterley, C. D. Pemmaraju, D. Neumark, S. Leone, D. Prendergast, O. Gessner","doi":"10.1063/1.5113798","DOIUrl":"https://doi.org/10.1063/1.5113798","url":null,"abstract":"UV pump–extreme UV (XUV) probe femtosecond transient absorption spectroscopy is used to study the 268 nm induced photodissociation dynamics of bromoform (CHBr3). Core-to-valence transitions at the Br(3d) absorption edge (∼70 eV) provide an atomic scale perspective of the reaction, sensitive to changes in the local valence electronic structure, with ultrafast time resolution. The XUV spectra track how the singly occupied molecular orbitals of transient electronic states develop throughout the C–Br bond fission, eventually forming radical Br and CHBr2 products. Complementary ab initio calculations of XUV spectral fingerprints are performed for transient atomic arrangements obtained from sampling excited-state molecular dynamics simulations. C–Br fission along an approximately CS symmetrical reaction pathway leads to a continuous change of electronic orbital characters and atomic arrangements. Two timescales dominate changes in the transient absorption spectra, reflecting the different characteristic motions of the light C and H atoms and the heavy Br atoms. Within the first 40 fs, distortion from C3v symmetry to form a quasiplanar CHBr2 by the displacement of the (light) CH moiety causes significant changes to the valence electronic structure. Displacement of the (heavy) Br atoms is delayed and requires up to ∼300 fs to form separate Br + CHBr2 products. We demonstrate that transitions between the valence-excited (initial) and valence + core-excited (final) state electronic configurations produced by XUV absorption are sensitive to the localization of valence orbitals during bond fission. The change in valence electron-core hole interaction provides a physical explanation for spectral shifts during the process of bond cleavage.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5113798","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45779336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14