Imaging ultrafast molecular dynamics with laser-induced electron diffraction

Establishing the structure of molecules and solids has always had an essential role in physics, chemistry and biology. The methods of choice are X-ray and electron diffraction, which are routinely used to determine atomic positions with sub-?ngstr?m spatial resolution. Although both methods are currently limited to probing dynamics on timescales longer than a picosecond, the recent development of femtosecond sources of X-ray pulses and electron beams suggests that they might soon be capable of taking ultrafast snapshots of biological molecules and condensed-phase systems undergoing structural changes. The past decade has also witnessed the emergence of an alternative imaging approach based on laser-ionized bursts of coherent electron wave packets that self-interrogate the parent molecular structure. Here we show that this phenomenon can indeed be exploited for laser-induced electron diffraction (LIED), to image molecular structures with sub-?ngstr?m precision and exposure times of a few femtoseconds. We apply the method to oxygen and nitrogen molecules, which on strong-field ionization at three mid-infrared wavelengths (1.7, 2.0 and 2.3?μm) emit photoelectrons with a momentum distribution from which we extract diffraction patterns. The long wavelength is essential for achieving atomic-scale spatial resolution, and the wavelength variation is equivalent to taking snapshots at different times. We show that the method has the sensitivity to measure a 0.1?? displacement in the oxygen bond length occurring in a time interval of ～5?fs, which establishes LIED as a promising approach for the imaging of gas-phase molecules with unprecedented spatio-temporal resolution.     

'Big Bang' tomography as a new route to atomic-resolution electron tomography

Until now it has not been possible to image at atomic resolution using classical electron tomographic methods, except when the target is a perfectly crystalline nano-object imaged along a few zone axes. The main reasons are that mechanical tilting in an electron microscope with sub-?ngstr?m precision over a very large angular range is difficult, that many real-life objects such as dielectric layers in microelectronic devices impose geometrical constraints and that many radiation-sensitive objects such as proteins limit the total electron dose. Hence, there is a need for a new tomographic scheme that is able to deduce three-dimensional information from only one or a few projections. Here we present an electron tomographic method that can be used to determine, from only one viewing direction and with sub-?ngstr?m precision, both the position of individual atoms in the plane of observation and their vertical position. The concept is based on the fact that an experimentally reconstructed exit wave consists of the superposition of the spherical waves that have been scattered by the individual atoms of the object. Furthermore, the phase of a Fourier component of a spherical wave increases with the distance of propagation at a known 'phase speed'. If we assume that an atom is a point-like object, the relationship between the phase and the phase speed of each Fourier component is linear, and the distance between the atom and the plane of observation can therefore be determined by linear fitting. This picture has similarities with Big Bang cosmology, in which the Universe expands from a point-like origin such that the distance of any galaxy from the origin is linearly proportional to the speed at which it moves away from the origin (Hubble expansion). The proof of concept of the method has been demonstrated experimentally for graphene with a two-layer structure and it will work optimally for similar layered materials, such as boron nitride and molybdenum disulphide.     

Structural studies of membranes and surface layers up to 1,000 A thick using X-ray standing waves

The X-ray standing wave (XSW) method, developed in the 1960s, was used originally to determine heavy atom positions in and on silicon and germanium single crystals. An X-ray standing wave generated by the interference of coherent incident and reflected beams excites X-ray fluorescence from the heavy atom, the intensity of which as a function of incident angle provides an indication of the atom's distance from the X-ray reflecting surface. The availability of X-ray mirrors and the ability to prepare layered synthetic microstructures has made possible the study of biologically relevant structures using the XSW technique on length scales of typically tens to hundreds of ?ngstr?ms, allowing heavy atoms in such structures to be located with ?ngstr?m or sub?ngstr?m resolution. Many model biological systems (such as Langmuir-Blodgett films, which mimic membranes) require access to still larger scales, but it is not obvious that an XSW will remain coherent over such length scales. Here we report studies of a lipid multilayer system using the XSW method, in which we have been able to locate the metal atoms in a zinc arachidate bilayer with ?ngstr?m resolution at a distance of almost 1,000 A above the surface of a gold mirror. Our results indicate that the XSW technique should be useful for structural studies of supramolecular aggregates, receptor-ligand interactions and multi-membrane stacks, in which length scales of this order are encountered.     

Electron tomography at 2.4-ångström resolution

Transmission electron microscopy is a powerful imaging tool that has found broad application in materials science, nanoscience and biology. With the introduction of aberration-corrected electron lenses, both the spatial resolution and the image quality in transmission electron microscopy have been significantly improved and resolution below 0.5??ngstr?ms has been demonstrated. To reveal the three-dimensional (3D) structure of thin samples, electron tomography is the method of choice, with cubic-nanometre resolution currently achievable. Discrete tomography has recently been used to generate a 3D atomic reconstruction of a silver nanoparticle two to three nanometres in diameter, but this statistical method assumes prior knowledge of the particle's lattice structure and requires that the atoms fit rigidly on that lattice. Here we report the experimental demonstration of a general electron tomography method that achieves atomic-scale resolution without initial assumptions about the sample structure. By combining a novel projection alignment and tomographic reconstruction method with scanning transmission electron microscopy, we have determined the 3D structure of an approximately ten-nanometre gold nanoparticle at 2.4-?ngstr?m resolution. Although we cannot definitively locate all of the atoms inside the nanoparticle, individual atoms are observed in some regions of the particle and several grains are identified in three dimensions. The 3D surface morphology and internal lattice structure revealed are consistent with a distorted icosahedral multiply twinned particle. We anticipate that this general method can be applied not only to determine the 3D structure of nanomaterials at atomic-scale resolution, but also to improve the spatial resolution and image quality in other tomography fields.     

Experimental measurements and theoretical calculations of the atomic structure of materials with subangstrom resolution and picometer precision

Lattice defects are unavoidable structural units in materials and play an important role in determining material properties. Compared with the periodic structure of crystals, the atomic configurations of the lattice defects are determined by the coordinates of a large number of atoms, making it difficult to experimentally investigate them. In computational materials science, multiparameter optimization is also a difficult problem and experimental verification is usually required to determine the possibility of obtaining the structure and properties predicted by cal- culations. Using our recent studies on oxide surfaces as examples, we introduce the method of integrated aberra- tion-corrected electron microscopy and the first-principles calculations to analyze the atomic structure of lattice defects. The atomic configurations of defects were mea- sured using quantitative high-resolution electron micros- copy at subangstrom resolution and picometer precision, and then the electronic structure and dynamic behavior of materials can be studied at the atomic scale using the first- principles calculations. The two methods complement each other and can be combined to increase the understanding of the atomic structure of materials in both the time and space dimensions, which will benefit materials design at the atomic scale.     

Anomalous properties in ferroelectrics induced by atomic ordering.

Complex insulating perovskite alloys are of considerable technological interest because of their large dielectric and piezoelectric responses. Examples of such alloys include (Ba1-xSrx)TiO3, which has emerged as a leading candidate dielectric material for the memory-cell capacitors in dynamic random access memories; and Pb(Zr1-xTix)O3 (PZT), which is widely used in transducers and actuators. The rich variety of structural phases that these alloys can exhibit, and the challenge of relating their anomalous properties to the microscopic structure, make them attractive from a fundamental point of view. Theoretical investigations of modifications to the atomic ordering of these alloys suggest the existence of further unexpected structural properties and hold promise for the development of new functional materials with improved electromechanical properties. Here we report ab initio calculations that show that a certain class of atomic rearrangement should lead simultaneously to large electromechanical responses and to unusual structural phases in a given class of perovskite alloys. Our simulations also reveal the microscopic mechanism responsible for these anomalies.     

原子结构参数的Xα法计算

本文推荐一种修改的Xα方法以计算分子中原子的结构参数,从而可进一步对分子的某些性质作出表征或者计算。所用的方法可计算不同化学环境下原子的参数。由于掌握了在分子中原子的波函数、径向分布函数、散射因子等基本参数和函数,故此法实际上可推广用到多种原子参数的计算上去。此计算可用微机实现,不像从头算那样耗时多,结果却不比从头算差,因此推荐此法是有益的。     

Zr_(55)Cu_(35)Al_(10)金属玻璃中紧键结合团簇的定量表征

定量表征金属玻璃的原子结构是深入理解和解释金属玻璃独特的物理性能和力学性能的关键.本文通过铜模吸铸法制备了Zr55Cu35Al10大块金属玻璃圆棒状试样,并利用中子衍射获得试样的对分布函数,从而定量地定义了金属玻璃紧键合团簇模型中的紧键合团簇.还通过第一性原理分子动力学模拟对Zr55Cu35Al10大块金属玻璃局域原子结构进行模拟计算,从模拟得到的结构中提取了许多紧键合团簇,并通过团簇尺寸对其定量地表征.     

Dodecagonal tiling in mesoporous silica

Recent advances in the fabrication of quasicrystals in soft matter systems have increased the length scales for quasicrystals into the mesoscale range (20 to 500 ?ngstr?ms). Thus far, dendritic liquid crystals, ABC-star polymers, colloids and inorganic nanoparticles have been reported to yield quasicrystals. These quasicrystals offer larger length scales than intermetallic quasicrystals (a few ?ngstr?ms), thus potentially leading to optical applications through the realization of a complete photonic bandgap induced via multiple scattering of light waves in virtually all directions. However, the materials remain far from structurally ideal, in contrast to their intermetallic counterparts, and fine control over the structure through a self-organization process has yet to be attained. Here we use the well-established self-assembly of surfactant micelles to produce a new class of mesoporous silicas, which exhibit 12-fold (dodecagonal) symmetry in both electron diffraction and morphology. Each particle reveals, in the 12-fold cross-section, an analogue of dodecagonal quasicrystals in the centre surrounded by 12 fans of crystalline domains in the peripheral part. The quasicrystallinity has been verified by selected-area electron diffraction and quantitative phason strain analyses on transmission electron microscope images obtained from the central region. We argue that the structure forms through a non-equilibrium growth process, wherein the competition between different micellar configurations has a central role in tuning the structure. A simple theoretical model successfully reproduces the observed features and thus establishes a link between the formation process and the resulting structure.     

Millisecond X-ray diffraction and the first electron density map from Laue photographs of a protein crystal

Attempts to use X-ray crystallography to extract three-dimensional information on transient phenomena in crystals have been hampered primarily by long data collection times. Here we report on the first difference Fourier map obtained from Laue diffraction photographs of a protein crystal, glycogen phosphorylase b. Data collection time was 3 s using the high-intensity white X-radiation generated on the wiggler magnet of the Daresbury Synchrotron Radiation Source (SRS), but data acquisition in the millisecond-submillisecond range is possible. The method presented here uses a simple difference technique and was designed to analyse structural changes relative to a known starting structure. The combination of this approach with cine techniques allows the recording of three-dimensional motion pictures at atomic resolution and opens up new areas in structural biology and chemistry.     

PDF法在SrBi2Ta2O9铁电薄膜结构分析中的应用

采用Sol—Gel法及spin—coating法制备出了SrBi2Ta2O9(SBT)铁电薄膜．通过对“对密度分布函数”(pairdistributionfunction，PDF)中结构因子的修正，利用X射线衍射的：PDF数据对铁电材料SrBi2Ta2O9的结构尺寸进行了分析，得出分布几率随陈化温度的变化呈现出不同的变化规律的结果．将2种陈化温度下的PDF数据和SrBi2Ta2O9扫描电镜的结果进行了对比分析，结果表明PDF法在分析局域结构以及局域结构和平均结构之间的关系方面更具优越性。     

Crystal structure of the ligand-free G-protein-coupled receptor opsin

In the G-protein-coupled receptor (GPCR) rhodopsin, the inactivating ligand 11-cis-retinal is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here we present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9 ?ngstr?m (A) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)(5,6)F regions and in TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 A, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganize the empty retinal-binding pocket to disclose two openings that may serve the entry and exit of retinal. The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation.     

Probing the chemistry of thioredoxin catalysis with force

Thioredoxins are enzymes that catalyse disulphide bond reduction in all living organisms. Although catalysis is thought to proceed through a substitution nucleophilic bimolecular (S(N)2) reaction, the role of the enzyme in modulating this chemical reaction is unknown. Here, using single-molecule force-clamp spectroscopy, we investigate the catalytic mechanism of Escherichia coli thioredoxin (Trx). We applied mechanical force in the range of 25-600 pN to a disulphide bond substrate and monitored the reduction of these bonds by individual enzymes. We detected two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulphide bond, causing a shortening of the substrate polypeptide by 0.79 +/- 0.09 A (+/- s.e.m.), and the second elongating the substrate disulphide bond by 0.17 +/- 0.02 A (+/- s.e.m.). These results support the view that the Trx active site regulates the geometry of the participating sulphur atoms with sub-?ngstr?m precision to achieve efficient catalysis. Our results indicate that substrate conformational changes may be important in the regulation of Trx activity under conditions of oxidative stress and mechanical injury, such as those experienced in cardiovascular disease. Furthermore, single-molecule atomic force microscopy techniques, as shown here, can probe dynamic rearrangements within an enzyme's active site during catalysis that cannot be resolved with any other current structural biological technique.     

Improved molecular replacement by density- and energy-guided protein structure optimization

Molecular replacement procedures, which search for placements of a starting model within the crystallographic unit cell that best account for the measured diffraction amplitudes, followed by automatic chain tracing methods, have allowed the rapid solution of large numbers of protein crystal structures. Despite extensive work, molecular replacement or the subsequent rebuilding usually fail with more divergent starting models based on remote homologues with less than 30% sequence identity. Here we show that this limitation can be substantially reduced by combining algorithms for protein structure modelling with those developed for crystallographic structure determination. An approach integrating Rosetta structure modelling with Autobuild chain tracing yielded high-resolution structures for 8 of 13 X-ray diffraction data sets that could not be solved in the laboratories of expert crystallographers and that remained unsolved after application of an extensive array of alternative approaches. We estimate that the new method should allow rapid structure determination without experimental phase information for over half the cases where current methods fail, given diffraction data sets of better than 3.2?? resolution, four or fewer copies in the asymmetric unit, and the availability of structures of homologous proteins with >20% sequence identity.     

Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment

Voltage-dependent K+ (Kv) channels repolarize the action potential in neurons and muscle. This type of channel is gated directly by membrane voltage through protein domains known as voltage sensors, which are molecular voltmeters that read the membrane voltage and regulate the pore. Here we describe the structure of a chimaeric voltage-dependent K+ channel, which we call the 'paddle-chimaera channel', in which the voltage-sensor paddle has been transferred from Kv2.1 to Kv1.2. Crystallized in complex with lipids, the complete structure at 2.4 ?ngstr?m resolution reveals the pore and voltage sensors embedded in a membrane-like arrangement of lipid molecules. The detailed structure, which can be compared directly to a large body of functional data, explains charge stabilization within the membrane and suggests a mechanism for voltage-sensor movements and pore gating.     

OCS分子基态(X3A'''')的势能函数

应用群论及原子分子反应静力学方法推导了OCS分子的电子态及其离解极限,采用B3P86方法,在CC-PVTZ水平上,优化出OCS基态分子稳定构型为三重态的Cs构型,其平衡核间距RC-S=0.1768nm、RC-O=0.1179nm、∠OCS=122.9,°能量为-512.0405 a.u.。同时计算出基态的简正振动频率:对称伸缩振动频率ν(A′)=354.5cm-1,弯曲振动频率ν(A′)=633.5cm-1和反对称伸缩振动频率ν(A′)=1792.8cm-1。在此基础上,使用多体项展式理论方法,导出了基态OCS分子的全空间解析势能函数,该势能函数准确再现了OCS(Cs)平衡结构。     

新颖深紫外二阶非线性光学材料的研究进展

深紫外非线性光学晶体在光刻、微加工及高分辨光电能谱仪等领域有重要的应用．本文将深紫外非线性光学材料按其结构基元的几何特点分为π共轭体系(硼酸盐、碳酸盐和硝酸盐)和非π共轭体系(磷酸盐、硫酸盐和硅酸盐)2大类，并总结和讨论了各类材料的晶体结构、线性和二阶非线性光学性能以及设计合成策略．希望能为探索新一代深紫外非线性光学材料提供有益的帮助．