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Protein secondary-structure description with a coarse-grained model: code and datasets in ActivePapers format 粗粒度模型的蛋白质二级结构描述:ActivePapers格式的代码和数据集
Pub Date : 2015-07-28 DOI: 10.5281/zenodo.21690
G. Kneller, K. Hinsen
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引用次数: 0
Advances in Crystallographic Image Processing for Scanning Probe Microscopy 扫描探针显微镜晶体图像处理研究进展
Pub Date : 2014-08-05 DOI: 10.1107/S2053273314083922
P. Moeck
This book chapter reviews progress in crystallographic image processing (CIP) for scanning probe microscopy (SPM) that has occurred since our description of the technique was first put into open access in this book series in the year 2010. The signal to noise ratio in all kinds of experimental images of more or less regular 2D periodic arrays is significantly enhanced by CIP and the technique is independent of the type of recording device. In the SPM imaging context, CIP can be understood as an a posteriori sharpening of the effective experimental scanning probe tip by computational means. It is now possible to remove multiple scanning probe mini-tip effects in images from 2D periodic arrays of physical objects that either self-assembled or were created artificially. Accepted within the scientific community is by now also the fact that SPM tips can change their shape and fine structure during the operation of a microscope and, thereby, obfuscate the recorded images in systematic ways. CIP restores much of the smeared out information in such images. The adaptation of a geometric Akaike Information Criterion from the robotics and computer vision community to the unambiguous detection of 2D translation symmetries enabled much of our recent progress. In the main body of this book chapter, we discuss this adaptation and briefly illustrate its utility on an example.
本章回顾了扫描探针显微镜(SPM)晶体图像处理(CIP)的进展,自从我们对该技术的描述于2010年首次在本系列书中开放获取以来。CIP技术与记录设备的类型无关,可显著提高较规则的二维周期阵列的各类实验图像的信噪比。在SPM成像环境中,CIP可以理解为通过计算手段对有效的实验扫描探针尖端进行后验锐化。现在有可能从自组装或人工创建的物理对象的二维周期性阵列中去除图像中的多个扫描探针微型尖端效应。科学界现在也接受了这样一个事实,即SPM尖端可以在显微镜操作过程中改变它们的形状和精细结构,从而以系统的方式混淆记录的图像。CIP可以恢复这些图像中大部分模糊的信息。机器人和计算机视觉社区对几何赤池信息准则的适应,使二维平移对称性的明确检测成为我们最近的进展。在本书这一章的主要部分,我们将讨论这种改编,并通过一个例子简要说明它的效用。
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引用次数: 0
3D Printing of Crystallographic Models for Interdisciplinary College Education 跨学科大学教育结晶模型的3D打印
Pub Date : 2014-08-05 DOI: 10.1107/S2053273314086203
P. Moeck, W. Kaminsky, Trevor J. Snyder
Crystallographic models of molecule and crystal structures, crystal morphologies, Bravais lattices, space and point group symmetries, highly local and extended crystal defects, ... can all be encoded in the Crystallographic Information Framework (CIF) file format. While 3D printing has been available for at least 20 years, cost and performance improvements have only recently made 3D printing practical for usage by college educators and the general public. There is also an industry wide 3D printing standard, the STL file format. Virtual reality freeware programs that include conversions from CIF to STL are openly available [1]. The more than 250,000 entries Crystallography Open Database (COD) has in recent years developed into the world’s premier open-access source for CIFs of structures of small molecules and small to medium sized unit cell crystals [2]. The International Advisory Board of the COD also supports a related project [3a], which provides CIFs for interdisciplinary college education. Three of these “COD offspring” databases have started to provide for free downloads of STL files of small molecules, crystal morphologies, and grain boundaries [3b]. These 3D printing files were created directly from the CIFs in these databases. It is now up to interested college educators to develop new pedagogy in teaching crystallography on the basis of 3D models that can be printed out from these files. To facilitate further developments in this field, there is a web portal of open-access crystallography resources to which all interested college educators are invited to contribute [3c].
分子和晶体结构的晶体学模型,晶体形态学,Bravais晶格,空间和点群对称性,高度局部和扩展晶体缺陷,…都可以用晶体学信息框架(CIF)文件格式进行编码。虽然3D打印已经有至少20年的历史,但成本和性能的改进直到最近才使3D打印实用于大学教育工作者和公众。还有一个行业通用的3D打印标准,即STL文件格式。包括从CIF到STL转换的虚拟现实免费软件程序是公开可用的[1]。近年来,超过25万条目的晶体学开放数据库(Crystallography Open Database, COD)已发展成为世界上最重要的小分子和中小型单胞晶体结构的开放获取资源[2]。COD的国际顾问委员会也支持一个相关的项目[3a],为跨学科的大学教育提供资金。其中三个“COD后代”数据库已经开始提供小分子、晶体形态和晶界的STL文件的免费下载[3b]。这些3D打印文件是直接从这些数据库中的CIFs创建的。现在,有兴趣的大学教育者可以在3D模型的基础上开发新的晶体学教学方法,这些模型可以从这些文件中打印出来。为了促进这一领域的进一步发展,有一个开放获取晶体学资源的门户网站,邀请所有感兴趣的大学教育工作者为其贡献[3c]。
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引用次数: 2
Supramolecular anion coordination networks with (6.3) cation-templated topologies 具有(6.3)阳离子模板拓扑的超分子阴离子配位网络
Pub Date : 2008-08-23 DOI: 10.1107/S0108767308084286
G. Resnati, P. Metrangolo, F. Meyer, T. Pilati, Giancarlo Terraneo, C. Ticozzi
1 etc. We are looking in particular for supramolecular organization in mixed crystals that can modify centrosymmetric structure of pure material into acentric structure of host-guest compound. Such approach can help to alter organization of strongly polarized donoracceptor molecules in crystals and make them useful for applications as optoelectronic materials. In the mixed crystals of I and II organic components are benzene derivatives such as isomers of nitrotoluene, low-melting or liquid at room temperature. Crystal growth of these materials has been done using zone melting technique and molecular structure of these materials in pure compounds was compared with their structures in mixed crystals. It was found that number of acentric crystals in the series mixed crystals of I with nitrobenzene derivatives is higher than statistical expectation. Explanation of this phenomenon can be found in specific intermolecular interactions forming supramolecular associates in these materials.
1等。我们特别关注混合晶体中的超分子组织,它可以将纯材料的中心对称结构修饰成主客体化合物的非中心结构。这种方法可以帮助改变晶体中强极化供体或受体分子的组织,并使其用于光电材料的应用。在I和II的混合晶体中,有机成分是苯衍生物,如硝基甲苯的异构体,在室温下低熔点或液态。用区域熔炼技术对这些材料进行了晶体生长,并比较了这些材料在纯化合物中的分子结构和在混合晶体中的结构。结果表明,在I与硝基苯衍生物的系列混合晶体中,非中心晶体的数量高于统计预期。这种现象的解释可以在这些材料中形成超分子缔合物的特定分子间相互作用中找到。
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引用次数: 0
The solid solution Co3.6Mg1.4Cl2(TeO3)4 固溶体Co3.6Mg1.4Cl2(TeO3)4
Pub Date : 2007-06-01 DOI: 10.1107/S1600536807024014
R. Takagi, D. Hjelmqvist, M. Johnsson
Complex transition metals oxyhalides containing a lone pair element, such as tellurium (IV), form an attractive research field because there is a high probability of finding new low-dimensionally arranged compounds and, particularly, a low-dimensionally arranged transition metals substructures, leading to interesting physical properties. Tellurium (IV) can drive the formation of many unusual structures because of its stereochemically active lone pair electrons, E. It commonly takes a coordination of three or four oxygen atoms to form either a TeO3E square pyramid or a TeO3+1E trigonal bipyramid. These lone pairs are very important players involved in lowering the dimensionality of crystal structures. Previous studies in transition metal tellurium (IV) oxohalide quarternary systems revealed a family of compounds, many of which exhibit interesting properties e.g. magnetic frustration. The unique point of this thesis is to employ alkaline earth elements (AE) to augment this ability of lone pair elements to lower the dimensionality of the transition metal arrangements. By this double usage of “chemical scissors” (a lone pair element used in conjunction with alkaline earth elements) we obtained new types of low-dimensionally arranged compounds.This thesis is focused on the syntheses and characterization of a series of compounds in the pentanary (five components) system AE-TeIV-TM-O-X (AE=alkaline earth metal, TM=transition metal and X=halogen), in which nine new compounds were found. The crystal structures of each of these compounds were determined by the single crystal X-ray diffraction data.
包含孤对元素的复杂过渡金属氧卤化物,如碲(IV),形成了一个有吸引力的研究领域,因为有很高的可能性发现新的低维排列的化合物,特别是低维排列的过渡金属子结构,导致有趣的物理性质。碲(IV)可以驱动许多不寻常结构的形成,因为它具有立体化学活性的孤对电子e。通常需要三个或四个氧原子配位才能形成TeO3E方形金字塔或TeO3+1E三角形双金字塔。这些孤对在降低晶体结构的维数方面起着非常重要的作用。先前对过渡金属碲(IV)氧化卤化物的研究揭示了一系列化合物,其中许多化合物表现出有趣的性质,例如磁挫败。本文的独特之处在于利用碱土元素(AE)来增强孤对元素的这种能力,从而降低过渡金属排列的维数。通过双重使用“化学剪刀”(与碱土元素结合使用的孤对元素),我们获得了新型的低维排列化合物。本文主要研究了五组分体系AE- teiv -TM- o -X (AE=碱土金属,TM=过渡金属,X=卤素)中一系列化合物的合成和表征,其中发现了9个新化合物。这些化合物的晶体结构都是由单晶x射线衍射数据确定的。
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引用次数: 2
3-Amino-4H-pyrido[2,3-e]-1,2,4-thiadiazine 1,1-dioxide 3-Amino-4H-pyrido [2, 3 e) 1、2、1-dioxide 4-thiadiazine 1日
Pub Date : 2001-07-01 DOI: 10.1107/S1600536801009904
L. Dupont, P. Tullio, S. Boverie, B. Pirotte
The title compound, C6H6N4O2S, was prepared for structural comparison with diazoxide (7-chloro-3-methyl-4H-1,2,4-benzo­thia­diazine 1,1-dioxide) and other 3-alkyl­amino­pyrido­thia­diazine 1,1-dioxides known to be potassium channel openers. Particular attention was paid to the tautomeric conformation adopted by the compound in the crystalline state, which is found to be the 4H-form.
制备了标题化合物C6H6N4O2S,并与已知的钾通道打开剂- 7-氯-3-甲基-1,2,4-苯并噻吩嘧啶1,1-二氧化二氮化合物(7-氯-3-甲基- 4h -1,2,4-苯并噻吩嘧啶1,1-二氧化二氮化合物)和其他3-烷基-氨基吡啶嘧啶1,1-二氧化二氮化合物进行结构比较。特别注意到化合物在结晶状态下采用的互变异构体构象,这是发现的4h型。
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引用次数: 1
a-Ammonium Vanadium Hydrogen Phosphate, a-NH4V(HPO4)2. a-磷酸氢钒铵,a-NH4V(HPO4)
Pub Date : 1998-09-15 DOI: 10.1107/S0108270198002856
Z. Bircsak, W. Harrison
α-Ammonium vanadium(III) bis(hydrogen phosphate) is a new ammonium vanadium(III) phosphate built up from a three-dimensional framework of VO6 octahedra and HPO4 tetrahedra [dav(V—O) = 2.008, dav(P—O) = 1.538, dav(N⋯O) = 3.086 A and θav(V—O—P) = 139.5°]. It is isostructural with α-RbV(HPO4)2 and complements the previously described β-NH4V(HPO4)2: α-NH4V(HPO4)2 contains both four-ring (two VO6 and two HPO4) and lantern (two VO6 and three HPO4) groupings, whereas β-NH4V(HPO4)2 contains only four-ring polyhedral groupings.
α-钒(III)二(磷酸氢)铵是由VO6八面体和HPO4四面体[dav(V-O) = 2.008, dav(P-O) = 1.538, dav(N⋯O) = 3.086 a和θav(V-O - p) = 139.5°]的三维框架构建而成的新型钒(III)磷酸铵。α-NH4V(HPO4)2与α-RbV(HPO4)2是同构的,并与先前描述的β-NH4V(HPO4)2互补:α-NH4V(HPO4)2含有四环(2个VO6和2个HPO4)和单环(2个VO6和3个HPO4)基团,而β-NH4V(HPO4)2只含有四环多面体基团。
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引用次数: 8
Experimental Electron Density study of NaH2PO4 at 30 K NaH2PO4在30k下的实验电子密度研究
Pub Date : 1998-02-01 DOI: 10.1107/S0108768197009622
M. Ichikawa, T. Gustafsson, I. Olovsson
The deformation electron density of sodium dihydrogen phosphate, NaHzPO4, at 30 K has been studied as a reference for the electron-density characteristics of hydrogen-bonded ferroelectrics containing phosphate ions. Clear peaks of deformation electron density (0.30.6 e A -3) are seen in the middle of each P--O bond and electron deficiency (-0.2 to -0.4 e A -3) on the opposite side of each P--O bond peak. The peak height is higher and the peak shape is more distinct in P--O bonds than in P---O(H) bonds as a whole; the distribution of deformation density in the region of lone-pair electrons is more diffuse. The O--H...O bond deformationdensity peaks of around 0.2 e A -3 appear in the middle of the O--H bond, followed by a deeper electron depletion of around -0.4 e A -3 on the H...O contract, just outside the H atom. The effective charges, defined as the integral of the deformation electron density, have the following values: around +0.2 for Na, +1.8 for P, -0.8 for O and +0.6 for H. The correlation of the deformationdensity peaks and the depth of the negative peak of the H atom with the hydrogen-bond distance are discussed.
研究了磷酸二氢钠(NaHzPO4)在30k下的变形电子密度,作为含磷酸盐离子的氢键铁电体电子密度特性的参考。在每个P—O键的中间可以看到明显的形变电子密度峰(0.30.6 e A -3),在每个P—O键的另一边可以看到电子缺乏症峰(-0.2 ~ -0.4 e A -3)。P—O键的峰高比P—O(H)键的峰高高,峰形比P—O(H)键更明显;变形密度在孤对电子区域的分布更为分散。O—H……O- H键中间出现了约0.2 e A -3的变形密度峰,随后在H键上出现了约-0.4 e A -3的更深的电子损耗。氧在氢原子外收缩。有效电荷,定义为变形电子密度的积分,有以下值:Na约为+0.2,P约为+1.8,O约为-0.8,H约为+0.6。讨论了变形密度峰和H原子负峰深度与氢键距离的关系。
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引用次数: 3
Li+/Na+β-alumina: A Combined Single Crystal Neutron and X-ray Diffraction Study Li+/Na+β-氧化铝:单晶中子和x射线联合衍射研究
Pub Date : 1997-08-01 DOI: 10.1107/S0108768197006629
K. Edström, T. Gustafsson, J. Thomas, G. Farrington
The crystal structure and ionic distribution in the conduction plane of the partially exchanged Na+ beta-alumina system Li0.75Na0.47Al11O17.11 has been determined from single-crystal X-ray diffraction at 30 and 298 K, in combination with a single-crystal
用单晶x射线衍射法测定了部分交换的Na+ β -氧化铝体系Li0.75Na0.47Al11O17.11在30和298 K下的晶体结构和离子分布
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引用次数: 7
Quantum chemical and experimental study of urea 尿素的量子化学及实验研究
Pub Date : 1996-08-08 DOI: 10.1107/S0108767396085455
D. Feil, R. D. Vries, V. Tsirelson, V. Zavodnik
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引用次数: 1
期刊
Acta Crystallographica
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