Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo‐Electron Microscopy Maps

In recent years, three‐dimensional density maps reconstructed from single particle images obtained by electron cryo‐microscopy (cryo‐EM) have reached unprecedented resolution. However, map interpretation can be challenging, in particular if the constituting structures require de‐novo model building or are very mobile. Herein, we demonstrate the potential of convolutional neural networks for the annotation of cryo‐EM maps: our network Haruspex has been trained on a carefully curated set of 293 experimentally derived reconstruction maps to automatically annotate RNA/DNA as well as protein secondary structure elements. It can be straightforwardly applied to newly reconstructed maps in order to support domain placement or as a starting point for main‐chain placement. Due to its high recall and precision rates of 95.1 % and 80.3 %, respectively, on an independent test set of 122 maps, it can also be used for validation during model building. The trained network will be available as part of the CCP‐EM suite.     

Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo-Electron Microscopy Maps

In recent years, three-dimensional density maps reconstructed from single particle images obtained by electron cryo-microscopy (cryo-EM) have reached unprecedented resolution. However, map interpretation can be challenging, in particular if the constituting structures require de-novo model building or are very mobile. Herein, we demonstrate the potential of convolutional neural networks for the annotation of cryo-EM maps: our network Haruspex has been trained on a carefully curated set of 293 experimentally derived reconstruction maps to automatically annotate RNA/DNA as well as protein secondary structure elements. It can be straightforwardly applied to newly reconstructed maps in order to support domain placement or as a starting point for main-chain placement. Due to its high recall and precision rates of 95.1 % and 80.3 %, respectively, on an independent test set of 122 maps, it can also be used for validation during model building. The trained network will be available as part of the CCP-EM suite.     

Inherent structures of condensed phases

The author’s subjective standpoint on the problem of inherent structure and on the history of this concept is expounded. The opinion is substantiated that basic regularities of the non-crystalline substances can be understood only on the level of inherent structures. In the case of structure of crystals this assertion is a triviality.     

Micro‐Scale Device—An Alternative Route for Studying the Intrinsic Properties of Solid‐State Materials: The Case of Semiconducting TaGeIr

An efficient application of a material is only possible if we know its physical and chemical properties, which is frequently obstructed by the presence of micro‐ or macroscopic inclusions of secondary phases. While sometimes a sophisticated synthesis route can address this issue, often obtaining pure material is not possible. One example is TaGeIr, which has highly sample‐dependent properties resulting from the presence of several impurity phases, which influence electronic transport in the material. The effect of these minority phases was avoided by manufacturing, with the help of focused‐ion‐beam, a μm‐scale device containing only one phase—TaGeIr. This work provides evidence for intrinsic semiconducting behavior of TaGeIr and serves as an example of selective single‐domain device manufacturing. This approach gives a unique access to the properties of compounds that cannot be synthesized in single‐phase form, sparing costly and time‐consuming synthesis efforts.     

Tailoring the Morphology and Fractal Dimension of 2D Mesh-like Gold Gels

As there is a great demand of 2D metal networks, especially out of gold for a plethora of applications we show a universal synthetic method via phase boundary gelation which allows the fabrication of networks displaying areas of up to 2 cm². They are transferred to many different substrates: glass, glassy carbon, silicon, or polymers such as PDMS. In addition to the standardly used web thickness, the networks are parametrized by their fractal dimension. By variation of experimental conditions, we produced web thicknesses between 4.1 nm and 14.7 nm and fractal dimensions in the span of 1.56 to 1.76 which allows to tailor the structures to fit for various applications. Furthermore, the morphology can be tailored by stacking sheets of the networks. For each different metal network, we determined its optical transmission and sheet resistance. The obtained values of up to 97 % transparency and sheet resistances as low as 55.9 Ω/sq highlight the great potential of the obtained materials.     

Tailoring the Morphology and Fractal Dimension of 2D Mesh‐like Gold Gels

As there is a great demand of 2D metal networks, especially out of gold for a plethora of applications we show a universal synthetic method via phase boundary gelation which allows the fabrication of networks displaying areas of up to 2 cm². They are transferred to many different substrates: glass, glassy carbon, silicon, or polymers such as PDMS. In addition to the standardly used web thickness, the networks are parametrized by their fractal dimension. By variation of experimental conditions, we produced web thicknesses between 4.1 nm and 14.7 nm and fractal dimensions in the span of 1.56 to 1.76 which allows to tailor the structures to fit for various applications. Furthermore, the morphology can be tailored by stacking sheets of the networks. For each different metal network, we determined its optical transmission and sheet resistance. The obtained values of up to 97 % transparency and sheet resistances as low as 55.9 Ω/sq highlight the great potential of the obtained materials.     

Two crystalline modifications of RuO4

RuO₄ was prepared by oxidation of elemental ruthenium. Two different modifications were obtained and investigated by X-ray single crystal diffraction. RuO₄-I has cubic symmetry , and two independent tetrahedral molecules are present in the unit cell. Within the standard uncertainties in both molecules the distances Ru-O are 1.695 Å. The second modification, RuO₄-II, is monoclinic and isotypic with OsO₄. There is one independent molecule in the unit cell, which shows distances Ru-O of 1.697 and 1.701 Å, respectively.     

Kristallstrukturen und chemische Bindung von AM2GeSe4 (A = Sr,Ba; M = Cu,Ag)

New Noncentrosymmetric Selenogermanates. I. Crystal Structures and Chemical Bonding of AM ₂GeSe₄ ( A = Sr, Ba; M = Cu, Ag) Three new quaternary selenogermanates were synthesized by heating the elements at 983–1073 K. Their crystal structures were determined by single crystal X‐ray methods. The dark red semiconductors crystallize in noncentrosymmetric space groups. SrCu₂GeSe₄ (Ama2, a = 10.807(4) Å, b = 10.735(4) Å, c = 6.541(2) Å, Z = 4) forms a new structure type, whereas BaCu₂GeSe₄ (P3₁, a = 6.490(1) Å, c = 16.355(3) Å, Z = 3) and BaAg₂GeSe₄ (I222, a = 7.058(1) Å, b = 7.263(1) Å, c = 8.253(2) Å, Z = 2) crystallize in structures known from thiostannates. Main structural features are almost regular GeSe₄‐, but distorted CuSe₄‐ or AgSe₄‐tetrahedra sharing corners or edges. Eight selenium atoms coordinate the alkaline earth atoms in the voids of these three dimensional tetrahedral networks. Chemical bonding and the electronic structure are elucidated by self‐consistent band structure calculations and the COHP method. The electron density and the electron localization function ELF of SrCu₂GeSe₄ reveal a significant stronger covalent character for the Ge–Se bonds compared with the Cu–Se bonds. For this reason the GeSe₄ tetrahedra appear as quasi molecular entities, arranged spatially according to the motifs of closest packing. The metal atoms occupy the tetrahedral and octahedral voids of these “tetrahedra packing”. This concept allows to derive the structures of AM₂GeSe₄‐compounds from simple binary structure types as Li₃Bi or Ni₂In.     

Helix Induction by Dirhodium: Access to Biocompatible Metallopeptides with Defined Secondary Structure

The use of carboxylate side chains to induce peptide helicity upon binding to dirhodium centers is examined through experimental and computational approaches. Dirhodium binding efficiently stabilizes α helicity or induces α helicity in otherwise unstructured peptides for peptides that contain carboxylate side chains with i, i+4 spacing. Helix induction is furthermore possible for sequences with i, i+3 carboxylate spacing, though in this case the length of the side chains is crucial: ligating to longer glutamate side chains is strongly helix inducing, whereas ligating the shorter aspartate side chains destabilizes the helical structure. Further studies demonstrate that a dirhodium metallopeptide complex persists for hours in cellular media and exhibits low toxicity toward mammalian cells, enabling exploitation of these metallopeptides for biological applications.     

LiAl的电子与几何结构

应用平面波展开和第一原理赝势法研究了锂铝单晶的电子和几何结构,给出LiAl各种可能结构的能量～体积关系图以及相关的能带结构,电子态密度和电荷密度分布等各种性质变化关系.讨论了B32结构与其他结构电子键合性质的不同,指出B32结构之所以成为LiAl最稳定的结构是由于Al＿Al原子形成了类似于Si＿Si的共价键合.计算得到的能量最低的稳定结构与实验以及其它的理论计算结果一致.     

Syntheses and crystal structures of mononuclear,tetranuclear and hexanuclear organotin compounds with derivatives of p -aminobenzoic acid

Four organotin(IV) compounds, [Bu₆Sn₆O₆(L¹)₆] (1), [Bu₆Sn₆O₆(L²)₄(L³)₂] (2), [Bu₈Sn₄O₂(L²)₄] (3) and [Ph₃Sn(L²)] (4), were obtained by reactions of BuSnOH, Bu₂SnO and Ph₃SnOH with 4-((6-chloropyridin-3-yl)methylamino)benzonic acid (HL¹), 4-((pyridin-2-yl)methylamino)benzonic acid (HL²) and p-aminobenzoic acid (HL³). 1 is a hexameric cluster, existing in a drum-like structure with prismatic Sn₆O₆ core. Compound 2 is a mixed drum, containing two kinds of carboxylic acid anions. Compound 3 possesses a Sn₄O₄ ladder structure. In 2 and 3, two-dimensional supramolecular structures are formed by the intermolecular hydrogen-bonding interactions. Compound 4 is a monomer with a dimer formed through π–π stacking between adjacent L² anions. Compounds 1–4 were characterized by elemental analyses and IR spectra.     

Synthesis and analysis of some adducts of 3,5-dinitrobenzamide

Adducts of 3,5-dinitrobenzamide, 1, with dimethylsulfoxide (DMSO), water and aza donor molecules like 4,4′-bipyridyl, 3, 1,2-bis(4-pyridyl)ethene, 4 and 1,2-bis(4-pyridyl)ethane, 5 are reported. While DMSO adduct was obtained by crystallization of 1 from DMSO, all other adducts were obtained by co-crystallization of 1 with the respective substrates from CH₃OH, except the water adduct. The water adduct, however, was obtained during the co-crystallization of 1 with 4-chloro or 4-aminobenzamide, but not upon crystallization from water directly. The adducts of aza donor compounds, 3-5 crystallize as solvates, incorporating solvent of crystallization. All these adducts were characterized by single crystal X-ray diffraction methods. All the adducts crystallize in centrosymmetric space groups with the amide moiety forming cyclic hydrogen bonds.     

Host-guest complexes of 3,5-dinitrobenzonitrile: channels and sandwich supramolecular architectures

Host-guest type complexes of 3,5-dinitrobenzonitrile, 1, with some hydrocarbons like benzene, naphthalene, p-xylene, o-xylene, and aza donor molecules (acridine, phenazine and phenothiazine) have been reported. In all the complexes, 1 forms a host network, yielding channels (in three-dimensional arrangement), which are filled by guest molecules, except in the complex of 1 with p-xylene. In this complex, although a host-guest type network is observed, the molecules of 1 and p-xylene are arranged in such a manner that the hydrocarbon is embedded between the layers of 1, like in inorganic clay structures. All the complexes have been characterized by single crystal X-ray diffraction methods.     

Artificial Antiferromagnets Possessing Extended Zero-, One-, Two-, and Three-Dimensional Structures

Layered (2D) artificial (or synthetic) antiferromagnets are fabricated by atom deposition techniques and possess very thin, nanometer-scale, magnetically ordered layers separated by a very thin nonmagnetic layer that antiferromagnetically couples the magnetic layers. Artificial antiferromagnets were crucial in the discovery of the giant magnetic effect (GMR), which had an incredible impact on the evolution of computer memory and its applications, and nucleated the dawn of spintronics (magnetoelectrics). The fundamental structural motif has been more recently achieved by using synthetic chemical methods that led to insulating artificial antiferromagnets. Examples of magnetically ordered layers that are antiferromagnetic coupled to form artificial antiferromagnets have been extended to isolated ions (0D) as well as extended chain (1D) and extended network 3D structures, and new phenomena and applications are anticipated as insulating antiferromagnets are more effective at propagating spin currents with respect to dielectric materials.     

Polycations Stabilised by Borosulfates: [Au3Cl4][B(S2O7)2] and the One-Dimensional Metal [Au2Cl4][B(S2O7)2](SO3)

(SO₄)-rich silicate analogue borosulfates are able to stabilise cationic cluster-like and chain-like aggregates. Single crystals of [Au₃Cl₄][B(S₂O₇)₂] and [Au₂Cl₄][B(S₂O₇)₂](SO₃) were obtained by solvothermal reaction with SO₃, and the electronic properties were investigated by means of density functional theory–based calculations. [Au₃Cl₄][B(S₂O₇)₂] exhibits a cluster-like cation, and the cationic gold-chloride strands in [Au₂Cl₄][B(S₂O₇)₂](SO₃) are found to resemble one-dimensional metallic wires. This is confirmed by polarisation microscopy.     

New Helical Folds in α‐Peptides with Alternating Chirality

In α‐peptides, the 8/10 helix is theoretically predicted to be energetically unstable and has not been experimentally observed so far. Based on our earlier studies on ‘helical induction’ and ‘hybrid helices’, we have adopted the ‘end‐capping’ strategy to induce the 8/10 helix in α‐peptides by using short α/β‐peptides. Thus, α‐peptides containing a regular string of α‐amino acids with alternating chirality were end capped by α/β‐peptides with 11/9‐helical motifs at the termini. Extensive NMR spectroscopy studies of these peptides revealed the presence of a hitherto unknown 8/10‐helical pattern; the H‐bonds in the shorter pseudorings were rather weak. The approach of using short helical motifs to induce new mixed helices in α‐peptides could provide avenues for more versatile design strategies.