An extended planar C5 conformation and a 310-helical structure of peptide foldamer composed of diverse alpha-ethylated alpha,alpha-disubstituted alpha-amino acids

Optically active peptide foldamers Tfa-[(S)-(alphaEt)Leu]-[(S)-(alphaEt)Nva]-Deg-[(S)-(alphaEt)Nle]-OEt (10) and Tfa-[(S)-(alphaEt)Val]-[(S)-(alphaEt)Leu]-[(S)-(alphaEt)Nva]-Deg-[(S)-(alphaEt)Nle]-OEt (11) composed of diverse alpha-ethylated alpha,alpha-disubstituted alpha-amino acids were synthesized. The dominant conformation of these peptides in solution was an unusual, fully extended planar conformation, and that in the crystal state was both right-handed (P) and left-handed (M) 3(10)-helical structures in 10 and a P 3(10)-helical structure in 11, respectively. The preferred planar C(5) conformation of the peptides prepared from chiral alpha-ethylated alpha,alpha-disubstituted alpha-amino acids was drastically different from the 3(10)-helical structure of the peptides prepared from chiral alpha-methylated alpha,alpha-disubstituted alpha-amino acids.     

Folding control in cyclic peptides through N-methylation pattern selection: formation of antiparallel beta-sheet dimers, double reverse turns and supramolecular helices by 3alpha,gamma cyclic peptides

Peptide foldamers constitute a growing class of nanomaterials with potential applications in a wide variety of chemical, medical and technological fields. Here we describe the preparation and structural characteristics of a new class of cyclic peptide foldamers (3alpha,gamma-CPs) that, depending on their backbone N-methylation patterns and the medium, can either remain as flat rings that dimerize through arrays of hydrogen bonds of antiparallel beta-sheet type, or can fold into twisted double reverse turns that, in the case of double gamma-turns, associate in nonpolar solvents to form helical supramolecular structures. A 3alpha,gamma-CP consists of a number of multiples of a repeat unit made up of four amino acid residues of alternating chirality: three corresponding to alpha-amino acids and one to a gamma-amino acid (a cis-3-aminocycloalkanecarboxylic acid).     

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.     

Low-valent niobium-catalyzed reduction of alpha,alpha,alpha-trifluorotoluenes

[reaction: see text] In the presence of 5 mol % of niobium(V) chloride, alpha,alpha,alpha-trifluorotoluene derivatives were reduced with lithium aluminum hydride to give toluene derivatives in good yields. Stepwise, partial reduction of bis(trifluoromethyl)benzene derivative was also demonstrated.     

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.     

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.