Structural polymorphism of crystalline polymers: Electron and atomic force microscopy contributions

The contribution of electron microscopy, electron diffraction and atomic force microscopy to the elucidation of the structure of polymers -in particular helical polyolefins- is briefly presented. Particular emphasis is put on the elucidation of rather subtle aspects of the structure, such as disorders introduced by packing of up and down, or left and right handed helices in the lattice. The spectroscopic and diffraction informations are evaluated and compared.     

Electron attachment induced proton transfer in a DNA nucleoside pair: 2'-deoxyguanosine-2'-deoxycytidine

To elucidate electron attachment induced damage in the DNA double helix, electron attachment to the 2'-deoxyribonucleoside pair dG:dC has been studied with the reliably calibrated B3LYP/DZP++ theoretical approach. The exploration of the potential energy surface of the neutral and anionic dG:dC pairs predicts a positive electron affinity for dG:dC [0.83 eV for adiabatic electron affinity (EAad) and 0.16 eV for vertical electron affinity (VEA)]. The substantial increases in the electron affinity of dG:dC (by 0.50 eV for EAad and 0.23 eV for VEA) compared to those of the dC nucleoside suggest that electron attachment to DNA double helices should be energetically favored with respect to the single strands. Most importantly, electron attachment to the dC moiety in the dG:dC pair is found to be able to trigger the proton transfer in the dG:dC- pair, surprisingly resulting in the lower energy distonic anionic complex d(G-H)-:d(C+H).. The negative charge for the latter system is located on the base of dC in the dG:dC- pair, while it is transferred to d(G-H) in d(G-H)-:d(C+H)., accompanied by the proton transfer from N1(dG) to N3(dC). The low energy barrier (2.4 kcal/mol) for proton transfer from dG to dC- suggests that the distonic d(G-H)-:d(C+H). pair should be one of the important intermediates in the process of electron attachment to DNA double helices. The formation of the neutral nucleoside radical d(C+H). is predicted to be the direct result of electron attachment to the DNA double helices. Since the neutral radical d(C+H). nucleotide is the key element in the formation of this DNA lesion, electron attachment might be one of the important factors that trigger the formation of abasic sites in DNA double helices.     

Elucidation of the structure of poly(γ-benzyl-l-glutamate) nanofibers and gel networks in a helicogenic solvent

The synthesis, characterization, self-assembly, and gel formation of poly(γ-benzyl-l-glutamate) (PBLG) in a molecular weight range from ca. 7,000–100,000 g/mol and with narrow molecular weight distribution are described. The PBLG is synthesized by the nickel-mediated ring-opening polymerization and is characterized by size-exclusion chromatography coupled with multiple-angle laser light scattering, NMR, and Fourier transform infrared spectroscopy. The self-assembly and thermoreversible gel formation in the helicogenic solvent toluene is investigated by transmission electron microscopy, atomic force microscopy, small-angle X-ray scattering, and synchrotron powder X-ray diffraction. At concentrations significantly below the minimum gelation concentration, spherical aggregates are observed. At higher concentrations, gels are formed, which show a 3D network structure composed of nanofibers. The proposed self-assembly mechanism is based on a distorted hexagonal packing of PBLG helices parallel to the axis of the nanofiber. The gel network forms due to branching and rejoining of bundles of PBLG nanofibers. The network exhibits uniform domains with a length of 200?±?42 nm composed of densely packed PBLG helices.      

Effect of the peptide secondary structure on the peptide amphiphile supramolecular structure and interactions

Bottom-up fabrication of self-assembled nanomaterials requires control over forces and interactions between building blocks. We report here on the formation and architecture of supramolecular structures constructed from two different peptide amphiphiles. Inclusion of four alanines between a 16-mer peptide and a 16 carbon long aliphatic tail resulted in a secondary structure shift of the peptide headgroups from α helices to β sheets. A concomitant shift in self-assembled morphology from nanoribbons to core-shell worm-like micelles was observed by cryogenic transmission electron microscopy (cryo-TEM) and atomic force microscopy (AFM). In the presence of divalent magnesium ions, these a priori formed supramolecular structures interacted in distinct manners, highlighting the importance of peptide amphiphile design in self-assembly.     

BUNDLE: A program for building the transmembrane domains of G-protein-coupled receptors

The only information available at present about the structural features of G-protein-coupled receptors (GPCRs) comes from low resolution electron density maps of rhodopsin obtained from electron microscopy studies on 2D crystals. Despite their low resolution, maps can be used to extract information about transmembrane helix relative positions and their tilt. This information, together with a reliable algorithm to assess the residues involved in each of the membrane spanning regions, can be used to construct a 3D model of the transmembrane domains of rhodopsin at atomic resolution. In the present work, we describe an automated procedure applicable to generate such a model and, in general, to construct a 3D model of any given GPCR with the only assumption that it adopts the same helix arrangement as in rhodopsin. The present approach avoids uncertainties associated with other procedures available for constructing models of GPCRs based on a template, since sequence identity among GPCRs of different families in most of the cases is not significant. The steps involved in the construction of the model are: (i) locate the centers of the helices according to the low-resolution electron density map; (ii) compute the tilt of each helix based on the elliptical shape observed by each helix in the map; (iii) define a local coordinate system for each of the helices; (iv) bring them together in an antiparallel orientation; (v) rotate each helix through the helical axis in such a way that its hydrophobic moment points in the same direction of the bisector formed between three consecutive helices in the bundle; (vi) rotate each helix through an axis perpendicular to the helical one to assign a proper tilt; and (vii) translate each helix to its center deduced from the projection map.     

涤纶与对乙酰氧基苯甲酸共聚酯的结构和性能的研究

本文对不同组成的涤纶与对乙酰氧基苯甲酸的无规共聚酯(PET-PHB)采用偏光显微镜、电子显微镜、X射线衍射及DSC等技术进行了研究。结果表明,当组成在～30(mol)％ PHB时开始出现热致性液晶,熔体变混浊,此时骤冷样品密度、平衡熔点、开始结晶的过冷程度及过热程度等与组成的关系都出现了突变。提出了液晶相中PHB-PHB链段可能存在以头尾相反方式形成的双链麻花棒按向列型方式排列。     

Design of Aromatic Helical Polymers for STM Visualization: Imaging of Single and Double Helices with a Pattern of π–π Stacking

From scanning tunneling microscopy (STM) images of rationally designed helical polymers with a pattern of π–π stacking, we successfully identified the single‐ and double‐helical superstructures. The STM images of the helical structures revealed the smallest helical architecture (diameter ca. 1.3 nm) that has been seen so far. Furthermore, the interconversion of single and double helices was further underpinned by experimental analyses. Significantly, the formation of double helices induced different supramolecular chirality to that observed for the single helices.     

A general procedure for building the transmembrane domains of G‐protein coupled receptors

The only results available at present about the structural features of G‐protein coupled receptors are the low resolution electron projection maps obtained from microscopy studies carried out on two‐dimensional crystals of rhodopsin. These studies support previous suggestions that these integral proteins are constituted by seven transmembrane domains. The low resolution electron density map of rhodopsin can be used to extract information about helix relative positions and tilt. This information, together with a reliable procedure to assess the residues involved in each of the transmembrane regions, can be used to construct a model of rhodopsin at atomic resolution. We have developed an algorithm that can be used to generate such a model in a completely automated fashion. The steps involved are: (i) locate the centers of the helices according to the low resolution electron density map; (ii) compute the tilt of each helix based on the elliptical shape observed by each helix in the map; (iii) define a local coordinate system for each of the helices; (iv) bring them together in an antiparallel orientation; (v) rotate each helix through the helical axis in such a way that its hydrophobic moment points in the same direction as the bisector formed between three consecutive helices in the bundle; (vi) rotate each helix through an axis perpendicular to the helical one to assign a proper tilt; (vii) translate each of the helix to its center deduced from the projection map. A major advantage of the procedure presented is its generality and consequently can be used to obtain a model of any G‐protein coupled receptor with the only assumption that the shape of the bundle is the same as found in rhodopsin. This avoids uncertainties found in other procedures that construct models of G‐protein coupled receptors based on sequence homology using rhodopsin as template. This revised version was published online in July 2006 with corrections to the Cover Date.     

High-resolution electron microscopic study of manganese silicides MnSi2−x

Several members of the family of Nowotny phases with compositions MnSi_2−x are studied by means of electron diffraction and high-resolution electron microscopy. The diffraction patterns exhibit spacing as well as orientation “anomalies.” From the corresponding high-resolution images it is concluded that the compounds exhibit a particular type of disorder. The spacing anomalies result from the fact that the manganese and silicon arrangements have different and to some extent independent periods along the c direction of the tetragonal structure. The orientation anomaly is due to the fact that the silicon helices can be shifted longitudinally along the c axis of the manganese sublattice. Dislocation-like arrangements of lattice fringes can consistently be explained by means of this model.     

Spectroscopic imaging techniques for characterization of polymer morphologies: a combination of infrared and electron microscopy

The morphological characterization of polymer blends consisting of polyamide and poly(tetrafluoroethylene) using FT-IR spectroscopy and electron microscopy is described. To enhance the lateral resolution - one of the main limits in infrared spectroscopy - a combination with scanning electron microscopy and analytical electron microscopic methods of a transmission electron microscope was made. The possibilities of electron energy loss spectroscopy and energy filtered transmission electron microscopy (EFTEM) in the area of polymer characterization are outlined.     

The microfibrillar network in gels of poly(γ-benzyl-L-glutamate) in benzyl alcohol

The gelation and gel-melting phenomena in semidilute isotropic solutions of poly(γ-benzyl-L -glutamate) (PBLG) in benzyl alcohol were studied by small-angle neutron scattering measurements, using a deuterated solvent, and by cryotransmission electron microscopy. The reversible gels are formed when the solution is cooled below the gelation temperature, and the gels melt upon heating. Hysteresis, of about 15°C, is observed between gelation and melting temperatures. In the isotropic solution, PBLG exists as isolated helices. Gelation is apparent as a large increase in the intensity scattered at low angles, signifying the heterogeneous microstructure of the gel. Direct visualization by electron microscopy of vitrified gel samples shows the formation of a microfibrillar network. The dimension of the observed microfibrils is about 10 nm. Upon melting, microstructural changes appear in a temperature range of about 10°C. The unique feature of the gel melting is that initially only the intensity in the mid-angle range decreases. This is interpreted as thickening of the microstructure due to melting of the thinner microfibrils. The final stage marks the melting of the thicker microfibrils. © 1996 John Wiley & Sons, Inc.     

Phosphonate lipid tubules II

We describe a new chiral tubule-forming lipid in which the C-O-P phosphoryl linkage of the archetypal tubule-forming molecule, 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine, "DC(8,9)PC", is replaced by a C-P linkage. Tubule formation with this phosphonate analogue proceeds under the same mild conditions as with DC(8,9)PC and produces similar yields, but synchrotron small-angle X-ray scattering, atomic force microscopy, and optical microscopy show the new tubules to have diameters 1.94 times as great, to be significantly shorter, and to be thinner-walled. A significant portion of the enantiomerically pure chiral phosphonate precipitate is in the form of stable open helices, and these helices are divided almost evenly between left- and right-handed members.     

Electron attachment to a hydrated DNA duplex: the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine

The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.     

Electron hole flow patterns through the RNA-cleaving 8-17 deoxyribozyme yield unusual information about its structure and folding

DNA double helices have been shown to conduct electron holes over significant distances. Here, we report on the hole flow patterns within a more intricately folded DNA complex, the 8-17 deoxyribozyme bound to a DNA pseudosubstrate, incorporating three helical elements and two catalytically relevant loops. The observed hole flow patterns within the complex permitted a quantitative assessment of the stacking preferences of the three constituent helices and provided evidence for significant transitions within the complex's global geometry. The patterns further suggested varying levels of solvent exposure of the complex's constituent parts, and revealed that a catalytically relevant cytosine within the folded complex exists in an unusual structural/electronic environment. Our data suggest that the study of charge flow may provide novel perspectives on the structure and folding of intricately folded DNAs and RNAs.     

Crystalline,Few-layer 2D Materials via Surfactant-monolayer-assisted Interfacial Synthesis

Prof. FENG Xinliang and coworkers from Dresden University of Technology reported surfactant-monolayer-assisted interfacial synthesis(SMAIS) as a general strategy for the controlled synthesis of few-layer 2D polymers to realize high crystallinity with large domain. The two-dimensional polyamide(Nature Chemistry, doi.org/10.1038/s41557-019-0327-5) and quasi-two-dimensional polyaniline(Nature Communication, doi.org/10.1038/s41467-019-11921-3) thin films were successfully obtained with the help of surfactants and fully characterized by optical microscopy, transmission electron microscopy, electron diffraction and atomic force microscopy.     

Superhard coatings — Production and analysis

In the development of diamond and c-BN products the analytical methods for characterizing the surface, bulk and interface of the diamond coatings are very important. SEM, Raman, XRD and IR are the methods used for characterization and SIMS, TEM, AES, NRA, RBS, XPS, STM, etc. are used for the investigation of special problems. The techniques for diamond and c-BN production are briefly summarized to give an idea of the complex interactions between production, application and analytical characterization. The analytical methods for diamond characterization and many relevant results are summarized in this paper; some physical properties (e.g. thermal conductivity, transparency, etc.) and their interaction with applications are also discussed.Abbreviations AES Auger electron spectroscopy - AFM atomic force microscopy - c-BN cubic boron nitride - CL cathodoluminescence - CVD chemical vapour deposition - EELS electron energy loss spectroscopy - EPMA electron probe microanalysis - ERDA elastic recoil detection analysis - h-BN hexagonal boron nitride - HP-HT high-pressure high-temperature - HF hot-filament - IR infra-red - LEED low energy electron diffraction - MW microwave - NAA neutron activation analysis - NRA nuclear reaction analysis - PL photoluminescence - PVD physical vapour deposition - RBS Rutherford backscattering spectrometry - RHEED reeflected high energy electron diffraction - SAD selected area diffraction - SEM scanning electron microscopy - SIMS secondary ion mass spectrometry - STM secondary ion mass spectrometry - TEM transmission electron microscopy - TMB trimethylborate - XPS X-ray photoelectron spectroscopy - XRD X-ray diffraction Dedicated to Professor Dr. rer. nat. Dr. h.c. Hubertus Nickel on the occasion of his 65th birthday     

Molecular packing and morphology of oligo(m-phenylene ethynylene) foldamers

Understanding and controlling solid-state morphologies and molecular conformations is the key to optimizing the properties of materials. As an example for the influence of small chemical changes on solid-state structures, we studied oligo(m-phenylene ethynylene) foldamers, where the introduction of an endo-methyl group induces a transition from an extended all-transoid to a helical all-cisoid conformation. The resulting structural changes were analyzed by X-ray diffraction (XRD), polarized optical microscopy (POM), and low-dose high-resolution electron microscopy (LD-HREM) over several length scales from the molecular to the mesoscopic level. The strong tendency of the endo-methyl oligomer 1 to form stable compact helices in solution resulted in round droplets with an ordered hexagonal columnar (Col(ho)) liquid crystalline structure, where shrinkage during the crystallization resulted in the formation of a banded texture. On the other hand, the endo-hydrogen oligomer 2 exhibited a very different morphology; its extended linear shape was maintained during crystallization and resulted in an extended lamellar structure, which was determined by a compromise between crystalline packing and minimization of the surface area. Another pronounced difference between both molecular structures was the ability of the extended lamellar "crystals" to bend, whereas the helices form either straight or disordered domains. In addition, both materials exhibit strong surface effects, which extend considerably inside the droplet and induce uniform bending of the supramolecular structures.     

Preparation and characterization of gadolinium hydroxide single-crystalline nanorods by a hydrothermal process

The Gd(OH)3 nanorods with diameters of ca.40-60 nm and lengths of more than 400-550 nm have been prepared by a novelhydrothermal technique.The structural features and chemical composition of the nanorods were investigated by X-ray diffraction(XRD),transmission electron microscopy(TEM),and field emission scanning electron microscope(FESEM),selected areaelectron diffraction(SAED),and high resolution transmission electron microscopy(HRTEM).The possible mechanism for theformation of Gd(OH)3 nanorods was proposed.     

Synthesis and characterization of cuprous selenide nanocrystals at room temperature

A simple method has been developed to prepare cuprous selenide nanocrystals by the reaction of copper nitrate trihydrate with selenium and sodium mercaptoacetate in aqueous ammonia system. Cu_2Se nanocrystals were characterized by transmission electron microscopy (TEM), high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), electron diffraction (ED), fluorescence spectrum and ultraviolet-visible absorption spectrum. Cu_2Se nanocrystals showed berzelianite structure with 20-40 nm in length and 10-20 nm in width. A possible mechanism is also discussed.     

Design of Chiral β-Double Helices from γ-Peptide Foldamers

Chirality is ubiquitous in nature, and homochirality is manifested in many biomolecules. Although β-double helices are rare in peptides and proteins, they consist of alternating L- and D-amino acids. No peptide double helices with homochiral amino acids have been observed. Here, we report chiral β-double helices constructed from γ-peptides consisting of alternating achiral (E)-α,β-unsaturated 4,4-dimethyl γ-amino acids and chiral (E)-α,β-unsaturated γ-amino acids in both single crystals and in solution. The two independent strands of the same peptide intertwine to form a β-double helix structure, and it is stabilized by inter-strand hydrogen bonds. The peptides with chiral (E)-α,β-unsaturated γ-amino acids derived from α-L-amino acids adopt a (P)-β-double helix, whereas peptides consisting of (E)-α,β-unsaturated γ-amino acids derived from α-D-amino acids adopt an (M)-β-double helix conformation. The circular dichroism (CD) signature of the (P) and (M)-β-double helices and the stability of these peptides at higher temperatures were examined. Furthermore, ion transport studies suggested that these peptides transport ions across membranes. Even though the structural analogy suggests that these new β-double helices are structurally different from those of the α-peptide β-double helices, they retain ion transport activity. The results reported here may open new avenues in the design of functional foldamers.