Dimorphic ErAgSn and TmAgSn – High‐Pressure and High‐Temperature Driven Phase Transitions

The stannides ErAgSn and TmAgSn have been investigated under high‐temperature (HT) and high‐pressure (HP) conditions in order to investigate their structural chemistry. ErAgSn and TmAgSn are dimorphic: normal‐pressure (NP) ErAgSn and HT‐TmAgSn crystallize into the NdPtSb type structure, P6₃mc, a = 466.3(1), c = 729.0(2) pm for NP‐ErAgSn and a = 465.4(1), c = 726.6(2) pm for HT‐TmAgSn. NP‐ErAgSn was obtained via arc‐melting of the elements and subsequent annealing at 970 K, while HT‐TmAgSn crystallized directly from the melt by rapidly quenching the arc‐melted sample. HT‐TmAgSn transforms to the ZrNiAl type low‐temperature modification upon annealing at 970 K. The high‐pressure (HP) modification of ErAgSn was synthesized under multianvil high‐pressure (11.5 GPa) high‐temperature (1420 K) conditions from NP‐ErAgSn: ZrNiAl type, , a = 728.7(2), c = 445.6(1) pm. The silver and tin atoms in NP‐ErAgSn and HT‐TmAgSn build up two‐dimensional, puckered [Ag₃Sn₃] networks (277 pm intralayer Ag–Sn distance in NP‐ErAgSn) that are charge‐balanced and separated by the erbium and thulium atoms. The fourth neighbor in the adjacent layer has a longer Ag–Sn distance of 298 pm. The [AgSn] network in HP‐ErAgSn is three‐dimensional. Each silver atom has four tin neighbors (281–285 pm Ag–Sn). The [AgSn] network leaves distorted hexagonal channels, which are filled with the erbium atoms. The crystal chemistry of the three phases is discussed.     

Oligosilane‐ and Oligosiloxane‐bridged Phosphines – Synthesis,Structures, and Metalation

The range of molecular silicon phosphorus compounds has been extended by some new species containing oligosilane ((R₂Si)_n; n ≥ 2) or oligosiloxane ((R₂SiO)_mSiR₂; m ≥ 1) fragments bound to phosphorus atoms. Primary and secondary compounds of these types allow for the synthesis of metal derivatives. Such metalated species usually form oligomers and exhibit a versatile structural chemistry with cyclic, polycyclic, and cage‐like patterns. The main results obtained in the field of oligosilane‐ and oligosiloxane‐bridged phosphines will be presented below and the structures of the metal derivatives will be discussed. Moreover, the synthesis of an inorganic ligand on the basis of siloxane‐bridged phosphines will be presented. This compound opens up a new chapter in host‐guest chemistry.     

A Phosphorus Analogue of p-Quinodimethane with a Planar P4 Ring: A Metal-Free Diphosphorus Source

Para-quinodimethane (pQDM) is a fundamental structural component in many π-conjugated organic molecules and materials. The incorporation of phosphorus atom into π-conjugated frameworks offers unique opportunities for controlling the properties of derived species. A phosphorus analogue of p-quinodimethane (pQDM), (IPrC)₂P₄ [ 5 , IPr=C{N(Ar)CH₂}₂; Ar=2,6-iPr₂C₆H₃] featuring a planar P₄ ring, was readily accessible by KC₈-reduction of (IPrC)(PCl₂)₂ ( 2 ). Base-mediated C−H functionalization of IPrCH₂ ( 1 ) with PCl₃ afforded 2 . The formation of 5 was expected to occur through a dimerization of the transient 3H-diphosphirene (IPrC)P₂ ( 4 ), which was theoretically suggested to have an intermediate diradical character. Compound 5 underwent photo-induced ring-contraction reaction to form the singlet diradicaloid (IPrCP)₂ VI and white phosphorus (P₄). The formation of and VI and P₄ suggested the formal diphosphorus (P₂) elimination from 5 . Indeed, photolysis of a mixture of 1,3-cyclohexadiene (CHD) and 5 led to the formation of P₂-entrapped product (CHD)₂P₂ ( 6 ). The compound 5 represents the first organophosphorus species that functions as a P₂ source.     

Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/trans orientation of Xaa–Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.

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Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series**

The use of fluorescence techniques has an enormous impact on various research fields including imaging, biochemical assays, DNA-sequencing and medical technologies. This has been facilitated by the development of numerous commercial dyes with optimized photophysical and chemical properties. Often, however, information about the chemical structures of dyes and the attached linkers used for bioconjugation remain a well-kept secret. This can lead to problems for research applications where knowledge of the dye structure is necessary to predict or understand (unwanted) dye-target interactions, or to establish structural models of the dye-target complex. Using a combination of optical spectroscopy, mass spectrometry, NMR spectroscopy and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we propose a structure for Alexa Fluor 555 and refine that of AF555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647 maleimide. We also conducted a comprehensive comparison between Alexa Fluor and AF dyes by continuous-wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein-attached dyes. All these data support the idea that Alexa Fluor and AF dyes have a cyanine core and are a derivative of Cy3 and Cy5. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single-molecule FRET applications. Both pairs showed excellent performance in solution-based smFRET experiments using alternating laser excitation. Minor differences in apparent dye-protein interactions were investigated by molecular dynamics simulations. Our findings clearly demonstrate that the AF-fluorophores are an attractive alternative to Alexa- and Cy-dyes in smFRET studies or other fluorescence applications.