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.     

Halogenomercury Salts of Sterically Crowded Triazenides – Convenient Starting Materials for Redox‐Transmetallation Reactions

Diaryl‐substituted triazenides Ar(Ar′)N₃HgX [Ar/Ar′ = Dmp/Mph, X = Cl ( 2a ), Br ( 3a ), I ( 4a ); Ar/Ar′ = Dmp/Tph, X = Cl ( 2b ), I ( 4b ) with Mph = 2‐MesC₆H₄, Mes = 2,4,6‐Me₃C₆H₂, Tph = 2′,4′,6′‐triisopropylbiphenyl‐2‐yl and Dmp = 2,6‐Mes₂C₆H₃] were synthesized by salt‐metathesis reactions in ethyl ether from the readily available starting materials Ar(Ar′)N₃Li and HgX₂. These compounds may be used for redox‐transmetallation reactions with rare‐earth or alkaline earth metals. Thus, reaction of 4b or 2b with magnesium or ytterbium in tetrahydrofuran afforded the triazenides Dmp(Tph)N₃MX(thf) ( 5b : M = Mg, X = I; 6b : M = Yb, X = Cl) in good yield. All new compounds were characterized by melting point, ¹H and ¹³C NMR spectroscopy and for selected species by IR spectroscopy or mass spectrometry. In addition, the solid‐state structures of triazenides 2a , 2b , 3a , 4b , 5b and 6b were investigated by single‐crystal X‐ray diffraction.     

Thermal,Magnetic, Electronic,and Superconducting Properties of Rare‐Earth Metal Pentagermanides REGe5 (RE = La,Nd, Sm,Gd) and Synthesis of TbGe5

A series of isotypic rare‐earth metal pentagermanides including the new compound TbGe₅ were prepared by high‐pressure synthesis. They crystallize in the orthorhombic space group Immm [No. 71; a = 395.70(9) pm; b = 611.1(2) pm, and c = 983.6(3) pm for TbGe₅]. The crystal structure is isotypic to LaGe₅ and consists of puckered germanium slabs, which sandwich a second germanium species and the rare‐earth metal atoms. At ambient pressure, the thermal decomposition of the phases REGe₅ (RE = La, Nd, Sm, Gd, and Tb) proceeds via discrete intermediate steps into Ge(cF8) and thermodynamically stable germanium‐poorer phases. The investigated compounds REGe₅ are paramagnetic metallic conductors, which order antiferromagnetically at low temperatures. Specific heat measurements reveal that the superconducting state of LaGe₅ below T_c = 7.1(1) K is characterized by a critical field of μ₀H_c2 = 0.2 T and weak electron‐phonon coupling. Density‐functional based band‐structure calculations yield a very similar electronic structure for all the isotypic REGe₅ compounds. Besides a slight increase in the width of the valence band for smaller RE atoms, only minor differences are found for the two different germanium environments.     

Structural Investigations and Thermal Behaviour of Mercury(II) Sulfito Complexes

The crystal structures of (NH₄)[HgSO₃Cl] ( 1 ) and of (NH₄)₂[Hg(SO₃)₂] ( 2 ) were determined from single crystal diffractometer data sets. 1 : 22 °C, Pnma, Z = 4, a = 15.430(3), b = 5.525(1), c = 6.679(1) Å, R(F) = 0.0256, R_w(F²) = 0.0642 (all 1056 unique reflections). 2 : ?108 °C, P2₁2₁2₁, Z = 4, a = 6.2240(4), b = 9.3908(6), c = 13.6110(8) Å, R(F) = 0.0179, R_w(F²) = 0.0493 (all 2699 unique reflections). The structure of 1 contains bent Cl‐Hg‐SO₃ entities (site symmetry m; d(Hg‐Cl) = 2.3403(13) Å, d(Hg‐S) = 2.3636(12) Å, ∠(Cl‐Hg‐S) = 164.51(5)°, d(S‐O) 2×1.458(3) Å, 1.468(4) Å, = 1.461Å) linked to undulated ribbons parallel to the b ‐axis by intermolecular secondary bonds SO···Hg (d(O···Hg) = 2×2.595(3) Å). These ribbons in turn aggregate to layers around the bc ‐plane. The layers are stacked along the a ‐axis with interlayer distances of a /2. The structure of 2 is made up of O₃S‐Hg‐SO₃ moieties (d(Hg‐S) = 2.3935(7), 2.3935(8) Å; ∠(Hg‐S‐Hg) = 174.41(3)°; = 1.474Å), that are linked to ribbons parallel to the a axis by coordination of Hg to three remote O atoms (2.801(4) < d(Hg‐O) < 2.844(3) Å). Adjacent ribbons are joined together by an additional Hg‐O contact of 2.733(3) Å, leading to a three‐dimensional anionic framework. Both crystal structures are stabilised by disordered NH₄⁺ cations, placed between the anionic layers or in the vacancies of the framework, via moderate hydrogen bonding interactions N‐H···O with donor‐acceptor distances ranging from 2.8 to 3.2Å. 1 and 2 were further characterised by thermal analysis (TG, DSC). They start to decompose at temperatures above 130 °C.