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1. Single-molecule fluorescence detection of a tricyclic nucleoside analogue

   https://doi.org/10.1039/D0SC03903A  

   Samaan, George N.; Wyllie, Mckenzie K.; Cizmic, Julian M.; Needham, Lisa-Maria; Nobis, David; Ngo, Katrina; Andersen, Susan; Magennis, Steven W.; Lee, Steven F.; Purse, Byron W. (February 2021, Chemical Science)

   null (Ed.)

   Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C -linked 8-(diethylamino)benzo[ b ][1,8]naphthyridin-2(1 H )-one nucleoside, which we name ABN, exhibits ε 442 = 20 000 M −1 cm −1 and Φ em,540 = 0.39 in water, increasing to Φ em = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities. 

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2. A folding motif formed with an expanded genetic alphabet

   https://doi.org/10.1038/s41557-024-01552-7  

   Wang, Bang; Rocca, James R; Hoshika, Shuichi; Chen, Cen; Yang, Zunyi; Esmaeeli, Reza; Wang, Jianguo; Pan, Xiaoshu; Lu, Jianrong; Wang, Kevin K; et al (October 2024, Nature Chemistry)

   Abstract Adding synthetic nucleotides to DNA increases the linear information density of DNA molecules. Here we report that it also can increase the diversity of their three-dimensional folds. Specifically, an additional nucleotide (dZ, with a 5-nitro-6-aminopyridone nucleobase), placed at twelve sites in a 23-nucleotides-long DNA strand, creates a fairly stable unimolecular structure (that is, the folded Z-motif, or fZ-motif) that melts at 66.5 °C at pH 8.5. Spectroscopic, gel and two-dimensional NMR analyses show that the folded Z-motif is held together by six reverse skinny dZ⁻:dZ base pairs, analogous to the crystal structure of the free heterocycle. Fluorescence tagging shows that the dZ⁻:dZ pairs join parallel strands in a four-stranded compact down–up–down–up fold. These have two possible structures: one with intercalated dZ⁻:dZ base pairs, the second without intercalation. The intercalated structure would resemble the i-motif formed by dC:dC⁺-reversed pairing at pH ≤ 6.5. This fZ-motif may therefore help DNA form compact structures needed for binding and catalysis. 

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3. A Nontemplated Route to Macrocyclic Dibridgehead Diphosphorus Compounds: Crystallographic Characterization of a “Crossed‐Chain” Variant of in / out Stereoisomers

   https://doi.org/10.1002/asia.201800739  

   Kharel, Sugam; Jia, Tiezheng; Bhuvanesh, Nattamai; Reibenspies, Joseph_H; Blümel, Janet; Gladysz, John_A (August 2018, Chemistry – An Asian Journal)

   Abstract Reactions of (O=)PH(OCH₂CH₃)₂and BrMg(CH₂)_mCH=CH₂(4.9–3.2 equiv;m=4 (a), 5 (b), 6 (c)) give the dialkylphosphine oxides (O=)PH[(CH₂)_mCH=CH₂]₂(2 a–c; 77–81 % after workup), which are treated with NaH and then α,ω‐dibromides Br(CH₂)_nBr (0.49–0.32 equiv;n=8 (a′), 10 (b′), 12 (c′), 14 (d′)) to yield the bis(trialkylphosphine oxides) [H₂C=CH(CH₂)_m]₂P(=O)(CH₂)_n(O=)P[(CH₂)_mCH=CH₂]₂(3 ab′,3 bc′,3 cd′,3 ca′; 79–84 %). Reactions of3 bc′and3 ca′with Grubbs’ first‐generation catalyst and then H₂/PtO₂afford the dibridgehead diphosphine dioxides(4 bc′,4 ca′; 14–19 %,n′=2m+2);³¹P NMR spectra show two stereoisomeric species (ca. 70:30). Crystal structures of two isomers of the latter are obtained,out,out‐4 ca′and a conformer ofin,out‐4 ca′that features crossed chains, such that the (O=)P vectors appearout,out. Whereas4 bc′resists crystallization, a byproduct derived from an alternative metathesis mode, (CH₂)₁₂P(=O)(CH₂)₁₂(O=)P(CH₂)₁₂, as well as3 ab′and3 bc′, are structurally characterized. The efficiencies of other routes to dibridgehead diphosphorus compounds are compared. 

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4. Clarifying the structures of imidines: using crystallographic characterization to identify tautomers and localized systems of π-bonding

   https://doi.org/10.1107/S2053229623002036  

   Aristov, Michael M.; Geng, Han; Harris, James W.; Berry, John F. (April 2023, Acta Crystallographica Section C Structural Chemistry)

   Nitrogen heterocycles are a class of organic compounds with extremely versatile functionality. Imidines, HN[C(NH) R ] 2 , are a rare class of heterocycles related to imides, HN[C(O) R ] 2 , in which the O atoms of the carbonyl groups are replaced by N—H groups. The useful synthesis of the imidine compounds succinimidine and glutarimidine, as well as their partially hydrolyzed imino–imide congeners, was first described in the mid-1950s, though structural characterization is presented for the first time in this article. In the solid state, these structures are different from the proposed imidine form: succinimidine crystallizes as an imino–amine, 2-imino-3,4-dihydro-2 H -pyrrol-5-amine, C 4 H 7 N 2 ( 1 ), glutarimidine as 6-imino-3,4,5,6-tetrahydropyridin-2-amine methanol monosolvate, C 5 H 9 N 3 ·CH 3 OH ( 2 ), and the corresponding hydrolyzed imino–imide compounds as amino–amides 5-amino-3,4-dihydro-2 H -pyrrol-2-one, C 4 H 6 N 2 O ( 3 ), and 6-amino-4,5-dihydropyridin-2(3 H )-one, C 5 H 8 N 2 O ( 4 ). Imidine 1 was also determined as the hydrochloride salt solvate 5-amino-3,4-dihydro-2 H -pyrrol-2-iminium chloride–2-imino-3,4-dihydro-2 H -pyrrol-5-amine–water (1/1/1), C 4 H 8 N 3 + ·Cl − ·C 4 H 7 N 3 ·H 2 O ( 1 ·HCl). As such, 1 and 2 show alternating short and long C—N bonds across the molecule, revealing distinct imino (C=NH) and amine (C—NH 2 ) groups throughout the C—N backbone. These structures provide definitive evidence for the predominant imino–amine tautomer in the solid state, which serves to enrich the previously proposed imidine-focused structures that have appeared in organic chemistry textbooks since the discovery of this class of compounds in 1883. 

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5. Synthesis, molecular and crystal structures of 4-amino-3,5-difluorobenzonitrile, ethyl 4-amino-3,5-difluorobenzoate, and diethyl 4,4′-(diazene-1,2-diyl)bis(3,5-difluorobenzoate)

   https://doi.org/10.1107/S2056989024006819  

   Novikov, Egor M; Guillen_Campos, Jesus; Read_de_Alaniz, Javier; Fonari, Marina S; Timofeeva, Tatiana V (August 2024, Acta Crystallographica Section E Crystallographic Communications)

   The crystal structures of two intermediates, 4-amino-3,5-difluorobenzonitrile, C₇H₄F₂N₂(I), and ethyl 4-amino-3,5-difluorobenzoate, C₉H₉F₂NO₂(II), along with a visible-light-responsive azobenzene derivative, diethyl 4,4′-(diazene-1,2-diyl)bis(3,5-difluorobenzoate), C₁₈H₁₄F₄N₂O₄(III), obtained by four-step synthetic procedure, were studied using single-crystal X-ray diffraction. The molecules ofIandIIdemonstrate the quinoid character of phenyl rings accompanied by the distortion of bond angles related to the presence of fluorine substituents in the 3 and 5 (ortho) positions. In the crystals ofIandII, the molecules are connected by N—H...N, N—H...F and N—H...O hydrogen bonds, C—H...F short contacts, and π-stacking interactions. In crystal ofIII, only stacking interactions between the molecules are found. 

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