Targeting RNA G‐Quadruplex in SARS‐CoV‐2: A Promising Therapeutic Target for COVID‐19?

The COVID‐19 pandemic caused by SARS‐CoV‐2 has become a global threat. Understanding the underlying mechanisms and developing innovative treatments are extremely urgent. G‐quadruplexes (G4s) are important noncanonical nucleic acid structures with distinct biofunctions. Four putative G4‐forming sequences (PQSs) in the SARS‐CoV‐2 genome were studied. One of them (RG‐1), which locates in the coding sequence region of SARS‐CoV‐2 nucleocapsid phosphoprotein (N), has been verified to form a stable RNA G4 structure in live cells. G4‐specific compounds, such as PDP (pyridostatin derivative), can stabilize RG‐1 G4 and significantly reduce the protein levels of SARS‐CoV‐2 N by inhibiting its translation both in vitro and in vivo. This result is the first evidence that PQSs in SARS‐CoV‐2 can form G4 structures in live cells, and that their biofunctions can be regulated by a G4‐specific stabilizer. This finding will provide new insights into developing novel antiviral drugs against COVID‐19.     

Evidence for d‐Orbital Aromaticity in Sn‐ and Pb‐Based Clusters: Is Sn2‐12 Aromatic?

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.     

Is the Excited‐State H‐atom Transfer in Hypericin Concerted?¶

The excited-state intramolecular H-atom transfer of hypericin (Hyp) was investigated as a function of pH in monodispersed reverse micelles formed by sodium bis(2-ethylhexyl)sulfosuccinate/heptane/water and in complexes with Tb3+ under conditions in which one of the two carbonyl groups of Hyp is incapable of accepting a hydrogen atom. The results of pump-probe transient absorption experiments provide no evidence for a concerted H-atom transfer mechanism.     

How Strong Are Hydrogen Bonds in Metalla‐β‐diketones?

The energies of the kinetically inert, electronically saturated Lukehart-type metalla-beta-diketone [Re{(COMe)2H}(CO)4] (9 a) and of the kinetically labile, electronically unsaturated platina-beta-diketones [Pt{(COMe)2H}Cl2]- (10 a), [Pt2{(COMe)2H}2(micro-Cl)2] (11 a), and [Pt{(COMe)2H}(bpy)]+ (12 a) have been calculated by DFT at the B3LYP/6-311++G(d,p) level using effective core potentials with consideration of relativistic effects for the transition metals. Analogously, energies of the requisite open (non-hydrogen-bonded) equilibrium conformers (9 b, 10 c, 11 b, 12 b) and energies which were obtained from the hydrogen-bonded conformers by rigid rotation of the OH group around the C--O bond by 180 degrees followed by relaxation of all bond lengths and angles (9 c, 10 d, 11 c, 12 d) have been calculated. These energies were found to be higher by 14.7/27.2 (9 b/9 c), 20.7/27.2 (10 c/10 d), 19.2/25.7 (11 b/11 c), and 9.4/19.6 kcal mol(-1) (12 b/12 d) than those of the intramolecularly O--HO hydrogen-bonded metalla-beta-diketones 9 a, 10 a, 11 a, and 12 a, respectively. In acetylacetone (Hacac), the generic organic analogue of metalla-beta-diketones, the energies of the most stable non-hydrogen-bonded enol isomer (6 b) and of the conformer derived from the H-bonded form by rigid rotation of the OH group by 180 degrees followed by subsequent relaxation of all bond lengths and angles (6 k) were found to be 10.9/16.1 kcal mol(-1) (6 b/6 k) higher compared to the intramolecularly O--HO bonded isomer 6 a. Thus, the hydrogen bonds in metalla-beta- diketones must be regarded as strong and were found to be up to twice as strong as that in acetylacetone. A linear relationship was found between the hydrogen-bond energies based on the rigidly rotated structures and the OO separation in the hydrogen-bonded structures. Furthermore, these energies were also found to be correlated with the electron densities at the OH bond critical points (rhobcp) in the O--HO bonds of metalla-beta-diketones 9 a, 10 a, 11 a, and 12 a (calculated using the AIM theory). The comparison of the energies of the doubly intermolecularly hydrogen-bonded dinuclear platina-beta-diketone [{Pt{(COMe)2H}(bpy)}2]2+ (14) with that of the mononuclear intramolecularly hydrogen-bonded cation [Pt{(COMe)2H}(bpy)]+ (12 a) showed that the intermolecular hydrogen bonds in 14 are weaker than the intramolecular hydrogen bond in 12.     

C?H/π‐Interaction‐Guided Self‐Assembly in π‐Conjugated Oligomers

We report CH/π hydrogen‐bond‐driven self‐assembly in π‐conjugated skeletons based on oligophenylenevinylenes (OPVs) and trace the origin of interactions at the molecular level by using single‐crystal structures. OPVs were designed with appropriate pendants in the aromatic core and varied by hydrocarbon or fluorocarbon tails along the molecular axis. The roles of aromatic π‐stack, van der Waals forces, fluorophobic effect and CH/π interactions were investigated on the theromotropic liquid crystallinity of OPV molecules. Single‐crystal structures of hydrocarbon OPVs provided direct evidence for the existence of CH/π interactions between the π‐ring (H‐bond acceptor) and alkyl C? H (H‐bond donor). The four important crystallographic parameters, d_c?x=3.79 Å, θ=21.49°, φ=150.25° and d_Hp?x=0.73 Å, matched in accordance with typical CH/π interactions. The CH/π interactions facilitate the close‐packing of mesogens in x–y planes, which were further protruded along the c axis producing a lamellar structure. In the absence of CH/π interactions, van der Waals interactions drove the assembly towards a Schlieren nematic texture. Fluorocarbon OPVs exhibited smectic liquid‐crystalline textures that further underwent Smectic A (SmA) to Smectic C (SmC) phase transitions with shrinkage up to 11 %. The orientation and translational ordering of mesogens in the liquid‐crystalline (LC) phases induced H‐ and J‐type molecular arrangements in fluorocarbon and hydrocarbon OPVs, respectively. Upon photoexcitation, the H‐ and J‐type molecular arrangements were found to emit a blue or yellowish/green colour. Time‐resolved fluorescence decay measurements confirmed longer lifetimes for H‐type smectic OPVs relative to that of loosely packed one‐dimensional nematic hydrocarbon‐tailed OPVs.     

Electronic Bond‐to‐Bond Fluxes in Pericyclic Reactions: Synchronous or Asynchronous?

One at a time or all at once? Electronic fluxes during a pericyclic reaction in the electronic ground state--exemplified for the degenerate Cope rearrangement of semibullvalene--may proceed either synchronously or asynchronously. Quantum simulations show that the mechanism is determined by the preparation of the reactants, for example, synchronous at cryogenic temperatures (tunneling) but asynchronous when induced by selective laser pulses (with energy over the barrier).     

6‐Chloroisocytosine and 5‐bromo‐6‐methylisocytosine: again,one or two tautomers present in the same crystal?

It is well known that pyrimidin‐4‐one derivatives are able to adopt either the 1H‐ or the 3H‐tautomeric form in (co)crystals, depending on the coformer. As part of ongoing research to investigate the preferred hydrogen‐bonding patterns of active pharmaceutical ingredients and their model systems, 2‐amino‐6‐chloropyrimidin‐4‐one and 2‐amino‐5‐bromo‐6‐methylpyrimidin‐4‐one have been cocrystallized with several coformers and with each other. Since Cl and Br atoms both have versatile possibilities to interact with the coformers, such as via hydrogen or halogen bonds, their behaviour within the crystal packing was also of interest. The experiments yielded five crystal structures, namely 2‐aminopyridin‐1‐ium 2‐amino‐6‐chloro‐4‐oxo‐4H‐pyrimidin‐3‐ide–2‐amino‐6‐chloropyrimidin‐4(3H)‐one (1/3), C₅H₇N₂⁺·C₄H₃ClN₃O⁻·3C₄H₄ClN₃O, (Ia), 2‐aminopyridin‐1‐ium 2‐amino‐6‐chloro‐4‐oxo‐4H‐pyrimidin‐3‐ide–2‐amino‐6‐chloropyrimidin‐4(3H)‐one–2‐aminopyridine (2/10/1), 2C₅H₇N₂⁺·2C₄H₃ClN₃O⁻·10C₄H₄ClN₃O·C₅H₆N₂, (Ib), the solvent‐free cocrystal 2‐amino‐5‐bromo‐6‐methylpyrimidin‐4(3H)‐one–2‐amino‐5‐bromo‐6‐methylpyrimidin‐4(1H)‐one (1/1), C₅H₆BrN₃O·C₅H₆BrN₃O, (II), the solvate 2‐amino‐5‐bromo‐6‐methylpyrimidin‐4(3H)‐one–2‐amino‐5‐bromo‐6‐methylpyrimidin‐4(1H)‐one–N‐methylpyrrolidin‐2‐one (1/1/1), C₅H₆BrN₃O·C₅H₆BrN₃O·C₅H₉NO, (III), and the partial cocrystal 2‐amino‐5‐bromo‐6‐methylpyrimidin‐4(3H)‐one–2‐amino‐5‐bromo‐6‐methylpyrimidin‐4(1H)‐one–2‐amino‐6‐chloropyrimidin‐4(3H)‐one (0.635/1/0.365), C₅H₆BrN₃O·C₅H₆BrN₃O·C₄H₄ClN₃O, (IV). All five structures show R₂²(8) hydrogen‐bond‐based patterns, either by synthon 2 or by synthon 3, which are related to the Watson–Crick base pairs.     

Electron ionization mass spectra of 8‐aryl‐3,4‐dioxo‐2H,8H‐6,7‐dihydroimidazo[2,1‐c][1,2,4]triazines. Do they exhibit tautomerism in the gas phase?

The electron ionization mass spectra of the title compounds (1: a R = H, b 2-CH(3), c 4-CH(3), d 2,3-diMe, e 2-OCH(3), f 4-OCH(3), g 2-Cl, h 3-Cl, i 4-Cl, j 3,4-diCl) were recorded at 70 eV to determine the effects of substituents and the possible keto-enol tautomerism. The compounds showed several common fragment ions but also fragment ions which divided them into three classes, namely 1a-1d (parent compound and Me-substituted derivatives), 1e and 1f (MeO-substituted derivatives), and 1g-1j (Cl-substituted derivatives). The presence of the HOCN(+.) ion as well as the exponential dependence of its total ion current in the case of p- and also 3-Cl-substituted compounds (1a, c, f, h-j) on the Hammett sigma constants and the loss of CHO or one or two HOCN moieties can be somewhat easier explained by the presence of the enol form but as a whole the results support the predominance of the keto form, in parallel to the situation in solution.     

Does Excited‐State Proton‐Transfer Reaction Contribute to the Emission Behaviour of 4‐Aminophthalimide in Aqueous Media?

4‐Aminophthalimide (AP) is an extensively used molecule both for fundamental studies and applications primarily due to its highly solvent‐sensitive fluorescence properties. The fluorescence spectrum of AP in aqueous media was recently shown to be dependent on the excitation wavelength. A time‐dependent blue shift of its emission spectrum is also reported. On the basis of these findings, the excited‐state solvent‐mediated proton‐transfer reaction of the molecule, which was proposed once but discarded at a later stage, is reintroduced. We report on the fluorescence behaviour of AP and its imide‐H protected derivative, N‐BuAP, to prove that a solvent‐assisted excited‐state keto–enol transformation does not contribute to the steady‐state and time‐resolved emission behaviour of AP in aqueous media. Our results also reveal that the fluorescence of AP in aqueous media arises from two distinct hydrogen‐bonded species. The deuterium isotope effect on the fluorescence quantum yield and lifetime of AP, which was thought to be a reflection of the excited‐state proton‐transfer reaction in the system, is explained by considering the difference in the influence of H₂O and D₂O on the nonradiative rates and ground‐state exchange of the proton with the solvent.