The Tautomeric State of N4-Hydroxycytidine within Base-Paired RNA.

Antiviral nucleoside analogues (e.g., Molnupiravir, Remdesivir) played key roles in the treatment of COVID-19 by targeting SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). The nucleoside of Molnupiravir, N4-hydroxycytidine (NHC), exists in two tautomeric forms that pair either with G or A within the RdRp active site, causing an accumulation of viral RNA mutations during replication. Detailed insights into the tautomeric states within base pairs and the structural influence of NHC in RNA are still missing. In this study, we investigate the properties of NHC:G and NHC:A base pairs in a self-complementary RNA duplex by UV thermal melting and NMR spectroscopy using atom-specifically 15N-labeled versions of NHC that were incorporated into oligonucleotides by solid-phase synthesis. NMR analysis revealed that NHC forms a Watson-Crick base pair with G via its amino form, whereas two equally populated conformations were detected for the NHC:A base pair: a weakly hydrogen-bonded Watson-Crick base pair with NHC in the imino form and another conformation with A shifted toward the minor groove. Moreover, we found a variable influence of NHC:G and NHC:A base pairs on the neighboring duplex environment. This study provides conclusive experimental evidence for the existence of two tautomeric forms of NHC within RNA base pairs.

π-π Catalysis Made Asymmetric-Enantiomerization Catalysis Mediated by the Chiral π-System of a Perylene Bisimide Cyclophane.

Enzymes actuate catalysis through a combination of transition state stabilization and ground state destabilization, inducing enantioselectivity through chiral binding sites. Here, we present a supramolecular model system which employs these basic principles to catalyze the enantiomerization of [5]helicene. Catalysis is hereby mediated not through a network of functional groups but through π-π catalysis exerted from the curved aromatic framework of a chiral perylene bisimide (PBI) cyclophane offering a binding pocket that is intricately complementary with the enantiomerization transition structure. Although transition state stabilization originates simply from dispersion and electrostatic interactions, enantiomerization kinetics are accelerated by a factor of ca. 700 at 295 K. Comparison with the meso-congener of the catalytically active cyclophane shows that upon configurational inversion in only one PBI moiety the catalytic effect is lost, highlighting the importance of precise transition structure recognition in supramolecular enzyme mimics.

Folding and fluorescence enhancement with strong odd-even effect for a series of merocyanine dye oligomers.

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy. Solvent-dependent UV/vis spectroscopic studies reveal folding processes for the MC oligomers driven by strong dipole-dipole interactions resulting in well-defined π-stacks with antiparallel orientation of the dyes. Whilst even-numbered tetramer 4 and hexamer 6 only show partial folding into dimeric units, odd-numbered trimer 3 and pentamer 5 fold into π-stacks of three and five MC units upon decreasing solvent polarity. In-depth 2D NMR studies provided insight into the supramolecular structure. For trimer 3, an NMR structure could be generated revealing the presence of a well-defined triple π-stack in the folded state. Concomitant with folding, the fluorescence quantum yield is increased for all MC oligomers in comparison to the single chromophore. Based on radiative and non-radiative decay rates, this fluorescence enhancement can be attributed to the rigidification of the chromophores within the π-stacks that affords a pronounced decrease of the non-radiative decay rates. Theoretical investigations for the double and triple dye stacks based on time-dependent density functional theory (TD-DFT) calculations indicate for trimer 3 a pronounced mixing of Frenkel and charge transfer (CT) states. This leads to significant deviations from the predictions obtained by the molecular exciton theory which only accounts for the Coulomb interaction between the transition dipole moments of the chromophores.

Defined Merocyanine Dye Stacks from a Dimer up to an Octamer by Spacer-Encoded Self-Assembly Approach.

A series of well-defined chromophore stacks is obtained upon self-assembly of merocyanine and bis(merocyanine) dyes in nonpolar solvents. Careful design of the spacer moieties linking the dipolar chromophores within the bis(merocyanine) dyes allows one to direct the dipole-dipole interaction driven aggregation into stacks of desired size from dimer up to octamer. The spacer-encoded self-assembly process was investigated by UV/vis absorption spectroscopy showing an increase of the hypsochromic shift with increasing stack size. The structure of the largest aggregate comprising eight chromophores was analyzed by 1D and 2D nuclear magnetic resonance spectroscopic studies revealing a perfectly interdigitated centrosymmetric organization of the dipolar dyes and concomitant annihilation of the ground state dipole moment is observed in the UV/vis absorption spectra. This unprecedented series of dye stacks from dimer to octamer enabled a systematic study of the optical absorption properties in dependence of the stack size disclosing that the absorption features can be rationalized by molecular exciton theory. Our results show that the noncovalent synthesis approach based on dipolar aggregation is suitable for the design of well-defined dye aggregates of specific size, allowing in-depth studies to manifest structure-property relationships.

Cyanohydridoborate Anions: Synthesis, Salts, and Low-Viscosity Ionic Liquids.

High-yield syntheses up to molar scales for salts of [BH(CN)3 ]- (2) and [BH2 (CN)2 ]- (3) starting from commercially available Na[BH4 ] (Na5), Na[BH3 (CN)] (Na4), BCl3 , (CH3 )3 SiCN, and KCN were developed. Direct conversion of Na5 into K2 was accomplished with (CH3 )3 SiCN and (CH3 )3 SiCl as a catalyst in an autoclave. Alternatively, Na5 is converted into Na[BH{OC(O)R}3 ] (R=alkyl) that is more reactive towards (CH3 )3 SiCN and thus provides an easy access to salts of 2. Some reaction intermediates were identified, for example, Na[BH(CN){OC(O)Et}2 ] (Na7 b) and Na[BH(CN)2 {OC(O)Et}] (Na8 b). A third entry to 2 and 3 uses ether adducts of BHCl2 or BH2 Cl such as the commercial 1,4-dioxane adducts that react with KCN and (CH3 )3 SiCN. Alkali metal salts of 2 and 3 are convenient starting materials for organic salts, especially for low viscosity ionic liquids (ILs). [EMIm]3 has the lowest viscosity and highest conductivity with 10.2 mPa s and 32.6 mS cm-1 at 20 °C known for non-protic ILs. The ILs are thermally, chemically, and electrochemically robust. These properties are crucial for applications in electrochemical devices, for example, dye-sensitized solar cells (Grätzel cells).

Perfluoroalkyltricyanoborate and Perfluoroalkylcyanofluoroborate Anions: Building Blocks for Low-Viscosity Ionic Liquids.

The potassium perfluoroalkyltricyanoborates K[Cn F2 n+1 B(CN)3 ] [n=1 (1 d), 2 (2 d)] and the potassium mono(perfluoroalkyl)cyanofluoroborates K[Cn F2 n+1 BF(CN)2 ] [n=1 (1 c), 2 (2 c)] and [Cn F2 n+1 BF2 (CN)]- [n=1 (1 b), 2 (2 b), 3 (3 b), 4 (4 b)] are accessible with perfect selectivities on multi-gram scales starting from K[Cn F2 n+1 BF3 ] and Me3 SiCN. The K+ salts are starting materials for the preparation of salts with organic cations, for example, [EMIm]+ (EMIm=1-ethyl-3-methylimidazolium). These [EMIm]+ salts are hydrophobic room-temperature ionic liquids (RTILs) that are thermally, chemically and electrochemically very robust, offering electrochemical windows up to 5.8 V. The RTILs described herein, exhibit very low viscosities with a minimum of 14.0 mPa s at 20 °C for [EMIm]1 c, low melting points down to -57 °C for [EMIm]2 b and extraordinary high conductivities up to 17.6 mS cm-1 at 20 °C for [EMIm]1 c. The combination of these properties makes these ILs promising materials for electrochemical devices as exemplified by the application of selected RTILs as component of electrolytes in dye-sensitised solar cells (DSSCs, Grätzel cells). The efficiency of the DSSCs was found to increase with a decreasing viscosity of the neat ionic liquid. In addition to the spectroscopic characterisation, single crystals of the potassium salts of the anions 1 b-d, 2 d, 3 b and 4 c as well as of [nBu4 N]2 c have been studied by X-ray diffraction.

Microtubular Self-Assembly of Covalent Organic Frameworks.

Despite significant progress in the synthesis of covalent organic frameworks (COFs), reports on the precise construction of template-free nano- and microstructures of such materials have been rare. In the quest for dye-containing porous materials, a novel conjugated framework DPP-TAPP-COF with an enhanced absorption capability up to λ=800 nm has been synthesized by utilizing reversible imine condensations between 5,10,15,20-tetrakis(4-aminophenyl)porphyrin (TAPP) and a diketopyrrolopyrrole (DPP) dialdehyde derivative. Surprisingly, the obtained COF exhibited spontaneous aggregation into hollow microtubular assemblies with outer and inner tube diameters of around 300 and 90 nm, respectively. A detailed mechanistic investigation revealed the time-dependent transformation of initial sheet-like agglomerates into the tubular microstructures.

Protonation versus Oxonium Salt Formation: Basicity and Stability Tuning of Cyanoborate Anions.

Anhydrous H[BH2 (CN)2 ] crystallizes from acidic aqueous solutions of the dicyanodihydridoborate anion. The formation of H[BH2 (CN)2 ] is surprising as the protonation of nitriles requires strongly acidic and anhydrous conditions but it can be rationalized based on theoretical data. In contrast, [BX(CN)3 ]- (X=H, F) gives the expected oxonium salts (H3 O)[BX(CN)3 ] while (H3 O)[BF2 (CN)2 ]/H[BF2 (CN)2 ] is unstable. H[BH2 (CN)2 ] forms chains via N-H⋅⋅⋅N bonds in the solid state and melts at 54 °C. Solutions of H[BH2 (CN)2 ] in the room-temperature ionic liquid [EMIm][BH2 (CN)2 ] contain the [(NC)H2 BCN-H⋅⋅⋅NCBH2 (CN)]- anion and are unusually stable, which enabled the study of selected spectroscopic and physical properties. [(NC)H2 BCN-H⋅⋅⋅NCBH2 (CN)]- slowly gives H2 and [(NC)H2 BCN-BH(CN)2 ]- . The latter compound is a source of the free Lewis acid BH(CN)2 , as shown by the generation of [BHF(CN)2 ]- and BH(CN)2 ⋅py.

A Star-shaped Oligo(phenylenevinylene) Liquid Crystal Host with an Anthracene Guest-A Double Nanosegregating Supermesogen.

Hexasubstituted C3 -symmetric benzenes with three elongated shape-persistent oligo(phenylenevinylene) arms and three pyridyl hydrogen-bond acceptors have been synthesized. These mesogens assemble in a double-helical columnar liquid crystal (LC) structure, owing to the compensation of free spaces between conjugated arms by dimer formation. The void is filled also by up to three anthracene carboxylic acids as guests forming hydrogen bonded supermesogens assembling in columnar LC and soft-crystal phases. Thin film fluorescence and solid-state NMR spectroscopy imply a transition from a disordered columnar LC to an unexpected double nanosegregated morphology of a filled soft columnar crystal phase. An additional intracolumnar separation of anthracene and oligo(phenylenevinylene) chromophores occurs, separate to the general segregation of aliphatic and aromatic building blocks in LC structures. The new type of supermesogens will enable the rational design of host-guest double cables with a wide range of different conjugated building blocks.

Crowded Star Mesogens: Guest-Controlled Stability of Mesophases from Unconventional Liquid-Crystal Molecules.

The molecular design of crowded hexasubstituted star mesogens based on a benzene core and alternating substitution with oligo(phenylenevinylene) arms and aryl units generates free space between the conjugated arm scaffolds. Various arylcarboxy building blocks, decorated with alkoxy chains, have been incorporated in the void by mixing, hydrogen bonding or covalent bonds to the aryl groups. The mesogens assemble in columnar stacks ranging from soft crystals to rectangular and hexagonal columnar liquid crystals, revealed by polarized optical microscopy, differential scanning calorimetry, X-ray scattering and modelling. The stability of the mesophases is crucially influenced by the binding mode of the arylcarboxy guest building blocks. The origin of the variation in clearing temperature is unravelled by modelling, cohesive energy density considerations and solid-state NMR spectroscopy. The control over the transition temperature is important for the formation of aligned thin films and thus for potential applications.

Generation of Dicoordinate Boron(I) Units by Fragmentation of a Tetra-Boron(I) Molecular Square.

Reduction of carbene-borane adduct [(cAAC)BBr2 (CN)] (cAAC=1-(2,6-diisopropylphenyl)-3,3,5,5-tetramethylpyrrolidin-2-ylidene) cleanly yielded the tetra(cyanoborylene) species [(cAAC)B(CN)]4 presenting a 12-membered (BCN)4 ring. The analysis of the Kohn-Sham molecular orbitals showed significant borylene character of the BI atoms. [(cAAC)B(CN)]4 was found to reduce two equivalents of AgCN per boron center to yield [(cAAC)B(CN)3 ] and fragmented into two-coordinate boron(I) units upon reaction with IMeMe (1,3,4,5-tetramethylimidazol-2-ylidene) to yield the corresponding tricoordinate mixed cAAC-NHC cyanoborylene. The analogous cAAC-phosphine cyanoborylene was obtained by reduction of [(cAAC)BBr2 (CN)] in the presence of excess phosphine.

Phenylene ethynylene-tethered perylene bisimide folda-dimer and folda-trimer: investigations on folding features in ground and excited states.

In this work, we have elucidated in detail the folding properties of two perylene bisimide (PBI) foldamers composed of two and three PBI units, respectively, attached to a phenylene ethynylene backbone. The folding behaviors of these new PBI folda-dimer and trimer have been studied by solvent-dependent UV/Vis absorption and 1D and 2D NMR spectroscopy, revealing facile folding of both systems in tetrahydrofuran (THF). In CHCl3 the dimer exists in extended (unfolded) conformation, whereas partially folded conformations are observed in the trimer. Temperature-dependent (1) H NMR spectroscopic studies in [D8 ]THF revealed intramolecular dynamic processes for both PBI foldamers due to, on the one hand, hindered rotation around CN imide bonds and, on the other hand, backbone flapping; the latter process being energetically more demanding as it was observed only at elevated temperature. The structural features of folded conformations of the dimer and trimer have been elucidated by different 2D-NMR spectroscopy (e.g., ROESY and DOSY) in [D8 ]THF. The energetics of folding processes for the PBI dimer and trimer have been assessed by calculations applying various methods, particularly the semiempirical PM6-DH2 and the more sophisticated B97D approach, in which relevant dispersion corrections are included. These calculations corroborate the results of NMR spectroscopic studies. Folding features in the excited states of these PBI foldamers have been characterized by using time-resolved fluorescence and transient absorption spectroscopy in THF and CHCl3 , exhibiting similar solvent-dependent behavior as observed for the ground state. Interestingly, photoinduced electron transfer (PET) process from electron-donating backbone to electron-deficient PBI core for extended, but not for folded, conformations was observed, which can be explained by a fast relaxation of excited PBI stacks in the folded conformation into fluorescent excimer states.

Perylene bisimide dimer aggregates: fundamental insights into self-assembly by NMR and UV/Vis spectroscopy.

A novel perylene bisimide (PBI) dye bearing one solubilizing dialkoxybenzyl and one bulky 2,5-di-tert-butylphenyl substituent was synthesized and its aggregation behavior was analyzed by NMR and UV/Vis spectroscopy in various chloroform/methylcyclohexane (MCH) solvent mixtures. In the presence of no less than 10 vol % chloroform, exclusive self-assembly of this PBI dye into π-stacked dimers was unambiguously confirmed by means of both concentration-dependent (1) H NMR and UV/Vis spectroscopic experiments. Based on ROESY NMR, a well-defined π-stacked dimer structure was determined and further corroborated by molecular modeling studies. By varying the solvent composition of chloroform and MCH, the solvent effects on the Gibbs free energy of PBI dimerization were elucidated and showed a pronounced nonlinearity between lower and higher MCH contents. This observation could be related to a further growth process of dimers into larger aggregates that occurs in the absence of chloroform, which is required to solvate the aromatic π surfaces. With the help of a single-crystal structure analysis for a related PBI dye, a structural model could be derived for the extended aggregates that are still composed of defined π-π-stacked PBI dimer entities.

Impact of molecular flexibility on binding strength and self-sorting of chiral π-surfaces.

In this work, we have explored for the first time the influence of conformational flexibility of π-core on chiral self-sorting properties of perylene bisimides (PBIs) that are currently one of the most prominent classes of functional dyes. For this purpose, two series of chiral macrocyclic PBIs 3a-c and 4a-c comprising oligoethylene glycol bridges of different lengths at the 1,7 bay positions were synthesized and their atropo-enantiomers (P and M enantiomers) were resolved. Single crystal analysis of atropo-enantiomerically pure (P)-3a not only confirmed the structural integrity of the ethylene glycol bridged macrocycle but also illustrated the formation of π-stacked dimers with left-handed supramolecular helicity. Our detailed studies with the series of highly soluble chiral PBIs 4a-c by 1- and 2-D (1)H NMR techniques, and temperature- and concentration-dependent UV/vis absorption and circular dichroism (CD) spectroscopy revealed that in π-π-stacking dimerization of these PBIs chiral self-recognition (i.e., PP and MM homodimer formation) prevails over self-discrimination (i.e., PM heterodimer formation). Our studies clearly showed that with increasing conformational flexibility of PBI cores imparted by longer bridging units, the binding strength for the dimerization process increases, however, the efficiency for chiral self-recognition decreases. These results are rationalized in terms of an induced-fit mechanism facilitating more planarized π-scaffolds of PBIs containing longer bridging units upon π-π-stacking.

Self-assembly of bis(merocyanine) tweezers into discrete bimolecular pi-stacks.

Examples of a novel class of tweezer molecules have been constructed through the tethering of two dipolar merocyanine chromophores by a naphthalenedimethylene or dimethylenediphenylmethane spacer. The electrostatic-interaction-directed self-assembly of these bis(merocyanine) tweezers affords centrosymmetric bimolecular complexes with very high dimerization constants of up to >10(9) M(-1), even in the good solvating solvent chloroform. This pronounced self-association of the bis(merocyanine) tweezers is attributed to the strongly dipolar nature of the merocyanine chromophores and a unique aggregate geometry of four pi-stacked chromophores with an alternating arrangement of their dipole moments. The structural assignment of the tetrachromophoric pi-stack has been accomplished by MALDI-TOF mass spectrometry and ROESY NMR spectroscopy. Furthermore, molecular modeling studies have accounted for the relationships between the dimerization constants and optical properties of the bimolecular complexes of the present bis(merocyanine) dyes and the structure of the spacer and the positions at which the merocyanine chromophores are attached.

Polyketide folding in higher plants: biosynthesis of the phenylanthraquinone knipholone.

The biosynthesis of knipholone, as an axially chiral phenylanthraquinone, in higher plants was examined by feeding experiments with [13C2]-labeled precursors. [13C2]-Acetate and advanced synthetic intermediates were fed to sterile cultures of Kniphofia pumila (Asphodelaceae), with subsequent NMR analysis on the isolated natural product involving 2D INADEQUATE and SELINQUATE experiments. Due to its uneven number of carbon atoms, and because of its uncertain decarboxylation site, the "northern" part of the molecule (i.e., the chrysophanol portion) might originate from four different cyclization modes. According to the labeling pattern of the product isolated after incorporation, this anthraquinone part of knipholone is formed by the so-called F folding mode (originally established for fungi). The acetophenone part of the molecule, which does not undergo a decarboxylation reaction, originates from four acetate units. The surprising lack of randomization of the intact [13C2] units in this "southern" part reveals the absence of a free symmetric intermediate as initially anticipated. This is in agreement with the intact incorporation of the "authentic" southern molecular portion, 4,6-dihydroxy-2-methoxyacetophenone, while the corresponding symmetrical candidate trihydroxyacetophenone was clearly not incorporated, showing that the O-methylation of the freshly cyclized tetraketide is the step that prevents symmetrization of the acetophenone.

Light-harvesting metallosupramolecular squares composed of perylene bisimide walls and fluorescent antenna dyes.

The fluorescent dye 4-dimethylamino-1,8-naphthalimide was incorporated at the bay area of N,N'-bispyridyl perylene bisimide to afford a fourfold-functionalized perylene bisimide ligand. Through self-assembly directed by metal-ion coordination, a multichromophore supramolecular entity composed of sixteen dimethylaminonaphthalimide antennas and a perylene bisimide-walled square core was subsequently constructed from this linear ditopic ligand and 90 degrees metal corner [Pd(dppp)](OTf)2 (dppp=1,3-bis(diphenylphosphino)propane; OTf=trifluoromethanesulfonate) in good yield. The isolated metallosupramolecular square was characterized by elemental analysis and 1H, 13C, and 31P{1H} NMR and UV/Vis spectroscopy. Furthermore, by means of 1H NMR diffusion-ordered spectroscopy (DOSY) the dimension of this assembly was evaluated by employing a previously reported perylene bisimide ligand and its square assembly as references. The results obtained confirm the square framework of the current assembly. The optical properties of this multichromophore dye assembly were investigated by UV/Vis and steady-state and time-resolved fluorescence spectroscopy. It was revealed that light captured by dimethylaminonaphthalimide antennas could be efficiently transported to the perylene bisimide core by a fluorescence resonance mechanism (energy-transfer efficiency E=95%), and this resulted in almost exclusive detection of intense perylene bisimide emission, irrespective of the excitation wavelength applied. The present square scaffold containing aminonaphthalimide antenna dyes exhibits more than seven times higher fluorescence quantum yield (Phifl=0.37) than a previously reported pyrene-bearing perylene bisimide-walled square (Phifl=0.05). Thus, this multichromophore square assembly with aminonaphthalimide antenna dyes is an artificial model for the cyclic light-harvesting complexes in purple bacteria.

Different polyketide folding modes converge to an identical molecular architecture.

Metabolic diversity is being studied intensively by evolutionary biologists, but so far there has been no comparison of biosynthetic pathways leading to a particular secondary metabolite in both prokaryotes and eukaryotes. We have detected the bioactive anthraquinone chrysophanol, which serves as a chemical defense in diverse eukaryotic organisms, in a bacterial Nocardia strain, thereby permitting the first comparative biosynthetic study. Two basic modes of folding a polyketide chain to fused-ring aromatic structures have so far been described: mode F (referring to fungi) and mode S (from Streptomyces). We have demonstrated that in eukaryotes (fungi, higher plants and insects), chrysophanol is formed via folding mode F. In actinomycetes, by contrast, the cyclization follows mode S. Thus, chrysophanol is the first polyketide synthase product that is built up by more than one polyketide folding mode.

Interaction of the fusogenic peptide B18 in its amyloid-state with lipid membranes studied by solid state NMR.

The interaction of the fusogenic polypeptide segment "B18" from the fertilization protein binding with lipid membranes was investigated by solid state 2H and 31P NMR, and by differential scanning calorimetry. B18 is known to adopt different conformations depending on peptide concentration, ionic conditions, pH and lipid environment. Here, the peptide was studied in its beta-stranded amyloid conformation. According to 31P NMR, the lamellar morphology of the DMPC bilayer remains intact in the presence of B18. In going from low (1:90) to high (1:10) peptide/lipid ratios, an increasing effect on several different 2H-labeled lipid segments was observed, reflecting changes in phase behavior and local dynamics. The strongest influence of B18 was detected at the acyl-chains, while no significant effect on the lipid headgroup conformation was observed. This suggests an insertion of B18 in its fibrillar state into the membrane driven by hydrophobic interactions, rather than a peripheral binding mediated by electrostatics.

Dioncophylline E from Dioncophyllum thollonii, the first 7,3'-coupled dioncophyllaceous naphthylisoquinoline alkaloid.

The isolation and structural elucidation of dioncophylline E, a novel naphthylisoquinoline alkaloid from the rare West African liana Dioncophyllum thollonii, is described. The alkaloid displays an unusual 7,3'-linkage between the naphthalene and the isoquinoline portions. Due to the resulting medium degree of steric hindrance exerted by the ortho-substituents next to the biaryl axis, the compound undergoes slow rotation about the axis at room temperature and thus is the first such alkaloid that occurs as a mixture of two configurationally semi-stable atropo-diastereomers. Dioncophylline E exhibits good antimalarial activity against both chloroquine-sensitive and -resistant strains of Plasmodium falciparum while its antitrypanosomal activity against Trypanosoma cruzi is weak and that against T. brucei rhodesiense is moderate. Furthermore, four additional naphthylisoquinoline alkaloids previously known from the related plant species Triphyophyllum peltatum, have been identified in D. thollonii.