Configuration and E/Z interconversion mechanism of O(S)-allyl-S(O)-methyl-N-(acridin-9-yl) iminothiocarbonate

The configuration and dynamic behavior of O-allyl-S-methyl-N-(acridin-9-yl)iminothiocarbonate (1) and its S-allyl-O-methyl regioisomer (2) were studied using quantum chemical calculations and by applying a novel graphical method to scatter maps obtained from MD simulations for evaluation of an NOE-weighted internuclear distance (r(NOE)). Energy calculations indicated that the Z configuration was predominant for each compound and, further, this was supported both by the calculated chemical shifts and the r(NOE). Both N-inversion- and rotation-type transition-state structures were also calculated for the E/Z isomerization process, the results indicating that the preferred interconversion mechanism for 1 is N-inversion, but contrastingly, interconversion via rotation is equally as probable as N-inversion for 2. This supports the notion that one or the other or both pathways can be active and each system needs to be assessed on a case-by-case basis.     

Alnumycins A2 and A3: new inverse-epimeric pairs stereoisomeric to alnumycin A1

Two new pairs of stereoisomeric alnumycin As, A2 {(2)-(1R,1′RS,4′SR,5′SR)} and A3 {(2)-(1R,1′RS,4′SR,5′RS)}, are described. Similar to alnumycin A1 {(2)-(1R,1′RS,4′RS,5′SR)}, each of these naturally occurring compounds is also a pair of C-1 inverse epimers. The relative configurations of the dioxane ring sidechains were assigned on the basis of ¹H NMR NOE contacts and molecular modeling using density functional theory (DFT) at the M06-2X/6-31G(d) level of theory. The absolute configurations of C-1 and the determination of inverse epimeric relationships were achieved by experimental electronic circular dichroism (ECD) measurements, with both aspects confirmed by using the chiral derivatizing agent (CDA) Mosher′s acid chloride {α-methoxy-α-trifluorophenylacetyl chloride (MTPACl)} to effect enantiodifferentiation. The absolute configurations of the dioxane ring using the CDA could only be effected in the case of alnumycin A1, the results of which were in agreement with previous assignments. The dioxane ring conformational mobility and the likely interaction between the MTPA groups coupled with the structural novelty of the diols in the dioxane ring with respect to CDA analysis precluded an absolute configuration assignment for alnumycins A2 and A3 based on empirical comparisons or by computational analysis of through-space NMR shieldings (TSNMRS) emanating from the phenyl groups of the MTPA moieties.     

TEAD–YAP Interaction Inhibitors and MDM2 Binders from DNA-Encoded Indole-Focused Ugi Peptidomimetics

DNA-encoded combinatorial synthesis provides efficient and dense coverage of chemical space around privileged molecular structures. The indole side chain of tryptophan plays a prominent role in key, or “hot spot”, regions of protein–protein interactions. A DNA-encoded combinatorial peptoid library was designed based on the Ugi four-component reaction by employing tryptophan-mimetic indole side chains to probe the surface of target proteins. Several peptoids were synthesized on a chemically stable hexathymidine adapter oligonucleotide “hexT”, encoded by DNA sequences, and substituted by azide-alkyne cycloaddition to yield a library of 8112 molecules. Selection experiments for the tumor-relevant proteins MDM2 and TEAD4 yielded MDM2 binders and a novel class of TEAD-YAP interaction inhibitors that perturbed the expression of a gene under the control of these Hippo pathway effectors.     

Synthesis and NMR characterization of the cis and trans isomers of [Pt(II)(N9-adeH)2(pz)2] and X-ray crystallography of the trans isomer

The reaction of tetrapyrazine Pt(II) with adenine under basic conditions yielded two products both disubstituted by adenine and bound in all cases to the N-9 nitrogen of adenine. Crystals amenable to X-crystallographic analysis were obtained for one product which was consequently identified as trans-[Pt(II)(N9-adeH)2(pz)2](NO3)(4).H2O. The other product, though, was identified as the cis isomer based on extensive and comparative NMR structural studies whereby the two compounds were examined as both neutral and tetraprotonated species in solution. The major product of the reaction was unexpectedly the cis isomer, thus obtained in contrast to the trans effect, and the reason for this result is speculated on. Computational calculations using DFT at the B3LYP/TZVP-MARI-J level of theory provided the head-to-tail conformer as the overwhelmingly more stable species over the head-to-head conformer for both compounds whilst the trans product was found to be more stable than the cis. Thus the reaction does not follow a thermodynamic course and rather is kinetically controlled in concert with the speculated mode of reaction.     

Composition, structure, and luminescence of montmorillonites saturated with different aggregates of methylene blue

The distribution of various aggregates (dimers, trimers, and tetramers) of methylene blue (MB) formed in aqueous solution at various concentrations of dye has been calculated using the equilibrium aggregation constants betaq. Two montmorillonite samples with different cation exchange capacities, surface areas, and interlayer distances d001, Na-SWy, and Ca-Cheto, were saturated with methylene blue (MB) solutions with various ratios between monomers and higher aggregates of dye. The total amount of MB in the intercalated montmorillonite samples (MB-SWy and MB-Cheto) increases with increasing concentration of dye in water solutions, i.e., with increasing aggregates/monomers ratio of MB in water solution. In all intercalated montmorillonite samples with methylene blue except guest qth aggregate cations [MBqq+] low contents of Na+ (in MB-SWy) and Ca2+ (in MB-Cheto) cations were also determined. A very good positive correlation between the basal spacing d001 and the MB/montmorillonite molar ratio was revealed for saturated MB-montmorillonite samples. Structural analysis using a combination of diffraction data with molecular modeling revealed the differences in the interlayer arrangement of MB guests in MB-SWy and MB-Cheto intercalates. Also, fluorescence measurements showed the strong effect of the silicate layer charge on the spectroscopic behavior of MB guests intercalated in montmorillonite. Methylene blue exhibits a certain luminescence in MB-SWy samples with cation exchange capacity 0.80 meq g-1 and almost no luminescence in MB-Cheto samples with higher cation exchange capacity 1.50 meq g-1.     

Tautomerism,regioisomerism, and cyclization reactions of acridinyl thiosemicarbazides

The regioselectivities of methyl‐ and phenylhydrazine with acridin‐9‐yl isothiocyanate (thus yielding thiosemicarbazides with acridine substituted on the urea‐type side) were examined. Methylhydrazine regioselectivity was high with the α‐nitrogen atom overwhelmingly more nucleophilic than the β‐nitrogen atom; phenylhydrazine regioselectivity was poor but varied with the solvent and only in the case of ethanol was nucleophilic predominance of the α‐nitrogen atom pronounced. Of note, whilst both phenyl thiosemicarbazides were present in solution only as spiro forms, the methyl product was present as an equilibrium mixture of open‐chain and spiro thiosemicarbazides. Reactions on the NH₂ blocked analogue of methyl acridin‐9‐ylthiosemicarbazide (1‐isopropylidene‐2‐methylthiosemicarbazide) were also examined. Interestingly, present in the starting material itself was a structural motif of novelty wherein a triazolethione represented the major species of an equilibrium between cyclic and open‐chain forms.