Solid state and solution conformation of 2-pyridinecarboxylic acid hydrazides: a new structural motif for foldamers

Mechanistic Insight toward Understanding the Role of Charge in Thiourea Organocatalysis

Pyranylation and glycosylation are pivotal for accessing a myriad of natural products, pharmaceuticals, and drug candidates. Catalytic approaches for enabling these transformations are of utmost importance and integral to advancing this area of synthesis. In exploring this chemical space, a combined experimental and computational mechanistic study of pyranylation and 2-deoxygalactosylation catalyzed by a cationic thiourea organocatalyst is reported. To this end, a thiourea-cyclopropenium organocatalyst was employed as a model system in combination with an arsenal of mechanistic techniques, including ¹³C kinetic isotope effect experiments, deuterated labeling studies, variable-temperature ¹H NMR spectroscopy, and density functional theory calculations. From these studies, two distinct reaction pathways were identified for this transformation corresponding to either dual hydrogen bond (H-bond) activation or Brønsted acid catalysis. The former involving thiourea orchestrated bifurcated hydrogen bonding proceeded in an asynchronous concerted fashion. In contrast, the latter stepwise mechanism involving Brønsted acid catalysis hinged upon the formation of an oxocarbenium intermediate accompanied by subsequent alcohol addition.

Conformation and Visual Distinction between Urea and Thiourea Derivatives by an Acetate Ion and a Hexafluorosilicate Cocrystal of the Urea Derivative in the Detection of Water in Dimethylsulfoxide

Structures of different solvates and solute-solvent interactions of 4-(3-(4-nitrophenyl)urido)benzoate (L ₁ ) and methyl-4-(3-(4-nitrophenyl)thiourido)benzoate (L ₂ ) with different solvents are analyzed. The solution of L ₁ with tetrabutylammonium acetate (TBAA) in dimethylsulfoxide (DMSO) is colorless, but a similar solution of L ₂ with TBAA is orange. On the other hand, respective solutions of these urea and thiourea derivatives with tetrabutylammonium fluoride (TBAF) in DMSO are orange. Urea derivative L ₁ facilitates the reaction of TBAF with glass to form tetrabutylammonium hexafluorosilicate, which on further interaction with L ₁ forms cocrystal 2L ₁ ·(TBA)₂SiF₆. Reorganization of hydrogen-bonded self-assembly of 2L ₁ ·(TBA)₂SiF₆ in DMSO caused by water is established by a dynamic light scattering study. With an increase in the amount of water in the solution, visual color changes from orange to colorless, and the color changes are reversed upon the addition of a dehydrating agent such as molecular sieves. Solvates of L ₁ with DMSO, dimethylformamide (DMF), and dimethylacetamide are quasi-isostructural. The respective self-assembly of these solvates differs due to orientations of aromatic rings and the carbomethoxy group across the thioamide/amide bond. Significant differences in self-assemblies of the respective DMSO solvate of L ₁ and L ₂ are observed; self-assembly of the former has dimeric subassemblies as repeat units, whereas the latter has monomeric subassemblies. DMF solvates of L ₁ and dimethylacetamide of L ₁ are built by dimeric subassemblies to form self-assembled structures, but these subassemblies differ in the orientation of the carbomethoxy group across the urea units.

Molecular recognition of nucleotides in water by scorpiand-type receptors based on nucleobase discrimination

The detection of nucleotides is of crucial importance because they are the basic building blocks of nucleic acids. Scorpiand-based polyamine receptors functionalized with pyridine or anthracene units are able to form stable complexes with nucleotides in water, based on coulombic, π-π stacking, and hydrogen-bonding interactions. This behavior has been rationalized by means of an exploration with NMR spectroscopy and DFT calculations. Binding constants were determined by potentiometry. Fluorescence spectroscopy studies have revealed the potential of these receptors as sensors to effectively and selectively distinguish guanosine-5'-triphosphate (GTP) from adenosine-5'-triphosphate (ATP).

Synthesis of crescent aromatic oligoamides

[structures: see text] This article describes the synthetic procedures for the preparation of crescent (and helical) aromatic oligoamides developed in recent years in our laboratory. The large-scale preparation of a variety of monomers derived from various tetrasubstituted benzenes is presented. Three different strategies for constructing various oligomers consisting of meta- and meta/para-linked benzene residues are discussed. Factors affecting coupling efficiency and yields are analyzed. The developed synthetic methods have provided the basis for the preparation of longer oligomers and for the development of solid-phase synthesis.

Aromatic Foldamers with Iminodicarbonyl Linkers: Their Structures and Optical Properties

[structure: see text] Carboxamides possessing naphthalene rings connected by multiple iminodicarbonyl linkers were synthesized. These molecules forced the naphthalene rings to be placed in the positions facing each other, and they form helical foldamers both in solution and in the crystalline state. Their folding structures were investigated by single-crystal X-ray analysis and (1)H NMR spectroscopy. Their absorption and fluorescence spectra showed a red shift as the number of naphthalene moieties increased. This remarkable change is based on the intramolecular interaction between naphthalene moieties. Helicity of the foldamer can be controlled by the introduction of chiral auxiliaries at imide nitrogen atoms, which results in an observation of induced circular dichroism.

Synthesis of oligomers derived from amide-linked neuraminic acid analogues

N-Fluoren-9-ylmethoxycarbonyl-protected sugar amino acids derived from alpha-O-methoxy- and 2,3-dehydroneuraminic acids have been prepared. Incorporation of these monomer units into solid-phase synthesis led to the efficient synthesis of two series of oligomers varying from one to eight units in length. The (1-->5)-linked amides of 2,3-dehydroneuraminic acid were further subjected to hydrogenation giving a third series of oligomers with a beta-hydrido substituent at the anomeric carbon.

A novel intramolecular hydrogen bonding between a side-chain pyridine ring and an amide hydrogen of the peptide backbone in tripeptides containing the new amino acid, α,α-di(2-pyridyl)glycine

Four tripeptides (Z-AA1-2Dpy-AA3-OMe; AA1, AA3 = Gly, Aib) containing a novel amino acid, alpha, alpha-di(2-pyridyl)glycine (2Dpy), were synthesized by the modified Ugi reaction. NMR analysis clearly indicated that the 2Dpy-containing tripeptides except the peptide in which AA1, AA3 = Aib, adopt a unique conformation with two intramolecular hydrogen bonds between 2Dpy-NH and a pyridine nitrogen and between AA3-NH and another pyridine nitrogen. This conformation has so far not been reported. On the other hand, the peptide Z-Aib-2Dpy-Aib-OMe probably adopts a beta-turn structure which is stabilized by two intramolecular hydrogen bonds between 2Dpy-NH and a pyridine nitrogen and between AA3-NH and the C=O of the Z group.