Substituent Effects on Pyrid-2-yl Ureas toward Intramolecular Hydrogen Bonding and Cytosine Complexation

Dual Chalcogen-Bonding Interactions for the Conformational Control of Urea

Dual chalcogen-bonding interactions is proposed as a novel means for the conformational control of urea derivatives. The formation of a chalcogen-bonding interaction at both sides of the urea carbonyl group was unambiguously confirmed by X-ray diffraction as well as computational studies including non-covalent interaction (NCI) plot index analysis, quantum theory of atoms in molecules (QTAIM) analysis, and natural bond orbital (NBO) analysis via DFT calculations. By virtue of this dual interaction, urea derivatives that bear chalcogen atoms (X=S and Se) adopt a planar structure via the carbonyl oxygen (O) with an X⋅⋅⋅O⋅⋅⋅X arrangement on the same side of the molecule. The rigidity of the conformational lock was evaluated using the molecular arrangement in the crystal and the rotational barrier of benzochalcogenophene ring, which indicated a stronger conformational lock in benzoselenophene than in benzothiophene urea derivatives. Furthermore, the acidity of the urea derivatives increases according to the Lewis-acidic properties of the chalcogen-bonding interactions, whereby benzoselenophene urea is more acidic than benzothiophene urea. Tweezer-shaped urea derivatives were prepared, and their stereostructure proved the viability of the conformational control for defining the location of the substituents on the urea framework.

Direct Detection of Hydrogen Bonds in Supramolecular Systems Using 1H-15N Heteronuclear Multiple Quantum Coherence Spectroscopy

Hydrogen-bonded supramolecular systems are usually characterized in solution through analysis of NMR data such as complexation-induced shifts and nuclear Overhauser effects (nOe). Routine direct detection of hydrogen bonding particularly in multicomponent mixtures, even with the aid of 2D NMR experiments for full assignment, is more challenging. We describe an elementary rapid ¹H-¹⁵N HMQC NMR experiment which addresses these challenges without the need for complex pulse sequences. Under readily accessible conditions (243/263 K, 50 mM solutions) and natural ¹⁵N abundance, unambiguous assignment of ¹⁵N resonances facilitates direct detection of intra- and intermolecular hydrogen bonds in mechanically interlocked structures and quadruply hydrogen-bonded dimers─of dialkylaminoureidopyrimidinones, ureidopyrimidinones, and diamidonaphthyridines─in single or multicomponent mixtures to establish tautomeric configuration, conformation, and, to resolve self-sorted speciation.

Rhodium-Catalyzed Synthesis of Unsymmetric Di(heteroaryl)ureas Involving an Equilibrium Shift

Unsymmetric di(heteroaryl)ureas such as HetAr¹-NHCONH-HetAr² are efficiently synthesized from two symmetric ureas, HetAr¹-NHCONH-HetAr¹ and HetAr²-NHCONH-HetAr², by rhodium-catalyzed exchange reactions. The equilibrium in some of the reactions can be shifted to the formation of unsymmetric ureas by the aggregation of the dimers formed by inter- and intramolecular hydrogen bonding.

Synthesis of unsymmetrical urea from aryl- or pyridyl carboxamides and aminopyridines using PhI(OAc)2via in situ formation of aryl- or pyridyl isocyanates

The synthesis of unsymmetrical ureas (N-aryl-N′-pyridylurea and N,N′-bipyridylurea) from aryl- or pyridyl carboxamides and aminopyridines in the presence of PhI(OAc)2 has been reported. The formation of pyridylisocyanates from their corresponding carboxamides via Hofmann rearrangement is confirmed.

Modular O- vs. N-coordination of pyridylidene amide ligands to iron determines activity in alcohol oxidation catalysis

A family of polydentate pyridine-substituted pyridylidene amide (PYA) complexes bound to iron(ii) was developed. The variation of the coordination set from NN-bidentate PYA to tridentate pincer-type pyPYA2 systems (pyPYA2 = 2,6-bis(PYA)pyridine) had a large influence on the binding mode to iron(ii), including a change from the N- to rare O-coordination of the PYA site and a concomitant shift of the predominant ligand resonance structure. These binding mode variations invoke changes in the reactivity of the complexes, which were probed in the peroxide-mediated oxidation of 1-phenylethanol to acetophenone. A comparison with uncomplexed FeCl2 indicated that bidentate NN coordination is unstable and presumably leads to the dissociation of FeCl2. In contrast, the tridentate ligand binding is robust. Remarkably, the tridentate PYA pincer coordination inhibits catalytic activity in the NNN binding mode, while the ONO coordination greatly enhances catalytic performance. Under optimized conditions, the bis-ligated ONO pincer iron complex [Fe(pyPYA2)2][2PF6] reaches full conversion within one hour (0.5 mol% catalyst loading) and under dilute conditions turnover numbers over 20 000 (0.005 mol% catalyst loading).

Synthesis, biological and molecular dynamics investigations with a series of triazolopyrimidine/triazole-based benzenesulfonamides as novel carbonic anhydrase inhibitors

In the presented work, we report the design and synthesis of different new sets of triazolopyrimidine-based (9a-d) and triazole-based (11a-h, 13a-c, 15a,b, 17a,b and 21a-g) benzenesulfonamides. The newly synthesized sulfonamides were assessed for their inhibitory activities toward four human (h) metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) isoforms; hCA I, II, IX and XII. The four examined isoforms were inhibited by the prepared sulfonamides (9a-d, 11a-h, 13a-c, 15a,b, 17a,b and 21a-g) in variable degrees with KIs ranges: 94.4-4953.5 nM for hCA I, 6.9-837.6 nM for hCA II, 3.3-85.0 nM for hCA XI, and 4.4-105.0 nM for hCA XII. In particular, sulfonamides 11e, 21a and 21e emerged as single-digit nanomolar hCA IX and hCA XII inhibitors. Interestingly, triazolopyrimidine-based sulfonamide 9d and triazole-based sulfonamide 21e were found to be the most selective hCA IX inhibitors over hCA I (SI = 100.85 and 210.58, respectively) and hCA II (SI = 18.54 and 38.36, respectively). Thereafter, sulfonamides 9d and 21e were docked into the active site of CAs II, IX and XII, then poses showing the best scoring values and favorable binding interactions were subjected to a MM-GBSA based refinement and, limited to CA IX and XII, to a cycle of 100 ns molecular dynamics.

Conversion of curved assemblies into two dimensional sheets

The design and preparation of organic two dimensional (O2D) sheets and their conversion to curved nanostructures is in its infancy. To convert a flat structure into a curved structure, the molecule must have multiple interaction possibilities and an in-built twist. The conjugated small molecule iso-Indigo (i-Indigo) comprises two phenyl rings that are twisted (the dihedral angle is 15°) at the junction. The i-Indigo has been connected with moieties that impart hydrogen bonding and van der Waals interactions. Due to the presence of the π cloud in i-Indigo, π-π interactions are also present in the molecule. While all three interactions are in operation, rings and toroids are formed. Upon addition of hydrogen bonding competing solvents, the rings and toroids unravel to form O2D sheets. Control molecules that don't have hydrogen bonding moieties and π-π interactions form random assemblies. Please note that the rings, toroids and O2D sheets are formed in a single solvent by simple dissolution, unlike previous approaches that involve multiple steps and solvents.

Conformational change in the association of a heterocyclic urea derivative forming two intramolecular hydrogen bonds in polar solvent

Competition of two urea moieties for the same counterpart including change of conformation upon binding in polar solvent.

Scalable, One-Pot, Microwave-Accelerated Tandem Synthesis of Unsymmetrical Urea Derivatives

We report a facile, microwave-accelerated, one-pot tandem synthesis of unsymmetrical ureas via a Curtius rearrangement. In this method, one-pot microwave irradiation of commercially available (hetero)aromatic acids and amines in the presence of diphenylphosphoryl azide enabled extremely rapid (1-5 min) construction of an array of unsymmetrical ureas in good to excellent yields. We demonstrate the utility of our method in the efficient, gram-scale synthesis of key biologically active compounds targeting the cannabinoid 1 and α7 nicotinic acetylcholine receptors.

Oxidative Carbonylation of Aromatic Amines with CO Catalyzed by 1,3-Dialkylimidazole-2-selenone in Ionic Liquids

1,3-Dialkylimidazole-2-selenone as a novel substituted selenium heterocyclic catalyst was used to catalyze oxidative carbonylation of aromatic amines with carbon monoxide in the presence of air to symmetrical ureas in up to 97% yield in ionic liquids.

Side-Chain Supramolecular Polymers Employing Conformer Independent Triple Hydrogen Bonding Arrays

Derivatives of thymine have been extensively used to promote supramolecular materials assembly. Such derivatives can be synthetically challenging to access and may be susceptible to degradation. The current article uses a conformer-independent acceptor-donor-acceptor array (ureidopyrimidine) which forms moderate affinity interactions with diamidopyridine derivatives to effect supramolecular blend formation between polystyrene and poly(methyl methacrylate) polymers obtained by RAFT which have been functionalized with the hydrogen bonding motifs.

A fluorescein-containing, small-molecule, water-soluble receptor for cytosine free bases

In this study, we synthesized small-molecule, water-soluble, fluorescein-containing ureido compounds 6 and 8 as target receptors for cytosine free bases and then investigated the binding of cytosine free bases with the receptors using (15)N NMR spectroscopy and partially labeled cytosine-2,4-(13)C-1,3,4-(15)N-cytosine. Binding with the receptor 6a (the disodium form of 6) caused the chemical shift of the nitrogen atom of the amino group of cytosine to move downfield; binding of the receptor 8a (the disodium form of 8), which is possessing no corresponding aryl nitrogen atom, had no effect on this signal. Fluorescence spectroscopy revealed that binding of cytosine and its derivatives led to quenching of the fluorescence of receptor 6a; in contrast, the quenching of receptor 8a was only slightly affected by cytosine. Because the fluorescence of 6a was not quenched by either deoxycytidine or uracil, it appears that this receptor is a specific for cytosine among the DNA bases. We used the fluorescence of 6a to measure the apparent binding constants for various cytosine derivatives, including the anticancer prodrug 5-fluorocytosine. Receptor 6a is the first small-molecule, water-soluble fluorescent receptor for the specific binding of cytosine free bases in aqueous solution.

Isocyanate diinsertion into the N-H bond of the 2-pyridylamino ligand of organolanthanides

[Cp2LnNHPy]2 (Py = 2-pyridyl) (1a-e) react with phenyl isocyanate to form the N-H diinsertion products Cp2Ln[eta2:eta1-PyNCON(Ph)CONHPh](THF) (Ln = Yb (3a), Er (3b), Y (3c), Dy (3d), Gd (3e)). It has been proven that nPr2NH can abstract one PhNCO unit from 3c to form Cp2Y[eta3-OC(NHPh)NPy] (2c) and nPr2NHCONHPh (4), representing a rare example of selective release of a functional group of ligands in organolanthanide chemistry. Hydrolysis of 2c gives the organic nitrogen-containing product PyNHCONHPh (5). Moreover, 3c can also be obtained by the reaction of 2c with PhNCO. These results demonstrate that the diinsertion of PhN=C=O into the N-H bond of coordinated amino ligands might proceed in a stepwise manner. All the compounds were characterized by elemental analysis and spectroscopic properties. The structures of compounds 3a-e and 4 are also determined through X-ray single-crystal diffraction analysis.

Molecular recognition of cationic phenothiazinium and phenoxazinium dyes with pi-extended 2'-deoxyadenosine nucleotides

N(6)-(N'-Arylcarbamoyl)-2'-deoxyadenosine-H-phosphonates displayed molecular recognition towards cationic phenothiazinium and phenoxazinium dyes in aqueous solutions; studies have shown that binding is driven mainly by aromatic interactions and that size and shape-complementarity of the aromatic rings in host and guest provides selectivity.

Non-covalent polymer assembly using arrays of hydrogen-bonds

Hydrogen-bond-mediated non-covalent polymer synthesis is an emerging area that presents new opportunities for the design of stimuli-responsive materials. Central to this is the ready availability of appropriate building blocks with which to link monomers together. This review discusses recent developments in the design, synthesis and use of arrays of hydrogen-bonds as supramolecular linking units.