Three-center Hydrogen Bonds Research Articles

Hydrogen-bonding-induced oligoanthranilamide foldamers. Synthesis, characterization, and complexation for aliphatic ammonium ions

The self-assembly of a novel series of intramolecular hydrogen bonding-driven foldamers have been described. Five linear aromatic amide oligomers 1– 5 , which bear two to six repeating benzoyl amide subunits, respectively, have been prepared by continuous amide-coupling reactions. The existence of three-centered hydrogen bonds in the oligomers and consequently, the folding conformation of the oligomers in the solid state and solution have been proved by the X-ray analysis (for 2 ) and the 1H NMR and IR experiments. Molecular modeling reveals a planar and rigid conformation for the oligomers and a cavity of 0.86 nm in diameter for 6-mer 5 . Fluorescent and 1H NMR experiments have demonstrated that the new aromatic oligo-amide foldamers can bind primary and secondary alkyl ammonium ions in chloroform and the associated binding constants have been determined. It is revealed that 5-mer 4 exhibits the largest binding ability. A face-to-face binding mode has been proposed for the complexes.

Tris(1H-imidazole-κN3)(DL-malato-κ3O,O′,O′′)nickel(II)

In the title complex, [Ni(C4H4O5)(C3H4N2)3], the NiII atom is coordinated by one tridentate malate dianion and three imidazole mol­ecules with a distorted octa­hedral geometry. The imidazole H atom links with both carbox­yl O atoms of the neighboring complex to form a three-centered hydrogen bond, which results in a long centroid–centroid distance of 4.447 (2) A between neighboring parallel imidazole rings.

Furan derivatives of substituted phenylthiourea: spectral studies, semi-empirical quantum-chemical calculations and X-ray structure analyses

Fifty new derivatives of 1-(furan-2-carbonyl)- and 1-(furan-3-carbonyl)-3-phenyl substituted thiourea have been synthesised and identified. Intramolecular hydrogen bonds were investigated in detail, using IR spectroscopy. The three-level Fermi resonance effect in the IR spectra was analysed after deconvolution and band separation. Semi-empirical quantum-chemical calculations (AM1 and PM3) support the results of the IR spectroscopic studies. X-ray single crystal diffraction analyses of four selected compounds, namely 1-(furan-3-carbonyl)-3-(2-trifluoromethyl-phenyl)-thiourea ( 1e), 1-(2-methyl-furan-3-carbonyl)-3-(2-trifluoromethyl-phenyl)-thiourea ( 2e), 1-(2,6-dichloro-phenyl)-3-(2-methyl-furan-3-carbonyl)-thiourea ( 2n) and 1-(4-methoxyphenyl)-3-(3-methyl-2-furan-carbonyl)-thiourea ( 3e), corroborated the molecular and crystal structure of these compounds. Relatively strong intramolecular hydrogen bonds of the N–H⋯O C type as well as intermolecular two-centred and bifurcated three-centred hydrogen bonds were observed, confirming the results of the IR spectral study and the semi-empirical quantum-chemical calculations. A variety of intermolecular interactions, yielding the supramolecular architectures in the four crystalline compounds, are discussed in detail.

Hydrogen bonding-mediated oligobenzamide foldamer receptors that efficiently bind a triol and saccharides in chloroform

The self-assembly of two novel intramolecular hydrogen bonding-driven foldamers is described. Two linear symmetric aromatic amide oligomers, 1 and 2, which are incorporated with benzene subunits, have been prepared by continuous amide-coupling reactions. The existence of three-centred hydrogen bonds in the oligomers and consequently the folding conformation of the oligomers in solution have been characterized by 1H NMR experiments and by comparing them with the reported solid state structure of the identical structural skeleton. Molecular modeling reveals a rigid crescent conformation for 1 with a cavity of ca. 0.9 nm in diameter and a helical conformation for 2 with a cavity of ca. 0.8 nm in diameter. Due to the existence of intramolecular hydrogen bonding, all the CO groups in both oligomers are located inwardly. The binding of 1 and 2 towards a trihydroxyl guest and four saccharide derivatives have been investigated with 1H NMR, fluorescence, and circular dichroism spectroscopy. The association constants of the corresponding 1 ∶ 1 complexes have been determined by fluorescence titration experiments.

L-Ornithinium sulfate monohydrate

In the title compound, C5H14N2O22+·SO42−·H2O, the ornithinium cation forms a strong O—H⋯O hydrogen bond with the sulfate anion. One backbone conformation angle is in an eclipsed conformation, while the other two are in a trans–trans staggered conformation. All the amino and carboxyl­ate groups and the sulfate anions are involved in hydrogen bonding. The amino groups are also involved in a three-centred hydrogen bond with the O atoms of the sulfate anion.

Highly efficient, one-step macrocyclizations assisted by the folding and preorganization of precursor oligomers.

Highly efficient, one-step macrocyclizations leading to the formation of macrocyclic hexa(aramides) in high yields (69-82%) are described. The one-step macrocyclizations were facilitated by the preorganization or folding of the backbones of uncyclized precursors in the course of macrocyclization. The preorganization of backbones was achieved by the presence of localized three-centered hydrogen bonds that were adopted in the design of a class of closely related, backbone-rigidified foldamers. The macrocyclization involved reactions between diacid chloride 1 and diamine 2. The crude reaction mixtures and products were conveniently examined by mass spectrometric method (MALDI-TOF). Compared to most traditional one-step macrocyclizations that usually require high dilution conditions and often lead to very low overall yields of the desired products, cyclic hexamers 3 were obtained as the overwhelmingly major product under a variety of reaction conditions, suggesting the generality of this approach.

Spectroscopic and structural investigations on [(DD18C6)H 2]I 8 formed in the reaction of N, N′-dibenzylated diazacrown ether (DD18C6) with iodine

Photometric titration measurements indicated in the reaction of diazacrown ether N, N ′-dibenzyl-1,4,10,13-tetraoxo-7,16-diazacyclooctadecane (DD18C6, 2) with iodine in chloroform that a complex was formed in the molar ratio DD18C6:I 2=1:4. This complex was also prepared on a preparative scale as dark brown compound and characterized by microanalysis, UV–Vis, IR, and Raman spectroscopy. By X-ray diffraction analysis the solid-state structure of the complex was shown to be [(DD18C6)H 2]I 8 ([ 3]I 8) consisting of a doubly protonated macrocycle and an octaiodide dianion (I 8 2− ) in the typical (nearly planar) Z-shaped geometry. The macrocycle is C i symmetric and the protonated nitrogen atoms adopt an endo– endo orientation that is stabilized by the three-center hydrogen bonds N–H(⋯O) 2, where the oxygen atoms of the macrocycle act as hydrogen acceptors. The orientation of the phenyl groups of the benzyl sidearms are turned above and below the macrocycle. Quantum chemical calculations on the DFT level of theory of the non-protonated and the doubly protonated macrocycle (DD18C6, 2c) and [(DD18C6)H 2] 2+ ( 3c), respectively, were performed and discussed for 3c in terms of conformational strain of the macrocycle, the strength of the intramolecular N–H⋯O hydrogen bonds and cation–π interactions.

The hydrogen bond stabilizing effect in enammonium salts of captodative aminoalkenes containing a carbonyl group

Enhanced stability of enammonium salts of captodative carbonyl-containing aminoalkenes as compared to the salts of simple enamines is discussed on the basis of 1H and 13C NMR, IR, UV spectroscopy and the results quantum chemical calculations. Stabilization of the N-protonated form of captodative aminoalkenes is due to either intramolecular (NH +⋯OC) or intermolecular (NH +⋯Solv or NH +⋯X −) hydrogen bonding, whereas the C-protonated form is destabilized due to umpolung of the carbon–carbon double bond. The formation of bifurcated (three-centered) hydrogen bond between the enammonium cation and the solvent is demonstrated. The three-centered solvate complex is characterized by nonclassical dependence of the chemical shift of the bridging hydrogen atom from the proton-acceptor power of the solvent.

The role of carbon‐donor hydrogen bonds in stabilizing tryptophan conformations

Although most side-chain torsion angles correspond to low-energy rotameric positions, deviations occur with significant frequency. One striking example arises in Trp residues, which have an important role in stabilizing protein structures because of their size and mixed hydrophobic/hydrophilic character. Ten percent of Trp side-chains have unexplained conformations with chi(2) near 0 degrees instead of the expected 90 degrees. The current work is a structural and energetic analysis of these conformations. It is shown that many Trp residues with these orientations are stabilized by three-center carbon-donor hydrogen bonds of the form C-H...X...H-C, where X is a polar hydrogen-bond acceptor in the environment of the side-chain. The bridging hydrogen bonds occur both within the Trp side-chain and between the side-chain and the local protein backbone. Free energy maps of an isolated Trp residue in an explicit water environment show a minimum corresponding to the off-rotamer peak observed in the crystallographic data. Bridging carbon-donor hydrogen bonds are also shown to stabilize on-rotamer Trp conformations, and similar bridging hydrogen bonds also stabilize some off-rotamer Asp conformations. The present results suggest a previously unrecognized role for three-center carbon-donor hydrogen bonds in protein structures and support the view that the off-rotamer Trp side-chain orientations are real rather than artifacts of crystallographic refinements. Certain of the off-rotamer Trp conformations appear to have a functional role.

Solvatochromism of Heteroaromatic Compounds: XXIII. Reversible Specific Solvatochromic Effect in the IR Spectra of 2-Nitrophenol and 2,4,6-Trinitrophenol

2-Nitrophenol and 2,4,6-trinitrophenol form with protophilic solvents complexes with a bifurcate (three-center) hydrogen bond. Their O-H stretching vibration frequencies nonlinearly and unsteadily vary with the H-bond acceptor ability of the medium, which is a spectroscopic evidence for three-center H-complex formation.

The crystal structure of 5-amino-2-nitrobenzoic acid

The crystal structure of 5-amino-2-nitrobenzoic acid (5A2NB) was determined by the X-ray diffraction method. The 5-amino-2-nitrobenzoic acid crystallizes in the monoclinic P21/c space group with a = 3.898(2) A, b = 13.531(3) A, c = 14.301(3) A, and β = 90.83(3)°. The adjacent molecules form a cyclic dimmer by intermolecular hydrogen bonds of type O—H⋅⋅⋅sO with their carboxyl groups. In the crystal structure NH2 group forms a three-center hydrogen bond with oxygen atoms of NO2 group. The IR spectrum and thermal properties of acid are discussed.

Hydrogen bond-induced rigid oligoanthranilamide ribbons that are planar and straight.

[structure: see text] A new series of oligoanthranilamides has been synthesized starting from suitably modified p-phenylenediamine and p-phthalic acid derivatives. Due to strong intramolecular three-center hydrogen bonds, the new oligomers self-assemble into highly stable straight and planar molecular ribbons, which have been characterized by X-ray crystallography and 1H NMR, IR, and UV-vis spectroscopy.

Polarized vibrational spectroscopy of fiber polymers: hydrogen bonding in cellulose II.

Vibrational spectroscopy using polarized incident radiation can be used to determine the orientation of X-H bonds with respect to coordinates such as crystallographic axes. The adaptation of this approach to polymer fibers is described here. It requires spectral intensity to be quantified around a 180 degrees range of polarization angles and not just recorded transversely and longitudinally as is normal in fiber spectroscopy. Mercerized cellulose II is used as an example. The unit cell of the cellulose II lattice contains six distinct hydroxyl groups engaged in a complex network of hydrogen bonds that hold the cellulose chains laterally together. A formalism is described to relate the variation in intensity of each O-H stretching mode to the angle between its transition moment and the chain axis as the polarization axis is rotated with respect to the fiber axis. It was necessary to include the effect of dispersion in chain orientation around the mean and the averaging of all rotational positions of the chains round their axis. The two crystallographically distinct O(2)-H groups, which are each hydrogen-bonded to only one acceptor oxygen, show a close match in orientation between the transition moments of their stretching bands and the O-H bond axis. The two O(3)-H groups each have a three-centered hydrogen bond to O-5 and O-6 of the next residue in the same chain. The transition moments of their stretching modes lay between the acceptor oxygens. Hydrogen bonding from the O(6)-H groups is still more complex but again the transition moment of each O-H bond lay within the cone of orientations described by the acceptor oxygens, provided that one additional acceptor oxygen excluded from the published crystal structure was considered. The transition moments for the O-H stretching modes were approximately aligned with the O-H bond axes, but the alignment was not necessarily exact. This approach is not restricted to hydroxyl groups, but it is particularly useful for the elucidation of hydrogen bonding in fibrous polymers for which crystallographic data on proton positions are not available.

Crucial role of three-center hydrogen bonding in a challenging chiral molecular recognition.

The enantio-discrimination of beta-chiral primary ammonium ions is achieved by a rational approach that utilizes three-center (bifurcated) hydrogen bonding. The extraction experiments on various selected guests reveal that the bifurcated H-bonding plays a crucial role for the chiral discrimination. The X-ray data obtained for an inclusion complex substantiate such interactions. Using the bifurcated H-bonding, the chiral molecular recognition with our C(3)-symmetric tripodal oxazoline receptors is extended generally toward ammonium ions of alpha-, beta-, and alpha,beta-chiral amines. Simple molecular models, evoking the bifurcated H-bonding, explain the chiral discrimination modes.

DiethylN,N′-m-phenylenedioxamate

The title compound, C14H16N2O6, crystallizes in the monoclinic space group, C2/c. C2 symmetry is imposed on the mol­ecule. The ethyl oxamate groups are twisted out of the aromatic ring plane by 34.53 (6)° and both carbonyl groups are antiperiplanar. The intramolecular hydrogen-bonding pattern is depicted by a soft C—H⋯O/O′ three-centered hydrogen bond, and N—H⋯O and C—H⋯O hydrogen-bonding interactions which form an S(5)S(5)S(6)S(6)′S(5)′S(5)′ motif. The mol­ecules are linked into C(3) and C(4) chain motifs, forming supramolecular layers in the ac plane.

Molecular Conformation of 2,2-Dinitrodiphenylamine According to Dielectric Studies and Ab Initio Quantum Chemical Calculations

According to the results of ab initio calculations employing the HF/6-31G* approach, the isolated 2,2'-dinitrodiphenylamine molecule exists as an sc, sc conformer stabilized by a symmetric intramolecular bifurcated (three-center) hydrogen bond. In protophilic solvents (1,4-dioxane), the conformational equilibrium is also shifted in the direction of this rotational isomer.

Polysulfonylamine, CLXI. Ein neuartiges 1,2-Dihydroimidazochinolinylium-Kation: Zufällige Isolierung und Kristallstruktur des entsprechenden Dimesylamids Polysulfonylamines, CLXI. A Novel 1,2-Dihydroimidazoquinolinylium Cation: Serendipitous Isolation and Crystal Structure of the Corresponding Dimesylamide

Orange-coloured 1,2-dihydro-2,2-dimethyl-imidazo[4,5,1-ij]quinolinylium dimesylamide (1) was accidentally obtained on treating 8-aminoquinoline with one equivalent of dimesylamine in acetone solution. To the best of the authors’ knowledge, the tricyclic cation in question or congeners thereof have not been reported previously. The crystal structure of 1 (monoclinic, space group P21/c, Z = 4; - 130 °C) consists of (MeSO2)N- layers, between which the cations are intercalated to form centrosymmetric (π-π)-bonded pairs. Each cation is connected to the adjacent anion layers by a conventional NDH···(O,N) three-centre hydrogen bond and a set of weak C(sp2)DH···O = S and CH2DH···O = S interactions.

Secondary interactions in N-(chloromethyl)pyridinium chlorides (n = 2, 3, 4).

In the isomeric title compounds, viz. 2-, 3- and 4-(chloromethyl)pyridinium chloride, C(6)H(7)ClN(+).Cl(-), the secondary interactions have been established as follows. Classical N-H.Cl(-) hydrogen bonds are observed in the 2- and 3-isomers, whereas the 4-isomer forms inversion-symmetric N-H(.Cl(-).)(2)H-N dimers involving three-centre hydrogen bonds. Short Cl.Cl contacts are formed in both the 2-isomer (C-Cl.Cl(-), approximately linear at the central Cl) and the 4-isomer (C-Cl.Cl-C, angles at Cl of ca 75 degrees ). Additionally, each compound displays contacts of the form C-H.Cl, mainly to the Cl(-) anion. The net effect is to create either a layer structure (3-isomer) or a three-dimensional packing with easily identifiable layer substructures (2- and 4-isomers).

Creating nanocavities of tunable sizes: hollow helices.

A general strategy for creating nanocavities with tunable sizes based on the folding of unnatural oligomers is presented. The backbones of these oligomers are rigidified by localized, three-center intramolecular hydrogen bonds, which lead to well-defined hollow helical conformations. Changing the curvature of the oligomer backbone leads to the adjustment of the interior cavity size. Helices with interior cavities of 10 A to >30 A across, the largest thus far formed by the folding of unnatural foldamers, are generated. Cavities of these sizes are usually seen at the tertiary and quaternary structural levels of proteins. The ability to tune molecular dimensions without altering the underlying topology is seen in few natural and unnatural foldamer systems.

Polysulfonylamine, CLV [1]. Starke und schwache Wasserstoffbrücken in den Kristallstrukturen von 2,2΄-Bipyridinium-, 1,10-Phenanthrolinium- und 1,8-Bis(dimethylamino)naphthalinium-dimesylamid / Polysulfonylamines, CLV [1]. Strong and Weak Hydrogen Bonding in the Crystal Structures of 2,2΄-Bipyridinium, 1,10-Phenanthrolinium and 1,8-Bis(dimethylamino)naphthalinium Dimesylamide

As a sequel to prior reports on strong and weak hydrogen bonding in onium di(methanesulfonyl) amide crystals, low-temperature X-ray structures are described for three salts of general formula BH+(MeSO2)2N-, where BH+ is 2,2΄-bipyridinium (1; monoclinic, space group P21/n, Z΄ = 1), 1,10-phenanthrolinium (2; monoclinic, P21/c, Z΄ = 2), or 1,8-bis(dimethylamino) naphthalinium (3; orthorhombic, P212121, Z΄ = 1). Monoprotonation of the organic bases by (MeSO2)2NH results in the formation of an intra-cation N-H···N hydrogen bond, which is asymmetric in 1 and 2, but approximately symmetric in the proton-sponge cation of 3. Moreover, the acidic H atom is engaged in a cation-anion contact N-H···N- in 1 and 2 or H+···Oδ- in 3, thus conferring three-centre character upon the strong hydrogen bonding. Each structure displays a multitude of close interionic C-H···O/N contacts that are geometrically consistent with weak hydrogen bonding. A salient feature is provided by short S-CH2-H···O-S inter-anion contacts, which lead to layers in 1 and to catemers in 2, but are non-existent in structure 3. The cations of both 1 and 2 form π-stacks that are intercalated between the anion layers or surrounded by six anion catemers, whereas in structure 3 each cation is octahedrally coordinated by six anions and vice-versa. The heteroionic connectivity comprises the aforementioned branches of the strong three-centre hydrogen bonds (in 1-3), numerous Car-H···A bonds (1, 2: A = O; 3: A = O, N), S-CH2-H···Nring interactions (1, 2), and close N-CH2-H···O=S contacts (3; possibly destabilizing).