1H NMR studies of intramolecular hydrogen bonding in N-(pyridyl)amides of 6-methylpicolinic acid N-oxide

The ¹H NMR spectra of seven N-(pyridyl)amides of 6-methylpicolinic acid N-oxide in chloroform were obtained. The influence on the chemical shifts of the N? H protons of temperature, concentration and the CH₃ substituent in the pyridine ring was studied. The N? H protons were found to be shifted to low fields (～14 ppm) owing to the formation of strong intramolecular hydrogen bonding. The influence of the pyridine ring on the chemical shift of the N? H proton is comparable with the inductive effect of the p-nitrophenyl group. The hindered rotation around the N-pyridyl bond of N-(α-pyridyl)amides of 6-methylpicolinic acid in solution is discussed.     

Shape of the proton potential in an intramolecular hydrogen-bonded system. Part II

The crystals of 5,5′-dibromo-3-diethylaminomethyl-2,2′-biphenol N-oxide were studied by X-ray and FT-IR spectroscopy. Within this molecule two short OHO intramolecular hydrogen bonds are formed. The NO?H⁺?O⁻ bond between the OH and the N-oxide groups is very strong, of 2.419(7) Å between the oxygen atoms. The proton potential of this hydrogen bond is flat, broad and has probably no barrier—consequently it could not be located from X-ray diffraction data. The other hydrogen bond formed between two hydroxyl groups appears asymmetrical from FT-IR spectra, and shows also relatively limited proton polarizability. The molecular conformation is non-planar, due to strong overcrowding effect between the oxygen atoms involved in the hydrogen bonds.     

Hydro­gen‐bonded adducts of ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol): a finite cyclic 1:1 adduct with 2,2′‐dipyridyl­amine

In ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–2,2′‐dipyridyl­amine (1/1), [Fe(C₁₈H₁₅O)₂]·C₁₀H₉N₃, (I), there is an intramolecular O—H?O hydrogen bond [H?O 2.03 Å, O?O 2.775 (2) Å and O—H?O 147°] in the ferrocenediol component, and the two neutral molecular components are linked by one O—H?N hydrogen bond [H?N 1.96 Å, O?N 2.755 (2) Å and O—H?N, 157°] and one N—H?O hydrogen bond [H?O 2.26 Å, N?O 3.112 (2) Å and N—H?O 164°] forming a cyclic R(8) motif. One of the pyridyl N atoms plays no part in the intermolecular hydrogen bonding, but participates in a short intramolecular C—H?N contact [H?N 2.31 Å, C?N 2.922 (2) Å and C—H?N 122°].     

Correlation between the reactivity and spectroscopic properties of N‐substituted secondary thioamides. New intramolecular N···H+···N binding approach and proton complexes based on thioamide ligation

On the basis of a comparison of chemical shifts and wavenumbers of several secondary thioamides and amides having monocationic substituents attached to thiocarbamoyl or carbamoyl groups by a polymethylene chain, new intramolecular unconventional N···H⁺···N hydrogen bonding effects were discovered. It is argued that the CH₂—N rotation is hindered and two ⁺H···NHCH₃ non‐equivalent protons occur in a proton spectrum of hydrochloride 1a (at 10.68 and 2.77 ppm, respectively) instead of two ⁺NH₂CH₃ protons. Presumably, the above steric factors inhibit the acidic hydrolysis of 1a (stabilized by strong intramolecular N···H⁺···N hydrogen bonds) to an amide and prevent intramolecular cyclization of 2a (stabilized by strong intramolecular neutral–neutral N···HN hydrogen bonds) to a cyclic amidine. Postulation of additional dihydrogen bond formation is helpful in understanding the spectroscopic differences of 4 and 5 . The above new bonding is also compared with intramolecular N···H—N⁺ hydrogen bonds in primary amine salts 7 and 8 . In contrast to 3 , a cooperative hydrogen bonded system is observed in 9 and 10 . The weak hydrogen bonds in 7 – 10 facilitate the hydrolysis and cyclization reactions of secondary thioamides. The spectroscopic data for secondary (thio)amides are especially useful for characterizing the electronic situation at the (thio)carbamoyl nitrogen atoms and they are perfectly correlated with the reactivity. Examples of chelation of protons by thioamides ( 11 and 12 ), which contain strongly electron‐donating pyrimidine groups, are presented to show the contribution of dihydrogen bonding in the protonation reaction similar to 1 and 4 . Copyright © 2003 John Wiley & Sons, Ltd.     

Hydro­gen‐bonded adducts of ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol): monomeric and polymeric adducts with 1,2‐bis(4‐pyridyl)­ethene and 1,6‐di­amino­hexane

In the adduct ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–1,2‐bis(4‐pyridyl)­ethene (1/1), [Fe(C₁₈H₁₅O)₂]·C₁₂H₁₀N₂, there is an intramolecular O—H?O hydrogen bond in the ferro­cene­diol component and a single O—H?N hydrogen bond linking the diol to the di­amine, which is disordered over two sets of sites, so forming a finite monomeric adduct. In the adduct ferrocene‐1,1′‐diyl­bis­(di­phenyl­methanol)–1,6‐di­amino­hexane (2/1), 2[Fe(C₁₈H₁₅O)₂]·C₆H₁₆N₂, the amine lies across a centre of inversion in space group P. There is an intramolecular O—H?O hydrogen bond in the ferrocenediol, and the molecular components are linked by O—H?N and N—H?O hydrogen bonds, one of each type, into a C(13)[R(12)] chain of rings.     

Piperidinium 3‐[(4‐hydroxy‐5,7‐di­methyl‐2‐oxo‐2H‐chromen‐3‐yl)­phenyl­methyl]‐5,7‐di­methyl‐2‐oxo‐2H‐chromen‐4‐olate

In the title salt, C₅H₁₂N⁺·C₂₉H₂₃O₆^?, both benzo­pyran systems are planar. Intermolecular N—H?O hydrogen bonds and a short O—H?O intramolecular hydrogen bond are observed in the structure.     

Conformational isomers of the [(5‐methyl‐2‐pyridinio)aminomethylene]diphosphonate dianion and [(5‐methyl‐2‐pyridyl)aminomethylene]diphosphonate trianion in salts with 4‐aminopyridine and ammonia

The crystal structures of two salts, products of the reactions between [(5‐methyl‐2‐pyridyl)aminomethylene]bis(phosphonic acid) and 4‐aminopyridine or ammonia, namely bis(4‐aminopyridinium) hydrogen [(5‐methyl‐2‐pyridinio)aminomethylene]diphosphonate 2.4‐hydrate, 2C₅H₇N₂⁺·C₇H₁₀N₂O₆P₂²⁻·2.4H₂O, (I), and triammonium hydrogen [(5‐methyl‐2‐pyridyl)aminomethylene]diphosphonate monohydrate, 3NH₄⁺·C₇H₉N₂O₆P₂³⁻·H₂O, (II), have been determined. In (I), the Z configuration of the ring N—C and amino N—H bonds of the bisphosphonate dianion with respect to the C_ring—N_amino bond is consistent with that of the parent zwitterion. Removing the H atom from the pyridyl N atom results in the opposite E configuration of the bisphosphonate trianion in (II). Compound (I) exhibits a three‐dimensional hydrogen‐bonded network, in which 4‐aminopyridinium cations and water molecules are joined to ribbons composed of anionic dimers linked by O—H...O and N—H...O hydrogen bonds. The supramolecular motif resulting from a combination of these three interactions is a common phenomenon in crystals of all of the Z‐isomeric zwitterions of 4‐ and 5‐substituted (2‐pyridylaminomethylene)bis(phosphonic acid)s studied to date. In (II), ammonium cations and water molecules are linked to chains of trianions, resulting in the formation of double layers.     

Chiral Transformation in Protonated and Deprotonated Adipic Acids through Multistep Internal Proton Transfer

Protonated and deprotonated adipic acids (PAA: HOOC? (CH₂)₄? COOH₂⁺ and DAA: HOOC? (CH₂)₄? COO^?) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H₂O???H???OH₂)⁺ Zundel‐like symmetric hydrogen bonding, whereas that of DAA has H₃O⁺ Eigen‐like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel‐like ions for PAA and Eigen‐like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH???O short hydrogen‐bond stretching peaks are predicted in the range of 1000–1700 cm^?1 in the Car–Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen‐bond peaks. The O? H? O stretching peaks in the range of 1800–2700 cm^?1 become insignificant above around 150 K and are almost washed out at about 300 K.     

3,4‐Di‐2‐pyridyl‐1,2,5‐oxadiazole and its perchlorate salt

In 3,4‐di‐2‐pyridyl‐1,2,5‐oxadiazole (dpo), C₁₂H₈N₄O, each mol­ecule resides on a twofold axis and inter­acts with eight neighbours via four C—H⋯N and four C—H⋯O inter­actions to generate a three‐dimensional hydrogen‐bonded architecture. In the perchlorate analogue, 2‐[3‐(2‐pyrid­yl)‐1,2,5‐oxadiazol‐4‐yl]pyridinium perchlorate, C₁₂H₉N₄O⁺·ClO₄⁻ or [Hdpo]ClO₄, the [Hdpo]⁺ cation is bisected by a crystallographic mirror plane, and the additional H atom in the cation is shared by the two pyridyl N atoms to form a symmetrical intra­molecular N⋯H⋯N hydrogen bond. The cations and perchlorate anions are linked through C—H⋯O hydrogen bonds and π–π stacking inter­actions to form one‐dimensional tubes along the b‐axis direction.     

Two‐component molecular crystals composed of chloronitrobenzoic acids and 4‐aminopyridine

The crystal structures of the four isomeric organic salts 4‐amino­pyridinium 2‐chloro‐4‐nitro­benzoate, (I), 4‐amino­pyridinium 2‐chloro‐5‐nitro­benzoate, (II), 4‐amino­pyridinium 5‐chloro‐2‐nitro­benzoate, (III), and 4‐amino­pyridinium 4‐chloro‐2‐nitro­benzoate, (IV), all C₅H₇N₂⁺·C₇H₃ClNO₄^?, are presented. Compound (I) has one intramolecular hydrogen bond, one intermolecular C—H?O hydrogen bond and π–π‐stacking interactions. Compound (II) has N—H?O, C—H?O and C—H?Cl hydrogen bonds, and Cl?O—C electrostatic interactions. Compound (III) has N—H?O and C—H?O hydrogen bonds. Compound (IV) has a π–π‐stacking interaction, but no C—H?O hydrogen bonds.     

Intramolecular easily polarizable hydrogen bonds with anilides of 1-piperidine carboxylic acids

IR spectra are plotted from anilides of 1-piperidine carboxylic acids C₅H₁₀N(CH₂)_n CONHC₆H₄R in CHCl₃ and CDCl₃ solutions. In the cases of n = 1 and n = 4, weak intramolecular (NH?N) hydrogen bonds are formed. An asymmetrical energy surface occurs and the proton is present at the N of the anilide group. In the cases of n = 2 and n = 3, intramolecular proton transfer hydrogen bonds of the types N_BH?N_P ? ^?N_B?H⁺N_p are formed. In contrast to the intramolecular OH? N ? O^?1 ? H⁺N bonds with 1-piperidine carboxylic acids, these bonds to not cause IR continua but two bands: one in the region 3250–3190 and one in the region 2500–2450 cm^?1. The fact that, instead of IR continua, bands are observed is explained by the following: (1) these hydrogen bonds are relatively long; (2) they show only a narrow distribution of bond length; (3) the electrical fields at these bonds are small, since they are strongly screened.     

Theoretical study of bifurcated hydrogen bonding effects on the 1J(N,H), 1hJ(N,H), 2hJ(N,N) couplings and 1H, 15N shieldings in model pyrroles

According to the density functional theory calculations, the X···H···N (X?N, O) intramolecular bifurcated (three‐centered) hydrogen bond with one hydrogen donor and two hydrogen acceptors causes a significant decrease of the ^1hJ(N,H) and ^2hJ(N,N) coupling constants across the N? H···N hydrogen bond and an increase of the ¹J(N,H) coupling constant across the N? H covalent bond in the 2,5‐disubsituted pyrroles. This occurs due to a weakening of the N? H···N hydrogen bridge resulting in a lengthening of the N···H distance and a decrease of the hydrogen bond angle at the bifurcated hydrogen bond formation. The gauge‐independent atomic orbital calculations of the shielding constants suggest that a weakening of the N? H···N hydrogen bridge in case of the three‐centered hydrogen bond yields a shielding of the bridge proton and deshielding of the acceptor nitrogen atom. The atoms‐in‐molecules analysis shows that an attenuation of the ^1hJ(N,H) and ^2hJ(N,N) couplings in the compounds with bifurcated hydrogen bond is connected with a decrease of the electron density ρ_H···N at the hydrogen bond critical point and Laplacian of this electron density ?²ρ_H···N. The natural bond orbital analysis suggests that the additional N? H···X interaction partly inhibits the charge transfer from the nitrogen lone pair to the σ*_{N? H} antibonding orbital across hydrogen bond weakening of the ^1hJ(N,H) and ^2hJ(N,N) trans‐hydrogen bond couplings through Fermi‐contact mechanism. An increase of the nitrogen s‐character percentage of the N? H bond in consequence of the bifurcated hydrogen bonding leads to an increase of the ¹J(N,H) coupling constant across the N? H covalent bond and deshielding of the hydrogen donor nitrogen atom. Copyright © 2010 John Wiley & Sons, Ltd.     

2,2′‐Bipyridinium(1+) bromide monohydrate

In the crystal structure of 2,2′‐bipyridinium(1+) bromide monohydrate, C₁₀H₉N₂⁺·Br⁻·H₂O, the cation has a cisoid conformation with an intramolecular N—H⋯N hydrogen bond. The cation also forms an N—H⋯O hydrogen bond to an adjacent water mol­ecule, which in turn forms O—H⋯Br⁻ hydrogen bonds to adjacent Br⁻ anions. In this way, a chain is formed extending along the b axis. Additional interactions (C—H⋯Br⁻ and π–π) serve to stabilize the structure further.     

Intramolecular N-H···O and N-H···N hydrogen bonding patterns in N-benzyl and N-(pyridin-2-ylmethyl) benzamides

This Letter reports the evidences for intramolecular six-membered N-H···O hydrogen bonding in N-benzyl benzamides and five-membered N-H···N hydrogen bonding in N-(pyridin-2-ylmethyl) benzamide. Intramolecular six-membered N-H···X (X = O or F) hydrogen bonding in 2-methoxyl- or 2-fluorobenzamides is used to lock the amide proton from forming strong intermolecular N-H···OC hydrogen bonding. As a result, for the first time the new intramolecular hydrogen bonding patterns are observed in the crystal structures of nine amides, whereas the whole molecules give rise to a new class of three-center hydrogen bonding motif. ¹H NMR study in chloroform-d also supports that this weak intramolecular hydrogen bonding pattern exists in solution.     

A novel hydrogen-bonding N-oxide–sulfonamide–nitro N—H…O synthon determining the architecture of benzenesulfonamide cocrystals

The structures of novel cocrystals of 4-nitropyridine N-oxide with benzenesulfonamide derivatives, namely, 4-nitrobenzenesulfonamide–4-nitropyridine N-oxide (1/1), C₅H₄N₂O₃·C₆H₆N₂O₄S, and 4-chlorobenzenesulfonamide–4-nitropyridine N-oxide (1/1), C₆H₆ClNO₂S·C₅H₄N₂O₃, are stabilized by N—H…O hydrogen bonds, with the sulfonamide group acting as a proton donor. The O atoms of the N-oxide and nitro groups are acceptors in these interactions. The latter is a double acceptor of bifurcated hydrogen bonds. Previous studies on similar crystal structures indicated competition between these functional groups in the formation of hydrogen bonds, with the priority being for the N-oxide group. In contrast, the present X-ray studies indicate the existence of a hydrogen-bonding synthon including N—H…O(N-oxide) and N—H…O(nitro) bridges. We present here a more detailed analysis of the N-oxide–sulfonamide–nitro N—H…O ternary complex with quantum theory computations and the Quantum Theory of Atoms in Molecules (QTAIM) approach. Both interactions are present in the crystals, but the O atom of the N-oxide group is found to be a more effective proton acceptor in hydrogen bonds, with an interaction energy about twice that of the nitro-group O atoms.     

catena‐Poly­[[di­aqua­lithium(I)]‐μ‐[9H‐purine‐2,6(1H,3H)‐dionato‐O2:N7]]

In the title compound, [Li(C₅H₃N₄O₂)(H₂O)₂]_n, the coordinate geometry about the Li⁺ ion is distorted tetrahedral and the Li⁺ ion is bonded to N and O atoms of adjacent ligand mol­ecules forming an infinite polymeric chain with Li—O and Li—N bond lengths of 1.901 (5) and 2.043 (6) Å, respectively. Tetrahedral coordination at the Li⁺ ion is completed by two cis water mol­ecules [Li—O 1.985 (6) and 1.946 (6) Å]. The crystal structure is stabilized both by the polymeric structure and by a hydrogen‐bond network involving N—H?O, O—H?O and O—H?N hydrogen bonds.     

Amide–Amide Hydrogen Bonding. Semirubin Amides

Summary. Semirubins are analogs for one-half of the bilirubin structure and capable of intramolecular hydrogen bonding. Semirubin amides of ammonia and primary amines are also capable of intramolecular hydrogen bonding. From a combination of spectroscopic methods (¹H NMR, NOE, and VPO), the primary amide is found to engage very effectively in intramolecular hydrogen bonding. The secondary and tertiary amides engage in both intramolecular (i) and intermolecular (ii) hydrogen bonding: N-methyl (i, monomer + ii, dimer), N-tert-butyl (ii, dimer), N,N-diethyl (i, monomer + ii, dimer). With an oxo-group at C(10), all of the amides are monomeric and most engage in intramolecular hydrogen bonding.     

4‐Aminopyridinium hydrogen maleate

The title compound, C₅H₇N₂⁺·C₄H₃O₄⁻, crystallizes in space group P2₁ with one ion pair in the asymmetric unit. The hydrogen maleate anion possesses nearly planar geometry and displays an extremely short intramolecular O—H...O hydrogen bond, with an O...O distance of 2.4198 (19) Å. Classical N—H...O hydrogen bonds, together with short C—H...O contacts, generate an extensive hydrogen‐bonding network.     

Temperature-dependent polymorphism of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide: experimental and theoretical studies on intermolecular interactions in the crystal state

X-ray analysis of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide reveals the temperature-dependent polymorphism associated with the crystallographic symmetry conversion. The observed crystal structure transformation corresponds to a symmetry reduction from I4₁ /a (I) to P4₃ (II) space groups. The phase transition mainly concerns the subtle but clearly noticeable reorganization of molecules in the crystal space, with the structure of individual molecules left almost unchanged. The Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, revealing graphically the differences in spatial arrangements of the molecules in both polymorphs. The N-oxide oxygen atom acts as a formally negatively charged hydrogen bonding acceptor in intramolecular hydrogen bond of N–H…O^? type. The combined crystallographic and theoretical DFT methods demonstrate that the observed intramolecular N-oxide N–H…O hydrogen bond should be classified as a very strong charge-assisted and closed-shell non-covalent interaction.     

Amide–Amide Hydrogen Bonding. Semirubin Amides

Semirubins are analogs for one-half of the bilirubin structure and capable of intramolecular hydrogen bonding. Semirubin amides of ammonia and primary amines are also capable of intramolecular hydrogen bonding. From a combination of spectroscopic methods (¹H NMR, NOE, and VPO), the primary amide is found to engage very effectively in intramolecular hydrogen bonding. The secondary and tertiary amides engage in both intramolecular (i) and intermolecular (ii) hydrogen bonding: N-methyl (i, monomer + ii, dimer), N-tert-butyl (ii, dimer), N,N-diethyl (i, monomer + ii, dimer). With an oxo-group at C(10), all of the amides are monomeric and most engage in intramolecular hydrogen bonding.