Amide hydrogen bonding: control of the molecular and extended structures of two symmetrical pyridine‐2‐carboxamide derivatives

The crystal structures of two symmetrical pyridine‐2‐carboxamides, namely N,N′‐(propane‐1,3‐diyl)bis(pyridine‐2‐carboxamide), C₁₅H₁₆N₄O₂, (I), and N,N′‐(butane‐1,4‐diyl)bis(pyridine‐2‐carboxamide), C₁₆H₁₈N₄O₂, (II), exhibit extended hydrogen‐bonded sequences involving their amide groups. In (I), conventional bifurcated amide–carbonyl (N—H)...O hydrogen bonding favours the formation of one‐dimensional chains, the axes of which run parallel to [001]. Unconventional bifurcated pyridine–carbonyl C—H...O hydrogen bonding links adjacent one‐dimensional chains to form a `porous' three‐dimensional lattice with interconnected, yet unfilled, voids of 60.6 (2) ų which combine into channels that run parallel to, and include, [001]. 4% of the unit‐cell volume of (I) is vacant. Compound (II) adopts a Z‐shaped conformation with inversion symmetry, and exhibits an extended structure comprising one‐dimensional hydrogen‐bonded chains along [100] in which individual molecules are linked by complementary pairs of amide N—H...O hydrogen bonds. These hydrogen‐bonded chains interlock viaπ–π interactions between pyridine rings of neighbouring molecules to form sheets parallel with (010); each sheet is one Z‐shaped molecule thick and separated from the next sheet by the b‐axis dimension [7.2734 (4) Å].     

Hydrogen‐bonded supramolecular polymers from derivatives of α‐amino‐ε‐caprolactam: A bio‐based material

Hydrogen‐bonded supramolecular polymers were prepared from the derivatives of α‐amino‐ε‐caprolactam (ACL), obtained from a renewable resource. Several self‐complimentary bis‐ or tetra‐caprolactam monomers were synthesized by varying the number of carbons of the spacer between the hydrogen‐bonding end groups. Physical properties of these hydrogen‐bonded polymers were clearly demonstrated by differential scanning colorimetry, solid‐state NMR, and X‐ray powder diffraction analyses. The supramolecular behavior was also supported by fiber formation from the melt for several of these compounds, and stable glassy materials were prepared from the physical mixtures of two different biscaprolactams. The self‐association ability of ACL was also used by incorporating ACL at the chain ends of low‐molecular weight Jeffamine (M_n = 900 g/mol) using urea and amide linkages. The transformation of this liquid oligomer at room temperature into a self‐standing, transparent film clearly showed the improvement in mechanical properties obtained by the introduction of terminal hydrogen‐bonding groups. Finally, the use of monomers with a functionality of four gave rise to network formation either alone or combination with bifunctional monomers. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

FTIR study on molecular structure of poly(N-isopropylacrylamide) in mixed solvent of methanol and water

The intrachain and interchain hydrogen bonding of poly(N-isopropylacrylamide) (PNIPA) and intermolecular hydrogen bonding between PNIPA chains and the solvent molecules in the mixed solvent of methanol and water have been quantitatively investigated by using Fourier transform infrared (FTIR) spectroscopy at 25 °C. In this spectroscopic system with curve fitting program, we found that in the C-H stretching region, both the N-isopropyl group and the backbone underwent conformational change upon the solvent composition. An analysis of the amide I band suggested that the amide groups of PNIPA were mainly involved in intermolecular hydrogen bonding with water molecules, and the polymer chains were flexible and disordered in the mixed solvent when the methanol volume fraction (χ_v) was lower than 15%. While χ_v was in the range of 15-65%, about 30% of these intermolecular hydrogen bonding between the polymer and water were replaced by intrachain and interchain hydrogen bonding, consequently, PNIPA shrinked as aggregates. If χ_v was above 65%, the interchain hydrogen bonding became predominant due to the solubility characteristics of amphiphilic methanol, and the PNIPA system was homogeneous solution again. We believe that the reentrant transition is related to the weaker interaction between PNIPA molecules and methanol-water complexes, (H₂O)_m(CH₃OH)_n (m/n = 5/1, 5/2, 5/3, 5/4, 5/5) as compared to that between PNIPA and free water or free methanol.     

Telechelic polynorbornenes with hydrogen bonding moieties by direct end capping of living chains

We present two novel symmetric olefins bearing hydrogen bonding moieties for the direct capping of living ring opening metathesis polymerization‐chains using Grubbs catalyst 1st‐ and 3rd‐generation. The symmetric olefins are generated via homo metathesis of the corresponding α‐olefins under aid of microwave irradiation and are used to prepare polynorbornene‐chains (M_n = 4,000–10,000 g/mol, M_w/M_n = 1.1–1.4) bearing barbiturate and thymine‐moieties. A qualitative and quantitative analysis of the generated polymers is done via MALDI‐TOF MS proving the introduction of hydrogen‐bonding moieties into the polymer chain and revealing the strong dependence of the desorption on the chemical structure of the different polymer species and high efficiencies for the end group introduction (90–99%). The efficiency of this process depends strongly on the reaction time and the equivalents of terminating agent with respect to the living end. The best results for the end group introduction are achieved by reacting the living chains with an excess of the terminating agent (5–20 equiv) for 100 h. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

Bonding of acetylene to copper atom,dimer, and trimer

The bonding of acetylene to copper atom, dimer, and trimer was investigated with a Kohn–Sham density functional approach. Full geometry optimization yielded the equilibrium structures of various Cu_nC₂H₂ species. Gradient corrections were included in the calculation of binding energies (BE ). The Cu—C₂H₂ complex was found to have a C_s structure and a BE of 10 kcal/mol. Three isomers of Cu₂C₂H₂ have similar total energies: a C_2v end-bonded structure with a BE of 18 kcal/mol, and two 1,2-dicupro ethylene isomers—a cis form with a BE of 12 kcal/mol and a trans form with a BE of 15 kcal/mol. Two stable C_2v isomers of Cu₃C₂H₂ were found. In both isomers, the Cu₃ ring relaxes from its isosceles structure, with two short bonds (2.247 Å) and one long bond (2.478 Å), and adopts a nearly equilateral geometry. In one isomer of Cu₃C₂H₂, the acetylene is bonded to one apex of the Cu₃ ring with a BE of 29 kcal/mol. In the other, it is bonded to two copper atoms of one side of the Cu₃ ring with a BE of 33 kcal/mol. © 1994 John Wiley & Sons, Inc.     

The effect of γ‐cyclodextrin addition in the self‐assembly behavior of pyrene labeled poly(acrylic) acid with different chain sizes

The interaction between poly(acrylic acid) polymers (PAA) of low‐ (2000 g/mol) and high‐ (450,000 g/mol) molecular weight (M_w) hydrophobically modified with pyrene (PAAMePy) and β‐ and γ‐cyclodextrins (β‐CD, γ‐CD) was investigated with fluorescent techniques. The interaction with β‐CD promotes little variation in the spectral and photophysical behavior of the polymer, whereas significant changes are observed upon addition of γ‐CD. The degree of inclusion (between the pyrene groups of the polymer and the cyclodextrins) is followed through the observation of the changes in the absorption, excitation (collected in the monomer and excimer emission regions) and emission (I_E/I_M ratio) spectra and from time‐resolved data. Within the studied range of γ‐CD concentration, the fluorescence decays of the long chain (high M_w) PAAMePy polymers were found tri‐exponential in the monomer and excimer emission regions in agreement with previous studies. In the case of the low M_w PAAMePy polymers, tri‐exponential decays were observed at the monomer and excimer emission wavelengths. However, when a γ‐CD concentration of 0.01 and 0.03 M is reached for, respectively, the low‐ and high‐labeled pyrene short chain (low M_w) polymers, the fluorescence decays in the excimer region become biexponential (two excimers) with no rising component, thus showing that all pyrene groups are encapsulated (and preassociated) into the γ‐CD cavity. In the case of the high M_w polymers, the addition of γ‐CD has been found to change the level of polymer interaction from pure intramolecular (water in the absence of cyclodextrin) to a coexistence of intra‐ with intermolecular interactions. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1402–1415, 2008     

Comparison of the Structural Information on Sol-Gel Systems Provided by Pyrene Labeled Fluorescent Probes

The influence of the acid catalyst concentration on the structural evolution of a sol-gel system was studied by doping TEOS based starting solutions with two fluorescent probes: a polystyrene chain (M _n =1700) and a much shorter alkane chain (M=172), both of them labeled at both ends with 1-pyrenyl. For this purpose, each probe was incorporated in two TEOS∶H₂O∶C₂H₅OH mixtures (molar ratios 1∶4∶1), one at pH 1.2 and the other at pH 2.5 (respectively below and above the isoelectric point of silica). Very low concentrations of the probes were used (≤10⁻⁶ M), so the pyrene dimmers and excimers were formed only intramolecularly. The ratios of excimer to monomer fluorescence intensities at excitation wavelength of 360 nm (where mainly the ground state pyrene dimmers are excited) were studied as a function of time. Different evolutions of these ratios were observed, which allowed us to predict that the silica structure developsvia the formation of primary particles, even at pH values below the isoelectric point of silica, where it is not possible to directly detect their formation.     

The role of hydroxyl groups in interchain interactions in cellulose Iα and Iβ

Complex networks of hydrogen bonds within the cellulose I_α and I_β contribute greatly to cellulose's anisotropic physical properties such as material stiffness. The interchain hydrogen bonding interactions through hydroxyl groups are isolated in each of the three lattice planes of the adjacent chains within the unit cell of two allomorphs of natural cellulose. In our density function theory study with dispersion corrected Perdew–Burke–Ernzerhof (PBE‐D2) functional, these hydroxyl groups participate in strong hydrogen bonding interactions (?24.8 and ?24.8 kcal/mol for cellulose I_α and I_β, respectively) in the side‐to‐side lattice plane. Unexpectedly, the hydroxyl groups also participate significantly in hydrogen bonding interactions (?11.0 and ?12.4 kcal/mol for cellulose I_α and I_β, respectively) in one of the diagonal lattice planes in both cellulose I_α and I_β. Both PM7 and PBE‐D2 method predict that the overall interaction is asymmetric and stronger in the right diagonal lattice plane. While hydrogen bonding interactions are strongest in side‐to‐side lattice plane as expected, the role of hydrogen bonding interactions for keeping the sheet together is more significant than previously thought.     

(S,S)‐4′′‐Cyano‐7,7′′‐dimethoxy‐3′,6′‐dioxodispiro[indane‐2,2′‐piperazine‐5′,2′′‐indane]‐4‐carboxamide methanol solvate: interrupting the amide‐to‐amide hydrogen‐bonded tape

The title methanol solvate, C₂₄H₂₂N₄O₅·CH₃OH, forms an extended three‐dimensional hydrogen‐bonded structure, assisted by the presence of several good donor and acceptor sites. It shows none of the crystal packing features typically expected of piperazinediones, such as amide‐to‐amide R₂²(8) hydrogen bonding. In this structure the methanol solvent appears to play only a space‐filling role; it is not involved in any hydrogen bonding and instead is disordered over several sites. This study reports, to the best of our knowledge, the first crystal structure of an indane‐containing piperazinedione compound which exhibits a three‐dimensional hydrogen‐bonded structure formed by classical (N—H...O and N—H...N) hydrogen‐bonding interactions.     

Three‐dimensional hydrogen‐bonded structures in the hydrated proton‐transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid homologues

The structures of the 1:1 hydrated proton‐transfer compounds of isonipecotamide (piperidine‐4‐carboxamide) with oxalic acid, 4‐carbamoylpiperidinium hydrogen oxalate dihydrate, C₆H₁₃N₂O⁺·C₂HO₄⁻·2H₂O, (I), and with adipic acid, bis(4‐carbamoylpiperidinium) adipate dihydrate, 2C₆H₁₃N₂O⁺·C₆H₈O₄²⁻·2H₂O, (II), are three‐dimensional hydrogen‐bonded constructs involving several different types of enlarged water‐bridged cyclic associations. In the structure of (I), the oxalate monoanions give head‐to‐tail carboxylic acid O—H...O_carboxyl hydrogen‐bonding interactions, forming C(5) chain substructures which extend along a. The isonipecotamide cations also give parallel chain substructures through amide N—H...O hydrogen bonds, the chains being linked across b and down c by alternating water bridges involving both carboxyl and amide O‐atom acceptors and amide and piperidinium N—H...O_carboxyl hydrogen bonds, generating cyclic R₄³(10) and R₃²(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water molecule. In the crystal structure, the two inversion‐related cations are interlinked through the two water molecules, which act as acceptors in dual amide N—H...O_water hydrogen bonds, to give a cyclic R₄²(8) association which is conjoined with an R₄⁴(12) motif. Further N—H...O_water, water O—H...O_amide and piperidinium N—H...O_carboxyl hydrogen bonds give the overall three‐dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen‐bonded structures. The presence of solvent water molecules in these structures is largely responsible for the non‐occurrence of the common hydrogen‐bonded amide–amide dimer, promoting instead various expanded cyclic hydrogen‐bonding motifs.     

Synthesis of arborescent polystyrene by “click” grafting

A method was developed for the synthesis of arborescent polystyrene by “click” coupling. Acetylene functionalities were introduced on linear polystyrene (M_n = 5300 g/mol, M_w/M_n = 1.05) by acetylation and reaction with potassium hydroxide, 18‐crown‐6 and propargyl bromide in toluene. Polymerization of styrene with 6‐tert‐butyldimethylsiloxyhexyllithium yielded polystyrene (M_n = 5200 g/mol, M_w/M_n = 1.09) with a protected hydroxyl chain end. Deprotection, followed by conversions to tosyl and azide functionalities, provided the side chain material. Coupling with CuBr and N,N,N′,N″,N″‐pentamethyldiethylenetriamine proceeded in up to 94% yield. Repetition of the grafting cycles led to well‐defined (M_w/M_n ≤ 1.1) polymers of generations G1 and G2 in 84% and 60% yield, respectively, with M_n and branching functionalities reaching 2.8 × 10⁶ g/mol and 460, respectively, for the G2 polymer. Coupling longer (M_n = 45,000 g/mol) side chains with acetylene‐functionalized substrates was also examined. For a linear substrate, a G0 polymer with M_n = 4.6 × 10⁵ g/mol and M_w/M_n = 1.10 was obtained in 87% yield; coupling with the G0 (M_n = 52,000 g/mol) substrate produced a G1 polymer (M_n = 1.4×10⁶ g/mol, M_w/M_n = 1.38) in 28% yield. The complementary approach using azide‐functionalized substrates and acetylene‐terminated side chains was also investigated, but proceeded in lower yield. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1730–1740     

catena‐Poly[[[triaquazinc(II)]‐μ‐2‐nitroterephthalato‐κO1:κ2O4,O4′] monohydrate]

The title complex, {[Zn(C₈H₃NO₆)(H₂O)₃]·H₂O}_n, has a one‐dimensional chain structure. The two carboxylate groups of the dianionic 2‐nitroterephthalate ligand adopt mono‐ and bidentate chelating modes. The Zn atom shows distorted octahedral coordination, bonded to three O atoms from two carboxylate groups and three O atoms of three non‐equivalent coordinated water molecules. The one‐dimensional chains are aggregated into two‐dimensional layers through inter‐chain hydrogen bonding. The whole three‐dimensional structure is further stabilized by inter‐layer hydrogen bonds.     

Self‐Assembled Multimetallic/Peptide Complexes: Structures and Unimolecular Reactions of [Mn(GlyGly−H)2n−1]+ and Mn+1(GlyGly−H2n]2+ Clusters in the Gas Phase

The unimolecular chemistry and structures of self‐assembled complexes containing multiple alkaline‐earth‐metal dications and deprotonated GlyGly ligands are investigated. Singly and doubly charged ions [M_n(GlyGly?H)_n‐1]⁺ (n=2–4), [M_n+1(GlyGly?H)_2n]²⁺ (n=2,4,6), and [M(GlyGly?H)GlyGly]⁺ were observed. The losses of 132 Da (GlyGly) and 57 Da (determined to be aminoketene) were the major dissociation pathways for singly charged ions. Doubly charged Mg²⁺ clusters mainly lost GlyGly, whereas those containing Ca²⁺ or Sr²⁺ also underwent charge separation. Except for charge separation, no loss of metal cations was observed. Infrared multiple photon dissociation spectra were the most consistent with the computed IR spectra for the lowest energy structures, in which deprotonation occurs at the carboxyl acid groups and all amide and carboxylate oxygen atoms are complexed to the metal cations. The N?H stretch band, observed at 3350 cm^?1, is indicative of hydrogen bonding between the amine nitrogen atoms and the amide hydrogen atom. This study represents the first into large self‐assembled multimetallic complexes bound by peptide ligands.     

Characterization of the ground state pyrene complex in ethylene-propylene copolymer solutions

Pyrene-labeled functionalized ethylene-propylene (EP) copolymer was prepared by grafting 1-pyrenebutyrylhydrazine onto EP copolymer through maleic anhydride pendants. The EP copolymer contained 60 mol % ethylene; its weight-average molecular weight (M^w) was 148,000. The pyrene-labeled amide functionalized EP copolymer, PA-EP(60/40), was made to simulate the amine functionalized EP copolymers that are commonly used as dispersant additives in motor oils. UV absorption spectra, fluorescence emission and excitation spectra, and fluorescence decay profiles of the pyrene were studied to determine the copolymer conformation and dynamics in methylcyclohexane and tetrahydrofuran (THF). The pyrene fluorescence characteristics of PA-EP(60/40) were highly dependent on the solvent. The dependence of fluorescence emission intensity on the excitation wavelength was large in methylcyclohexane and moderate in THF. A frequency shift of about 2 nm was observed between the excitation spectrum obtained with the emission line at 377 nm and that at 550 nm in the methylcyclohexane solutions, but no shift was found in the corresponding tetrahydrofuran solutions. The ratios of the preexponential factors (a₂₁/a₂₂) of the excimer decays obtained in both methylcyclohexane and THF solutions were different from ?1.0. However, the deviation of the excimer formation process from the Birks scheme is small in THF but large in methylcyclohexane. In addition, the Huggins constants obtained from intrinsic viscosity measurements of the PA-EP(60/40) copolymer solutions suggest that copolymer aggregation occurs in methylcyclohexane but not in THF. H-bonding between two pyrene-containing pendants is apparently the main driving force for the formation of the ground state pyrene complex. THF is found to be effective in inhibiting the H-bonding formation. © 1995 John Wiley & Sons, Inc.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the N? H…O?C, C? H…O?C, N? H…OH₂, and C?O…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Poly[[triaquazinc(II)]‐μ3‐4‐nitrophthalato‐κ3O1:O2:O2′]

In the title complex, [Zn(C₈H₃NO₆)(H₂O)₃]_n, the two carboxylate groups of the 4‐nitrophthalate dianion ligands have monodentate and 1,3‐bridging modes, and Zn atoms are interconnected by three O atoms from the two carboxylate groups into a zigzag one‐dimensional chain along the b‐axis direction. The Zn atom shows distorted octahedral coordination as it is bonded to three O atoms from carboxylate groups of three 4‐nitrophthalate ligands and to three O atoms of three non‐equivalent coordinated water molecules. The one‐dimensional chains are aggregated into two‐dimensional layers through inter‐chain hydrogen bonding. The whole three‐dimensional structure is further maintained and stabilized by inter‐layer hydrogen bonds.     

Hydrogen bonding interaction between 1,4‐dioxane and water

This work reports an interaction of 1,4‐dioxane with one, two, and three water molecules using the density functional theory method at B3LYP/6‐311++G* level. Different conformers were studied and the most stable conformer of 1,4‐dioxane‐(water)_n (n = 1–3) complex has total energies ?384.1964038, ?460.6570694, and ?537.1032381 hartrees with one, two, and three water molecules, respectively. Corresponding binding energy (BE) for these three most stable structures is 6.23, 16.73, and 18.11 kcal/mol. The hydrogen bonding results in red shift in O? O stretching and C? C stretching modes of 1,4‐dioxane for the most stable conformer of 1,4‐dioxane with one, two, and three water molecules whereas there was a blue shift in C? O symmetric stretching and C? O asymmetric stretching modes of 1,4‐dioxane. The hydrogen bonding results in large red shift in bending mode of water and large blue shift in symmetric stretching and asymmetric stretching mode of water. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

The first suberate lanthanum(III) complex without uncoordinated water

catena‐Poly­[[aqua­lanthanum(III)]‐μ‐(8‐carboxy­octanoato)‐μ‐octanedioato], [La(C₈H₁₂O₄)(C₈H₁₃O₄)(H₂O)]_n, is, to our knowledge, the first reported rare‐earth complex containing a flexible long‐chain ligand that crystallizes without water of crystallization. The layered polymeric structure is built from infinite chains of one‐edge‐sharing LaO₈(H₂O) polyhedra, connected through the carbon backbone chains of the ligands. The two chemically different ligands act in the same coordination modes, exhibiting chelating bonds and μ‐1,1‐bridging monodentate linkage, and adopting the same extended conformation. In the relatively limited hydrogen‐bonding network, a very strong hydrogen bond between the deprotonated and protonated ligand ends stabilizes the framework.