Hydrogen bonding in noncovalent synthesis: selectivity and the directed organization of molecular strands

Amino Acid Polymerization on Silica Surfaces

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.

Synthetically encoded complementary oligomers

Creating the next generation of advanced materials will require controlling molecular architecture to a degree typically achieved only in biopolymers. Sequence-defined polymers take inspiration from biology by using chain length and monomer sequence as handles for tuning structure and function. These sequence-defined polymers can assemble into discrete structures, such as molecular duplexes, via reversible interactions between functional groups. Selectivity can be attained by tuning the monomer sequence, thereby creating the need for chemical platforms that can produce sequence-defined polymers at scale. Developing sequence-defined polymers that are specific for their complementary sequence and achieve their desired binding strengths is critical for producing increasingly complex structures for new functional materials. In this Review Article, we discuss synthetic platforms that produce sequence-defined, duplex-forming oligomers of varying length, strength and association mode, and highlight several analytical techniques used to characterize their hybridization.

Self-assembly of secondary aryl amides in cocrystals with perfluoroaryl coformers: structural analysis and synthon preferences

Lactams 1–3 readily form cocrystals with pentafluorophenol (pfp) or pentafluorobenzoic acid (pfba) and the observed crystal packings result from concerted aryl⋯perfluoroaryl stacking interactions combined with hydrogen bonding.

Melamine-Barbiturate Supramolecular Assembly as a pH-Dependent Organic Radical Trap Material

In the last two decades, a large number of self-assembled materials were synthesized and they have already found their way into large-scale industry and science. Hydrogen-bond-based supramolecular adducts are found to have unique properties and to be perfect host structures for trapping target molecules or ions. Such chemical systems are believed to resemble living matter and can substitute a living cell in a number of cases. Herein, a report on an organic material based on supramolecular assembly of barbituric acid and melamine is presented. Surprisingly, the structure is found to host and stabilize radicals under mild conditions allowing its use for biological applications. The number of free radicals is found to be easily tuned by changing the pH of the environment and it increases when exposed to light up to a saturation level. We describe a preparation method as well as stability properties of melamine-barbiturate self-assembly, potentiometric titration, and hydrogen ions adsorption data and EPR spectra concerning the composite.

Just add sugar for carbohydrate induced self-assembly of curcumin

In nature, self-assembly processes based on amphiphilic molecules play an integral part in the design of structures of higher order such as cells. Among them, amphiphilic glycoproteins or glycolipids take on a pivotal role due to their bioactivity. Here we show that sugars, in particular, fructose, are capable of directing the self-assembly of highly insoluble curcumin resulting in the formation of well-defined capsules based on non-covalent forces. Simply by mixing an aqueous solution of fructose and curcumin in an open vessel leads to the generation of capsules with sizes ranging between 100 and 150 nm independent of the initial concentrations used. Our results demonstrate that hydrogen bonding displayed by fructose can induce the self-assembly of hydrophobic molecules such as curcumin into well-ordered structures, and serving as a simple and virtually instantaneous way of making nanoparticles from curcumin in water with the potential for template polymerization and nanocarriers.

Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations

The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

Ethynyl hydrogen bonds and iodoethynyl halogen bonds: a case of synthon mimicry

The common electrostatic features of ethynyl and iodoethynyl hydrogen- and halogen-bond donors, respectively, lead to synthon mimicry which can be employed in synthetic crystal engineering for the construction of identical supramolecular assemblies in the solid-state.

H-Bond: Τhe Chemistry-Biology H-Bridge

H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.

Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations

The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations

The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N–H⋯F–C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments.

Dinuclear organogold(i) complexes bearing uracil moieties: chirality of Au(i)–Au(i) axis and self-assembly

Dinuclear organogold(i) complexes bearing uracil moieties were designed, wherein the chirality of the Au(i)–Au(i) axis was induced by coordination regulation of the axially chiral bidentate diphosphine ligand, and intermolecular hydrogen-bonded assemblies were formed between the uracil moieties.

Supramolecular assemblies of nucleoside functionalized carbon nanotubes: synthesis, film preparation, and properties

Nucleoside-functionalized multi-walled carbon nanotubes (N-MWCNTs) were synthesized and characterized. A self-organization process using hydrogen bonding interactions was then used for the fabrication of self-assembled N-MWCNTs films free of stabilizing agents, polymers, or surfactants. Membranes were produced by using a simple water-dispersion-based vacuum-filtration method. Hydrogen-bond recognition was confirmed by analysis with IR spectroscopy and TEM images. Restoration of the electronic conduction properties in the N-MWCNTs membranes was performed by removing the organic portion by thermal treatment under an argon atmosphere to give d-N-MWCNTs. Electrical conductivity and thermal gravimetric analysis (TGA) measurements confirmed the efficiency of the annealing process. Finally, oxidative biodegradation of the films N-MWCNTs and d-N-MWCNTs was performed by using horseradish peroxidase (HRP) and low concentrations of H2 O2 . Our results confirm that functional groups play an important role in the biodegradation of CNT by HRP: N-MWCNTs films were completely biodegraded, whereas for d-N-MWCNTs films no degradation was observed, showing that the pristine CNT undergoes minimal enzyme-catalyzed oxidation This novel methodology offers a straightforward supramolecular strategy for the construction of conductive and biodegradable carbon nanotube films.

NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water

An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.

Biguanide and squaric acid as pH-dependent building blocks in crystal engineering

Biguanides and squaric acid are attractive partners for crystal engineering: they incorporate multiple sites that can donate or accept hydrogen bonds. Protonation equilibria in their solutions and the outcome of crystallization experiments are pH dependent: 10 different salts have been obtained from N,N-dimethylbiguanide, N-phenylbiguanide and N-o-tolylbiguanide.

Synthesis and characterization of thermally stable aromatic polyamides and poly(1,3,4-oxadiazole-amide)s nanoparticles containing pendant substituted bezamides

Background

The introduction of pendent bulky groups along the polymer backbone results in a less ordered polymer matrix and increases the solubility characteristics without affecting thermal properties. The inclusion of chromogenic chemical moieties in the chains can give rise to the luminescent converter material which permits the preparation of materials with potential applications. Aromatic polymers containing heterocyclic rings in the main chain are known for their high thermal resistance, good hydrolytic stability, low dielectric and tough mechanical properties. There is currently much research directed towards the discovery of new blue light-emitting polymers, with characteristics of high efficiency and high reliability. Herein, we describe the preparation of aromatic polyamides and poly (1,3,4-oxadiazole-amide)s nanoparticles with pendant structures comprised of m- and p-acetoxybenzamide groups, where the acetoxybenzamide groups act as signaling units due to their fluorescent and chromogenic characteristics.

Results

Aromatic polyamides and poly(1,3,4-oxadiazole-amide)s nanoparticles with pendant structures comprised of m- and p-acetoxybenzamide groups were successfully prepared and characterized using different analytical methods. Most polyamides were obtained as well-separated spherical nanoparticles while aramide containing pyridine produced aggregated particles attributed to the molecular self assembly via H-bond directed organization of molecular precursors. The thermal behavior of all polymers exhibited two major thermal decompositions due to the subsequent breakage of the acetoxy group in the lateral chain and cleavage of the main amide bonds. Photoluminescence studies revealed that the blue emissions for the polyamide derived from benzidine were blue-shifted (shifted to a lower wavelength) compared to that of polyamides containing flexible linkages.

Conclusions

We report the synthesis of aromatic polyamides and poly(1,3,4-oxadiazole-amide)s nanoparticles with pendant structures comprised of m- and p-acetoxybenzamide groups. The thermal behavior of all polymers exhibited two major decompositions due to breakage of the acetoxy group in the lateral chain and cleavage of the main amide bonds. Structure- photoluminescence correlation demonstrated an interesting connection between structural modification and optical properties. The blue emissions for the polyamide derived from benzidine, attributed to the highly conjugation system, was blue shifted with the introduction of flexible linkages. The prepared polymers dissolved in warm polar aprotic solvents. Further investigations to obtain films with reasonably good mechanical properties for different applications are in progress.

Antioxidant activity of new aramide nanoparticles containing redox-active N-phthaloyl valine moieties in the hepatic cytochrome P450 system in male rats

We report the synthesis of aramide nanoparticles containing a chiral N-phthaloyl valine moiety and their antioxidant activities on hepatic contents of cytochrome P₄₅₀, amidopyrene N-demethylase, aniline-4-hyroxylase and induced the hepatic content of cytochrome b5 and nicotinamide adenine dinucleotide phosphate (NADPH) cytochrome C-reductase. Polymers were obtained as well-separated spherical nanoparticles while highly aggregated particles via H-bonding organization of the aramide-containing pyridine led to a thin layer formation. The effects of the nanoparticles and CCl₄ on enzyme activities and thiobarbituric acid reactive substances (TBARS) levels of male rat liver were studied. Pretreatments of rats with the polyamides prior to the administration of CCl₄ decreased the hepatic content of the tested enzymes. Doses reduced the toxic effects exerted by (•CCl₃) upon the liver through inhibition of the cytochrome P₄₅₀ system. Inhibition of such metabolizing enzymes could reduce the carcinogenic effects of chemical carcinogens.

Design of ferrocene-dipeptide bioorganometallic conjugates to induce chirality-organized structures

The highly ordered molecular assemblies in proteins can have a variety of functions, as observed in enzymes, receptors, and the like. Synthetic scientists are constructing bioinspired systems by harnessing the self-assembling properties of short peptides. Secondary structures such as alpha-helices, beta-sheets, and beta-turns are important in protein folding, which is mostly directed and stabilized by hydrogen bonding and the hydrophobic interactions of side chains. The design of secondary structure mimics that are composed of short peptides has attracted much attention, both for gaining fundamental insight into the factors affecting protein folding and for developing pharmacologically useful compounds, artificial receptors, asymmetric catalysts, and new materials. Ferrocenes are an organometallic scaffold with a central reverse-turn unit based on the inter-ring spacing of about 3.3 A, which is a suitable distance for hydrogen bonding between attached peptide strands. The conjugation of organometallic compounds with biomolecules such as amino acids, peptides, and DNA should provide novel systems that reflect properties of both the ferrocene and the biologically derived moieties. In this Account, we focus on recent advances in the design of ferrocene-peptide bioconjugates, which help illustrate the peptidomimetic basis for protein folding and the means of constructing highly ordered molecular assemblies. Ferrocene-peptide bioconjugates are constructed to form chirality-organized structures in both solid and solution states. The ferrocene serves as a reliable organometallic scaffold for the construction of protein secondary structures via intramolecular hydrogen bonding: the attached dipeptide strands are constrained within the appropriate dimensions. The introduction of the chiral dipeptide chains into the ferrocene scaffold induces the conformational enantiomerization of the ferrocenyl moiety; the chirality-organized structure results from intramolecular hydrogen bonding. The configuration and sequence of the amino acids are instrumental in the process. Regulation of the directionality and specificity of hydrogen bonding is a key component in the design of various molecular assemblies. Ferrocene-peptide bioconjugates also have a strong tendency to self-assemble through the contributions of available hydrogen-bonding donors in the solid state. Some ferrocene-peptide bioconjugates bearing only one dipeptide chain exhibit a helically ordered molecular assembly through a network of intermolecular (rather than intramolecular) hydrogen bonds. The propensity to form the chiral helicity appears to be controlled by the chirality of the dipeptide chains. Organization of host molecules is a useful strategy for forming artificial receptors. The conformationally regulated ferrocene-peptide bioconjugate provides the chirality-organized binding site for size-selective and chiral recognition of dicarboxylic acids through multipoint hydrogen bonds. Metal ions serve a variety of purposes in proteins, including structural stabilization for biological function. The complexation of ferrocene-peptide bioconjugates with palladium(II) compounds not only stabilizes the chirality conformational regulation but also induces conformational regulation of the dipeptide chain through complexation and intramolecular chirality organization. Construction of the chirality-organized ferrocene-peptide bioconjugates is also achieved by metal-directed assembly. These varied examples amply demonstrate the value of ferrocene-peptide bioconjugates in asserting architectural control over highly ordered molecular assemblies.

Melamine toxicity

Melamine contamination of infant formula in China and its health effects highlight the safety of the global food supply especially as it relates to formula-fed infants. Melamine is a widely used industrial chemical not considered acutely toxic with a high LD(50) in animals. The data available on acute and chronic human exposure to melamine have been limited and extrapolated from animal data. Pet food contamination in 2004 and 2007 showed stone formation and illness in animals when melamine was co-ingested with cyanuric acid. The recent outbreak in infants showed that melamine ingested in large doses may cause stones and illness without significant ingestion of cyanuric acid or other melamine-related chemicals. This may be due to increased uric acid excretion in infants and formation of melamine-uric acid stones. Diagnosis and treatment of infants exposed to melamine requires further study. Clinical signs and symptoms in infants are nonspecific. The stones may be radiolucent and are not consistently seen on ultrasound. The use of alkalinization of the urine for treatment has been proposed, but is of unproven benefit. The FDA and other regulatory agencies have recommended acceptable levels of melamine in foods for consumption. Melamine ingestion has been implicated in stone formation when co-ingested with cyanuric acid, but will cause urinary stones in infants when large amounts of melamine alone are ingested.