Molecular Engineering of Free‐Base Porphyrins as Ligands—The N−H⋅⋅⋅X Binding Motif in Tetrapyrroles

The core N?H units of planar porphyrins are often inaccessible to forming hydrogen‐bonding complexes with acceptor molecules. This is due to the fact that the amine moieties are “shielded” by the macrocyclic system, impeding the formation of intermolecular H‐bonds. However, methods exist to modulate the tetrapyrrole conformations and to reshape the vector of N?H orientation outwards, thus increasing their availability and reactivity. Strategies include the use of porpho(di)methenes and phlorins (calixphyrins), as well as saddle‐distorted porphyrins. The former form cavities due to interruption of the aromatic system. The latter are highly basic systems and capable of binding anions and neutral molecules via N?H???X‐type H‐bonds. This Review discusses the role of porphyrin(oid) ligands in various coordination‐type complexes, means to access the core for hydrogen bonding, the concept of conformational control, and emerging applications, such as organocatalysis and sensors.     

Hydrogen‐Bond‐Guided Self‐Assembly of Nucleotides on a Receptor‐Array Surface

The hydrogen‐bond‐guided self‐assembly of 5′‐ribonucleotides bearing adenine(A), cytosine (C), uracil (U), or guanine (G) bases from aqueous solution on a lipid‐like surface decorated with synthetic bis(Zn^II–cyclen) (cyclen=1,4,7,10‐tetraazacyclodododecane) metal–complex receptor sites is described. The process was studied by using surface plasmon resonance spectroscopy. The data show that the mechanism of nucleotide binding to the 2D template is influenced by the chemistry of the bases and the pH value of the solution. In a neutral solution of pH 7.5, the process is cooperative and selective with respect to Watson–Crick pairs (A–U and C–G), which form stable double planes in accordance with the Chargaff rule. In a more acidic solution at pH 6.0, the interactions between complementary partners become non‐cooperative and the surface also stabilizes mismatched and wobble pairs due to the pH‐induced changes in the receptor coordination state. The results suggest that hydrogen bonding plays a key role in the self‐assembly of complementary nucleotides at the lipid‐like interface, and the cooperative character of the process stems from the ideal matching of the orientation and chemistry of all the interacting components with respect to each other in neutral solution.     

Phase behavior and properties of polyvinyl alcohol/gelatin blends with novel pH‐dependence

A novel change of phase behavior and properties of polyvinyl alcohol (PVA)/gelatin blends as a function of pH was reported. The PVA/gelatin blends were found to be completely miscible in acidic condition (pH < 4), partially miscible in basic condition (pH > 8), and immiscible in neutral condition (pH was ca. 6). As a result, the membranes cast from acidic condition showed the highest tensile strength and the lowest alcohol vapor permeation (AVP) rate; those obtained from neutral condition showed the lowest tensile strength and highest AVP rate; the properties of membranes cast from basic condition lay in between. The interaction between PVA and gelatin was investigated via Fourier transform infrared spectrum (FTIR), differential scanning calorimetry (DSC), and Zetasizer measurement. The novel pH‐dependence of the blends was ascribed to the protonation of amino groups of gelatin in acidic condition, which resulted in a strong electrostatic attraction between ? NH of gelatin and ? OH of PVA. The partial miscibility in basic condition was due to the ionization of carboxyl groups of gelatin, which caused a stretching of gelatin via electrostatic repulsive force and a breakage of the H‐bonding among the molecular chains, leading to a limited interaction between PVA and gelatin and forming a partially miscible blend. In neutral conditions, there were almost no charges (very limited protonation and ionization) at the weak polyampholyte gelatin, and the strong H‐bonding among gelatin molecules themselves or PVA molecules themselves caused the phase separation between gelatin and PVA. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 239–247, 2009     

Hydrogen bonding in 4‐nitrobenzene‐1,2‐diamine and two hydrohalide salts

The structures of 4‐nitrobenzene‐1,2‐diamine [C₆H₇N₃O₂, (I)], 2‐amino‐5‐nitroanilinium chloride [C₆H₈N₃O₂⁺·Cl⁻, (II)] and 2‐amino‐5‐nitroanilinium bromide monohydrate [C₆H₈N₃O₂⁺·Br⁻·H₂O, (III)] are reported and their hydrogen‐bonded structures described. The amine group para to the nitro group in (I) adopts an approximately planar geometry, whereas the meta amine group is decidedly pyramidal. In the hydrogen halide salts (II) and (III), the amine group meta to the nitro group is protonated. Compound (I) displays a pleated‐sheet hydrogen‐bonded two‐dimensional structure with R₂²(14) and R₄⁴(20) rings. The sheets are joined by additional hydrogen bonds, resulting in a three‐dimensional extended structure. Hydrohalide salt (II) has two formula units in the asymmetric unit that are related by a pseudo‐inversion center. The dominant hydrogen‐bonding interactions involve the chloride ion and result in R₄²(8) rings linked to form a ladder‐chain structure. The chains are joined by N—H...Cl and N—H...O hydrogen bonds to form sheets parallel to (010). In hydrated hydrohalide salt (III), bromide ions are hydrogen bonded to amine and ammonium groups to form R₄²(8) rings. The water behaves as a double donor/single acceptor and, along with the bromide anions, forms hydrogen bonds involving the nitro, amine, and ammonium groups. The result is sheets parallel to (001) composed of alternating R₅⁵(15) and R₆⁴(24) rings. Ammonium N—H...Br interactions join the sheets to form a three‐dimensional extended structure. Energy‐minimized structures obtained using DFT and MP2 calculations are consistent with the solid‐state structures. Consistent with (II) and (III), calculations show that protonation of the amine group meta to the nitro group results in a structure that is about 1.5 kJ mol⁻¹ more stable than that obtained by protonation of the para‐amine group. DFT calculations on single molecules and hydrogen‐bonded pairs of molecules based on structural results obtained for (I) and for 3‐nitrobenzene‐1,2‐diamine, (IV) [Betz & Gerber (2011). Acta Cryst. E 67 , o1359] were used to estimate the strength of the N—H...O(nitro) interactions for three observed motifs. The hydrogen‐bonding interaction between the pairs of molecules examined was found to correspond to 20–30 kJ mol⁻¹.     

trans‐Aquachloro[(1R,4R,8S,11S)‐6,13‐diammonio‐6,13‐dimethyl‐1,4,8,11‐tetra­azacyclo­tetra­decane‐κ4N1,4,8,11]nickel(II) trichloride trihydrate

The title compound, [NiCl(C₁₂H₃₂N₆)(H₂O)]Cl₃·3H₂O, has the bis­(diamine)‐substituted cyclic tetra­amine in a planar coordination to triplet ground‐state Ni^II [average Ni—N = 2.068 (3) Å], with a chloride ion [Ni—Cl = 2.4520 (5) Å] and a water mol­ecule [Ni—O = 2.177 (2) Å] coordinated in the axial sites. The amine substituents are protonated and equatorially oriented. The amine groups, ammonium groups, water molecules and chloride ions are linked by an extensive hydrogen‐bonding network.     

Bis[bis(methoxycarbimido)aminato]copper(II) 1‐methylpyrrolidin‐2‐one disolvate

The title compound, [Cu(C₄H₈N₃O₂)₂]·2C₅H₉NO, consists of a neutral copper complex, in which the Cu^II centre coordinates to two bis(methoxycarbimido)aminate ligands, solvated by two molecules of 1‐methylpyrrolidin‐2‐one. The complex is planar and centrosymmetric, with the Cu^II centre occupying a crystallographic inversion centre and adopting approximately square‐planar geometry. N—H...O hydrogen‐bonding interactions exist between the amine NH groups of the ligands and the O atoms of the 1‐methylpyrrolidin‐2‐one molecules. The associated units pack to form sheets.     

Double Hydrogen‐Bonding pH‐Sensitive Hydrogels Retaining High‐Strengths Over a Wide pH Range

Traditional pH‐sensitive hydrogels inevitably suffer strength deterioration while the responsive weak acid or base groups are in the ionized state. In this study, we report on a facile approach to fabricate a novel pH‐sensitive high‐strength hydrogel from copolymerization of two hydrogen‐bonding motif‐containing monomers, 3‐acrylamidophenylboronic acid and 2‐vinyl‐4,6‐diamino‐1,3,5‐triazine with a crosslinker N,N‐methylenebisacrylamide through hydrophilic optimization of the comonomer oligo(ethylene glycol) methacrylate. The double hydrogen bonding hydrogel exhibits both high tensile and compressive strengths over a broad pH range due to the unique ability to maintain at least one type of hydrogen‐bonding crosslink over the whole course of pH change.     

7‐Cyclopropyl‐2′‐deoxytubercidin: a carbocyclic side‐chain derivative of 7‐deaza‐2′‐deoxyadenosine

The title compound {systematic name: 4‐amino‐5‐cyclopropyl‐7‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine}, C₁₄H₁₈N₄O₃, exhibits an anti glycosylic bond conformation, with the torsion angle χ = −108.7 (2)°. The furanose group shows a twisted C1′‐exo sugar pucker (S‐type), with P = 120.0 (2)° and τ_m = 40.4 (1)°. The orientation of the exocyclic C4′—C5′ bond is ‐ap (trans), with the torsion angle γ = −167.1 (2)°. The cyclopropyl substituent points away from the nucleobase (anti orientation). Within the three‐dimensional extended crystal structure, the individual molecules are stacked and arranged into layers, which are highly ordered and stabilized by hydrogen bonding. The O atom of the exocyclic 5′‐hydroxy group of the sugar residue acts as an acceptor, forming a bifurcated hydrogen bond to the amino groups of two different neighbouring molecules. By this means, four neighbouring molecules form a rhomboidal arrangement of two bifurcated hydrogen bonds involving two amino groups and two O5′ atoms of the sugar residues.     

Hydrogen‐bonded networks in 5‐chloropyridin‐2‐amine–fumaric acid (2/1) and 2‐aminopyridinium dl‐malate

Crystals of 5‐chloropyridin‐2‐amine–(2E)‐but‐2‐enedioate (2/1), 2C₅H₅ClN₂·C₄H₄O₄, (I), and 2‐aminopyridinium dl ‐3‐carboxy‐2‐hydroxypropanoate, C₅H₇N₂⁺·C₄H₅O₅⁻, (II), are built from the neutral 5‐chloropyridin‐2‐amine molecule and fumaric acid in the case of (I) and from ring‐N‐protonated 2‐aminopyridinium cations and malate anions in (II). The fumaric acid molecule lies on an inversion centre. In (I), the neutral 5‐chloropyridin‐2‐amine and fumaric acid molecules interact via hydrogen bonds, forming two‐dimensional layers parallel to the (100) plane, whereas in (II), oppositely charged units interact via ionic and hydrogen bonds, forming a three‐dimensional network.     

Dual‐responsive copolymer poly(2,2,3,4,4,4‐hexafluorobutyl methacrylate)‐block‐poly[2‐(dimethylamino)ethyl methacrylate] synthesized via photoATRP for surface with tunable wettability

In this work, a series of block copolymers of poly(2,2,3,4,4,4‐hexafluorobutyl methacrylate)‐block‐poly[2‐(dimethylamino)ethyl methacrylate] (PHFBMA‐b‐PDMAEMA) were synthesized via photo‐induced atom transfer radical polymerization (photoATRP) at room temperature. By the introduction of PDMAEMA segment, the hydrophilicity of the silicon wafer surface spin‐coated with PHFBMA homopolymer was improved. Furthermore, the study of tunable surface wettability showed that the surface wettability was pH‐dependent and thermal‐independent at pH 2 and 10. The as‐fabricated surface coated with PHFBMA₁₁₀‐b‐PDMAEMA₁₈₇ showed switchable water contact angle from 85.4° at pH > 4 to 55.0° at pH 2 due to the protonation and deprotonation of tertiary amine groups of PDMAEMA. However, because of the ascendancy of protonated PDMAEMA at pH 2 and the decreased LCST at pH 10, the wettability of the as‐prepared surfaces was thermal‐insensitive. Finally, surface morphology and composition investigation showed that the property of wettability‐controllable surface was not only influenced by surface composition, but also affected by chain conformation. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 3868–3877     

1,3‐Bis(ethylamino)‐2‐nitrobenzene, 1,3‐bis(n‐octylamino)‐2‐nitrobenzene and 4‐ethylamino‐2‐methyl‐1H‐benzimidazole

1,3‐Bis(ethylamino)‐2‐nitrobenzene, C₁₀H₁₅N₃O₂, (I), and 1,3‐bis(n‐octylamino)‐2‐nitrobenzene, C₂₂H₃₉N₃O₂, (II), are the first structurally characterized 1,3‐bis(n‐alkylamino)‐2‐nitrobenzenes. Both molecules are bisected though the nitro N atom and the 2‐C and 5‐C atoms of the ring by twofold rotation axes. Both display intramolecular N—H...O hydrogen bonds between the amine and nitro groups, but no intermolecular hydrogen bonding. The nearly planar molecules pack into flat layers ca 3.4 Å apart that interact by hydrophobic interactions involving the n‐alkyl groups rather than by π–π interactions between the rings. The intra‐ and intermolecular interactions in these molecules are of interest in understanding the physical properties of polymers made from them. Upon heating in the presence of anhydrous potassium carbonate in dimethylacetamide, (I) and (II) cyclize with formal loss of hydrogen peroxide to form substituted benzimidazoles. Thus, 4‐ethylamino‐2‐methyl‐1H‐benzimidazole, C₁₀H₁₃N₃, (III), was obtained from (I) under these reaction conditions. Compound (III) contains two independent molecules with no imposed internal symmetry. The molecules are linked into chains via N—H...N hydrogen bonds involving the imidazole rings, while the ethylamino groups do not participate in any hydrogen bonding. This is the first reported structure of a benzimidazole derivative with 4‐amino and 2‐alkyl substituents.     

Electrochemically‐controlled DNA Release under Physiological Conditions from a Monolayer‐modified Electrode

An indium tin oxide (ITO) electrode prepared on a flexible polymeric support was modified with an amino‐silane and then functionalized with trigonelline and 4‐carboxyphenylboronic acid covalently bound to the amino groups. The trigonelline species containing quarterized ammonium group produced positive charge on the electrode surface regardless of the pH value, while the phenylboronic acid species were neutral below pH 8 and negatively charged above pH 9 (note that their pK_a=8.4). The total charge on the monolayer‐modified electrode was positive at the neutral pH and negative at pH>9 (note that 4‐carboxyphenylboronic acid was attached to the electrode surface in excess to trigonelline, thus allowing the negative charge to dominate on the electrode surface at basic pH). Single‐stranded DNA molecules were loaded on the modified electrode at pH 7.0 due to their electrostatic attraction to the positively charged surface. By applying electrolysis at −1.0 V (vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase in the vicinity of the electrode surface. The process resulted in the transition to the total negative charge due to the negative charges formed on the phenylboronic acid species. This resulted in the electrostatic repulsion and release of the loaded DNA. The developed approach allowed the electrochemically‐triggered DNA release not only in the aqueous solutions, but also in human serum solution, thus giving promise for future biomedical applications.     

Hydrogen‐Bonding‐Induced Polymorphous Phase Transitions in 2D Organic Nanostructures

The 2D self‐assembly of various 2‐hydroxy‐7‐alkoxy‐9‐fluorenone (HAF) molecules has been investigated by scanning tunneling microscopy (STM) at the liquid/solid interface. A systematic study revealed that HAF molecules with different numbers of carbon atoms in their alkoxy chains could form two or three different kinds of nanostructures, that is, less‐ordered, flower‐like, and zig‐zag patterns, owing to the formation of different types of intermolecular hydrogen bonds. The observed structural transition was found to be driven by molecular thermodynamics, surface diffusion, and the voltage pulse that was applied to the STM tip. The zig‐zag pattern was the most stable of these configurations. An odd–even effect on the flower‐like structure, as induced by the odd and even number of carbon atoms in the side chain, was observed by STM. The influence of the odd–even effect on the melting point has a close relationship with the molecular self‐assembled pattern. Our results are significant for understanding the influence of hydrogen‐bonding interactions on the dominant adsorption behavior on the surface and provide a new visual approach for observing the influence of the odd–even effect on the phase transition.     

The effect of hydrogen bonding on the conformations of 2‐(1H‐indol‐3‐yl)‐2‐oxoacetamide and 2‐(1H‐indol‐3‐yl)‐N,N‐dimethyl‐2‐oxoacetamide

In the title compounds, C₁₀H₈N₂O₂, (I), and C₁₂H₁₂N₂O₂, (II), the two carbonyl groups are oriented with torsion angles of −149.3 (3) and −88.55 (15)°, respectively. The single‐bond distances linking the two carbonyl groups are 1.528 (4) and 1.5298 (17) Å, respectively. In (I), the molecules are linked by an elaborate system of N—H...O hydrogen bonds, which form adjacent R²₂(8) and R⁴₂(8) ring motifs to generate a ladder‐like construct. Adjacent ladders are further linked by N—H...O hydrogen bonds to build a three‐dimensional network. The hydrogen bonding in (II) is far simpler, consisting of helical chains of N—H...O‐linked molecules that follow the 2₁ screw of the b axis. It is the presence of an elaborate hydrogen‐bonding system in the crystal structure of (I) that leads to the different torsion angle for the orientation of the two adjacent carbonyl groups from that in (II).     

On‐Surface Self‐Assembly of a C3‐Symmetric π‐Conjugated Molecule Family Studied by STM: Two‐Dimensional Nanoporous Frameworks

The on‐surface self‐assembled behavior of four C ₃‐symmetric π‐conjugated planar molecules ( Tp , T12 , T18 , and Ex ) has been investigated. These molecules are excellent building blocks for the construction of noncovalent organic frameworks in the bulk phase. Their hydrogen‐bonded 2D on‐surface self‐assemblies are observed under STM at the solid/liquid interface; these structures are very different to those in the bulk crystal. Upon combining the results of STM measurements and DFT calculations, the formation mechanism of different assemblies is revealed; in particular, the critical role of hydrogen bonding in the assemblies. This research provides us with not only a deep insight into the self‐assembled behavior of these novel functional molecules, but also a convenient approach toward the construction of 2D multiporous networks.     

Cooperative Formation of Long‐Range Ordering in Water Ad‐layers on Fe3O4(111) Surfaces

The initial stages of water adsorption on magnetite Fe₃O₄(111) surface and the atomic structure of the water/oxide interface remain controversial. Herein, we provide experimental results obtained by infrared reflection–absorption spectroscopy (IRAS) and temperature‐programmed desorption (TPD), corroborated by density functional theory (DFT) calculations showing that water readily dissociates on Fe_tet sites to form two hydroxo species. These act as an anchor for water molecules to form a dimer complex which self‐assembles into an ordered (2×2) structure. Water ad‐layer ordering is rationalized in terms of a cooperative effect induced by a hydrogen‐bonding network.     

Water‐mediated intermolecular interactions in 1,2‐O‐cyclohexylidene‐myo‐inositol: a quantitative analysis

The syntheses of new myo‐inositol derivatives have received much attention due to their important biological activities. 1,2‐O‐Cyclohexylidene‐myo‐inositol is an important intermediate formed during the syntheses of certain myo‐inositol derivatives. We report herein the crystal structure of 1,2‐O‐cyclohexylidene‐myo‐inositol dihydrate, C₁₂H₂₀O₆·2H₂O, which is an intermediate formed during the syntheses of myo‐inositol phosphate derivatives, to demonstrate the participation of water molecules and hydroxy groups in the formation of several intermolecular O—H…O interactions, and to determine a low‐energy conformation. The title myo‐inositol derivative crystallizes with two water molecules in the asymmetric unit in the space group C 2/c , with Z = 8. The water molecules facilitate the formation of an extensive O—H…O hydrogen‐bonding network that assists in the formation of a dense crystal packing. Furthermore, geometrical optimization and frequency analysis was carried out using density functional theory (DFT) calculations with B3LYP hybrid functionals and 6‐31G(d), 6‐31G(d,p) and 6‐311G(d,p) basis sets. The theoretical and experimental structures were found to be very similar, with only slight deviations. The intermolecular interactions were quantitatively analysed using Hirshfeld surface analysis and 2D (two‐dimensional) fingerplot plots, and the total lattice energy was calculated.     

Effect of differently terminal groups of poly(amido‐amine) dendrimers on dispersion stability of nano‐silica and ab initio calculations

To investigate the effect of differently terminal groups of the lowest‐order generation poly(amido‐amine) dendrimers on dispersion stability of nano‐silica, the four types of G0‐CH₂CH₃ (G0E), G0‐CH₂CH₂CH₂CH₃ (G0B), G0‐NH₂ (G0N), and G0‐COOH (G0C) dendrimer molecules are used to modify the silica based on the dry modification. The zeta potential, the surface charge density, and the storage stability of kinds of modified SiO₂ dispersion systems have been studied. The results show that the effect of carboxyl groups on dispersion stability is stronger than that of the other groups such as the amine and alkyl groups. Mulliken charge distributions of the main active sites are analyzed through the conductor‐like polarizable calculation model (CPCM) on basis of the density functional theory (DFT) method, indicating the formation of chemical bonding between the modifiers and SiO₂ particles. The most stable SiO₂ dispersion system modified by G0‐COOH dendrimer molecule is obtained due to the combined effect including the hydrogen bonding, electrostatic repulsive force, and the steric hindrance of the terminal groups. Copyright © 2015 John Wiley & Sons, Ltd.     

Inner Workings of a Cinchona Alkaloid Catalyzed Oxa‐Michael Cyclization: Evidence for a Concerted Hydrogen‐Bond‐Network Mechanism

Cinchona alkaloids catalyze the oxa‐Michael cyclization of 4‐(2‐hydroxyphenyl)‐2‐butenoates to benzo‐2,3‐dihydrofuran‐2‐yl acetates and related substrates in up to 99 % yield and 91 % ee (ee=enantiomeric excess). Catalyst and substrate variation studies reveal an important role of the alkaloid hydroxy group in the reaction mechanism, but not in the sense of a hydrogen‐bonding activation of the carbonyl group of the substrate as assumed by the Hiemstra–Wynberg mechanism of bifunctional catalysis. Deuterium labeling at C‐2 of the substrate shows that addition of RO? H to the alkenoate occurs with syn diastereoselectivity of ≥99:1, suggesting a mechanism‐based specificity. A concerted hydrogen‐bond network mechanism is proposed, in which the alkaloid hydroxy group acts as a general acid in the protonation of the α‐carbanionic center of the product enolate. The importance of concerted hydrogen‐bond network mechanisms in organocatalytic reactions is discussed. The relative stereochemistry of protonation is proposed as analytical tool for detecting concerted addition mechanisms, as opposed to ionic 1,4‐additions.     

DNA Computing Systems Activated by Electrochemically‐triggered DNA Release from a Polymer‐brush‐modified Electrode Array

An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA‐based Identity, AND and XOR logic gates. Single‐stranded DNA molecules were loaded on the mixed poly(N ,N ‐dimethylaminoethyl methacrylate) (PDMAEMA)/poly(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAEMA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at −1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.