Resonance‐Assisted Hydrogen Bonding as a Driving Force in Synthesis and a Synthon in the Design of Materials

Resonance‐assisted hydrogen bonding (RAHB), a concept introduced by Gilli and co‐workers in 1989, concerns a kind of intramolecular H‐bonding strengthened by a conjugated π‐system, usually in 6‐, 8‐, or 10‐membered rings. This Review highlights the involvement of RAHB as a driving force in the synthesis of organic, coordination, and organometallic compounds, as a handy tool in the activation of covalent bonds, and in starting moieties for synthetic transformations. The unique roles of RAHB in molecular recognition and switches, E/Z isomeric resolution, racemization and epimerization of amino acids and chiral amino alcohols, solvatochromism, liquid‐crystalline compounds, and in synthons for crystal engineering and polymer materials are also discussed. The Review can provide practical guidance for synthetic chemists that are interested in exploring and further developing RAHB‐assisted synthesis and design of materials.     

Carbohydrate–DNA Interactions at G‐Quadruplexes: Folding and Stability Changes by Attaching Sugars at the 5′‐End

Quadruplex DNA structures are attracting an enormous interest in many areas of chemistry, ranging from chemical biology, supramolecular chemistry to nanoscience. We have prepared carbohydrate–DNA conjugates containing the oligonucleotide sequences of G‐quadruplexes (thrombin binding aptamer (TBA) and human telomere (TEL)), measured their thermal stability and studied their structure in solution by using NMR and molecular dynamics. The solution structure of a fucose–TBA conjugate shows stacking interactions between the carbohydrate and the DNA G‐tetrad in addition to hydrogen bonding and hydrophobic contacts. We have also shown that attaching carbohydrates at the 5′‐end of a quadruplex telomeric sequence can alter its folding topology. These results suggest the possibility of modulating the folding of the G‐quadruplex by linking carbohydrates and have clear implications in molecular recognition and the design of new G‐quadruplex ligands.     

Bifunctional Iodoazolium Salts: Searching for Cooperation Between Halogen Bonding and Hydrogen Bonding

Non-covalent interactions play an important role in all sub-fields of chemistry, including catalysis, where interactions of different natures can work together to improve reactivitiy and selectivity. Several families of molecules that incorporate both hydrogen bond (HB) and halogen bonding (XB) donors have already been studied. However, there is a lack of data on how grafting HB donors to iodoazolium salts could impact their association and reactivity properties. Herein, we disclose the synthesis of a library of iodoazolium salts bearing varied HB donors, along with a study of their physico-chemical properties using different techniques (X-ray diffraction, ³¹P NMR, ITC) and their behavior in catalysis. Even though no clear-cut evidence of cooperation between XB and HB could be obtained through physico-chemical evaluations, a iodoazolium salt bearing a urea function displayed better conversion and product selectivity in a Ritter reaction than all other activators lacking one or the other function.     

Glucose–Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside–RNA recognition, glucose‐nucleobase pairs have been examined. Deoxyoligonucleotides with a 6‐deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6‐Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6‐deoxyglucose‐guanine pair closely resembles a purine‐pyrimidine geometry. Quantum chemical calculations indicate that glucose‐purine pairs are as stable as a natural T‐A pair.     

Dimeric Calixarenes: A New Family of Major‐Groove Binders

A new class of potent DNA binding agents is presented. Dimeric calix[4]arenes with cationic groups at their upper rims and flexible alkyl bridges can be synthesized from triply acyl‐protected calix[4]arene tetramines in relatively short synthetic sequences (3–5 steps). The compounds attach themselves to double‐stranded nucleic acids in a noncovalent fashion, with micro‐ to nanomolar affinities. Guanidinium headgroups with their extended hydrogen‐bonding “fingers” are more powerful than ammonium groups, and the benzylamine series is superior to the anilinium series (see below). The new ligands easily distinguish between RNA and various DNA types, and produce characteristic changes in UV/Vis, fluorescence, CD, as well as NMR spectra. Especially extended oligonucleotides of more than 100 base pairs are bound with affinities increasing from RNA (10 μM K_d)<AT‐rich (1 μM )<GC‐rich DNA double strands (100–10 nM ). Ethidium bromide displacement studies confirm this order. CE₅₀ values are remarkably low (1–4 μM ), and are more than 300 times lower than that of spermine, which is a typical backbone binder. Stoichiometries are rather high (one calixarene dimer per two BP), suggesting a potential aggregation of bound ligands inside the major groove. Most UV/Vis melting curves display an inverted shape, and start from drastically enhanced absorption intensities for the DNA complexes. DAPI displacement studies prove that up to one equivalent of calixarene dimer can be accommodated in the dye‐loaded DNA. RNA complexation by calixarene dimers is accompanied by a drastic CD spectral transition from the typical A‐form to a perfect B‐signature, providing further experimental evidence for major‐groove binding. The orientation of the ligands can be deduced from NMR titrations and is reproduced in Monte‐Carlo simulations on 1:1 complexes in water.     

Selectivity of DNA Replication: The Importance of Base-Pair Geometry over Hydrogen Bonding

The polymerase enzyme hardly differentiates between thymine and difluorotoluene nucleotides with respect to the replication selectivity. X-ray structure analysis show the importance of the Watson–Crick geometry for the replication fidelity; base selection is determined by the spatial prerequisite of the substrate pocket and directed protein interactions in the minor groove (schematically shown on the right).     

Enhanced Room-Temperature Phosphorescence through Intermolecular Halogen/Hydrogen Bonding

Room-temperature phosphorescence (RTP) materials with high efficiency have attracted much attention because they have unique characteristics that cannot be realized in conventional fluorescent materials. Unfortunately, efficient RTP in metal-free organic materials is very rare and it has traditionally been considered as the feature to divide purely organic compounds from organometallic and inorganic compounds. There has been increasing research interest in the design and preparation of metal-free organic RTP materials in recent years. It has been reported that intermolecular interactions make a big difference to the photophysical behavior of organic molecules. In this regard, herein, the parameters that affect RTP efficiency are discussed, and a brief review of recent intermolecular halogen-/hydrogen-bonding strategies for efficient RTP in metal-free organic materials are provided. The opportunities and challenges are finally elaborated in the hope of guiding promising directions for the design and application of RTP materials.     

Hydrogen Peroxide Coordination to Cobalt(II) Facilitated by Second‐Sphere Hydrogen Bonding

M(H₂O₂) adducts have been postulated as intermediates in biological and industrial processes; however, only one observable M(H₂O₂) adduct has been reported, where M is redox‐inactive zinc. Herein, direct solution‐phase detection of an M(H₂O₂) adduct with a redox‐active metal, cobalt(II), is described. This Co^II(H₂O₂) compound is made observable by incorporating second‐sphere hydrogen‐bonding interactions between bound H₂O₂ and the supporting ligand, a trianionic trisulfonamido ligand. Thermodynamics of H₂O₂ binding and decay kinetics of the Co^II(H₂O₂) species are described, as well as the reaction of this Co^II(H₂O₂) species with Group 2 cations.     

Guest–Host Hydrogen Bonding in Structure H Clathrate Hydrates

Molecular dynamics simulations of the structure H (sH) clathrate of tert‐butylmethylether show the prevalence of ether–water hydrogen bonding (see picture), absent in the neo‐hexane sH clathrate. This affects guest–cage dynamics and host–water dielectric relaxation dynamics. The ¹³C and ¹H NMR relaxation times for both guests are measured, and the differences are explained in terms of guest–host interactions in the two clathrates.

     

CH‐Directed Anion–π Interactions in the Crystals of Pentafluorobenzyl‐Substituted Ammonium and Pyridinium Salts

Simple pentafluorobenzyl‐substituted ammonium and pyridinium salts with different anions can be easily obtained by treatment of the parent amine or pyridine with the respective pentafluorobenzyl halide. Hexafluorophosphate is introduced as the anion by salt metathesis. In the case of the ammonium salt 4 , water co‐crystallisation seems to suppress effective anion–π interactions of bromide with the electron‐deficient aromatic system, whereas with salts 5 and 6 such interactions are observed despite the presence of water. However, due to asymmetric hydrogen‐bonding interactions with ammonium side chains, the anion of 5 is located close to the rim of the pentafluorophenyl group (η¹ interaction). In 6 the CH–anion hydrogen bonding is more symmetric and fixes the anion on top of the ring (η⁶). A similar structure‐controlling effect is observed in case of the 1,4‐diazabicyclo[2.2.2]octane derivatives 7 . Here the position of the anion (Cl, Br, I) is shifted according to the length of the weak CH–halide interaction. The hexafluorophosphate 7 d reveals that this “non‐coordinating” anion can be located on top of an aromatic π system. In the methyl‐substituted pyridinium salts 9 and 10 different locations of the bromide anions with respect to the π system are observed. This is due to different conformations of the mono‐ versus disubstituted pyridine, which leads to different directions of the weak, but structurally important, H_Me? Br bonds.     

Hydrogen Bonding in Phosphine Oxide/Phosphate–Phenol Complexes

To develop a new solvent‐impregnated resin (SIR) system for the removal of phenols and thiophenols from water, complex formation by hydrogen bonding of phosphine oxides and phosphates is studied using isothermal titration calorimetry (ITC) and quantum chemical modeling. Six different computational methods are used: B3LYP, M06‐2X, MP2, spin component‐scaled (SCS) MP2 [all four with 6‐311+G(d,p) basis set], a complete basis set extrapolation at the MP2 level (MP2/CBS), and the composite CBS‐Q model. This reveals a range of binding enthalpies (ΔH) for phenol–phosphine oxide and phenol–phosphate complexes and their thio analogues. Both structural (bond lengths/angles) and electronic elements (charges, bond orders) are studied. Furthermore, solvent effects are investigated theoretically by the PCM solvent model and experimentally via ITC. From our calculations, a trialkylphosphine oxide is found to be the most promising extractant for phenol in SIRs, yielding ΔH=?14.5 and ?9.8 kcal mol^?1 with phenol and thiophenol, respectively (MP2/CBS), without dimer formation that would hamper the phenol complexation. In ITC measurements, the ΔH of this complex was most negative in the noncoordinating solvent cyclohexane, and slightly less so in π–π interacting solvents such as benzene. The strongest binding is found for the dimethyl phosphate–phenol complex [?15.1 kcal mol^?1 (MP2/CBS)], due to the formation of two H‐bonds (P?O???H‐O‐ and P‐O‐H???O‐H); however, dimer formation of these phosphates competes with complexation of phenol, and would thus hamper their use in industrial extractions. CBS‐Q calculations display erroneous trends for sulfur compounds, and are found to be unsuitable. Computationally relatively cheap SCS‐MP2 and M06‐2X calculations did accurately agree with the much more elaborate MP2/CBS method, with an average deviation of less than 1 kcal mol^?1.     

Cooperative Self‐Assembly‐Assisted Formation of Monodisperse Optically Active Spherical and Anisotropic Nanoparticles

We report a new method in which spontaneous self‐assembly is employed to synthesize monodisperse polymer nanoparticles with controlled size (<50 nm), shape, tunable functionality, and enhanced solvent and thermal stability. Cooperative noncovalent interactions, such as hydrogen bonding and aromatic π–π stacking, assist self‐assembly of amphiphilic macromolecules (polystyrene‐block‐polyvinylpyridine, PS? PVP) and structure directing agents (SDAs) to form both spherical and anisotropic solid polymer nanoparticles with SDAs residing in the particle core surrounded by the polymers. Through detailed investigations by scanning electron microscopy and transmission electron microscopy (TEM), we have rationalized nanoparticle morphology evolution and dependence on factors such as SDA concentration and PVP size. By keeping the PS chain size constant, the particle morphology progresses from continuous films to spherical particles, and on to cylindrical nanowires or rods with increasing the PVP chain size. The final nanoparticles are very stable and can be redispersed in common solvents to form homogenous solutions and thin films of ordered nanoparticle arrays through solvent evaporation processes. These nanoparticles exhibit tunable fluorescent colors (or emissions) depending on the choices of the central SDAs. Our method is simple and general without requiring complicated synthetic chemistry, stabilizing surfactants, or annealing procedures (e.g., temperature or solvent annealing), making scalable synthesis feasible.     

Hydrogen Bonding versus Halogen Bonding: Spectroscopic Investigation of Gas-Phase Complexes Involving Bromide and Chloromethanes

Hydrogen bonding and halogen bonding are important non-covalent interactions that are known to occur in large molecular systems, such as in proteins and crystal structures. Although these interactions are important on a large scale, studying hydrogen and halogen bonding in small, gas-phase chemical species allows for the binding strengths to be determined and compared at a fundamental level. In this study, anion photoelectron spectra are presented for the gas-phase complexes involving bromide and the four chloromethanes, CH₃Cl, CH₂Cl₂, CHCl₃, and CCl₄. The stabilisation energy and electron binding energy associated with each complex are determined experimentally, and the spectra are rationalised by high-level CCSD(T) calculations to determine the non-covalent interactions binding the complexes. These calculations involve nucleophilic bromide and electrophilic bromine interactions with chloromethanes, where the binding motifs, dissociation energies and vertical detachment energies are compared in terms of hydrogen bonding and halogen bonding.     

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A⁻ and the analogous hydrogen-bonded complexes DH⋅⋅⋅A⁻ (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A⁻ arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A⁻ and the σ* orbital of D–X.     

Hydrogen Bonding between Metal‐Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies

The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal‐ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground‐state molecules, prior to interaction, can provide considerable insight into the interactions.