CH Hydrogen Bond Research Articles

Neighboring Effects of Sulfur Oxidation State on Dynamic Covalent Bonds and Assemblies.

The impact of a varied sulfur oxidation state (sulfide, sulfoxide, and sulfone) on imine dynamic covalent chemistry is presented. The role of noncovalent interactions, including chalcogen bonds and CH hydrogen bonds, on aldehyde/imine structures and imine exchange reactions was elucidated through experimental and computational evidence. The change in the sulfur oxidation state and diamine linkage further allowed the regulation of imine macrocycles, providing a platform for controlling molecular assemblies.

Selectivity Rule of Cryptands for Anions: Molecular Rigidity and Bonding Site.

Cryptands utilize inside CH or NH groups as hydrogen bond (H-bond) donors to capture anions such as halides. In this work, the nature and selectivity of confined hydrogen bonds inside cryptands were computationally analyzed with the energy decomposition scheme based on the block-localized wavefunction method (BLW-ED), aiming at an elucidation of governing factors in the binding between cryptands and anions. It was revealed that the intrinsic strengths of inward hydrogen bonds are dominated by the electrostatic attraction, while the anion preferences (selectivity) of inner CH and NH hydrogen bonds are governed by the Pauli exchange repulsion and electrostatic interaction, respectively. Typical conformers of cages are classified into two groups, including the C3(h) -symmetrical conformers, in which all halide anions are located near the centroids of cages, and the "semi-open" conformers, which exhibit shifted bonding sites for different halide anions. Accordingly, the difference in governing factors of selectivity is attributed to either the rigidity of cages or the binding site of anions for these two groups. In details, the C3 conformers of NH cryptands can be enlarged more remarkably than the C3(h) -symmetrical conformers of CH cryptands as the size of anion (ionic radius) increases, resulting in the relaxation of the Pauli repulsion and a dramatic reduction in electrostatic attraction, which eventually rules the selectivity of NH cryptands for halide anions. By contrary, the CH cryptands are more rigid and cannot effectively reduce the Pauli repulsion, which subsequently governs the anion preference. Unlike C3 conformers whose rigidity determines the selectivity, semi-open conformers exhibit different binding sites for different anions. From F- to I- , the bonding site shifts toward the outside end of the pocket inside the semi-open NH cryptand, leading to the significant reduction of the electrostatic interaction that dominates the anion preference. Differently, binding sites are much less affected by the size of anion inside the semi-open CH cryptand, in which the Pauli exchange repulsion remains the key factor for the selectivity of inner hydrogen bonds.

Synthesis, Single Crystal Structural Investigation, Hirshfeld Surface Analysis, Thermoanalysis and Spectroscopic Study of Two New Cu(II) and Co(II) Transition-Metal Complexes

Two new complexes, [Cu(dimpyr)2(H2O)2](NO3)2.2H2O (1) and (Hamdimpy)2[CoCl4].H2O (2), with the monodentate ligand 2-amino-6-methylpyrimidin-4-(1H)-one (dimpyr) and the countercation 4-amino-2,6-dimetylpyrimidium (Hamdimpy), respectively, were prepared and characterized by single crystal X-ray diffraction, elemental analysis and IR spectroscopy. In (1), the Cu(II) cation is tetracoordinated, in a square plan fashion, by two nitrogen atoms from the pyrimidine ring of the organic ligand and two oxygen atoms of two coordinated water molecules. In the atomic arrangement, the CuO2N2 square planes are interconnected via the formation of O-H…O hydrogen bonds involving both coordinated and free water molecules and NO3− nitrate anions to form inorganic layers parallel to the (a, b) plane at z = (2n + 1)/4. In (2), the central atom Co(II) is four-coordinated in a distorted tetrahedral fashion by four Cl− ions. The [CoCl4]2− tetrahedra are arranged parallel to the plane (1¯10) at x = (2n + 1)/2 and the organic cations are grafted between them by establishing with them hydrogen bonds of CH…Cl and NH…Cl types. The vibrational absorption bands were identified by infrared and Raman spectroscopy. Intermolecular interactions were investigated via Hirshfeld surfaces and electronic properties such as HOMO and LUMO energies were derived. The two compounds were characterized by thermal analysis to determine their thermal behavior with respect to temperature.

Darren Johnson.

"The best advice I have ever been given is in two parts: 1) while it is important in life to learn how to connect dots, you have to collect dots first, and 2) don't forget to give yourself time to think …" Find out more about Darren Johnson in his Author Profile.

The road to aryl CH⋯anion binding was paved with good intentions: fundamental studies, host design, and historical perspectives in CH hydrogen bonding

Throughout the design and development of supramolecular receptors for anion binding, many different non-covalent anion-binding motifs have been employed. One motif seen in many host-guest systems is the sometimes weaker, 'non-traditional' aryl CH hydrogen bond. From June Sutor's discovery of the interaction and its subsequent dismissal by the field in the 1960s to today's use of the aryl CH hydrogen bond in synthetic anion receptors, the path our lab took to begin studying this interaction has been influenced by many other researchers in the field. This feature article highlights the history and properties of the CH hydrogen bond, with a particular focus on aryl CH hydrogen bonds in anion recognition. We highlight select recent developments in the field of anion receptors utilizing aryl CH hydrogen bonds, with an emphasis on how this has influenced the evolution of our approach in designing fundamental studies on CH hydrogen bonding and exploiting this interaction in efforts aimed toward preferential anion binding.

Cinchona-Based Primary Amine Catalyzed a Proximal Functionalization of Dienamines: Asymmetric α-Fluorination of α-Branched Enals

Fluorination of dienamines generated by α-branched enals and 6′-hydroxy-9-amino-9-deoxy-epi-quinidine (30 mol %) with NSFI show excellent α-regioselectivity to construct allylic fluorides containing a highly stereocontrolled quaternary fluorinated carbon (E/Z ≥ 20/1 and up to 93% enantiometric excess (ee)). By DFT calculation, the quinuclidine moiety of the catalyst was shown to function as a coordinating group to promote a reaction at the proximal α-position, and the nonclassical CH hydrogen bond plays an important role in the high enantioselectivity.

N-acetylglyoxylic amide bearing a nitrophenyl group as anion receptors: NMR and X-ray investigations on anion binding and selectivity

N-Nitrophenylglyoxylic amides 1 and 2 in presence of tetrabutylammonium cation (TBA) act as receptors for anions HSO4−, Cl−, Br− and NO3− as investigated by NMR studies. The receptors formed 1:1 host-guest complexes in solution. X-ray structure of 1 along with TBA that bind a chloride anion is reported. Molecule 1 showed the highest selectivity for HSO4− anion over others measured. X-ray structure of the bound Cl− revealed a pocket containing the anion making strong (NH⋯Cl) and weak hydrogen bonds (CH⋯Cl) that contribute to the recognition of the chloride anion. NH and CH hydrogen bonds resulted in a relatively strong binding for chloride ions.

Synthesis, crystal and molecular-electronic structure, and kinetic investigation of two new sterically hindered isomeric forms of the dimethyl[methyl(phenylsulfonyl)amino]benzenesulfonyl chloride

Two new structural isomers – 2,4-dimethyl-5-[methyl(phenylsulfonyl)amino]benzenesulfonyl chloride (1) and 2,4-dimethyl-3-[methyl(phenylsulfonyl)amino]benzenesulfonyl chloride (2) were synthesized by interaction of N-(2,4-dimethylphenyl)-N-methyl-benzenesulfonamide or N-(2,6-dimethylphenyl)-N-methylbenzenesulfonamide with chlorosulfonic acid. Both compounds have been structurally characterized by X-ray single crystal diffraction at 100 K. The crystals of 1 are triclinic: space group P1¯, a = 8.1542(2), b = 11.0728(3), c = 11.2680(3) Å, α = 116.557(3), β = 95.155(2), γ = 108.258(2)°, V = 831.97(4) Å3, Z = 2, R = 0.0251 for 2429 reflections; the crystals of 2 are monoclinic: space group P21/c, a = 11.7428(2), b = 11.3518(2), c = 12.5886(2) Å, β = 93.659(2)°, V = 1674.66(5) Å3, Z = 4, R = 0.0269 for 2622 reflections. The structure of both isomers is organized as molecular crystals. These sterically hindered organic molecules are cross-linked into framework by means of hydrogen bonds of CH⋯O type (H⋯O distances are in range 2.27(2)–2.76(2) Å). The ab initio quantum-chemical calculations of an electronic structure of the isomeric molecules of 1 and 2 have been performed using the restricted Hartree-Fock method with a 6-31G* basis set. The calculated values of charge density concentrated on the electronegative atoms of the sterically hindered molecules are in good agreement with parameters of the intramolecular hydrogen bonds. The obtained data of the kinetic investigations of the substitution reactions in aqueous solution well correlate with stereo-chemical characteristics of the both molecules of the dimethyl[methyl(phenylsulfonyl)amino]-benzenesulfonyl chloride.

Self-assembled structures of ferrocene-l-carnosine conjugates

Ferrocene-l-carnosine conjugates, Fc-l-Carnosine-OEt and Fc2-l-Carnosine-OEt, were synthesized and characterized by X-ray crystallographic analyses. The single-crystal X-ray structure determination of Fc-l-Carnosine-OEt was demonstrated to reveal the formation of antiparallel β-sheet-like 12-membered intermolecularly hydrogen-bonded ring between NH (β-alanine) and CO (β-alanine of another molecule). Furthermore, the self-assembled structure through antiparallel β-sheet-like hydrogen bonding network of β-alanyl moieties and homomeric association of the imidazole moieties through the one-dimensional hydrogen-bonded chain was formed in the crystal packing. The self-assembled structure based on antiparallel β-sheet-like hydrogen bonding between NH (histidine) and CO (the ferrocenoyl moiety of another molecule) was also observed in the crystal packing of Fc2-l-Carnosine-OEt. In the case of Fc2-l-Carnosine-OEt, which has the N-ferrocenoyl imidazole moiety, each molecule is connected through the intermolecular hydrogen bonds of CH⋯N pattern between the ferrocene and the imidazole moieties.

Why are sec-alkylperoxyl bimolecular self-reactions orders of magnitude faster than the analogous reactions of tert-alkylperoxyls? The unanticipated role of CH hydrogen bond donation.

High-level ab initio calculations are used to identify the mechanism of secondary (and primary) alkylperoxyl radical termination and explain why their reactions are much faster than their tertiary counterparts. Contrary to existing literature, the decomposition of both tertiary and non-tertiary tetroxides follows the same asymmetric two-step bond cleavage pathway to form a caged intermediate of overall singlet multiplicity comprising triplet oxygen and two alkoxyl radicals. The alpha hydrogen atoms of non-tertiary species facilitate this process by forming unexpected CHO hydrogen bonds to the evolving O2. For non-tertiary peroxyls, subsequent alpha hydrogen atom transfer then yields the experimentally observed non-radical products, ketone, alcohol and O2, whereas for tertiary species, this reaction is precluded and cage escape of the (unpaired) alkoxyl radicals is a likely outcome with important consequences for autoxidation.

Substituent Effects in CH Hydrogen Bond Interactions: Linear Free Energy Relationships and Influence of Anions.

Aryl CH hydrogen bonds (HBs) are now commonly recognized as important factors in a number of fields, including molecular biology, stereoselective catalysis, and anion supramolecular chemistry. As the utility of CH HBs has grown, so to has the need to understand the structure-activity relationship for tuning both their strength and selectivity. Although there has been significant computational effort in this area, an experimental study of the substituent effects on CH HBs has not been previously undertaken. Herein we disclose a systematic study of a single CH HB by using traditional urea donors as directing groups in a supramolecular binding cavity. Experimentally determined association constants are examined by a combination of computational (electrostatic potential) and empirical (σm and σp) values for substituent effects. The dominance of electrostatic parameters, as observed in a computational DFT study, is consistent with current CH HB theory; however, a novel anion dependence of the substituent effects is revealed in solution.

Crystal structure of tetra-butyl-ammonium bromide-1,2-di-iodo-3,4,5,6-tetra-fluoro-benzene-di-chloro-methane (2/2/1).

The crystallization of a 1:1 molar solution of 1,2-di­iodo-3,4,5,6-tetra­fluoro­benzene (o-DITFB) and tetra­butyl­ammonium bromide (n-Bu4NBr) from di­chloro­methane yielded pure white crystals of a halogen-bonded compound, C16H36N+·Br−·C6F4I2·0.5CH2Cl2 or [(n-Bu4NBr)(o-DITFB)]·0.5CH2Cl2. The compound may be described as a quaternary system and may be classified as a salt–cocrystal solvate. The asymmetric unit contains one mol­ecule of solvent, two o-DITFB mol­ecules, two cations (n-Bu4N+) and two crystallographically distinct bromide ions [θI ⋯ Br- ⋯ I = 144.18 (1) and 135.35 (1)°]. The bromide ion is a bidentate halogen-bond acceptor which inter­acts with two covalently bonded iodines (i.e. halogen-bond donors), resulting in a one-dimensional polymeric zigzag chain network approximately along the a axis. The observed short contacts and angles are characteristic of the non-covalent inter­action [d C—I⋯Br = 3.1593 (4)–3.2590 (5) Å; θC—I⋯Br = 174.89 (7) and 178.16 (7)°]. It is noted that iodine acts as both a halogen-bond donor and a weak CH hydrogen-bond acceptor, while the bromide ions act as acceptors for weak CH hydrogen bonds and halogen bonds.

Conformation and interactions of dopamine hydrochloride in solution.

The aqueous solution of dopamine hydrochloride has been investigated using neutron and X-ray total scattering data together with Monte-Carlo based modelling using Empirical Potential Structure Refinement. The conformation of the protonated dopamine molecule is presented and the results compared to the conformations found in crystal structures, dopamine-complexed protein crystal structures and predicted from theoretical calculations and pharmacophoric models. It is found that protonated dopamine adopts a range of conformations in solution, highlighting the low rotational energy barrier between different conformations, with the preferred conformation being trans-perpendicular. The interactions between each of the species present (protonated dopamine molecules, water molecules, and chloride anions) have been determined and are discussed with reference to interactions observed in similar systems both in the liquid and crystalline state, and predicted from theoretical calculations. The expected strong hydrogen bonds between the strong hydrogen bond donors and acceptors are observed, together with evidence of weaker CH hydrogen bonds and π interactions also playing a significant role in determining the arrangement of adjacent molecules.

How many water molecules does it take to ionise HCN/HNC? An NCI exploration.

How many water molecules does it take to ionise HCN/HNC? An NCI exploration.

Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR.

Pulsed field gradient (PFG) NMR has been used to probe self-diffusion of molecular and ionic species in aqueous mixtures of choline chloride (ChCl) based deep eutectic solvents (DESs), in order to elucidate the effect of water on motion and inter-molecular interactions between the different species in the mixtures, namely the Ch(+) cation and hydrogen bond donor (HBD). The results reveal an interesting and complex behaviour of such mixtures at a molecular level. In general, it is observed that the hydroxyl protons ((1)H) of Ch(+) and the hydrogen bond donor have diffusion coefficients significantly different from those measured for their parent molecules when water is added. This indicates a clear and significant change in inter-molecular interactions. In aqueous Ethaline, the hydroxyl species of Ch(+) and HBD show a stronger interaction with water as water is added to the system. In the case of Glyceline, water has little effect on both hydroxyl proton diffusion of Ch(+) and HBD. In Reline, it is likely that water allows the formation of small amounts of ammonium hydroxide. The most surprising observation is from the self-diffusion of water, which is considerably higher that expected from a homogeneous liquid. This leads to the conclusion that Reline and Glyceline form mixtures that are inhomogeneous at a microscopic level despite the hydrophilicity of the salt and HBD. This work shows that PFG NMR is a powerful tool to elucidate both molecular dynamics and inter-molecular interactions in complex liquid mixtures, such as the aqueous DES mixtures.

Neutral CH and cationic CH donor groups as anion receptors.

The design and synthesis of anion selective receptors and chemosensors continues to attract considerable interest within the supramolecular community. In recent years, increasing attention has focused on the use of neutral and cationic CH hydrogen bond donors as anion recognition elements. Over the last five years, motifs that support CHX (X = anion) hydrogen bonds have been actively used in various shape persistent macrocycles, foldamers and "molecular machines". This tutorial review highlights recent developments in host-guest chemistry based on the use of neutral and cationic CH hydrogen bond donors. Also discussed are various structural classifications, including alkyl CH, phenyl CH, triazole-based CH, imidazolium (CH)(+) and triazolium (CH)(+) hydrogen bond donor systems.

On the role of noncovalent interactions in electrocatalysis. Two cases of mediated reductive dehalogenation

Two cases of mediated electron transfer are presented: chloroform reduction catalysed by MoII/I alkoxy scorpionates and debromination of hexabromocyclododecane (HBCD) in the presence of free-base tetraphenylporphyrin (H2TPP). Although H2TPP should act as a typical outer-sphere mediator, it is not active towards analogous dehalogenation of 1,2-dibromocyclododecane. The observed phenomena can be rationalised by considering the catalytically relevant transient adducts formed owing to noncovalent interactions (CH hydrogen bonds and dispersive Chalogen⋯π interactions or directional halogen bonding), which warrants the close and prolonged contact between the catalyst and its substrate, thus increases the probability of electron transfer, and decisively accelerates the reaction. Crucial for this action is thermodynamic stability of the adducts, which can only be explained if dispersive van der Waals interactions are properly accounted for, e.g., as by dispersion-corrected density functional theory (DFT-D) calculations. The structures involving strong and anisotropic interactions, like the surprisingly short CH⋯Oalkoxide H-bonding in the MoI–chloroform adduct, may be reasonably well described by standard DFT calculations and the energy needs only be corrected for dispersion without the need for structure re-optimisation at the DFT-D level. The latter is, however, a method of choice for the prediction of supramolecular structures chiefly controlled by weak non-directional van der Waals forces.

ChemInform Abstract: Shape Persistence Delivers Lock‐and‐Key Chloride Binding in Triazolophanes

AbstractReview: 98 refs.

Selective Recognition of Cyanide Anion via Formation of Multipoint NH and Phenyl CH Hydrogen Bonding with Acyclic Ruthenium Bipyridine Imidazole Receptors in Water

Five imidazole-based anion receptors A-E are designed for cyanide anion recognition via hydrogen bonding interaction in water. Only receptors A [Ru(bpy)(2)(mpipH)](ClO(4))(2) (bpy is bipyridine and mpipH is 2-(4-methylphenyl)-imidazo[4,5-f]-1,10-phenanthroline) and E [Ru(2)(bpy)(4)(mbpibH(2))](ClO(4))(4) (mbpibH(2) is 1,3-bis([1,10]-phenanthroline-[5,6-d]imidazol-2-yl)benzene) selectively recognize CN(-) from OAc(-), F(-), Cl(-), Br(-), I(-), NO(3)(-), HSO(4)(-), ClO(4)(-), H(2)PO(4)(-), HCO(3)(-), N(3)(-), and SCN(-) anions in water (without organic solvent) at physiological conditions via formation of multiple hydrogen bonding interaction with binding constants of K(A(H2O)) = 345 ± 21 and K(E(H2O)) = 878 ± 41, respectively. The detection limits of A and E toward CN(-) in water are 100 and 5 μM, respectively. Receptor E has an appropriate pK(a2)* value (8.75) of N-H proton and a C-shape cavity structure with three-point hydrogen bonding, consisting of two NH and one cooperative phenyl CH hydrogen bonds. Appropriate acidity of N-H proton and multipoint hydrogen bonding are both important in enhancing the selectivity and sensitivity toward CN(-) in water. The phenyl CH···CN(-) hydrogen bonding interaction is observed by the HMBC NMR technique for the first time, which provides an efficient approach to directly probe the binding site of the receptor toward CN(-). Moreover, CN(-) induced emission lifetime change of the receptor has been exploited in water for the first time. The energy-optimized structure of E-CN adduct is also proposed on the basis of theoretical calculations.

Structure and phosphorescence of meta-bromobenzophenone crystal

Solid state properties of meta-bromobenzophenone crystals were studied, including X-ray diffraction, integrated phosphorescence spectrometry, and ab initio calculations. The structure of meta-bromobenzophenone crystals has been determined by powder X-ray diffraction to be orthorhombic (space group Pbca) with a=11.70461(15)Å, b=7.70025(9)Å, c=24.0055(2)Å, Z=8. This structure includes a supramolecular network formed by weak hydrogen bonds of CH⋯O and CH⋯π short contacts. A tight π–π short contact between virtually parallel substituted and unsubstituted phenyl rings of neighbor molecules is another distinguishing feature of the crystal structure, which might be the cause of the unusual very broad lonely band in the room-temperature phosphorescence spectrum. The low-temperature (1.6K) phosphorescence spectra are of monomeric character, revealing sharp lines superimposed on broad 0→ν bands, which is a signature of emission from some traps.