Hydrogen-bonded Dimers Research Articles

Metastable Charged Dimers in Organometallic Species: A Look into Hydrogen Bonding between Metallocene Derivatives.

Multiply charged complexes bound by noncovalent interactions have been previously described in the literature, although they were mostly focused on organic and main group inorganic systems. In this work, we show that similar complexes can also be found for organometallic systems containing transition metals and deepen in the reasons behind the existence of these species. We have studied the structures, binding energies, and dissociation profiles in the gas phase of a series of charged hydrogen-bonded dimers of metallocene (Ru, Co, Rh, and Mn) derivatives isoelectronic with the ferrocene dimer. Our results indicate that the carboxylic acid-containing dimers are more strongly bonded and present larger barriers to dissociation than the amide ones and that the cationic complexes tend to be more stable than the anionic ones. Additionally, we describe for the first time the symmetric proton transfer that can occur while in the metastable phase. Finally, we use a density-based energy decomposition analysis to shine light on the nature of the interaction between the dimers.

From liquid to crystal via mechanochemical grinding: unique host-guest (HOF) cocrystal.

Mechanochemical synthesis via grinding of trimesic acid (TA, C9H6O6) and 4-chlorophenyl diphenyl phosphate (4CDP, C18H14ClO4P) (liquid at room temperature) in a 1:1 ratio resulted in the formation of an inclusion type of cocrystal. The crystallization of this phase via slow evaporation at low temperature (276-277 K) from methanol resulted in a rare `stairstep morphology' during the process of crystal growth. This morphology was not observed after crystallization of the compound from other solvents like toluene, dichloromethane, acetone, hexane and isooctane, and hence this was characteristically observed in methanol only. The characterization from single-crystal X-ray diffraction revealed the formation of a cocrystal with five molecules of TA and two molecules of 4CDP in the asymmetric unit. The trimesic acid molecules form hydrogen-bonded dimers resulting in hexagonal rings, and these rings are stacked through π-π intermolecular interactions to make a hexagonal honeycomb-like structure. The phosphate molecules, 4CDP, were found to be trapped as guests in these hexagonal channels. The similarity in the packing of trimesic acid is compared in the cocrystal and the free acid quantitatively via Xpac analysis, which establishes the relationship of a `2D supramolecular construct' between them. This signifies a unique type of arrangement in which the voids created by the trimesic acid moiety do not undergo distortion by the inclusion of the guest molecules. The quantitative analysis of the intermolecular interactions using Hirshfeld surfaces and fingerprint plots deciphers the role of both strong O-H...O hydrogen bonds and weak intermolecular interactions in the crystal packing.

Hydrogen bonded dimer of an alcohol with the derived carboxylic acid triggering their sorption by nanoporous-crystalline PPO films.

Films exhibiting nanoporous-crystalline (NC) phases of poly(2,6-dimethyl-1,4-phenylene) oxide (PPO), which are highly effective to absorb apolar organic guest molecules, are also able to absorb polar molecules (like alcohols and carboxylic acids) but only from concentrated organic solutions. NC PPO films, which do not absorb alcohols and carboxylic acids from diluted aqueous solutions, exhibits a huge uptake (even above 30wt%) of benzyl alcohol (BAL) and benzoic acid (BA), if BA is obtained by spontaneous room temperature oxidation of BAL in aqueous solution. This phenomenon is rationalized by an easy uptake, mainly by the PPO intrahelical crystalline empty channels, of a BAL/BA 1/1 hydrogen-bonded dimer. This huge uptake of BAL/BA dimer by NC PPO films, which is also fast for films exhibiting the orientation of the crystalline helices perpendicular to the film plane (c^ orientation), can be exploited for purification of water from BAL, when present in traces. High and fast sorption of a hydrogen bonded dimer and negligible sorption of the two separate compounds is possibly unprecedented for absorbent materials.

Robust Single-Supermolecule Switches Operating in Response to Two Different Noncovalent Interactions.

Supramolecular electronics provide an opportunity to introduce molecular assemblies into electronic devices through a combination of noncovalent interactions such as [π···π] and hydrogen-bonding interactions. The fidelity and dynamics of noncovalent interactions hold considerable promise when it comes to building devices with controllable and reproducible switching functions. Here, we demonstrate a strategy for building electronically robust switches by harnessing two different noncovalent interactions between a couple of pyridine derivatives. The single-supermolecule switch is turned ON when compressing the junction enabling [π···π] interactions to dominate the transport, while the switch is turned OFF by stretching the junction to form hydrogen-bonded dimers, leading to a dramatic decrease in conductance. The robustness and reproducibility of these single-supermolecule switches were achieved by modulating the junction with Ångström precision at frequencies of up to 190 Hz while obtaining high ON/OFF ratios of ∼600. The research presented herein opens up an avenue for designing robust bistable mechanoresponsive devices which will find applications in the building of integrated circuits for microelectromechanical systems.

The inter-molecular hydrogen bonds modulated reversible ACQ-AIE conversion and dual-states sensing applications of shikimic acid derived hydrogen bond dimers

Smart molecules with adjustable and reversible ACQ-AIE transformation which could be used as luminescence sensors both in solvent and solid-state are rarely reported. Planar luminophores with strong inter-molecular hydrogen bonds and a rotor might exhibit reversible ACQ-AIE conversion by modulating the inter-molecular hydrogen bonds. As a proof of concept, herein, two smart hydrogen bond dimers (Qufu-1 and Qufu-2) with reversible ACQ-AIE transformation were derived from the renewable bio-feedstock shikimic acid. Qufu-1 and Qufu-2 possessing a novel 4-oxo-3,4-dihydrobenzofuro[2,3-d]pyrimidine key structure and both exhibit crystallization induced ACQ (CIACQ) and precipitation induced AIE (PIAIE) in solid-state. Single crystal analysis indicates that the large planar configuration formed in the dimers of Qufu-1 and Qufu-2 due to the inter-molecular hydrogen bonds, which would result in the strong π-π stacking and ACQ in crystal. The AIE state could be facile realized by breaking the inter-molecular hydrogen bonds and changing the aggregation state from crystal to precipitation. Moreover, ACQ to AIE transformation could also accomplish for Qufu-1 and Qufu-2 in solution by modulating the inter-molecular hydrogen bonds with acid. In addition, three-level structures latent fingerprint identification in real environment and fluorescent sensing of hazardous biogenic amines in food samples were performed with Qufu-1.

Crystal structure of a (carb-oxy-meth-yl)tri-ethyl-aza-nium bromide-2-(tri-ethyl-aza-n-ium-yl)acetate (1/1) hydrogen-bonded dimer.

The title compound, C8H18NO2 +·Br-·C8H17NO2, crystallizes as the bromide salt of a 50:50 mixture of (tri-ethyl-azaniumyl)-carb-oxy-lic acid and the zwitterionic (tri-ethyl-azaniumyl)-carboxyl-ate. The two organic entities are linked by a half-occupied bridging carb-oxy-lic acid hydrogen atom that is hydrogen-bonded to the carboxyl-ate group of the second mol-ecule. The tetra-lkyl-ammonium group adopts a nearly perfect tetra-hedral shape around the nitro-gen atom with bond lengths that agree with known values. The carb-oxy-lic acid/carboxyl-ate group is oriented anti to one of the ethyl groups on the ammonium group, and the carbonyl oxygen atom is engaged in intra-molecular C-H⋯O hydrogen bonds.

Tautomeric mixture coordination enables efficient lead-free perovskite LEDs.

Lead halide perovskite light-emitting diodes (PeLEDs) have demonstrated remarkable optoelectronic performance1-3. However, there arepotential toxicity issues with lead4,5 and removing lead from the best-performing PeLEDs-without compromising their high external quantum efficiencies-remains a challenge. Here we report a tautomeric-mixture-coordination-induced electron localization strategy to stabilize thelead-free tinperovskiteTEA2SnI4 (TEAI is2-thiopheneethylammonium iodide) by incorporating cyanuric acid. We demonstrate that a crucial function of the coordination is to amplify theelectronic effects, even for those Sn atoms that aren't strongly bonded with cyanuric acidowing to the formation of hydrogen-bonded tautomeric dimer and trimer superstructures on the perovskite surface. This electron localization weakens adverse effects from Anderson localization and improves ordering in the crystal structure of TEA2SnI4. These factors result in a two-orders-of-magnitude reduction in thenon-radiative recombination capture coefficient and an approximately twofold enhancement inthe exciton binding energy. Our lead-free PeLED has an external quantum efficiency of up to 20.29%, representing a performance comparable to that of state-of-the-art lead-containing PeLEDs6-12. We anticipate that these findings will provide insights into the stabilization of Sn(II) perovskites and further the development of lead-free perovskite applications.

Mn(III)–Salen Complexes with Metallophilic Interactions

We synthesized a series of five novel Mn–salen-based compounds (1a–1c, 2a, 2b) through the reaction between precursor chloride complexes and potassium silver/gold dicyanide. The prepared compounds were structurally and magnetically characterized. Our findings revealed that all the Mn(III) central atoms exhibited an axially elongated coordination polyhedron, leading to the observation of axial magnetic anisotropy as indicated by the negative axial magnetic parameter D, which was determined through fitting the experimental magnetic data and supported by theoretical CASSCF/NEVPT2 calculations. Furthermore, we observed magnetic-exchange interactions only in compounds with a special supramolecular topology involving O–H···O hydrogen-bonded dimers. In these cases, the weak magnetic exchange (J/cm−1 = −0.58(2) in 1b and −0.73(7) in 2b) was mediated by the O–H···O hydrogen bonds. These findings were further supported by BS–DFT calculations, which predicted weak antiferromagnetic exchanges in these complexes and ruled out exchange interactions mediated by diamagnetic cyanido metallo–complex bridges. Additionally, we investigated the observed Ag···π (1b) and Au···Au (2b) interactions using QT–AIM calculations, confirming their non-covalent nature. We compared these results with previously reported Mn–salen-based compounds with metallophilic interactions arising from the presence of the [Ag/Au(CN)2]− bridging units.

Potential energy surfaces of antiparallel water-water interactions

Antiparallel water-water interaction is a significant interaction between two water molecules and plays an important role in liquid water. The potential energy surface of antiparallel water-water interaction was calculated at accurate CCSD(T)/CBS level of theory by systematic changes of the torsion angle THOHO, parallel displacement r, normal distance R, and water-water dihedral angle Pa/Pb. The results show that the most stable geometry of antiparallel water-water interaction has an interaction energy of −4.22 kcal/mol and THOHO = 140°. A significant portion of the antiparallel interactions have interaction energies more negative than −2.0 kcal/mol. The angle α of the most stable geometries of antiparallel water-water interactions is in the range 110°–120°. Comparison with classical hydrogen bonds in water dimers shows that hydrogen bonds with values of angle α < 140° have interaction energies up to −3.2 kcal/mol, while a significant number of antiparallel water-water interactions is stronger than it. The antiparallel geometry is a low barrier transition state between two hydrogen bonded minima with changed acceptor–donor roles of two water molecules.

Enhanced SO2 adsorption performance on nitrogen-doped biochar: Insights from generalized two-dimensional correlation infrared spectroscopy

Nitrogen-doped biochar is considered as a renewable, cost-effective, and promising SO2 adsorbent. However, it is difficult to improve the physicochemical properties of biochar synergistically and clarify the adsorption mechanism. Therefore, in this study, a one-step high-temperature CO2-NH3 modification method was proposed for biochar to improve its SO2 adsorption, and the in situ Diffuse Reflectance Infrared Fourier Transform Spectroscopy (in situ DRIFTS) was used to reveal the interface reaction mechanism between SO2 and nitrogen-doped biochar. The results showed that when the modification temperature exceeded 700 °C, CO2 and NH3 exhibited significant thermal activation and nitrogen doping on biochar simultaneously. Under a modification temperature of 800 °C (BCAN-800), the microporous surface area and nitrogen content of modified biochar reached the highest value of 563.83 m2/g and 6.63 wt%. The SO2 adsorption capacities of BCAN-800 were up to 201.89 mg/g and 145.68 mg/g at 30 °C and 120 °C, respectively. The results of in situ DRIFTS showed that dimeric and bridge hydrogen bonds were the main SO2 adsorption sites on nitrogen-doped biochar at 30 °C. With the increase of adsorption temperature, nitrogen-containing groups as the main adsorption site could combine with SO2 to form sulfamide (60 °C), which eventually existed in a more stable form of SO42−/R-O-SO2-OR′ (120 °C).

4-Methyl-2-(2-methyl-anilino)benzoic acid.

The title compound, C15H15NO2, was obtained by the reaction of 2-chloro-4-methyl-benzoic acid and o-toluidine using 2-eth-oxy-ethanol as solvent. Crystals of the title compounds were obtained from crystallization in acetone. The mol-ecule in the crystal is twisted with a dihedral angle between the aromatic rings of 50.86 (5)°. In the crystal structure, the mol-ecules associate to form acid-acid hydrogen-bonded dimers linked by pairwise O-H⋯O hydrogen bonds.

"Magic Numbers" in Self-Faceting of Alcohol-Doped Emulsion Droplets.

Oil-in-water emulsion droplets spontaneously adopt, below some temperature Td , counterintuitive faceted and complex non-spherical shapes while remaining liquid. This transition is driven by a crystalline monolayer formed at the droplets' surface. Here, weshow that ppm-level doping of the droplet's bulk by long-chain alcohols allows tuning Td by >50 °C, implying formation of drastically different interfacial structures. Furthermore, "magic" alcohol chain lengths maximize Td . This weshow to arise from self-assembly of mixed alcohol:alkane interfacial structures of stacked alkane layers, co-crystallized with hydrogen-bonded alcohol dimers. These structures are accounted for theoretically and resolved by direct cryogenic transmission electron microscopy (cryoTEM), confirming the proposed structures. The discovered tunability of key properties of commonly-used emulsions by minute concentrations of specific bulk additives should benefit these emulsions' technologicalapplicability.

Synthesis and crystal structure studies of 5-(tri-fluoro-meth-yl)-1,3,4-thia-diazol-2(3H)-one at 180 K.

The synthesis and crystal structure of C3HF3N2OS, systematic name 5-(tri-fluoro-meth-yl)-1,3,4-thia-diazol-2(3H)-one (5-TMD-2-one), a compound containing the pharmacologically important heterocycle 1,3,4-thia-diazole, is presented. The asymmetric unit comprises six independent mol-ecules (Z' = 6), all of which are planar. The r.m.s. deviations from each mean plane range from 0.0063 to 0.0381 Å, not including the CF3 fluorine atoms. Within the crystal, two of the mol-ecules form hydrogen-bonded dimers that in turn combine with inversion-related copies to form tetra-meric constructs. Similar tetra-mers, but lacking inversion symmetry, are formed by the remaining four mol-ecules. The tetra-mers are linked into tape-like motifs by S⋯O and O⋯O close contacts. The environments of each symmetry-independent mol-ecule were compared via a Hirshfeld surface analysis. The most abundant atom-atom contacts are between fluorine atoms, while the strongest result from N-H⋯O hydrogen bonds.

Structural Elucidation of 2-(6-(Diethylamino)benzofuran-2-yl)-3-hydroxy-4H-chromen-4-one and Labelling of Mycobacterium aurum Cells

Trehalose conjugates of 3-hydroxychromone (3HC) dyes have previously been utilized as fluorescence labels to detect metabolically active mycobacteria with a view to facilitating point-of-care detection of mycobacterial pathogens, especially Mycobacterium tuberculosis. We subjected the 3HC dye 2-(6-(diethylamino)benzofuran-2-yl)-3-hydroxy-4H-chromen-4-one (3HC-2) to a combined X-ray crystallography and density functional theory (DFT) study, and conducted preliminary fluorescence labelling experiments with the model organism Mycobacterium aurum. In the crystal, 3HC-2 exhibits an s-cis conformation of the chromone and the benzofuran moieties about the central C–C bond. According to DFT calculations, the s-cis conformer is about 1.8 kcal mol−1 lower in energy than the s-trans conformer. The solid-state supramolecular structure features hydrogen-bonded dimers and π…π stacking. Fluorescence microscopy revealed fluorescence of M. aurum cells treated with the dye trehalose conjugate 3HC-2-Tre in the GFP channel. It was concluded that s-cis is the preferred conformation of 3HC-2 and that the generally considered non-pathogenic M. aurum can be labelled with the fluorescence probe 3HC-2-Tre for convenient in vitro drug screening of new antimycobacterial agents.

Crystal packing and mechanofluorochrmism of distyrylanthracene derivatives modulated by hydrogen bonds

Two distyrylanthracene derivatives with ester and carboxyl moieties (AnDMB and AnDBA) were synthesized to investigate the influence of terminal group on their photophysical, crystal stacking and mechanofluorochromic (MFC) properties. Spectral and theory calculation results indicate that two compounds have similar absorption because their similar energy levels although they have different terminal groups. Both compounds exhibited crystallization-induced emission enhancement (CIEE). AnDMB crystals are rod-like and emitted strong blue-green fluorescence because of weak π-stacking. The blocky AnDBA crystals with DMAC (N, N-dimethylacetamide) molecules have a red-shifted emission. Moreover, instead of forming a hydrogen bond dimer between the carboxyl groups, a strong hydrogen bond is formed between the carbonyl group of DMAC and the carboxyl group. Crystal structure indicates that enhanced π-stacking should be responsible for its longer wavelength emission. Moreover, the crystals of two compounds could change their emission colors under force stimuli, but AnDMB exhibited higher color contrast than that of AnDBA. A shift of 40 nm might be observed when the AnDMB crystals were ground, while an emission spectral shift of 18 nm emerged after AnDBA crystals were ground. These results indicated that hydrogen bond did not only regulate molecular stacking and fluorescence properties in crystals, but also adjusted force-stimuli responsiveness.

Diethyl 2-Cyano-3-oxosuccinate

The titular compound was characterized for the first time using a full range of spectroscopic methods, including UV, IR, 1H, and 13C NMR spectra. In solution, all methods showed a keto–enol equilibrium strongly shifted to the enol form. The X-ray structures determined for all simple 2-oxosuccinates showed only the enol form packed as hydrogen-bonded dimer stacks.

A Peptide Potential Based on a Bond Dipole Representation of Electrostatics

A potential based on a bond dipole representation of electrostatics is reported for peptides. Different from those popular force fields using atom-centered point-charge or point-multipole to express the electrostatics, our peptide potential uses the chemical bond dipole–dipole interactions to express the electrostatic interactions. The parameters for permanent and induced bond dipoles are derived from fitting to the MP2 three-body interaction energy curves. The parameters for van der Waals are taken from AMBER99sb and further refined from fitting to the MP2 stacking interaction energy curve. The parameters for bonded terms are taken from AMBER99sb without any modification. The scale factors for intramolecular dipole–dipole interactions are determined from reproducing the highly qualified ab initio conformational energies of dipeptides and tetrapeptides. The resulting potential is validated by use to evaluate the conformational energies of polypeptides containing up to 15 amino acid residues. The calculation results show that our peptide potential produces the conformational energies much closer to the famous density functional theory M06-2X/cc-pVTZ results than the famous AMBER99sb and AMOEBAbio18 force fields. Our potential also produces accurate intermolecular interaction energies for hydrogen-bonded and stacked dimers. We anticipate the peptide potential proposed here could be helpful in computer simulations of polypeptides and proteins.

On the structures of free-base lepidine and some mineral acid salts

The crystal and molecular structures of free-base lepidine (4-methylquinoline, 1) and the mineral acid salts lepidinium chloride (2), nitrate (3) and dihydrogen phosphate (4) are reported. Compound 1 was studied by differential scanning calorimetry and in situ capillary cryocrystallography. In the crystal structures, the molecules of free-base lepidine in 1 and the lepidinium cations in 2–4 are face-to-face π⋅⋅⋅π-stacked. The quinoline nitrogen atom is not involved in directional intermolecular interactions such as weak hydrogen bonds in 1. In the salts 2–4, proton transfer to the quinoline nitrogen atom and N−H⋅⋅⋅Cl (in 2) and N−H⋅⋅⋅O (in 3 and 4) hydrogen bonding is observed. Hirshfeld surface analysis reveals that lepidinium salts 2 and 3 form hydrogen-bonded dimers in the crystal and confirms that the packing of 4 is dominated by hydrogen-bonded dihydrogen phosphate anion chains.

(η5-Carb-oxy-cyclo-penta-dien-yl)(η7-cyclo-hepta-trien-yl)manganese(I) hexa-fluorido-phosphate.

The title compound, [Mn(C7H7)(C6H5O2)]PF6 or [(Cht)Mn(Cp'CO2H)]PF6, with Cht = cyclo-hepta-trienyl and Cp' = C5H4, is an air-stable, purple, heteroleptic, cationic sandwich complex with manganese in oxidation state +I and π-coordinating cyclo-hepta-trienyl and cyclo-penta-dienyl ligands. The latter ligand carries the carb-oxy-lic acid functionality. This 'tromancenium-8-carb-oxy-lic acid' with hexa-fluorido-phosphate as counter-ion represents a rare case of a cationic carb-oxy-lic acid. Structurally, this organometallic carb-oxy-lic acid displays the common motif of planar Osp 2⋯H-Osp 3/Osp 3-H⋯Osp 2 hydrogen-bonded carb-oxy-lic acid dimers with anti-oriented metallocenyl moieties, the cationic charge of which is balanced by octa-hedrally shaped hexa-fluorido-phosphate anions. Positional disorder is observed in the cyclo-hepta-trienyl ring and the PF6 - anion.

Experimental FTIR-MI and Theoretical Studies of Isocyanic Acid Aggregates.

Homoaggregates of isocyanic acid (HNCO) were studied using FTIR spectroscopy combined with a low-temperature matrix isolation technique and quantum chemical calculations. Computationally, the structures of the HNCO dimers and trimers were optimized at the MP2, B3LYPD3 and B2PLYPD3 levels of theory employing the 6-311++G(3df,3pd) basis set. Topological analysis of the electron density (AIM) was used to identify the type of non-covalent interactions in the studied aggregates. Five stable minima were located on the potential energy surface for (HNCO)2, and nine were located on the potential energy surface for (HNCO)3. The most stable dimer (D1) involves a weak, almost linear N-H⋯N hydrogen bond. Other structures are bound by a N-H⋯O hydrogen bond or by O⋯C or N⋯N van der Waals interactions. Similar types of interactions as in (HNCO)2 were found in the case of HNCO trimers. Among nine stable (HNCO)3 structures, five represent cyclic forms. The most stable T1 trimer structure is characterized by a six-membered ring formed by three N-H⋯N hydrogen bonds and representing high symmetry (C3h). The analysis of the HNCO/Ar spectra after deposition indicates that the N-H⋯O hydrogen-bonded dimers are especially prevalent. Upon annealing, HNCO trimers were observed as well. Identification of the experimentally observed species relied on previous experimental data on HNCO complexes as well as computed data on HNCO homoaggregates' vibrational spectra.