Classical Hydrogen Bonds Research Articles

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.

The role of halogen bonding in the interaction landscape directing the crystal packing in a homologous series of halogenated coumarin derivatives

The role of halogen bonding as a supramolecular directing interaction was investigated in a series of ten 3-halogenocoumarin derivatives using X-ray diffraction analysis. Halogen bonds might not be as strong as classical hydrogen bonds in molecules such as substituted coumarins but are nevertheless expected to play a certain role in the supramolecular assemblies. Hirshfeld surface analysis, full interaction maps and quantum calculations are used to identify halogen interactions such as X···O, X···π or interhalogen contacts of type I and II, where X is a halogen atom. The halogen interactions in this series appear to be in competition with other supramolecular interactions which leads to a larger structural diversity than expected. This might be due to the steric shielding by the ortho substituents of the halogen atom in the 3-position on the lactone ring of the coumarin motif which are themselves strong hydrogen bond acceptors or donors, but also to the relatively abundant presence of π- π interactions between the aromatic coumarin moieties.

Structural, Hirshfeld surface and molecular docking studies of a new organotin(IV)-phosphoric triamide complex and an amidophosphoric acid ester proposed as possible SARS-CoV-2 and Monkeypox inhibitors

Phosphoramides and their complexes are attractive compounds due to their significant inhibiting functionality in biological medicine. In this paper, a novel organotin(IV)-phosphoramide complex (Sn(CH3)2Cl2{[(3-Cl)C6H4NH]P(O)[NC4H8O]2}2, 1), derived from a reaction between phosphoric triamide ligand with dimethyltin dichloride, and a new amidophosphoric acid ester ([OCH2C(CH3)2CH2O]P(O)[N(CH3)CH2C6H5], 2), prepared from the condensation of a cyclic chlorophosphate reagent with N-methylbenzylamine, are structurally characterized and in silico investigated as potential SARS-CoV-2 and Monkeypox inhibitors by molecular docking simulation. Both compounds crystallize in the monoclinic crystal system with space group P21/c. The asymmetric unit of the complex 1 consists of one-half molecule, where SnIV is located on an inversion center, while the asymmetric part of 2 consists of one whole molecule. In the complex 1, the tin atom adopts a six-coordinate octahedral geometry with trans groups of (Cl)2, (CH3)2 and (PO)2 (PO = phosphoric triamide ligand). The molecular architecture consists of the N–H⋯Cl hydrogen bonds stretching as a 1D linear arrangement along the b axis with intermediate R22(12) ring motifs, whereas in the case of 2, the crystal packing is devoid of any classical hydrogen bond interaction. Furthermore, a graphical analysis by using Hirshfeld surface method identifies the most important intermolecular interactions being of the type H⋯Cl/Cl⋯H (for 1) and H⋯O/O⋯H (for 1 and 2), covering the hydrogen bond interactions N–H⋯Cl and C–H⋯O═P, respectively, which turn out to be favoured. A biological molecular docking simulation on the studied compounds provides evidence to suggest a significant inhibitory potential against SARS-COV-2 (6LU7) and Monkeypox (4QWO) especially for 6LU7 with a binding energy around −6 kcal/mol competing with current effective drugs against this virus (with a binding energy around −5 and −7 kcal/mol). It is worth noting that this report is the first case of an inhibitory potential evaluation of phosphoramide compounds on Monkeypox.

Exploiting Blood Transport Proteins as Carborane Supramolecular Vehicles for Boron Neutron Capture Therapy.

Carboranes are promising agents for applications in boron neutron capture therapy (BNCT), but their hydrophobicity prevents their use in physiological environments. Here, by using reverse docking and molecular dynamics (MD) simulations, we identified blood transport proteins as candidate carriers of carboranes. Hemoglobin showed a higher binding affinity for carboranes than transthyretin and human serum albumin (HSA), which are well-known carborane-binding proteins. Myoglobin, ceruloplasmin, sex hormone-binding protein, lactoferrin, plasma retinol-binding protein, thyroxine-binding globulin, corticosteroid-binding globulin and afamin have a binding affinity comparable to transthyretin/HSA. The carborane@protein complexes are stable in water and characterized by favorable binding energy. The driving force in the carborane binding is represented by the formation of hydrophobic interactions with aliphatic amino acids and BH-π and CH-π interactions with aromatic amino acids. Dihydrogen bonds, classical hydrogen bonds and surfactant-like interactions also assist the binding. These results (i) identify the plasma proteins responsible for binding carborane upon their intravenous administration, and (ii) suggest an innovative formulation for carboranes based on the formation of a carborane@protein complex prior to the administration.

Influence of halogen atoms and hydrogen bonds in the crystal structure of 1,2,4-trisubstituted imidazoles having haloaryl groups

A new family of trisubstituted imidazoles having the privileged 1-haloarylethanol group at position 1 was synthesized by a microwave-assisted reduction reaction of N-aroyilmethyl-imidazoles. Structures of halogenated precursors (4-FPh, 4-ClPh, 4-BrPh) and the reduction product 4-bromophenyl substituted were studied via single X-ray crystallography (SXRC) and computational calculations. The halogen atoms’ effect on the crystal structure was analyzed using electrostatic potentials mapped over Hirshfeld surfaces, allowing us to confirm that fluorine atoms do not form σ-holes; instead, these atoms have negative electrostatic potentials all over the atomic position favoring the formation of short CH‧‧‧F hydrogen bonds that are similar in length to classic hydrogen bonds. However, such σ-hole effects in chlorine and bromine atoms induce the formation of CCl‧‧‧π and C-Br‧‧‧O interactions in the absence of strong hydrogen bonding. This remark is confirmed in 4c, where the hydroxyl group forms strong OH‧‧‧N hydrogen bonds avoiding the bromine atoms to form other interactions apart from the typical CH‧‧‧Br contacts despite their potential behavior to induce other interactions via σ-holes.

The 2′-C-methylribonucleoside of 5-aza-7-deaza-7-iodoguanine: Hydrogen and halogen bonding in nucleoside crystals, synthesis and physical properties

The single-crystal X-ray structure of the 5-aza-7-deaza-7-iodoguanine 2′-C-methylribonucleoside 1 is described. The nucleoside was synthesized by stereoselective nucleobase anion glycosylation, yielding the protected nucleoside (70%), which was then deprotected to 1. By the same route, the non-iodinated 2′-C-methylribonucleoside 2 was obtained. In solution, the CD-spectrum of the iodinated 2′-C-methylribonucleoside 1 displays an almost mirror-like Cotton effect compared to the non-halogenated 2, revealing the strong impact of the iodo substituent to the molecule. Suzuki-Miyaura cross-coupling of 1 with pyrene boronic acid yielded a dye conjugate. The pyrene conjugate shows solvent dependent exciplex fluorescence. From the single-crystal X-ray structure of 1, conformational parameter were determined in solid state. The molecule shows anti conformation, a C3’-endo (N) sugar pucker and an antiperiplanar orientation of the 5′‑hydroxyl group. Apart from classical hydrogen bonds, nucleoside 1 possesses a halogen bond from the iodo substituent to the sugar oxygen O3’. A Hirshfeld surface analysis supports this finding. Nucleoside 1 forms a regular, tightly packed structure with stacking interactions between nucleobases and among sugar residues. A comparison of crystal packing of the iodinated 2′-C-methylribonucleoside 1 with the corresponding ribo- and 2′-deoxyribonucleosides demonstrates that halogen bonding depends on the sugar structure and determines the connectivity in crystal layers.

Supramolecular Structure of Tris(1,10-phenanthroline)zinc(II)-Cation and N,N′,N″-tris(carboxymethyl)-1,3,5-benzenetricarboxamide-Anion: Synthesis, Crystal Structure, Vibrational Spectra, and Theoretical Investigations

The present work reports on the synthesis, structural, spectroscopic, and theoretical studies of a new solid state ionic compound mainly composed of tris(1,10-phenanthroline)zinc(II) cations and N,N′,N″-tris(carboxymethyl)-1,3,5-benzenetricarboxamide anions. Colorless and well-shaped crystals were obtained from an alkaline aqueous methanolic solution, and single-crystal X-ray diffraction revealed a distinct supramolecular network. Powder diffraction techniques and Rietveld analysis confirmed the phase purity of the crystalline probes. The compound crystallizes in the orthorhombic space group Pbca with a cell volume of 9517.0 Å3. The complex cations [Zn(phen)3]2+ are interconnected via π–π-interactions and form a cationic layer network with holes. The organic counterion, as a dianion, forms dimeric units through π–π-interactions and hydrogen bonds, which also form an anionic layer network with honeycomb-like holes through cooperative classical hydrogen bonds of the O∙∙∙H–O and O∙∙∙H–N type with attractive secondary electrostatic interactions. Using the holes, the resulting supramolecular framework can be described as an interpenetrated network of separate anionic and cationic layers linked by further weaker non-covalent interactions such as C–H∙∙∙π and lone-pair∙∙∙π interactions. DFT calculations confirmed the experimentally observed spectroscopic (IR and Raman) findings. For a deeper insight into the structural arrangement in the crystal, the different Hirshfeld surfaces of the cation and anion, the pairwise interaction energies as well as the energy framework were calculated, supporting the dominance of attractive and repulsive electrostatic forces between the ions.

A Comprehensive Ab Initio Study of Halogenated A···U and G···C Base Pair Geometries and Energies.

Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of "Atoms in Molecules" (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.

NMR and DFT studies of monounsaturated and ω-3 polyunsaturated free fatty acids in the liquid state reveal a novel atomistic structural model of DHA

Structures of low-energy conformers of caproleic acid (CA; 10:1 cis-9), oleic acid (OA; 18:1 cis-9), α-linolenic acid (ALA; 18:3 cis-9,12,15 ω-3), eicosapentaenoic acid (EPA; 20:5 cis-5,8,11,14,17 ω-3), and docosahexaenoic acid (DHA; 22:6 cis-4,7,10,13,16,19 ω-3) in the liquid state, based on detailed 1D NOE and density functional theory calculations of 1H NMR chemical shifts are presented. Transient 1D NOE experiments with variable mixing time showed significant through-space proximity of the CH2–COOH protons and the terminal CH3– groups. Variable temperature 1H NMR experiments revealed strong intermolecular centro-symmetric cyclic hydrogen bond interactions of the carboxylic groups of the monounsaturated oleic and caproleic acids (δ(COOH) ∼ 12.0–12.4 ppm), ALA and EPA (δ(COOH) ∼ 11.0 ppm). On the contrary, the carboxylic proton of DHA is strongly shielded with δ(COOH) ∼ 8.5 ppm. DFT calculations were interpreted in terms of aggregates of dimerized fatty acids with parallel and antiparallel interdigitated structures. The antiparallel arrangement was found to be in excellent agreement with experimental 1D NOE NMR data. For the dimeric DHA, a flip-flop process between a classical intermolecular centro-symmetric hydrogen bond through carboxylic groups and a novel intramolecular hydrogen bond between the carboxylic group and the terminal ω-3 double bond is demonstrated.

Subtle hydrogen bond preference and dual Franck-Condon activity - the interesting pairing of 2-naphthol with anisole.

The hydrogen-bonded complexes between 2-naphthol (or β-naphthol) and anisole are explored by detecting their IR absorption in the OH stretching range as well as their UV absorption by means of laser-induced fluorescence and resonance-enhanced two-photon UV ionisation. For the more stable cis and the metastable trans conformations of the OH group in 2-naphthol, hydrogen bonding to the oxygen atom of anisole is consistently detected in different supersonic jet expansions. Alternative hydrogen bonding to the aromatic ring of anisole remains elusive, although the majority of state-of-the-art hybrid DFT functionals with London dispersion correction and - less surprisingly - MP2 wavefunction theory predict it to be slightly more stable at zero-point level, unless three-body dispersion correction is added to the B3LYP-D3(BJ) approach. This changes at the CCSD(T) level, which forecasts an energy advantage of 1-3 kJ mol-1 for the classical hydrogen bond arrangement even after including (DFT) zero-point energy contributions. The UV and IR spectra of the cis complex exhibit clear evidence for intensity redistribution of the primary OH stretch oscillator to combination states with the same low-frequency intermolecular bending mode by Franck-Condon-type vertical excitation mechanisms. This rare case of dual (vibronic and vibrational) Franck-Condon activity of a low-frequency mode invites future studies of homologues where aromatic ring docking of the OH group may be further stabilised, e.g. through anisole ring methylation.

Involvement of the -C(O)-CH=CH- linker chain in different π interactions in crystalline chalcones, (2E)-phenyl-C(=O)-CH=CH-benzene derivatives. Importance of anti-parallel layered motifs in benzyloxy substituted compounds

X-ray crystallographic, Hirshfeld surface and PIXEL study is reported on five benzyloxy substituted compounds, namely (E)-3-[2 methoxy‑5-benzyloxyphenyl]-1-(2‑hydroxy-4-methoxyphenyl)-2-ene-1-one, compound 1, (E)-3-[2,5-bis(benzyloxy)phenyl]-1-(2-hydroxyphenyl)-2-ene-1-one, compound 2, (E)-3-[2,5-bis(benzyloxy)phenyl]-1-(2‑hydroxy-4-methoxyphenyl)-2-ene-1-one, compound 3, (E)-3-[2,5-bis(benzyloxy)phenyl]-1-(2‑hydroxy-3,4-dimethoxyphenyl)-2-ene-1-one, compound 4, and (E)-3-[2,5-bis(benzyloxy)phenyl]-1-(2‑hydroxy-4,5-dimethoxyphenyl)-2-ene-1-one, compound 5. All five compounds exhibit intramolecular O—H(hydroxyl)···O(carbonyl) classical hydrogen bonds, (E)-arrangements about the olefinic bond and near planar chalcone cores, with the interplanar angles between chalcone rings A and B all less than 10°. The phenyl groups in the benzyloxy substituents make much greater interplanar angles with the chalcone core rings, A and B. The linker units, -C(O)-CH=CH-, between the terminal phenyl rings in the chalcone cores, exhibit electronic delocalization as indicated by the bond lengths being between single and double bonds. Motifs having molecules aligned in antiparallel arrangements in layers, with perpendicular distances between the two layers of ca.3.5 Å are amongst the most important motifs. The molecular slippage of the antiparallel molecules in these motifs varies significantly, which results in different functionality, e.g., the terminal phenyl rings, or segments in the linker unit, such as the carbonyl or the olefinic groups, in one layer being suitably placed to interact with functionality in the other. This series of motifs illustrate a great range of slippage distances which is reflected in the variety of interactions present in the motifs, including off-set, face-to-face π···π, π(CO)···π, π(CO)···π(CO) and π(C=C)···π(C=C) interactions. PIXEL calculations reveal the important motifs and their energies, and generally indicate the much greater importance of the dispersive contribution than Coulombic and polarization contributions to the overall energies of these molecules.

Stereochemistry Controls Dihydrogen Bonding Strengths in Chiral Amine Boranes Adducts.

The growing interest in exploiting novel concepts of non-covalent interactions in catalysts and supramolecular chemistry made us revisit a special kind of hydrogen bonding: the dihydrogen bond (DHB), formed between a classical hydrogen bond donor and a hydridic hydrogen as acceptor. Herein, we investigate how the strength of the N-Hδ+ ⋅⋅⋅δ- H-B interaction and hence the DHB-driven self-aggregation of amine-borane adducts is governed by steric effects by comparing the structures and binding enthalpies of various chiral derivatives. For a diastereomeric pair of amine-boranes prepared from a chiral secondary amine, we show that the stereochemistry at the nitrogen has significant influence on the interaction enthalpy. Based on this finding, N-chiral amine boranes can be envisioned to become interesting building blocks in supramolecular chemistry to fine-tune the formation dynamics of assemblies.

Crystal structure of vismodegib, C19H14Cl2N2O3S

The crystal structure of vismodegib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Vismodegib crystallizes in space group P21/a (#14) with a = 16.92070(20), b = 10.20235(4), c = 12.16161(10) Å, β = 108.6802(3)°, V = 1988.873(9) Å3, and Z = 4. The crystal structure consists of corrugated layers of molecules parallel to the bc-plane. There is only one classical hydrogen bond in the structure, between the amide nitrogen atom and the N atom of the pyridine ring. Pairs of these hydrogen bonds link the molecules into dimers, with a graph set R2,2(14) &gt; a &gt; a. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Conformational fidelity and hydrogen bond associability of L-histidine with sulfamate anion studied through XRD, quantum chemical, spectroscopic and molecular docking simulation as a cdk-4 inhibitor against retinoblastoma

L-histidinium sulfamate, (C6H10N3O2)+.SO3NH2−,crystallizes in the orthorhombic space group, P212121, with four molecules per unit cell. The asymmetric part of unit cell comprises a diprotonated monovalent histidinium cation and a sulfamate anion. The amino nitrogen of the cation is deviated from the carboxylate group plane. The backbone conformations are observed to be cis and trans conformations. The side chain conformations are witnessed to be gauche I / gauche II / gauche I rotomers. The conformations of the cation are dominated by the three dimensional intermolecular hydrogen bonding network in the crystal packing. The classical hydrogen bonds are observed in the crystalline landscapes categorically cation-cation, anion-anion and cation-anion interactions leading to chain C(4), C(5) and C(7) motifs and ring R33(10), R33(14), R33(21) and R55(30) motifs. The molecular structure, FT-IR, FT-Raman, Frontier Molecular Orbitals (FMO), Natural Bond Orbital (NBO) analysis Mulliken charge analysis, Electrostatic potential analysis (ESP), Non-Linear Optical (NLO) properties of L-histidinium sulfamate have been evaluated using the (DFT) calculations with B3LYP/6‒311++G (d, p) basis set. TD-DFT in gas phase with the same basis set was used to analyze electronic parameters such as excitation energy, wavelength, band gap, and oscillator strength from the theoretical UV–Visible spectrum. The Fukui function was also used to investigate the molecule's local reactivity. The contribution of distinct interactions within the molecule and the strength of molecular packing in the compound have been evaluated through Hirshfeld surface (HS) analysis .Retinoblastoma is the most well-known pediatric malignant development of the eye. The protein cyclin dependent kinase (Cdk) plays a role in the phosphorylation process; its inhibition triggers the retinoblastoma protein's suppressor function, which stops tumor development. Molecular docking simulation has been performed through PyRx software and the new single crystal L-histidinium sulfamate showed effective binding to the Cdk-4 protein with the binding score of -6.7 Kcal/mol and pharmacokinetic studies showed a good safety profile of L-histidinium sulfamate.

Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations.

Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor–lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O–HC, O–Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor–lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand–lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor–lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.

Three Zn(II) luminescent coordination polymers as sensors for the sensing of levofloxacin and benzaldehyde

Three new ternary Zn(Ⅱ)-based coordination polymers (CPs), [Zn(L)(PA)]n (1), [Zn4(L)2(IP)3(OH)2]n (2), and [Zn(L)(TP)]n (3) (H2PA = phthalic acid, H2IP = isophthalic acid, H2TP = terephthalic acid, L = 2-(2-Pyridin-4-yl-vinyl)-1H-benzimidazole, BZH = benzaldehyde, and LEV = levofloxacin), were hydrothermally synthesized and characterized. 1 exhibits a 1D trapezoidal chain, which is further expanded by π-π stacking interaction into a 2D supramolecular layer. While 2 displays an unusual 3, 5, 6-coordinated simplified underlying cgh7 network, 3 reveals a 2D hcb sheet and extended into a 3D supramolecular framework via classic hydrogen bond interactions. Three CPs and their paper-based sensors are dual-functional luminescent probes for the detecting of levofloxacin and benzaldehyde with high sensitivity and selectivity.

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2- Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2- Methoxylated Homologue

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6- trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

Synthesis and crystallographic study of six quaternary salts of N-halomethylated and non-N-halomethylated ammonium: Importance of C-H‧‧‧X (X=F, I) and I‧‧‧I− halogen interactions in the supramolecular structures

The syntheses of six salts, N-halomethylated (1a,1b,1c) and non-N-halomethylated (2a,2b,2c), are achieved by a four-step sequence involving: (i) Grignard reaction starting from p-(F)C6H4MgBr and Br(CH2)n+1COOEt; (ii) acid-catalyzed dehydration of the resulting tertiary alcohols Br(CH2)n+1C(OH) (C6H4-p-F)2; (iii) bromide substitution by aqueous dimethylamine in the resulting olefins Br(CH2)nCH=C(C6H4-pF)2; and (iv) displacement of an iodide anion by reaction of the resulting amines of (CH3)2N(CH2)nCH=C(C6H4-pF)2 with CH2I2. These compounds were crystallized in a binary mixture of water-isopropanol in slow evaporation. Crystallographic studies show that the crystal growth of these compounds is controlled by C-H‧‧‧X (X=F, I or I−) and I‧‧‧I− interactions with a complete absence of classic hydrogen bonds. The detected H‧‧‧X and I‧‧‧I− distances are very short compared with the values normally observed in literature. The results suggest that, in the lack of other hydrogen bonds, halogen atoms form strong interactions and, in the case of these salts, control completely the supramolecular structure. Moreover, it was found that the length of (CH2)n chains influences the intermolecular interactions, being longer for lengthy chains. Hirshfeld surface (HS) analysis support this observation showing that these halogenated intermolecular interactions conform in high proportion the contacts in the crystal. Additionally, HS allowed the detection of σ-holes were I‧‧‧I− act as Lewis´s acid-base pair, respectively.

Water: new aspect of hydrogen bonding in the solid state.

All water-water contacts in the crystal structures from the Cambridge Structural Database with d OO ≤ 4.0 Å have been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d OH ≤ 3.0 Å and α ≥ 120°) with most being stronger than -3.3 kcal mol-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O-H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (β1, β2 ≥ 160°, 80 ≤ α ≤ 140° and T HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry.

Hydrogen bonds in aqueous choline chloride solutions by DFT calculations and X-ray scattering

Choline chloride (ChCl) is a common hydrogen bond acceptor (HBA) for deep eutectic solvents (DESs), and the hydrogen bonds between ChCl and H2O impact the physicochemical properties of DES-water mixtures. In the present work, the hydrogen bonds in aqueous ChCl solutions were investigated combining with Raman spectroscopy, density functional theory (DFT) calculations, X-ray scattering and empirical potential structure refinement (EPSR). The Ch+ in aqueous ChCl solutions mainly exists as the gauche conformation. The aqueous ChCl solutions were found to be stabilized by both classical hydrogen bonds (O-H⋯Y, Y = Cl, OW) and carbon-hydrogen bonds (C-H⋯Y, Y = OW) between the components. The orientation of the hydrogen bonds is close to linear (∼180°), while the orientation of the carbon-hydrogen bonds is relatively weak (150°∼176°). The existence of carbon-hydrogen bonds elucidates the high coordination of quaternary ammonium group with H2O. Carbon-hydrogen bonds are found in the partial radial distribution functions, the angle distribution functions and the atoms in molecules analysis. Hydrogen bonds and carbon-hydrogen bonds can affect the physicochemical properties of aqueous ChCl solutions and DES-H2O mixtures. This fundamental understanding of the aqueous ChCl solutions will enable future developments in functional design and application of choline-based DESs.