2‐(2‐Oxazolin‐2‐yl)benzene‐1,4‐diol: X‐ray and density functional theory studies

In the crystal structure of the title compound, C₉H₉NO₃, there are strong intra­molecular O—H⋯N and inter­molecular O—H⋯O hydrogen bonds which, together with weak inter­molecular C—H⋯O hydrogen bonds, lead to the formation of infinite chains of mol­ecules. The calculated inter­molecular hydrogen‐bond energies are −11.3 and −2.7 kJ mol⁻¹, respectively, showing the dominant role of the O—H⋯O hydrogen bonding. A natural bond orbital analysis revealed the electron contribution of the lone pairs of the oxazoline N and O atoms, and of the two hydr­oxy O atoms, to the order of the relevant bonds.     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.     

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate, 2C₂H₇N₄O⁺·FO₃P²⁻·2H₂O, are presented. Polymorph (I), crystallizing in the space group Pnma, is slightly less densely packed than polymorph (II), which crystallizes in Pbca. In (I), the fluorophosphonate anion is situated on a crystallographic mirror plane and the O atom of the water molecule is disordered over two positions, in contrast with its H atoms. The hydrogen‐bond patterns in both polymorphs share similar features. There are O—H...O and N—H...O hydrogen bonds in both structures. The water molecules donate their H atoms to the O atoms of the fluorophosphonates exclusively. The water molecules and the fluorophosphonates participate in the formation of R⁴₄(10) graph‐set motifs. These motifs extend along the a axis in each structure. The water molecules are also acceptors of either one [in (I) and (II)] or two [in (II)] N—H...O hydrogen bonds. The water molecules are significant building elements in the formation of a three‐dimensional hydrogen‐bond network in both structures. Despite these similarities, there are substantial differences between the hydrogen‐bond networks of (I) and (II). The N—H...O and O—H...O hydrogen bonds in (I) are stronger and weaker, respectively, than those in (II). Moreover, in (I), the shortest N—H...O hydrogen bonds are shorter than the shortest O—H...O hydrogen bonds, which is an unusual feature. The properties of the hydrogen‐bond network in (II) can be related to an unusually long P—O bond length for an unhydrogenated fluorophosphonate anion that is present in this structure. In both structures, the N—H...F interactions are far weaker than the N—H...O hydrogen bonds. It follows from the structure analysis that (II) seems to be thermodynamically more stable than (I).     

Cover Feature: An Exploration of the Hydrogen Bond Donor Ability of Ammonia (ChemPhysChem 20/2023)

Ammonia is an important molecule due to its wide use in the fertiliser industry. It is also used in aminolysis reactions. Theoretical studies of the reaction mechanism predict that in reactive complexes and transition states, ammonia acts as a hydrogen bond donor forming N−H⋅⋅⋅O hydrogen bond. Experimental reports of N−H⋅⋅⋅O hydrogen bond, where ammonia acts as a hydrogen bond donor are scarce. Herein, the hydrogen bond donor ability of ammonia is investigated with three chalcogen atoms i. e. O, S, and Se using matrix isolation infrared spectroscopy and electronic structure calculations. In addition, the chalcogen bond acceptor ability of ammonia has also been investigated. The hydrogen bond acceptor molecules used here are O(CH₃)₂, S(CH₃)₂, and Se(CH₃)₂. The formation of the 1 : 1 complex has been monitored in the N−H symmetric and anti-symmetric stretching modes of ammonia. The nature of the complex has been delineated using Atoms in Molecules analysis, Natural Bond Orbital analysis, and Energy Decomposition Analysis. This work presents the first comparison of the hydrogen bond donor ability of ammonia with O, S, and Se.     

(6‐Oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylato‐κ2O5,O6)bis[2‐(2‐pyridyl)‐1H‐benzimidazole‐κ2N2,N3]manganese(II) monohydrate

In the title compound, [Mn(C₅H₂N₂O₄)(C₁₂H₉N₃)₂]·H₂O, the Mn^II centre is surrounded by three bidentate chelating ligands, namely, one 6‐oxido‐2‐oxo‐1,2‐dihydropyrimidine‐5‐carboxylate (or uracil‐5‐carboxylate, Huca²⁻) ligand [Mn—O = 2.136 (2) and 2.156 (3) Å] and two 2‐(2‐pyridyl)‐1H‐benzimidazole (Hpybim) ligands [Mn—N = 2.213 (3)–2.331 (3) Å], and it displays a severely distorted octahedral geometry, with cis angles ranging from 73.05 (10) to 105.77 (10)°. Intermolecular N—H...O hydrogen bonds both between the Hpybim and the Huca²⁻ ligands and between the Huca²⁻ ligands link the molecules into infinite chains. The lattice water molecule acts as a hydrogen‐bond donor to form double O...H—O—H...O hydrogen bonds with the Huca²⁻ O atoms, crosslinking the chains to afford an infinite two‐dimensional sheet; a third hydrogen bond (N—H...O) formed by the water molecule as a hydrogen‐bond acceptor and a Hpybim N atom further links these sheets to yield a three‐dimensional supramolecular framework. Possible partial π–π stacking interactions involving the Hpybim rings are also observed in the crystal structure.     

2‐{[(3‐Fluorophenyl)amino]methylidene}‐3‐oxobutanenitrile and 5‐{[(3‐fluorophenyl)amino]methylidene}‐2,2‐dimethyl‐1,3‐dioxane‐4,6‐dione: X‐ray and DFT studies

In the crystal structures of the title compounds, C₁₁H₉FN₂O, (I), and C₁₃H₁₂FNO₄, (II), the molecules are joined pairwise via different hydrogen bonds and the constituent pairs are crosslinked by weak C—H...O hydrogen bonds. The basic structural motif in (I), which is partially disordered, comprises pairs of molecules arranged in an antiparallel fashion which enables C—H...N[triple‐bond]C interactions. The pairs of molecules are crosslinked by two weak C—H...O hydrogen bonds. The constituent pair in (II) is formed by intramolecular bifurcated C—H...O/O′ and combined inter‐ and intramolecular N—H...O hydrogen bonds. In both structures, F atoms form weak C—F...H—C interactions with the H atoms of the two neighbouring methyl groups, the H...F separations being 2.59/2.80 and 2.63/2.71 Å in (I) and (II), respectively. The bond orders in the molecules, estimated using the natural bond orbitals (NBO) formalism, correlate with the changes in bond lengths. Deviations from the ideal molecular geometry are explained by the concept of non‐equivalent hybrid orbitals. The existence of possible conformers of (I) and (II) is analysed by molecular calculations at the B3LYP/6–31+G** level of theory.     

Molecular Structure of 1-Germatrahol and its Complex With Chloroform

The crystal structures of anhydrous 1-germatranol and its complex with HCCl₃ are centrosymmetrical dimers because of their intermolecular hydrogen bonds. In the germatranol crystal, the axial and equatorial oxygen atoms of its two molecules are hydrogen bonded into an eight-membered coordination cycle. In the complex with HCCl₃, the two molecules of germatranol are likewise linked in dimers, and both axial oxygen atoms are H bonded with HCCl₃. In the investigated structures, the axial Ge—O bond is shorter than the equatorial ones. Depending on the number and strength of the hydrogen bonds, the interatomic Ge—O and Ge ← N distances change markedly. The quantitative estimates of the H bond energy are obtained from quantum chemical calculations of the model systems containing 1-germatranol and HCCl₃ molecules.     

Complexes H2CO:PXH2 and HCO2H : PXH2 for X=NC,F, Cl,CN, OH,CCH, CH3, and H: Pnicogen Bonds and Hydrogen Bonds

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to investigate H₂CO : PXH₂ pnicogen-bonded complexes and HCO₂H : PXH₂ complexes that are stabilized by pnicogen bonds and hydrogen bonds, with X=NC, F, Cl, CN, OH, CCH, CH₃, and H. The binding energies of these complexes exhibit a second-order dependence on the O−P distance. DFT-SAPT binding energies correlate linearly with MP2 binding energies. The HCO₂H : PXH₂ complexes are stabilized by both a pnicogen bond and a hydrogen bond, resulting in greater binding energies for the HCO₂H : PXH₂ complexes compared to H₂CO : PXH₂. Neither the O−P distance across the pnicogen bond nor the O−P distance across the hydrogen bond correlates with the binding energies of these complexes. The nonlinearity of the hydrogen bonds suggests that they are relatively weak bonds, except for complexes in which the substituent X is either CH₃ or H. The pnicogen bond is the more important stabilizing interaction in the HCO₂H : PXH₂ complexes except when the substituent X is a more electropositive group. EOM-CCSD spin-spin coupling constants ^1pJ(O−P) across pnicogen bonds in H₂CO:PXH₂ and HCO₂H : PXH₂ complexes increase as the O−P distance decreases, and exhibit a second order dependence on that distance. There is no correlation between ^2hJ(O−P) and the O−P distance across the hydrogen bond in the HCO₂H : PXH₂ complexes. ^2hJ(O−P) coupling constants for complexes with X=CH₃ and H have much greater absolute values than anticipated from their O−P distances.     

Strong N−H⋅⋅⋅O Hydrogen Bonding in a Model Compound of the Catalytic Triad in Serine Proteases

Low-barrier hydrogen bond (LBHB) involvement in enzyme catalysis is examined by analysis of experimental nuclear and electron densities of a model compound for the catalytic triad in serine proteases (shown schematically), which is based on a cocrystal of betaine, imidazole, and picric acid. The three short, strong N−H⋅⋅⋅O hydrogen bonds in the structure have varying degrees of covalent bonding contributions suggesting a gradual transition to the LBHB situation.     

Dinicotinamidium squarate

The crystal structure determination of the dinicotinamidium squarate salt, 2C₆H₇N₂O⁺·C₄O₄²⁻, is reported, with the squarate dianion residing on an inversion centre and the unique cation in a general position. Salt formation occurs by donation of two H atoms from squaric acid to the nicotin­amide base. The crystal packing is derived from three types of hydrogen bonding. The primary hydrogen bond involves a squarate anion O atom and an H atom of the protonated pyridine group of the nicotin­amide, with an N⋯O distance of 2.5760 (13) Å. The second hydrogen bond involves a second anion O atom and an amide H atom, with an N⋯O distance of 2.8374 (14) Å. Thirdly, an intermolecular interaction between two coplanar nicotin­amide moieties occurs between an amide O atom and a symmetry‐related amide H atom, with an N1⋯O3 distance of 2.8911 (15) Å. These hydrogen bonds are also responsible for the planarity of the nicotin­amide moiety in the salt.     

The charge density distribution in a model compound of the catalytic triad in serine proteases

Combined low temperature (28(1) K) X-ray and neutron diffraction measurements were carried out on the co-crystallised complex of betaine, imidazole, and picric acid (1). The experimental charge density was determined and compared with ab initio theoretical calculations at the B3LYP/6-311G(d,p) level of theory. The complex serves as a model for the active site in, for example, the serine protease class of enzymes, the so-called catalytic triad. The crystal contains three short strong N-H...O hydrogen bonds (HBs) with dN...O < 2.7 A. The three HBs have energies above 13 kcalmol(-1), although the hydrogen atoms are firmly localized in the "nitrogen wells". This suggests that low-barrier hydrogen bonding in catalytic enzyme reactions may be a sufficient, but not a necessary, condition for obtaining transition-state stabilization. Structural analysis (e.g., covalent N-H bond lengthening) indicates that the hydrogen bond between H3A and 08 of imidazole and betaine respectively (HB2) is slightly stronger than the bond between H1A and O1A of imidazole and picric acid (HB1), although HB1 is shorter than HB2: (dN...O(HB1)= 2.614(1) A, dN...O(HB2) = 2.684(1) A, dH...O(HB1) = 1.630(1) A, dH...O(HB2)= 1.635(1) A, dN-H(HB1) = 1.046(1) A, dN-H(HB2) = 1.057(1) A). Furthermore, the charge density analysis reveals that HB2 has a larger covalent character than HB1, with considerable polarization of the density towards the acceptor atom. The Gatti and Bader source function (S) is introduced to the analysis of strong HBs. The source function is found to be a sensitive measure for the nature of a hydrogen bond, and comparison with low-barrier and single-well hydrogen bonding systems (e.g., benzoylacetone and nitromalonamide) shows that the low-barrier hydrogen bond (LBHB) state is characterized by an enormously increased hydrogen atom source contribution to the bond critical point in the HB. In this context, HB2 can be characterized as intermediate between localized HBs and delocalized LBHBs.     

Structural,Hirshfeld surface and spectroscopic studies of the noncentrosymmetric 1-ethylpiperazinediium pentachloroantimonate (III) monohydrate

1-Ethylpiperazinediium pentachloroantimonate (III) monohydrate, C₆H₁₆N₂SbCl₅·H₂O, has been synthesized by the reaction of antimony trioxide (Sb₂O₃) and 1-ethylpiperazine in an aqueous solution of hydrochloric acid. The structure crystallizes in orthorhombic system, in the non-centrosymmetric space group Pca2₁ and consists of isolated [C₆H₁₆N₂]²⁺ cations, square pyramidal [SbCl₅]²⁻ anions and lattice water molecules. OH⋯Cl hydrogen bonds link the [SbCl₅]²⁻ anions and water molecules to form double chains stretching along the [101] direction. The chains in turn are linked to the organic cations via NH⋯Cl, CH⋯Cl, CH⋯O and NH⋯O hydrogen bonds to form a three-dimensional network. This structure presents an example of a general square pyramidal complex ion containing a stereo-chemically active lone pair of electrons. Solid state ¹³C and ¹⁵N CP-MAS NMR spectra are in agreement with the X-ray structure, and vibrational absorption bands were identified by infrared spectroscopy. DFT calculations allowed the attribution of the NMR peaks and IR absorption bands. The interactions variability of the two independent cations and ten chloride atoms is analyzed via Hirshfeld surface analysis.     

Conformation of cationic N,N‐di­methyl­glycine in di­methyl­glycinium tri­fluoro­acetate

In the title compound, C₄H₁₀NO₂⁺·C₂F₃O₂^?, the main N—C—COOH skeleton of the protonated amino acid is nearly planar. The C=O/C—N and C=O/O—H bonds are syn and the two methyl groups are gauche to the methyl­ene H atoms. The conformation of the cation in the crystal is compared to that given by ab initio calculations (Hartree–Fock, self‐consistent field molecular‐orbital theory). The tri­fluoro­acetate anion has the typical staggered conformation with usual bond distances and angles. The cation and anion form dimers through a strong O—H?O hydrogen bond which are further interconnected in infinite zigzag chains running parallel to the a axis by N—H?O bonds. Weaker C—H?O interactions involving the methyl groups and the carboxy O atoms of the cation occur between the chains.     

Insights and Activation Energy Surface of the Dehydrogenation of C2HxO Species in Ethanol Oxidation Reaction on Ir(100)

Dehydrogenation of an organic compound is the first and the most fundamental elementary reaction in many organic reactions. In ethanol oxidation reaction (EOR) to form CO₂, there are a total of 46 pathways in C₂H_xO (x=1–6) species leading to the removal of all six hydrogen atoms in five C−H bonds and one O−H bond. To investigate the degree of dehydrogenation in EOR under operando conditions, we performed density function theory (DFT) calculations to study 28 dehydrogenation steps of C₂H_xO on Ir(100). An activation energy surface was then constructed and compared with that of the C−C bond cleavages to understand the importance of the degree of dehydrogenation in EOR. The results show that there are likely 28 dehydrogenations in EOR under fuel cell temperatures and the last two hydrogens in C₂H₂O are less likely cleaved. On the other hand, deep dehydrogenation including 45 dehydrogenations can occur under ethanol steam reforming conditions.     

Methyl 4‐[(1‐acetyl‐3‐tert‐butyl‐1H‐pyrazol‐5‐yl)amino]‐3‐nitrobenzoate

In the molecule of the title compound, C₁₇H₂₀N₄O₅, there are two intramolecular N—H...O hydrogen bonds having amidic and nitro‐group O atoms as the acceptors and together forming a three‐centre N—H...(O)₂ system. These interactions appear to play an important role in controlling the relative orientation of the pyrazole and aryl rings. The bond distances provide evidence for some polarization of the electronic structure. Molecules are linked into simple chains by a single C—H...O hydrogen bond.     

N‐tert‐Butyl‐N′‐(5,7‐di­methyl‐1,8‐naphthyridin‐2‐yl)­urea

The title compound, C₁₅H₂₀N₄O, has been synthesized as an AADD recognition unit for quadruple hydrogen bonds. All non‐H atoms of the mol­ecule apart from two methyl groups of the tert‐butyl group lie in a common plane. An intramolecular hydrogen bond is formed connecting two N atoms. In the solid state, the title compound crystallizes as a centrosymmetric dimer connected by N—H?O=C interactions with an N?O distance of 2.824 (2) Å.     

Crystal structure of 1:1 Complexes between urea and two crown ether derivatives of phthalic acid, 2,3,5,6,8,9,11,12,14,15-decahydrobenzo[1,4,7,10,13,16]hexaoxacyclo-octadecin-18,19-dicarboxylic acid (i) and 2,3,5,6,8,9,11,12-octahydro-benzo[1,4,7,10,13]pentaoxacyclopentadecin-15,16-dicarboxylic acid (II)

The crystal structures of the titlke compounds have been determined by X-ray diffraction. Urea, I crystallizes in the triclinic PI space group with cell dimensions a = 8.336(2), b = 11.009(2), c = 13.313(2) Å, α = 105.55(3), β = 103.62(3), γ = 104.63(3)° and Z = 2 final R value 0.072 for 2105 observations. Urea, II crystallizes in the orthorhombic P2₁2₁2₁ space group with cell dimensions a = 8.750(2), b = 10.844(3) and c = 21.215(3) Å and Z = 4, final R value 0.083 for 599 observations. All the hydrogen atoms were located in the complex urea, I ; urea molecules form hydrogen bonded dimers about centers of symmetry, these dimers are sandwiched between macrocyclic rings forming one simple and one bifurcated hydrogen bond from the “endo” hydrogen atoms to the ether oxygen atoms. These units are held by hydrogen bonding between the urea molecules and carboxylic acids in two other units; these hydrogen bonds are cyclic involving eight atoms -(N-H(exo)…O(keto)-C-O-H…O(urea)-C)-. Only one carboxylic acid group per molecule takes part in these hydrogen bonds, the other forms a short, 2.490(7) Å, internal bond to the acceptor keto oxygen atom. N(H)…O bonds range from 2.930(7) to 3.206(7) Å, O(H)…O is 2.475(6) Å. In the complex urea, II each urea is hydrogen bonded to three different host molecules and vice versa; the urea “endo” hydrogen atoms bond to the ether oxygen atoms, while both “exo” hydrogen atoms take part in cyclic hydrogen bonds to carboxylic acids. There is not internal hydrogen bond. N(H)…O bonds range from 2.83 to 3.26(2) A and the O-…O bonds are 2.55 and 2.56(2) Å.     

The synergistic co‐operation of N—H…O=P hydrogen bonds and C—H…OX weak intermolecular interactions (X is =P or —C) in the (CH3O)2P(O)(NH–NHC6F5) amidophosphoester: a combined X‐ray crystallographic and theoretical study

The asymmetric unit of O,O′‐dimethyl [(2,3,4,5,6‐pentafluorophenyl)hydrazinyl]phosphonate, C₈H₈F₅N₂O₃P, is composed of two symmetry‐independent molecules with significant differences in the orientations of the C₆F₅ and OMe groups. In the crystal structure, a one‐dimensional assembly is mediated from classical N—H…O hydrogen bonds, which includes R₂²(8), D(2) and some higher‐order graph‐set motifs. By also considering weak C—H…O=P and C—H…O—C intermolecular interactions, a two‐dimensional network extends along the ab plane. The strengths of the hydrogen bonds were evaluated using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6‐311G(d,p) level of theory. The LP(O) to σ*(NH) and σ*(CH) charge‐transfer interactions were examined according to second‐order perturbation theory in natural bond orbital (NBO) methodology. The hydrogen‐bonded clusters of molecules, including N—H…O and C—H…O interactions, were constructed as input files for the calculations and the strengths of the hydrogen bonds are as follows: N—H…O [R₂²(8)] > N—H…O [D(2)] > C—H…O. The decomposed fingerprint plots show that the contribution portions of the F…H/H…F contacts in both molecules are the largest.     

Bis(μ‐5‐carboxybenzene‐1,3‐dicarboxylato‐κ2O1:O3)bis[(2,2′‐bi‐1H‐imidazole‐κ2N3,N3′)zinc]

The title compound, [Zn₂(C₉H₄O₆)₂(C₆H₆N₄)₂], consists of two Zn^II ions, two 5‐carboxybenzene‐1,3‐dicarboxylate (Hbtc²⁻) dianions and two 2,2′‐bi‐1H‐imidazole (bimz) molecules. The Zn^II centre is coordinated by two carboxylate O atoms from two Hbtc²⁻ ligands and by two imidazole N atoms of a bimz ligand, in a distorted tetrahedral coordination geometry. Two neighbouring Zn^II ions are bridged by a pair of Hbtc²⁻ ligands, forming a discrete binuclear [Zn₂(Hbtc)₂(bimz)₂] structure lying across an inversion centre. Hydrogen bonds between carboxyl H atoms and carboxylate O atoms and between imidazole H atoms and carboxylate O atoms link the binuclear units. These binuclear units are further extended into a three‐dimensional supramolecular structure through extensive O—H...O and N—H...O hydrogen bonds. Moreover, the three‐dimensional nature of the crystal packing is reinforced by the π–π stacking. The title compound exhibits photoluminescence in the solid state, with an emission maximum at 415 nm.     

A novel tubular hydrogen‐bond pattern in a new diazaphosphole oxide: a combination of X‐ray crystallography and theoretical study of hydrogen bonds

In the structure of 2‐(4‐chloroanilino)‐1,3,2λ⁴‐diazaphosphol‐2‐one, C₁₂H₁₁ClN₃OP, each molecule is connected with four neighbouring molecules through (N—H)₂…O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R ³₃(12) and R ₄³(14) hydrogen‐bond ring motifs, combined with a C (4) chain motif. The hole constructed in the tubular architecture includes a 12‐atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co‐operating in classical hydrogen bonding, takes part in an N—H…π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen‐bond pattern. The energies of the N—H…O and N—H…π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen‐bonded cluster of molecules as the input file for the chemical calculations. In the ¹H NMR experiment, the nitrogen‐bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the ²J _H–P coupling constant.