Hydrogensquarate Anions Research Articles

Interactions of pyridoxine (Vitamin B6) with squaric acid and water. Experimental and theoretical studies

Pyridoxine (Vitamin B6, 3‑hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine) forms a hydrate adduct with squaric acid (3,4-dihydroxy-3-cyclobuten-1,2‑dione). The proton from squaric acid is transferred to the pyridoxine nitrogen atom. Two hydrogen squarate anions form a centrosymmetric α-dimer, which interacts symmetrically with two pyridoxinium cations and two water molecules, through several hydrogen bonds of the lengths from 2.498(3) to 2.843(3) Å. The molecular structure of the 2:2:2 adduct (dimer) was studied by a single-crystal X-ray diffraction, DFT calculations, FTIR and NMR spectroscopies. Structures of three models of the monomer of pyridoxinium hydrogen squarate monohydrate (1:1:1) were optimized at the APF-D/6–311++G(d,p) level of theory. Their molecular geometries, hydrogen bond distances, IR spectra, natural atomic charges, frontier molecular orbitals (HOMO and LUMO) were analyzed. The quantum theory of atoms in molecule (QTAIM) was used to classify the strength of the hydrogen bonds in the dimer and monomers of the optimized adducts. The studied compound was screened for antifungal activities and showed inhibiting properties against A. niger and P. placenta.

Regarding configuration and hydrogen atom placement in “Development of new L-Serine Squarate single crystal” [Tyagi et al., J. Mol. Struct. 1224 (2021) 129190

The crystal structure of L-serinium hydrogensquarate (CSD refcode: HUQNIT), published in this journal very recently [Tyagi et al., J. Mol. Struct. 1224 (2021) 129190], is revised. Problems arise from the assignment of the absolute configuration of the serinium cation and the positioning of disordered hydrogen atoms of the hydrogensquarate anion. The correct structure of L-serinium hydrogensquarate was published more than 20 years ago [CSD refcode: PAZCUO; Kolev et al., Z. Kristallogr. NCS 213 (1998) 169-170].

Structural, vibrational and DFT studies of di-(pipecolinium acid) squarate

A racemic mixture of (R)- and (S)-pipecolic acid (piperidine-2-carboxylic acid, P2C) forms a stable crystalline complex with squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione, H2SQ), at the 2:1 ratio (1). The crystals are built of two pipecolic acid cations (P2C+H) and squarate dianion (SQ2−). Complex 1 has been characterized by single-crystal X-ray analysis, Raman, FTIR and 13C CP MAS spectroscopy. The title complex crystallizes in monoclinic C2/c space group with Z=4 and Z’=0.5. In the crystal structure two types of C2-symmetric complexes with different chirality are identified as [(R)-P2C+H]2SQ2− and [(S)-P2C+H]2SQ2−. The molecules are linked through the COOH⋯O–C of 2.587(1) Å and two N+H⋯O–C hydrogen bonds of 2.756(1) and 2.759(1) Å. In the optimized structure, at the B3LYP/6–311++G(d,p) level of theory, pipecolic acid zwitterion and cation interact with the hydrogen squarate anion. Charge delocalization has been analysed using the Natural Bond Orbital (NBO) method. Solid-state Raman, FTIR and 13C CP MAS spectra have been measured. The potential energy distributions (PED) have been used to assign the vibrational spectra. The crystal and optimized structures have been compared.

Structural and spectroscopic properties of piperidinium-4-carboxylic acid hydrogen squarate

The 1:1 complex of protonated piperidine-4-carboxylic acid (P4C+H) with hydrogen squarate anion (HSQ−) was prepared and characterized by a single-crystal X-ray diffraction, B3LYP/6-311++G(d,p) calculations, FTIR and NMR spectroscopies. The crystals are orthorhombic, Pbcn space group. The molecules are linked through the OH⋯O hydrogen bonds of 2.723(1) and 2.574(1)Å formed between P4C+H and HSQ−, and between HSQ− anions linked into a β-chain, respectively. The hydrogen squarate anion is surrounded by four P4C+H cations which are involved in the N+H⋯O hydrogen bonds of the lengths from 2.815(1) to 3.183(2)Å. The potential energy distributions (PED), calculated for the optimized structure of the title complex at B3LYP/6-311++G(d,p) level of theory, were used for the assignments of IR bands in the experimental and calculated spectra. The FTIR spectrum was consistent with the X-ray results. The theoretical and experimental IR spectra have been compared. The NMR spectra in an aqueous solution and in the solid-state have been studied.

New structural motif of hydrogensquarate anions in the presence of dl-Serinium cation. Spectral and structural elucidation

A new crystalline complex of dl-serine and squaric acid (H2Sq) in stoichiometric ratio 1:1 (dl-Ser·HSq) was synthesized, isolated and structurally characterized by single crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P21/n and its structure consists of a 3D supramolecular network of hydrogensquarate anions and serinium cations directed by intermolecular hydrogen bonding interactions. The 3D network is formed by hydrogen bonds with participation of CO–OH, hydrogensquarate ion and NH3+ group, (Sq) CO…OC (OH) (2.525 Å), –NH3+…OC (Sq) (2.915, 2.985 and 3.016 Å), hydroxyl group CH2–OH…OC (Sq) (2.739 Å), O…H–N+ (3.016 Å) and (C–OHA…OC (Sq) (3.242), respectively. The structural information shows a new structural motif, a non-classic α-chain of the hydrogensquarate anions with dihedral angle between neighbouring HSq− anions 43.66°. The Raman and infrared spectra of the new crystal were measured in the 4000–50 cm−1and 4000–400 cm−1 region frequency range respectively. The assignment of bands in infrared and Raman spectra of the crystal was performed on the basis of DFT (B3LYP) calculations, X-ray structural results and by the comparison with literature data.

Synthesis, an experimental and quantum chemical computational study: Proton sharing in 4-Morpholinium bis(hydrogen squarate)

The experimental and theoretical investigation results of a novel organic squarate salt of 4-Morpholinium bis(hydrogen squarate) (1), C6H14ON+·C8H3O8-, were reported in this study. The crystal structure of the title compound was found to crystallize in the triclinic P−1 space group. In the crystals of 1 the morpholine ring adopts the chair conformation with the ethyl group in the equatorial and hydrogen atoms in axial positions. The hydrogen squarate anions are linked into a homoconjugated anion, [(HSQ)2H], by a short symmetric, nonlinear O8⋯H2⋯O2 hydrogen bond of 2.444 (2)Å. The structural and vibrational properties of the compound were also studied by computational methods of ab-initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The obtained calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 obtained are presented and compared with the X-ray analysis result. On the other hand the molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.

Synthesis, an experimental and quantum chemical computational study of a new nonlinear optical material: 2-Picolinium hydrogensquarate

The experimental and theoretical investigation results of a novel organic non-linear optical (NLO) organic squarate salt of 2-Picolinium hydrogensquarate (1), C6H8N+·C4HO4-, were reported in this study. The space group of the title compound was found in the monoclinic C2/c space group. It was found that the asymmetric unit consists of one monohydrogen squarate anion together with mono protonated 2-Picolinium, forming the (1) salt. The X-ray analysis clearly indicated that the crystal packing has shown the hydrogen bonding ring pattern of D22(10) (α-dimer) through NH⋯O interactions. The hydrogensquarate anions form α-dimer, while 2-Picolinium molecule interacts through NH⋯O and CH⋯O with the hydrogensquarate anion. The structural and vibrational properties of the compound were also studied by computational methods of ab initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 obtained are presented and compared with the X-ray analysis result. On the other the molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.

Supramolecular structure of the 1:2 complex of 1,4-dimethylpiperazine mono-betaine with squaric acid

The 1:2 complex of 1,4-dimethylpiperazine mono-betaine (MBPZ) with squaric acid (H2SQ) has been characterised by single-crystal X-ray analysis, FTIR and NMR spectroscopies, and by DFT calculations. The crystals are monoclinic, space group P21/c. Two MBPZ cations and four hydrogen squarate anions (HSQ− ) are linked by strong O(1)–H…O(13) (2.525(4) Å), O(14)–H…O(21) (2.511(4) Å) and N(4)–H…O(23) (2.607(3) Å) hydrogen bonds into a cyclamer . In turn, the cyclamers are linked into a helix through two O(24)–H…O(11) hydrogen bonds of 2.516(4) Å. The piperazinium ring has a chair conformation with N(4)–CH3 and N(1)–CH2COOH substituents in the equatorial positions, and N(1)–CH3 in the axial position. The FTIR spectrum is consistent with the crystal data. Two models of the 1:2 complex of MBPZ with H2SQ have been optimised at the B3LYP/6-311++G(d,p) level of theory and have been used to calculate harmonic IR frequencies. One of the models (2) is dominated by electrostatic attraction between NH(4)+ and HSQ− , whereas in the other (3) squaric acid interacts with a zwitterionic MBPZ through the O–H…O and O–H…N hydrogen bonds.

The 2:2 complex of pyridine betaine with squaric acid studied by X-ray diffraction, FTIR, NMR and DTG methods

The 2:2 ionic crystals of pyridine betaine (PyB) with squaric acid (H2SQ) belong to monoclinic space group C2/c. Supramolecular structure of the crystals investigated is formed by the loss of one proton from every two squaric acid molecules. Pyridine betaines form a homoconjugated cation, [(PyB)2H]+, through a short, symmetric COO⋯H⋯OOC hydrogen bond of 2.463(2)Å. The hydrogen squarate anions are linked into a homoconjugated anion, [(HSQ)2H]−, by a short symmetric, non-linear O⋯H⋯O hydrogen bond of 2.453(1)Å, with the H-atom located on the twofold axis. The bis(hydrogen squarate)hydrogen anions are linked into a centrosymmetric cyclic dimer by two identical asymmetric OH⋯O hydrogen bonds of 2.536(2)Å. The (PyB)2H cation and cyclic dimer of hydrogen squarate anions are placed around two different systems of inversion centers in the unit cell. The FTIR spectrum is consistent with the X-ray results. The 13C chemical shift of the CO atom confirms the presence of the hydrogen squarate anion in the complex studied. The complex decomposed in three thermal stages.

Hydrogen bonds and electrostatic interactions in the 1:1 complex of DABCO di-betaine with squaric acid: Crystallographic, theoretical and spectroscopic studies

► Hydrogen squarate anions are bonded to homoconjugated DABCO di-betaine cations. ► O H···O and C H···O hydrogen bonds and N + ···O electrostatic interactions are present. ► C H···O hydrogen bonds are confirmed by the νC H···O vibrations in the IR spectrum. ► DABCO moiety has a propeller conformation. ► The crystal structure is more extended than optimized ones. The molecular structure of the 1:1 complex of DABCO di-betaine (1,4-dicarboxymethyl-1,4-diazabicyclo[2.2.2]octane inner salt) with squaric acid ( 1 ) has been characterized by single-crystal X-ray diffraction, infrared spectroscopy and DFT calculations. Crystals 1 are monoclinic, space group P 2 1 / c . One proton of squaric acid is transferred to one of the carboxylate groups of DABCO di-betaine. The mono-protonated DABCO di-betaine cation is further engaged in the COOH⋯OOC hydrogen bond of 2.526(2) Å with the neighboring cations, linking them into a zigzag chain. The hydrogen squarate anion interacts with the oxygen atom of the carboxylate group of DABCO di-betaine cation, through the O H⋯O C hydrogen bonds of 2.600(2) Å. The structures of monomer 1a , dimer 2 and cation 3 have been optimized at the B3LYP/6-31G(d,p) level of theory. The FTIR spectrum is consistent with the X-ray results. The second-derivative spectrum of 1 and calculated frequencies for the optimized structure 1a are used to explain the frequencies in the experimental FTIR spectrum.

Poly[[μ-aqua-tetraaquabis(μ-2-hydroxy-4-oxocyclobut-1-ene-1,3-diolato)strontium] hemihydrate

In the title coordination polymer, {[Sr(C4HO4)2(H2O)5]·0.5H2O}n, the Sr2+ ion is coordinated by three monodentate hydrogensquarate (hsq) anions and six aqua ligands in a distorted SrO9 monocapped square-anti­prismatic geometry. The hsq anions and water mol­ecules bridge the metal ions into infinite sheets lying parallel to (100). The O atom of the uncoordinated water mol­ecule lies on a crystallographic twofold axis. The packing is stabilized by numerous O—H⋯O hydrogen bonds.

Three forms of squaric acid with pyrazine and pyridine derivatives: an experimental and theoretical study

Three new squarate salts were synthesized and combined with experimental and theoretical study on molecular, vibrational, and electronical properties. Squaric acid was crystallized as HSQ− [SQ: squarate] monoanion in [(C13H12NO2)(HC4O4)] (I), as uncharged H2SQ in [(C5H5N3O)(H2C4O4)] (II), and as SQ2− dianion form in [C6H9N2)2(C4O4)] (III). They crystallize in the triclinic and monoclinic crystal system with space group P−1, P21/c, and P21/c, respectively. Crystal structure analysis reveals that, far from forming discrete ionic species in (I) and (II), it is likely that there is large degree of proton sharing between the two hydrogen squarate anions in (I) and between the neutral moieties in (II), with the H atom lying almost symmetrically between the donor and acceptor sites, as evidenced by the long O–H and N–H bonds and short H···O distances. Ab initio calculations have been carried out for three compounds by using DFT/B3LYP and HF methods at 6-31++G(d,p) basis set. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, calculated data show that the predicted geometries can reproduce the structural parameters. The results of the optimized molecular structure for three compounds obtained on the basis of two models are presented and compared with the experimental X-ray data. Calculated vibrational frequencies are consistent with each other and experimental IR data. The theoretical electronic absorption spectra have been calculated by both TD–DFT and HF–CIS methods. Molecular orbital coefficients analysis suggest that the electronic transitions are mainly assigned to n → π* and π → π* electronic transitions.

A second monoclinic polymorph of ethylenediammonium bis(hydrogen squarate) monohydrate

The title compound, C2H10N2 2+·2HC4O4 −·H2O, a new polymorph of ethyl­enediammonium bis­(hydrogen squarate) monohydrate, was synthesized by slow evaporation of an acid solution. The asymetric unit contains two hydrogen squarate anions, two half-mol­ecules of protonated ethyl­enediamine arranged around a twofold axis and one water mol­ecule. In the crystal, N—H⋯O and O—H⋯O hydrogen bonds between the hydrogen squarate anions, protonated N atoms from the amine group and water mol­ecules lead to a three-dimensional framework. In particular, the cohesion between the squarate groups is ensured by very short intermolecular hydrogen bonds bonds. The title compound crystallized together with the previously reported polymorph [Mathew et al. (2002 ▶). J. Mol. Struct. 641, 263–279].

Stacking Structure of Quinolinium Hydrogensquarate

A new proton‐transfer organic salt, quinolinium hydrogensquarate (C13H9NO4), has been synthesized and fully characterized by single crystal x‐ray diffraction. The salt crystallizes in the monoclinic space group P21/n with the parameters: a = 3.8290(12) Å, b = 20.960(6) Å, c = 13.802(4) Å, β = 95.452(5)°, V = 1102.7(6) Å3, Z = 4 formula units. The structure consists of uncommon supramolecular neutral dimers which pile up parallel to [100] forming infinite sheets. These centrosymmetric dimers are held together by lateral hydrogen‐bonds whereby two neighboring coplanar hydrogensquarate anions act as a bridge between two terminal quinolinium cations and C‐H…O bridgings interlink next neighboring sheets. The bulk structure of this salt is consolidated by weak π—π interactions within the sheets which are neatly ordered side‐by‐side relative to one another.

2-(Phenylethyl)ammonium hydrogensquarate hemihydrate: crystal structure, solid-state IR-spectroscopic and theoretical characterization

The title compound, 2-(phenylethyl)ammonium hydrogensquarate hemihydrate, was synthesized and structurally and spectroscopically characterized by a single crystal X-ray diffraction and solid-state polarized IR spectroscopy of oriented colloids in a nematic host. The crystal structure consists of two crystallographically independent 2-(phenylethyl)ammonium cations, joined in a 2D hydrogen-bonded network with hydrogensquarate anions and solvent water molecules. Surprisingly, the crystallographically non-equivalent cations exhibit differing pseudo T and G trans configurations.

Polymorphs of 4-(dihydroxymethyl)pyridinium hydrogensquarate – Crystal structures and spectroscopic properties

The novel salt of a geminal diol 4-(dihydroxymethyl)pyridinium hydrogensquarate was derived from isonicotinaldehyde and squaric acid in water. Two polymorphs were characterized by means of single crystal X-ray diffraction and linear-polarized infrared (IR-LD) spectroscopy of oriented colloids in nematic host. UV spectroscopy was employed to confirm the stabilization of the geminal diol form in aqueous solution. Depending of the reaction conditions two polymorphs of 4-(dihydroxymethyl)pyridinium hydrogensquarate are determined – monoclinic ( 1) and a triclinic ( 2) polymorph. The monoclinic ( 1) crystallizes in the centrosymmetric space group P2 1/ c, while ( 2) crystallizes in the centrosymmetric space group P 1 ¯ , respectively. The hydrogensquarate anions in both forms form the α chain motif via interanionic hydrogen bonding interactions 2.664(7) Å ( 1) and 2.517(5) Å ( 2), respectively. The geminal diol group of the cations in ( 1) are directed to an adjacent hydrogensquarate ion via two O–H···O hydrogen bonds with an averaged donor–acceptor distances forming an eight membered ring. In contrast to ( 1), in ( 2) the infinite hydrogen bonded two-dimensional layers formed by cations and anions are connected via a hydrogen bond between hydroxyl groups of adjacent symmetry related cations.

1,10-Phenanthrolinium hydrogensquarate monohydrate—A non-centrosymmetric structure from two non-chiral agents

The novel hydrogensquarate salt of 1,10-phenanthroline has been synthesized, isolated and structurally elucidated by single crystal X-ray diffraction. 1,10-Phenanthrolinium hydrogensquarate monohydrate ( 1) crystallizes in the non-centrosymmetric P2 1 space group. Its hydrogensquarate anions form a stable dimer by means of (Sq)OH⋯O C (Sq) hydrogen bonds with lengths of 2.509, 2.526, 2.510, and 2.524 Å. The solvent water molecule interacts with the anion dimers by means of strong and moderate hydrogen bonds HOH⋯O C (Sq) with bond lengths of 2.782 and 2.845 Å, respectively. The 1,10-phenanthrolinium cation participates in NH⋯OH 2 interactions with the water molecule (bond lengths of 2.810, 2.758, 2.779 and 2.760 Å). Surprisingly, compound contains four independent molecules in the unit cell. Optical properties were elucidated by means of linear-polarized solid-state IR-spectroscopy and UV-spectroscopy. In addition TGA, DSC, DTA data, positive and negative ESI mass spectra as well as 1H- and 13C NMR spectra are presented. Quantum chemical methods were used to calculate the electronic structure, vibrational data and electronic spectra as well as non-linear optical properties of neutral 1,10-phenanthroline and its protonated cation. Second harmonic generation measurements of the novel compound demonstrate that the compound possesses effective d coefficients of 1.9 ± 0.5 pm V −1, value that is about three times higher that of the low temperature form of potassium dideuterophosphate.

Spectroscopic and structural elucidation of 4-dimethylaminopyridine and its hydrogensquarate

A distortion of the aromatic character and stabilization of the imino-form as a result of the protonation of 4-dimethylaminopyridine was established by IR-, UV- and 1H NMR-spectral analysis of 4-diaminopyridinium hydrogensquarate. Quantum chemical calculations were carried out at MP2 and B3LYP levels of theory and a 6-311++G** basis set with a view to determining the changes in geometrical parameters and IR-spectroscopic characteristics resulting from N py protonation. Linear-dichroic IR-spectroscopy coupled with the orientation techniques of solid samples as liquid crystal suspensions and melted solid polycrystalline films was applied for the identification of the IR-bands, characteristic for the structural fragments of the neutral and imino-form of the pyridine derivative. The spectral results were compared with the structure, obtained by a single crystal X-ray analysis. The salt contains dimmers of hydrogensquarate anions and N py protonated cations of which the former are stabilized by strong intermolecular OH…O interactions (2.552 Å and 143.1(2)°). The 4-diaminopyridinium cation interacts with the anion through moderate NH…O bonds (2.729 Å and 165.0(0)°). Individual cations are π–π stacked with their neighbors at a distance of 3.406 Å.

Cyclohexylammonium hydrogensquarate hemihydrate

The components of the title compound, C6H14N+·C4HO4−·0.5H2O, are connected by moderate inter­molecular N—H⋯O hydrogen bonds between the anions and cations into infinite three-dimensional networks. The cyclo­hexyl­ammonium cation inter­acts with the solvent mol­ecule by means of an N—H⋯O hydrogen bond. The hydrogensquarate anions form α chains through strong O—H⋯O inter­actions.

Synthesis, spectroscopic, structural and theoretical characterization of hydrogensquarate and mononuclear Au(III)-complex of dipeptide phenylalanyltyrosine

The mononuclear Au(III)-complex ([Au(C 18H 18N 2O 4)Cl]) and hydrogensquarate ([C 22H 21N 2O 8]) of dipeptide phenylalanyltyrosine ( H–Phe–Tyr–OH) have been synthezised, characterized spectroscopically and structurally by means of solid-state linear-polarized IR-spectroscopy, 1H- and 13C-NMR, ESI-MS, HPLC-MS–MS, FAB-MS, TGS and DSC methods. The structure of the Au(III)-complex has been predicted theoretically by DFT calculations. The dipeptide coordinated in a tridentate manner via –NH 2, –COO − and N −-groups. One Cl − ion is attached to the metal centre as a terminal ligand, yielding a planar AuN 2OCl chromophor. The hydrogensquarate consists in positive charged dipeptide moiety and negative one hydrogensquarate (HSq −) anion stabilizing by strong intermolecular hydrogen bonds.