Structure of the complex of dimethylphenyl betaine with dichloroacetic acid studied by X-ray diffraction,DFT calculations,infrared and Raman spectra

The structure of the complex of dimethylphenyl betaine (DMPB) with dichloroacetic acid (DCA) (1) has been investigated by X-ray diffraction, FTIR and Raman spectroscopy, and B3LYP/6-311 + + G(d,p) calculations. The crystal is monoclinic, space group P2₁. The acid is connected with betaine through the OH⋯O hydrogen bond of 2.480(2) Å. In the optimized structure the short, asymmetric O⋯O distance is 2.491 Å. FTIR spectrum shows a broad absorption in the 1500–400 cm⁻¹ region characteristic of very short OH⋯O hydrogen bond caused by Fermi resonance between νOH and overtones of δOH and γOH. In the Raman spectrum this broad absorption is not observed. The potential energy distributions (PED) were used for the assignments of IR and Raman frequencies in the experimental and calculated spectra. The FTIR and Raman spectra of the crystal complex are consistent with the X-ray results.     

Crystal and molecular structure, hydrogen bonding and electrostatic interactions of bis(pyridine betaine) perchlorate

Bis(pyridine betaine) perchlorate, (PB)₂H·ClO₄, has been characterized by X-ray diffraction, B3LYP and MP2 calculations, FTIR, Raman and NMR spectroscopy and DSC. The complex crystallizes in space group C2/c. A pair of PB molecules is bridged by a short symmetric O·H·O hydrogen bond of the length 2.456(5) Å. Three conformers (I-III), with respect to the N⁺?O distances, of (PB)₂H cation have been analyzed at the DFT and MP2 level of theory and compared with the C(1)?O distances in the (PhCH₂COO)₂H anion. The calculated O?O distances for the analyzed cations are slightly shorter than that in the crystal. The type of hydrogen bond depends on the cation conformation and the method of calculations. The FTIR spectra of (PB)₂H·ClO₄ and (PBd₅)₂H·ClO₄ (bis(pyridine-d₅ betaine) perchlorate) show a broad and intense absorption in the 1500-400 cm⁻¹ range, which is similar to the type A acid salts of carboxylic acids and other 2:1 betaine complexes with mineral acids. In the Raman and second FTIR-derivative spectra (d²) the broad absorption is absent. A linear unit-slope correlation between d² negative band and Raman band is found. This confirms that derivative spectrometry can be used to estimate frequencies of the narrow bands covered by the broad absorption due to the O·H·O stretching and bending vibrations.     

X-Ray, MP2 and DFT studies of the structure and vibrational spectra of homarinium chloride

The effects of hydrogen bonding, inter- and intramolecular electrostatic interactions on the structure of homarinium chloride, HOMH·Cl, in the crystal and its isolated molecule have been studied by X-ray diffraction, FT-IR, Raman, ¹H and ¹³C NMR spectroscopies, and by the MP2 and DFT theoretical methods. In the crystal, the Cl⁻ anion is connected with protonated homarine via the O–HCl⁻ hydrogen bond of the length of 2.937(4) Å, and two N⁺Cl⁻ intermolecular electrostatic interactions. In the isolated molecule, according to the MP2 and B3LYP calculations, the Cl⁻ anion is engaged in a shorter hydrogen bond (O–HCl⁻ of 2.811–2.861 Å) and in one type of intramolecular electrostatic interactions. The calculated bond lengths and bond angles at the MP2 and B3LYP levels of theory are in good agreement with the X-ray data, except the conformation of the COOH group, which is cis (syn) in the crystal and trans (anti) in the isolated molecule. The tentative assignments for the experimental solid state vibrational spectra of HOMH·Cl and HOMD·Cl have been made on the basis of the B3LYP/6-31G(d,p) calculated frequencies and intensities. The effect of quaternization of picolinic acid on the chemical shifts of the ring protons and carbons is analyzed.     

DFT studies of the structure, vibrational and NMR spectra of 2-amino-pyridine betaine monohydrate

Four of the most stable conformers of 2-amino-pyridine betaine (1-carboxymethyl-2-amino-pyridinium inner salt) monohydrates, 2-NH₂PB·H₂O, and one anhydrous were analyzed by the B3LYP/6-31G(d,p) calculations and compared with the X-ray data. Two types of optimized conformers can be distinguished: (a) with NH₂ and COO groups and (b) an imino tautomer with NH and COOH groups. A common feature of the optimized molecules are intramolecular hydrogen bonds between the COO⁻ and H₂N or COOH and HN groups. In the crystal both NH₂ and COO groups participate in intermolecular hydrogen bonds. The probable assignments of the anharmonic experimental solid state vibrational frequencies of 2-NH₂PB·H₂O and 2-ND₂PB·D₂O (conformer 2) based on the calculated B3LYP/6-31G(d,p) harmonic frequencies have been made. Correlations between experimental chemical shifts for 2-NH₂PB, its hydrochloride and 1-carboxyethyl-2-amino-pyridinium inner salt (¹³C and ¹H in D₂O) and GIAO/B3LYP/6-31G(d,p) calculated isotropic shielding constants, δ_exp=a+bσ_calc, are reported. Good linear regression between experimental and theoretical results for ¹³C was obtained. Only in 2-NH₂PB the hydrogen at -position is outside the linear correlation.     

Molecular structures, hydrogen bonding and electrostatic interactions of 3-(2-bromo-pyridinium)-propionic acid and 3-(pyridinium)-pivalic acid halides

Intra- and intermolecular interactions and the conformations of 3-(2-bromo-pyridinium)-propionic acid bromide (1) and 3-(pyridinium)-pivalic acid chloride (2) have been studied by X-ray diffraction and theoretically. In these complexes, Br⁻ and Cl⁻ anions are H-bonded to the COOH group and interact electrostatically with the positively charged nitrogen atoms of neighbouring molecules. To analyse these interactions theoretically, the structures of monomers and dimers in various configurations were optimized by PM3 and BLYP/6-31G(d,p) methods. The analysis confirmed the vital role of both the H-bonds and electrostatic interactions (intra- and intermolecular) for the molecular conformation and the ionic aggregation in the solid state.     

X-ray diffraction studies of two azametallatranes. Peculiarities of structures of N,N′,N″-tris(trimethylsilyl)azametallatranes using DFT calculations

Single crystal structures of N(CH₂CH₂NSiMe₃)₃Si-Vinyl (1) and N(CH₂CH₂NSiMe₃)₃Si-n-Butyl (2) were determined by X-ray diffraction studies: both compounds show weak transannular N_ax→M interactions (1, d(N_ax→Si)=2.712(1) Å, 2, d(N_ax→Ge)=2.743(3) Å). General trends for molecular structures of the group 14 elements (Si, Ge, Sn) azametallatranes are discussed with also included DFT calculations data.     

Tricarbonyl rhenium complexes of bis(pyrazol-1-yl)methane and bis(3,5-dimethylpyrazol-1-yl)methane – Synthesis,spectroscopic characterization,X-ray structure and DFT calculations

Two novel tricarbonyl rhenium complexes based on the bidentate heterocyclic N–N ligands [bis(pyrazol-1-yl)methane(bpzm) and bis(3,5-dimethylpyrazol-1-yl)methane(bdmpzm)] have been synthesized by heating at reflux [Re(CO)₅Cl] with the appropriate N–N ligand in toluene. The compounds have been characterized by IR and UV–Vis spectroscopy and X-ray analysis. Density functional theory (DFT) and time-dependent (TD) DFT calculations have been carried out for the [Re(CO)₃(bdmpzm)Cl] complex.     

Copper(II) complexes of bis(pyrazol-1-yl)methane - Synthesis, spectroscopic characterization, X-ray structure and DFT calculations

Two novel copper(II) complexes incorporating bis(pyrazol-1-yl)methane ligand (bpzm) have been synthesized. The compounds [CuCl(bpzm)₂(H₂O)]Cl·H₂O (1) and [Cu(N₃)₂(bpzm)]_n (2) have been studied by IR, UV-Vis spectroscopy and X-ray crystallography. The experimental studies on the compounds 1 and 2 have been accompanied computationally by the density functional theory (DFT) calculations.     

Synthesis, spectroscopic characterization, X-ray structure and DFT calculations of rhenium(III) complex with bis(3,5-dimethylpyrazol-1-yl)methane

[ReCl₃(MeCN)(PPh₃)₂] reacts with bis(3,5-dimethypyrazol-1-yl)methane (bdmpzm) in acetone to give [ReCl₃(bdmpzm)(PPh₃)]. The compound has been studied by IR, UV–Vis spectroscopy and X-ray crystallography. The molecular orbital diagram of [ReCl₃(bdmpzm)(PPh₃)] has been calculated with the density functional theory (DFT) method.     

X-ray crystal structure and vibrational spectra of hydrazides and their metal complexes. Part II. Hexaaquacobalt(II)bis(phthalhydrazidato)tetrahydrate

The hexaaquacobalt(II)bis(phthalhydrazidato)tetrahydrate, [Co(H₂O)₆](C₈N₂O₂H₅)₂·4H₂O is examined using single crystal X-ray diffraction analysis. The crystals are triclinic, space group , with a = 9.757(1), b = 10.955(2), c = 11.106(1),  = 100.79(2), β = 90.35(3), γ = 91.54(1) and Z = 2. In [Co(H₂O)₆](C₈N₂O₂H₅)₂·4H₂O, the cobalt(II) is coordinated by six water ligands and the [Co(H₂O)₆]²⁺ is associated with the two O-deprotonated phthalhydrazidato ions only by hydrogen bonds. The infrared and Raman spectra of phthalhydrazide (PH) and infrared spectra of deuterated derivative phthalhydrazide (PD) and of [Co(H₂O)₆](C₈N₂O₂H₅)₂·4H₂O are reported. The theoretical wavenumbers, infrared intensities and Raman scattering activities have been calculated using density functional (B3LYP) method with the 6-311++G(d,p) basis set. The calculated potential energy distribution has proved to be of great help in assigning the spectra PH, its deuterated derivative and [Co(H₂O)₆](C₈N₂O₂H₅)₂·4H₂O. The results from natural bond orbital (NBO) analysis for keto-hydroxy form of PH are presented.     

Polymorphism of N,N'-diacetylbiuret studied by solid-state 13C and 15N NMR spectroscopy, DFT calculations, and X-ray diffraction

The molecular configuration and crystal structure of solid polycrystalline N,N′′‐diacetylbiuret (DAB), a potential nitrogen‐rich fertilizer, have been analyzed by a combination of solid‐ and liquid‐state NMR spectroscopy, X‐ray diffraction, and DFT calculations. Initially a pure NMR study (“NMR crystallography”) was performed as available single crystals of DAB were not suitable for X‐ray diffraction. Solid‐state ¹³C NMR spectra revealed the unexpected existence of two polymorphic modifications (α‐ and β‐DAB) obtained from different chemical procedures. Several NMR techniques were applied for a thorough characterization of the molecular system, revealing chemical shift anisotropy (CSA) tensors of selected nuclei in the solid state, chemical shifts in the liquid state, and molecular dynamics in the solid state. Dynamic NMR spectroscopy of DAB in solution revealed exchange between two different configurations, which raised the question, is there a correlation between the two different configurations found in solution and the two polymorphic modifications found in the solid state? By using this knowledge, a new crystallization protocol was devised which led to the growth of single crystals suitable for X‐ray diffraction. The X‐ray data showed that the same symmetric configuration is present in both polymorphic modifications, but the packing patterns in the crystals are different. In both cases hydrogen bonds lead to the formation of planes of DAB molecules. Additional symmetry elements, a two‐fold screw in the case of α‐DAB and a c‐glide plane in the case of β‐DAB, lead to a more symmetric (α‐DAB) or asymmetric (β‐DAB) intermolecular hydrogen‐bonding pattern for each molecule.     

Synthesis,spectroscopic characterization,X-ray structure and DFT calculations of five-coordinated chlorocopper(II) complex with bis(3,5-dimethylpyrazol-1-yl)methane

The reaction of copper dichloride dihydrate and bis(3,5-dimethylpyrazol-1-yl)methane affords [Cu{H₂C(3,5-Me₂pz)₂}₂Cl]Cl · 3H₂O. The compound has been studied by IR, UV–Vis spectroscopy and X-ray crystallography. The electronic structure of the [Cu{H₂C(3,5-Me₂pz)₂}₂Cl]⁺ cation has been calculated with the density functional theory (DFT) method. The spin-allowed doublet–doublet electronic transitions of [Cu{H₂C(3,5-Me₂pz)₂}₂Cl]⁺ have been calculated with the time-dependent DFT method, and the UV–Vis spectrum of the title compound has been discussed on this basis.     

X-ray and spectroscopic studies of the molecular structure of bis(8-oxy-1-methylquinolinium) hydroiodide

Bis(8-oxy-1-methylquinolinium) hydroiodide has been studied by X-ray diffraction, FT-IR, ¹H and ¹³C NMR spectroscopy. In the crystalline state a homoconjugated OH  O⁻ hydrogen bond is formed. As indicated by the X-ray data this hydrogen bond is very short (2.457 Å) and structurally symmetrical. The existence of this bond is manifested in the FT-IR spectra by an intense and broad band in the 1500–400 cm⁻¹ region. This type of absorption indicates that this hydrogen bond can be described by one very broad potential energy minimum in which the proton shows a large proton polarizability due to its fast fluctuations, i.e., it shows the so-called Zundel’s polarizability.     

X-ray diffraction, DFT theoretical, and IR polarized spectroscopic studies of the crystal-like E-mesophase of 4′-hexyloxy-isothiocyanatotolane (6OTOLT)

The dynamics of 6OTOLT molecules was analyzed based on IR absorption spectra and DFT calculations. Of particular interest was the mode ascribed to the ν_as(NCS) vibrations, the transition dipole moment of which is directed along the long axes of the molecules. Polarized IR spectra in the region of this mode allowed a characterization of the ordering of molecules in the analyzed phases. In a case of the smectic E phase, a random distribution of molecules aligned laterally in two-dimensional space between KRS-5 windows was found. The crystals of 6OTOLT were successfully grown and are characterized by an interesting Pc space group. The molecules are parallely arranged in layers and cross the adjoining ones underneath at an angle of 86.04°. The distance between the ring planes is 3.48 Å. The packing of molecules indicates a tendency to maintain short contacts between NCS groups and alkyl chains. The crystals grown do not correspond to the ordering of the smectic E phase and thus to the solid state obtained after cooling the smectic phase. Calculations of the interaction energy for three possible arrangements of dimeric species show a predominance of the core-to-core units. It was also shown that in this case an increase in ν_as(NCS) frequency should be expected, in good agreement with experimental data.     

X-ray diffraction,spectroscopic (IR,Raman) and DSC studies of bis(betainium) p-toluenesulfonate monohydrate crystal

Bis(betainium) p-toluenesulfonate monohydrate (abbreviated as BBTSH) was studied at various temperatures by X-ray diffraction, differential scanning calorimetry and vibrational spectroscopy methods. DSC curves of BBTSH show a peak at about 349 K which corresponds to water escape from the crystal, and reveal the “cold crystallization” phenomenon. BBTSH crystallizes in the P2₁/c space group of monoclinic system. After heating above 349 K the compound dehydrates, the crystal system changes to triclinic, the monocrystalline samples become non-merohedral twins. The BBTSH crystal comprises p-toluenesulfonic anions, monoprotonated betaine dimers and water molecules. Three kinds of hydrogen bonds are present in the crystal: strong, asymmetric and almost linear OH⋯O hydrogen bond (R(O⋯O) = 2.463(2) Å), weak O_wH⋯O hydrogen bonds (R(O_w⋯O) = 2.820(2) − 2.822(2) Å) and weak CH⋯O hydrogen bonds (R(C⋯O) = 3.295(2) − 3.416(2) Å). The ν_aOHO vibration of the strongest hydrogen bond in the crystal gives rise to an intense broad absorption with numbers of transmission windows in the low wavenumber region of the infrared spectra. Coupling between νCO stretching vibrations of two COO groups of the betaine dimer was detected. The process corresponding to the loss of water is accompanied by the breakage of strong OH⋯O hydrogen bonds in betaine dimers and rearrangement inside half of the betaine dimers. This rearrangement results in formation of the new betaine dimers with OH∙∙∙O hydrogen bond of similar strength as corresponding bond in the hydrated form (BBTSH).     

Study of hydrogen bonds in N-methylacetamide by DFT calculations of oxygen, nitrogen, and hydrogen solid-state NMR parameters

Solid-state nuclear magnetic resonance (NMR) parameters of ¹⁷O, ¹⁴N/¹⁵N, and ²H/¹H nuclei were evaluated in two available neutron crystalline structures of N-methylacetamide (NMA) at 250 and 276 K, NMA-I and NMA-II, respectively. Density functional theory calculations were performed by B3LYP method and 6-311++G** and IGLO-II type basis sets to calculate the electric field gradient (EFG) and chemical shielding (CS) tensors at the sites of mentioned nuclei. In order to investigate hydrogen bonds (HBs) effects on NMR tensors, calculations were performed on four-model systems of NMA: an optimized isolated gas-phase, crystalline monomers, crystalline dimers, and crystalline trimers. Comparing the calculated results reveal the influence of N–H···O=C and C–H···O=C HB types on the NMR tensors which are observable by the evaluated parameters including quadrupole coupling constant, C _Q, and isotropic CS, σ _iso. Furthermore, the results demonstrate more influence of HB on the EFG and CS tensors of NMA at 276 K rather than that of 250 K.     

Synthesis,spectroscopic characterization,X-ray structure and DFT calculations of rhenium(III) complex with 1-isoquinolinyl phenyl ketone

The [ReCl₃(MeCN)(PPh₃)] complex reacts with 1-isoquinolinyl phenyl ketone (N–O) to give [ReCl₃(N–O)(PPh₃)]. The compound has been studied by IR, UV–Vis spectroscopy, magnetic measurements and X-ray crystallography. The magnetic behavior is characteristic of mononuclear octahedral Re(III) complex with d⁴ low-spin (³T_1g ground state) and arises because of the large spin–orbit coupling, which gives diamagnetic ground state. The molecular orbital diagram of [ReCl₃(N–O)(PPh₃)] has been calculated with the density functional theory (DFT) method, and time-dependent DFT (TD-DFT) calculations have been employed in order to discussion of its spectroscopic properties in more detail.     

Theoretical study of the strong intramolecular hydrogen bond and metal-ligand interactions in group 10 (Ni, Pd, Pt) bis(dimethylglyoximato) complexes

The structural and bonding characteristics of the bis(dimethylglyoximato) complexes of group 10 transition metals ([M(dmg)₂], where M = Ni, Pd and Pt) were investigated by means of quantum chemical computations. The equilibrium geometries, energetic and bonding properties were computed using the B3P86 exchange-correlation density functional in conjunction with a 6-311+(+)G^∗∗ basis set. The computations revealed that the strong O⁻?H-O hydrogen bond exists only in the presence of the metal cations. The free (dmg)₂²⁻ ligand has significantly different geometry in which the O⁻?H-O interaction is replaced by N?O-H bonds. The characteristics of the metal-ligand interactions were determined by natural bond orbital analysis.