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.     

Crystal and molecular structure, hydrogen bond and electrostatic interactions of bis(1-methylisonicotinate)hydrogen perchlorate studied by X-ray diffraction, DFT calculations, FT-IR, Raman and NMR spectroscopes

The crystal structure of bis(1-methylisonicotinate)hydrogen perchlorate, (MIN)₂H·ClO₄, has been studied by X-ray diffraction, DFT calculations, FT-IR, Raman, ¹H and ¹³C NMR spectra. The crystals are monoclinic, space group P2₁/n, with a pair of MIN molecules bridged by a short asymmetrical O·H·O hydrogen bond of 2.461(5) Å. The COO groups are twisted by 80.55° with respect to the plane of the pyridine ring. The anion interacts electrostatically with the positively charged nitrogen atoms of the neighbouring MIN molecules. The most stable conformer of isolated (MIN)₂H·ClO₄ and two homoconjugated cations, (MIN)₂H, have been analyzed by the B3LYP/6-31G(d,p) calculations in order to determine the influence of the anion on the hydrogen bonds in MIN·H·MIN unit. The FT-IR spectrum of the (MIN)₂H·ClO₄ shows a broad and intense absorption in the 1500–400 cm⁻¹ region, typical of short hydrogen bonds. The isotopic ratio, νOHO/νODO, is close to unity, indicating that the hydrogen bond is acentric (pseudo-type A).     

Copper(II), nickel(II) and cobalt(II) complexes of 4-cyanobenzonic acid: syntheses, crystal structures and spectral properties

Three new metal complexes, Cu(4-Hcba)₂(4-cba)₂(Py)₂ (4-Hcba=4-cyanobenzoic acid) 1 and M[H(4-cba)₂]₂(Py)₂ (M=Ni 2, Co 3), have been prepared by the treatment of 4-Hcba with the respective metal nitrate M(NO₃)₂ (M=Cu, Ni, Co) in the presence of pyridine (Py). Single-crystal X-ray diffraction analyses (3 is isostructural to 2) show that the obtained complexes are of isolated mononuclear and the metal atoms have distorted octahedral coordination environment. Two different types of intramolecular hydrogen bonds exist: asymmetrical O–HO for 1 and symmetrical OHO for 2 and 3. The crystal packing between the molecular complexes is controlled mainly by T-shaped C–Hπ interactions between pyridine and phenyl rings. Preliminary discussions on IR, UV–VIS and fluorescent spectra have also been carried out.     

Syntheses,crystal structures,and IR spectra of isonicotinamide-isonicotinamidium bis(isonicotinamide)-tetrakis(isothiocyanato)ferrate(III) and isonicotinamidium chloride

Reaction of iron(III) thiocyanate with isonicotinamide (inia) in ethanol leads to formation of a dark red, air stabile crystalline iron(III) compound of composition [iniaH·inia][Fe(inia)₂(NCS-N)₄]. Single-crystal X-ray diffraction analysis shows the triclinic P–1 space group with unit cell parameters: a?=?8.2440(4)?Å, b?=?9.5540(3)?Å, c?=?11.2590(5)?Å, α?=?93.945(4)°, β?=?95.554(4)°, γ?=?96.285(3)°, and Z?=?1. The iron compound contains [iniaH·inia]⁺ cations and [Fe(inia)₂(NCS-N)₄]^– anions, which are held together by ionic interactions and hydrogen bonding. The Fe(III) is octahedrally coordinated by six nitrogens, four from NCS^– in the equatorial plane and two from inia occupying axial positions. The [iniaH]Cl has been formed by reaction of inia with hydrochloric acid. [iniaH]Cl crystallized in the monoclinic C2/c space group with unit cell parameters: a?=?25.156(5)?Å, b?=?5.095(1)?Å, c?=?12.747(3)?Å, and Z?=?8. Both compounds have also been characterized by elemental analyses and infrared spectroscopy. Structural and infrared spectral data are compared with data of similar compounds in the literature.     

Electronic structure and vibrational spectra of cis-diammine(orotato)platinum(II), a potential cisplatin analogue: DFT and experimental study

Orotic acid (vitamin B₁₃) is a key intermediate in biosynthesis of the pyrimidine nucleotides in living organisms, moreover, it may serve as the biological carrier for some metal ions. cis-Diammine(orotato)platinum(II), cis-[Pt(C₅H₂N₂O₄)(NH₃)₂] can be considered as a new potential cisplatin analogue. The FT-Raman and FT-IR spectra of the title complex are reported, for the first time. The molecular structure, vibrational frequencies, and the theoretical infrared and Raman intensities have been calculated by the density functional mPW1PW91 method. The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution. The theoretically predicted IR and Raman spectra show very good agreement with experiment. Natural bond orbital (NBO) analyses were performed for cisplatin, carboplatin and the title complex. The results provided new data on the nature of platinum–ligand bonding in these compounds. Strong intramolecular hydrogen bond between the orotate ligand and the coordinated ammonia group stabilizes the structure of the platinum(II) complex. Thus, it is suggested that the orotate ligand in the title complex is more inert to the substitution reactions than the chloride ligands in cisplatin.     

Unusual co-ordination behaviour of imidazole-4-acetic acid. Synthesis, crystal structure and vibrational studies of one-dimensional co-ordination polymer of zinc(II) with two different ligand forms

This work is devoted to structural and vibrational studies of novel 1D polymeric zinc(II) complex [ZnCl(ia)(Hia)]·H₂O (infinity) [Hia=imidazole-4-acetic acid]. It has been found for the first time that the ia anion is acting as bidentate bridging ligand with N1 and carboxylate oxygen atoms as binding centres. The quasi-tetrahedral coordination polyhedron is completed by one chloride anion and monodentate Hia ligand bonded with zinc(II) cation via carboxylate oxygen atom. The compound crystallise in the triclinic P space group with Z=2. The polymer chains are held together by hydrogen bonding network involving the N---H and carboxylate groups, chloride ions and water molecules. The differences between normal vibrations of two ligand forms present in the complex are discussed on the basis of the density functional calculations (DFT) performed for natural and N-deuterated isotopomers. The assignment of the observed MIR and Raman bands is given in terms of potential energy distribution (PED).     

Three Ag(I) and Cu(II) complexes of 4-pyridin-4-yl-(1,3) dithiol-2-one

Single crystals of Ag(I) and Cu(II) complexes with 4-pyridin-4-yl-(1,3) dithiol-2-one (PYDO), [Ag(PYDO)₂]ClO₄, [Ag(PYDO)₂(NO₃)], and [Cu(PYDO)₂(NO₃)₂] have been prepared and characterized. PYDO displays excellent coordination to Cu(II) and Ag(I). The 1,3-dithiol five-member ring is an electron donor that enhances the coordination ability of the py group. HOMO-1 σ coordination and d–π electron back-donating from metal to ligand (LUMO) are suggested based on the calculation. Weak interactions and secondary bonds from the anion to cation play an important role in the molecular assembly.     

Characterization and crystal structures of copper(II), cobalt(II), and nickel(II) complexes with two kinds of piperidine carboxylic acids

Copper(II) complex with -piperidine-3-carboxylic acid ( -Hpipe-3):[Cu( -pipe-3)₂(H₂O)] and cobalt(II) and nickel(II) complexes with piperidine-4-carboxylic acid (Hpipe-4):[M(Hpipe-4)₂(H₂O)₄]Cl₂ (M: Co, Ni) have been prepared and characterized by means of IR and powder diffuse reflection spectra, thermal analysis, and magnetic susceptibility. The crystal structures of these complexes have been determined by X-ray diffraction. The crystal of [Cu( -pipe-3)₂(H₂O)] is orthorhombic with the space group Pbcn. The copper atom is in a square pyramidal geometry, ligated by two carboxylato oxygen atoms, two nitrogen atoms, and a water molecule. One molecule of this complex consists of either -piperidine-3-carboxylic acid or -piperidine-3-carboxylic acid. The crystals of [M(Hpipe-4)₂(H₂O)₄]Cl₂ are monoclinic with space group P2₁/n. In these complexes the metal atom is in an octahedral geometry ligated by two carboxylato oxygen atoms and four water molecules.     

Electronic spectra of Cu(II) crystal complexes with S-methylthiosemicarbazones

Electronic spectra for a series of coordination compounds of copper(II) with tridentant ligands of salicyl aldehyde S-methylthiosemicarbazone and 8-quinoline aldehyde S-methylthiosemicarbazone were investigated. Coordinations of central ions were determined on the basis of X-ray data and IR spectra. Electronic transitions were detected by processing the diffusion-reflection spectra according to theKubelka-Munk theory. Identifications proved the presence of bands corresponding to intraligand transition, charge transfer spectra and the transition of d-d type which are the result of the elimination of d-orbital degeneration for Cu(II) ions in the crystal field. The effect of the symmetry of coordination polyhedrons is discussed.

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Elektronenspektren von Cu(II) Kristall-Komplexen mit S-Methylthiosemicarbazonen

Zusammenfassung Es wurden Elektronenspektren einer Serie von Koordinationsverbindungen des Kupfer(II) mit tridentaten Liganden (Salizylaldehyd-S-methylthiosemicarbazon und 8-Chinolinylaldehyd-S-methylthiosemicarbazon) untersucht. Die Zentralionkoordination wurde durch Röntgenstrahlenuntersuchungen und auf Grund der IR-Spektren festgestellt. Die Elektronenübergänge wurden nach derKubelka-Munk-Theorie aus den diffusen Reflexionsspektren ermittelt. Die Banden wurden den Intraligandübergängen, dem charge-transfer-Spektrum und den d-d-Typ-Übergängen, die als Resultat der Entartungsbeseitigung der Cu(II)-d-Orbitale im Kristallfeld verschiedener Symmetrie entstehen, zugeschrieben.

     

Experimental and theoretical studies on vibrational spectra of 4-(2-furanylmethyleneamino)antipyrine, 4-benzylideneaminoantipyrine and 4-cinnamilideneaminoantipyrine

This work deals with the IR and Raman spectroscopy of 4-(2-furanylmethyleneamino) antipyrine (FAP), 4-benzylideneaminoantipyrine (BAP) and 4-cinnamilideneaminoantipyrine (CAP) by means of experimental and quantum chemical calculations. The equilibrium geometries, harmonic frequencies, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-31G(d) basis set. The comparisons between the calculated and experimental results covering molecular structures, assignments of fundamental vibrational modes and thermodynamic properties were investigated. The optimized molecular geometries have been compared with the experimental data obtained from XRD data, which indicates that the theoretical results agree well with the corresponding experimental values. For the three compounds, comparisons and assignments of the vibrational frequencies indicate that the calculated frequencies are close to the experimental data, and the IR spectra are comparable with some slight differences, whereas the Raman spectra are different clearly and the strongest Raman scattering actives are relative tightly to the molecular conjugative moieties linked through their Schiff base imines. The thermodynamic properties (heat capacities, entropies and enthalpy changes) and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized strucutres.     

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).     

Analysis of vibrational spectra of 2 and 3-methylpiperidine based on density functional theory calculations

The experimental and theoretical vibrational spectra of 2 and 3-methylpiperidine (abbreviated as 2-MP and 3-MP) were studied. The FT-Infrared spectra of 2-MP and 3-MP molecules were recorded in the liquid phase. The structural and spectroscopic analysis of the title molecules were made by using density functional harmonic calculations. For the title molecules, only one form was found most stable structure by using B3LYP level with the 6-311G (d,p) basis set. Selected experimental bands were assigned and characterized based on the scaled theoretical wave numbers by their total energy distribution (TED).     

Synthesis and crystal structure of two novel nickel (imidazole) complexes having hydrogen-bonded networks

Two nickel (imidazole) complexes, Ni(im)₆Cl₂·4H₂O (1) and Ni(im)₆(NO₃)₂ (2) (im=imidazole) have been synthesized and characterized by elemental analysis, IR, UV, TG and single crystal X-ray diffraction. 1 crystallizes in the triclinic space group P-1 with a=8.800(6) Å, b=9.081(6) Å, c=10.565(7) Å, =75.058(9)°, β=83.143(8)°, γ=61.722(8)°, V=718.3(8) Å³, Z=1 and R₁ (wR₂)=0.0469 (0.1497). 2 crystallizes in the trigonal space group R-3 with a=12.370(6) Å, b=12.370(6) Å, c=14.782(14) Å, =90.00°, β=90.00°, γ=120.00°, V=1959(2) Å³, Z=3 and R₁ (wR₂)=0.0358 (0.0955). 1 and 2 exhibit different supramolecular network due to their different counter anions and different hydrogen bonding connection. In compound 1, [Ni(im)₆]²⁺ cation and counter anions Cl⁻ alternatively array in an ABAB fashion via N–HCl hydrogen bonding. In compound 2, the plane of each NO₃²⁻ is almost parallel and each NO₃²⁻ connect three different [Ni(im)₆]²⁺ cations via N–HO hydrogen bonding.     

Synthesis and study of trinuclear Pd(II) and Pt(II) complexes with 2-mercaptonicotinic acid: Crystal and molecular structure of [Pd3(mercaptonicotinic acid)3Cl3]

Pd(II) and Pt(II) complexes of 2-mercaptonicotinic acid of formulae [M₃(mercaptonicotinic acid)₃Cl₃] were synthesized and characterized by the usual spectroscopic techniques including mass spectrometry. The crystal structure was obtained for the palladium complex. The molecule has a ternary symmetry, and mercaptonicotinic acid coordinates in a bidentate (N,S) mode to each palladium ion. The sulfur atom acts as a bridge between two palladium atoms. The fourth coordination site in the plane square geometry of the Pd(II) is occupied by a chloride ion. Identical molecular structure is proposed for the platinum compound in agreement with the spectroscopic and theoretical results.     

Structure and vibrational spectra of the bis(betaine)-selenic acid molecular crystal

The crystal structure of bis(betaine)-selenic acid has been determined by X-ray diffraction as orthorhombic, space group Pbca, with a = 11.591(2), b = 22.930(5), c = 12.045(2) Å and Z = 8. The crystal comprises hydrogen selenate ions, HSeO⁻₄, and two distinct betaine molecules, which are held together into a complex by short hydrogen bonds. One of the betaine molecules is present as the zwitterion form (CH₃)₃N⁺---CH₂---COO⁻ and the second occurs as the protonated form (CH₃)₃N⁺---CH₂---COOH. Powder FTIR and Raman spectra were measured. An assignment of the observed bands to vibrations of the hydrogen bonds and internal vibrations of the hydrogen selenate ion and the betaine molecules is proposed.     

Vibrational spectra of mixed (phthalocyaninato)(porphyrinato) yttrium(III) double-decker complexes: Density functional theory calculations

The vibrational (IR and Raman) spectra of neutral and reduced mixed (phthalocyaninato)(porphyrinato) yttrium(III) double-decker complexes Y(Pc)(Por) and [Y(Pc)(Por)]⁻ [the simplified models of mixed (phthalocyaninato)(porphyrinato) rare earth(III) complexes] are studied using density functional theory (DFT) calculations. The simulated IR and Raman spectra of Y(Pc)(Por) are compared with the experimental IR spectrum of Tb(Pc)(TClPP) and Raman spectrum of Y(Pc)(TClPP), respectively, and many bands can acceptably fit in spite of the different species. On the basis of comparison with the simulated spectra of PbPc and PbPor together with the assistance of normal coordinate analysis, the calculated frequencies in their IR and Raman spectra are identified in terms of the vibrational mode of different ligand for the first time. The calculated frequency at 1048 cm⁻¹ in the IR spectrum of [Y(Pc)(Por)]⁻ with contribution from both Pc and Por vibrational modes is the characteristic IR vibrational mode of the reduced double-decker, while the characteristic IR vibrational mode of Y(Pc)(Por) attributed from the vibration of phthalocyanine monoanion radical Pc⁻ appears at 1257 cm⁻¹. In line with our previous experimental findings that the Raman spectra of M(Pc)(TPP) and M(Pc)(TClPP) are dominated by the Pc vibrational modes, theoretical calculations indicate that most of the Raman vibrational modes contributed from Por ring are covered up by those of Pc ring and thus are hard to be recognized in the Raman spectra of [Y(Pc)(Por)]⁻ and Y(Pc)(Por) due to their much weaker intensity in comparison with that of Pc ligand. Comparison in the IR and Raman spectra between [Y(Pc)(Por)]⁻ and Y(Pc)(Por) also suggests the localization of hole on the Pc ring in the neutral double-decker Y(Pc)(Por). The present work, representing the first detailed DFT study on the vibrational spectra of mixed (phthalocyaninato)(porphyrinato) rare earth(III) double-decker complexes, is useful in helping to understand the vibrational spectroscopic properties of this series of mixed tetrapyrrole ring complexes.     

Synthesis,crystal structure and magnetism of 1D cobalt(II) coordination polymer with thiocyanate as bridging ligand

A one-dimensional coordination polymer [Co(μ _1,3-NCS)₂(npdo)₂] _n (npdo?=?4-nitropyridine N-oxide) has been synthesized and structurally determined by X-ray crystallography. The complex crystallizes in the orthorhombic space group of Pbcn with a?=?22.688(5)?Å, b?=?7.2636(17)?Å, c?=?10.299(2)?Å. Adjacent Co(II) ions are coordinated by two μ _1,3-SCN^? bridging ligands, forming a one-dimensional chain along the c axis and the npdo coordinates to Co(II) ion as a terminal ligand. The thermal variation of the magnetic moments of the complex reflects the antiferromagnetic interaction between the bridged Co(II) ions above 20?K and the ferromagnetic transition or the strong short-range spin interaction below 20?K.     

Synthesis and crystal structure of bis(m-hydroxybenzoato(1-))bis(benzimidazole) copper(II) dihydrate

The crystal structure of the title complex was determined by single-crystal X-ray diffraction methods. The unit cell contains two independent molecules, A and B. B is a mononuclear Cu(II) complex with square-planar coordination geometry formed by two benzimidazole molecules and two hydroxylbenzoate anions. A is a dimer of B, formed by bridging hydroxybenzoate, and copper assumes square-pyramidal geometry. Aromatic π–π stacking is observed between parallel benzimidazole rings of neighboring A molecules. IR spectra of the compound are assigned in line with the crystal structure.