Barbara Morzyk-Ociepa

Revised molecular structure and vibrational spectra of tetraaqua(orotato)nickel(II) monohydrate: band assignment based on density functional calculations

Abstract The crystal and molecular structure and vibrational spectra of [Ni(orotato)(H2O)4]·H2O have been reinvestigated. Single crystal X-ray diffraction studies have revealed new structural features. It is shown that two uracilate rings from the orotate ligands are linked through the pair of N3–H3⋯O2 (−x+1, −y, −z+1) hydrogen bonds which lead to the formation of centrosymmetric dimer of the title complex in the crystal unit cell. The nickel atom is bound to the deprotonated N1 pyrimidine atom and to the carboxylate oxygen atom of the orotate ligand, and to four water molecules. The lattice water molecule is involved in hydrogen bond to the coordinated water molecule, and not to the N3H group, as previously reported. The Raman and infrared spectra (4000–50xa0cm−1) of the title complex are presented, for the first time. The theoretical frequencies, infrared intensities and Raman scattering activities have been calculated by the second-order Moller–Plesset and density functional (B3LYP) methods with the LanL2DZ and D95V∗∗/LanL2DZ basis sets, respectively. The B3LYP-predicted infrared and Raman spectra show a very good agreement with experiment. Detailed band assignment has been made on the basis of the calculated potential energy distribution (PED). The results provide new information on the strength of nickel–ligand bonding in this complex. The Ni–N1(pyrimidine) stretching vibration is assigned to the strong Raman band at 256xa0cm−1, and the Ni–O(carboxylate) stretching vibration is assigned at 357xa0cm−1. It is demonstrated that B3LYP method is extremely helpful in the reliable assignment of vibrational spectra of the Ni(II) complex with orotic acid.

Vibrational spectra of 1-methyluracilate complex with silver(I) and theoretical studies of the 1-MeU anion.

The FT-Raman and FT-infrared spectra of (1-methyluracilato)silver, [Ag(C(5)H(5)N(2)O(2))] in the solid state have been studied. The complex is a polymer in which one silver ion is linearly bonded to two 1-MeU ligands through the deprotonated N(3) sites and another silver ion is tetrahedrally coordinated to the four 1-MeU ligands through the O2 and O4 carbonyl oxygen atoms. The harmonic vibrational frequencies, infrared intensities and Raman scattering activities of the N(3)-deprotonated 1-methyluracilate anion have been calculated using density functional (B3LYP) and ab initio (HF and MP2) methods with the 6-31G(d,p) and 6-31++G(df,pd) basis sets. The calculated potential energy distribution (PED) for the 1-MeU anion has proved to be of great help in assigning the spectra of the title complex. It can be concluded that the two strong Raman bands at 1263 and 796 cm(-1) are diagnostic for the N3-deprotonation of the 1-methyluracilate ring and complexation with silver ion. The linear N-Ag-N stretching vibrations are assigned to the bands at 448 and 362 cm(-1) (IR) and 453, 362 cm(-1) (Raman). The Ag-O stretching vibrations are assigned to the bands in the range of 280-250 cm(-1).

FT-Raman and infrared spectra of silver(I) complexes with glutarimidate and 3,3-dimethylglutarimidate anions

Abstract FT-Raman and FT-IR spectra are reported for glutarimidato-Ag(I) and 3,3-dimethyl-glutarimidato-Ag(I) complexes, which show very close structural similarity to the corresponding Ag(I) complexes with pyrimidine nucleobases. The spectra indicate that in both complexes the deprotonated nitrogen atom and two oxygen atoms of the glutarimide ring are involved in binding with silver atoms. Vibrational assignment is supported by normal coordinate analysis based on a general valence force field. The linear Nue5f8Ague5f8N stretching vibrations are assigned to the bands at 479 cm−1 (infrared) and 485 cm−1 (Raman). The silver–oxygen stretching vibrations are assigned to the bands in the range 253–206 cm−1.

Vibrational spectra of 1-methylthyminate complexes with mercury(II) and potassium and ab initio calculations of the 1-MeT anion

Abstract The FT-Raman and FT-infrared spectra of bis(1-methylthyminato)mercury(II), Hg(1-MeT) 2 , and potassium 1-methylthyminate, K(1-MeT), are reported. The molecular structure, harmonic vibrational frequencies, infrared intensities and Raman scattering activities of the N 3 -deprotonated 1-MeT anion have been calculated at the HF/6-31++G ∗∗ and MP2/D95V ∗∗ levels of theory. A rigorous normal coordinate analysis of the 1-MeT anion has been made. The ab initio predicted frequencies and intensity patterns of the IR and Raman bands as well as the calculated potential energy distribution (PED) have proved to be of great help in assigning the spectra of the title compounds. It is concluded that the potassium cation binds to the oxygen atom of the N 3 -deprotonated ligand in K(1-MeT). It also follows that the exocyclic C O bonds in the N 3 -coordinated mercury(II) complex, Hg(1-MeT) 2 , are more ionic than those in the neutral 1-methylthymine.

Vibrational spectroscopic studies of indolecarboxylic acids and their metal complexes: Part VIII. 5-Methoxyindole-2-carboxylic acid and its Zn(II) complex

The complex of 5-methoxyindole-2-carboxylic acid with Zn(II) has been synthesized and characterized by the infrared and Raman spectroscopic methods. Moreover, the infrared and Raman spectra of 5-methoxyindole-2-carboxylic acid (5-MeOI2CAH) and the infrared spectrum of deuterated derivative of 5-metoxyindole-2-carboxylic acid (5-MeOI2CA-d2) are recorded in the solid phase. The theoretical wavenumbers, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-311++G(df,p) basis set for 5-MeOI2CAH and 5-MeOI2CA-d2 and with the 6-311++G(df,p)/LanL2DZ basis sets for the theoretical model of [Zn(5-MeOI2CA)(2)(H(2)O)(2)](n). The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution for 5-MeOI2CAH, 5-MeOI2CA-d2 and [Zn(5-MeOI2CA)(2)(H(2)O)(2)](n). The results from natural bond orbitals (NBO) analyses for indole-2-carboxylic acid (I2CAH) and 5-MeOI2CAH are discussed.

X-ray crystal structure, vibrational spectra and DFT calculations of 3-chloro-7-azaindole: A case of dual N-H N hydrogen bonds in dimers

3-Chloro-7-azaindole (3Cl7AI) is the carrier ligand in a new anticancer platinum(II) agent cis-[PtCl2(3Cl7AI)2]. In this work 3Cl7AI has been studied by a single crystal X-ray diffraction, infrared and Raman spectroscopy and density functional calculations. The compound crystallizes in the monoclinic system, space group P21/n, with a=12.3438(3), b=3.85964(11), c=14.4698(4)Å, β=100.739(2)°, V=677.31(3)Å(3) and Z=4. In the crystal, a pair of 3Cl7AI molecules forms a centrosymmetric dimer linked by the moderately strong dual N-H⋯N hydrogen bonds. The nitrogen atom in the pyrrole ring acts as the proton donor, while the nitrogen atom in the pyridine ring is the proton acceptor. The FT-IR and FT-Raman spectra (3500-60 cm(-1)) have been recorded. The theoretical studies on the molecular structures and vibrational spectra of the monomeric and dimeric forms of 3Cl7AI and its N-deuterated derivative were performed using the B3LYP method with 6-311++G(d,p) basis set. The theoretically predicted Raman spectrum for the dimer shows very good agreement with experiment. Detailed vibrational assignments for the two isotopomers have been made on the basis of the calculated potential energy distributions (PEDs). The dual N-H⋯N hydrogen bonds in 3Cl7AI dimer are characterized by a very broad and complicated structure of the absorption band between 3300 and 2500 cm(-1), which is caused by multiple Fermi resonances between the N-H stretching vibration and various combinations bands.