Małgorzata Ratajczak-Sitarz

Stereochemistry and transformations of NH:N hydrogen bonds Part II. Proton stability in the monosalts of 1,4-diazabicyclo[2.2.2]octane

Abstract Crystal structures of three monosalts of 1,4-diazabicyclo[2.2.2]octane, perchlorate, tetrafluoroborate and bromide, have been studied by X-ray diffraction. The orthorhombic perchlorate and tetrafluoroborate salts are isostructural, while the bromide salt crystallizes in the hexagonal system. Varying stabilities of the acidic proton in the NH:N hydrogen bonds, linking the cations into chains, have been observed: in the perchlorate salt the H-atom is ordered, in the tetrafluoroborate it is 0.75:0.25 disordered at two N-sites, and in the hydrobromide the H-atom is 50:50 disordered between the symmetry-related sites. Possible mechanisms leading to the disorder of the protons and their stabilizing factors are discussed.

Crystal structure of Schiff base derivative of gossypol with 3,6,9-trioxa-decylamine

Abstract Crystals of the Schiff base derivative of gossypol with 3,6,9-trioxa-decylamine were examined using X-ray diffraction, FT-IR and CPMAS spectroscopy. The Schiff base crystallizes as a racemate in the space group C2/c with a =24.390(5), b =12.026(2), c =14.810(3) A, β =102.78(3)°, and Z =4. The results of the FT-IR, and CPMAS study of the crystals are in agreement with the X-ray data. The FT-IR spectrum of the crystals shows that the OH groups at position 1,1′ and 6,6′ as well as the N 16 –H proton are involved in weak intermolecular and intramolecular hydrogen bonds, respectively. The FTIR and CP-MAS spectral behaviour is in agreement with the crystallographic results demonstrating the existence of the enamine-enamine tautomeric form of the Schiff base studied.

Synthesis, crystal structures and antibacterial activity studies of aza-derivatives of phytoalexin from cotton plant - gossypol.

Using Gossypol (GOS) extracted from cotton seeds, a series of its Schiff bases (1-18) and hydrazones (19-27) have been synthesized and evaluated for their antimicrobial activities against Gram-positive bacteria, Gram-negative bacteria and yeast-like organisms. Of the 27 aza-derivatives of gossypol, 11 have been found active against the microorganisms tested, similar to gossypol. Crystal structures of the new Schiff base (compound 7) and hydrazone (compound 25) of gossypol reveal the presence of two different tautomers within two types of the aza-derivatives studied. The newly synthesized aza-derivatives of gossypol are characterized by the FT-IR, NMR and MS methods.

Reinvestigation of the structure of monensin A phenylurethane sodium salt based on X-ray crystallographic and spectroscopic studies, and its activity against hospital strains of methicillin-resistant S. epidermidis and S. aureus

Monensin A phenylurethane sodium salt (MON-UR1-Na) crystals were studied by the X-ray, NMR, FT-IR and PM5 semi-empirical methods. The X-ray data show that the compound forms a pseudocyclic structure, stabilized by three intramolecular hydrogen bonds, and the sodium cation coordinated by five oxygen atoms in the hydrophilic sphere. The NMR and FT-IR data demonstrate that this pseudocyclic structure is also conserved in CH2Cl2 solution. This structure of MON-UR1-Na is significantly different than the ones previously proposed by Westley et al. and Tanaka et al. The semi-empirical calculations of the MON-UR1-Na structures indicate that the one of the crystal is the most energetically favorable one. Other parameters, such as the size, chemical and biological nature of the urethane substituent, and especially the free carbonyl urethane group, may have a role in the biological activity of MON-UR1-Na. The in vitro microbiological tests provide evidence that MON-UR1-Na shows higher antibacterial activity against human pathogenic bacteria, including antibiotic-resistant Staphylococcus aureus and Staphylococcus epidermidis than the parent unmodified antibiotic—Monensin A.

Molecular structure of a complex formed between hydrobromide of 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene and 5,5'-dibromo-2,2'-biphenol in crystal and solutions

Abstract A complex of 5,5′-dibromo-2,2′-biphenol with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene hydrobromide has been studied using X-ray diffraction, FT-IR, and 1 H NMR spectroscopy. In the crystal structure, a bromide anion is hydrogen-bonded with MTBDH + cation and two hydroxyl groups of two 5,5′-dibromo-2,2′-biphenol molecules. In the solid state, the Br − anion is an acceptor in N + –H⋯Br − , and two O–H⋯Br − intermolecular hydrogen bonds. In chloroform and acetonitrile, the structure of the complex assumes a new structure due to almost complete dissociation of protonated MTBD molecule. In chloroform, the MTBDH + cation is hydrogen-bonded with 5,5′-dibromo-2,2′-biphenol whereas in acetonitrile it is free and solvated by the solvent. In both cases, the 5,5′-dibromo-2,2′-biphenol molecule is hydrogen-bonded to the bromide anion.

Shape of the proton potential in an intramolecular hydrogen-bonded system. Part II

Abstract 5,5′-dibromo-3-diethylaminomethyl-2,2′-biphenol N-oxide was studied by IR and NMR spectroscopy in chloroform and acetonitrile solutions. Two intramolecular hydrogen bonds are present in these molecules. The NO⋯H + ⋯O − bond formed between the OH and the N-oxide groups is very strong. The proton potential is flat and broad and has probably no barrier. This hydrogen bond shows only slight proton polarizability. The other hydrogen bond formed between two hydroxyl groups OH⋯O − ⇌ − O⋯HO is weaker and show large proton polarizability. The proton motions in both hydrogen bonds are not coupled and therefore these hydrogen bonds are not cooperative.

MOLECULAR AND CRYSTAL STRUCTURES OF DITHIOSUCCINIMIDE AND 2,2,3,3-TETRAMETHYLDITHIOSUCCINIMIDE

Abstract The crystal structures of dithiosuccinimide ( 1 ) and 2,2,3,3-tetramethyldithiosuccinimide ( 2 ) have been determined by X-ray diffraction. The molecules of 1 are located on mirror planes and are planar, while the molecules of the tetramethyl derivative lie in general positions and their five-membered rings are distorted towards a twist conformation. In the crystalline state the molecules of both compounds are similarly linked by pairs of NH···S hydrogen bonds into C i -symmetric dimers. The molecular geometries have been calculated by several semiempirical methods, of which MNDO gave the most reliable dimensions.

Structure and conformation of 2,3-diethoxycarbonyl-1-methylpyridinium iodide studied by NMR, FTIR, Raman, X-ray diffraction and DFT methods.

Computational and spectroscopic properties of 2,3-diethoxycarbonyl-1-methylpyridinium iodide, 1, were studied. The crystal structure of 1 was analyzed by X-ray diffraction. Molecular geometry of title compound has been calculated using the density functional theory (DFT) at B3LYP/6-311G(d,p) level of theory and was compared with the experimental data. Iodide anion interacts electrostatically with the positively charged pyridinium nitrogen atom and via weak CH⋯I(-) hydrogen bonds. In crystals the N-methyl and ethoxycarbonyl groups are disordered in two orientations. The structures of 2 (in vacuum), 3 (in CHCl3) and 4 (in DMSO) optimized by the B3LYP/6-311G(d,p) approach are different than that in crystal 1. The experimental (13)C and (1)H chemical shifts (δexp) of the investigated ester in CDCl3 and DMSO-d6 correlate linearly with GIAO/B3LYP/6-311G(d,p) magnetic isotropic shielding constants calculated according to the screening solvation model (COSMO), δexp=a+b σcalc. The FTIR and Raman spectra of the solid compound are consisted with the X-ray structure.

Crystal structure and physical properties of 1-methyl-3-(carboxymethyl)benzimidazolium betaine·CuBr2 in crystal and water solution

A new Cu(II) carboxylate coordinating compound [1-methyl-3-carboxymethyl benzimidazolium betaine]2CuBr2 was synthesized and crystallized. The crystal has the triclinic symmetry P, with unit cell dimensions a = 7.9693, b = 8.4129, c = 9.1302 A, α = 68.058, β = 85.402 and γ = 71.258 deg. (Z = 1), and molecules stacked along the a-axis. Cu(II)-complexes are planar and four-coordinated with chromophore CuO2Br2, where two oxygen atoms belong to the carboxylate groups of two betaines acting as unidentate ligands. The compound was characterized by two-dimensional 1H and 13C NMR spectroscopy for the determination of the correlation between protons of a ligand molecule. NMR spectra confirm the coordination of Cu(II) ions and allow identification of H(2) proton as easily detached in basic conditions. FT-IR spectra confirm the unidentate coordination of the betaine carboxylate group. UV-Vis spectra show three bands in d–d-transition region. Energies of these transitions were used in the interpretation of the EPR results. From powder and single crystal EPR measurements the g-factors were determined as gx = 2.072, gy = 2.030, gz = 2.241. A non-typical g-factor sequence is a consequence of the orbital mixing in the ground state of Cu(II) complex of D2h symmetry. The g-factors were interpreted in terms of the Molecular Orbital (MO) theory which delivered the Cu(II) unpaired electron density delocalization onto the ligand molecules. A strong delocalization on betaine molecules via in-plane ground-state orbital was found and unexpectedly also via out-of plane orbital directed towards the non-coordinating oxygen of the betaine carboxylate group.

Spectroscopic and structural investigation of 2,5-dicarboxy-1-methylpyridinium inner salt.

The structure of 2,5-dicarboxy-1-methylpyridinium inner salt (1), has been studied by X-ray diffraction, B3LYP/6-311G(d,p) calculations, FTIR, Raman and NMR spectroscopy. The molecules are linked by short intermolecular and asymmetric O-H⋯O hydrogen bonds of 2.486(2)Å between carboxyl and carboxylate groups of neighboring molecules into infinite chains. The hydrogen bonds in the molecules optimized by the B3LYP/6-311G(d,p) approach in trimer (2) and dimer (3) are slightly longer than in the crystal. The FTIR spectrum of the investigated inner salt is dominated by a broad and intense absorption in the 1500-800 cm(-1) region attributed to the ν(as)(OHO) and γ(OHO) vibrations of the strong hydrogen bond. In the Raman spectrum the broad absorption is absent. Linear correlations, δ(exp)=a+b σ(calc) between the experimental (1)H and (13)C NMR chemical shifts (δ(exp)) of the investigated inner salt in D2O and the calculated magnetic isotropic shielding constants (σ(calc)) for the optimized monomer (4a) solvated in water are reported. The pKa value for 1 of 2.31±0.02 was determined by the potentiometric titration.