Complex Formation Equilibria of Unusual Seven Coordinate Fe(III) Complexes with DNA Constituents

Seven-coordinate Fe(III) complexes [Fe(dapsox)(H₂O)₂]⁺, where [dapsox = 2,6-diacetylpyridine-bis(semioxamazide)] is an equatorial pentadentate ligand with five donor atoms (2O and 3N), were studied with regard to their acid–base properties and complex formation equilibria. Stability constants of the complexes and the pK _a values of the ligands were measured by potentiometric titration. The interaction of [Fe(dapsox)(H₂O)₂]⁺ with the DNA constituents, imidazole and methylamine·HCl were investigated at 25 °C and ionic strength 0.1 mol·dm^?3 NaNO₃. The hydrolysis constants of the [Fe(dapsox)(H₂O)₂]⁺ cation (pK _a1 = 5.94 and pK _a2 = 9.04), the induced ionization of the amide bond and the formation constants of the complexes formed in solution were calculated using the nonlinear least-squares program MINIQUAD-75. The stoichiometry and stability constants for the complexes formed are reported. The results show the formation of 1:1 and 1:2 complexes with DNA constituents supporting the hepta-coordination mode of Fe(III). The concentration distributions of the various complex species were evaluated as a function of pH. The thermodynamic parameters ΔH° and ΔS° calculated from the temperature dependence of the equilibrium constants were investigated for interaction of [Fe(dapsox)(H₂O)₂] with uridine.     

Infrared spectrometric study of the interaction between 2-dimethylamino-3,3-dimethyl-1 azirine and some phenol derivatives

The H-bonded complexes between 2-dimethylamino-3,3-dimethyl-1-azirine (TMAAZ) and some phenol derivatives have been studied by IR spectrometry in carbon tetrachloride. The equilibrium constants at 300, 315 and 328 K and the ? ΔH°, ? Δν_OH and Δν_CN values have been determined. The comparison with previously studied OH … N complexes shows that TMAAZ forms stronger complexes than would be expected from the pK_a value. These facts are discussed in terms of steric, hybridization, solvation and charge transfer effects. From a pK_a of 8, the IR spectrum shows the appearance of ion pairs N⁺-H …^?O. A predominance of protonated species can be calculated for a pK_a of 6. This can explain why 1,2-ring cleavage whose first step is probably the formation of an azirinium cation, occurs for acids characterized by pK_a values lower than 5 but not for enolizable ketones having pK_a values higher than 9.     

Structure and proton-donating ability of trifluoro-<Emphasis Type="Italic">N</Emphasis>-(2-phenylacetyl)methanesulfonamide

According to the data of quantum-chemical calculations and IR spectroscopy the trifluoro-N-(2-phenylacetyl)methanesulfonamide CF₃SO₂NHC(O)CH₂Ph in the isolated state and in inert media exists in the form of two conformers with the syn- and antiperiplanar orientation of the C=O and N-H bonds. Its self-associates in the CCl₄ solution and in molecular crystals constitute cyclic dimers formed by the NH···O=S bonds and chain dimers with the NH···O=C bonds. As a hydrogen bond donor, trifluoro-N-(2-phenylacetyl)methanesulfonamide is stronger than N-methyltrifluoromethanesulfonamide. Its pK _a in methanol is 5.45, that is 5 pK units lower than for amides CF₃SO₂NHR and 2 pK units higher than for imide (CF₃SO₂)₂NH.     

Two polymorphic modifications of 1-(N-morpholiniomethyl)spirobi- (3-oxo-2,5-dioxa-1-silacyclopentan)- ate hydrate

The compound 1-(N-morpholiniomethyl)spirobi(3-oxo-2,5-dioxa-1-silacyclopentan)ate crystallizes from aqueous solution of γ-butyrolactone in the form of two crystal hydrate modifications: monoclinic (with D = 1.53 g/cm³, space group P 2₁/n) and triclinic (D = 1.45 g/cm³, space group P1^-). For the monoclinic form, an X-ray structural study at -100°C has been performed. For both structures the coordination polyhedron of the silicon atom is a trigonal bipyramid. In the crystal structures there are strong intermolecular hydrogen bonds of NH···O and OH···O types.     

Estimates for systematic empirical corrections of consistent 4–21G ab initio geometries and their correlations to total energy group increments

The structural parameters of the completely relaxed 4–21G ab initio geometries of more than 30 basic organic compounds are compared to experimental results. Some ranges for systematic empirical corrections, which relate 4–21G bond distances to experimental parameters, are associated with total energy increments. In general, for the currently feasible comparisons, the following corrections can be given which relate calculated distances to experimental r_g parameters and calculated angles to r_s-structures For CC single bond distances, deviations between calculated and observed parameters (r_g) are in the ranges of ?0.006(2) to ?0.010(2) Å for normal or unstrained hydrocarbons; ?0.011(3) to ?0.016(3) Å for cyclobutane type compounds; and +0.001(5) to +0.004(4) Å for CH₃ conjugated with CO. For CO single bonds the ranges are ?0.006(9) to +0.002(3) Å for CO conjugated with CO; and ?0.019(3) to ?0.027(9) Å for aliphatic and ether compounds. A very large and exceptional discrepancy exists for the highly strained ethylene oxide, r_s — r_e = ?0.049(5) Å and in CH₃OCH₃ and C₂H₅OCH₃ the r_s — r_e differences are ?0.029(5), ?0.040(10) and ?0.025(10) Å. Some of these discrepancies may also be due to deficiencies of the microwave substitution method caused by atomic coordinates close to inertial planes. For CN bonds, two types of NCH₃ corrections are from +0.005(6) to ?0.006(6) and from ?0.009(2) to ?0.014(6) Å; and the range for NCO is +0.012(3) to +0.028(4) Å. For isolated CC double bonds the range is + 0.025(2) to +0.028(2) Å. For conjugated CC double bonds the correction is less positive (+0.014(1) Å for benzene). For CO double bonds the corrections are ?0.004(3) to +0.003(3) Å. For bond angles of type HCH, CCH, CCC, CCO, CCO, OCO, NCO and CCC the corrections are of the order of magnitude about 1–2° (or better). Angles centered at heteroatoms are less accurate than that, when hydrogen atoms are involved. Differences in HOC and NHC angles were found in a range of ?2.3(5)° to ?6.2(4)°.     

Crystal structure and luminescence of europium(III) acrylate

The atomic structure of europium acrylate crystals [Eu₂(Acr)₅OH·3H₂O]·2(0.5H₂O) was studied by X-ray analysis (a = 24.360(3) Å, b = 18.466(2) Å, c = 8.5818(9) Å, β = 96.087(2)°, space group C2/c, Z = 6, ρ_calc = 2.036 g/cm³). The crystal structure involves chains of binuclear [Eu₂(C₃H₃O₂)₅OH·3H₂O] molecules, running infinitely in the [101] direction and having pairs of C₉H₉EuO₇H₂O molecules alternating with C₆H₆EuO₄OH·2H₂O molecules that link the pairs. The infinite chains are linked by hydrogen bonds and van der Waals interactions. The thermal behavior of luminescence of the europium(III) complex is discussed.     

Derivatographic studies on dehydration of salt hydrates and their deuterium oxide analogues. VI

Non-isothermal studies of the dehydration of double salt hydrates of the type K₂AB₄·M(II)SO₄·6H₂O where AB₄BeF^2?₄ or SeO^2?₄ and M(II)Mg(II), Co(II), Ni(II), Cu(II) or Zn(II) and their D₂O analogues were carried out. Thermal parameters like activation energy, order of reaction, enthalpy change, etc., for each step of dehydration were evaluated from the analysis of TG, DTA and DTG curves. These parameters were compared with the corresponding double sulphate, i.e., K₂SO₄·M(II)SO₄·6H₂O and their D₂O analogues. The role of divalent cation on the thermal properties of dehydration of the salt hydrates and also the effect on the thermal properties due to deuteration were discussed. The order of reaction was always found unity. The values of ΔH were within ～11-～19 kcal mol^?1     

A gas-phase electron diffraction study of the molecular structure of tetravinylsilane

The molecular structure of tetravinylsilane has been studied by gas-phase electron diffraction. The radial distribution curve suggests the absence of conformers having vinyl double bonds staggered with respect to the SiC₄ skeleton. Of the eclipsed or approximately-eclipsed conformers, the one with S₄ symmetry gives the best fit with experiment, although a small admixture of a C₁ conformation cannot be ruled out. Least-squares refinement gave the following values for the independent structural parameters (lengths, r_a basis; angles, r_α basis): C-H = 1.118 ± 0.003 Å, CC = 1.355 ± 0.002 Å, Si-C = 1.855 ±0.002 Å, ∠SiCC = 124.0 ± 0.3°, ∠SiCH = 118.4 ± 1.0°, torsion angles CSiCC are 17.5 ± 0.6° from the eclipsed conformation. During the refinement the vibrational amplitudes u and perpendicular amplitude corrections K were held constant at calculated values. The CC bond length provides evidence of interaction between the vinyl π-bonds and the vacant d-orbitals of silicon.     

Analytical applications of the reaction of thorium with benzenephosphonic acid

Benzenephosphonic acid quantitatively precipitates thorium as Th(C₆H₅PO₃)₂·3H₂O at pH values as low as 0.5. The compound may be dried at 140° to 180° C and weighed, as a gravimetric means of determining thorium. On ignition, Th (C₂H₅PO₃)₂ 3 H₂O undergoes decomposition at 240° to 300° C to form Th(C₆H₅PO₃)₂·2H₂O, at 450° to 650° C to form Th(HPO₄)₂·2H₂O and finally at 800° to 1000° C to form Th(HPO₄)₂. The latter compound is stable to 1200° C.Potentiometrically (pK₁' = 0.91, pK₂' = 6.41) and spectrophotometrically (pK₁' = 0.96, pK₂' = 6.51) determined pK' values are reported. Absorption spectra of C₆H₅PO₃H₂, C₆H₅PO₃H^- and C₆H₅PO₃^-2 are reported. The solubility of Th (C₆H₅PO₃)₂·3H₂O was studied as a function of pH and the average value of the solubility product (K_sp = 4s³) was found to be 3.24·10^-31.     

The molecular structure of gaseous tetrachloro-p-benzoquinone and tetrachloro-o-benzoquinone by electron diffraction

The structures of tetrachloro-p-benzoquinone and tetrachloro-o-benzoquinone (p- and o-chloranil) have been investigated by gas electron diffraction. The ring distances are slightly larger and the carbonyl bonds slightly smaller than in the corresponding unsubstituted quinones. The molecules are planar to within experimental error, but small deviations from planarity such as those found for the para compound in the crystal are completely compatible with the data. Values for the geometrical parameters (r_a distances and bond angles) and for some of the more important amplitudes (l) with parenthesized uncertainties of 2σ including estimated systematic error and correlation effects are as follows. Tetrachloro-p-benzoquinone: D_2h symmetry (assumed); r(CO) = 1.216 Å(4), r(CC) = 1.353 Å(6), r(C-C) = 1.492 Å(3), r(C-Cl) = 1.701 Å(3), ∠C-C-C = 117.1° (7), ∠CC-C1 = 122.7° (2), l(CO)= 0.037 Å(5), l(CC) = l(C-C) - 0.008 Å(assumed) = 0.049 Å(7), and l(C-Cl) = 0.054 Å(3). Tetrachloro-o-benzoquinone: C_2v symmetry (assumed); r(CO) = 1.205 Å(5), r(CC) = 1.354 Å(9), r(C_cl-C_cl) = 1.478 Å(28), r(Co-C_cl) = 1.483 Å(24), r(C_o-C_o) = 1.526 Å(2), r(C-Cl)= 1.705 Å(3), <C_o-CO = 121.0° (22), ∠C-C-C = 117.2° (9), ∠C_co, ClC-Cl = 118.9° (22), ∠C_ccl, ClC-Cl = 122.2°(12), l(CO) = 0.039 Å(5), and l(C_cl-C_cl) = l(C_o-C_cl) = l( Co-Co) = l(CC) + 0.060 Å(equalities assumed) = 0.055 Å(9). Vibrational'shortenings (shrinkages) of a few of the long non-bond distances have also been measured.     

Sesquiterpenoids — XVI: Conformations of cycloheptane and α-methylene-γ-lactone rings in sesquiterpenoids: X-ray determination of the constitution,absolute stereochemistry,and conformation of euparotin bromoacetate

The molecular structure of euparotin, a highly oxygenated sesquiterpene of the guaianolide type, has been determined by crystal-structure analysis of euparotin bromoacetate. The bromo-derivative crystallizes from benzene-petrol as a benzene solvate, C₂₂H₂₅O₈Br·$\text{1}\text{2}$C₆H₆, crystals of which are monoclinic, of space group C2, with a = 34·85, b = 7·04, c = 10·90 Å, β = 106°35′, and Z = 4. The atomic co-ordinates were determined by Fourier and least-squares calculations which employed 1947 photographic |F₀| values and converged at R = 12·8% with isotropic thermal parameters for the C and O atoms and anisotropic parameters for the Br atom. The absolute configuration was established by the anomalous-dispersion effect. The cycloheptane ring of the sesquiterpenoid has a conformation which is closer to a twist chair (C₂) than a chair (C_s) form, and a survey shows that this is also true for other perhydroazulene sesquiterpenoids. In the α-methylene-γ-lactone of euparotin and several other sesquiterpenoids the CCCO torsion angle has the same sign as the C(α)C(β)C(γ)-O torsion angle, establishing the basis for Stöcklin et al's correlation between the position and stereochemistry of lactone fusion and the sign of the Cotton effect of the n → π* transition of the CCCO chromophore.     

Competition between H<Subscript>2</Subscript>O and CH<Subscript>3</Subscript>OH molecules in the formation of the simplest stable proton disolvates and their solvation in aqueous methanol solutions of KOH and CH<Subscript>3</Subscript>OK

IR spectroscopic and quantum chemical methods are used to study the competition between water and methanol molecules in the formation of the simplest stable proton disolvates and their subsequent solvation in the case of solutions of KOH in CH₃OH and CH₃OK in H₂O with similar stoichiometries (~1:3-3.5). The complexes found in these solutions are analysed to determine their composition and structure: they are found to be heteroions (CH₃O?H?OH)^– solvated by two similar solvent molecules. In both cases, there are virtually no complexes of the second possible type (CH₃OH·(CH₃O?H?OCH₃)^–··H₂O or CH₃OH·(HO?H?OH)^–·H₂O), which appears to be due to the stoichiometric compositions of the solutions. It is shown that a DFT calculation (B3LYP/6-31++G(d,p)) of linear complexes with strong (~15-30 kcal/mol) H bonds reproduces, with good accuracy, the IR spectra of the solutions, which consist mainly of these complexes.     

β-Cyclodextrin Inclusion Complexes of 2-Hydroxyfluorene and 2-Hydroxy-9-fluorenone: Differences in Stoichiometry and Excited State Prototropic Equilibrium

We report that 1:1 and 1:2 complexes are formed for 2-hydroxy-9-fluorenone with β-cyclodextrin (β-CD) and that there is an unusual red shift in emission at higher concentrations of β-CD. Between different stoichiometries of the complexes the titrimetric curves for the neutral–anionic equilibria for the guests differ drastically and so do the excited state pK values. The formation of an 1:1 inclusion complex with 2-hydroxy-9-fluorenone (2HFN) as the guest in β-CD with the binding constant (K) of 606.65 L·mol^?1 was determined. The ground and excited state pK _a values for the neutral–mono-anion equilibrium are not affected by β-CD. Hence the hydroxyl group is considered exposed in the aqueous environment. Two different types of inclusion complexes of 2HFN were observed in β-CD. The 1:2 complex of 2HFN shows a red shift from the 1:1 complex and is less fluorescent that the 1:1 complex. The red shift reveals that the 1:2 complex is more stabilized than the 1:1 complex. The excited state pK _a values in both complexes with β-CD are higher that those in aqueous solution. This shows that the complexation makes the molecule less acidic in the S1 state. The β-CD molecule is perceived as not able to encapsulate the 2HFN molecule fully, but the larger rim of the β-CD comes closer to the C=O group. The other half of the 2HFN molecule is encapsulated by the second β-CD molecule and thus there is formation of the 1:2 inclusion complex at higher concentrations of β-CD.     

The molecular structure of fumaric acid and the deformation of carboxyl group geometry on crystallization

The molecular structure of fumaric acid was studied by means of gas electron diffraction at 260° C. The molecular parameters and their standard deviations obtained for a C_2h model are (r_a distances in Å, angles in degrees): CO: 1.202(0.002), C-O: 1.341(0.006), C-C: 1.486(0.004), CC: 1.356(0.016). C-C-O: 112.1(1.0), C-CO: 124.4(1.1), C-CC: 121.8(1.2). From the available data on carboxylic acids the weighted average deformation of the structure of a carboxylic group on crystallization was determined; a significant expansion of the O-H bond (0.040 Å ), the CO bond (0.010 Å ) and the C-C-O bond angle (1.5° ) and a shrinkage of the C-O bond (0.041 Å ), the C_α-C bond (0.012 Å ) and the C-CO bond angle (2.0° ) was found. The energy for these deformations was estimated to be 1.8 kcal mol^?1.     

Molecular and crystal structures of two organoarsenic compounds with AsO bonds: Triphenylarsinoxide hydrate and p-carbomethoxyphenylarsinoxide

The full X-ray structure analysis of two organoarsenic compounds with AsO bonds has been performed. I, (C₆H₅)₃AsO · H₂O (a redetermination, see ref. 1), monoclinic, a 11.155, b 9.461, c 16.621 », γ 113.24°, Z = 4, space group P2₁/n; II, (CH₃OCOC₆H₄) (C₂H₅)₂AsO, triclinic, a 5.973, b 9.179, c 11.818 », α 86.78, β 83.88, γ 97.76°, Z = 2, space group P$\text{1}$. The final R values are 0.034 (I) and 0.042 (II). In structure I there are centrosymmetric dimers formed by intermolecular hydrogen bonds between H₂O and I (OH…O 2.795 and 2.820 »).     

Theoretical study of hydrolysis of an imine oxime in aqueous solution and crystal structure and spectroscopic characterization of a platinum(II) complex containing the hydrolysis product

The hydrolysis of an imine oxime (ppeieoH) in neutral and acidic aqueous solutions was studied using DFT at the B3LYP/6-311G(d,p) level. The rate-determining step at the neutral and acidic aqueous solutions is the nucleophilic attack of the water molecules to the neutral or protonated imine C atom of ppeieoH. The activation energy is much lower in the acidic hydrolysis. The hydrolysis of ppeieoH results in the parent carbonyl oxime (inapH) and amine compounds with ΔG _cal values of 8.66 and 11.02 kJ mol^?1 in the neutral and acidic solutions, respectively. The hydrolysis of ppeieoH was observed experimentally during its reaction with K₂[PtCl₄] in an aqueous solution. The reaction yielded [PtCl(inap)(DMSO)], which contains only the hydrolysis product inap. The new platinum(II) complex was characterized spectroscopic techniques and X-ray diffraction. The platinum(II) ion is coordinated by chlorido, carbonyl oxime (inap), and DMSO ligands forming a distorted square-planar arrangement. The molecules of the platinum(II) complex were connected by weak non-conventional C–H···O and C–H···π hydrogen bonds.     

INTRAMOLECULAR OH···S HYDROGEN BONDS AND MOLECULAR CONFORMATIONS IN 2-METHYLMERCAPTOETHANOL

Abstract

The infrared absorption spectrum of monomeric 2-methylmercaptoethanol in dilute CC1₄, solution exhibits four overlapped bands in the fundamental OH stretching region. The individual band components were resolved using digital computing techniques [1], and the relative band intensities are temperature dependent. The “free” OH bands at 3634 and 3623 cm correspond to gauche and trans orientations about the C-O bond, respectively, by analogy with similar band components in the infrared spectrum of ethanol in dilute CC1₄, solution. The OH bands at 3539 and 3446 cm^?1 are assigned to gGt and gGg¹ conformers, respectively, each involving an intramolecular OH···S hydrogen bond (conformer notation refers to the orientation about the C-O, C-C and C-S(CH₃) bonds, respectively). A similar interpretation of the matrix isolated infrared spectra of ethylene glycol, involving two conformers with intramolecular OH···O hydrogen bonds and differing principally in the orientation of the proton-acceptor OH group, has been presented recently [2]. The microwave spectrum of 2-mercaptoethanol in the vapour phase arises from an all-gauche conformation with an intramolecular OH···S hydrogen bond [3].     

Determination of pK a of benzoic acid- and p-aminobenzoic acid-modified platinum surfaces by electrochemical and contact angle measurements

Acidity constant values of benzoic acid (BA)-modified platinum electrode (Pt-BA) and p-aminobenzoic acid (pABA)-modified platinum electrode (Pt-NHBA) surfaces were determined using cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and contact angle measurements (CAM). Diazonium tetrafluoroborate salt reduction and pABA oxidation reactions were used to prepare (Pt-BA) and (Pt-NHBA) surfaces, respectively. Both surfaces exhibited pH dependence with [Fe(CN)₆]^3?/4? redox probe solutions at different pH; this allowed us to estimate the surface pK _a values. Acidity constants for Pt-BA surface were found to be pK _a (3.09 ± 0.25), (4.89 ± 0.11), and (3.91 ± 0.54) by CV, EIS, and CAM techniques, respectively, while the values for Pt-NHBA surface were pK _a (3.16 ± 0.45), (4.24 ± 0.40), and (5.64 ± 0.12). The Pt-BA surface pK _a values were lower in CV and CAM measurements relative to the bulk solution of BA, while a higher value was observed in EIS for Pt-BA surface. The pK _a values determined for Pt-NHBA surface via both CV and EIS were lower than the bulk value; however, the result obtained from CAM was one unit higher than pK _a of bulk pABA.     

Copper(I) complexes with 2-butyne-1,4-diol: Synthesis and crystal structure of the anionic π-complex (ImH)[CuCl2(HOCH2C≡CCH2OH)] (ImH[CuCl2(HOCH2C≡CCH2OH)] (ImH+ is imidazolium cation)

The crystalline complex ImH[CuCl₂(HOCH₂C≡CCH₂OH)] has been synthesized by the direct interaction of 2-butyne-1,4-diol with CuCl in concentrated aqueous solution of (ImH)Cl (ImH⁺ is imidazolium cation) and studied by X-ray crystallography. The crystals are triclinic, space group P $\overline 1 $ , a = 7.08(2) Å, b = 7.49(1) Å, c = 10.962(8) Å, α = 101.76(8)°, β = 95.85(8)°, γ = 99.57(8)°, Z = 2. The structure consists of stacks of discrete anions [CuCl₂(HOCH₂C≡CCH₂OH)]^? arranged along the [100] axis and [ImH]⁺ cations occupying the free space. The environment of π-coordinated Cu(I) atoms is trigonal and consists of two chlorine atoms and the C≡C bond of 2-butyne-1,4-diol molecule. The alcohol groups do not participate in the coordination, but they form strong hydrogen bonds N-H···O (H···O, 1.76(6) Å) and O-H···Cl(H···Cl, 2.29(5) Å).     

Hydrogen-bonding interaction in a complex of amino acid with urea studied by DFT calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine, and leucine) and urea in gas phase have been carried out using density functional theory (DFT) and ab initio methods at the B3LYP/6-311++g** and MP2/6-311++g** theory levels. The structures, binding energy, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution, and bond characteristics of the mentioned complexes were calculated. Urea is a good H-bond donor and an excellent receptor for highly electronegative atoms like O and N, through the formation of two or more hydrogen bonds. The NH₂ and COOH groups of amino acids can form several different types of H-bonds with urea molecular, as well as C^αH and alkyl side chains. The calculated high binding energy also suggests multiple H-bonds formed in one complex. The OH···O contact is the strongest hydrogen bond interaction with H···O separation around 1.65 Å and its relevant angle close to 176°. The closely linear amide H-bonds NH···O and OH···N strongly stabilize the amino acid–urea complex with H···O separation between 1.89 and 2.38 Å. The weaker CH···O/N H-bonds are also discussed as significant interaction in biological systems involving amino acids.