Double-bonded Oxygen Atom Research Articles

Kinetics and mechanism of a macrocyclic chromium(III) complex oxidation to chromium(IV) by hexacyanoferrate(III) in strongly alkaline media

Oxidation of the macrocyclic Cr(III) complex cis-[Cr(cycb)(OH)2]+, where cycb=rac-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane, by an excess of the hexacyanoferrate(III) in basic solution, slowly produces Cr(V) species. These species, detected using e.p.r. spectroscopy, are stable under ambient conditions for many hours, and the hyperfine structure of the e.p.r. spectrum is consistent with the interaction of the d-electron with four equivalent nitrogen nuclei. Electro-spray ionization mass spectrometry suggests a concomitant oxidation of the macrocyclic ligand, in which double bonds and double bonded oxygen atoms have been introduced. By comparison basic chromate(III) solutions are oxidized rapidly to chromate(VI) by hexacyanoferrate(III) without any detectable generation of stable Cr(V) intermediates.

Alkali and alkali–lead oxynitride phosphate glasses: a comparative structural study by NMR and XPS

Nitrided phosphate glasses are characterized by tetrahedral units P(O,N) 4 in which nitrogen atoms have substituted for both bridging and non-bridging double bonded oxygen atoms. 31P magic angle spinning (MAS) nuclear magnetic resonance (NMR) shows that PO 4, PO 3N and PO 2N 2 tetrahedra may coexist within the glass network. The relative proportion of these structural units as a function of the N/P ratio depends on the composition of the oxide base glass, as illustrated in sodium, lithium–sodium and lithium–sodium–lead phosphate glasses. Furthermore, 31P double quantum (DQ) MAS NMR shows that the nitrogen/oxygen substitution is not a random process. The modifier cations influence the connections between tetrahedra throughout the overall nitrided glass network, and, therefore, the final structure. N 1s X-ray photoelectron spectroscopy (XPS) shows that nitrogen atoms may exist in the P(O,N) 4 tetrahedra as doubly coordinated (–N= ) and triply coordinated (–N<) species, bonded to two and three phosphorus atoms, respectively. The relation between both kinds of nitrogen as a function of the N/P ratio depends also on the oxide-base glass composition. In this work, the thermal nitridation in flowing ammonia of alkali and alkali–lead metaphosphate glasses is studied. The results deduced from the NMR and XPS experiments make it possible, in addition to a comparison between the nitridation kinetics, to follow and to compare the structural evolution of oxynitride glasses resulting from a progressive nitrogen incorporation. In particular, the important role of PbO in the nitridation mechanism is revealed, demonstrating in this case that the nitridation is not random, its beginning included.

Surface control of optical properties in silicon nanoclusters

Density functional and quantum Monte Carlo calculations are employed to determine the effect of surface passivants on the optical gap of silicon nanoclusters. Our results show that quantum confinement is only one mechanism responsible for visible photoluminescence and that the specific surface chemistry must be taken into account in order to interpret experimental results. Significant changes occur in the optical gap of fully hydrogenated silicon nanoclusters when the surface contains passivants that change the bonding network at the surface. In the case of just one double-bonded oxygen atom, the gap reduction computed as a function of the nanocluster size demonstrates that one contaminant can greatly alter the optical gap. A further significant reduction of the gap occurs with multiple double-bonded oxygen contamination, providing a consistent interpretation of several recent experiments. We predict that other passivants that distort the tetrahedral bonding network at the surface, including other double-bonded groups and in some cases bridged oxygen, will also significantly affect the optical gap. Conversely, single-bonded passivants will have a minimal influence on the optical gap. A discussion of the difference in the strength of the optical transitions for clusters with different passivants is presented.

‘Strain effect’ descriptors for ATP and ADP derivatives with modified phosphate groups

Semiempirical AM1 calculations were carried out for quantum chemically optimized conformations of ATP and ADP and their modified phosphate derivatives with the oxygen atoms intervening between phosphorus atoms substituted by imido or methylene groups or the double-bonded oxygen atoms substituted by sulfur. In addition to the calculation of conventional geometric and energetic parameters, the effect of these substitutions was quantified in terms of conformational ‘strain energy’. The latter has been defined as the energy of transformation of the parent nucleotide (ATP or ADP) from the optimum conformation to the conformation optimized for its phosphate-modified analog. The results of calculations revealed that conformational ‘strain’ of phosphate-modified nucleotides depends not only on the nature of the substituent but also on its position. The respective effect had the largest magnitude when the substitution was made between two terminal phosphorus atoms. Given that the ‘strain energy’ characterizes the geometrical aspects of the interaction of nucleotide molecules with receptors and enzymes, an attempt was made to correlate it with the corresponding biological activities. Such correlation was significant in the case of highly specific binding sites for universal ligands like ATP.

CH2 + CO2 → CH2O + CO, One-Step Oxygen Atom Abstraction or Addition/Fragmentation via α-Lactone?

Ab initio G2 calculated pathways are presented for the reaction CH2 + CO2 → CH2O + CO in which net transfer of a double bonded oxygen atom occurs from CO2 to the carbene. Of particular interest are the electronic state of the attacking methylene, the structure of the possible intermediates, and the lowest energy path(s) available for this reaction. As expected, our results support the assignment of α-lactone 1 as the intermediate observed by IR in the matrix isolation experiments of Milligan and Jacox; analogous reactions involving substituted carbenes have more recently been reported by Sander et al. We obtain ΔHf(1) = −43.3 kcal/mol based on the G2 atomization energy, while a variety of isodesmic reactions point to slightly higher values (averaged −42.7 kcal/mol). Acyclic ·CH2O(CO)· (methylene-oxycarbonyl) and ·CH2CO2· (acetoxyl) biradicals 2 and 3, respectively, were also considered on both singlet and triplet potential energy surfaces. According to the calculations, the singlet reaction proceeds with little or no barrier to form 1; subsequent ring fragmentation (ΔH⧧ = 27.5 kcal/mol) yields the products CH2O + CO. Collision orientation must play a role, however; Wagner et al. have reported that reaction is only half as fast as collisional deactivation of 1:CH2 to 3:CH2 which presumably occurs via nonproductive encounter geometries. An activated channel (ΔH⧧ = 23.2 kcal/mol) was also located in which 1:CH2 directly abstracts oxygen from CO2 via an ylide-like TS 12. The lowest energy 3:CH2 + CO2 attack is endothermic by 7.8 kcal/mol, forming the triplet acetoxyl diradical 33; a higher energy path leads to methylene-oxycarbonyl diradical 32. Barriers for these two processes are ΔH⧧ = 19.3 and 57.7 kcal/mol, respectively. No path for isomerization of 33 to 32 was found. Attempts to locate regions on the triplet approach surface where the singlet crosses to become the lower energy spin state were complicated by the difficulty of optimizing geometries within the composite G2 model. Preliminary efforts, however, indicate that such crossings occur at geometries higher in energy than separated 1:CH2 + CO2, suggesting that their role should be relatively unimportant in this reaction.

First-Principles Theory of Muon and Muonium Trapping in the Protein Chain of Cytochrome c and Associated Hyperfine Interactions

The microscopic details of the electron transfer in cytochrome c (cyt c) are being investigated by the Muon Spin Relaxation (μSR) technique. We are using the Hartree–Fock Cluster Procedure to determine the most likely trapping sites for μ+ and muonium (Mu) in the protein chain, and have performed extensive calculations in single amino acid molecules of the protein chain of cyt c. The double-bonded oxygen atom of the carboxyl group was identified as the trapping site for both μ+ and Mu. Utilizing the wave functions we obtained from the Hartree–Fock calculations, we have determined the hyperfine field that the μ+ in Mu experiences while the latter is trapped at the oxygen.

Local Structure and Electronic State of Oxygens in Lithium Phosphate Glasses Calculated by Molecular Orbital Theory.

The validity of separating O1s photoelectron spectra of alkaline phosphate glasses into three peaks assigned to bridging, non-bridging and double-bonded oxygen atoms was discussed on the basis of the molecular orbital calculations by density functional method. Models used for the calculations were lithium metaphosphate chain clusters consisting of 2, 4 and 5 PO4 units. Two oxygen atoms around a Li+ ion, non-bridging oxygen and double-bonded oxygen, were structurally indistinguishable, and were considered to be classified into the same terminal atoms. The O1s orbital energies of these terminal oxygen atoms were consistent to each other within 0.4eV. The variation in orbital energies probably results from inhomogeneous broadening caused by the statistically distributed surroundings around PO4 units. From these results, it was concluded that in O1s photoelectron spectra of phosphate glasses, the separation of the lower binding energy side peak into two bands is not appropriate.

Studies on peroxomolybdates. XIX. Crystal structure of potassium heptaoxotetraperoxotrimolybdate(VI)-water( [formula omitted]) K 4[Mo 3O 7(O 2) 4]·2H 2O

The crystal structure of potassium heptaoxotetraperoxotrimolybdate(VI)-water( 1 2 ), K 4[Mo 3O 7(O 2) 4]·2H 2O, has been determined from single-crystal X-ray diffraction data. The yellow compound crystallizes in the triclinic space group P 1 with a = 8.470(1), b = 12.297(3), c = 8.407(2) A ̊ , α = 103.56(2)°, β = 104.32(1)°, γ = 103.40(1)°, V = 784.8(3) A ̊ 3 and Z = 2. Full-matrix least-squares refinement of 218 structural parameters gave R = 0.026 for 4415 observed [ I > 3 σ( I)], independent reflections. In the [Mo 3O 7(O 2) 4] 4− anion two molybdenum atoms are seven-coordinated and one molybdenum atom is four-coordinated. The anion can be described as being composed of two edge-sharing pentagonal bipyramids sharing one common corner with a tetrahedron. In the pentagonal bipyramids the molybdenum atoms are displaced 0.314–0.317 Å from the equatorial plane towards the double-bonded apical oxygen atom. The three molybdenum atoms are situated at the corners of an isosceles triangle with the two seven-coordinated molybdenum atoms (Mo pbp) at the base. Selected bond distances: MoO peroxo 1.933(3)-1.991(3) Å, Mo pbpO apical 1.683(3)–1.695(3) Å, Mo pbpO apical 2.301(2)–2.334(2) Å and (OO) peroxo 1.460(5)–1.487(4) Å. Mo ⋯ Mo is 3.3612(4), 3.7037(5) and 3.7306(7) Å.

Studies on peroxomolybdates XVIII. Crystal structure of ammonium μ-fluoro- μ-oxo-bis[oxodiperoxomolybdate(VI)]- water(2/1), [formula omitted], a dibridged peroxodimolybdate

The crystal structure of ammonium μ- fluoro-μ- oxo-bis[oxodiperoxomolybdate(VI)]-water (2 1) , (NH 4) 3[FO{MoO(O 2) 2} 2]· 1 4 H 2O , has been determined from single-crystal X-ray diffraction data. The yellow compound crystallizes as multiple-twins in the monoclinic space group P2 1/ c with a = 13.803(3) A ̊ , b = 11.230(2) A ̊ , c = 15.975(3) A ̊ , β = 109.46(2)° and Z = 8. Full-matrix least-squares refinement of 316 structural parameters gave R = 0.057 for 3265 observed [ I > 3 σ( I)], independent reflections. The [FO{MoO(O 2) 2} 2] 3− anions, of which there are two crystallographically different ones in the asymmetric unit, have approximately C 2v symmetry and are composed of two edge-sharing pentagonal bipyramids, the molybdenum atoms thus being seven-coordinated. The molybdenum atoms are displaced 0.312–0.365 Å from the equatorial planes towards the respective double-bonded apical oxygen atom. Bond distances are as follows: MoO peroxo 1.884(10)–1.975(8) Å, Mo = O apical 1.670(8)–1.682(8) Å, MoF bridge 2.246(6)–2.313(6) Å, MoO bridge 1.925(7)–1.941(7) Å and (OO) peroxo 1.436(15)–1.465(12) Å. Mo ··· Mo is 3.369(1)–3.379(1) Å, MoOMo 120.5(4)–122.6(4)° and MoFMo 94.0(2)–95.5(2)°. The powder photograph of the title compound was recorded at room temperature and was indexed.

Studies on peroxomolybdates. XV. Crystal structure of ammonium difluorooxodiperoxomolybdate(VI), (NH4)2[MoF2O(O2)2], and a survey of important distances in pentagonal-bipyramidal peroxomolybdates

The crystal structure of ammonium difluorooxodiperoxomolybdate(VI), (NH4)2[MoF2O(O2)2], has been determined by single-crystal X-ray diffraction methods. The yellow compound crystallizes in the triclinic space groupP¯1 witha=7.752(2),b=7.498(3),c=6.066(2) A,α=86.37(3),β=109.60(3),γ=94.45(3)°, andZ=2. A total of 3857 reflexion intensities was recorded on a SyntexP21 diffractometer using MoKα radiation at room temperature. The structure was solved by the Patterson method and successive electron density calculations. Full-matrix least-squares refinement yielded a finalR value of 0.027 for 3729 observed [I>3σ(I)] reflexions. In the complex anion molybdenum is surrounded by a pentagonal-bipyramidal arrangement of ligand atoms. Two side-on bonded peroxo groups and a fluorine atom form the equatorial plane and one fluorine atom and a double-bonded oxygen atom occupy the apical positions. The molybdenum atom is displaced 0.311(1) A from the equatorial plane in the direction of the double-bonded oxygen atom. Bond distances: Mo-Operoxo 1.931(2)-1.976(2) A, Mo=Oapical 1.688(2) A, Mo-Fequatorial 1.979 (1) A, Mo-Fapical 2.199(1) A and (O-O)peroxo 1.474(2)-1.480(2) A.

Studies on peroxomolybdates. XVI: A new fluoro-bridged tetraperoxodimolybdate. Crystal structure of ammonium μ-fluoro-bis(fluorooxodiperoxomolybdate(VI)), (NH4)3[F{MoFO(02)2}2

Abstract The crystal structure of ammonium μ-fluoro-bis(fluorooxodiperoxomolybdate(VI)), (NH4)3[F{MoFO(O2)2}2], was determined by single-crystal X-ray diffraction methods. The yellow compound crystallizes in the mono-clinic space group P2/n with a = 10.686(7) A , b = 6.604(5) A , c = 8.338(7) A , β = 106.39° (at 170 K) and Z = 2. Two data sets were collected, one at 170 K (1797 reflections; R = 0.025) and one at 290 K (2757 reflections; R = 0.042). The complex anion is composed of two identical corner-sharing pentagonal bipyramids. Each molydenum atom is surrounded by a pentagonal bipyramidal arrangement of ligand atoms. Two side-on bonded peroxo groups and a fluorine atom form the equatorial plane, and the bridging fluorine atom and a double-bonded oxygen atom occupy the apical positions. The molybdenum atom is displaced by 0.324(1) A from the equatorial plane towards the double-bonded oxygen atom. Bond distances at 170 K are MoO peroxo = 1.934(2)–1.972(2) A , MoO apical = 1.670(2) A , MoF equatorial = 1.964(2) A , MoF apical = 2.196(1) A and (OO) peroxo = 1.473(2)–1.487(2) A . The angle MoFMo is 146.2(1)°.

Molecular orbital study for short and medium range order of P 2O 5 glass

The short- and medium-range order of pure P2O5 glass was investigated by the molecular orbital (MO) methods with the cluster approximation. The shape of a basic structural PO4 unit and the conformation of the two corner-sharing units were determined by means of the geometrical optimization using the ab initio SCF-MO GAUSSIAN-80 method. In the three corner-sharing units, the total energy for several conformations was calculated by the semi-empirical SCF-MO CNDO/2 method. The stable conformation was discussed in relation to the results thus obtained. The double-bonded P-O length was shorter than that of the single-bonded P-O, and the O-P-O bond angle was smaller than the regular tetrahedral value. It was proved that the shape of a PO4 unit was distorted as compared with that of a regular tetrahedron. The P-O-P intertetrahedral bond-angle was estimated to be smaller than the most probable value of the Si-O-Si angle in SiO2 glass. It was also found that two doublebonded oxygen atoms were situated closely to each other, and that the variations in dihedral angles contribute significantly to the value of the total energy and all three dihedral angles were divergent.

Interaction of phospholipids (Lysophosphatidylethanolamines) with water and sodium cation

We have performed detailed ab initio SCF calculations on the intermolecular interaction energies for one Na+ ion and one water molecule with two molecular fragments, one exemplifying a phospholipid (PL) head (PLHD) and the other, a phospholipid tail (PLTL). A 6-12-1 atom-atom pair potential for the interaction of a Na+ ion and water with a lysophosphatidyl-ethanolamine (LPEA) was derived from these results by a fitting procedure. This fitted potential was used to obtain isoenergy maps that provide energy profiles of the Na+ ion and the water around the phospholipids. The interaction of the Na+ ion with PL, as well as the interaction of water with the PL, can be visualized from these maps, which, as expected, show regions of hydrophilicity and hydrophobicity for the water and indicate a very strong binding site for the Na+ ion on the phosphate. It appears to be a stationary site that would limit the Na+ ion mobility. This binding site is located near the double-bonded oxygen atom of the phosphate group; its binding energy for Na+ is 67 kcal/mol. On the other hand the NH+ group of PLHD ahows strong electrostatic repulsion of Na+ while interacting with water with a binding energy of 13 kcal/mol. This potential energy well region for water is separated from another of similar depth near the phosphate by a barrier and both regions are expected to act as binding sites for water.

XPS measurements and structural aspects of silicate and phosphate glasses

Detailed measurements of the shape of the 01s photoelectron lines from a range of silicate, alumino silicate, and phosphate glasses have been made. In the case of the silicate glasses contributions from bridging and non bridging oxygen atoms were separated. For phosphate glasses an additional component due to double bonded oxygen atoms could be determined by curve fitting procedures and by comparison with selected crystalline phosphates. The intensities of the photoelectrons from these oxygen types bonded in different ways and the chemical shifts between them could be correlated with alkali and alkaline earth oxide contents and with the cation field strength. The ionic binding character introduced into the glass networks is a non-localized effect because not only the non bridging oxygen atoms are influenced by the alkali and alkaline earth ions but also the bridging and double bonded oxygen atoms. In the case of the sodium alumino silicate glasses a coordination change is indicated at Al 2O 3/Na 2O ∼ 0.4.

Oxidation of silicon: New electron spectroscopy results

New X-ray photoemission spectroscopy data and high resolution electron scattering spectroscopy data are presented which indicate that a peroxide-like model of the oxygen chemisorption on silicon surface is correct. These results are discussed in light of a recent double-bonded oxygen atom model due to Ludeke and Koma.

The Crystal Structure of Tripotassium bis(Oxalato)dioxovanadate(V) Trihydrate

The potassium salt of bis(oxalato)dioxovanadate(V), K3[V(O)2(C2O4)2]•3H2O crystallizes in a triclinic lattice with space group [Formula: see text] Two formula units make up the asymmetric unit which has dimensions a = 7.851(2), b = 11.603(2), c = 7.778(2) Å, α = 94.26(1), β = 110.07(1), γ = 91.25(1)°. Three-dimensional single-crystal X-ray diffraction counter data was refined by full-matrix least-squares techniques to R = 0.039. Hydrogen atomic parameters were included in the 213 variables used. A total of 3869 reflections was measured of which 85.4% were classed observed by the criterion I ≥ 2.3σ. The 563 unobserved reflections were included in the final cycle of structure-factor calculations but were not used in the refinement.The anion has irregular octahedral geometry with the two double-bonded oxygen atoms (V=O, 1.628(2) and 1.639(2) Å) cis to each other. The V—O (oxalate) bonds are of two significantly different types: (i) those that are trans to each other (2.009(2), 1.995(2) Å) and (ii) those that are trans to oxo ligands (2.158(2), 2.230(2) Å). The non-coplanar oxalate ligands are twisted about the C—C single bonds (1.550(3) and 1.551(4) Å), while the terminal C—O bonds average to 1.226(9) Å, and the inner ones to 1.274(16) Å. The anions exhibit an approximate non-crystallographic two-fold axis, though distortions from regularity are found. These distortions may best be attributed to hydrogen bonding with the three water molecules and, to a much lesser extent, by contact with the potassium ions.