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Dieter Cremer

Publications and source records attributed to Dieter Cremer.

At least 19 recordsLinked to original sources

The ozonation of silanes and germanes: an experimental and theoretical investigation.

Ozonation of various silanes and germanes produced the corresponding hydrotrioxides, R3SiOOOH and R3GeOOOH, which were characterized by 1H, 13C, 17O, and 29Si NMR, and by infrared spectroscopy in a two-pronged approach based on measured and calculated data. Ozone reacts with the E-H (E = Si, Ge) bond via a concerted 1,3-dipolar insertion mechanism, where, depending on the substituents and the environment (e.g., acetone-d6 solution), the H atom transfer precedes more and more E-O bond formation. The hydrotrioxides decompose in various solvents into the corresponding silanols/germanols, disiloxanes/digermoxanes, singlet oxygen (O2(1delta(g))), and dihydrogen trioxide (HOOOH), where catalytic amounts of water play an important role as is indicated by quantum chemical calculations. The formation of HOOOH as a decomposition product of organometallic hydrotrioxides in acetone-d6 represents a new and convenient method for the preparation of this simple, biochemically important polyoxide. By solvent variation, singlet oxygen (O2(1delta(g))) can be generated in high yield.

Germanium↗

Calculation of spin-densities within the context of density functional theory. The crucial role of the correlation functional.

It is demonstrated that the LYP correlation functional is not suited to be used for the calculation of electron spin resonance hyperfine structure (HFS) constants, nuclear magnetic resonance spin-spin coupling constants, magnetic, shieldings and other properties that require a balanced account of opposite- and equal-spin correlation, especially in the core region. In the case of the HFS constants of alkali atoms, LYP exaggerates opposite-spin correlation effects thus invoking too strong in-out correlation effects, an exaggerated spin-polarization pattern in the core shells of the atoms, and, consequently, too large HFS constants. Any correlation functional that provides a balanced account of opposite- and equal-spin correlation leads to improved HFS constants, which is proven by comparing results obtained with the LYP and the PW91 correlation functional. It is suggested that specific response properties are calculated with the PW91 rather than the LYP correlation functional.

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Docking, triggering, and biological activity of dynemicin A in DNA: a computational study.

The triggering and biological activity of the naturally occurring enediyne dynemicin A (1) was investigated, both inside and outside the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG).d(CCAGTAGTAG), using density functional theory (B3LYP with the 3-21G and 6-31G(d) basis set), BD(T)/cc-pVDZ (Brueckner doubles with a perturbative treatment of triple excitations), and the ONIOM approach. Enediyne 1 is triggered by NADPH in a strongly exothermic reaction (-88 kcal/mol), which involves a number of intermediate steps. Untriggered 1 has a high barrier for the Bergman cyclization (52 kcal/mol) that is lowered after triggering to 16.7 kcal/mol due to an epoxide opening and the accompanying strain relief. The Bergman reaction of triggered 1 is slightly exothermic by 2.8 kcal/mol. The singlet biradical formed in this reaction is kinetically stable (activation enthalpies of 19.5 and 21.8 kcal/mol for retro-Bergman reactions) and is as reactive as para-benzyne. The activity-relevant docking mode is an edge-on insertion into the minor groove, whereas the intercalation between base pairs, although leading to larger binding energies, excludes a triggering of 1 and the development of its biological activity. Therefore, an insertion-intercalation model is developed, which can explain all known experimental observations made for 1. On the basis of the insertion-intercalation model it is explained why large intercalation energies suppress the biological activity of dynemicin and why double-strand scission can be achieved only in a two-step mechanism that involves two enediyne molecules, explaining thus the high ratio of single-strand to double-strand scission observed for 1.

Algorithms↗

The structures of m-benzyne and tetrafluoro-m-benzyne.

The structures of m-benzyne and its fluorinated derivative, tetrafluoro-m-benzyne, were investigated using coupled cluster methods including triple excitations [CCSD(T) and CCSDT], different reference wave functions (spin-restricted Hartree-Fock, spin-unrestricted Hartree-Fock, and Brueckner), and different basis sets [6-31G(d,p) and correlation-consistent valence triple-zeta (cc-pVTZ)]. The inclusion of triple excitations in conjunction with d- and f-type polarization functions is paramount to correctly describe through-bond delocalization of the monocyclic form. At the highest level of theory, the C1-C3 distance of the minimum energy form of m-benzyne is 2.0 A and the profile of the potential energy surface along the C1-C3 distance is that of an asymmetric, single well, in agreement with previous density-functional theory and coupled cluster studies. In addition, the calculated CCSD(T) fundamental frequencies are in excellent agreement with the measured infrared frequencies, thus confirming the monocyclic form of m-benzyne. For tetrafluoro-m-benzyne, however, the increased eclipsing strain between the ring-external C-X bonds stabilizes the bicyclo[3.1.0]hexatriene form: the C1-C3 distance is calculated at the CCSD(T)/cc-pVTZ level to be approximately 1.75 A, which is in the range of elongated CC bonds. Computed harmonic vibrational frequencies compare reasonably well with the experimental neon-matrix difference spectrum and provide further evidence for the existence of a bicyclic form.

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Elucidation of the electronic structure of molecules with the help of NMR spin-spin coupling constants: the FH molecule.

It is demonstrated how the one-bond NMR spin-spin coupling constant (SSCC) (1)J(FH) can be used as a source of information on the electronic structure of the FH molecule. For this purpose, the best possible agreement between measured and calculated SSCC is achieved by large basis set coupled perturbed density functional theory calculations. Then, the calculated value is dissected into its four Ramsey terms: Fermi contact, the paramagnetic spin-orbit term, the diamagnetic spin-orbit term, and the spin dipole term, which in turn are decomposed into orbital contributions and then described by their spin densities and orbital current densities. In this way, the SSCC gives detailed information about the electronegativity of F, the bond polarity, the bond polarizability, the volume and the polarizability of sigma and pi lone pair orbitals, the s- or p-character of the bond orbital, the nature of the LUMO, and the density distribution around F.

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Connection between the regular approximation and the normalized elimination of the small component in relativistic quantum theory.

The regular approximation to the normalized elimination of the small component (NESC) in the modified Dirac equation has been developed and presented in matrix form. The matrix form of the infinite-order regular approximation (IORA) expressions, obtained in [Filatov and Cremer, J. Chem. Phys. 118, 6741 (2003)] using the resolution of the identity, is the exact matrix representation and corresponds to the zeroth-order regular approximation to NESC (NESC-ZORA). Because IORA (=NESC-ZORA) is a variationally stable method, it was used as a suitable starting point for the development of the second-order regular approximation to NESC (NESC-SORA). As shown for hydrogenlike ions, NESC-SORA energies are closer to the exact Dirac energies than the energies from the fifth-order Douglas-Kroll approximation, which is much more computationally demanding than NESC-SORA. For the application of IORA (=NESC-ZORA) and NESC-SORA to many-electron systems, the number of the two-electron integrals that need to be evaluated (identical to the number of the two-electron integrals of a full Dirac-Hartree-Fock calculation) was drastically reduced by using the resolution of the identity technique. An approximation was derived, which requires only the two-electron integrals of a nonrelativistic calculation. The accuracy of this approach was demonstrated for heliumlike ions. The total energy based on the approximate integrals deviates from the energy calculated with the exact integrals by less than 5 x 10(-9) hartree units. NESC-ZORA and NESC-SORA can easily be implemented in any nonrelativistic quantum chemical program. Their application is comparable in cost with that of nonrelativistic methods. The methods can be run with density functional theory and any wave function method. NESC-SORA has the advantage that it does not imply a picture change.

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A gauge-independent zeroth-order regular approximation to the exact relativistic Hamiltonian--formulation and applications.

A simple modification of the zeroth-order regular approximation (ZORA) in relativistic theory is suggested to suppress its erroneous gauge dependence to a high level of approximation. The method, coined gauge-independent ZORA (ZORA-GI), can be easily installed in any existing nonrelativistic quantum chemical package by programming simple one-electron matrix elements for the quasirelativistic Hamiltonian. Results of benchmark calculations obtained with ZORA-GI at the Hartree-Fock (HF) and second-order Moller-Plesset perturbation theory (MP2) level for dihalogens X(2) (X=F,Cl,Br,I,At) are in good agreement with the results of four-component relativistic calculations (HF level) and experimental data (MP2 level). ZORA-GI calculations based on MP2 or coupled-cluster theory with single and double perturbations and a perturbative inclusion of triple excitations [CCSD(T)] lead to accurate atomization energies and molecular geometries for the tetroxides of group VIII elements. With ZORA-GI/CCSD(T), an improved estimate for the atomization energy of hassium (Z=108) tetroxide is obtained.

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One-electron versus electron-electron interaction contributions to the spin-spin coupling mechanism in nuclear magnetic resonance spectroscopy: analysis of basic electronic effects.

For the first time, the nuclear magnetic resonance (NMR) spin-spin coupling mechanism is decomposed into one-electron and electron-electron interaction contributions to demonstrate that spin-information transport between different orbitals is not exclusively an electron-exchange phenomenon. This is done using coupled perturbed density-functional theory in conjunction with the recently developed J-OC-PSP [=J-OC-OC-PSP: Decomposition of J into orbital contributions using orbital currents and partial spin polarization)] method. One-orbital contributions comprise Ramsey response and self-exchange effects and the two-orbital contributions describe first-order delocalization and steric exchange. The two-orbital effects can be characterized as external orbital, echo, and spin transport contributions. A relationship of these electronic effects to zeroth-order orbital theory is demonstrated and their sign and magnitude predicted using simple models and graphical representations of first order orbitals. In the case of methane the two NMR spin-spin coupling constants result from totally different Fermi contact coupling mechanisms. (1)J(C,H) is the result of the Ramsey response and the self-exchange of the bond orbital diminished by external first-order delocalization external one-orbital effects whereas (2)J(H,H) spin-spin coupling is almost exclusively mitigated by a two-orbital steric exchange effect. From this analysis, a series of prediction can be made how geometrical deformations, electron lone pairs, and substituent effects lead to a change in the values of (1)J(C,H) and (2)J(H,H), respectively, for hydrocarbons.

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Hemiortho esters and hydrotrioxides as the primary products in the low-temperature ozonation of cyclic acetals: an experimental and theoretical investigation.

Low-temperature ozonation (-78 degrees C) of 1,3-dioxolanes 1a-1f and 1,3-dioxanes 1g and h in acetone-d6, methyl acetate, and tert-butyl methyl ether produced both the corresponding hemiortho esters (2a-h, ROH) and acetal hydrotrioxides (3a-h, ROOOH) in molar ratios ROH/ROOOH ranging from 0.5 to 23. Both types of intermediates were fully characterized by 1H, 13C, and 17O NMR spectroscopy. DFT calculations suggest that ozone abstracts a hydride ion from 1 to form an ion pair, R+ -OOOH, which subsequently collapses to either the corresponding hemiortho ester (ROH) or the acetal hydrotrioxide (ROOOH). Hemiortho esters decomposed quantitatively into the corresponding hydroxy esters. Experimentally obtained activation parameters for the decomposition of 2a (E(a) = 13.5 +/- 1.0 kcal/mol, log A = 8.3 +/- 1.0) are in accord with a highly oriented transition state involving, according to B3LYP calculations (deltaH(a)(298) = 13.2 kcal/mol), two molecules of water as a bifunctional catalyst. This mechanism is also supported by the magnitude of the solvent isotope effect for the decomposition of 2e, i.e., k(H2O)/k(D2O) = 4.6 +/- 1.2. Besides the hydroxy esters and oxygen (3O2/1O2), dihydrogen trioxide (HOOOH) was formed in the decomposition of most of the acetal hydrotrioxides (ROOOH) investigated. The activation parameters for the decomposition of the hydrotrioxides 3a-e in various solvents were E(a) = 20 +/- 2 kcal/mol, log A = 13.5 +/- 1.5. Several mechanistic possibilities for the decomposition of ROOOH were tested by experiment and theory. The formation of the hydroxy esters and oxygen could be explained by the intramolecular transfer of the proton to form the hydroxy ester. The assistance of water in the decomposition of ROOOH to form the hydroxy esters, either directly or via hemiortho esters, was also investigated. According to DFT calculations, the formation of a hydroxy ester via hemiortho ester is energetically more favorable (deltaH(a)(298) = 14.5 kcal/mol), again due to the catalytic effect of two water molecules. HOOOH generation requires the involvement of water in the decomposition of ROOOH where the direct formation out of ROOOH is energetically preferred. The energy for a reaction between two molecules of water and singlet oxygen (delta1O2) is too high to occur in solution.

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Revision of the dissociation energies of mercury chalcogenides--unusual types of mercury bonding.

Mercury chalcogenides HgE (E=O, S, Se, etc.) are described in the literature to possess rather stable bonds with bond dissociation energies between 53 and 30 kcal mol(-1), which is actually difficult to understand in view of the closed-shell electron configuration of the Hg atom in its ground state (...4f(14)5d(10)6s(2)). Based on relativistically corrected many body perturbation theory and coupled-cluster theory [IORAmm/MP4, Feenberg-scaled IORAmm/MP4, IORAmm/CCSD(T)] in connection with IORAmm/B3LYP theory and a [17s14p9d5f]/aug-cc-pVTZ basis set, it is shown that the covalent HgE bond is rather weak (2-7 kcal mol(-1)), the ground state of HgE is a triplet rather than a singlet state, and that the experimental bond dissociation energies have been obtained for dimers (or mixtures of monomers, dimers, and even trimers) Hg2E2 rather than true monomers. The dimers possess association energies of more than 100 kcal mol(-1) due to electrostatic forces between the monomer units. The covalent bond between Hg and E is in so far peculiar as it requires a charge transfer from Hg to E (depending on the electronegativity of E) for the creation of a single bond, which is supported by electrostatic forces. However, a bonding between Hg and E is reduced by strong lone pair-lone pair repulsion to a couple of kcal mol(-1). Since a triplet configuration possesses somewhat lower destabilizing lone pair energies, the triplet state is more stable. In the dimer, there is a Hg-Hg pi bond of bond order 0.66 without any a support. Weak covalent Hg-O interactions are supported by electrostatic bonding. The results for the mercury chalcogenides suggests that all experimental dissociation energies for group-12 chalcogenides have to be revised because of erroneous measurements.

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Relativistically corrected hyperfine structure constants calculated with the regular approximation applied to correlation corrected ab initio theory.

The infinite-order regular approximation (IORA) and IORA with modified metric (IORAmm) is used to develop an algorithm for calculating relativistically corrected isotropic hyperfine structure (HFS) constants. The new method is applied to the calculation of alkali atoms Li-Fr, coinage metal atoms Cu, Ag, and Au, the Hg(+) radical ion, and the mercury containing radicals HgH, HgCH(3), HgCN, and HgF. By stepwise improvement of the level of theory from Hartree-Fock to second-order Møller-Plesset theory and to quadratic configuration interaction theory with single and double excitations, isotropic HFS constants of high accuracy were obtained for atoms and for molecular radicals. The importance of relativistic corrections is demonstrated.

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Calculation of indirect nuclear spin-spin coupling constants within the regular approximation for relativistic effects.

A new method for calculating the indirect nuclear spin-spin coupling constant within the regular approximation to the exact relativistic Hamiltonian is presented. The method is completely analytic in the sense that it does not employ numeric integration for the evaluation of relativistic corrections to the molecular Hamiltonian. It can be applied at the level of conventional wave function theory or density functional theory. In the latter case, both pure and hybrid density functionals can be used for the calculation of the quasirelativistic spin-spin coupling constants. The new method is used in connection with the infinite-order regular approximation with modified metric (IORAmm) to calculate the spin-spin coupling constants for molecules containing heavy elements. The importance of including exact exchange into the density functional calculations is demonstrated.

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Decomposition of nuclear magnetic resonance spin-spin coupling constants into active and passive orbital contributions.

The theory of the J-OC-PSP (decomposition of J into orbital contributions using orbital currents and partial spin polarization) method is derived to distinguish between the role of active, passive, and frozen orbitals on the nuclear magnetic resonance (NMR) spin-spin coupling mechanism. Application of J-OC-PSP to the NMR spin-spin coupling constants of ethylene, which are calculated using coupled perturbed density functional theory in connection with the B3LYP hybrid functional and a [7s,6p,2d/4s,2p] basis set, reveal that the well-known pi mechanism for Fermi contact (FC) spin coupling is based on passive pi orbital contributions. The pi orbitals contribute to the spin polarization of the sigma orbitals at the coupling nuclei by mediating spin information between sigma orbitals (spin-transport mechanism) or by increasing the spin information of a sigma orbital by an echo effect. The calculated FC(pi) value of the SSCC (1)J(CC) of ethylene is 4.5 Hz and by this clearly smaller than previously assumed.

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Investigation of the NMR spin-spin coupling constants across the hydrogen bonds in ubiquitin: the nature of the hydrogen bond as reflected by the coupling mechanism.

The indirect scalar NMR spin-spin coupling constants across the H-bonds of the protein ubiquitin were calculated, including the Fermi contact, the diamagnetic spin-orbit, the paramagnetic spin-orbit, and the spin dipole term, employing coupled perturbed density functional theory in combination with the B3LYP functional and different basis sets: (9s,5p,1d/5s,1p)[6s,4p,1d/3s,1p] and (11s,7p,2d/5s,1p)[7s,6p,2d/4s,2p]. Four different models based on either the crystal or the aqueous solution structure of ubiquitin were used to describe H-bonding for selected residue pairs of ubiquitin. Calculated and measured 3hJ(NC') coupling constants differ depending on the model used, which is due to the fact that the geometry of ubiquitin is different in the solid state and in aqueous solution. Also, conformational averaging leads to a decrease of the magnitude of the measured 3hJ(NC') constants, which varies locally (larger for -sheets, smaller for -helix). Two different spin-spin coupling mechanisms were identified. While mechanism I transmits spin polarization via an electric field effect, mechanism II involves also electron delocalization from the lone pair of the carbonyl oxygen to the antibonding orbital of the N-H bond. Mechanism I is more important in the crystal structure of ubiquitin, while in aqueous solution, mechanism II plays a larger role. It is possible to set up simple relationships between the spin-spin coupling constants associated with the H bond in proteins and the geometrical features of these bonds. The importance of the 3hJ(NC') and 1J(N-H) constants as descriptors for the H-bond is emphasized.

Amides↗

Can one assess the pi character of a C-C bond with the help of the NMR spin-spin coupling constants?

Measured one-bond spin-spin coupling constants (SSCC) 1J(CC) can be used to describe the nature of the C-C bond, provided one is able to separate the various coupling mechanisms leading to 1J(CC). The Fermi-contact (FC) term probes the first-order density at the positions of the coupling nuclei, whereas the noncontact terms (the paramagnetic spin orbit (PSO) and the spin-dipole (SD) terms) probe the pi character of the C-C bond (the diamagnetic spin orbit (DSO) term can mostly be neglected). A model is tested, in which the value of the FC(CC) term is estimated with the help of measured SSCCs 1J(CH). The difference between the measured J(CC) and the estimated FC(CC) values, delta(CC) = PSO(CC) + SD(CC) + DSO(CC), provides a semiquantitative measure of the pi character of a C-C multiple bond. The applicability and limitations of this approach are discussed by partitioning the four Ramsey terms of the SSCC 1J(CC) into one- and two-orbital contributions. The FC, PSO, and SD terms of 1J(CC) are explained and analyzed with regard to their relationship to other C-C bond properties. It is shown that empirical relationships between measured SSCCs and the s character of a bond need reconsideration.

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The impact of the self-interaction error on the density functional theory description of dissociating radical cations: ionic and covalent dissociation limits.

Self-interaction corrected density functional theory was used to determine the self-interaction error for dissociating one-electron bonds. The self-interaction error of the unpaired electron mimics nondynamic correlation effects that have no physical basis where these effects increase for increasing separation distance. For short distances the magnitude of the self-interaction error takes a minimum and increases then again for decreasing R. The position of the minimum of the magnitude of the self-interaction error influences the equilibrium properties of the one-electron bond in the radical cations H2+ (1), B2H4+ (2), and C2H6+ (3), which differ significantly. These differences are explained by hyperconjugative interactions in 2 and 3 that are directly reflected by the self-interaction error and its orbital contributions. The density functional theory description of the dissociating radical cations suffers not only from the self-interaction error but also from the simplified description of interelectronic exchange. The calculated differences between ionic and covalent dissociation for 1, 2, and 3 provide an excellent criterion for determining the basic failures of density functional theory, self-interaction corrected density functional theory, and other methods. Pure electronic, orbital relaxation, and geometric relaxation contributions to the self-interaction error are discussed. The relevance of these effects for the description of transition states and charge transfer complexes is shown. Suggestions for the construction of new exchange-correlation functionals are given. In this connection, the disadvantages of recently suggested self-interaction error-free density functional theory methods are emphasized.

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Systematic strategy for decoding the NMR spin-spin coupling mechanism: the J-OC-PSP method.

Criteria for analyzing the NMR spin-spin coupling mechanism were derived. Advantages and disadvantages of parallel- and post-processing analytical methods are discussed. An orbital decomposition into just one-orbital contributions provides less information than a decomposition into one-, two- and m-orbital effects. If just the last orbital in an orbital path leading from the perturbing to the responding nucleus is considered, the physics of the transport of spin information cannot be described. The theory of the J-OC-PSP (decomposition of J into Orbital Contributions using Orbital Currents and Partial Spin Polarization) is described to demonstrate the role of orbital contributions, orbital spin densities and orbital currents for the coupling mechanism. J-OC-PSP1 provides a decomposition into one- and two-orbital contributions with distinct physical reference (Ramsey perturbation of orbitals, steric exchange interactions, etc.) whereas J-OC-PSP2 introduces distinct orbital paths from perturbing to responding nucleus, clarifies the difference between active, passive and frozen orbitals and makes it possible to separate through-space from through-bond spin-spin coupling mechanism. Fermi contact coupling in hydrocarbons over more than two bonds is found to occur preferentially through space by tail interactions of the orbitals, as was anticipated in the early work of Barfield.

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Mechanism of formation of hydrogen trioxide (HOOOH) in the ozonation of 1,2-diphenylhydrazine and 1,2-dimethylhydrazine: an experimental and theoretical investigation.

Low-temperature (-78 degrees C) ozonation of 1,2-diphenylhydrazine in various oxygen bases as solvents (acetone-d(6), methyl acetate, tert-butyl methyl ether) produced hydrogen trioxide (HOOOH), 1,2-diphenyldiazene, 1,2-diphenyldiazene-N-oxide, and hydrogen peroxide. Ozonation of 1,2-dimethylhydrazine produced besides HOOOH, 1,2-dimethyldiazene, 1,2-dimethyldiazene-N-oxide and hydrogen peroxide, also formic acid and nitromethane. Kinetic and activation parameters for the decomposition of the HOOOH produced in this way, and identified by (1)H, (2)H, and (17)O NMR spectroscopy, are in agreement with our previous proposal that water participates in this reaction as a bifunctional catalyst in a polar decomposition process to produce water and singlet oxygen (O(2), (1)delta(g)). The possibility that hydrogen peroxide is, besides water, also involved in the decomposition of hydrogen trioxide is also considered. The half-life of HOOOH at room temperature (20 degrees C) is 16 +/- 1 min in all solvents investigated. Using a variety of DFT methods (restricted, broken-symmetry unrestricted, self-interaction corrected) in connection with the B3LYP functional, a stepwise mechanism involving the hydrotrioxyl (HOOO(*)) radical is proposed for the ozonation of hydrazines (RNHNHR, R = H, Ph, Me) that involves the abstraction of the N-hydrogen atom by ozone to form a radical pair, RNNHR(*) (*)OOOH. The hydrotrioxyl radical can then either abstract the remaining N(H) hydrogen atom from the RNNHR(*) radical to form the corresponding diazene (RN=NR), or recombines with RNNHR(*) in a solvent cage to form the hydrotrioxide, RN(OOOH)NHR. The decomposition of these very labile hydrotrioxides involves the homolytic scission of the RO-OOH bond with subsequent "in cage" formation of the diazene-N-oxide and hydrogen peroxide. Although 1,2-diphenyldiazene is unreactive toward ozone under conditions investigated, 1,2-dimethyldiazene reacts with relative ease to yield 1,2-dimethyldiazene-N-oxide and singlet oxygen (O(2), (1)delta(g)). The subsequent reaction sequence between these two components to yield nitromethane as the final product is discussed. The formation of formic acid and nitromethane in the ozonolysis of 1,2-dimethylhydrazine is explained as being due to the abstraction of a methyl H atom of the CH(3)NNHCH(3)(*) radical by HOOO(*) in the solvent cage. The possible mechanism of the reaction of the initially formed formaldehyde methylhydrazone (and HOOOH) with ozone/oxygen mixtures to produce formic acid and nitromethane is also discussed.

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