Joze Koller

University of Ljubljana, Lubliano, Ljubljana, Slovenia

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Publications (16)98.17 Total impact

  • Tell Tuttle · Janez Cerkovnik · Joze Koller · Bozo Plesnicar ·
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    ABSTRACT: Protonated dihydrogen trioxide (HOOOH) has been postulated in various forms for many years. Protonation can occur at either the terminal (HOOO(H)H(+)) or central (HOOH(OH)(+)) oxygen atom. However, to date there has been no definitive evidence provided for either of these species. In the current work we have employed ab initio methods, CCSD(T) and MP2, with a large basis set (6-311++G(3df,3pd)) to determine the relative stabilities of these species. It is shown that the terminally protonated species is strongly favored relative to the centrally protonated species (DeltaE = 15.8 kcal/mol, CCSD(T)//MP2). The mechanism of formation of HOOO(H)H(+) was determined to occur with a low barrier with the H(3)O(+) occurring in a thermoneutral reaction (DeltaE = -0.3 kcal/mol, CCSD(T)//MP2). Although HOOO(H)H(+) exists as a stable intermediate, it is extremely short-lived and rapidly decomposes (DeltaE* = 8.6 kcal/mol, MP2) to H(3)O(+) and O(2)((1)Delta(g)). The decomposition reaction is stabilized by solvent water molecules. The short-lived nature of the intermediate implies that the intermediate species can not be observed in (17)O NMR spectra, which has been demonstrated experimentally.
    The Journal of Physical Chemistry A 08/2010; 114(30):8003-8. DOI:10.1021/jp103882e · 2.69 Impact Factor
  • Miklos Kertesz · Joze Koller · Andrej Azman ·
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    ABSTRACT: The presence of nonsinglet instabilities of the restricted Hartree-Fock ground-state wavefunction may be an indication of strong correlation effects. We have recently observed that such instabilities persist in some conjugated polymers even with localizable electronic structure, like strongly alternating polyene [(CH)x] or its isoelectronic analog (polymethineimine) by performing ab initio STO-3G unrestricted Hartree-Fock (UHF) calculations for these chain systems, using different geometrical arrangements. We suggest that coupled-cluster calculations might give a resolution to this problem.
    International Journal of Quantum Chemistry 03/2009; 18(S14):463-466. DOI:10.1002/qua.560180848 · 1.43 Impact Factor
  • Janez Cerkovnik · Bozo Plesnicar · Joze Koller · Tell Tuttle ·
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    ABSTRACT: We demonstrate in this work by theory and experiment that benzaldehyde hydrotrioxide (PhC(O)OOOH), the intermediate most likely formed in the low-temperature ozonation of benzaldehyde, is too unstable to be detected by NMR (1H, 13C, and 17O) spectroscopy in various organic solvents at temperatures > or = -80 degrees C and that its previous detection must have been erroneous. Several plausible mechanisms for the formation of this polyoxide were explored by using density functional theory. We found that the formation of the hydrotrioxide involves the facile 1,3-dipolar insertion of ozone into the C-H bond (deltaH(double dagger) = 11.1 kcal/mol) in a strongly exothermic process (deltaH(R) = -57.0 kcal/mol). The hydrotrioxide then quickly decomposes in a second concerted, exothermic reaction involving an intramolecular H transfer to form benzoic acid and singlet oxygen (O2(1delta(g))) (deltaH(double dagger) = 5.6 kcal/mol), deltaH(R) = -14.0 kcal/mol). The equilibrium is thus expected to be shifted toward the products; therefore, this intermediate cannot be observed experimentally. Peroxybenzoic acid, still another major reaction product formed in the ozonation reaction, is formed as a result of the surprising instability of the RC(O)O-OOH bond (deltaH(R) = 23.5 kcal/mol), generating HOO* and benzoyloxyl radicals. Both of these radicals can then initiate the chain autoxidation reaction sequence--the abstraction of a H atom from benzaldehyde to form either a benzoyl radical and HOOH or a benzoyl radical and benzoic acid. Because only very small amounts of HOOH were detected in the decomposition mixtures, the recombination of the benzoyl radical with the HOO* radical (deltaH(R) = -80.7 kcal/mol) appears to be the major source of peroxybenzoic acid. A theoretical investigation of the mechanistic possibility of the involvement of still another intermediate, a cyclic tetraoxide (tetraoxolane) formed as a primary product in the 1,3-dipolar cycloaddition of ozone to the carbonyl group of the aldehyde, revealed that the tetraoxide is a "real" molecular entity with the five-membered ring adopting an envelope conformation. The tetraoxide is destabilized by 7.0 kcal/mol relative to the reactant complex, and the transition state for its formation is 17.4 kcal/mol above the reactant complex, which, although accessible under the reaction conditions, is not expected to be competitive with the reaction generating the hydrotrioxide.
    The Journal of Organic Chemistry 12/2008; 74(1):96-101. DOI:10.1021/jo801594n · 4.72 Impact Factor
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    ABSTRACT: Hydrogen-bonded gas-phase molecular clusters of dihydrogen trioxide (HOOOH) have been investigated using DFT (B3LYP/6-311++G(3df,3pd)) and MP2/6-311++G(3df,3pd) methods. The binding energies, vibrational frequencies, and dipole moments for the various dimer, trimer, and tetramer structures, in which HOOOH acts as a proton donor as well as an acceptor, are reported. The stronger binding interaction in the HOOOH dimer, as compared to that in the analogous cyclic structure of the HOOH dimer, indicates that dihydrogen trioxide is a stronger acid than hydrogen peroxide. A new decomposition pathway for HOOOH was explored. Decomposition occurs via an eight-membered ring transition state for the intermolecular (slightly asynchronous) transfer of two protons between the HOOOH molecules, which form a cyclic dimer, to produce water and singlet oxygen (Delta (1)O 2). This autocatalytic decomposition appears to explain a relatively fast decomposition (Delta H a(298K) = 19.9 kcal/mol, B3LYP/6-311+G(d,p)) of HOOOH in nonpolar (inert) solvents, which might even compete with the water-assisted decomposition of this simplest of polyoxides (Delta H a(298K) = 18.8 kcal/mol for (H 2O) 2-assisted decomposition) in more polar solvents. The formation of relatively strongly hydrogen-bonded complexes between HOOOH and organic oxygen bases, HOOOH-B (B = acetone and dimethyl ether), strongly retards the decomposition in these bases as solvents, most likely by preventing such a proton transfer.
    The Journal of Physical Chemistry A 10/2008; 112(35):8129-35. DOI:10.1021/jp8036928 · 2.69 Impact Factor
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    ABSTRACT: Binding of a small molecule to a macromolecular target reduces its conformational freedom, resulting in a negative entropy change that opposes the binding. The goal of this study is to estimate the configurational entropy change of two minor-groove-binding ligands, netropsin and distamycin, upon binding to the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). Configurational entropy upper bounds based on 10-ns molecular dynamics simulations of netropsin and distamycin in solution and in complex with DNA in solution were estimated using the covariance matrix of atom-positional fluctuations. The results suggest that netropsin and distamycin lose a significant amount of configurational entropy upon binding to the DNA minor groove. The estimated changes in configurational entropy for netropsin and distamycin are -127 J K(-1) mol(-1) and -104 J K(-1) mol(-1), respectively. Estimates of the configurational entropy contributions of parts of the ligands are presented, showing that the loss of configurational entropy is comparatively more pronounced for the flexible tails than for the relatively rigid central body.
    Biophysical Journal 09/2006; 91(4):1460-70. DOI:10.1529/biophysj.105.074617 · 3.97 Impact Factor
  • M. Kertesz · J. Koller · A. Azman ·
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    ABSTRACT: The most wide-spread ab initio technique for polymers, the LCAO Hartree-Fock-Roothaan-type crystal orbital method is reviewed with emphasis on its convergence properties (mainly on basis sets and lattice sums). Questions of numerical realization including a symmetry problem are mentioned. Possibilities for obtaining physical parameters other than total energy are discussed. Problems associated with evaluation of localized one-particle orbitals (Wannier functions) are presented including their possible use as basis functions in electronic correlation calculations. Some examples of Hartree-Fock instabilities for polymers with partly filled energy band are given. The paper is supplemented by a bibliography of applications of ab initio techniques for ground state calculations on polymers and one-dimensional models of solids.
    Recent Advances in the Quantum Theory of Polymers, 01/2006: pages 56-79;
  • Urban Bren · Milan Hodoscek · Joze Koller ·
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    ABSTRACT: The netropsin molecule preferentially binds to the four consecutive A.T base pairs of the DNA minor groove and could therefore inhibit the expression of specific genes. The understanding of its binding on a molecular level is indispensable for computer-aided design of new antitumor agents. This knowledge could be obtained via molecular dynamics (MD) and docking simulations, but in this case appropriate force field parameters for the netropsin molecule should be explicitly defined. Our parametrization was based on the results of quantum chemical calculations. The resulting set of parameters was able to reproduce bond lengths, bond angles, torsional angles of the ab initio minimized geometry within 0.03 A, 3 deg and 5 deg, respectively, and its vibrational frequencies with a relative error of 4.3% for low and 2.8% for high energy modes. To show the accuracy of the developed parameters we calculated an IR spectrum of the netropsin molecule using MD simulation and found it to be in good agreement with the experimental one. Finally, we performed a 10 ns long MD simulation of the netropsin-DNA complex immersed in explicit water. The overall complex conformation remained stable at all times, and its secondary structure was well retained.
    Journal of Chemical Information and Modeling 11/2005; 45(6):1546-52. DOI:10.1021/ci050151r · 3.74 Impact Factor
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    ABSTRACT: Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than netropsin, the loss of ligand-solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding.
    Nucleic Acids Research 02/2005; 33(2):725-33. DOI:10.1093/nar/gki195 · 9.11 Impact Factor
  • M. Kertész · J. Koller · A. Ažman ·
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    ABSTRACT: The occurrence of broken-symmetry Hartree-Fock solutions may indicate instability of the lattice depending on the symmetry of the charge-density wave (CDW). In case of polyacetylene, (CH)x, we have found such solutions having an off-diagonal CDW. It is pointed out that this sort of instability is principally different from the Peierls instability. The importance of correct (symmetrical) cutoff of interactions in direct space (“finite neighbor's approximation”) is emphasized. A basic difference in the potential-energy curve of trans-(CH)x and the isoelectronic (HCN)x around the equidistant configuration is shown.
    International Journal of Quantum Chemistry 10/2004; 18(2):645 - 650. DOI:10.1002/qua.560180240 · 1.43 Impact Factor
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    ABSTRACT: 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.
    Journal of the American Chemical Society 10/2003; 125(38):11553-64. DOI:10.1021/ja036801u · 12.11 Impact Factor
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    Elfi Kraka · Dieter Cremer · Joze Koller · Bozo Plesnicar ·
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    ABSTRACT: The HOOO(-) anion (1) can adopt a triplet state (T-1) or a singlet state (S-1), where the former is 9.8 kcal/mol (DeltaH(298) = 10.3 kcal/mol) more stable than the latter. S-1 possesses a strong O-OOH bond with some double bond character and a weakly covalent OO-OH bond (1.80 A) according to CCSD(T)/6-311++G(3df,3pd) calculations (the longest O-O bond ever found for a peroxide). In aqueous solution, S-1 adopts a geometry closely related to that of HOOOH (OO(O), 1.388 A; (O)OO(H), 1.509 A; tau(OOOH), 78.3 degrees ), justifying that S-1 is considered the anion of HOOOH. Dissociation into HO anion and O(2)((1)Delta(g)) requires 15.4 (DeltaH(298) = 14.3; DeltaG(298) = 8.9) kcal/mol. Structure T-1 corresponds to a van der Waals complex between HO anion and O(2)((3)Sigma(g)(-)) having a binding energy of 2.7 (DeltaH(298) = 2.1) kcal/mol. Modes of generating S-1 in aqueous solution are discussed, and it is shown that S-1 represents an important intermediate in ozonation reactions.
    Journal of the American Chemical Society 08/2002; 124(28):8462-70. DOI:10.1021/ja012553v · 12.11 Impact Factor
  • Nina Lah · Joze Koller · Gerald Giester · Primoz Segedin · Ivan Leban ·
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    ABSTRACT: Reactions of copper(II) carboxylates with 4-aminopyridine (4-apy) were investigated and their products structurally characterized by single crystal X-ray diffraction. Reaction of copper(II) acetate resulted in two isomers of a monomeric complex of composition Cu(ac)2(4-apy)2 with markedly different stabilities: the violet form, 1, unstable in air and the blue, stable form, 2. In both isomers the ligands are arranged around the copper atom in a trans geometry. The 4-apy ligands lie almost in the plane in 1, while they are twisted with respect to each other in 2. Variations were observed also in the coordination of the acetate groups to the copper ion. The energy difference between the two isomers was obtained on the basis of ab initio MO calculations. The result agrees well with the observed relative stabilities in the solid state. Monomeric complexes of the same stoichiometry were obtained also by the reaction of Cu(II) hexanoate and heptanoate with 4-apy. The violet Cu(hex)2(4-apy)2, 3, and Cu(hep)2(4-apy)2, 4, are isostructural and possess trans geometry of the ligands around the copper centre. Reaction of 4-apy with Cu(II) octanoate lead to formation of a novel, unprecedented basic centrosymmetric tetranuclear compound of composition Cu4(oct)6(OH)2(4-apy)2, 5. Complex 5 contains bidentate bridging and monoatomic bridging carboxylate groups, triply bridging hydroxyl groups and 4-aminopyridine as a terminal ligand. In all five compounds 4-apy is coordinated through the endocyclic nitrogen atom only.
    New Journal of Chemistry 06/2002; 26(7):933-938. DOI:10.1039/b110051c · 3.09 Impact Factor
  • Janez Cerkovnik · Evgen Erzen · Joze Koller · Bozo Plesnicar ·
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    ABSTRACT: Low-temperature ozonation of cumene (1a) in acetone, methyl acetate, and tert-butyl methyl ether at -70 degrees C produced the corresponding hydrotrioxide, C(6)H(5)C(CH(3))(2)OOOH (2a), along with hydrogen trioxide, HOOOH. Ozonation of triphenylmethane (1b), however, produced only triphenylmethyl hydrotrioxide, (C(6)H(5))(3)COOOH (2b). These observations, together with the previously reported experimental evidence, seem to support the "radical" mechanism for the first step of the ozonation of the C-H bonds in hydrocarbons, i.e., the formation of the caged radical pair (R(**)OOOH), which allows both (a) collapse of the radical pair to ROOOH and (b) the abstraction of the hydrogen atom from alkyl radical R(*) by HOOO(*) to form HOOOH. The B3LYP/6-311++G(d,p) (ZPE) calculations revealed that HOOO radicals are considerably stabilized by forming intermolecularly hydrogen-bonded complexes with acetone (BE = 8.55 kcal/mol) and dimethyl ether (7.04 kcal/mol). This type of interaction appears to be crucial for the relatively fast reactions (and the formation of the polyoxides in relatively high yields) in these solvents, as compared to the ozonations run in nonbasic solvents. However, HOOO radicals appear to be not stable enough to abstract hydrogen atoms outside the solvent cage, as indicated by the absence of HOOOH among the products in the ozonolysis of triphenylmethane. The decomposition of alkyl hydrotrioxides 2a and 2b involves a homolytic cleavage of the RO-OOH bond with subsequent "in cage" reactions of the corresponding radicals, while the decomposition of HOOOH is most likely predominantly a "pericyclic" process involving one or more molecules of water acting as a bifunctional catalyst to produce water and singlet oxygen (Delta(1)O(2)).
    Journal of the American Chemical Society 02/2002; 124(3):404-9. DOI:10.1021/ja017320l · 12.11 Impact Factor
  • E Erzen · J Koller · B Plesnicar ·
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    ABSTRACT: The oxidation of thianthrene 5-oxide, i.e., a mechanistic probe for the assessment of the electronic character of various oxidants, with peroxybenzoic acids in various oxygen bases as solvents was investigated. The nucleophilicity (X(SO)) of peroxy acids was increasing with increasing basicity of the oxygen base. A good linear correlation was observed by plotting X(SO) values vs either the Kamlet-Taft beta values or the OOH (1)H NMR chemical shifts of m-chloroperoxybenzoic acid (m-CPBA) in solvents of various basicity. These observations, together with the results of IR and (1)H NMR spectroscopic studies of peroxybenzoic acids, and DFT (B3LYP/6-311++G) studies of the intramolecular hydrogen bonding in peroxyformic, peroxyacetic, and m-CPBA, as well as the intermolecular hydrogen bonding in the complexes of the these peroxy acids with dimethyl ether as a model oxygen base, support the involvement of the peroxy acid-oxygen base complexes in the transition states of these reactions. The increased nucleophilicity (X(SO)) of peroxy acids in basic solvents is most likely due to the increased negative charge on the terminal "electrophilic" peroxycarboxylic oxygen atom (OH), and/or the increased LUMO and HOMO energies of the peroxy acid in the complexes, as compared to those parameters in the intramolecularly hydrogen-bonded form of peroxy acids, believed to be operative in inert solvents.
    The Journal of Organic Chemistry 08/2001; 66(15):5155-62. · 4.72 Impact Factor
  • Bozo Plesnicar · Janez Cerkovnik · Joze Koller · Franci Kovac ·
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    ABSTRACT: The preparation and H-1, C-13, and Si-29 NMR spectroscopic characterization of dimethylphenylsilyl hydrotrioxides (2), produced by the low temperature (-78-degrees-C) ozonation of dimethylphenylsilanes (1) in acetone-d6, methyl acetate, and dimethyl ether, is reported. H-1 NMR spectroscopic evidence for the involvement of a transient polyoxide, tentatively assigned to hydrogen trioxide (HOOOH), in the decomposition of 2 is given. All attempts to characterize both types of hydrotrioxides by O-17 NMR spectroscopy failed. The calculated relatively strong binding energy for the intermolecularly hydrogen-bonded cyclic dimer of HOOOH (BE = 7.7 kcal/mol, 6-31G**//6-31G) support the belief that self-association is, similarly to previously studied hydrotrioxides, H3SiOOOH and CH3OOOH, the characteristic structural feature of this species. Kinetic and activation parameters for the decomposition of 2, i.e., large negative activation entropies, a rather significant substituent effect on the decomposition of 2a in methyl acetate (Hammett rho-value 1.2 +/-0.1) as well as the observed dependence of the rate of the decomposition of 2a on solvent polarity, indicate the importance of polar decomposition pathways. The results of ESR spin trapping experiments are, together with product studies, discussed in terms of possible contributions of homolytic processes to the overall mechanism of the decomposition of 2. The negative Hammett rho-values for the oxidation of phenyl methyl sulfides to sulfoxides and the latter to the corresponding sulfones with 2 as well as the reactivity order 4-XPhSMe >> 4-XPhSOMe indicate an electrophilic nature of the oxidant.
    Journal of the American Chemical Society 06/1991; 113(13). DOI:10.1021/ja00013a034 · 12.11 Impact Factor
  • Joze Koller · Milan Hodoscek · Bozo Plesnicar ·
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    ABSTRACT: Ab initio calculations have been carried out to predict the equilibrium structures of monomeric and dimeric CHâOOOH, HâSiOOOH, CHâOOH, and HâSiOOH. The calculated relatively strong binding energies for the intermolecularly hydrogen-bonded cyclic dimers of the hydrotrioxides and hydroperoxides investigated (BE = 6-8 kcal/mol) support the belief that self-association is the characteristic structural feature of these species. Ab initio calculations of the theoretical acidities, defined as the energy differences between the energy minima for the neutral molecules and those for the corresponding anions, reveal the following order of the gas-phase acidities: HâSiOOOH > CHâOOOH > HâSiOOH > CHâOOH. The investigation of relative bond strengths indicates that the RO-OOH bonds in the hydrotrioxides are weaker than the ROO-OH bonds, supporting the predictions from the previous thermochemical and kinetic studies that the split into RO{sm bullet} and {sm bullet}OOH radicals is the lowest energy radical decomposition pathway available for these polyoxides.
    Journal of the American Chemical Society 03/1990; 112(6):2124-2129. DOI:10.1021/ja00162a013 · 12.11 Impact Factor