Homolytic Dissociation Research Articles

Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments

Development and applications of a new approach to hybrid quantum mechanical and molecular mechanical (QM/MM) theory based on the effective fragment potential (EFP) technique for modeling properties and reactivity of large molecular systems of biochemical significance are described. It is shown that a restriction of frozen internal coordinates of effective fragments in the original formulation of the theory (Gordon, M. S.; Freitag, M. A.; Bandyopadhyay, P.; Jensen, J. H.; Kairys, V.; Stevens, W. J. J. Phys. Chem. A 2001, 105, 293) can be removed by introducing a set of small EFs and replacing the EFP−EFP interactions by the customary MM force fields. The concept of effective fragments is also utilized to solve the QM/MM boundary problem across covalent bonds. The buffer fragment, which is common for both subsystems, is introduced and treated specially when energy and energy gradients are computed. An analysis of conformations of dipeptide−water complexes, as well as of dipepties with His and Lys residues, confirms the reliability of the theory. By using the Hartree−Fock and MP2 quantum chemistry methods with the OPLS-AA molecular mechanical force fields, we calculated the energy difference between the enzyme−substrate complex and the first tetrahedral intermediate for the model active site of the serine protease catalytic system. In another example, the multiconfigurational complete active space self-consistent field (CASSCF) method was used to model the homolytic dissociation of the peptide helix over the central C−N bonds. Finally, the potentials of internal rotation of the water dimer considered as a part of the water wire inside a polyglycine analogue of the ion channel gramicidin A were computed. In all cases, an importance of the peptide environment from MM subsystems on the computed properties of the quantum parts is demonstrated.

Synthesis, X-ray structure, and properties of the singly bonded C60 dimer having diethoxyphosphorylmethyl groups utilizing the chemistry of C60(2-).

[reaction: see text] A singly bonded C60 dimer having a diethoxyphosphorylmethyl group on each C60 cage was obtained by the reaction of C60(2-) dianion with diethyl iodomethylphosphonate followed by the treatment with iodine. The precise structure of the dimer was determined for the first time by X-ray crystallography, and its homolytic dissociation as well as spectroscopic and electrochemical properties were clarified.

Thermodynamics and kinetics of homolytic cleavage of carbon–oxygen bonds in radical anions obtained by electrochemical reduction of alkyl aryl ethers

The properties and the reactivity of the radical anions of 4-cyanophenyl alkyl ethers and naphthyl alkyl ethers have been determined by electrochemical methods. Under electrochemical conditions homolytic dissociation is the only observed process. Cyclic voltammetry studies lead to the conclusion that this process is a stepwise one, the initially produced radical anion cleaving by a slow first order reaction followed by a second electron transfer in a DISP1 mechanism. A Marcus type relationship between the cleavage rate constants and the standard free energy of the reaction leads to an intrinsic barrier in the range of 0.7 to 0.8 eV. The analysis of the intrinsic barrier values indicates that solvent organisation represents a modest contribution, the bond dissociation energy of the radical anion (structural contribution) being the main factor in the total barrier. Previously unknown bond dissociation energies of naphthyl ethers have been estimated using the correlations established in this work.

Aromatic cyanation in contact glow discharge electrolysis of acetonitrile

Contact glow discharge electrolysis of acetonitrile solution containing a variety of aromatic compounds was carried out. A stable discharge was sustained around a platinum wire anode in contact with a surface of solution, when a d.c. high voltage over 500 V was applied between the anode and cathode immersed in the solution under ambient pressure of argon. An aromatic substitution involving radicals produced through the homolytic dissociation of acetonitrile significantly occurred to result in the formation of corresponding cyanoaromatics as well as propionitrile, succinonitrile, and acrylonitrile. The effects of reaction conditions on the current yields of products were discussed in association with the reaction mechanism.

Grignard Reaction as a Result of Tunneling of the Triplet Branch of the Reaction Through a Singlet Barrier

Quantum-chemical calculations were carried out to study the mechanism of the Grignard reaction Mg + CH3F. The reaction between Mg, CH3F gives rise to a triplet complex which has a lower energythan the corresponding singlet complex at MgFCH3 angles ranging from 60 to 139°. The transition from thesinglet branch of the reaction to the nonequilibrium triplet branch results in decomposition of CH3F with formation of various final products. A linear Grignard reagent CH3-Mg-F is formed by simultaneous homolytic CH3-F dissociation and ionic covalent interaction of the methyl group and the fluorine atom with the magnesium cation arising in the course of the reaction. Normal mode frequencies for the Mg + CH3F complex at various MgFCH3 are were calculated. The calculation results nicely agree with experimental data.

Electron-spin conservation and methyl-substitution effects on bonds in closed- and open-shell systems — A G3 ab initio study of small boron-containing molecules and radicals

High level ab initio molecular orbital theory calculations have been used to study the geometries and thermochemistry of molecules and free radicals substituted by BH2, BHCH3, and B(CH3)2. The heats of formation and RR'B—X bond strengths (RR' = H, H; H, CH3; CH3, CH3 and X = CH3, NH2, OH, F, SiH3, PH2, SH, and Cl) together with those for the open-shell systems RR'B—Y· (RR' = H, H; H, CH3; CH3, CH3 and Y = CH2, NH, O, SiH2, PH, and S) have been calculated at the G3 level of theory. The trends observed for the homolytic bond strengths in the closed-shell systems are those expected from electronegativity arguments, i.e., as the difference in electronegativity between the two atoms in the B—X bond increases, the bond strength increases. Methyl substitution on B in the closed- and open-shell species increases the ionic contribution to the bond thereby decreasing the bond strength. The lowest possible homolytic dissociation energy for the free radicals RR'BY· is lower than those of their closed-shell counterparts, yet the B—Y· bonds are shorter. This is due to the demands of spin conservation in the dissociation of the radicals favouring the formation of higher energy products.Key words: ab initio calculations, bond dissociation energy, organoboron compounds, thermochemistry.

Laser flash photolysis study of azides derived from Cr(iii) and Mn(iii) salen complexes

Laser flash photolysis of (salen)Cr(III) and (salen)Mn(III) azides has shown that photodenitrogenation occurs through the intermediacy of triplet metal nitrenes. A minor competing pathway consisting in the formation of tetra-coordinated Mn(II) and Cr(II) fragments has also been observed. Both reaction paths are explained through two sorts of photocleavages centered on the azido apical ligand: (a) rupture of the N–N2 bond to form the coordinated triplet nitrene and (b) homolytic dissociation of the metal–N3 bond.

P–P bond cleavage; energetics and structural changes in tetramethyldiphosphine and tetrasilyldiphosphine from ab initio MO calculations

The molecular structures and conformations of tetramethyldiphosphine and tetrasilyldiphosphine and their corresponding dimethylphosphido and disilylphosphido radicals were computed by high-level ab initio molecular orbital calculations utilising a range of methods (HF, MP2, B3LYP) and different basis sets. The thermodynamic properties of the homolytic dissociation reaction were also calculated at the G2 level and compared with those computed by other theoretical methods. The results indicate that although the MP2/6-311+G* calculations are superior in reproducing experimental structural and high-level theoretical thermodynamic data, the thermodynamic properties computed using the B3LYP method with effective core potentials for Si and P or even with a small (3-21G*) basis set are on a par with calculations employing larger basis sets and more elaborate treatment of electron correlation at the MP2 level. This offers the possibility of quick reasonable estimation of thermodynamic properties of large dissociating systems. An estimation of bond energies based on the energetics of structural changes upon dissociation of the diphosphines gives values in agreement with the previously estimated P–P bond energies in organic compounds. The current ab initio calculations demonstrated the existence of two conformers of tetramethyldiphosphine, gauche and anti, with the anti form being more stable by 6.1 kJ mol−1 as computed at the MP2/6-311+G* level, in disagreement with the previous results of the electron diffraction structure investigation. This disagreement in the conformational composition and the large difference in computed and experimental values of the P–P–C angles indicate that the structure of tetramethyldiphosphine in the gas phase may need re-determination.

Thermal Decomposition of Secondary N-nitramines Having 1,2,4-Triasole and Tetrazole Substituents

Thermal decomposition of secondary N-nitramines having azole substituents in the β position is faster by almost two orders of magnitude than the decomposition of γ-substituted analogs. The rate-determining stage is homolytic dissociation of the NANO2 bond. An alternative route of thermal decomposition of γ-tetrazolyl-substituted N-nitramines involves initial clavage of the tetrazole ring.

A theoretical study on the homolytic dissociation energies of H–N+ bonds

Various levels of theoretical calculations were performed to study the N+–H bond dissociation energies (BDEs) of protonated amines in order to check the experimental results and to investigate the substituent effects. It was found that the reported experimental N+–H BDEs in the gas phase are possibly not accurate. Our best predictions on the basis of CBS-Q and G3 calculations for the N+–H BDEs of NH4+, CH3NH3+, (CH3)2NH2+, (CH3)3NH+, PhNH3+, and pyridinium are 125 ± 1, 110 ± 1, 107 ± 1, 95 ± 1, 75 ± 2, and 124 ± 1 kcal mol−1, respectively. In agreement with a previous study, it was also found that the solvent effects on the N+–H homolysis in acetonitrile are large, which significantly increases the N+–H BDEs compared to the gas phase. Further studies on the N+–H BDEs of protonated para-substituted anilines indicated that the substituent effects should have a slope of about 8.7 kcal mol−1 against the substituent σp+ constants. This value is larger than that for the O–H BDEs of phenols (6.7–6.9 kcal mol−1) and N–H BDEs of neutral anilines (3.0 kcal mol−1). The pattern of substituent effects is also completely different from that for the C–H BDEs of toluenes, as the C–H BDEs of toluenes are reduced by both the electron-withdrawing and -donating groups. Thus, we concluded that it is the electron demand of the system that dictates the substituent effects on BDEs. For the protonated aniline case, the origin of the substituent effects was found to be that an electron-withdrawing group destabilizes X–C6H4–NH2+˙ more than X–C6H4–NH3+, whereas an electron-donating group stabilizes X–C6H4–NH2+˙ more than X–C6H4–NH3+.

Kinetic Modeling of the Effect of H2S and of NH3 on Toluene Hydrogenation in the Presence of a NiMo/Al2O3 Hydrotreating Catalyst. Discrimination between Homolytic and Heterolytic Models

Toluene hydrogenation was studied within a wide range of hydrogen sulfide, hydrogen, toluene, and ammonia partial pressures on a standard sulfided NiMo/Al2O3 hydrotreating catalyst at 350 °C under a total pressure of 4.9−9.8 MPa. The results showed a complex inhibiting effect of H2S on the hydrogenation activity with an order of reaction relative to H2S varying between −0.05 and −0.5. Unexpectedly, this inhibiting effect was enhanced by the presence of ammonia. Several kinetic models based on the homolytic or heterolytic dissociation of hydrogen and hydrogen sulfide were investigated and discriminated by using the CHEMKIN/SURFACE CHEMKIN II tool. The heterolytic dissociation was supposed to occur on centers composed of an unsaturated Mo ion (on which hydride ions and organic molecules can adsorb) and of a sulfur anion, host of the proton generated by the heterolytic dissociation of hydrogen or hydrogen sulfide. It was concluded that toluene hydrogenation was most likely to occur through a heterolytic mech...

Selective Hydrogenation of Methyl Oleate into Unsaturated Alcohols in the Presence of Cobalt–Tin Supported over Zinc Oxide Catalysts

The hydrogenation of methyl oleate (methyl-9-octadecenoate) into oleyl alcohol (methyl-9-octadecen-1-ol) was studied in the presence of a bimetallic CoSn supported over a zinc oxide catalyst in a stainless steel batch reactor at 270°C and 8.0 MPa. Zinc oxide can activate the carbonyl group and also the hydrogen by a possible heterolytic and homolytic dissociation of dihydrogen. The selectivity to unsaturated alcohol (oleyl alcohol) was significantly enhanced by adding tin to cobalt. The activity and the selectivity to unsaturated alcohols was maximum for an atomic Sn/Co ratio of 1, as for the CoSn alumina sol–gel catalyst. For all CoSn catalysts, the selectivity to unsaturated alcohols goes through a maximum for a surface Sn/Co ratio close to 2, the active species being a mixed Me0–(SnOx)2, where the oxidation of tin is close to 0. The reduction of CoSn solids with sodium borohydride increased the activity of the catalyst.

Theoretical evaluation of the hydrogen kinetic isotope effect on the first step of the methylmalonyl-CoA mutase reaction

We have calculated hydrogen kinetic isotope effects (KIEs) for the first step of the methylmalonyl-CoA mutase reaction, including multidimensional tunneling correction at the zero curvature (ZCT) level, and compared them with the experimental values. Both alternative mechanisms of this step, concerted and stepwise, can be accommodated. It turned out to be essential to include Arg207 hydrogen-bonded to the reactant in the mechanism predicting simultaneous breaking of the Co–C bond of AdoCbl and hydrogen atom transfer. The consequence of the stepwise mechanism is a much larger facilitation of the homolytic dissociation of the carbon–cobalt bond by the enzyme than currently appreciated; our results suggest lowering of the activation energy by about 23 kcal mol−1. We have also shown that large hydrogen KIEs of tunneling origin do not necessarily break the Swain–Schaad equation. Furthermore, when this equation does not hold, the exponent may be smaller in the presence of tunneling than it is at the semi-classical limit, indicating that nonclassical behavior may be a more common phenomenon than expected.

A Periodic Density Functional Theory Analysis of the Effect of Water Molecules on Deprotonation of Acetic Acid over Pd(111)

Nonlocal gradient corrected periodic density functional theory (DFT) was used to investigate the effect of water on the dissociation of acetic acid to the acetate anion and its corresponding proton on the Pd(111) surface. In the gas phase, the homolytic dissociation of acetic acid into acetate and hydrogen radicals (+468 kJ/mol) is clearly favored over its heterolytic dissociation into the acetate anion and proton (+1483 kJ/mol). In the presence of water, however, the heterolytic dissociation of acetic acid was found to be thermoneutral. The charged products (acetate ion and proton) are strongly stabilized by water. The metal surface acts to lower the endothermicity of the dissociation step. The energy of dissociation of acetic acid over Pd(111) was found to be +28 kJ/mol in the vapor phase. An analysis of the charge indicates that the dissociation of acetic acid over Pd(111) in the vapor phase is homolytic, forming products which are free radical like. The dissociation of acetic acid over Pd in the presence of water molecules, however, was found to be more heterolytic than in the vapor phase, forming products that have ionic characteristics. The dissociation of acetic acid over Pd(111) in the presence of solvating water molecules was calculated to be +37 kJ/mol. The metal surface stabilizes the acetate species but to a relatively weaker extent than the stabilization provided by the water solvent. The acetate anion was found to be 57 kJ/mol more stable when completely solvated by water molecules than on Pd(111). In the vapor phase, the acetate anion binds with an energy of over −198 kJ/mol on Pd(111). The surface acts as a “solvent” to shield the negative charge of the ion. In the presence of a solvent, however, the interaction between the acetate ion and the Pd(111) surface is weakened considerably. The interaction between acetate and the surface, however, is nevertheless attractive at −114 kJ/mol. While the acetate anion is thermodynamically more stable when completely solvated by water molecules, there appears to be a barrier for it to desorb from the metal surface.

Does the interconversion of polysulfur compounds proceed via hypervalent intermediates? An ab initio MO study.

Ab initio MO calculations at the CCSD(T)/6-311++G(2df,p)//MP2/6-311++G** level have been carried out to determine the reaction energies and Gibbs energies of the homolytic dissociation of the S-S bonds in the chainlike sulfanes H2Sn (n = 2-4). Good agreement with the experimental data is observed. At the same level of theory, the formation of the hypothetical sulfuranes H2S(SH)2, H2S(SSH)2, and S(SH)4 from H2S and the mentioned sulfanes has been studied. Species of this type had been proposed as intermediates in the interconversion reactions of polysulfur compounds (e.g., formation of S7 from S8 and vice versa). The three sulfuranes serve here as model compounds. On the basis of the Gibbs energies and activation energies at 298 K, it is shown that the formation of the three sulfuranes from sulfanes requires too much energy and activation energy to successfully compete with homolytic dissociation reactions. In addition, the formation of the methylsubstituted sulfurane S(SMe)4 from the sulfanes Me2S2 and Me2S3 was studied to elucidate the mechanism of the formal exchange of sulfur atoms between polysulfane molecules. However, both the reaction energy of 199 kJ mol(-1) and the activation energy of 287 kJ mol(-1), calculated at the MP2/6-31G* level, are much higher than the homolytic dissociation energy of the S-S bonds in chain- and ringlike polysulfur compounds, such as Me2S4 (140 kJ mol(-1)) and sulfur homocycles (150 kJ mol(-1)). Therefore, it is concluded that the observed interconversion reactions of sulfur rings and of chainlike polysulfanes do not proceed via sulfurane-type intermediates. Instead, these reactions will take place by a radical chain mechanism at high temperatures, while at temperatures below 100 degrees C they are most probably initiated either by traces of nucleophiles that are present as impurities or by the polar surface groups usually present on the walls of the vessels used.

Direct semiclassical simulation of photochemical processes with semiempirical wave functions

We describe a new method for the simulation of excited state dynamics, based on classical trajectories and surface hopping, with direct semiempirical calculation of the electronic wave functions and potential energy surfaces (DTSH method). Semiempirical self-consistent-field molecular orbitals (SCF MO’s) are computed with geometry-dependent occupation numbers, in order to ensure correct homolytic dissociation, fragment orbital degeneracy, and partial optimization of the lowest virtuals. Electronic wave functions are of the MO active space configuration interaction (CI) type, for which analytic energy gradients have been implemented. The time-dependent electronic wave function is propagated by means of a local diabatization algorithm which is inherently stable also in the case of surface crossings. The method is tested for the problem of excited ethylene nonadiabatic dynamics, and the results are compared with recent quantum mechanical calculations.

Low-temperature surface-active complex-radical oligodert.Alkylperoxidic initiators

Carbon-chain functional surface-active oligoperoxides (FSAP) with ditertiary peroxidic, carboxyl or hydroxyl groups form stable oligoperoxidic metal complexes (OMC) through their interaction with transition metal salts in organic solutions. The mole fraction and formation constants of OMC are interrelated with the microstructures of FSAP, first of all, with the disposition of complex forming groups. Increasing the set of FSAP conformational structures promotes the enhancement of the local concentrations of reactants in the reaction zone during complex formation, thereby increasing the probability that the reaction will proceed. The kinetic and thermodynamic characteristics of the decomposition of peroxide fragments of FSAP in the aqueous medium providing the formation of controlled amount of free radicals, thereby the initiation of emulsion polymerization processes were investigated. The realization of the process of decomposition of – O:O – bonds as a result of homolytic dissociation or/and Red-Ox reactions depending media polarity and OMC nature were assumed.

Homolytic dissociation of 1-substituted cyclohexa-2,5-diene-1-carboxylic acids: an EPR spectroscopic study of chain propagation†

Hydrogen abstraction from 1-substituted cyclohexa-2,5-diene-1-carboxylic acids containing linear, branched and cyclic alkyl substituents, as well as allyl, propargyl (prop-2-ynyl), cyanomethyl and benzyl substituents, has been studied by EPR spectroscopy. For each carboxylic acid, EPR spectra of the corresponding cyclohexadienyl radicals were observed at lower temperatures, followed by spectra due to ejected carbon-centred radicals at higher temperatures. Rate constants, for release of the carbon-centred radicals from the cyclohexadienyl radicals, were determined from radical concentration measurements for the above range of substituents. The rate of cyclohexadienyl radical dissociation increased with branching in the 1-alkyl substituent and with electron delocalisation in the ejected carbon-centred radical; 3,5- and 2,6-dimethyl-substitution of the cyclohexadienyl ring led to reductions in the dissociation rate constants. Rate data for abstraction of bisallylic hydrogens from the cyclohexadienyl acids were also obtained for ethyl, n-propyl and isopropyl radicals. These results indicated a sharp drop in the rate of hydrogen abstraction as the degree of branching in the attacking radical increased. Small decreases in the hydrogen abstraction rate constants were observed for cyclohexadienes containing CO2R substituents.

The expectation value of the spin operator [formula omitted] as a diagnostic tool in coupled cluster theory : The advantages of using UHF-CCSD theory for the description of homolytic dissociation

Coupled cluster (CC) theory carried out with a spin-unrestricted Hartree–Fock (UHF) reference wave function suffers less from spin contamination because infinite order electron correlation effects covered by the CC method in question reduce spin contamination. For example, UHF-CCSD, contrary to UHF, is not contaminated by a S+1 state. However, the value of 〈 S ̂ 2〉 CCSD , is strongly influenced by the response of the UHF-CCSD wave function on the spin contamination present at UHF and, therefore, adopts a relatively large value. A reliable diagnostic tool correctly reflecting the influence of spin contamination on the UHF-CCSD energy is obtained by just considering the energy related part of 〈 S ̂ 2〉 CCSD .

FTIR study of thermally induced transformations of trimethylsilylmethyl acetate in the temperature range 623–813 K

The chemistry of trimethylsilylmethyl acetate in the gas phase in the temperature range 623–813 K has been investigated under static conditions using Fourier transform IR spectroscopy. Little change occurs at temperatures lower than 623 K, at which temperature a thermally induced isomerization to form ethyldimethylsilyl acetate occurs. Some ethanoic acid is also produced at this temperature. The ethyldimethylsilyl acetate produced undergoes thermolysis at temperatures >723 K giving methane, ethene, carbon monoxide, carbon dioxide, ethanoic acid, 1,3-diethyl-1,1,3,3-tetramethyldisiloxane, cyclohexamethyltrisiloxane, and cyclooctamethyltetrasiloxane as products. Loss of ethyldimethylsilyl acetate is first order over the whole temperature range, and first-order rate constants vary from 4.87×10 −5 s −1 at 723 K to 33.5×10 −5 s −1 at 813 K, respectively, leading to an activation energy, E a, of 110(4) kJ mol −1. An intramolecular five-centre process is proposed for the isomerization reaction. The thermolysis is interpreted in terms of principally radical reactions involving initial homolytic dissociation of the EtMe 2SiOC(O)CH 3 bond.