MODELS FOR BACTERIAL PHOTOSYNTHESIS: ELECTRON TRANSFER FROM PHOTOEXCITED SINGLET BACTERIOPHEOPHYTIN TO METHYL VIOLOGEN AND m-DINITROBENZENE

Abstract. As a model for the primary reactions of photosynthesis, we studied photochemical electron transfer from bacteriopheophytin (BPh) to methyl viologen (MVC1₂) and to m-dinitrobenzene (m-DNB) in solution. Both MVC1₂ and m-DNB cause reductions in the lifetime of the first excited singlet state of BPh (BPh*), in the fluorescence quantum yield, and in the quantum yield of the triplet state, BPh ⁺. The quenching of BPh* probably results from electron transfer, which generates short-lived radical pairs involving the BPh radical cation (BPh⁺) and the reduced form of the quencher. Electron transfer from BPh* is thermodynamically favorable, but that from BPh^T is not. From the magnitude of the quenching, we calculate rate constants for electron transfer in collision complexes formed between BPh* and MVC1₂ or m-DNB. Measurements of the quantum yield of the free BPh⁺ radical indicate that about 3/4 of the [BPh⁺ MV⁺] radical pairs decay by reverse electron transfer, rather than dissociating to give the free radicals. Essentially all of the [BPh⁺m-DNB ⁺] radical pairs must decay by reverse electron transfer, because free BPh⁺ cannot be detected in this case. From these data, we estimate the rate constants for the reverse electron transfer reactions. The higher probability of dissociation in the [BPh⁺ MV⁺] radical pair can be explained by coulombic repulsion. The rate of the primary electron transfer reaction in photosynthetic bacteria is comparable to that of forward electron transfer in the BPh* collision complexes. Reverse electron transfer, however, is at least 10³-times slower in the radical pair formed in the bacterial reaction center than it is in [BPh⁺m-DNB^?], and more than 10⁴-times slower than in [BPh⁺ MV⁺]. The explanation for this dramatic and crucially important difference remains unclear, but several possibilities are discussed.     

Isomerization of chemically activated bicyclo[3.1.0]hex-2-ene and related C6H8 isomers

Singlet methylene was reacted with cyclopentadiene to give chemically activated bicyclo[3.1.0]hex-2-ene (BCH). The rate of isomerization of BCH to 1,4-cyclohexadiene, 1,3-cyclohexadiene, cis-1,3,5-hexatriene, and l-methylcyclopentadiene is compared with calculated rate constants using the RRKM theory and measured or estimated thermal Arrhenius parameters. Subsequent isomerizations of the C₆H₈ products are also measured and calculated. These include 1,4-cyclohexadiene to benzene and the reversible reactions between 1,3-cyclohexadiene, cis-1,3,5-hexatriene, and trans-1,3,5-hexatriene. The results provide new data for several of these reactions which have not been observed in thermal studies. Agreement between the observed and calculated rates using the strong collision assumption is satisfactory except for the trans-1,3,5-hexatriene to cis-1,3,5-hexatriene reaction.     

Removal of Model Pollutants in Aqueous Solution by Gliding Arc Discharge. Part II: Modeling and Simulation Study

Plasma Chemistry and Plasma Processing - The aim of this work is the modeling of plasma-chemical reactions taking place between highly oxidizing gaseous species (·OH, ·NO and...     

Application of Forst's method to the calculation of thermal unimolecular reaction rates and isotope effects in the falloff region

A method proposed in 1972 by W. Forst is used to calculate the experimentally accessible pressure dependence of thermal unimolecular rate constants. The specification of an activated complex always employed in RRKM calculations is avoided. This allows for a more consistent comparison between the results obtained by the application to various unimolecular processes. In order to bring experimental and calculated curves into agreement, fourcenter eliminations of hydrogen halides from alkyl halides require the formal introduction of a collision efficiency factor λ ? 0.2, and for the concerted ring opening of 1,1-dichlorocyclopropane λ ? 0.4 must be assumed. The isotope effects for the decomposition of CD₃CD₂Cl and CH₃CD₂Cl have been studied, and the pressure dependence of k_H/k_D is reported. Studying the biradical ring opening of oxetan, cyclobutane, and cyclopropane, the falloff curves and isotope effects are predicted within the experimental uncertainty by the use of λ ? 1.0. This different behavior of concerted and biradical reactions against falloff calculations can hardly be attributed to experimental uncertainties in the Arrhenius parameters and/or the collision frequency alone.     

A quantum‐chemical DFT study of the mechanism and regioselectivity of the 1,3‐dipolar cycloaddition reaction of nitrile oxide with electron‐rich ethylenes

The 1,3‐dipolar cycloaddition (13DC) reactions of nitrile‐oxide NO 1 with two ethylenes, enamine 2a and enamine 2b , were computationally studied using B3LYP/6‐31G(d) DFT methods. The two possible ortho and meta regioselective channels were characterized and analyzed. The moderate polarity of these 13DC reactions is related to the high nucleophilic character of both ethylenes, and the moderate electrophilic nature of the NO 1 , that accounts for the relatively low calculated activation energies. Analysis of different forms of energies along the different reaction channels indicates that the present 13DC reactions are completely ortho regioselective, accordingly to the experimental outcomes. Electron localization function analysis indicates that these 13DC reactions proceed via a nonconcerted (two‐stage) one‐step mechanism.     

Calculation of strong-collision dissociation rate constants from NASA thermodynamic polynomials

A new method for calculating low-pressure strong-collision rate constants of dissociation and recombination reactions was proposed. The method is based on determining the density of states of the internal degrees of freedom of the reactant molecule by applying the inverse Laplace transform to the respective partition function, which, in turn, is calculated from the thermodynamic properties in the form of NASA polynomials. The proposed model is universal in the sense that the required NASA polynomials can be calculated using molecular properties obtained by various methods, both theoretical and experimental or a combination thereof. In the present study, the NASA polynomials were taken from the available databases or calculated from thermodynamic functions, either tabulated or determined by statistical mechanics in the rigid-rotor harmonic-oscillator approximation, with a simple anharmonicity correction introduced when necessary. In addition, a model for calculating the rotational factor is developed and tested. It is based on determination of the centrifugal barrier as a function of the dissociating bond length at a given rotational energy through calculating the principal moments of inertia of the molecule at each step of elongation of the bond. The proposed approach is exemplified for the dissociation of the H₂O, HO₂, and H₂O₂ molecules and the corresponding reverse reactions. A comparison with the available experimental data made it possible to estimate the weak-collision efficiency. At high temperatures, for all the reactions studied, the weak collision efficiency appears to be quite reasonable, whereas, at low temperatures, the situation is unsatisfactory, except perhaps for H₂O dissociation. Given that the energy threshold E₀ of dissociation reactions is typically well known, the calculated and measured dissociation rate constants are represented and handled in terms of the preexponential factor A(T) in the expression k(T) = A(T)exp(−E₀/RT). A new formula for fitting A(T) was proposed: log A(T) = a + b(1000/T) + c(1000/T)^p, which turned out to be a good approximation for the preexponential factors of not only the rate constants but also the equilibrium constants.     

Dipolar DC induced collisional activation of non‐dissociated electron‐transfer products

The application of electron transfer and dipolar direct current induced collisional activation (ET‐DDC) for enhanced sequence coverage of peptide/protein cations is described. A DDC potential is applied across one pair of opposing rods in the high‐pressure collision cell of a hybrid quadrupole/time‐of‐flight tandem mass spectrometer (QqTOF) to induce collisional activation, in conjunction with electron transfer reactions. As a broadband technique, DDC can be employed for the simultaneous collisional activation of all the first‐generation charge‐reduced precursor ions (eg, electron transfer no‐dissociation or ETnoD products) from electron transfer reactions over a relatively broad mass‐to‐charge range. A systematic study of ET‐DDC induced collision activation on peptide/protein cations revealed an increase in the variety (and abundances) of sequence informative fragment ions, mainly c‐ and z‐type fragment ions, relative to products derived directly via electron transfer dissociation (ETD). Compared with ETD, which has low dissociation efficiency for low‐charge‐state precursor ions, ET‐DDC also showed marked improvement, providing a sequence coverage of 80% to 85% for all the charge states of ubiquitin. Overall, this method provides a simple means for the broadband collisional activation of ETnoD ions in the same collision cell in which they are generated for improved structural characterization of polypeptide and protein cations subjected to ETD.     

Kinetic model of a DC oxygen glow discharge

A simple kinetic model predicting the concentration of oxygen atoms, metastable singlet molecules O₂(a ¹) and negative ions O — in the positive column of a DC glow discharge is developed. The calculated O and O₂(a ¹) concentrations are compared to previously reported measurements for pressuresp=0.2–2 Torr and discharge currentsI=10–80 mA. The electron density calculated from the continuity equationj=n _e e v _d agrees well with experiment. The rate coefficients for electron impact processes used in the balance equations of O, O₂(a ¹), and O^– were taken from the literature as a function of the reduced electric fieldE/N forE/N=40–80 Td. A reasonable agreement is obtained between the model and the experiment with a set of 10 reactions for the production and destruction of the above-mentioned species     

Destruction of sulfonol in its aqueous solutions by contact glow discharge treatment: 1. Product formation kinetics

Degradation of the anionic surfactant Sulfonol (sodium alkylbenzenesulfonate) in its aqueous solutions acting as a liquid cathode of atmospheric-pressure dc discharge in air has been studied. The products of plasma-chemical decomposition of Sulfonol in the liquid phase have been identified. The kinetic characteristics of the formation of products of plasma-chemical reactions at a substrate concentration of 5 × 10^?3 g/L (0.014 mmol/L) and a discharge current of 40 mA have been determined.     

The influence of the effective potential on the strong collision limiting low–pressure rate coefficients

The influence of the effective potential energy curves on the calculation of the strong collision limiting low-pressure rate coefficients of thermal dissociation-recombination reactions was analyzed in terms of the factorized formalism of Troe. An analysis of 26 reactions employing a Morse potential coupled with a quasitriatomic molecular model and an explicit account of the adiabatic zero-point barriers, as originallyproposed by Troe, was performed. A comparison between calculations realizedwith an exactly fitted looseness parameter, α, and with a standard value of α = 1.0 Å^?1, indicates that the use of this last value is satisfactorily justified in the evaluation of thestrong collision limiting low-pressure rate coefficients. A study interms of restrictive relationships between the looseness and Morse parameters and ab initio, radial potentials (for CH₄, CH₃O₂, and HO₂) was also realized. The uncertainties in the evaluation of termolecular rate coefficients due to the lack of a complete knowledge of the long-range potentials are also briefly discussed.     

Dipole–reaction field interaction model for the solvent reorganization energy and its application to the benzoquinone–benzoquinone anion radical system

 Based on the spherical cavity approximation and the Onsager model, a dipole–reaction field interaction model has been proposed to elucidate the solvent reorganization energy of electron transfer (ET). This treatment only needs the cavity radius and the solute dipole moment in the evaluation of the solvent reorganization energy, and fits spherelike systems well. As an application, the ET reaction between p-benzoquinone and its anion radical has been investigated. The inner reorganization energy has been calculated at the level of MP2/6–31+G, and the solvent reorganization energies of different conformations have been evaluated by using the self-consistent reaction field approach at the HF/6–31+G level. Discussions have been made on the cavity radii and the values are found to be reasonable when compared with the experimental ones of some analogous intramolecular ET reactions. The ET matrix element has been determined on the basis of the two-state model. The fact that the value of the ET matrix element is about 10 times larger than RT indicates that this ET reaction can be treated as an adiabatic one. By invoking the classical Marcus ET model, a value of 4.9 × 10⁷M⁻¹s⁻¹ was obtained for the second-order rate constant, and it agrees quite well with the experimental one. Received: 19 October 2001 / Accepted: 17 January 2002 / Published online: 3 May 2002     

Analysis of the electron density redistribution in the course of nucleophilic addition reactions of H− and F− to acetylene and methylacetylene molecules according toab initio calculations

Energy characteristics and peculiarities of variation of structural parameters along the minimum energy pathways (MEP) calculated earlier of six reactions of nucleophilic addition of H^– and F^– to acetylene and methylacetylene have been analyzed. The electronic mechanism of the reactions, the character of the electron density redistribution, and its relation with the changes in structural parameters have been discussed. It has been found for all six reactions that the structural reorganization of an alkyne + Nu system is completed before the barriers. However, the increase in the alkyne multiple bond length and changes in electronic characteristics for the reactions with F^– (endothermic reactions) take place before the barrier (late transition state) and for the reaction with H^– (exothermic reactions), after the barrier (early transition state).Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2373–2377, December, 1995.     

Electron-transfer and chemical reactivity following collisions of Ar with C2H2

The reaction between Ar²⁺ and C₂H₂ has been studied, at centre-of-mass collision energies ranging from 3 to 7 eV, using a position-sensitive coincidence technique to detect the monocation pairs, which are formed. Sixteen different reaction channels generating pairs of monocations have been observed, these channels arise from double-electron-transfer, single-electron-transfer and chemical reactions forming ArC⁺. Examination of the scattering diagrams and energetic information extracted from the coincidence data indicate that double-electron-transfer is a direct process, which does not involve a collision complex, and the derived energetics point towards a concerted, not stepwise, mechanism for the two-electron-transfer. As is commonly observed, single-electron-transfer from C₂H₂ to Ar²⁺ takes place via a direct mechanism, again not involving complexation. Most of the C₂H₂⁺ products that are formed in the single-electron-transfer reactions possess significant (12–15 eV) internal energy and fragment rapidly within the electric field of the partner Ar⁺ ion. The chemical reactions appear to proceed via a direct mechanism involving the initial formation of ArCH⁺, which subsequently fragments to form ArC⁺.     

Formation of the iron-oxo hydroxylating species in the catalytic cycle of aromatic amino acid hydroxylases

The first part of the catalytic cycle of the pterin‐dependent, dioxygen‐using nonheme‐iron aromatic amino acid hydroxylases, leading to the Fe^IV?O hydroxylating intermediate, has been investigated by means of density functional theory. The starting structure in the present investigation is the water‐free Fe? O₂ complex cluster model that represents the catalytically competent form of the enzymes. A model for this structure was obtained in a previous study of water‐ligand dissociation from the hexacoordinate model complex of the X‐ray crystal structure of the catalytic domain of phenylalanine hydroxylase in complex with the cofactor (6R)‐L ‐erythro‐5,6,7,8‐tetrahydrobiopterin (BH₄) (PAH‐Fe^II‐BH₄). The O? O bond rupture and two‐electron oxidation of the cofactor are found to take place via a Fe‐O‐O‐BH₄ bridge structure that is formed in consecutive radical reactions involving a superoxide ion, O₂^?. The overall effective free‐energy barrier to formation of the Fe^IV?O species is calculated to be 13.9 kcal mol^?1, less than 2 kcal mol^?1 lower than that derived from experiment. The rate‐limiting step is associated with a one‐electron transfer from the cofactor to dioxygen, whereas the spin inversion needed to arrive at the quintet state in which the O? O bond cleavage is finalized, essentially proceeds without activation.     

A perturbation molecular orbital theory of gas-phase dissociative electron-transfer rates

Gasphase dissociative electron-transfer (ET) reactions are examined in the light of modern electron-transfer theory and a perturbation molecular orbital (PMO) model for ion-molecule collision rates. Two dissociative ET reactions reported by Knighton and Grimsrud—the reaction of azulene anion with dibromodifluoromethane and with carbon tetrachloride—happened in the inverted region of the relationship between reaction rate and free energy. Carbon-halogen vibration participation in dissociative ET reactions is demonstrated in two reaction series. Carbon-hydrogen stretch (3050 cm^?1) activation of electron transfer happened in the most exothermic reaction series: dissociative capture to form bromide from bromotrichloromethane The reasons for the failure of classical ion-molecule collision theory to give a quantitative account of reactive ion-molecule collision rates are presented in some detail. The fundamental failure is a result of a previously unappreciated change in the polarizability of a molecule when the orbitals on the molecule overlap with those on an adjacent ion. The molecular orbital-based collision model used here avoids the need to evaluate the changes in the polarizability tensor with overlap.     

Plasma-chemical methane conversion under nonthermal and thermal conditions: An attempt toward uniform kinetic modeling

It is shown that it is basically possible to model plasma-chemical methane conversion using a kinetic concept regardless of the kind of plasma, i.e., the kind of activation. While the temporal plasma-chemical decomposition of methane is controlled by a first-order rate equation, the temporal product formation can be described by a set of first-order consecutive reactions. Prolonged portions of constant product concentrations in the temporal product formation curves were explained by the assumption of an equilibrium between forward and reverse reactions. The modeling revealed the special role of the re-formation of dissociated molecules.     

How Oriented External Electric Fields Modulate Reactivity

A judiciously oriented external electric field (OEEF) can catalyze a wide range of reactions and can even induce endo/exo stereoselectivity of cycloaddition reactions. The Diels–Alder reaction between cyclopentadiene and maleic anhydride is studied by using quantitative activation strain and Kohn–Sham molecular orbital theory to pinpoint the origin of these catalytic and stereoselective effects. Our quantitative model reveals that an OEEF along the reaction axis induces an enhanced electrostatic and orbital interaction between the reactants, which in turn lowers the reaction barrier. The stronger electrostatic interaction originates from an increased electron density difference between the reactants at the reactive center, and the enhanced orbital interaction arises from the promoted normal electron demand donor–acceptor interaction driven by the OEEF. An OEEF perpendicular to the plane of the reaction axis solely stabilizes the exo pathway of this reaction, whereas the endo pathway remains unaltered and efficiently steers the endo/exo stereoselectivity. The influence of the OEEF on the inverse electron demand Diels–Alder reaction is also investigated; unexpectedly, it inhibits the reaction, as the electric field now suppresses the critical inverse electron demand donor–acceptor interaction.     

Size-dependent reactivity of cobalt cluster ions with nitrogen monoxide: Competition between chemisorption and decomposition of NO

Reactions of NO molecules on cobalt cluster ions were studied in a beam-gas geometry by using a tandem mass spectrometer. Single-particle collision reactions of Co_mNO⁺ (m = 3–10) with NO were found to proceed in such a manner that NO decomposition dominates at m = 4–6 with the maximum reaction cross section at m = 5 and chemisorption dominates in m ≥ 7. On the other hand, in two-particle collision reactions of Co_n⁺ (n = 2–10) with NO, NO decomposition at n ≥ 5 and chemisorption of two NO molecules with Co atoms loss at n ≥ 8 were found to proceed. These results indicate that the size-dependency of the multiple collision reactions originates from secondary attacking of an NO molecule to primary products of the initial single collision reactions. The DFT calculation supports the scheme that both the decomposition and chemisorption of two-particle collision reactions proceed via a common intermediate, Co_mN₂O₂⁺, in which the two NO molecules are dissociatively chemisorbed on the cobalt cluster ion, and the size-dependency of the two-particle collision reactions is explained in terms of the structure of this reaction intermediate.     

Determination of the energy distribution in unimolecular reactions under soft collision conditions

The effective energy distribution of activated molecules at the time of reaction under soft collision conditions ?′(E, ω) is pressure dependent and therefore difficult to recover from unimolecular decomposition data obtained at different pressures. We show in this work that the part of this function restricted to the condition that the collision frequency ω has to be equal to the microscopic rate constant k(E) at the energy given ?″[E,ω = k(E)] is a reasonable approximation to the input energy distribution ?(E) for quite soft collisions. This function is not pressure dependent and then recoverable at least in principle and as a matter of fact is not conceptually far from the function that the already reported deconvolution methods based in physical approximations attempt to recover. The deconvolution methods have been checked under soft collision conditions. We have found that the input energy distribution is recovered with reasonable accuracy for energies transferred by collision 〈ΔE〉 above 5 kcal mol^?1, conditions common in polyatomic systems.