Comparative dissociation of peptide polyanions by electron impact and photo-induced electron detachment

We compare product-ion mass spectra produced by electron detachment dissociation (EDD) and electron photodetachment dissociation (EPD) of multi-deprotonated peptides on a Fourier transform and a linear ion trap mass spectrometer, respectively. Both methods, EDD and EPD, involve the electron emission-induced formation of a radical oxidized species from a multi-deprotonated precursor peptide. Product-ion mass spectra display mainly fragment ions resulting from backbone cleavages of C_α-C bond ruptures yielding a and x ions. Fragment ions originating from N-C_α backbone bond cleavages are also observed, in particular by EPD. Although EDD and EPD methods involve the generation of a charge-reduced radical anion intermediate by electron emission, the product ion abundance distributions are drastically different. Both processes seem to be triggered by the location and the recombination of radicals (both neutral and cation radicals). Therefore, EPD product ions are predominantly formed near tryptophan and histidine residues, whereas in EDD the negative charge solvation sites on the backbone seem to be the most favorable for the nearby bond dissociation.     

Insights into the mechanism of O₂ formation and release from the Mn₄O₄L₆ "cubane" cluster

To probe photoinduced water oxidation catalyzed by the Mn?O?L? cubane clusters, we have computationally studied the mechanism and controlling factors of the O? formation from the [Mn?O?L?] catalyst, 6. It was demonstrated that dissociation of an L = H?PO?? ligand from 6 facilitates the direct O-O bond formation that proceeds with a 28.3 (33.4) kcal/mol rate-determining energy barrier at the transition state TS1. This step (the O-O single bond formation) of the reaction is a two-electron oxidation/reduction process, during which two oxo ligands are transformed into to μ2:η2-O?2? unit, and two ("distal") Mn centers are reduced from the 4+ to the 3+ oxidation state. Next two-electron oxidation/reduction occurs by "dancing" of the resulted O?2? fragment between the Mn1 and Mn2/Mn(2')-centers, keeping its strong coordination to the Mn(1')-center. As a result of this four-electron oxidation/reduction process Mn centers of the Mn?-core of I transform from {Mn1(III)-Mn(1')(III)-Mn2(IV)-Mn(2')(IV)} to {Mn1(II)-Mn(1')(II)-Mn2(III)-Mn(2')(III)} in IV. In other words, upon O? formation in cationic complex [Mn?O?L?](+), I, all four Mn-centers are reduced by one electron each. The overall reaction I → TS1 → II → III → TS2 → IV → TS3 → V → VI + O? is found to be exothermic by 15.4 (10.5) kcal/mol. We analyze the lowest spin states and geometries of all reactants, intermediates, transition states, and products of the targeted reaction.     

Novel efficient synthesis of β-fluoro-β-(trifluoromethyl)styrenes

CF₃CFBr₂ was employed in catalytic olefination reactions of aromatic aldehydes. In situ prepared hydrazones of aldehydes were transformed to β-fluoro-β-(trifluoromethyl)styrenes by reaction with CF₃CFBr₂ under CuCl catalysis. Based on this reaction, a novel stereoselective approach towards β-fluoro-β-(trifluoromethyl)styrenes was elaborated. Nucleophilic vinylic substitution of fluorine by secondary amines, thiolates and alkoxides in β-fluoro-β-(trifluoromethyl)styrenes was also tested.     

Mechanistic study of multi-step nucleophilic substitution for trifluoromethylated styrenes

The key steps of the reactions of nitrogen nucleophiles with β-halogen-β-trifluoromethylstyrenes have been studied by ¹⁹F and ¹H NMR monitoring and quantum-chemical calculations. In contrast to the mechanism proposed earlier for nucleophilic vinylic substitution of captodative carbonyl-bearing haloalkenes, this reaction proceeds via either E–Ad or Ad–E sequence depending on the nature of aromatic substituents of the parent styrenes.     

Calculation of chemical potentials of chain molecules by the incremental gauge cell method

The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)], and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.     

Ab initio calculations of the electronic states of AsH2 including dissociation characteristics

Multireference configuration interaction calculations have been carried out for low-lying electronic states of AsH(2). Bending potentials for the ten lowest states of AsH(2) are obtained in C(2v) symmetry for As-H distances fixed at the the ground state equilibrium value of 2.845 a(0), as well as for the minimum energy path constrained to R(1) = R(2). The calculated equilibrium geometries for the X?(2)B(1) ground state and the A?(2)A(1) excited state agree very well with the previous experimental and theoretical results, whereas the data for the higher-lying states are obtained for the first time. Asymmetric potential energy surface (PES) cuts (at R(1) = 2.845 a(0), θ = 90.7°) and two-dimensional (2D) PESs for the lowest three states are also new. The calculated ab initio data are used for analysis of possible AsH(2) photodissociation channels and predissociation effects. It is shown that the A?(2)A(1)-X?(2)B(1) transition dipole moment decreases with increasing bending angle, which influences the intensity distribution in the A?(0,0,0)→X? emission spectrum (v(2)' bending series), shifting its maximum to smaller v(2)' quantum numbers.     

Polynomial approximation of nonlinear differential systems with prefixed accuracy

This paper presents a method for constructing polynomial approximations of the solutions of nonlinear initial value systems of differential equations. Given an a priori chosen accuracy, the degree of the vector polynomial can be adapted so that the approximate solution has the required precision. The method is based on the AI-method of Dzyadyk developed for the scalar case, and the computational cost is shown to be competitive with other methods.     

Cavitation and crystallization in a metastable Lennard-Jones liquid at negative pressures and low temperatures

Molecular dynamics simulations have been used to investigate the kinetics of spontaneous cavitation and crystallization in a Lennard-Jones liquid at negative pressures in the temperature range where these processes compete with each other. The nucleation rate has been calculated in NVE and NpT ensembles by the method of mean lifetime and the transition interface sampling method with parallel path swapping. The data obtained have been used to determine in the framework of classical nucleation theory the value of the ratio of the solid-liquid and the liquid-void interfacial free energy for critical crystals and cavities and the values of their volumes at points where the cavitation rate of the liquid is equal to the rate of its crystallization.