Protonation and electronic structure of 2,6-dichlorophenolindophenolate during reduction. A theoretical study including explicit solvent.

Protonation in the two-electron/two-proton reduction processes of 2,6-dichlorophenolindophenolate (DCIP) is investigated combining density functional theory (DFT) and molecular dynamics (MD) methods. DCIP (anion), DCIP•- (radical anion), and DCIP2- (dianion) are considered, including the electronic structure analysis from the prospective of quantum theory of atoms and molecules (QTAIM). It is shown that oxygen on the indophenolate moiety and nitrogen are the first and/or the second proton acceptor sites and their energetic order depends on the total charge of the system. MD simulations of differently charged species interacting with the solvent molecules have been performed for methanol, water, and oxonium cation (H3O+). Methanol and water molecules are found to form only hydrogen bonds with the solute irrespective of its charge. The calculated pKa values show that the imino group of DCIPH- is a weaker acid than water. While in the case of DCIP (and DCIP•-) plus oxonium cation, proton transfer from the solvent to the solute was evidenced for both aforementioned acceptor sites. In addition, MD simulations of bulks containing 15 and 43 molecules of water around the DCIP molecule have been performed, revealing the formation of 2-4 hydrogen bonds. Graphical Abstract 2,6-Dichlorophenolindophenolate interacts with solvent molecules (water, oxonium cation and methanol). Hydrogen transfer and electronic structure are studied by DFT and molecular dynamics methods.

Calculations of hyperfine coupling constant of copper(II) in aqueous environment. Finite temperature molecular dynamics and relativistic effects.

The presented paper is focused on the calculation of hyperfine coupling constants (HFCC) of Cu (2+) ion in water environment. To simulate the conditions of the electron paramagnetic resonance (EPR) experiment in aqueous phase, molecular dynamics using the density functional theory (DFT) was employed. In total three different functionals (BLYP, B3LYP, M06) were employed for studying their suitability in describing coordination of Cu (2+) by water molecules. The system of our interest was composed of one Cu (2+) cation surrounded by a selected number (between thirty and fifty) of water molecules. Besides the non-relativistic HFCCs (Fermi contact terms) of Cu (2+) also the four-component relativistic HFCC calculations are presented. The importance of the proper evaluation of HFCCs, the inclusion of spin-orbit term, for Cu (2+) containing systems (Neese, J. Chem. Phys. 118, 3939 2003; Almeida et al., Chem. Phys. 332, 176 2007) is confirmed at the relativistic four-component level of theory.

Ab initio calculation of structure and transport properties of He X (X = Zn, Cd, Hg) van der Waals complexes.

The ground state ab initio CCSD(T) potential curves using various basis sets (aug-cc-pVXZ-PP (X = D, T, Q, 5)) is obtained for the dimers of helium with IIb group metals. The effect of the position of the (mid) bond-functions on the interaction energy is discussed. A Symmetry Adapted Perturbation Theory decomposition of the interaction energy is provided and the trends in the dimer stabilizing and destabilizing contributions are depicted. The spline fitted potential curves are applied together with rigorous statistical formulae in order to obtain the transport coefficients (viscosity coefficients, diffusion coefficients) and the second virial coefficient both for pure constituents and mixtures. The obtained theoretical results are compared with available experimental data. Molecular dynamics is used to obtain reliable values of the diffusion coefficients for all the systems under study.

Relativistic effects in HgHe and HgXe CCSD(T) ground state potential curves. Low-density viscosity simulations of Hg:Xe mixture.

The comparison of coupled cluster with single and double excitations and with perturbative correction of triple excitations [CCSD(T)] ground state potential curves of mercury with rare gases (RG): HgHe and HgXe, at several levels of theory is presented. The scalar relativistic (REL) effects and spin-orbit coupling effects in the ground state potential curves of these weakly bounded dimers are considered. The CCSD(T) ground state potential curves at the level of the Dirac-Coulomb Hamiltonian (DCH) are compared with CCSD(T) curves at the level of 4-component spin-free modified DCH, the scalar 2nd order Douglas-Kroll-Hess (DKH2) and the nonrelativistic (NR-LL) (Lévy-Leblond) Hamiltonian. In addition, London-Drude formula and SCF interaction energy curves are employed in the analysis of different contributions of REL effects in dissociation energies of HgRG and Hg(2) dimers. Moreover, the large anharmonicity of the HgHe ground state potential curve is highlighted. The computationally less demanding scalar DKH2 Hamiltonian is employed to calculate the HgXe, Hg(2) , and Xe(2) all electron CCSD(T) ground state potential curves in highly augmented quadruple zeta basis sets. These potential curves are used to simulate the shear viscosity of mercury, xenon, and mercury-xenon (Hg:Xe) mixture.

Picture change error correction of radon atom electron density.

The importance of the picture change error (PCE) correction in the quasirelativistic electron density of radon atom is presented. PCE correction is considered for the infinite order two-component (IOTC) and second order Douglas-Kroll-Hess (DKH2) wave functions. Implementation details of PCE correction of electron density are outlined. The result section presents the radial distributions of electron density ρ(r) and the 4πr(2)ρ(r) function of the radon atom in the nuclear region. The PCE corrected and contaminated DKH2, IOTC electron densities are presented and compared with the Dirac-Coulomb Hamiltonian and nonrelativistic electron densities. Besides, some additional effects in electron density and SCF energy are considered, such as spin-orbit coupling, the inclusion of the Gaunt term, and the finite nucleus model effects. The effects of p(2)Vp(2) and p(2)ρ(r)p(2) analytic integral classes within IOTC Hamiltonian and PCE correction of IOTC electron density are considered.

X-ray constrained unrestricted Hartree-Fock and Douglas-Kroll-Hess wavefunctions.

The extension of the X-ray constrained (XC) wavefunction approach to open-shell systems using the unrestricted Hartree-Fock formalism is reported. The XC method is also extended to include relativistic effects using the scalar second-order Douglas-Kroll-Hess approach. The relativistic effects on the charge and spin density on two model compounds containing the copper and iron atom are reported. The size of the relativistic effects is investigated in real and reciprocal space; in addition, picture-change effects are investigated and discussed for the isolated Cu atom. It is found that the relativistic terms lead to changes in the densities that are much smaller than those from the X-ray constraint. Nevertheless, the use of the relativistic corrections in the ab initio model always leads to an improvement in the agreement statistics. An interesting result of the unrestricted XC technique is the possibility of obtaining experimentally derived spin densities from X-ray data.

Electron transfer: a primary step in the reactions of sodium hydrosulphide, an H2S/HS(-) donor.

Endogenously produced H2S/HS(-), a newly found gasotransmitter, is well represented by NaHS. In deoxygenated media it terminated semi-stable oxidant radicals up to stoichiometric ratios of 1:1. In the presence of oxygen the antioxidant activities of NaHS were impaired considerably due to its competitive reactions with molecular oxygen. The primary reaction steps of NaHS were investigated using two different spin traps, 5,5-dimethylpyrroline-N-oxide and sodium 3,5-dibromo-4-nitrosobenzenesulphonate (DBNBS), in protolytic and aprotic solvents (water and dimethylsulphoxide, DMSO) under argon and oxygen. Sulphhydryl radicals (HS(*)/S(* -)) were primarily formed (S(* -) in water and HS(*) in DMSO), probably coupled to the formation of superoxide radical anions. The DBNBS spin trap acted also as an electron acceptor and formed its radical anions in the presence of NaHS. Hence, one of the primary steps in the reactions of sulphides is the electron transfer from H2S/HS(-) species to a suitable acceptor, which may play a fundamental role in their biological functions.

On relativistic effects in ground state potential curves of Zn2, Cd2, and Hg2 dimers. A CCSD(T) study.

The ground state potential curves of the Zn2, Cd2, and Hg2 dimers calculated at different levels of theory are presented and compared with each other as well as with experimental and other theoretical studies. The calculations at the level of Dirac-Coulomb Hamiltonian (DCH), 4-component spin-free Hamiltonian, nonrelativistic Lévy-Leblond Hamiltonian and at the level of simple Coulombic correction to DCH are presented. The potential curves are calculated in an all-electron supermolecular approach including the correction to basis set superposition error (BSSE). Electron correlation is treated at the coupled cluster level including single and double excitations and noniterative triple corrections, CCSD(T). In addition, simulations of the temperature dependence of dynamic viscosities in the low-density limit using the obtained ground state potential curves are presented.

The potential pitfalls of using 1,1-diphenyl-2-picrylhydrazyl to characterize antioxidants in mixed water solvents.

Approaching living systems, aqueous solutions are appropriate to characterize antioxidants, whereas the frequently used standard 1,1-diphenyl-2-picrylhydrazyl (DPPH) is insoluble in water. Therefore, mixed water-ethanol solvents were investigated using the electron paramagnetic resonance (EPR) spectroscopy. Two forms of DPPH were identified: at higher ethanol ratios a quintet spectrum characteristic of solutions, and at lower ratios, a singlet spectrum typical for solid DPPH, were found. Mixed solvents with 0-50% (v/v) water reproduced the same antioxidant equivalent points well and the reaction rate between DPPH and the antioxidant may increase considerably with increasing water ratios, as demonstrated using vitamin E as an antioxidant. But at still higher water ratios (70-90% (v/v)) the antioxidant activities dropped, since a part of the DPPH in the aggregated form does not react sufficiently with the antioxidants. Characteristics of the most common antioxidants were determined in ethanol or its 50% (v/v) aqueous solution.

On the structure and physical origin of the interaction in H(2) ... Cl(-) and H(2) ... Br(-) van der Waals anion complexes.

The ab initio three-dimensional potential energy surface (PES) for the weak interaction of hydrogen molecule with bromine anion is presented. The surface was obtained by the supermolecular method at the coupled cluster with single and double excitations and noniterative correction to triple excitations (CCSD(T)) level of theory. Our calculations indicate the van der Waals (vdW) system for the linear orientation at R=3.37 A with a well depth of D(e)=660.1 cm(-1). The presented PES reveals also transition state for the perpendicular orientation at R=4.22 A with a barrier of 607.1 cm(-1). The physical origin of the stability of vdW H(2) ... Br(-) structure with respect to the H(2) ... Cl(-) one was analyzed by the symmetry adapted perturbation theory based on the single determinant Hartree-Fock (HF) wave function. The separation of the interaction energy shows that the dispersion forces play slightly more important role in the stabilization of the vdW system with Br(-) than with Cl(-).