Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions

In this paper we have developed an effective computational procedure for the structural and dynamical investigation of ions in aqueous solutions. Quantum mechanical potential energy surfaces for the interaction of a transition metal ion with a water molecule have been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective ion-water interactions have been fitted by suitable analytical potentials, and have been utilized in molecular dynamics (MD) simulations to obtain structural and dynamical properties of the ionic aqueous solutions. This procedure has been successfully applied to the Co2+-H2O open-shell system and, for the first time, Co-oxygen and Co-hydrogen pair potential functions have been determined and employed in MD simulations. The reliability of the whole procedure has been assessed by applying it also to the Zn2+ and Ni2+ aqueous solutions, and the structural and dynamical properties of the three systems have been calculated by means of MD simulations and have been found to be in very good agreement with experimental results. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to extended X-ray absorption fine structure (EXAFS) experiments.     

Methylene radical cation transfer from ionized oxirane to CH3SCH3 and C6H5SCH3 in the gas phase: Formation of sulphur distonic ions and/or insertion in a carbon–sulphur bond

The α-distonic sulphur-containing ion $ {}^ \cdot {\rm CH}_2 \mathop {\rm S}\limits^ + \left({{\rm CH}_3 } \right)_2 $ has been generated by transfer of CH from ionized oxirane to dimethyl thioether and distinguished from the molecular ion of ethyl methyl thioether by collision induced dissociation (CID) experiments. In particular, the α-distonic ion expels CH₂ to a minor extent following collision, whereas the molecular ion of ethyl methyl thioether does not undergo this reaction. The metastable C₃H₈S^+˙ ions formed by CH transfer to dimethyl thioether and ionization of ethyl methyl thioether decompose by competing losses of CH₃R˙, CH₄ and C₂H₄. The elimination of ethene is taken as evidence for isomerization of the α-distonic ion to the molecular ion of ethyl methyl thioether prior to spontaneous dissociation. Evidence for the formation of stable α-distonic sulphur-containing ions by transfer of CH from ionized oxirane to methyl phenyl thioether has not been obtained. The collision-induced and spontaneous reactions of the ions formed by CH transfer to methyl phenyl thioether indicate that a mixture of the radical cations of CH₃C₆H₄SCH₃, C₆H₅SCH₂CH₃ and C₆H₅CH₂SCH₃ is generated implying that attack on the phenyl group occurs in addition to a formal insertion of a methylene entity in a C? S bond.     

SLIM: A Short-Linked,Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements

The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site-directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in-cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide-functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm , and shows high stability against reduction. Using this label, the guanine-nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.     

Scope and Limitations of the s-Block Metal-Mediated Pudovik Reaction

The hydrophosphorylation of phenylacetylene with di(aryl)phosphane oxides Ar₂P(O)H (Pudovik reaction) yields E/Z-isomer mixtures of phenylethenyl-di(aryl)phosphane oxides ( 1 ). Alkali and alkaline-earth metal di(aryl)phosphinites have been studied as catalysts for this reaction with increasing activity for the heavier s-block metals. The Pudovik reaction can only be mediated for di(aryl)phosphane oxides whereas P-bound alkyl and alcoholate substituents impede the P−H addition across alkynes. The demanding mesityl group favors the single-hydrophosphorylated products 1-Ar whereas smaller aryl substituents lead to the double-hydrophosphorylated products 2-Ar . Polar solvents are beneficial for an effective addition. Increasing concentration of the reactants and the catalyst accelerates the Pudovik reaction. Whereas Mes₂P(O)H does not form the bis-phosphorylated product 2-Mes , activation of an ortho-methyl group and cyclization occurs yielding 2-benzyl-1-mesityl-5,7-dimethyl-2,3-dihydrophosphindole 1-oxide ( 3 ).     

Complexes of helium with neutral molecules: Progress toward a quantitative scale of bonding character

The complexes of helium with nearly 30 neutral molecules (M) were investigated by various techniques of bonding analysis and symmetry-adapted perturbation theory (SAPT). The main investigated function was the local electron energy density H( r ), analyzed, in particular, so to estimate the degree of polarization (DoP) of He in the various He(M). As we showed recently (Borocci et al., J. Comput. Chem., 2019, 40, 2318–2328), the DoP is a quantitative index that is generally informative about the role of polarization (induction plus charge transfer [CT]) and dispersion in noncovalent noble gas complexes. As further evidence in this regard, we presently ascertained quantitative correlations between the DoP(He) of the He(M) and indices based on the electron density ρ( r ), including the molecular electrostatic potential at the He M bond critical point, as well as the percentage contributions of induction and dispersion to the SAPT binding energies. Based also on the explicit evaluation of the CT, accomplished through the study of the charge-displacement function, we derived a quantitative scale that ranks the He(M) according to their dispersive, inductive, and CT bonding character. Our taken approach could be conceivably extended to other types of noncovalent complexes.     

Study of the rate of methyl loss and the structure of the product ion as a function of the lifetime of the molecular ion of pent-3-en-2-ol

The normalized unimolecular rate constant for loss of a methyl radical from pent-3-en-2-ol molecular ions with lifetimes ranging from 10^?11 to 10^?9 s was studied by field ionization kinetics (FIK). The normalized rate curve shows maxima at molecular ion lifetimes of 10^?10.5 and 10^?10.1 s. Based on results for deuterium and ¹³C-labelled pent-3-en-2-ol, the maximum at 10^?10.5 s is ascribed to loss of the methyl group at the 1-position by a direct cleavage reaction. The maximum at 10^?10.1 s is attributed to a 1,2-H shift-initiated rearrangement of the molecular ion, which leads to loss of the methyl group at the 5- and 1-positions. The time dependence of the processes in the form of the maxima on the normalized rate curve is discussed qualitatively in terms of a lower critical energy and a tighter transition state of the 1,2-H shift than those of the direct cleavage reaction. Collision-induced dissociation of the [C₄H₇O]⁺ product ions in combination with FIK provides evidence that at molecular ion lifetimes corresponding to the first maximum on the rate curve protonated crotonaldehyde is formed, whereas protonated methyl vinyl ketone and the butyryl cation are formed at times corresponding to the second maximum.     

Site of gas-phase methylation of l-phenyl-2-aminopropane

The regioselectivity of methyl cation transfer from (CH₃)₂F⁺, (CH₃)₂Cl⁺ and (CH₃)₃O⁺ to 1-phenyl-2-aminopropane was studied by Fourier transform ion cyclotron resonance in combination with collision-induced dissociation and neutralization-reionization mass spectrometry of the stable [M + CH₃]⁺ ions formed in a chemical ionization source. The (CH₃)₂F⁺ ion transfers a methyl cation to the NH₂ group and the phenyl ring with almost equal probability. Predominant CH₃⁺ transfer to the NH₂ group is observed for the (CH₃)₂Cl⁺ ion whereas the (CH₃)₃O⁺ ion reacts almost exclusively at the amino group. The preference for methylation at NH₂ is discussed in terms of a lower methyl cation affinity of the phenyl ring than of the amino group and the existence of an energy barrier for methylation of the phenyl moiety.