Dimer Ions Research Articles

Generation of soluble oligomeric β-amyloid species via copper catalyzed oxidation with implications for Alzheimer’s disease: A DFT study

A mechanism for the oxidation of a dimeric beta-amyloid copper ion complex is proposed based on DFT calculations. It involves the Met35 residue, which is believed to be important in the neurotoxicity causing Alzheimer's disease. Oxidation of Met35 is found to proceed readily with dioxygen when two Met35 residues are close to each other and the copper ion. This indicates that oxidants, such as hydrogen peroxide, are not necessary for oxidation of beta-amyloid copper ion complexes. Understanding these processes could be pivotal in gaining more knowledge of this complex disease and for the development of therapeutic treatments.

Generation and dissociation of oxygen‐ and chloride‐bridged iron(III) and manganese(III) tetraphenylporphyrin dimer ions in the gas phase

Electrospray ionization mass spectrometry (ESI/MS) has allowed the discovery of novel dimer ions emerging from solutions of metalloporphyrin salts and their investigation by collision-induced dissociation (CID) with N(2) molecules. ESI mass spectra have been recorded for the formation of the oxygen or chloride-bridged dimer ions [(FeTPP)(2)OH](+), [(MnTPP)(2)OH](+), [(FeTPP)(2)Cl](+) and [(MnTPP)(2)Cl](+) derived from various solutions of FeTPPCl and MnTPPCl salts. The CID of [(FeTPP)(2)OH](+) proceeds mainly by neutral loss of (FeTPP)OH to form [FeTPP](+) and, to a minor extent, to form the charge-reversed products. The CID of [(MnTPP)(2)OH](+) exhibits exclusively the product ion [MnTPP](+) by loss of neutral (MnTPP)OH. [(FeTPP)(2)Cl](+) and [(MnTPP)(2)Cl](+) dissociate by loss of (Fe/MnTPP)Cl to give rise to [Fe/MnTPP](+). [(FeTPP)(2)O](+) and [(FeTPP)(2)OH](+) were generated from a solution of the dimer, (FeTPP)(2)O. Dissociation of [(FeTPP)(2)O](+) yields two product ions, [FeTPP](+) and [(FeTPP)O](+), with higher onsets compared to the equivalent fragments formed from [(FeTPP)(2)OH](+).

Metallic microwires obtained as replicas of etched ion tracks in polymer matrixes: Microscopy and emission properties

Specially prepared porous matrixes (with through and dead-end pores of cylindrical or conical forms) were used as the templates for making ensembles of microwires. The process of electrodeposition of metal (Cu) into these pores was investigated. AFM technique was used for studying the “composite material” (metal microwires embedded into the polymer matrix). It was shown that the combination of different modes of AFM (tapping with phase-contrast mode, contact with lateral force mode) makes it possible to detect metal in the polymer matrix. Additional spread resistance mode in the contact regime allowed to measure the electrical conductivity of a single wire. The ensembles of free-standing microwires (metallic replicas of the pores obtained after removing of the polymer matrix) were used as the substrates (for deposition of the probe) for ion emission in the mass-spectrometer. It was shown that the intensity of formed ion beam increases with increasing of power of the laser pulse and with increasing of the mass of the probe. The intensity of mass-spectra signal on the power of laser pulse has a threshold character with saturation accompanied with the appearance of dimer ions. At the same time this intensity decreases with the increasing of the surface density of wires. The effect of degradation of wires during the laser pulse irradiation was found.

Collision-Induced Dissociation of Dimeric G-Quadruplexes of HIV-1 Integrase Inhibitors and Their Complexes by Tandem-in-Time Mass Spectrometry

The collision-dissociation behavior of two novel dimeric G-quadruplexes of HIV-1 integrase inhibitors and their noncovalent complex ions with a perylene derivative (Tel03), polyamides (ImImImbetaDp and PyPyPybetaDp) was investigated by tandem-in-time electrospray ionization mass spectrometry (ESI-MS). It was found that the dimeric ion loses five ammonium ions one by one at activation energy of 10%, so the loss of NH(4)(+) is the predominant fragmentation pathway at lower collision energy. When the activation amplitude is increased to 16%, the loss of guanine nucleobases from backbones of the oligonucleotide is the predominant fragmentation pathway. And the stability of the complex ion of the dimeric G-quadruplex and Tel03 is higher than that of ImImImbetaDp and PyPyPybetaDp. The results of the MS/MS spectra of the complex ion indicated that Tel03 binding molecule favor the stabilization of the novel G-quadruplex structure.

Alkali-helium snowball complexes formed on helium nanodroplets

We systematically investigate the formation and stability of snowballs formed by femtosecond photoionization of small alkali clusters bound to helium nanodroplets. For all studied alkali species Ak = (Na,K,Rb,Cs) we observe the formation of snowballs Ak(+)He(N) when multiply doping the droplets. Fragmentation of clusters Ak(N) upon ionization appears to enhance snowball formation. In the case of Na and Cs we also detect snowballs Ak(2) (+)He(N) formed around Ak dimer ions. While the snowball progression for Na and K is limited to less than 11 helium atoms, the heavier atoms Rb and Cs feature wide distributions at least up to Ak(+)He(41). Characteristic steps in the mass spectra of Cs-doped helium droplets are found at positions consistent with predictions on the closure of the first shell of helium atoms around the Ak(+) ion based on variational Monte Carlo simulations.

Ion core structure in (N2O)n+(n=2–8) studied by infrared photodissociation spectroscopy

IR photodissociation (IRPD) spectra of (N(2)O)(2)(+) x Ar and (N(2)O)(n)(+) with n=3-8 are measured in the 1000-2300 cm(-1) region. The (N(2)O)(2)(+) x Ar ion shows an IRPD band at 1154 cm(-1), which can be assigned to the out-of-phase combination of the nu(1) vibrations of the N(2)O components in the N(4)O(2)(+) ion; the positive charge is delocalized over the two N(2)O molecules. The geometry optimization and the vibrational analysis at the B3LYP/6-311+G(*) level show that the N(4)O(2)(+) ion has a C(2h) structure with the oxygen ends of the N(2)O components bonded to each other. The IRPD spectra of the (N(2)O)(n)(+) (n=3-8) ions show three prominent bands at approximately 1170, approximately 1275, and approximately 2235 cm(-1). The intensity of the approximately 1170 cm(-1) band relative to that of the other bands decreases with increasing the cluster size. Therefore, the approximately 1170 cm(-1) band is ascribed to the N(4)O(2)(+) dimer ion core and the approximately 1275 and approximately 2235 cm(-1) bands are assigned to the nu(1) and nu(3) vibrations of solvent N(2)O molecules, respectively. Since the band of the N(4)O(2)(+) ion core is located at almost the same position for all the (N(2)O)(n)(+) (n=2-8) clusters, the C(2h) structure of the dimer ion core does not change so largely by the solvation of N(2)O molecules, which is quite contrastive to the isoelectronic (CO(2))(n)(+) case.

Cassini detection of Enceladus' cold water‐group plume ionosphere

This study reports direct detection by the Cassini plasma spectrometer of freshly‐produced water‐group ions (O+, OH+, H2O+, H3O+) and heavier water dimer ions (HxO2)+ very close to Enceladus where the plasma begins to emerge from the plume. The data were obtained during two close (52 and 25 km) flybys of Enceladus in 2008 and are similar to ion data in cometary comas. The ions are observed in detectors looking in the Cassini ram direction exhibiting energies consistent with the Cassini speed, indicative of a nearly stagnant plasma flow in the plume. North of Enceladus the plasma slowing commences about 4 to 6 Enceladus radii away, while south of Enceladus signatures of the plasma interaction with the plume are detected 22 Enceladus radii away.

Electronic structure of the noble-gas dimer ions

A systematic study of the electronic structure and chemical binding in the dimer ion sequence, Ne2+, Ar2+, Kr2+, and Xe2+, has been carried out using both density functional and ab initio configuration interaction computational approaches. This study includes detailed calculations of the pertinent potential energy curves and an analysis of the calculated spectroscopic properties of the bound A2Σ+u (1/2u I) state of these ions.

Interparticle forces in spherical monodispersed silica dispersions: Effects of branched polyethylenimine and molecular weight

The effect of branched polyethylenimine (PEI) of molecular weight (Mw) 600, 1800 and 70,000 on the surface forces interacting between ‘uniform size’ spherical silica particles in water was investigated via the yield stress and zeta potential techniques. This silica has a point of zero charge at pH ∼ 2.0. All PEIs caused the zeta potential–pH curve and the high pH zero zeta potential to shift to a higher pH and the extent of the shift increases with increasing PEI concentration and is not affected by PEI Mw. PEI adsorption on silica is low or negligible at pH less than 3.5 and this is due to a very low negative charge density. Adsorption of PEI beyond 3.5 caused a maximum zeta potential to occur at pH between 4 and 6. The maximum yield stress located at the point zero zeta potential is many times larger than that with no added PEI. It ranged from 20 to 42 times for low Mw PEI and as high as 68 times for Mw 70,000. At low surface coverages, the force responsible for the high yield stress is charged patch–bridging attraction. At complete surface coverage, particle bridging via hydrogen bond and unlike charged attraction between monomeric, dimeric and tetrameric silicate ions with the adsorbed PEI layers of the interacting particles was responsible.

A study of exchange interactions in alkali molecular ion dimers with application to charge transfer in cold Cs

The formulation of Bardsley et al (Phys. Rev. A 11 1911) for evaluating the asymptotic electron exchange interaction between an alkali ion and its parent atom is extended by the use of a more accurate representation of the asymptotic wavefunction of the isolated atom and also by the inclusion of a further term in the series that accounts for the presence of the ion. The Bardsley analysis is compared with a purely numerical approach in which the Holstein–Herring integrand is constructed from a polarized wavefunction built from numerical solutions of the differential equations of Rayleigh–Schrödinger perturbation theory and the required quadrature is performed numerically. Values of the asymptotic exchange interactions are given for the molecular ions Li+2, Na+2, K+2, Rb+2 and Cs+2. As an example, exchange interactions for Cs+2 evaluated by an ab initio method are compared to those predicted by the Bardsley formula. Potentials for the lowest states of Cs+2 are constructed from the ab initio values matched to the asymptotic exchange and long-range polarization interactions, and these potentials are used to predict the 12Σ+g and 12Σ+u scattering lengths and low-energy charge transfer cross sections.

The covalently bound HC [tbnd]N dimer ions HC [dbnd]N−N [dbnd]CH [rad]+ and HC [dbnd]N−C( [dbnd]N)H [rad]+ are stable species in the gas-phase, but the neutral counterparts are not

Tandem mass spectrometry based experiments and computational chemistry (CBS-QB3/APNO methods) indicate that ionized s-tetrazine eliminates N 2 to yield the elusive linear HC N dimer ion HC N–N CH + ( 1). The ion is stable in the rarefied gas-phase but, as it is generated with considerable internal energy, it readily interconverts with HC N–C( N)H + ( 2), via a 1,2-HCN shift. This more stable HCN dimer ion was generated independently by loss of HCN from ionized s-triazine. Whereas the HN C dimer ion HN C C NH + has a (kinetically) stable neutral counterpart, theory and experiment (neutralization–reionization mass spectrometry) agree that the HC N dimer ions 1 and 2 do not.

Gas-Phase Reactivity of Acylphenols in Electrospray and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry

Acylphenols from Myristica crassa were identified based on liquid chromatography high-resolution mass spectrometry and liquid chromatography tandem mass spectrometry (MS/MS) experiments. Two types of compound were found in the extract of the plant: monomeric (malabaricone B and C) and dimeric compounds (C-C bonded biphenyl and C-C bonded phenyl-linear carbon chain). Evidence of formation of covalent dimeric ions during the electrospray ionization and matrix-assisted laser desorption ionization (MALDI) processes was established. [2M-3H](-) dimeric ions were detected on the mass spectra of each monomeric compound during high-performance liquid chromatography separation. The MS/MS spectra of those species were compared to the MS/MS spectra obtained for the dimeric compounds synthesized by the plant. Fragmentation pathways were studied for the two classes of dimer. The dimeric ions formed in the ion source were C-C bonded biphenyl compounds. Further evidence was obtained from MALDI experiments: increase in the extraction delay time leads to an increase of the dimeric ions relative abundance. Their formation is based on the high reactivity of phenols or phenolate ions which are easily oxidized yielding phenoxy radicals.

Theoretical study of the dimers of ferriporphyrin analogues (MC34H31N4O4)2 and their positive ions with 3d-metal atoms M

The electronic and geometric structures and the energetic characteristics of isolated dimeric molecules and positive ions of ferriporphyrin analogues (MC34H31O4N4) 2 0,+ and corresponding monomers MC34H31O4N 4 0,+ with 3d-metal atoms M = Sc-Ni in states with different multiplicities were calculated by the density functional theory B3LYP method with the Gen-1 = 6-31G*(Fe) + 6-31G(C,H,N,O) basis set. Their energies were refined with the use of the extended basis set Gen-2 = 6-311+G*(Fe) + 6-31G*(C,H,N,O). The computation results were compared with the analogous calculated data on the dimers of heme analogues (MC34H32O4N4) 2 0,+ and MC34H32O4N 4 0,+ with the same M atoms. The behavior of the above-mentioned properties was analyzed in going along the 3d series, upon ionization and a change in multiplicity, and in other related series. Trends were traced in the calculated energies D 1 of dissociation of the ferriporphyrin analogue dimers into monomers, (MC34H31O4N4) 2 0,+ → MC34H31O4N 4 0,+ MC34H31O4N 4 0 , and in the energies D 2 of removal of two hydrogen atoms from heme analogue dimers resulting in ferriporphyrin analogues, (MC34H32O4N4) 2 0,+ → (MC34H31O4N4) 2 0,+ + 2H. It was shown that, in going along the 3d series, the D 1 energy rapidly decreases from ∼210 kcal/mol for M = Sc to a few tens of kcal/mol for M = Ni, with a small minimum for Mn and a small maximum for Fe, as the energy of the pair of broken covalent (polar) bonds M-O decreases. Conversely, the D 2 energy increases rapidly and rather monotonically from ∼45 kcal/mol for M = Sc to ∼135 kcal/mol for M = Fe, as the difference between the energies of the pair of forming covalent bonds M-O and the pair of broken donor-acceptor bonds M ← O decreases. For the positive ions, the D 1 and D 2 values are, as a rule, 5–10 kcal/mol higher than those for the parent neutral analogues. The character of the spin density distribution in states with different multiplicities was considered.

Charge Trapping in Imidazolium Ionic Liquids

Room-temperature ionic liquids (ILs) are a promising class of solvents for applications ranging from photovoltaics to solvent extractions. Some of these applications involve the exposure of the ILs to ionizing radiation, which stimulates interest in their radiation and photo- chemistry. In the case of ILs consisting of 1,3-dialkylimidazolium cations and hydrophobic anions, ionization, charge transfer and redox reactions yield charge-trapped species thought to be radicals resulting from neutralization of the constituent ions. Using computational chemistry methods and the recent results on electron spin resonance (ESR) and transient absorption spectroscopy of the ionized ILs, we argue that electron localization in the imidazolium ILs yields a gauche dimer radical cation with the elongated C(2)-C(2) bond. This species is shown to absorb in the near-infrared and the visible regions and accounts for the observed ESR spectra. We suggest that the excess electron in these aromatic ILs is localized as such a dimeric ion, and consider the chemical implications of this attribution. We also suggest that three-electron N-N bonding with the formation of a dimer radical anion occurs for amide anions, such as dicyanamide, when the parent anion traps holes; steric hindrance prevents the analogous reaction for bis(triflyl)amide anion. For another anion of practical importance, bis(oxalato)borate, a pathway involving the elimination of CO(2) is suggested. Together, these results indicate the unanticipated tendency of the ILs to localize primary charges as radical ions as opposed to neutral radicals. Thus, it appears that secondary chemistry in the ionized ILs may be dominated by radical ion reactions, similarly to the previously studied conventional organic liquids, depending on the composition of the IL.

Flowing afterglow studies of the electron recombination of protonated cyanides (RCN)H + and their proton-bound dimer ions (RCN) 2H + where R is H, CH 3, and CH 3CH 2

A study has been made of the electron–ion dissociative recombination of the protonated cyanides (RCNH +, R = H, CH 3, C 2H 5) and their proton-bound dimers (RCN) 2H + at 300 K. This has been accomplished with the flowing afterglow technique using an electrostatic Langmuir probe to determine the electron density decay along the flow tube. For the protonated species, the recombination coefficients, α e(cm 3 s −1), are (3.6 ± 0.5) × 10 −7, (3.4 ± 0.5) × 10 −7, (4.6 ± 0.7) × 10 −7 for R = H, CH 3, C 2H 5, respectively. For the proton-bound dimers, the α e are substantially greater being (2.4 ± 0.4) × 10 −6, (2.8 ± 0.4) × 10 −6, (2.3 ± 0.3) × 10 −6 for R = H, CH 3, C 2H 5, respectively. Fitting of the electron density decay data to a simple model has shown that the rate coefficients for the three-body association of RCNH + with RCN are very large being (2.0 ± 0.5) × 10 −26 cm 6 s −1. The significance of these data to the Titan ionosphere is discussed.

Free Energy Barrier Estimation for the Dissociation of Charged Protein Complexes in the Gas Phase

Free energies are calculated for the protonated cytochrome c' dimer ion in the gas phase as a function of the center of mass distance between the monomers. A number of different charge partitionings are examined as well as the behavior of the neutral complex. It is found that monomer unfolding competes with complex dissociation and that the relative importance of these two factors depends upon the charge partitioning in the complex. Symmetric charge partitionings preferentially suppress the dissociation barrier relative to unfolding, and complexes tend to dissociate promptly with little structural changes occurring in the monomers. Alternatively, asymmetric charge partitionings preferentially lower the barrier for monomer unfolding relative to the dissociation barrier. In this case, the monomer with the higher charge unfolds before the complex dissociates. For the homodimer considered here, this pathway has a large free energy barrier. The results can be rationalized using schematic two-dimensional free energy surfaces. Additionally, for large multimeric complexes, it is argued that the unfolding and subsequent charging of a single monomer is a favorable process, cooperatively lowering both the unfolding and dissociation barriers at the same time.

Pb9CdCdPb9]6−: A Zintl cluster anion with an unsupported cadmium–cadmium bond

Reaction of an ethylenediamine solution of the intermetallic Zintl phase K4Pb9 with dimesitylcadmium yielded the dimeric Zintl ion [Pb9Cd-CdPb9]6- in low crystalline yield. The cluster anion exhibits a Cd-Cd bond and was structurally characterised by single crystal X-ray diffraction in [K(2,2,2-crypt)]6[Cd2Pb18].2en (1). DFT was also used to explore the bonding in the hexa-anionic cluster.

Study on sublimation of solid electrolyte (AgI)0.5‐(AgPO3)0.5with Knudsen effusion mass spectrometry

Knudsen high-temperature mass spectrometry was used to study the process of sublimation of a solid electrolyte (AgI)(0.5-)(AgPO(3))(0.5). Monoatomic iodine ions were found to be the dominant species in the electron ionization mass spectra below 600 degrees C. With an increase in temperature, the relative content of phosphorus oxide ions, mainly [PO](+) and [P(4)O(10)](+), increased. Under further heating, we observed silver iodide and iodine dimer ions together with phosphorus dimer and tetramer ions and clusters [IPO(2)](+), [IP(2)](+), [I(3)P](+). Using the experimental logarithmic dependencies of ion signal intensities versus the reciprocal absolute temperature of the effusion cell, the apparent sublimation enthalpies Delta(s)H of the ions giving the most intense signals were estimated.

Gas-Phase H/D Exchange and Collision Cross Sections of Hemoglobin Monomers, Dimers, and Tetramers

The conformations of gas-phase ions of hemoglobin, and its dimer and monomer subunits have been studied with H/D exchange and cross section measurements. During the H/D exchange measurements, tetramers undergo slow dissociation to dimers, and dimers to monomers, but this did not prevent drawing conclusions about the relative exchange levels of monomers, dimers, and tetramers. Assembly of the monomers into tetramers, hexamers, and octamers causes the monomers to exchange a greater fraction of their hydrogens. Dimer ions, however, exchange a lower fraction of their hydrogens than monomers or tetramers. Solvation of tetramers affects the exchange kinetics. Solvation molecules do not appear to exchange, and solvation lowers the overall exchange level of the tetramers. Cross section measurements show that monomer ions in low charge states, and tetramer ions have compact structures, comparable in size to the native conformations in solution. Dimers have remarkably compact structures, considerably smaller than the native conformation in solution and smaller than might be expected from the monomer or tetramer cross sections. This is consistent with the relatively low level of exchange of the dimers.

Kinetic study of proton-bound dimer formation using ion mobility spectrometry

A method to measure the rate constant for the formation of symmetrical proton-bound dimers at ambient pressure was proposed. The sample is continuously delivered to the drift region of an ion mobility spectrometer where it reacts with a swarm of monomer ions injected by the shutter grid. Dimer ions are formed in the drift tube and a tail appears in the ion mobility spectrum. The rate constant is derived from the mobility spectra. The proposed approach was typically examined for methyl isobutyl ketone (MIBK), 2,4-dimethyl pyridine (DMP), and dimethyl methyl phosphonate (DMMP). The rate constants measured in this study were: 0.25 × 10 −9, 0.86 × 10 −10, and 0.47 × 10 −10 cm 3 s −1 for MIBK, DMP and DMMP, respectively. The logarithm of the measured rate constants were found to be almost independent of reciprocal temperature within 303 to 343 K, indicating that no activation energy is involved in the formation of proton-bound dimers.