Dimer Ions Research Articles

Effects of high-fluence ion implantation on colorless diamond self-standing films

Self-standing polycrystalline diamond films fabricated by chemical vapor deposition, which were transparent up to the intrinsic band edge of ∼5.5 eV, were implanted with boron negative dimer ions (B2−) of 60 keV at various fluences ranging from 1×1014 to 3×1017 B/cm2. Even at the lowest fluence of 1×1014 B/cm2, a weak color darkening was observed by the naked eye, indicating the optical absorption due to damage, not to implants. The subbandgap absorption tail increases with the fluence to the powers of ∼0.5 and ∼0.2 in the fluence regions lower and higher, respectively, than the transition fluence of ∼1×1016 B/cm2. The implanted regions also show large surface swelling of up to ∼60 nm in height. The swelling shows the same two-step power-law dependence with the same transition fluence. The same two-step power-law fluence dependence with the same transition fluence is also observed in the intensity of the defect Raman band around 1520 cm−1. From the good agreement between the estimated volume change due to graphitization and the measured swelling, the transition fluence is ascribed to the fluence where all the diamond structures in the implanted layer are transformed to graphitelike structures.

Density Functional Study of Intradimer Proton Transfers in Hydrated Adenine Dimer Ions, A2+(H2O)n (n = 0−2)

Structures of mono- and dihydrated adenine dimers and their cations were calculated using B3LYP density functional theory with the 6-31+G(d,p) basis set, in order to help understand photofragmentation experiments of hydrated adenine dimers from the energetics point of view. Several important pathways leading to the major fragmentation product, protonated adenine ion (AH(+)), thermodynamically at minimum costs were investigated at the ground-state electronic potential surface of hydrated adenine dimer cations. Our calculations suggest that the proton transfer from one adenine moiety to the other in hydrated dimer ions readily occurs with negligible barriers in normal hydration conditions. In asymmetrically hydrated ions, however, the proton transfer to more hydrated adenine moieties is kinetically hindered due to heightened transition-state barriers, while the other way is still barrierless. Such directional preference in proton transfer may be characterized as a unique dimer ion property, stemming from the difference in basicity of the two nitrogen atoms involved in the double hydrogen bond that would be equivalent without hydration. We also found that dimer cleavage requires about 4 times larger energy than evaporation of individual water molecules, so it is likely that most solvent molecules evaporate before the eventual dimer cleavage when available internal energy is limited.

Formation of an Ion-Pair Molecule with a Single NH+···Cl− Hydrogen Bond: Raman Spectra of 1,1,3,3-Tetramethylguanidinium Chloride in the Solid State, in Solution, and in the Vapor Phase

Some ionic compounds (salts) form liquids when heated to temperatures in the range of 200-300 degrees C. They may be referred to as moderate temperature ionic liquids. An example of such a compound is the 1,1,3,3-tetramethylguanidinium chloride, [TMGH]Cl, melting at approximately 212 degrees C. The chemistry of this compoundcontaining a dimeric ion-pair "molecule"was investigated in the solid state, in solutions in water and ethanol, and in the vapor phase, based on ab initio molecular orbital density functional theory (DFT)-type calculations with 6-311+G(d,p) basis sets. Calculations on the monomeric [TMGH] (+) ion and the dimeric chloride ion-pair salt converged to give geometries near the established crystal structure of [TMGH]Cl. The structures and their binding energies are given as well as calculated vibrational harmonic normal modes (IR and Raman band wavenumbers and intensities). Experimentally obtained Raman scattering spectra are presented and assigned, by comparing to the quantum mechanical calculations. It is concluded that dimeric molecular ion pairs with four N-H (+)...Cl (-) hydrogen bonds probably exist in the solutions and are responsible for the relatively high solubility of the "salt" in ethanol. It was discovered that the compound can be easily sublimed by heating to about 200-230 degrees C. In the Raman spectrum of the vapor at 225 degrees C, a characteristic strong band at 2229 cm (-1) was found and interpreted to show that the gas phase consists of monomeric ion-pair "molecules" held together by a single N-H (+)...Cl (-) hydrogen bond, the stretching band of which is causing the band.

The covalently bound HNC dimer ion HN [dbnd]C [dbnd]C [dbnd]NH [rad]+ has a kinetically stable neutral counterpart

Neutralization-reionization mass spectrometry (NRMS) and computational chemistry (CBS-QB3/APNO methods) have been used to show that HN C C NH (ethenediimine) and its isomer H 2N–C–C N (aminocyanocarbene) are generated as kinetically stable molecules in the rarefied gas-phase by one electron reduction of their ionic precursors. One route to the very stable ion HN C C NH + involves loss of HC N from the hydrogen-bridged radical cation [ HN C ⋯ H 2 N – C – C N ] + via a remarkable quid-pro-quo catalysis in which both the ion and the neutral undergo isomerization.

The reversible [4 + 4] photocycloaddition of acridizinium derivatives

Several aspects of the photoinduced dimerization of acridizinium ions, also known as benzo[ b]quinolizinium ions or 4a-azoniaanthracenes, are reviewed. In particular, the photochemical and photophysical studies of the [4 + 4] photocycloaddition and the cycloreversion of the corresponding acridizinium dimers in solution, in the solid state and in other organized media are presented and discussed. Examples are given for the possible application of this photochromic system for data storage or for photoinduced switching of material properties.

Molecular Basis of Prodrug Activation by Human Valacyclovirase, an α-Amino Acid Ester Hydrolase

Chemical modification to improve biopharmaceutical properties, especially oral absorption and bioavailability, is a common strategy employed by pharmaceutical chemists. The approach often employs a simple structural modification and utilizes ubiquitous endogenous esterases as activation enzymes, although such enzymes are often unidentified. This report describes the crystal structure and specificity of a novel activating enzyme for valacyclovir and valganciclovir. Our structural insights show that human valacyclovirase has a unique binding mode and specificity for amino acid esters. Biochemical data demonstrate that the enzyme hydrolyzes esters of alpha-amino acids exclusively and displays a broad specificity spectrum for the aminoacyl moiety similar to tricorn-interacting aminopeptidase F1. Crystal structures of the enzyme, two mechanistic mutants, and a complex with a product analogue, when combined with biochemical analysis, reveal the key determinants for substrate recognition; that is, a flexible and mostly hydrophobic acyl pocket, a localized negative electrostatic potential, a large open leaving group-accommodating groove, and a pivotal acidic residue, Asp-123, after the nucleophile Ser-122. This is the first time that a residue immediately after the nucleophile has been found to have its side chain directed into the substrate binding pocket and play an essential role in substrate discrimination in serine hydrolases. These results as well as a phylogenetic analysis establish that the enzyme functions as a specific alpha-amino acid ester hydrolase. Valacyclovirase is a valuable target for amino acid ester prodrug-based oral drug delivery enhancement strategies.

Inelastic electron collisions of the isotopically symmetric helium dimer ionHe2+4in a storage ring

Rate coefficients for dissociative recombination (DR), dissociative excitation (DE), and vibrational excitation between the helium dimer ion He-4(2)+ and electrons from a few meV up to 40 eV were measured using fast (3.8 and 8.3 MeV) ion beams stored for up to 85 s. Vibrational relaxation to greater than 95% in the v = 0 level was achieved by collisions with cold electrons over 50 s. Low-energy, strongly v-dependent DR rate coefficients are given for v = 0, 1, and >= 2. The rate coefficients at higher energies for v = 0, with DR and DE given on an absolute scale, are compared to results from recent wave-packet calculations on the fast dissociation dynamics of the doubly excited helium dimer, where the three processes occur as competing reaction channels. Also given are rate coefficients for vibrationally superelastic electron collisions at near 10 meV average energy and the approximate vibrational excitation cross section for fast collisions with the residual gas.

The effect of ion molecule reactions on peaks in ion mobility spectrometry

The peak width, shape and position are heavily affected by ion-molecule reactions which are inevitable in the drift region of an ion mobility spectrometer. This paper discusses three major types of reactions occurring in drift tube and their effects on the shape and displacement of the peaks. The first reaction is the dissociation of dimer ions during their flight time creating a tail for the monomer peak. The second one is the reaction between the monomer ions with molecules of the same kind in the drift region. Such a process shifts the peak to longer drift times and causes a tail for the peak as well as its broadening. The last one is the reaction of ions with molecules of different types such as dopant which may exist in the drift region. Depending on the reactivity of the ions, this kind of reaction displaces the peaks differently so that peak-to-peak resolution is lost or, in some cases, gained.

Mechanisms of Water Oxidation Catalyzed by Ruthenium Diimine Complexes

(18)O-isotope-labeling studies have led to the conclusion that there exist two major pathways for water oxidation catalyzed by dimeric ruthenium ions of the general type cis, cis-[L2Ru(III)(OH2)]2O(4+). We have proposed that both pathways involve concerted addition of H and OH fragments derived from H 2O to the complexes in their four-electron-oxidized states, i.e., [L2Ru(V)(O)]2O(4+), ultimately generating bound peroxy intermediates that decay with the evolution of O2. The pathways differ primarily in the site of addition of the OH fragment, which is either a ruthenyl O atom or a bipyridine ligand. In the former case, water addition is thought to give rise to a critical intermediate whose structure is L2Ru(IV)(OH)ORu(IV)(OOH)L2(4+); the structures of intermediates involved in the other pathway are less well defined but may involve bipyridine OH adducts of the type L2Ru(V)(O)ORu(IV)(OH)(L(*)OH)L(4+), which could react further to generate unstable dioxetanes or similar endoperoxides. Published experimental and theoretical support for these pathways is reviewed within the broader context of water oxidation catalysis and related reactions reported for other diruthenium and group 8 monomeric diimine-based catalysts. New experiments that are designed to probe the issue of bipyridine ligand "noninnocence" in catalysis are described. Specifically, the relative contributions of the two pathways have been shown to correlate with substituent effects in 4,4'- and 5,5'-substituted bipyridine complexes in a manner consistent with the formation of a reactive OH-adduct intermediate in one of the pathways, and the formation of OH-bipyridine adducts during catalytic turnover has been directly confirmed by optical spectroscopy. Finally, a photosensitized system for catalyzed water oxidation has been developed that allows assessment of the catalytic efficiencies of the complex ions under neutral and alkaline conditions; these studies show that the ions are far better catalysts than had previously been assumed based upon reported catalytic parameters obtained with strong oxidants in acidic media.

Co(II) and Cu(II) complexes of 2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidine

The Co(II) and Cu(II) complexes of 2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidine (trimethoprim) were synthesized and characterized by elemental analysis, UV-Vis and IR spectroscopy, magnetic susceptibility measurements, EPR (Cu complexes) and single crystal X-ray studies. The molecular structures of the compounds consist of dimeric metal ions in distorted octahedral environments, bridged with four acetate ions and each metal ion coordinated to one trimethoprim through the pyrimidinyl nitrogen atom.

Structure of Protonated Carbon Dioxide Clusters: Infrared Photodissociation Spectroscopy and ab Initio Calculations

The infrared photodissociation spectra (IRPD) in the 700 to 4000 cm(-1) region are reported for H+ (CO2)n clusters (n = 1-4) and their complexes with argon. Weakly bound Ar atoms are attached to each complex upon cluster formation in a pulsed electric discharge/supersonic expansion cluster source. An expanded IRPD spectrum of the H+ (CO2)Ar complex, previously reported in the 2600-3000 cm(-1) range [Dopfer, O.; Olkhov, R.V.; Roth, D.; Maier, J.P. Chem. Phys. Lett. 1998, 296, 585-591] reveals new vibrational resonances. For n = 2 to 4, the vibrational resonances involving the motion of the proton are observed in the 750 to 1500 cm(-1) region of the spectrum, and by comparison to the predictions of theory, the structure of the small clusters are revealed. The monomer species has a nonlinear structure, with the proton binding to the lone pair of an oxygen. In the dimer, this nonlinear configuration is preserved, with the two CO2 units in a trans configuration about the central proton. Upon formation of the trimer, the core CO2 dimer ion undergoes a rearrangement, producing a structure with near C2v symmetry, which is preserved upon successive CO2 solvation. While the higher frequency asymmetric CO2 stretch vibrations are unaffected by the presence of the weakly attached Ar atom, the dynamics of the shared proton motions are substantially altered, largely due to the reduction in symmetry of each complex. For n = 2 to 4, the perturbation due to Ar leads to blue shifts of proton stretching vibrations that involve motion of the proton mostly parallel to the O-H+-O axis of the core ion. Moreover, proton stretching motions perpendicular to this axis exhibit smaller shifts, largely to the red. Ab initio (MP2) calculations of the structures, complexation energies, and harmonic vibrational frequencies are also presented, which support the assignments of the experimental spectra.

The low-lying electronic states of ArXe+ and their potential energy functions

Photoionization and pulsed-field-ionization zero-kinetic-energy (PFI-ZEKE) photoelectron spectra of ArXe have been recorded between 96 400 and 108 200 cm(-1) following resonance-enhanced two-photon excitation via selected vibrational levels of the C 1 and D 0+ Rydberg states. The PFI-ZEKE photoelectron spectra consist of three vibrational progressions corresponding to the X 1/2<--X 0+, A1 3/2<--X 0+, and A2 1/2<--X 0+ transitions. From these progressions, adiabatic ionization energies, equilibrium internuclear distances, and vibrational constants have been derived for the lowest three electronic states of ArXe+. The photoionization spectra reveal long progressions of autoionizing Rydberg states converging to the lowest vibrational levels of the A1 3/2 state. A potential model has been developed that enables a global description of the low-lying electronic states of the heteronuclear rare gas dimer ions. The model explicitly treats the effects of the spin-orbit, charge-exchange, and long-range interactions. This model was used to obtain potential energy functions for all six low-lying electronic states of ArXe+ from the experimental positions of the vibrational levels of the X 1/2, A1 3/2, and A2 1/2 states relative to the ground neutral state and existing spectroscopic data on the B 1/2, C1 3/2, and C2 1/2 states.

The hydration of the mercury(I)-dimer – A quantum mechanical charge field molecular dynamics study

The complex and labile hydration structure of the dimeric mercury ion Hg 2 2 + has been studied by means of the novel quantum mechanical charge field molecular dynamics approach (QMCF MD). This system has been chosen as a challenging target to assess and evaluate the applicability of the QMCF approach, as standard MM and QM/MM protocols face obstacles in the formulation of accurate ion–solvent interaction potentials, while the application of the QMCF approach allows to renounce these potentials as the respective contributions are all included in the quantum mechanical framework. The results of the simulation show that the Hg(I) dimer forms a very labile hydration structure. In average 3.7 ligands are bound to each of the Hg atoms, and the water molecules are exchanged on the picosecond timescale.

Bis{μ-2,2'-[1,1'-(ethane-1,2-diyldinitrilo)diethyl-idyne]diphenolato}bis-[(benzoato-κO)manganese(III)] dihydrate.

The title compound, [Mn2(C18H18N2O2)2(C7H5O2)2]·2H2O, was synthesized by the reaction between manganese(II) benzoate and the Schiff base generated in situ by the condensation of ethane-1,2-diamine and o-hydroxy­aceto­phen­one. The Jahn–Teller-distorted manganese(III) ions of the centrosymmetric dimer are connected through phen­oxy bridges. Hydrogen-bonding inter­actions between the uncoord­in­ated C=O of the benzoate and uncoordinated water mol­ecules link the dimers into a chain running parallel to the c axis.

Study on the formation of an amoxicillin adduct with methanol using electrospray ion trap tandem mass spectrometry

The possibility of using the protonated methanol-adduct of antimicrobial amoxicillin for its identification and quantification at residue levels has been investigated, since it is impossible to completely suppress the formation of these adducts when methanol is present in the solvent system. This process has been monitored over time and as a function of concentration. It was determined that adducts were instantly formed and that the abundance of the protonated methanol-adduct at m/z 398 increased at the expense of the protonated molecule m/z 366 with storage time. The effect of several common solvents and mobile-phase additives on the ionization efficiency of amoxicillin and the formation of the methanol adduct has also been investigated. It was shown that the mass spectra of amoxicillin were strongly influenced by the solvent in which the analyte is dissolved and by the analyte concentration, as well as by the composition of mobile phase. Methanol was determined to be the best spray solvent, as it provided spectra with the lowest abundance of dimer ions. It was also determined that acetic acid as the mobile-phase additive provided the highest signal intensities, while ammonium acetate should not be used as an additive for the determination of amoxicillin at residue levels. Using high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS), fragmentation of the protonated molecules and the protonated methanol-adduct ions, in both positive and negative ion mode, has been performed. The fragmentation was stable and strong product ion spectra were obtained. The linearity of the MS detector response, and that of the chromatographic method, was tested. Due to the linear behaviour it was concluded that the protonated methanol-adduct ion can be used for analytical purposes, i.e. for identification and quantification of amoxicillin at trace levels.

Photodissociation dynamics of adenine dimer radical ions and hydrated adenine dimer ions, [formula omitted] ( n = 0–6)

We studied photodissociation dynamics of adenine dimer radical ions, A 2 + , and hydrated adenine dimer ions, A 2 + ( H 2 O ) n ( n = 1–6), at three wavelengths. The most abundant daughter ion is found to be protonated adenines, (AH) +, which implies that proton transfer is followed by dissociation in A 2 + and A 2 + ( H 2 O ) n . Theoretical calculations support that the most stable structures of A 2 + and A 2 + ( H 2 O ) 1 are formed by proton transfer. As cluster size of A 2 + ( H 2 O ) n becomes larger, the intensity of A 2 + as a daughter ion increases with the decrease in the intensity of (AH) +. Upon photoexcitation of A 2 + by 266 nm, adenine monomer ion (A +) is also observed along with (AH) +, which suggests that electronically excited states of (AH) + moiety in A 2 + promotes the hydrogen abstraction from (AH) +.

Fragmentation Dynamics of Size-Selected Pyrrole Clusters Prepared by Electron Impact Ionization: Forming a Solvated Dimer Ion Core

Structure and dynamics of size-selected charged pyrrole clusters have been studied by means of molecular beam scattering experiments and ab initio calculations. Small neutral Pyn clusters were produced in Py/He mixture expansions, and the scattering experiment with a secondary beam of He-atoms was exploited to select the neutral clusters of different sizes. The complete size-selected fragmentation patterns for the neutral dimer to the tetramer after an electron impact ionization at 70 eV were obtained from the measurements of the angular and velocity distributions at different fragment masses. All the investigated cluster sizes decay mainly to the monomer ions Py+1 (from 60 to 80% of the corresponding neutral size) and to the dimer ion Py+2 (20-30%). The trimer ions Py+3 are generated to less than 10% from the neutral trimer and tetramer. To explain the observed results, we have calculated the structures and energetics of pyrrole clusters up to the trimer for the neutral and the ionic state using DFT and PMP2 methods. The ab initio calculations show that ionized pyrrole clusters are formed with a dimeric core that is solvated by neutral pyrrole molecules. In addition, the ground and ionic state of Py-Ar complexes were calculated at CCSD(T) level with extended basis in relevance to the mixed clusters produced in supersonic expansions of Py seeded in Ar. The calculated dissociation energies of the Py-Ar and (Py-Ar)+ complexes indicate that Ar atoms are able to rapidly evaporate after ionization. The combined analysis of the fragmentation probabilities, and calculations allowed us to estimate the distribution of energy deposited in the clusters after the electron impact, which peaks above 1 eV and has a tail up to 5 eV.

Theoretical and infrared spectroscopic investigation of the O2−∙benzene and O4−∙benzene complexes

The infrared spectra of the O(2) (-).benzene and O(4) (-).benzene complexes are determined by means of Ar predissociation spectroscopy. Several transitions due to CH stretch fundamentals and various combination bands are observed in the 2700-3100 cm(-1) region. The experimental results are interpreted with the aid of electronic structure calculations. A comparison of the calculated and experimental spectra reveals that the spectrum of O(2) (-).benzene most likely arises from an isomer where the superoxide molecule binds preferentially to one CH group of benzene. In contrast, the spectrum of O(4) (-).benzene yields a CH pattern remarkably similar to that displayed by the C(2nu) X(-).benzene (X=halogen) complexes, consistent with a structure with two CH groups equally involved in the bonding. The lower energy vibrational fundamental transitions of the O(4) (-) anion are recovered with a slight redshift in the O(4) (-).benzene spectrum, establishing that this charge-delocalized dimer ion retains its identity upon complexation.

Structural Effects in the Analysis of Supported Lipid Bilayers by Time-of-Flight Secondary Ion Mass Spectrometry

We contribute to the rapidly emerging interest in the application of time-of-flight secondary ion mass spectrometry (TOF-SIMS) for chemical analysis of biological materials by presenting a careful TOF-SIMS investigation of structurally different SiO2-supported phospholipid assemblies. Freeze-dried supported 1-oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine (POPC) bilayers, Langmuir-Blodgett POPC monolayers, and disordered thick POPC films were investigated. Compared with the two latter structures, the supported bilayer showed a strong (5-10 times) enhancement in the yield of both the molecular and the dimer ion peaks of POPC, suggesting that the molecular peak may be used as a sensitive indicator for changes in the membrane structure and, in particular, an indicator for the presence of bilayer structures in, e.g., cell and tissue samples. The detection efficiency and the useful lateral resolution indicate that a lateral resolution of around 100 nm can be obtained on all structures by imaging the phosphocholine ion at 184 u using Bi3+ primary ions. For the chemically specific molecular peak at 760 u, the measured detection efficiencies correspond to a useful lateral resolution of around 2 microm for the bilayer structure. The results are discussed in relation to recent dynamic SIMS (nano-SIMS) analysis of freeze-dried supported lipid bilayers, displaying similar or higher lateral resolution, but which in contrast to TOF-SIMS requires isotopic labeling of the analyzed lipids.

Isotope effects in the metastable decay of Ne2 +

Neon dimer ions undergo spontaneous dissociation (metastable decay) several microseconds after formation by electron impact ionization of neon clusters. In this contribution we compare the kinetic energy release distribution (KERD) of the previously reported isotopomer 20Ne2 + with that of 22Ne2 +. The heavy isotopomer shows the same two components in the KERD as the lighter ones. However, the high-energy component that is due to electronic pre-dissociation is reduced in intensity. The decrease is attributed to a reduced predissociation rate from the II(1/2u) state into I(3/2u).