Keto-to-enol isomerization in the molecular ion of dimethylmethylphosphonate

A mechanism for keto-to-enol isomerization in dimethylmethylphosphonate (DMMP) has been proposed based on deuterium-labeling studies, a model compound and thermodynamic data. An electron ionization study of H/D exchange occurring in CD₃-labeled DMMP suggests that rapid keto-to-enol isomerization occurs in the ion source and a reaction mechanism based on sequential 1,4-H migrations rather than by the direct 1,3-H transfer or by sequential 1,2-H migrations is proposed. The examination of the mass-analyzed ion kinetic energy/collision-induced dissociation spectrum of the methylphosphonic acid molecular ion suggests that keto-to-enol isomerization does not occur for this species and that 1,2- and 1,3-H migrations are not favored. Available thermodynamic data were employed to construct a potential energy surface for keto-to-enol isomerization of the DMMP molecular ion. The thermodynamic data show that the energy barrier to isomerization is below the internal energy required for decomposition of the DMMP molecular ion. Additionally, the ΔH_f° for the intermediate and enolic isbmers are shown to be significantly less than the ΔH_f° for the keto form of the DMMP molecular ion.     

The molecular scanner in microscope mode

The combination of microscope mode matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) with protein identification methodology: the molecular scanner, was explored. The molecular scanner approach provides improvement of sensitivity of detection and identification of high-mass proteins in microscope mode IMS. The methodology was tested on protein distributions obtained after separation by sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE). High-quality, high-spatial-resolution ion images were recorded on a TRIFT-II ion microscope after gold coating of the MALDI sample preparation on the poly(vinylidenedifluoride) capture membranes. The sensitivity of the combined method is estimated to be 5 pmol. The minimum amount of sample consumed, needed for identification, was estimated to be better than 100 fmol. Software tools were developed to analyze the spectral data and to generate broad mass range and single molecular component microscope mode ion images and single mass-to-charge ratio microprobe mode images.     

A simple erosion dynamics model of molecular sputter depth profiling

A simple model which describes the essential features commonly observed in a molecular sputter depth profile is presented. General predictions of the dependence of measured molecular ion signals on the primary ion fluence are derived for the specific case where a mass spectrometric technique such as SIMS or secondary neutral mass spectrometry (SNMS) is used to analyze the momentary surface. The results are compared with recent experimental data on molecular depth profiles obtained by cluster‐ion‐initiated SIMS of organic overlayers. Copyright © 2008 John Wiley & Sons, Ltd.     

Collision-induced dissociation of the phenylsilane molecular ion

The high-energy collision-induced dissociation of the phenylsilane molecular ion generated by electron ionization has been investigated using tandem mass spectrometry (MS/MS). It was observed that the dissociation of the molecular ion (M(+*)) occurs mainly via [M-H](+), [M-2H](+*), and [M-3H](+), followed by two consecutive losses of C(2)H(2). The structures of the precursors for the [M-CH(3)](+), [M-SiH](+), and [M-SiH(2)](+*) ions are proposed. The data suggest that the molecular ion undergoes rearrangements to several isomers prior to dissociation, including the ion containing a five-membered carbon ring. Reaction mechanisms are proposed for the dissociations via the isomeric molecular ions.     

Numerical simulation of molecular uptake via electroporation

A numerical study of electroporation-mediated molecular delivery is presented. The model consists of the Nernst-Planck equations for species transport, coupled with an asymptotic Smoluchowski equation for membrane permeabilization. The transfer of calcium ions into a Chinese Hamster Ovary cell is simulated. The results reveal important physical insights. First, for this particular case, ion electrophoresis plays an important role, and is an order of magnitude faster than free diffusion on a comparable time scale. Second, the maximum achievable concentration within the cell is reciprocally correlated with the extracellular electrical conductivity. This behavior is mediated by an electrokinetic mechanism known as field-amplified sample stacking. Through this mechanism, the intracellular ion concentration can reach a level higher than the extracellular one provided that the intra-to-extracellular conductivity ratio is greater than unity. The results corroborate well with data in the literature, and offer a mechanistic interpretation to previous experimental observations. This work is a step toward the quantification of molecular delivery via electroporation.     

The elimination of carbon monoxide from molecular ions of phenol and other [C6H6O]+˙ isomers

Phenol and five acyclic isomeric compounds have been investigated using electron impact and field ionization techniques, mass analysed ion kinetic energy spectrometry and collision induced dissociation mass analysed ion kinetic energy spectrometry. The kinetic energy release data corresponding to the elimination of carbon monoxide from the molecular ions show that at least two structures of the reactant ion are involved. The electron impact and field ionization collision induced dissociation mass analysed ion kinetic energy spectra indicate that under electron impact conditions, the phenol ion partially isomerizes to another ion structure. An isomerization of about 40% to the structure of cis-2-hexen-4-yn-1-al is in good accordance with the spectral data.     

A wavelet‐PCA method saves high mass resolution information in data treatment of SIMS molecular depth profiles

A detailed depth characterization of multilayered polymeric systems is a very attractive topic. Currently, the use of cluster primary ion beams in time‐of‐flight secondary ion mass spectrometry allows molecular depth profiling of organic and polymeric materials. Because typical raw data may contain thousands of peaks, the amount of information to manage grows rapidly and widely, so that data reduction techniques become indispensable in order to extract the most significant information from the given dataset. Here, we show how the wavelet‐based signal processing technique can be applied to the compression of the giant raw data acquired during time‐of‐flight secondary ion mass spectrometry molecular depth‐profiling experiments. We tested the approach on data acquired by analyzing a model sample consisting of polyelectrolyte‐based multilayers spin‐cast on silicon. Numerous wavelet mother functions and several compression levels were investigated. We propose some estimators of the filtering quality in order to find the highest ‘safe’ approximation value in terms of peaks area modification, signal to noise ratio, and mass resolution retention. The compression procedure allowed to obtain a dataset straightforwardly ‘manageable’ without any peak‐picking procedure or detailed peak integration. Moreover, we show that multivariate analysis, namely, principal component analysis, can be successfully combined to the results of the wavelet‐filtering, providing a simple and reliable method for extracting the relevant information from raw datasets. Copyright © 2016 John Wiley & Sons, Ltd.     

Time of flight secondary ion mass spectrometric determination of molecular weight distributions of low polydispersity poly(dimethyl siloxane) with polyatomic primary ions

This work reports a comparison of oligomer and fragment ion intensities resulting from primary ion bombardment with several primary ion sources (Bi_n⁺, C₆₀⁺, and Cs⁺) at various energies in secondary ion mass spectrometry (SIMS). Although the use of polyatomic primary ions are of great interest due to increased secondary ion efficiency and yield, we demonstrate that monatomic primary ions result in increased oligomer ion yield for polymers prepared as submonolayer films on silver substrates. The enhancement of oligomer secondary ion yield with monatomic ions is evidence that monatomic primary ions have a shallower sampling depth than polyatomic ions, resulting from a collision cascade that is less energetic at the sample surface. The results are also consistent with a lower degree of fragmentation of the resultant secondary ions, which is observed when evaluating the fragmentation data and the spectral data.     

Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

The combination of small-angle X-ray solution scattering (SAXS) experiments and molecular dynamics (MD) simulations is now becoming a powerful tool to study protein conformations in solution at an atomic resolution. In this study, we investigated effects of ionic strength on SAXS data theoretically by using MD simulations of hen egg white lysozyme at various NaCl concentrations from 0 to 1 M. The calculated SAXS excess intensities showed a significant dependence on ion concentration, which originates from the different solvent density distributions in the presence and absence of ions. The addition of ions induced a slow convergence of the SAXS data, and a ～20 ns simulation is required to obtain convergence of the SAXS data with the presence of ions whereas only a 0.2 ns simulation is sufficient in the absence of ions. To circumvent the problem of the slow convergence in the presence of ions, we developed a novel method that reproduces the SAXS excess intensities with the presence of ions from short MD trajectories in pure water. By applying this method to SAXS data for the open and closed forms of transferrin at 1 M ion concentration, the correct form could be identified by simply using short MD simulations of the protein in pure water for 0.2 ns.     

Nonadiabatic molecular dynamics study of electron transfer from alizarin to the hydrated Ti4+ ion

Ab initio real-time nonadiabatic (NA) molecular dynamics (MD) simulations are performed in order to investigate the photoinduced electron transfer (ET) from alizarin to the hydrated Ti4+ ion and compare it with the ET into bulk TiO2 that forms the basis of the Gr?tzel type solar cell. The experimental data and electronic structure calculations indicate that the photoexcitation spectra of alizarin attached to either bulk TiO2 or the Ti4+ ion in solution are very similar. In contrast, the NAMD simulations at ambient temperature predict marked differences between the ET dynamics that follow the photoexcitation in the two systems. The simulation of ET between alizarin and the TiO2 surface shows predominantly adiabatic transfer that occurs within 8 fs (Duncan et al. J. Am. Chem. Soc. 2005, 127, 7941), in agreement with the time-resolved experimental data. The simulation of alizarin attached to the hydrated Ti4+ ion reported presently predicts that the ET does occur, but on a slower 30 fs time scale, with a substantially reduced amplitude and by a predominantly NA mechanism. The differences are attributed to the disparity in the acceptor states of bulk TiO2 and the Ti4+ ion in solution. It is shown that the predicted alizarin-Ti4+ ET dynamics can be verified experimentally.     

Quantitative ion mobility spectroscopy based on molecular collision rate theory

Atmospheric pressure chemical ionization and ion mobility spectrometry (IMS) have traditionally been viewed as a qualitative analytical technique for identifying specific chemicals in the atmosphere. This work employs a nonlinear model based on molecular collision rate theory for quantitative modeling of chemical analyte concentrations. The collision rate between any two molecules depends on the relative populations of each chemical species in the volume of air analyzed where most collisions between ions, or neutral molecules and ions, result in no charge transfer. The rate constants for formation of product ions and consumption of source ions are estimated using empirical data over a wide concentration range for several analytes and reagent gases. The rate constants are unique to the analyte and the reagent gas as well as the sensitivity of the particular IMS instrument and provide a quantitative model to relate the mobility peak amplitudes to the analyte concentration. The rate constants can also be normalized by the reaction ion consumption rate constant to remove the IMS instrument sensitivity and provide a qualitative metric for analyte identification independent of a particular IMS instrument. A quantitative example is given for an acetic acid plume measured by a hand-held IMS detector outdoors has the plume passes. The quantitative rate constants provide a reasonable basis for estimating analyte concentration from the ion mobility spectra over a wide range of analyte concentrations.     

Gas chromatography-mass spectrometry with supersonic molecular beams

Gas chromatography-mass spectrometry (GC-MS) with supersonic molecular beams (SMBs) (also named Supersonic GC-MS) is based on GC and MS interface with SMBs and on the electron ionization (EI) of vibrationally cold analytes in the SMBs (cold EI) in a fly-through ion source. This ion source is inherently inert and further characterized by fast response and vacuum background filtration capability. The same ion source offers three modes of ionization including cold EI, classical EI and cluster chemical ionization (CI). Cold EI, as a main mode, provides enhanced molecular ions combined with an effective library sample identification, which is supplemented and complemented by a powerful isotope abundance analysis method and software. The range of low-volatility and thermally labile compounds amenable for analysis is significantly increased owing to the use of the contact-free, fly-through ion source and the ability to lower sample elution temperatures through the use of high column carrier gas flow rates. Effective, fast GC-MS is enabled particularly owing to the possible use of high column flow rates and improved system selectivity in view of the enhancement of the molecular ion. This fast GC-MS with SMB can be further improved via the added selectivity of MS-MS, which by itself benefits from the enhancement of the molecular ion, the most suitable parent ion for MS-MS. Supersonic GC-MS is characterized by low limits of detection (LOD), and its sensitivity is superior to that of standard GC-MS, particularly for samples that are hard for analysis. The GC separation of the Supersonic GC-MS can be improved with pulsed flow modulation (PFM) GC x GC-MS. Electron ionization LC-MS with SMB can also be combined with the Supersonic GC-MS, with fast and easy switching between these two modes of operation.     

Pulsed flow modulation two-dimensional comprehensive gas chromatography-tandem mass spectrometry with supersonic molecular beams

Pulsed flow modulation (PFM) two-dimensional comprehensive gas chromatography (GC x GC) was combined with quadrupole-based mass spectrometry (MS) via a supersonic molecular beam (SMB) interface using a triple-quadrupole system as the base platform, which enabled tandem mass spectrometry (MS-MS). PFM is a simple GC x GC modulator that does not consume cryogenic gases while providing tunable second GC x GC column injection time for enabling the use of quadrupole-based mass spectrometry regardless its limited scanning speed. The 20-ml/min second column flow rate involved with PFM is handled, splitless, by the SMB interface without affecting the sensitivity. The combinations of PFM GC x GC-MS with SMB and PFM GC x GC-MS-MS with SMB were explored with the analysis of diazinon and permethrin in coriander. PFM GC x GC-MS with SMB is characterized by enhanced molecular ion and tailing-free fast ion source response time. It enables universal pesticide analysis with full scan and data analysis with reconstructed single ion monitoring on the enhanced molecular ion and another prominent high mass fragment ion. The elimination of the third fragment ion used in standard three ions method results in significantly reduced matrix interference. GC x GC-MS with SMB improves the GC separation, and thereby our ability for sample identification using libraries. GC-MS-MS with SMB provides better reduction (elimination) of matrix interference than GC x GC-MS. However, it is a target method, which is not always applicable. GC x GC-MS-MS does not seem to further reduce matrix interferences over GC-MS-MS and unlike GC x GC-MS, it is incompatible with library identification, but it is beneficial to have both GC x GC and MS-MS capabilities in the same system.     

An experimental and indo molecular orbital study of variable response of the p-phenyl substituent to electron demand. Relative conformations of two p-arylacetophenones as neutral molecules and +1 molecular ions

The INDO molecular orbital method suggests that the rings of p-phenylacetophenone and 2-fluoro-4′-acetylbiphenyl are more nearly coplanar in the +1 molecular ion than in the neutral molecule. This is indicated by old experimental data for the former and new data for the latter, based on the cleavage to [CH₃CO]⁺.     

Distorted five-fold coordination of Cu2+(aq) from a Car-Parrinello molecular dynamics simulation

The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car-Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 A and one axial water molecule at 2.45 A from the Cu2+ ion is found. A "hole" without water molecules is found on the opposite side of the axial water. The ion-water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm-1 below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.     

Quantum molecular dynamics

Electron or ion dynamics are treated using spin‐dependent quantum trajectories. These trajectories are inferred from the Dirac current, which contributes Schroedinger's current and additional spin‐dependent terms, all of which are of order c⁰ in the nonrelativistic regime of particle velocity, where c is the speed of light. The many‐body problem is treated precisely as in classical dynamics. Each electron or ion has its own equation of motion, which is the time‐dependent Dirac or the time‐dependent Schroedinger equation in the relativistic or nonrelativistic regime of particle velocity, respectively. As an example the theory is applied to the electronic structure of the helium atom, in which two electrons with opposite spin states are shown to correlate such that their quantum trajectories keep them on average on opposite sides of the nucleus. As the theory is time dependent, excited states are also generated. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A set of molecular models for alkali and halide ions in aqueous solution

This work presents new molecular models for alkali and halide ions in aqueous solution. The force fields were parameterized with respect to the reduced liquid solution density at 293.15 K and 1 bar, considering all possible ion combinations simultaneously. The experimental target data are reproduced with a high accuracy over a wide range of salinity. The ion models predict structural properties of electrolyte solutions well, such as pair correlation functions and hydration numbers. The force fields provide good predictions of the properties studied here in combination with different models for water.     

Pt-tetraethynylethene molecular scaffolding: synthesis and characterization of a novel class of organometallic molecular rods

The series of monodisperse Pt-bridged TEE oligomers 3a-f was prepared by oxidative Glaser-Hay oligomerization of monomer 7 under end-capping conditions. These novel molecular rods extend in length from 3.3 nm (monomeric 3a) to 12.1 nm (hexameric 3 f). Their isolation was achieved by high performance gel permeation chromatography (GPC), and their purification was best monitored by analytical GPC in combination with matrix-assisted laser-desorption-ionization mass spectrometry (MALDI-TOF MS). The mass spectra of each oligomer revealed the molecular ion or its sodium complex as parent ion together with a clean, highly characteristic fragmentation pattern. Delayed addition of the end-capping reagent PhC(triple bond)CH to the oligomerization mixture afforded polymer 10 with an average of approximately 32 repeat units and a remarkably narrow molecular weight distribution (Mw/Mn=1.06), which is indicative of a living polymerization process. UV/Vis spectral data as well as measurements of the second hyperpolarizability gamma by third harmonic generation (THG) revealed a nearly complete lack of pi-electron delocalization along the oligomeric backbone. The Pt atoms act as true insulating centers, and the Pt-C(sp) bonds hardly possess any pi character. The synthesis of the molecular rods 3a-f provides another demonstration of the power of oxidative acetylenic homocouplings for the preparation of unusual nanoarchitecture.     

Fourier transform laser microprobe mass spectrometry for the molecular identification of inorganic compounds

This study attempted to determine the molecular composition of inorganic analytes at the surface of solids by Fourier transform laser microprobe mass spectrometry (FT LMMS) with an external ion source. A database was established from the analysis of pure compounds. FT LMMS uses a similar ionization as the older LMMS instruments with time-of-flight (TOF) mass analyzer. However, apart from the mass resolution, the mass spectral patterns can be significantly different in FT LMMS compared to TOF LMMS. FT LMMS yields detailed information on the analyte by means of structural fragments, enabling us to specify the main building blocks, as well as adduct ions, consisting of the analyte molecule and a stable ion. Hence, deductive reasoning allows tentative characterization of the analogs without reference spectra, except for compounds with the same elements in different stoichiometries. In that case comparative data are needed.     

Three-dimensional depth profiling of molecular structures

Molecular time of flight secondary ion mass spectrometry (ToF-SIMS) imaging and cluster ion beam erosion are combined to perform a three-dimensional chemical analysis of molecular films. The resulting dataset allows a number of artifacts inherent in sputter depth profiling to be assessed. These artifacts arise from lateral inhomogeneities of either the erosion rate or the sample itself. Using a test structure based on a trehalose film deposited on Si, we demonstrate that the “local” depth resolution may approach values which are close to the physical limit introduced by the information depth of the (static) ToF-SIMS method itself.