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The Oak Ridge National Laboratory (ORNL) Laboratory Directed Research and Development (LDRD) Program reports its status to the U.S. Department of Energy (DOE) in March of each year. The program operates under the authority of DOE Order 413.2B, “Laboratory Directed Research and Development” (April 19, 2006), which establishes DOE’s requirements for the program while providing the Laboratory Director broad flexibility for program implementation. LDRD funds are obtained through a charge to all Laboratory programs. This report includes summaries all ORNL LDRD research activities supported during FY 2008. The associated FY 2008 ORNL LDRD Self-Assessment (ORNL/PPA-2008/2) provides financial data and an internal evaluation of the program’s management process.

An experimental capability is being developed at the Oak Ridge National Laboratory Multi-Charged Ion Research Facility (ORNL MIRF) to enable stored cooling and state characterization of molecular ions of essentially any mass. Ions selected from a variety of available sources are injected from the side into a 1.5 meter long electrostatic mirror trap, where excited internal states are cooled by radiative cooling. An electron beam target located near the middle of the ion-trap region, coupled with neutral fragment imaging detector systems at each end of the trap, permits state-specific studies of electron-molecular ion dissociation.

The operational characteristics and imaging performance are described for a new instrument comprising an atomic force microscope coupled with a pulsed laser and a linear ion trap mass spectrometer. The operating mode of the atomic force microscope is used to produce topographic surface images having sub-micrometer spatial and height resolution. Spatially resolved mass spectra of ions, produced from the same surface via microprobe-mode laser desorption/ionization at atmospheric pressure, are also used to create a 100 x 100 microm chemical image. The effective spatial resolution of the image (approximately 2 microm) was constrained by the limit of detection (estimated to be 10(9)-10(10) molecules) rather than by the diameter of the focused laser spot or the step size of the sample stage. The instrument has the potential to be particularly useful for surface analysis scenarios in which chemical analysis of targeted topographic features is desired; consequently, it should have extensive application in a number of scientific areas. Because the number density of desorbed neutral species in laser desorption/ionization is known to be orders-of-magnitude greater than that of ions, it is expected that improvements in imaging performance can be realized by implementation of post-ionization methods.

We report on the development of a versatile scanning apparatus for nanoscale surface sampling that utilizes the interaction of laser radiation at a sharp probe tip to effect desorption/ablation on opaque substrates. The process, which currently yields surface craters as small as approximately 50 nm diameterx5 nm deep, has been demonstrated with both metal-coated and bare silicon tips. Desorption/ablation under the tip occurs at illumination intensities below the corresponding optical far-field threshold, suggesting that the latter process should not degrade the spatial resolution attainable for proposed chemical imaging methods based on the scanning surface probe.

A theoretical calculation is reported of the time and space dependence of the reaction rate coefficient in a stretched quadrupole ion trap. The system consists of Ag+ ions moving in trace amounts through a dilute gas consisting primarily of He or Ar buffer gas, but with a small amount of a reactive neutral, D2. These systems were chosen because there are available now accurate potential energy curves for Ag+ ions interacting with He and Ar gas and because the cross section for Ag+ reaction with D2 is known over a wide range of collision energy.

Recent moment theories of ion motion in traps and similar devices are extended to mixtures of neutral gases in which one or more components can undergo infrequent reaction with the ion of interest. Expressions are developed for the position and time dependence of the ion-neutral reaction rate coefficient in such circumstances. These expressions are incorporated into the sets of coupled differential equations that govern the average ion velocity and kinetic and internal energies. This provides a consistent description of the ion transport and reaction coefficients.

The two-temperature moment theory of ion motion in devices where the external fields vary with position and time is applied to ideal quadrupole ion traps. In first approximation, the theory gives differential equations with collision frequencies that vary with the effective temperature characterizing the relative kinetic energy of the ion–neutral collisions. Solutions of the set of coupled differential equations provide the ion number density, average velocities, average energy and average temperature as functions of time and of position in the apparatus. That information also enables the effective temperature for the ion ensemble and the position-dependent energy density to be determined as a function of time. Solutions of the coupled equations are discussed for the Maxwell model, rigid spheres and general ion–neutral interactions.

Fundamental aspects are presented of a two-temperature moment theory for quadrupole ion traps developed via transformation of the Boltzmann equation. Solutions of the moment equations correspond to changes in the ensemble average for any function of ion velocity, because the Boltzmann equation reflects changes to an ion distribution as a whole. The function of primary interest in this paper is the ion effective temperature and its behavior during ion storage and resonance excitation. Calculations suggest that increases in ion effective temperature during resonance excitation are due primarily to power absorption from the main RF trapping field rather than from the dipolar excitation signal. The dipolar excitation signal apparently serves mainly to move ions into regions of the ion trap where the RF electric field, and thus ion RF heating, is greater than near the trap center. Both ideal and non-ideal ion trap configurations are accounted for in the moment equations by incorporating parameterized variables ã and \(\tilde q\), which are modified versions of the commonly used forms for the DC and AC ring voltages, and \(\tilde b\) and \(\tilde d\), which are new forms that account for the voltages applied to the endcaps. Besides extending the applicability of the moment equations to non-ideal quadrupole ion traps, the modified versions of the parameterized variables can have additional utility. Calculation of the spatial dependence of ion secular oscillation frequencies is demonstrated as an example.

There is currently a great need for rapid detection and positive identification of biological threat agents, as well as microbial species in general, directly from complex environmental samples. This need is most urgent in the area of homeland security, but also extends into medical, environmental, and agricultural sciences. Mass-spectrometry-based analysis is one of the leading technologies in the field with a diversity of different methodologies for biothreat detection. Over the past few years, "shotgun"proteomics has become one method of choice for the rapid analysis of complex protein mixtures by mass spectrometry. Recently, it was demonstrated that this methodology is capable of distinguishing a target species against a large database of background species from a single-component sample or dual-component mixtures with relatively the same concentration. Here, we examine the potential of shotgun proteomics to analyze a target species in a background of four contaminant species. We tested the capability of a common commercial mass-spectrometry-based shotgun proteomics platform for the detection of the target species (Escherichia coli) at four different concentrations and four different time points of analysis. We also tested the effect of database size on positive identification of the four microbes used in this study by testing a small (13-species) database and a large (261-species) database. The results clearly indicated that this technology could easily identify the target species at 20% in the background mixture at a 60, 120, 180, or 240 min analysis time with the small database. The results also indicated that the target species could easily be identified at 20% or 6% but could not be identified at 0.6% or 0.06% in either a 240 min analysis or a 30 h analysis with the small database. The effects of the large database were severe on the target species where detection above the background at any concentration used in this study was impossible, though the three other microbes used in this study were clearly identified above the background when analyzed with the large database. This study points to the potential application of this technology for biological threat agent detection but highlights many areas of needed research before the technology will be useful in real world samples.

This paper extends the momentum-transfer theory of drift tubes to ion traps and similar devices where the electric fields vary with both position and time. The collision frequencies that are incorporated into two-temperature and multi-temperature moment theories are given precise microscopic definitions instead of being treated as adjustable parameters.

A kinetic theory based on the Boltzmann equation is developed for the trapping of atomic ions in a radio-frequency quadrupole ion trap containing enough neutral atoms that ion-neutral collisions cannot be ignored. The collisions are treated at the same level of sophistication and detail as is used to deal with the time- and space-dependent electric fields in the trap. As a result, microscopic definitions are obtained for the damping and stochastic forces that originate from such collisions. These definitions contrast with corresponding phenomenological terms added ad hoc in previous treatments to create damped Mathieu and Langevin equations, respectively. Furthermore, the theory indicates that either collisional cooling or heating of the ions is possible, depending upon details of the ion-neutral mass ratios and interaction potential. The kinetic theory is not dependent on any special assumptions about the electric field strengths, the ion-neutral interaction potentials, or the ion-neutral mass ratio. It also provides an ab initio way to describe the ion kinetic energies, temperatures, and other properties by a series of successive approximations.

A kinetic model is developed for the dynamic events occurring within an atmospheric sampling glow discharge that affect its performance as an ion source for analytical mass spectrometry. The differential equations incorporate secondary electron generation and thermalization, reagent and analyte ion formation via electron capture and ion-molecule reactions, ion loss via recombination processes, diffusion, and ion-molecule reactions with matrix components, and the sampling and pumping parameters of the source. Because the ion source has a flow-through configuration, the number densities of selected species can be estimated by applying the steady-state assumption. However, understanding of its operation is aided by knowledge of the dynamic behavior, so numerical methods are applied to examine the time dependence of those species as well. As in other plasma ionization sources, the ionization efficiency is essentially determined by the ratio of the relevant ion formation and recombination rates. Although thermal electron and positive reagent ion number densities are comparable, the electron capture/ion-molecule reaction rate coefficient ratio is normally quite large and the ion-electron recombination rate coefficient is about an order of magnitude greater than that for ion-ion recombination. Consequently, the efficiency for negative analyte ion formation via electron capture is generally superior to that for positive analyte ion generation via ion-molecule reaction. However, the efficiency for positive analyte ion formation should be equal to or better than that for negative analyte ions when both ionization processes occur via ion-molecule reaction processes (with comparable rate coefficients), since the negative reagent ion density is considerably less than that for positive reagent ions. Furthermore, the particularly high number densities of thermal electrons and reagent ions leads to a large dynamic range of linear response for the source. Simulation results also suggest that analyte ion number densities might be enhanced by modification of the standard physical and operating parameters of the source.

Reaction pathways and rate constants of gas-phase uranium and uranium oxide ions with O-2 and H2O have been investigated using a quadrupole ion trap mass spectrometer (QIT-MS). A new reaction pathway is identified for the reaction between U2+ and H2O, which leads to the formation of UO+ via the intermediate UOH2+. Reaction rate constants are determined for several reactions by measuring the reaction rate at different partial pressures of the reagent gas and are found to be in reasonable agreement with the literature. These rate constants include the first known measurement for the reaction of U2+ with H2O (similar to0.4 k(ADO)). New limits on thermochemical values are also provided for certain species. These include DeltaH(f) (UO2+) less than or equal to 1742 kJ mol(-1) and 1614 less than or equal to DeltaHf (UOH2+) less than or equal to 1.818 kJ mol(-1) and are based on the assumption that only exothermic or thermoneutral reactions are possible under the conditions used. This assumption is supported by simulations of the root-mean-square (RMS) ion kinetic energy of stored uranium ions in the QIT. Only a slight increase in the RMS ion kinetic energies, from 0.1 to 0.2 eV, is predicted over the range of trapping conditions studied (0.05 less than or equal to q(z) less than or equal to 0.75) corresponding to a theoretical reaction temperature of similar to384 K. The simulations also compare helium and neon as bath gases and show that the RMS kinetic energies are found to be very similar at long trapping times (>20 ms), although neon establishes steady state conditions in approximately half the time.

Collision-induced dissociation (CID) rates are measured for a suite of lanthanide (plus yttrium) monoxide ions stored in a quadrupole ion trap. Yttrium, neodymium, and gadolinium oxides, having the same nominal dissociation energy (D0 ≈ 735kJmol−1) but different masses, provide an empirical correction of −1.2s−1amu−1 for the measured CID rates. The CID rate correction enables the correlation of bond dissociation energy with CID rate, allowing quantitative determinations of bond dissociation energies for lanthanide metal monoxide ions. For bond dissociation energies in the range of 567–849kJmol−1, mass corrected rates range from 50 to 120s−1. The calibration sensitivity is equivalent to 5kJmol−1s−1, and the measurement precision is ∼25kJmol−1. Bond energy determinations are found to agree with the average values reported for lanthanide oxide ions.

Dissociation of the tantalum oxide cation, a strongly bound diatomic, is simulated for the multiple-collision environment of a quadrupole ion trap mass spectrometer using a model based on thermal unimolecular reaction theory. The intact diatomic ion is assigned a specific internal temperature at which it undergoes collisional activation and deactivation during a random walk in energy space. Collisional energy transfer is assumed to proceed via independent vibrational and rotational processes, as described by the refined impulse approximation and exponential transition probability, with dissociation occurring when the vibrational energy exceeds the rotational-energy-dependent barrier for dissociation. Processing the data from many such random walks yields the simulated dissociation kinetics and time-dependent internal energy distribution of an ion population at the specified internal temperature. Comparison of experimental dissociation rates with those obtained via simulations performed over a series of temperatures enables prediction of internal temperatures and corresponding internal energy distributions for tantalum oxide ion populations undergoing resonance excitation. Although the simulations indicate that rotational-energy transfer can lead to significantly higher dissociation rates than those associated with purely vibrational-energy transfer, the results obtained in this study suggest that ion internal temperatures in the tens of thousands of degrees are required nonetheless to dissociate a strongly bound diatomic ion such as tantalum oxide, and the experimental data demonstrate that resonance excitation in a quadrupole ion trap can achieve the necessary temperatures.