2009. "The Infrared Spectra of Bacillus Bacteria Part II: Sporulated Bacillus-the Effect of Vegetative Cells and Contributions of Calcium Dipicolinate Trihydrate, CaDP•3H2O ." Applied Spectroscopy 63(8):908-915. Abstract Our previous paper showed that certain IR peaks, e.g. the peak at 1739 cm-1, are due to varying (trace) amounts of vegetative cells amongst the Bacillus spores and that these and other vegetative bands are associated with lipid-soluble compounds, likely phosphatidyl glycerol or phosphatidyl ethanolamine. This work investigates the infrared spectra of eight different sporulated Bacillus bacteria. For the endospores it is observed that peaks at 1441, 1277, 1015 cm-1 along with a distinct quartet of peaks at 766, 725, 701, and 659 cm-1 are clearly associated with calcium dipicolinate trihydrate, CaDP•3H2O. It is emphasized that the spore peaks, especially the quartet, arise from the calcium dipicolinate trihydrate and not from dipicolinic acid or other dipicolinate hydrate salts. The CaDP•3H2O vibrational peaks and the effects of hydration are studied using quantum chemistry in the PQS software package. The quartet is associated with many modes including contributions from the Ca2+ counterion and hydration waters including Ca-O-H bends, H2O-Ca-O torsions and O-C-O bends. The 1441 and 1015 cm-1 modes are planar pyridine modes with the 1441 mode primarily a ring C-N stretch and the 1015 mode primarily a ring C-C stretch.
2009. "The Infrared Spectra of Bacillus Bacteria Part I: Vegetative Bacillus versus Sporulated Cells and the Contributions of Phospholipids to Vegetative Infrared Spectra ." Applied Spectroscopy 63(8):899-907. Abstract This paper highlights the distinctions between the IR absorption spectra of vegetative versus sporulated Bacillus bacteria. It is observed that there are signatures clearly associated with either the sporulated or the vegetative state, and that vegetative cell (debris) can contribute to the spore spectra. A distinct feature at ~1739 cm-1 appears to be unique to vegetative cell spectra, and can also be used as an indicator of vegetative cells or cell debris in the spore spectra. The data indicate the band is caused by a phospholipid carbonyl bond and are consistent with, but do not prove, it to be either phosphatidyl ethanolamine (PE) or phosphatidyl glycerol (PG), the two major classes of phospholipids found in vegetative cells of Bacillus species. A companion paper discusses features associated with the sporulated state.
2009. "Absolute integrated intensities of vapor-phase hydrogen peroxide (H202) in the mid-infrared at atmospheric pressure." Analytical and Bioanalytical Chemistry 395(2):377-386. doi:doi:10.1007/s00216-009-2805-x Abstract We report quantitative broadband infrared spectra of vapor-phase hydrogen peroxide (H2O2) with all spectra pressure broadened to atmospheric pressure. The spectra were generated by flowing a concentrated solution (83 weight%) of H2O2 into a gently heated disseminator and diluting with a flow of pure nitrogen carrier gas. The water vapor lines were subtracted from the resulting spectra to yield the spectrum of pure H2O2. Comparison with previous results for the ν6 band strength (including hot bands) compares favorably with the results of Klee et al. [(1999) J. Mol. Spectr. 195, 154] as well as HITRAN. The present results are 433 and 467 cm-2 atm-1 (±8% and ±3% at 298 and 323 K, respectively) for the band strength, matching well the Klee value (S = 467 cm-2 atm-1 at 296 K) for the integrated band. Other bands in the 520-7500 cm-1 interval and their potential for atmospheric monitoring are discussed.
2009. "Passive Standoff Detection of RDX Residues on Metal Surfaces via Infrared Hyperspectral Imaging." Analytical and Bioanalytical Chemistry 395(2):337-348. doi:10.1007/s00216-009 Abstract Hyperspectral images of galvanized steel plates, each containing a stain of RDX, were recorded using a commercial longwave infrared imaging spectrometer. Demonstrations of passive RDX chemical detection at areal dosages between 16 and 90 µg / cm2 were carried out over practical stand-off ranges between 14 and 50 m. Efforts to develop better chemical anomaly and target detection through chemometric analyses are described.
2008. "INFRARED SPECTRAL SIGNATURES: CREATION OF REFERENCE DATA FOR VAPORS AND LIQUIDS." International Journal of High Speed Electronics and Systems 18(2):231-250. doi:10.1142/S012915640800531X Abstract Two primary goals of infrared spectroscopic dection are chemical identification and quantification. In order to accomplish these goals, a comprehensive and quantitative spectral library suitable for digital manipulation is required. To a large degree, the contents of such a library depend on the application. Since the primary application of the PNNL/DOE spectral library is for environmental monitoring, we have focused our efforts on hazardous pollutants, as well as a large variety of natural and anthropogenic chemicals. As a spin-off project and in collaboration with Dugway Proving Ground, we also had the opportunity to analyze a limited set of chemical warfare agents (CWAs).
2007. "Relative Raman Intensities in C6H6, C6D6, and C6F6: A Comparison of Different Computational Methods." Theoretical Chemistry Accounts 117(2):283-290. doi:10.1007/s00214-006-1350-z Abstract In order to determine which models can best emulate Raman spectra, the accuracy of various computational methods (Hartee-Fock, MP2, CCSD, CAS-SCF, and several types of DFT) for predicting relative intensities in the Raman spectra of C6H6, C6D6, and C6F6 were compared. In particular, the predicted relative intensities for v1 and v2 were compared with relative intensities measured by an FT-Raman spectrometer. While none of these methods excelled at this prediction, Hartee-Fock with a large basis set was most successful for C6H6, and C6D6, while PW91PW91 with the aug-cc-pVTZ basis set was most successful for C6F6.
2007. "Rapid Bacterial Identification Using Fourier Transform Infrared Spectroscopy." SPIE Newsroom. doi:10.1117/2.1200701.0559 Abstract Recent studies at Pacific Northwest National Laboratory (PNNL) using infrared spectroscopy combined with statistical analysis have shown the ability to identify and discriminate vegetative bacteria, bacterial spores and background interferents from one another. Since the anthrax releases in 2001, rapid identification of unknown powders has become a necessity. Bacterial endospores are formed by some Bacillus species as a result of the vegetative bacteria undergoing environmental stress, e.g. a lack of nutrients. Endospores are formed as a survival mechanism and are extremely resistant to heat, cold, sunlight and some chemicals. They become airborne easily and are thus readily dispersed which was demonstrated in the Hart building. Fourier Transform Infrared (FTIR) spectroscopy is one of several rapid analytical methods used for bacterial endospore identification. The most common means of bacterial identification is culturing, but this is a time-consuming process, taking hours to days. It is difficult to rapidly identify potentially harmful bacterial agents in a highly reproducible way. Various analytical methods, including FTIR, Raman, photoacoustic FTIR and Matrix Assisted Laser Desorption/Ionization (MALDI) have been used to identify vegetative bacteria and bacterial endospores. Each has shown certain areas of promise, but each has shortcomings in terms of sensitivity, measurement time or portability. IR spectroscopy has been successfully used to distinguish between the sporulated and vegetative state. [1,2] It has also shown its utility at distinguishing between the spores of different species. [2-4] There are several Bacillus species that occur commonly in nature, so it is important to be able to distinguish between the many different species versus those that present an imminent health threat. The spectra of the different sporulated species are all quite similar, though there are some subtle yet reproducible spectroscopic differences. Thus, a more robust and reliable method is needed for differentiation. Using chemometrics, a classification scheme was developed and performed on samples sporulated in glucose broth. PNNL has demonstrated that vegetative bacteria and endospores have unique infrared (IR) signatures that can be used to identify to the species-, and in some cases, even to the strain-level. We have shown that the IR spectra of spores of different species tend to be quite similar, yet the small but reproducible differences in the spectra allow for a certain degree of differentiation. Further studies have shown that the culture medium can also have an effect on the spectra. For the distinction between vegetative and endospores, we have consistently observed a series of four peaks at 766, 725, 702, and a fairly sharp peak (FWHM 7 cm-1) at 660 cm-1, present only in the endospore spectra.
2006. "The Quantitative Infrared and NIR Spectrum of CH2I2 Vapor: Vibrational Assignments and Potential for Atmospheric Monitoring." Atmospheric Chemistry and Physics 6(9):2581-2591. Abstract Diiodomethane (CH2I2) photolysis in the presence of ozone is a suggested precursor to new particle aerosol formation, particularly in coastal areas. As part of the PNNL database of gas-phase infrared spectra, the quantitative absorption spectrum of CH2I2 has been acquired at 0.1 cm-1 resolution. Two strong b2 symmetry A-type bands at 584 and 1114 cm-1 are observed, but are not resolved at 760 Torr and appear as B-type. In contrast, the b1 symmetry C-type bands near 5953, 4426 and 3073 cm-1 are resolved with rotational structure, including Q-branches with widths ≤ 1 cm-1. The quantitative infrared and near-infrared vapor-phase spectra (600 - 10,000 cm-1) are reported for the first time and discussed in terms of ambient monitoring. FT-Raman spectra and ab initio calculations are used to complete vibrational assignments.
2006. "A Disseminator for Rapid, Selectable and Quantitative Delivery of Low-and Semi-Volatile Liquid Species to the Vapor Phase." Review of Scientific Instruments 77(09):094103. doi:10.1063/1.2349298 Abstract Nelson and co-workers introduced a quantitative method for disseminating liquid samples to the vapor phase using a lead screw to depress the plunger of a syringe whose tip was mounted into the flow of a carrier gas. In order to measure quantitative vapor-phase infrared spectra, we have modified a commercial device to improve the accuracy and precision for quantitative vapor delivery. Design changes have focused on disseminating reactive or low-volatility liquids by heating only the syringe tip and dispensed liquid. Performance features include quantitative vapor-phase generation with >3 orders of magnitude concentration range, including for low volatility species, with most equilibration times <40 s. The method has been vetted by comparing the gas-phase IR data versus IR spectra taken using both gravimetric (NIST) and vapor (PNNL) generation techniques. Quantitative vapor spectra of low volatility samples are reported.
2005. "18O Effects on the Infrared Spectrum and Skeletal Tunneling of Tropolone." Journal of Chemical Physics 122:224311. Abstract Infrared absorption profiles observed for vibrational transitions of gaseous tropolone often show sharp Q branch peaks, some of them ultra-narrow spikes, indicative of the band origins for vibrational state-specific spectral tunneling doublets. In this work oxygen isotope effects for two CH wagging fundamentals, the COH torsion fundamental, and the skeletal contortion fundamental are reported. They allow considerations to be given: (1) oxygen isotope effects on the vibrational frequencies and state-specific tunneling splittings; (2) the asymmetry offset of the potential energy minima for 16O, 18O-tropolone; and (3) additional details concerning previously proposed high J rotation-contortion fundamental. The new results help to characterize the skeletal contortion fundamental and support the jo9nt participation of skeletal tunneling with H tunneling in the vibrational state-specific tautomerization processes of tropolone in its ground electronic state.
2005. "Mid-Infrared Versus Far-Infrared (THz) Relative Intensities of Room-temperature Bacillus Spores." Chemical Physics Letters 403(1-3):152-157. Abstract We have simultaneously recorded the mid-IR and far-IR (sometimes called terahertz, THz) spectra of the sporulated form of five common Bacillus bacteria: Bacillus subtilis ATCC 49760, Bacillus subtilis ATCC 6051, B. thuringiensis subsp. kurstaki ATCC 35866, Bacillus globigii 01, and B. atrophaeus 49337. The 295 K spectra were recorded from ~8 to 6,000 cm-1 of samples deposited onto windows transparent in both the mid- and far-infrared. The results indicate that any room-temperature THz absorption features due to the bacterial spores are at least 28 times weaker (based on p-p noise) than the corresponding mid-IR amide I band.
2004. "Gas-Phase Database for Quantitative Infrared Spectroscopy." Applied Spectroscopy 58(12):1452-1461. Abstract The National Institute of Standards and Technology (NIST) and the Pacific Northwest National Laboratory (PNNL) are each creating quantitative databases containing the vapor-phase infrared spectra of pure chemicals. The digital databases have been created with both laboratory and remote-sensing applications in mind. A spectral resolution of ≈0.1 cm-1 was selected to avoid degrading sharp spectral features, while also realizing that atmospheric broadening typically limits line widths to 0.1 cm-1. Calculated positional (wave number, cm-1) uncertainty is ≤0.005 cm-1, while the 1σ statistical uncertainty in absorbance values is <2% for most compounds. The latter was achieved by measuring multiple (typically ≥9) path length-concentration burdens and fitting a weighted Beer’s law plot to each wave number channel. The two databases include different classes of compounds and were compared using 12 samples. Though these 12 samples span a range of polarities, absorption strengths, and vapor pressures, the data agree to within experimental uncertainties with only one exception.
2004. "Semiactive Infrared Remote Sensing: A Practical Prototype and Field Comparison ." Applied Optics 43(3):638-650. Abstract A semiactive method of Fourier-transform (FTIR) remote sensing has been developed and field tested. The method replaces the sender telescope of an active technique with an extended, heated broadband source. The output of the extended source (a commercial griddle) is not collimated and thus facilitates alignment by having the detector optics simply point at the griddle. The present source fills the detector's field of view at 100 m and maintains a temperature ~80 K warmer than ambient. In field tests with live CO releases, the method was ~30 times less sensitive than active methods, but ~30 times more sensitive than passive methods, with far greater sensitivity in the midwave infrared.
2004. "Identification of Sporulated and Vegetative Bacteria using Statistical Analysis of Fourier Transform Mid-Infrared Transmission Data ." Applied Spectroscopy 58(2):203-211. Abstract A combined mid-infrared spectroscopic/statistical modeling approach for the discrimination and identification, at the strain level, of both sporulated and vegetative bacterial samples is presented. Transmission mode spectra of bacteria dried on ZnSe windows were collected using a Fourier-transform mid-infrared (FTIR) spectrometer. Five Bacillus bacterial strains (B. atrophaeus 49337, B. globigii, B. thuringiensis ssp. kurstaki, B. subtilis 49780, and B. subtilis 6051) were used to construct a reference spectral library and to parameterize a four-step statistical model for the systematic identification of bacteria. The statistical methods used included principal-component analysis (PCA), classification and regression trees (CART), and Mahalanobis-distance calculations. Internal cross-validation studies successfully classified 100% of the samples into their correct physiological state (sporulated or vegetative) and identified 67% of the samples correctly as to their bacterial strain. Analysis of thirteen blind samples, which included reference and other bacteria, nonbiological materials, and mixtures of both nonbiological and bacterial samples, yielded comparable accuracy. The chief advantage of this approach is the accurate identification of unknown bacteria, including spores, in a matter of minutes.
2003. "Identification of Bacterial Spores using Statistical Analysis of Fourier Transform Infrared Photoacoustic Spectroscopy Data ." Applied Spectroscopy 57(8):893-899. Abstract Fourier Transform Infrared Photoacoustic Spectroscopy (FTIR-PAS) has been applied for the first time to the identification and speciation of bacterial spores. With minimal preparation the spores were deposited into the photoacoustic sample cup and their spectra recorded. A total of 40 different samples of 5 different strains of Bacillus spores were analyzed: Bacillus subtilis ATCC 49760, Bacillus atrophaeus ATCC 49337, Bacillus subtilis 6051, Bacillus thuringiensis ssp. kurstaki, and Bacillus globigii Dugway. The statistical methods used included principal-component analysis (PCA), classification and regression trees (CART), and Mahalanobis-distance calculations. Internal cross-validation studies successfully classify the spores according to their bacterial strain in 38 of 40 cases (95%) and 36 of 40 (90%) in cross-validation. Analysis of fifteen blind samples, which included library and other spores, and nonbacterial materials, resulted in correct strain classification the blind samples that were members of the library and correct rejection of the nonbacterial samples.
2003. "Gas-Phase Hydrolysis of SOCL₂ at 297 and 309 K: Implications for Its Atmospheric Fate ." Journal of Physical Chemistry A 107(32):6183-6190. Abstract The gas-phase hydrolysis of thionyl chloride (SOCl₂) has been investigated at 297 K and 309 K in a mixing chamber using FTIR spectroscopy. Reagent concentrations of ~80 ppmv SOCl2 at 1, 18, 45 and 63% relative humidity (RH) were studied at 309 K, while humidities of ~3, 6, 10, 12, 18, 34, 48, 68 and 85% were used in the 297 K studies, all at a total pressure of ~1 atm in synthetic air. In each experiment, an aliquot of SOCl₂(g) was rapidly introduced into a chamber at fixed RH, quickly reaching a maximum and then decreasing exponentially as monitored by time-resolved infrared spectroscopy. The only observed reaction products were HCl(g) and SO₂(g) which were formed in a molar ratio of ~2:1. The exponential SOCl₂ decay curves directly showed the reaction to be first order in SOCl₂, and together with the RH-dependent data reveal the reaction to be first order in H₂O as well. The 297 K and 309 K hydrolysis rate constants were measured as 5.0 ? 1.3 x 10-21 and 4.3 ? 1.5 x 10-21 cm3/molecule-sec, respectively. Confirming previous results, SOCl₂ absorbed only at lambda < 290 nm, which suggests hydrolysis as the main loss mechanism in the troposphere at ambient temperatures and humidities.
2002. "Removing Aperture-Induced Artifacts from Fourier Transform Infrared Intensity Values." Applied Optics 41(15):2831-2839. Abstract Two FTIR intensity artifacts have been observed at moderately high (0.1 cm-1) spectral resolution, 1) light reflected off the aperture back was double modulated by the interferometer productin a 2f alias and 2) the warm (~310 K) annulus of the aperture seen by a cooled detector resulted in both distorted line shapes and anomalous intensities in the fingerprint region. Although the second artifact has been alluded to before, we report corrections to remove both anomalies and demonstrate the efficacy of these corrections. Prior to correction, integrated band intensities were found to be in error by up to 12%. Presumably all medium resolution (<0.5cm-1) optical-flat mid-IR spectrometers suffer from these artifacts.
2001. "Atmospheric Measurements of HONO by Tunable Diode Laser Absorption Spectroscopy." Journal of Atmospheric Chemistry 40(3):275-293. Abstract Ambient gas phase nitrous acid (HONO) has been measured by Tunable Diode Laser Spectroscopy with sub-ppbv detection limits. An R-branch line in the 1263.4 cm-1 v(sub 3) band was found to be free of interference and suitable for ambient HONO measurements. Nitrous Acid was measured during the night and early morning at an urban site in Toronto, Canada, during the summer of 1998. During the night of June 19, 1998, the concentration of HONO increased by as much as 0.5 ppbv/hr. The usual decrease in HONO after sunrise was delayed by a few hours, possibly due to a combination of an increase in the production rate of HONO with rush hour, and attenuation of the early morning light by hgh NO2 within the aerosol fog/haze.