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Vacuum-ultraviolet (VUV) photoionization of small methanol and methanol-water clusters

Description: In this work we report on thevacuum-ultraviolet (VUV) photoionization of small methanol and methanol-water clusters. Clusters of methanol with water are generated via co-expansion of the gas phase constituents in a continuous supersonic jet expansion of methanol and water seeded in Ar. The resulting clusters are investigated by single photon ionization with tunable vacuumultraviolet synchrotron radiation and mass analyzed using reflectron mass spectrometry. Protonated methanol clusters of the form (CH3OH)nH + (n=1-12) dominate the mass spectrum below the ionization energy of the methanol monomer. With an increase in water concentration, small amounts of mixed clusters of the form (CH3OH)n(H2O)H + (n=2-11) are detected. The only unprotonated species observed in this work are the methanol monomer and dimer. Appearance energies are obtained from the photoionization efficiency (PIE) curves for CH3OH +, (CH 3OH)2 +, (CH3OH)nH + (n=1-9), and (CH 3OH)n(H2O)H + (n=2-9 ) as a function of photon energy. With an increase in the water content in the molecular beam, there is an enhancement of photoionization intensity for methanol dimer and protonated methanol monomer at threshold. These results are compared and contrasted to previous experimental observations.
Date: May 12, 2008
Creator: Ahmed, Musahid; Ahmed, Musahid; Wilson, Kevin R.; Belau, Leonid & Kostko, Oleg
Partner: UNT Libraries Government Documents Department

A VUV photoionization measurement and ab-initio calculation of the ionization energy of gas phase SiO2

Description: In this work we report on the detection and vacuum-ultraviolet (VUV) photoionization of gas phase SiO2 generated in situ via laser ablation of silicon in a CO2 molecular beam. The resulting species are investigated by single photon ionization with tunable VUV synchrotron radiation and mass analyzed using reflectron mass spectrometry. Photoionization efficiency (PIE) curves are recorded for SiO and SiO2 and ionization energy estimates are revealed from such measurements. A state-to-state ionizationenergy of 12.60 (+-0.05) eV is recorded by fitting two prominent peaks in the PIE curve for the following process: 1SUM O-Si-O --> 2PRODg [O-Si-O]+. Electronic structure calculations aid in the interpretation of the photoionization process and allow for identification of the symmetric stretch of 2PRODg [O-Si-O]+ which is observed in the PIE spectrum to be 0.11 eV (890 cm-1) above the ground state of the cation and agrees with the 892 cm-1 symmetric stretch frequency calculated at the CCSD(T)/aug-cc-pVTZ level.
Date: December 5, 2008
Creator: Kostko, Oleg; Ahmed, Musahid & Metz, Ricardo B.
Partner: UNT Libraries Government Documents Department

Ionization of Water Clusters is Mediated by Exciton Energy Transfer from Argon Clusters

Description: The exciton energy deposited in an argon cluster, (Arn ,< n=20>) using VUV radiation is transferred to softly ionize doped water clusters, ((H2O)n, n=1-9) leading to the formation of non-fragmented clusters. Following the initial excitation, electronic energy is channeled to ionize the doped water cluster while evaporating the Ar shell, allowing identification of fragmented and complete water cluster ions. Examination of the photoionization efficiency curve shows that cluster evaporation from excitons located above 12.6 eV are not enough to cool the energized water cluster ion, and leads to their dissociation to (H2O)n-2H+ (protonated) clusters.
Date: January 25, 2012
Creator: Golan, Amir & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Desorption Dynamics, Internal Energies and Imaging of Organic Molecules from Surfaces with Laser Desorption and Vacuum Ultraviolet (VUV) Photoionization

Description: There is enormous interest in visualizing the chemical composition of organic material that comprises our world. A convenient method to obtain molecular information with high spatial resolution is imaging mass spectrometry. However, the internal energy deposited within molecules upon transfer to the gas phase from a surface can lead to increased fragmentation and to complications in analysis of mass spectra. Here it is shown that in laser desorption with postionization by tunable vacuum ultraviolet (VUV) radiation, the internal energy gained during laser desorption leads to minimal fragmentation of DNA bases. The internal temperature of laser-desorbed triacontane molecules approaches 670 K, whereas the internal temperature of thymine is 800 K. A synchrotron-based VUV postionization technique for determining translational temperatures reveals that biomolecules have translational temperatures in the range of 216-346 K. The observed low translational temperatures, as well as their decrease with increased desorption laser power is explained by collisional cooling. An example of imaging mass spectrometry on an organic polymer, using laser desorption VUV postionization shows 5 mu m feature details while using a 30 mu m laser spot size and 7 ns duration. Applications of laser desorption postionization to the analysis of cellulose, lignin and humic acids are briefly discussed.
Date: April 5, 2011
Creator: Kostko, Oleg; Takahashi, Lynelle K. & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Direct Determination of the Ionization Energies of PtC, PtO, and PtO2 with VUVRadiation

Description: Photoionization efficiency curves were measured for gas-phase PtC, PtO, and PtO2 using tunable vacuum ultraviolet (VUV) radiation at the Advanced Light Source. The molecules were prepared by laser ablation of a platinum tube, followed by reaction with CH4 or N2O and supersonic expansion. These measurements providethe first directly measured ionization energy for PtC, IE(PtC) = 9.45 +- 0.05 eV. The direct measurement also gives greatly improved ionization energies for the platinum oxides, IE(PtO) = 10.0 +- 0.1 eV and IE(PtO2) = 11.35 +- 0.05 eV. The ionization energy connects the dissociation energies of the neutral and cation, leading to greatly improved 0 K bond dissociation energies for the neutrals: D0(Pt-C) = 5.95 +- 0.07 eV, D0(Pt-O)= 4.30 +- 0.12 eV, and D0(OPt-O) = 4.41 +- 0.13 eV, as well as enthalpies of formation for the gas-phase molecules Delta H0 f,0(PtC(g)) = 701 +- 7 kJ/mol, Delta H0f,0(PtO(g)) = 396 +- 12 kJ/mol, and Delta H0f,0(PtO2(g)) = 218 +- 11 kJ/mol. Much of the error in previous Knudsen cell measurements of platinum oxide bond dissociation energies is due to the use of thermodynamic second law extrapolations. Third law values calculated using statistical mechanical thermodynamic functions are in much better agreement with values obtained from ionization energies and ion energetics. These experiments demonstrate that laser ablation production with direct VUV ionization measurements is a versatile tool to measure ionization energies and bond dissociation energies for catalytically interesting species such as metal oxides and carbides.
Date: July 21, 2008
Creator: Citir, Murat; Metz, Ricardo B.; Belau, Leonid & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Vacuum-Ultraviolet (VUV) Photoionization of Small Methanol and Methanol-Water Clusters

Description: In this work, we report on the vacuum-ultraviolet (VUV) photoionization of small methanol and methanol-water clusters. Clusters of methanol with water are generated via co-expansion of the gas phase constituents in a continuous supersonic jet expansion of methanol and water seeded in Ar. The resulting clusters are investigated by single photon ionization with tunable vacuum-ultraviolet synchrotron radiation and mass analyzed using reflectron mass spectrometry. Protonated methanol clusters of the form (CH3OH)nH+(n = 1-12) dominate the mass spectrum below the ionization energy of the methanol monomer. With an increase in water concentration, small amounts of mixed clusters of the form (CH3OH n(H2O)H+ (n = 2-11) are detected. The only unprotonated species observed in this work are the methanol monomer and dimer. Appearance energies are obtained from the photoionization efficiency (PIE) curves for CH3OH+, (CH3OH)2+, (CH3OH)nH+ (n = 1-9), and (CH3OH)n(H2O)H+ (n = 2-9) as a function of photon energy. With an increasein the water content in the molecular beam, there is an enhancement of photoionization intensity for the methanol dimer and protonated methanol monomer at threshold. These results are compared and contrasted to previous experimental observations.
Date: April 24, 2008
Creator: Kostko, Oleg; Belau, Leonid; Wilson, Kevin R. & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

On the Ionization Energies of C4H3 Isomers

Description: We have conducted a combined experimental and theoretical study on the formation of distinct isomers of resonantly stabilized free radicals, C4H3, which are important intermediates in the formation of polycyclic aromatic hydrocarbons in combustion flames and possibly in the interstellar medium. Our study utilized laser ablation of graphite in combination with seeding the ablated species in neat methylacetylene gas which also acted as a reagent. Photoionization efficiency (PIE) curves were recorded of the C4H3 isomers at the Advanced Light Source from 8.0 to 10.3 eV. The experimental PIE curve was compared with theoretical ones suggesting the formation of four C4H3 radicals: two acyclic structures i-C4H3 [1] and E/Z-n-C4H3 [2E/2Z]and two cyclic isomers 3 and 4. These molecules are likely formed via an initial addition of ground state carbon atoms to the carbon-carbon triple bond of the methylacetylene molecule followed by isomerization via hydrogen migrations and ring opening and emission of atomic hydrogen from these intermediates.
Date: September 16, 2009
Creator: Kaiser, Ralf I.; Mebel, Alexander; Kostko, Oleg & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

The effect of pi-stacking, h-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers

Description: A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Adiabatic and vertical ionization energies(IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions stronglyaffect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largestchanges in vertical IEs (0.4 eV) occur in asymmetric h-bonded and symmetric pi- stacked isomers, whereas in the lowest-energy symmetric h-bonded dimer the shiftin IEs is much smaller (0.1 eV). The origin of the shift and the character of the ionized states is different in asymmetric h-bonded and symmetric stacked isomers. Inthe former, the initial hole is localized on one of the fragments, and the shift is due to the electrostatic stabilization of the positive charge of the ionized fragment by thedipole moment of the neutral fragment. In the latter, the hole is delocalized, and the change in IE is proportional to the overlap of the fragments' MOs. The shifts in AAare much smaller due to a less effcient overlap and a smaller dipole moment. The ionization of the h-bonded dimers results in barrierless (or nearly barrierless) protontransfer, whereas the pi-stacked dimers relax to structures with the hole stabilized by the delocalization or electrostatic interactions.
Date: September 2, 2009
Creator: Bravaya, Ksenia B.; Kostko, Oleg; Ahmed, Musahid & Krylov, Anna I.
Partner: UNT Libraries Government Documents Department

Imaging with Mass Spectrometry: A SIMS and VUV-Photoionization Study of Ion-Sputtered Atoms and Clusters from GaAs and Au

Description: A new mass spectrometry surface imaging method is presented in which ion-sputtered neutrals are postionized by wavelength-tunable vacuum ultraviolet (VUV) light from a synchrotron source. Mass spectra and signal counts of the photoionized neutrals from GaAs (100) and Au are compared to those of the secondary ions. While clusters larger than dimers are more efficiently detected as secondary ions, certain species, such as As2, Au and Au2, are more efficiently detected through the neutral channel. Continuously tuning the photon wavelength allows photoionization efficiency (PIE) curves to be obtained for sputtered Asm (m=1,2) and Aun (n=1-4). From the observed ionization thresholds, sputtered neutral As and Au show no clear evidence of electronic excitation, while neutral clusters have photoionization onsets shifted to lower energies by ~;;0.3 eV. These shifts are attributed to unresolved vibrational and rotational excitations. High-spatial resolution chemical imaging with synchrotron VUV postionization is demonstrated at two different photon energies using a copper TEM grid embedded in indium. The resulting images are used to illustrate the use of tunable VUV light for verifying mass peak assignments by exploiting the unique wavelength-dependent PIE of each sputtered neutral species. This capability is valuable for identifying compounds when imaging chemically complex systems with mass spectrometry-based techniques.
Date: December 5, 2008
Creator: Takahashi, Lynelle; Zhou, Jia; Wilson, Kevin R.; Leone, Stephen R. & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Mass-Analyzed Threshold Ionization (MATI) Spectroscopy of Atoms and Molecules using VUV Synchrotron Radiation

Description: Mass-analyzed threshold ionization (MATI) spectroscopy using synchrotron radiation (Advanced Light Source, Lawrence Berkeley National Laboratory) has been performed for Ar, N2, O2, N2O, H2O, C2H2, and C6H6. MATI allows for a better determination of ionization energies compared to those derived from photoionization efficiency curves traditionally used in synchrotron photoionization mass spectrometry. The separation of the long-lived Rydberg state from the directly-formed prompt ion, essential for a meaningful MATI spectrum, has been accomplished by employing an arrangement of ion optics coupled to unique electric-field pulsing schemes. For Ar, a number of resolved bands below the ionization energy are observed, and these are ascribed to high-n,l Rydberg states prepared in the MATI scheme. The first vibrational stateresolved MATI spectra of N2 and O2 are reported and spectral characteristics are discussed in comparison with previously-reported threshold photoelectron spectroscopic studies. While MATI performed with synchrotron radiation is intrinsically less sensitive compared to laser based sources, this work demonstrates that MATI spectroscopy performed with widely tunable VUV radiation is a complementary technique for studying the ionization spectroscopy of polyatomic molecules.
Date: January 28, 2009
Creator: Kostko, Oleg; Kim, Sang Kyu; Leone, Stephen R. & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

Description: Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Date: March 14, 2010
Creator: Leone, Stephen R.; Ahmed, Musahid & Wilson, Kevin R.
Partner: UNT Libraries Government Documents Department

Internal Energies of Ion-Sputtered Neutral Tryptophan and Thymine Molecules Determined by Vacuum Ultraviolet Photoionization

Description: Vacuum ultraviolet photoionization coupled to secondary neutral mass spectrometry (VUV-SNMS) of deposited tryptophan and thymine films are performed at the Chemical Dynamics Beamline. The resulting mass spectra show that while the intensity of the VUV-SNMS signal is lower than the corresponding secondary ion mass spectroscopy (SIMS) signal, the mass spectra are significantly simplified in VUV-SNMS. A detailed examination of tryptophan and thymine neutral molecules sputtered by 25 keV Bi3 + indicates that the ion-sputtered parent molecules have ~;;2.5 eV of internal energy. While this internal energy shifts the appearance energy of the photofragment ions for both tryptophan and thymine, it does not change the characteristic photoionizaton efficiency (PIE) curves of thymine versus photon energy. Further analysis of the mass spectral signals indicate that approximately 80 neutral thymine molecules and 400 tryptophan molecules are sputtered per incident Bi3 + ion. The simplified mass spectra and significant characteristic ion contributions to the VUV-SNMS spectra indicate the potential power of the technique for organic molecule surface analysis.
Date: March 11, 2010
Creator: Zhou, Jia; Takahashi, Lynelle; Wilson, Kevin R.; Leone, Stephen R. & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

Description: We report a combined theoretical and experimental study of ionization of cytosine monomers and dimers. Gas-phase molecules are generated by thermal vaporization of cytosine followed by expansion of the vapor in a continuous supersonic jet seeded in Ar. The resulting species are investigated by single photon ionization with tunable vacuum-ultraviolet (VUV) synchrotron radiation and mass analyzed using reflectron mass spectrometry. Energy onsets for the measured photoionization efficiency (PIE) spectra are 8.60+-0.05 eV and 7.6+-0.1 eV for the monomer and the dimer, respectively, and provide an estimate for the adiabatic ionization energies (AIE). The first AIE and the ten lowest vertical ionization energies (VIEs) for selected isomers of cytosine dimer computed using equation-of-motion coupled-cluster (EOM-IP-CCSD) method are reported. The comparison of the computed VIEs with the derivative of the PIE spectra, suggests that multiple isomers of the cytosine dimer are present in the molecular beam. The calculations reveal that the large red shift (0.7 eV) of the first IE of the lowest-energy cytosine dimer is due to strong inter-fragment electrostatic interactions, i.e., the hole localized on one of the fragments is stabilized by the dipole moment of the other. A sharp rise in the CH+ signal at 9.20+-0.05 eV is ascribed to the formation of protonated cytosine by dissociation of the ionized dimers. The dominant role of this channel is supported by the computed energy thresholds for the CH+ appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.
Date: December 14, 2009
Creator: Kostko, Oleg; Bravaya, Ksenia; Krylov, Anna & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Spectroscopic signatures of proton transfer dynamics in the water dimer cation

Description: Using full dimensional EOM-IP-CCSD/aug-cc-pVTZ potential energy surfaces, the photoelectron spectrum, vibrational structure, and ionization dynamics of the water dimer radical cation, (H2O)+2, were computed. We also report an experimental photoelectron spectrum which is derived from photoionization efficiency measurements and compares favorably with the theoretical spectrum. The vibrational structure is also compared with the recent experimental work of Gardenier et al. [J. Phys. Chem. A 113, 4772 (2009)] and the recent theoretical calculations by Cheng et al. [J. Phys. Chem. A 113 13779 (2009)]. A reduced dimensionality nuclear Hamiltonian was used to compute the ionization dynamics for both the ground state and first excited state of the cation. The dynamics show markedly different behavior and spectroscopic signatures depending on which state of the cation is accessed by the ionization. Ionization to the ground-state cation surface induces a hydrogen transfer which is complete within 50 femtoseconds, whereas ionization to the first excited state results in a much slower process.
Date: December 21, 2009
Creator: Kamarchik, Eugene; Kostko, Oleg; Bowman, Joel M.; Ahmed, Musahid & Krylov, Anna I.
Partner: UNT Libraries Government Documents Department

Photodissociation of NO{sub 2} near 225 nm by Velocity Map Imaging

Description: In this paper we present a study of the photodissociation dynamics for NO{sub 2} in the region of 221-226 nm using velocity map imaging (VELMI) in conjunction with resonance enhanced multiphoton ionization (REMPI). We chose this region because it allowed us to use a single laser to photodissociate and probe the NO and O({sup 3}P) products using REMPI. Probing the angular and energy distributions of both fragments under state resolved conditions allows for detailed investigations of the product state distributions in the photodissociation dynamics of NO{sub 2}.
Date: October 1, 1998
Creator: Ahmed, Musahid; Peterka, D.S. & Suits, A.G.
Partner: UNT Libraries Government Documents Department

Oxygen isotope fractionation in the vacuum ultraviolet photodissociation of carbon monoxide: Wavelength, pressure and temperature dependency.

Description: Several absorption bands exist in the VUV region of Carbon monoxide (CO). Emission spectra indicate that these bands are all predissociative. An experimental investigation of CO photodissociation by vacuum ultraviolet photons (90 to 108 nm; ~13 to 11 eV) from the Advanced Light Source Synchrotron and direct measurement of the associated oxygen isotopic composition of the products are presented here. A wavelength dependency of the oxygen isotopic composition in the photodissociation product was observed. Slope values (δ'{sup 18}O/ δ'{sup 17}O) ranging from 0.76 to 1.32 were observed in oxygen three-isotope space (δ'{sup 18}O vs. δ'{sup 17}O) which correlated with increasing synchrotron photon energy, and indicate a dependency of the upper electronic state specific dissociation dynamics (e.g., perturbation and coupling associated with a particular state). An unprecedented magnitude in isotope separation was observed for photodissociation at the 105 and 107 nm synchrotron bands and are found to be associated with accidental predissociation of the vibrational states ({nu} = 0 and 1) of the upper electronic state E{sup 1}Π. For each synchrotron band, a large (few hundred per mil) extent of isotopic fractionation was observed and the range of fractionation is a combination of column density and exposure time. A significant temperature dependency in oxygen isotopic fractionation was observed, indicating a rotational level dependency in the predissociation process.
Date: January 3, 2012
Creator: Chakraborty, Subrata; Davis, Ryan; Ahmed, Musahid; Jackson, Teresa L. & Thiemens, Mark H.
Partner: UNT Libraries Government Documents Department

Discrete Dipole Approximation for Low-Energy Photoelectron Emission from NaCl Nanoparticles

Description: This work presents a model for the photoemission of electrons from sodium chloride nanoparticles 50-500 nm in size, illuminated by vacuum ultraviolet light with energy ranging from 9.4-10.9 eV. The discrete dipole approximation is used to calculate the electromagnetic field inside the particles, from which the two-dimensional angular distribution of emitted electrons is simulated. The emission is found to favor the particle?s geometrically illuminated side, and this asymmetry is compared to previous measurements performed at the Lawrence Berkeley National Laboratory. By modeling the nanoparticles as spheres, the Berkeley group is able to semi-quantitatively account for the observed asymmetry. Here however, the particles are modeled as cubes, which is closer to their actual shape, and the interaction of an emitted electron with the particle surface is also considered. The end result shows that the emission asymmetry for these low-energy electrons is more sensitive to the particle-surface interaction than to the specific particle shape, i.e., a sphere or cube.
Date: September 22, 2011
Creator: Berg, Matthew J.; Wilson, Kevin R.; Sorensen, Chris; Chakrabarti, Amit & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Experimental observation of guanine tautomers with VUV photoionization

Description: Two methods of preparing guanine in the gas phase, thermal vaporization and laser desorption, have been investigated. The guanine generated by each method is entrained in a molecular beam, single photon ionized with tunable VUV synchrotron radiation, and analyzed using reflectron mass spectrometry. The recorded photoionization efficiency (PIE) curves show a dramatic difference for experiments performed via thermal vaporization compared to laser desorption. The calculated vertical and adiabatic ionization energies for the eight lowest lying tautomers of guanine suggest the experimental observations arise from different tautomers being populated in the two different experimental methods.
Date: December 1, 2008
Creator: Zhou, Jia; Kostko, Oleg; Nicolas, Christophe; Tang, Xiaonan; Belau, Leonid; de Vries, Mattanjah S. et al.
Partner: UNT Libraries Government Documents Department

Laser Desorption Postionization Mass Spectrometry of Antibiotic-Treated Bacterial Biofilms using Tunable Vacuum Ultraviolet Radiation

Description: Laser desorption postionization mass spectrometry (LDPI-MS) with 8.0 ? 12.5 eV vacuum ultraviolet synchrotron radiation is used to single photon ionize antibiotics andextracellular neutrals that are laser desorbed both neat and from intact bacterial biofilms. Neat antibiotics are optimally detected using 10.5 eV LDPI-MS, but can be ionized using 8.0 eV radiation, in agreement with prior work using 7.87 eV LDPI-MS. Tunable vacuum ultraviolet radiation also postionizes laser desorbed neutrals of antibiotics and extracellular material from within intact bacterial biofilms. Different extracellular material is observed by LDPI-MS in response to rifampicin or trimethoprim antibiotic treatment. Once again, 10.5 eV LDPI-MS displays the optimum trade-off between improved sensitivity and minimum fragmentation. Higher energy photons at 12.5 eV produce significant parent ion signal, but fragment intensity and other low mass ions are also enhanced. No matrix is added to enhance desorption, which is performed at peak power densities insufficient to directly produce ions, thus allowing observation of true VUV postionization mass spectra of antibiotic treated biofilms.
Date: August 4, 2010
Creator: Gasper, Gerald L.; Takahashi, Lynelle K.; Zhou, Jia; Ahmed, Musahid; Moore, Jerry F. & Hanley, Luke
Partner: UNT Libraries Government Documents Department

Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

Description: We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.
Date: August 2, 2010
Creator: Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid & Krylov, Anna I.
Partner: UNT Libraries Government Documents Department

The effect of microhydration on ionization energies of thymine

Description: A combined theoretical and experimental study of the effect of microhydration on ionization energies (IEs) of thymine is presented. The experimental IEs are derived from photoionization efficiency curves recorded using tunable synchrotron VUV radiation. The onsets of the PIE curves are 8.85+-0.05, 8.60+-0.05, 8.55+-0.05, and 8.40+-0.05 eV for thymine, thymine mono-, di-, and tri-hydrates, respectively. The computed (EOM-IP-CCSD/cc-pVTZ) AIEs are 8.90, 8.51, 8.52, and 8.35 eV for thymine and the lowest isomers of thymine mono-, di-, and tri-hydrates. Due to large structural relaxation, the Franck-Condon factors for the 0<-- 0 transitions are very small shifting the apparent PIE onsets to higher energies. Microsolvation strongly affects IEs of thymine -- addition of each water molecule reduces the first vertical IE by 0.10-0.15 eV. The adiabatic IE decreases even more (up to 0.4 eV). The magnitude of the effect varies for different ionized states and for different isomers. For the ionized states that are localized on thymine the dominant contribution to the IE reduction is the electrostatic interaction between the delocalized positive charge on thymine and the dipole moment of the water molecule.
Date: January 3, 2011
Creator: Khistyev, Kirill; Bravaya, Ksenia B.; Kamarchik, Eugene; Kostko, Oleg; Ahmed, Musahid & Krylov, Anna I.
Partner: UNT Libraries Government Documents Department

Vacuum-Ultraviolet Photoionization and Mass Spectrometric Characterization of Lignin Monomers Coniferyl and Sinapyl Alcohols

Description: The fragmentation mechanisms of monolignols under various energetic processes are studied with jet-cooled thermal desorption molecular beam (TDMB) mass spectrometry (MS), 25 keV Bi3+ secondary ion MS (SIMS), synchrotron vacuum-ultraviolet secondary neutral MS (VUV-SNMS) and theoretical methods. Experimental and calculated appearance energies of fragments observed in TDMB MS indicate that the coniferyl alcohol photoionization mass spectra contain the molecular parent and several dissociative photoionization products. Similar results obtained for sinapyl alcohol are also discussed briefly. Ionization energies of 7.60 eV ? 0.05 eV for coniferyl alcohol and<7.4 eV for both sinapyl and dihydrosinapyl alcohols are determined. The positive ion SIMS spectrum of coniferyl alcohol shares few characteristic peaks (m/z = 137 and 151) with the TDMB mass spectra, shows extensive fragmentation, and does not exhibit clear molecular parent signals. VUV-SNMS spectra, on the other hand, are dominated by the parent ion and main fragments also present in the TDMB spectra. Molecular fragmentation in VUV-SNMS spectra can be reduced by increasing the extraction delay time. Some features resembling the SIMS spectra are also observed in the desorbed neutral products. The monolignol VUV-SNMS peaks shared with the TDMB mass spectra suggest that dissociative photoionization of ion-sputtered neutral molecules predominate in the VUV-SNMS mass spectra, despite the extra internal energy imparted in the initial ion impact. The potential applications of these results to imaging mass spectrometry of bio-molecules are discussed.
Date: February 9, 2011
Creator: Takahashi, Lynelle K.; Zhou, Jia; Kostko, Oleg; Golan, Amir; Leone, Stephen R. & Ahmed, Musahid
Partner: UNT Libraries Government Documents Department

Brominated Tyrosine and Polyelectrolyte Multilayer Analysis by Laser Desorption VUV Postionization and Secondary Ion Mass Spectrometry

Description: The small molecular analyte 3,5-dibromotyrosine (Br2Y) and chitosan-alginate polyelectrolyte multilayers (PEM) with and without adsorbed Br2Y were analyzed by laser desorption postionization mass spectrometry (LDPI-MS). LDPI-MS using 7.87 eV laser and tunable 8 ? 12.5 eV synchrotron vacuum ultraviolet (VUV) radiation found that desorption of clusters from Br2Y films allowed detection by&#8804;8 eV single photon ionization. Thermal desorption and electronic structure calculations determined the ionization energy of Br2Y to be ~;;8.3?0.1 eV and further indicated that the lower ionization energies of clusters permitted their detection at&#8804;8 eV photon energies. However, single photon ionization could only detect Br2Y adsorbed within PEMs when using either higher photon energies or matrix addition to the sample. All samples were also analyzed by 25 keV Bi3 + secondary ion mass spectrometry (SIMS), with the negative ion spectra showing strong parent ion signal which complemented that observed by LDPI-MS. The negative ion SIMS depended strongly on the high electron affinity of this specific analyte and the analyte?s condensed phase environment.
Date: March 14, 2011
Creator: Chicago, University of Illinois at; Blaze, Melvin M. T.; Takahashi, Lynelle; Zhou, Jia; Ahmed, Musahid; Gasper, Gerald et al.
Partner: UNT Libraries Government Documents Department

Comparing Vacuum and Extreme Ultraviolet Radiation for Postionization of Laser Desorbed Neutrals from Bacterial Biofilms and Organic Fullerene

Description: Vacuum and extreme ultraviolet radiation from 8 - 24 eV generated at a synchrotron was used to postionize laser desorbed neutrals of antibiotic-treated biofilms and a modified fullerene using laser desorption postionization mass spectrometry (LDPI-MS). Results show detection of the parent ion, various fragments, and extracellular material from biofilms using LDPI-MS with both vacuum and extreme ultraviolet photons. Parent ions were observed for both cases, but extreme ultraviolet photons (16-24 eV) induced more fragmentation than vacuum ultraviolet (8-14 eV) photons.
Date: December 8, 2010
Creator: Gaspera, Gerald L.; Takahashi, Lynelle K.; Zhou, Jia; Ahmed, Musahid; Moored, Jerry F. & Hanley, Luke
Partner: UNT Libraries Government Documents Department