Femtosecond Photoelectron Spectroscopy of the Dynamics of Electron Attachment and Photodissociation in Iodide-Nucleobase Clusters

DNA and RNA photodamage mechanisms are of significant importance but remain relatively poorly understood. The attachment of low-energy electrons to nucleic acid constituents has been shown to induce single and double strand breaks, although the mechanism of electron attachment and subsequent fragmentation remains debated. Nucleobases have been suggested to be the most likely target for attachment. The transient negative ions (TNIs) that form as a result of attachment have been implicated as important species in the damage mechanism. In addition, nucleobases exhibit strong photoabsorption cross-sections for UV light that may create a photoexcited species vulnerable to electron attachment. In vivo, local water molecules may stabilize TNIs and affect dissociation barriers, among other effects.Time-resolved photoelectron spectroscopy (TRPES) of gas phase iodide-nucleobase clusters is a powerful tool to probe ultrafast reductive damage pathways in nucleic acid constituents. This femtosecond pump-probe technique employs an ultraviolet (UV) pump pulse to either initiate charge transfer from the iodide to the nucleobase or directly photoexcite the nucleobase species. A UV or infrared (IR) probe pulse can photodetach nascent transient negative ions (TNIs) or anionic photofragments to trace the ultrafast dynamics of TNI formation, decay, and cluster dissociation. In this thesis, we employ TRPES in conjunction with excited state calculations and photofragment action spectroscopy to probe the dynamics of electron attachment and photodissociation in a variety of iodide-nucleobase clusters, including iodide-uracil, iodide-uracil-water, and the simpler model system iodide-nitromethane. Photofragment action spectroscopy and excited state calculations have revealed two distinct regimes of UV photoabsorption in iodide-nucleobase clusters: near the cluster vertical detachment energy (VDE) and near 4.8 eV. Near-VDE photoexcitation corresponds to optical excitation from an I(5p) orbital to form a dipole-bound (DB) anion, in which the excess electron is bound by the large dipole moment of the base. Photoexcitation from 4.6 - 5.2 eV is expected to correspond to base-centered pi-pi* photoexcitation of the nucleobase. In addition to DB anions, the canonical nucleobases are known to support conventional, valence-bound (VB) anionic states. Like the canonical nucleobases, nitromethane (CH3NO2) also possesses a large dipole moment and is known to support both DB and VB anion states and thus serves as a valuable small molecule model for the dynamics in larger nucleobase species. TRPES of iodide-nitromethane clusters with a near-VDE photon energy UV pump pulse yields instantaneous formation of the iodide-nitromethane DB anion with complete or nearly complete conversion to form a VB state in 400 - 500 fs. The VB state exhibits bi-exponential decay in 2 ps and 1200 ps. A UV probe pulse measures the formation of iodide as the major dissociation channel of the cluster, with mono-exponential formation in approximately 20 ps. Rice-Ramsperger-Kassel-Marcus (RRKM) calculations to model the statistical unimolecular dissociation of the cluster predict dissociation to form iodide in only 300 fs. The lack of a charged intermediate decay state suggests that intramolecular vibrational energy redistribution (IVR) in the cluster is the rate-limiting step in the nonstatistical dissociation of the cluster. TRPES of iodide-uracil binary clusters shows some similarities to iodide-nitromethane, with only partial DB to VB anion conversion following near-VDE photoexcitation likely due to the reversed energetic ordering of the two TNI states. In this pump energy regime, bi-exponential formation of iodide in 15 ps and 150 ps is measured and is expected to correspond to internal conversion and dissociation from each of the two relatively long-lived TNIs. Based on our TRPES results for iodide-nitromethane, we expect the long dissociation time constant to correspond to decay of the VB anion, with delayed dissociation due to inefficient IVR from vibrationally excited ring modes to the iodide---uracil stretch coordinate. In the pi-pi* photoexcitation regime, the VB anion of the iodide-uracil complex is found to form instantaneously despite the lack of a direct optical excitation to form this state. No DB anion is detected in this pump regime. We have suggested that VB anion formation occurs by charge transfer from iodide to fill the empty hole in the pi orbital following base-centered excitation. Autodetachment decay signal is measured in this photoexcitation regime to be approximately commensurate with the prompt formation and decay of the VB state. Thus, we expect that the decay of the nascent VB state is by autodetachment. Iodide formation is measured to occur in 10s of ps, and we expect that cluster dissociation to form iodide likely occurs as a result of internal conversion of the pi-pi* photoexcited base. The addition of a single water molecule to iodide-uracil is found to have two major effects: near-VDE photoexcitation yields a somewhat more pronounced DB to VB anion conversion in iodide-uracil-water than in iodide-uracil, and pi-pi* photoexcitation yields bi-exponential formation of iodide. In the near-VDE photoexcitation regime, the nascent DB anion may undergo relatively prompt water binding site reorientation to reach a conformer with a lower DB to VB anion conversion barrier resulting in delayed VB anion formation and thus more prominent conversion. Pi-pi* photoexcited iodide-uracil-water clusters may have other decay channels that can contribute to the bi-exponential formation of iodide such as the formation of iodide-water

Photodissociation dynamics of the iodide-uracil (I-U) complex

Photofragment action spectroscopy and femtosecond time-resolved photoelectron imaging are utilized to probe the dissociation channels in iodide-uracil (I− ⋅ U) binary clusters upon photoexcitation. The photofragment action spectra show strong I− and weak [U- H]− ion signal upon photoexcitation. The action spectra show two bands for I− and [U- H]− production peaking around 4.0 and 4.8 eV. Time-resolved experiments measured the rate of I− production resulting from excitation of the two bands. At 4.03 eV and 4.72 eV, the photoelectron signal from I− exhibits rise times of 86 ± 7 ps and 36 ± 3 ps, respectively. Electronic structure calculations indicate that the lower energy band, which encompasses the vertical detachment energy (4.11 eV) of I−U, corresponds to excitation of a dipole-bound state of the complex, while the higher energy band is primarily a π-π∗ excitation on the uracil moiety. Although the nature of the two excited states is very different, the long lifetimes for I− production suggest that this channel results from internal conversion to the I− ⋅ U ground state followed by evaporation of I−. This hypothesis was tested by comparing the dissociation rates to Rice-Ramsperger-Kassel-Marcus calculations

The Impact of Prenatal Nicotine Exposure on Impulsivity and Neural Firing in the Medial Prefrontal Cortex

Prenatal nicotine exposure (PNE) is linked to a large number of psychiatric disorders, including attention deficit hyperactivity disorder (ADHD). Current literature suggests that core deficits observed in ADHD reflect abnormal inhibitory control governed by the prefrontal cortex (PFC) of the brain. The PFC is structurally altered by PNE, but it is still unclear how neural firing is affected during tasks that test behavioral inhibition, such as the stop-signal task, or if neural correlates related to inhibitory control are affected after PNE in awake behaving animals. To address these questions, we recorded from single medial PFC (mPFC) neurons in control rats and PNE rats as they performed our stopsignal task. We found that PNE rats were faster for all trial types and were less likely to inhibit the behavioral response on STOP trials. Neurons in mPFC fired more strongly on STOP trials and were correlated with accuracy and reaction time. Although the number of neurons exhibiting significant modulation during task performance did not differ between groups, overall activity in PNE was reduced. We conclude that PNE makes rats impulsive and reduces firing in mPFC neurons that carry signals related to response inhibition

Livestock-associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 in Humans, Canada

Recent emergence of infections resulting from this strain is of public health concern

Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment

Christian R. Voolstra is with King Abdullah University of Science and Technology, Shinichi Sunagawa is with the European Molecular Biology Laboratory, Mikhail V. Matz is with UT Austin, Till Bayer is with King Abdullah University of Science and Technology, Manuel Aranda is with King Abdullah University of Science and Technology, Emmanuel Buschiazzo is with University of California Merced, Michael K. DeSalvo is with University of California San Francisco, Erika Lindquist is with the Department of Energy Joint Genome Institute, Alina M. Szmant is with University of North Carolina Wilmington, Mary Alice Coffroth is with State University of New York at Buffalo, Mónica Medina is with University of California Merced.Background -- Corals worldwide are in decline due to climate change effects (e.g., rising seawater temperatures), pollution, and exploitation. The ability of corals to cope with these stressors in the long run depends on the evolvability of the underlying genetic networks and proteins, which remain largely unknown. A genome-wide scan for positively selected genes between related coral species can help to narrow down the search space considerably. Methodology/Principal Findings -- We screened a set of 2,604 putative orthologs from EST-based sequence datasets of the coral species Acropora millepora and Acropora palmata to determine the fraction and identity of proteins that may experience adaptive evolution. 7% of the orthologs show elevated rates of evolution. Taxonomically-restricted (i.e. lineage-specific) genes show a positive selection signature more frequently than genes that are found across many animal phyla. The class of proteins that displayed elevated evolutionary rates was significantly enriched for proteins involved in immunity and defense, reproduction, and sensory perception. We also found elevated rates of evolution in several other functional groups such as management of membrane vesicles, transmembrane transport of ions and organic molecules, cell adhesion, and oxidative stress response. Proteins in these processes might be related to the endosymbiotic relationship corals maintain with dinoflagellates in the genus Symbiodinium. Conclusion/Relevance -- This study provides a birds-eye view of the processes potentially underlying coral adaptation, which will serve as a foundation for future work to elucidate the rates, patterns, and mechanisms of corals' evolutionary response to global climate change.This work was supported by DEB-1054766 to M.V.M. and National Science Foundation grants IOS-0644438 and OCE-0313708 to M.M., and by a Collaborative Travel Fund to C.R.V. made by King Abdullah University of Science and Technology (KAUST). The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

Femtosecond Photoelectron Spectroscopy of the Dynamics of Electron Attachment and Photodissociation in Iodide-Nucleobase Clusters

DNA and RNA photodamage mechanisms are of significant importance but remain relatively poorly understood. The attachment of low-energy electrons to nucleic acid constituents has been shown to induce single and double strand breaks, although the mechanism of electron attachment and subsequent fragmentation remains debated. Nucleobases have been suggested to be the most likely target for attachment. The transient negative ions (TNIs) that form as a result of attachment have been implicated as important species in the damage mechanism. In addition, nucleobases exhibit strong photoabsorption cross-sections for UV light that may create a photoexcited species vulnerable to electron attachment. In vivo, local water molecules may stabilize TNIs and affect dissociation barriers, among other effects.Time-resolved photoelectron spectroscopy (TRPES) of gas phase iodide-nucleobase clusters is a powerful tool to probe ultrafast reductive damage pathways in nucleic acid constituents. This femtosecond pump-probe technique employs an ultraviolet (UV) pump pulse to either initiate charge transfer from the iodide to the nucleobase or directly photoexcite the nucleobase species. A UV or infrared (IR) probe pulse can photodetach nascent transient negative ions (TNIs) or anionic photofragments to trace the ultrafast dynamics of TNI formation, decay, and cluster dissociation. In this thesis, we employ TRPES in conjunction with excited state calculations and photofragment action spectroscopy to probe the dynamics of electron attachment and photodissociation in a variety of iodide-nucleobase clusters, including iodide-uracil, iodide-uracil-water, and the simpler model system iodide-nitromethane. Photofragment action spectroscopy and excited state calculations have revealed two distinct regimes of UV photoabsorption in iodide-nucleobase clusters: near the cluster vertical detachment energy (VDE) and near 4.8 eV. Near-VDE photoexcitation corresponds to optical excitation from an I(5p) orbital to form a dipole-bound (DB) anion, in which the excess electron is bound by the large dipole moment of the base. Photoexcitation from 4.6 - 5.2 eV is expected to correspond to base-centered pi-pi* photoexcitation of the nucleobase. In addition to DB anions, the canonical nucleobases are known to support conventional, valence-bound (VB) anionic states. Like the canonical nucleobases, nitromethane (CH3NO2) also possesses a large dipole moment and is known to support both DB and VB anion states and thus serves as a valuable small molecule model for the dynamics in larger nucleobase species. TRPES of iodide-nitromethane clusters with a near-VDE photon energy UV pump pulse yields instantaneous formation of the iodide-nitromethane DB anion with complete or nearly complete conversion to form a VB state in 400 - 500 fs. The VB state exhibits bi-exponential decay in 2 ps and 1200 ps. A UV probe pulse measures the formation of iodide as the major dissociation channel of the cluster, with mono-exponential formation in approximately 20 ps. Rice-Ramsperger-Kassel-Marcus (RRKM) calculations to model the statistical unimolecular dissociation of the cluster predict dissociation to form iodide in only 300 fs. The lack of a charged intermediate decay state suggests that intramolecular vibrational energy redistribution (IVR) in the cluster is the rate-limiting step in the nonstatistical dissociation of the cluster. TRPES of iodide-uracil binary clusters shows some similarities to iodide-nitromethane, with only partial DB to VB anion conversion following near-VDE photoexcitation likely due to the reversed energetic ordering of the two TNI states. In this pump energy regime, bi-exponential formation of iodide in 15 ps and 150 ps is measured and is expected to correspond to internal conversion and dissociation from each of the two relatively long-lived TNIs. Based on our TRPES results for iodide-nitromethane, we expect the long dissociation time constant to correspond to decay of the VB anion, with delayed dissociation due to inefficient IVR from vibrationally excited ring modes to the iodide---uracil stretch coordinate. In the pi-pi* photoexcitation regime, the VB anion of the iodide-uracil complex is found to form instantaneously despite the lack of a direct optical excitation to form this state. No DB anion is detected in this pump regime. We have suggested that VB anion formation occurs by charge transfer from iodide to fill the empty hole in the pi orbital following base-centered excitation. Autodetachment decay signal is measured in this photoexcitation regime to be approximately commensurate with the prompt formation and decay of the VB state. Thus, we expect that the decay of the nascent VB state is by autodetachment. Iodide formation is measured to occur in 10s of ps, and we expect that cluster dissociation to form iodide likely occurs as a result of internal conversion of the pi-pi* photoexcited base. The addition of a single water molecule to iodide-uracil is found to have two major effects: near-VDE photoexcitation yields a somewhat more pronounced DB to VB anion conversion in iodide-uracil-water than in iodide-uracil, and pi-pi* photoexcitation yields bi-exponential formation of iodide. In the near-VDE photoexcitation regime, the nascent DB anion may undergo relatively prompt water binding site reorientation to reach a conformer with a lower DB to VB anion conversion barrier resulting in delayed VB anion formation and thus more prominent conversion. Pi-pi* photoexcited iodide-uracil-water clusters may have other decay channels that can contribute to the bi-exponential formation of iodide such as the formation of iodide-water

Time-Resolved Dynamics in Iodide-Uracil-Water Clusters upon Excitation of the Nucleobase

The dynamics of iodide-uracil-water (I−·U·H2O) clusters following π-π* excitation of the nucleobase are probed using time-resolved photoelectron spectroscopy (TRPES). Photoexcitation of this cluster at 4.77 eV results in electron transfer from the iodide moiety to the uracil, creating a valence-bound (VB) anion within the cross-correlation of the pump and probe laser pulses. This species can decay by a number of channels, including autodetachment and dissociation to I− or larger anion fragments. Comparison of the energetics of the photoexcited cluster and its decay dynamics with those of the bare iodide-uracil (I−·U) complex provide a sensitive probe of the effects of microhydration on these species

OBSERVATION OF NEW DYNAMICS IN THE STATE-RESOLVED COLLISIONAL RELAXATION OF HIGHLY EXCITED MOLECULES

Author Institution: Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742The dynamics of collisional deactivation of highly energized molecules, pyrazine-h$_{4}$ and pyrazine-d$_{4}$, by HCl molecules at 300 K show evidence of a new mechanism for collisional energy transfer. Highly vibrationally excited (E$_{vib}$ = 37,900 \wn) pyrazine-h$_{4}$ and pyrazine-d$_{4}$ molecules are produced in separate experiments by pulsed excitation with the fourth harmonic output of a Nd:YAG laser at $\lambda$ = 266 nm. Collisions between the energized isotopes and HCl molecules are monitored by measuring the nascent transient IR absorption of scattered HCl in individual rotational states. The results indicate that HCl molecules are scattered with a gain in rotational and translational energy, but the largest recoil energies are observed for the lowest rotational energy states of HCl. This behavior is opposite to that seen for other bath molecules including DCl and CO$_{2}$. The results point to differences in intermolecular interactions between the energy donor and acceptor molecules as contributing factors to the observed differences in the mechanism of energy transfer