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  • 1. Ahmed, Towfiq
    et al.
    Haraldsen, Jason T.
    Zhu, Jian-Xin
    Balatsky, Alexander V.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Royal Institute of Technology, Sweden; Los Alamos National Laboratory, USA.
    Next-Generation Epigenetic Detection Technique: Identifying Methylated Cytosine Using Graphene Nanopore2014In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 5, no 15, p. 2601-2607Article in journal (Refereed)
    Abstract [en]

    DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells. For adult somatic cells, the location and dynamics of methylation have been very precisely pinned down with the 5-cytosine markers on cytosine-phosphate-guanine (CpG) units. Unusual methylation on CpG islands is identified as one of the prime causes for silencing the tumor suppressant genes. Early detection of methylation changes can diagnose the potentially harmful oncogenic evolution of cells and provide promising guideline for cancer prevention. With this motivation, we propose a cytosine methylation detection technique. Our hypothesis is that electronic signatures of DNA acquired as a molecule translocates through a nanopore would be significantly different for methylated and nonmethylated bases. This difference in electronic fingerprints would allow for reliable real-time differentiation of methylated DNA. We calculate transport currents through a punctured graphene membrane while the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyanocytosine for comparison. Our calculations of transmission, current, and tunneling conductance show distinct signatures in their spectrum for each molecular type. Thus, in this work, we provide a theoretical analysis that points to a viability of our hypothesis.

  • 2. Ahn, Chi Woo
    et al.
    Ki, Hosung
    Kim, Joonghan
    Kim, Jeongho
    Park, Sungjun
    Lee, Yunbeom
    Kim, Kyung Hwan
    Stockholm University, Faculty of Science, Department of Physics. Institute for Basic Science (IBS), Republic of Korea.
    Kong, Qingyu
    Moon, Jiwon
    Pedersen, Martin Nors
    Wulff, Michael
    Ihee, Hyotcherl
    Direct Observation of a Transiently Formed Isomer During lodoform Photolysis in Solution by Time-Resolved X-ray Liquidography2018In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, no 3, p. 647-653Article in journal (Refereed)
    Abstract [en]

    Photolysis of iodoform (CHI3) in solution has been extensively studied, but its reaction mechanism remains elusive. In particular, iso-iodoform (iso-CHI2-I) is formed as a product of the photolysis reaction, but its detailed structure is not known, and whether it is a major intermediate species has been controversial. Here, by using time-resolved X-ray liquidography, we determined the reaction mechanism of CHI3 photodissociation in cyclohexane as well as the structure of iso-CHI2-I. Both iso-CHI2-I and CHI2 radical were found to be formed within 100 ps with a branching ratio of 40:60. Iodine radicals (I), formed during the course of CHI3 photolysis, recombine nongeminately with either CHI2 or I. Based on our structural analysis, the I-I distance and the C-I-I angle of iso-CHI2-I were determined to be 2.922 +/- 0.004 angstrom and 133.9 +/- 0.8 degrees, respectively.

  • 3. Amaya, Andrew J.
    et al.
    Pathak, Harshad
    Modak, Viraj P.
    Laksmono, Hartawan
    Loh, N. Duane
    Sellberg, Jonas A.
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, United States; KTH Royal Institute of Technology, Sweden.
    Sierra, Raymond G.
    McQueen, Trevor A.
    Hayes, Matt J.
    Williams, Garth J.
    Messerschmidt, Marc
    Boutet, Sebastien
    Bogan, Michael J.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Acceleratory Laboratory, United States.
    Stan, Claudiu A.
    Wyslouzil, Barbara E.
    How Cubic Can Ice Be?2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 14, p. 3216-3222Article in journal (Refereed)
    Abstract [en]

    Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r approximate to 10 nm) at similar to 225 K The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 mu s of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, chi, in the range of 0.78 +/- 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. The high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a similar to 1 mu s time scale in single nanodroplets.

  • 4. Beye, Martin
    et al.
    Öberg, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Xin, Hongliang
    Dakovski, Georgi L.
    Dell'Angela, Martina
    Föhlisch, Alexander
    Gladh, Jörgen
    Stockholm University, Faculty of Science, Department of Physics.
    Hantschmann, Markus
    Hieke, Florian
    Kaya, Sarp
    Kuehn, Danilo
    LaRue, Jerry
    Mercurio, Giuseppe
    Minitti, Michael P.
    Mitra, Ankush
    Stockholm University, Faculty of Science, Department of Physics.
    Moeller, Stefan P.
    Ng, May Ling
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, United States.
    Nordlund, Dennis
    Norskov, Jens
    Östrom, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Ogasawara, Hirohito
    Persson, Mats
    Schlotter, William F.
    Sellberg, Jonas A.
    Stockholm University, Faculty of Science, Department of Physics. KTH Royal Institute of Technology, Sweden; SLAC National Accelerator Laboratory, United States.
    Wolf, Martin
    Abild-Pedersen, Frank
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Wurth, Wilfried
    Chemical Bond Activation Observed with an X-ray Laser2016In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 18, p. 3647-3651Article in journal (Refereed)
    Abstract [en]

    The concept of bonding and antibonding orbitals is fundamental in chemistry. The population of those orbitals and the energetic difference between the two reflect the strength of the bonding interaction. Weakening the bond is expected to reduce this energetic splitting, but the transient character of bond-activation has so far prohibited direct experimental access. Here we apply time-resolved soft X-ray spectroscopy at a free electron laser to directly observe the decreased bonding antibonding splitting following bond-activation using an ultrashort optical laser pulse.

  • 5.
    Eilert, André
    et al.
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, United States; Stanford University, United States.
    Cavalca, Filippo
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, United States; Stanford University, United States.
    Roberts, F. Sloan
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, United States; Stanford University, United States.
    Osterwalder, Jürg
    Liu, Chang
    Stockholm University, Faculty of Science, Department of Physics.
    Favaro, Marco
    Crumlin, Ethan J.
    Ogasawara, Hirohito
    Friebel, Daniel
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, United States; Stanford University, United States.
    Subsurface Oxygen in Oxide-Derived Copper Electrocatalysts for Carbon Dioxide Reduction2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 1, p. 285-290Article in journal (Refereed)
    Abstract [en]

    Copper electrocatalysts derived from an oxide have shown extraordinary electrochemical properties for the carbon dioxide reduction reaction (CO2RR). Using in situ ambient pressure X-ray photoelectron spectroscopy and quasi in situ electron energy loss spectroscopy in a transmission electron microscope, we show that there is a substantial amount of residual oxygen in nanostructured, oxide-derived copper electrocatalysts but no residual copper oxide. On the basis of these findings in combination with density functional theory simulations, we propose that residual subsurface oxygen changes the electronic structure of the catalyst and creates sites with higher carbon monoxide binding energy. If such sites are stable under the strongly reducing conditions found in CO2RR, these findings would explain the high efficiencies of oxide-derived copper in reducing carbon dioxide to multicarbon compounds such as ethylene.

  • 6. Eilert, André
    et al.
    Roberts, F. Sloan
    Friebel, Daniel
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, United States; Stanford University, United States.
    Formation of Copper Catalysts for CO2 Reduction with High Ethylene/Methane Product Ratio Investigated with In Situ X-ray Absorption Spectroscopy2016In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 8, p. 1466-1470Article in journal (Refereed)
    Abstract [en]

    Nanostructured copper cathodes are among the most efficient and selective catalysts to date for making multicarbon products from the electrochemical carbon dioxide reduction reaction (CO2RR). We report an in situ X-ray absorption spectroscopy investigation of the formation of a copper nanocube CO2RR catalyst with high activity that highly favors ethylene over methane production. The results show that the precursor for the copper nanocube formation is copper(I)-oxide, not copper(I)-chloride as previously assumed. A second route to an electrochemically similar material via a copper(II)-carbonate/hydroxide is also reported. This study highlights the importance of using oxidized copper precursors for constructing selective CO2 reduction catalysts and shows the precursor oxidation state does not affect the electrocatalyst selectivity toward ethylene formation.

  • 7. Harada, Y.
    et al.
    Miyawaki, J.
    Niwa, H.
    Yamazoe, K.
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Probing the OH Stretch in Different Local Environments in Liquid Water2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 22, p. 5487-5491Article in journal (Refereed)
    Abstract [en]

    We use resonant inelastic X-ray scattering (RIXS) to resolve vibrational losses corresponding to the OH stretch where the X-ray absorption process allows us to selectively probe different structural subensembles in liquid water. The results point to a unified interpretation of X-ray and vibrational spectroscopic data in line with a picture of two classes of structural environments in the liquid at ambient conditions with predominantly close-packed high-density liquid (HDL) and occasional local fluctuations into strongly tetrahedral low-density liquid (LDL).

  • 8. Jay, Raphael M.
    et al.
    Norell, Jesper
    Stockholm University, Faculty of Science, Department of Physics.
    Eckert, Sebastian
    Hantschmann, Markus
    Beye, Martin
    Kennedy, Brian
    Quevedo, Wilson
    Schlotter, William F.
    Dakovski, Georgi L.
    Minitti, Michael P.
    Hoffmann, Matthias C.
    Mitra, Ankush
    Moeller, Stefan P.
    Nordlund, Dennis
    Zhang, Wenkai
    Liang, Huiyang W.
    Kunnus, Kristian
    Kubicek, Katharina
    Techert, Simone A.
    Lundberg, Marcus
    Wernet, Philippe
    Gaffney, Kelly
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Föhlisch, Alexander
    Disentangling Transient Charge Density and Metal-Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering2018In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, no 12, p. 3538-3543Article in journal (Refereed)
    Abstract [en]

    Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal-ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. pi-Back-donation is found to be mainly determined by the metal site occupation, whereas the ligand hole instead influences sigma-donation. Our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes.

  • 9.
    Josefsson, Ida
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kunnus, Kristjan
    Schreck, Simon
    Föhlisch, Alexander
    de Groot, Frank
    Wernet, Philippe
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Ab Initio Calculations of X-ray Spectra: Atomic Multiplet and Molecular Orbital Effects in a Multiconfigurational SCF Approach to the L-Edge Spectra of Transition Metal Complexes2012In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 3, no 23, p. 3565-3570Article in journal (Refereed)
    Abstract [en]

    A new ab initio approach to the calculation of X-ray spectra is demonstrated. It combines a high-level quantum chemical description of the chemical interactions and local atomic multiplet effects. We show here calculated L-edge X-ray absorption (XA) and resonant inelastic X-ray scattering spectra for aqueous Ni2+ and XA spectra for a polypyridyl iron complex. Our quantum chemical calculations on a high level of accuracy in a post-Hartree–Fock framework give excellent agreement with experiment. This opens the door to reliable and detailed information on chemical interactions and the valence electronic structure in 3d transition-metal complexes also in transient excited electronic states. As we combine a molecular-orbital description with a proper treatment of local atomic electron correlation effects, our calculations uniquely allow, in particular, identifying the influence of interatomic chemical interactions versus intra-atomic correlations in the L-edge X-ray spectra.

  • 10.
    Jämbeck, Joakim P. M.
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Exploring the Free Energy Landscape of Solutes Embedded in Lipid Bilayers2013In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, no 11, p. 1781-1787Article in journal (Refereed)
    Abstract [en]

    Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.

  • 11. Laksmono, Hartawan
    et al.
    McQueen, Trevor A.
    Sellberg, Jonas A.
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, USA.
    Loh, N. Duane
    Huang, Congcong
    Schlesinger, Daniel
    Stockholm University, Faculty of Science, Department of Physics.
    Sierra, Raymond G.
    Hampton, Christina Y.
    Nordlund, Dennis
    Beye, Martin
    Martin, Andrew V.
    Barty, Anton
    Seibert, M. Marvin
    Messerschmidt, Marc
    Williams, Garth J.
    Boutet, Sebastien
    Arnann-Winkel, Katrin
    Stockholm University, Faculty of Science, Department of Physics. University of Innsbruck, Austria.
    Loerting, Thomas
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Bogan, Michael J.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, USA; .
    Anomalous Behavior of the Homogeneous Ice Nucleation Rate in No-Man's Land2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 14, p. 2826-2832Article in journal (Refereed)
    Abstract [en]

    We present an analysis of ice nucleation kinetics from near-ambient pressure water as temperature decreases below the homogeneous limit T-H by cooling micrometer-sized droplets (microdroplets) evaporatively at 10(3)-10(4) K/s and probing the structure ultrafast using femtosecond pulses from the Linac Coherent Light Source (LCLS) free-electron X-ray laser. Below 232 K, we observed a slower nucleation rate increase with decreasing temperature than anticipated from previous measurements, which we suggest is due to the rapid decrease in water's diffusivity. This is consistent with earlier findings that microdroplets do not crystallize at <227 K, but vitrify at cooling rates of 10(6)-10(7) K/s. We also hypothesize that the slower increase in the nucleation rate is connected with the proposed fragile-to-strong transition anomaly in water.

  • 12.
    LaRue, Jerry
    et al.
    Stockholm University, Faculty of Science, Department of Physics. SLAC National Accelerator Laboratory, USA; Chapman University, USA; Fritz-Haber Institute of the Max-Planck-Society, Germany.
    Krejčí, O.
    Stockholm University, Faculty of Science, Department of Physics. Charles University in Prague, Czech Republic; Institute of Physics of the Czech Academy of Sciences, Czech Republic.
    Yu, L.
    Beye, M.
    Ng, M. L.
    Öberg, H.
    Stockholm University, Faculty of Science, Department of Physics.
    Xin, H.
    Mercurio, G.
    Moeller, S.
    Turner, J. J.
    Nordlund, D.
    Coffee, R.
    Minitti, M. P.
    Wurth, W.
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Öström, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Abild-Pedersen, F.
    Ogasawara, H.
    Real-Time Elucidation of Catalytic Pathways in CO Hydrogenation on Ru2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 16, p. 3820-3825Article in journal (Refereed)
    Abstract [en]

    The direct elucidation of the reaction pathways in heterogeneous catalysis has been challenging due to the short-lived nature of reaction intermediates. Here, we directly measured on ultrafast time scales the initial hydrogenation steps of adsorbed CO on a Ru catalyst surface, which is known as the bottleneck reaction in syngas and CO2 reforming processes. We initiated the hydrogenation of CO with an ultrafast laser temperature jump and probed transient changes in the electronic structure using real-time X-ray spectroscopy. In combination with theoretical simulations, we verified the formation of CHO during CO hydrogenation.

  • 13. Li, Xin
    et al.
    Hede, Thomas
    Stockholm University, Faculty of Science, Department of Meteorology .
    Tu, Yaoquan
    Leck, Caroline
    Stockholm University, Faculty of Science, Department of Meteorology .
    Ågren, Hans
    Surface-Active cis-Pinonic Acid in Atmospheric Droplets: A Molecular Dynamics Study2010In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 1, no 4, p. 769-773Article in journal (Refereed)
    Abstract [en]

    Water vapor in the atmosphere can condensate and form cloud droplets when there is a certain amount of humidity and a presence of cloud condensation nuclei, and organic solutes called surfactants can significantly lower the surface tension of water-one of the parameters determining cloud droplet population. We here present a molecular dynamics study of the behavior of cis-pinonic acid, a commonly found organic compound in cloud condensation nuclei, and its effect on the surface tension of water clusters. Specifically, the decrease in surface tension is found to depend on not only the concentration of the organic compound but also the droplet size due to the spontaneous assembly of the surfactant molecules on the droplet surface. This leads to the conclusion that the partitioning of the surfactant between the bulk and surface plays an important role in the behavior of atmospheric aerosol particles and thus in their availability for cloud formation.

  • 14. Li, Xin
    et al.
    Leck, Caroline
    Stockholm University, Faculty of Science, Department of Meteorology .
    Sun, Lu
    Hede, Thomas
    Stockholm University, Faculty of Science, Department of Meteorology .
    Tu, Yaoquan
    Ågren, Hans
    Cross-Linked Polysaccharide Assemblies in Marine Gels: An Atomistic Simulation2013In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, no 16, p. 2637-2642Article in journal (Refereed)
    Abstract [en]

    Marine polymeric gels or colloidal nano- and microgels have been shown to contribute significantly to the primary marine aerosol and cloud condensation nuclei over remote marine areas. A microscopic understanding of such biologically derived matter at the sea air interface is important for future development of global climate models, but unfortunately cannot be obtained from modern characterization techniques. In this contribution, we employ molecular dynamics simulations to reveal the atomistic details of marine polymeric gels represented by anionic polysaccharide assemblies. The ionic bonds formed between polysaccharides and metal ions in seawater as well as the hydrophobic contribution to surface area are investigated in detail, and destabilization of the assemblies upon removal of Ca2+ or acidification is explained. These results provide insight into physicochemical properties of polysaccharide-Ca2+ structures and enable future studies of their roles of in the wetting process of cloud droplet activation.

  • 15. Lindbad, Rebecka
    et al.
    Bi, Dongqin
    Park, Byung-wook
    Oscarsson, Johan
    Gorgoi, Mihaela
    Siegbahn, Hans
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Johansson, Erik M. J.
    Rensmo, Håkan
    Electronic Structure of TiO2/CH(3)NH(3)Pbl(3) Perovskite Solar Cell Interfaces2014In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 5, no 4, p. 648-653Article in journal (Refereed)
    Abstract [en]

    The electronic structure and chemical composition of efficient CH(3)NH(3)Pbl(3) perovskite solar cell materials deposited onto mesoporous TiO2 were studied using photoelectron spectroscopy with hard X-rays. With this technique, it is possible to directly measure the occupied energy levels of the perovskite as well as the TiO2 buried beneath and thereby determine the energy level matching of the interface. The measurements of the valence levels were in good agreement with simulated density of states, and the investigation gives information on the character of the valence levels. We also show that two different deposition techniques give results indicating similar electronic structures.

  • 16. McFarland, Hannah L.
    et al.
    Ahmed, Towfiq
    Zhu, Jian-Xin
    Balatsky, Alexander V.
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Los Alamos National Laboratory, New Mexico.
    Haradsen, Jason T.
    First-Principles Investigation of Nanopore Sequencing Using Variable Voltage Bias on Graphene-Based Nanoribbons2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 13, p. 2616-2621Article in journal (Refereed)
    Abstract [en]

    In this study, we examine the mechanism of nanopore-based DNA sequencing using a voltage bias across a graphene nanoribbon. Using density function theory and a nonequilibrium Green's function approach, we determine the transmission spectra and current profile for adenine, guanine, cytosine, thymine, and uracil as a function of bias voltage in an energy minimized configuration. Utilizing the transmission current, we provide a general methodology for the development of a three nanopore graphene-based device that can be used to distinguish between the various nucleobases for DNA/RNA sequencing. From our analysis, we deduce that it is possible to use different transverse currents across a multinanopore device to differentiate between nucleobases using various voltages of 0.5, 1.3, and 1.6 V. Overall, our goal is to improve nanopore design to further DNA/RNA nucleobase sequencing and biomolecule identification techniques.

  • 17. Meyer, Benjamin
    et al.
    Barthel, Senja
    Mace, Amber
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). École Polytechnique Fédérale de Lausanne (EPFL), Switzerland.
    Vannay, Laurent
    Guillot, Benoit
    Smit, Berend
    Corminboeuf, Clémence
    DORI Reveals the Influence of Noncovalent Interactions on Covalent Bonding Patterns in Molecular Crystals Under Pressure2019In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 7, p. 1482-1488Article in journal (Refereed)
    Abstract [en]

    The study of organic molecular crystals under high pressure provides fundamental insight into crystal packing distortions and reveals mechanisms of phase transitions and the crystallization of polymorphs. These solid-state transformations can be monitored directly by analyzing electron charge densities that are experimentally obtained at high pressure. However, restricting the analysis to the featureless electron density does not reveal the chemical bonding nature and the existence of intermolecular interactions. This shortcoming can be resolved by the use of the DORI (density overlap region indicator) descriptor, which is capable of simultaneously detecting both covalent patterns and noncovalent interactions from electron density and its derivatives. Using the biscarbonyt[14]annulene crystal under pressure as an example, we demonstrate how DORI can be exploited on experimental electron densities to reveal and monitor changes in electronic structure patterns resulting from molecular compression. A novel approach based on a flood-fill-type algorithm is proposed for analyzing the topology of the DORI isosurface. This approach avoids the arbitrary selection of DORI isovalues and provides an intuitive way to assess how compression packing affects covalent bonding in organic solids.

  • 18. Monti, Susanna
    et al.
    Srifa, Pemikar
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kumaniaev, Ivan
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Samec, Joseph S. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    ReaxFF Simulations of Lignin Fragmentation on a Palladium-Based Heterogeneous Catalyst in Methanol-Water Solution2018In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, no 18, p. 5233-5239Article in journal (Refereed)
    Abstract [en]

    The interaction of fragments derived from lignin depolymerization with a heterogeneous palladium catalyst in methanol-water solution is studied by means of experimental and theoretical methodologies. Quantum chemistry calculations and molecular dynamics simulations based on the ReaxFF approach are combined effectively to obtain an atomic level characterization of the crucial steps of the adsorption of the molecules on the catalyst, their fragmentation, reactions, and desorption. The main products are identified, and the most important routes to obtain them are explained through extensive computational procedures. The simulation results are in excellent agreement with the experiments and suggest that the mechanisms comprise a fast chemisorption of identified fragments from lignin on the metal interface accompanied by bond breaking, release of some of their hydrogens and oxygens to the support, and eventual desorption depending on the local environment. The strongest connections are those involving the aromatic rings, as confirmed by the binding energies of selected representative structures, estimated at the quantum chemistry level. The satisfactory agreement with the literature, quantum chemistry data, and experiments confirms the reliability of the multilevel computational procedure to study complex reaction mixtures and its potential application in the design of high-performance catalytic devices.

  • 19. Rudy, Delaunay
    et al.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Rousseau, Patrick
    Domaracka, Alicja
    Maclot, Sylvain
    Wang, Yang
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Chen, Tao
    Stockholm University, Faculty of Science, Department of Physics.
    Adoui, Lamri
    Manuel, Alcami
    Martin, Fernando
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Huber, Bernd A.
    Molecular growth inside polycyclic aromatic hydrocarbon clusters induced by ion collisions2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 9, p. 1536-1542Article in journal (Refereed)
    Abstract [en]

    The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn’s moon Titan.

  • 20.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics. National Research Council Canada.
    Boguslavskiy, Andrey E.
    Stolow, Albert
    Two-Photon Excited State Dynamics of Dark Valence, Rydberg, and Superexcited States in 1,3-Butadiene2014In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 5, no 3, p. 560-565Article in journal (Refereed)
    Abstract [en]

    Two-photon absorption in systems with parity permits access to states that cannot be prepared by one-photon absorption. Here we present the first time-resolved photoelectron spectroscopy study using this technique, applied to 1,3-butadiene, in which we investigated the dynamics of its dark valence, Rydberg, and superexcited states. The dark valence state dynamics are accessed via the Rydberg manifold, excited by two photons of 400 nm. We find that the 'dark' 2(1)A(g) state populated in this manner has a much longer lifetime than when accesses via the 1(1)B(u) 'bright' valence state when populated by one photon of 200 nm. In addition, we compared the dynamics of the 3s pi- and 3d pi-Rydberg states. These Rydberg states relax to the valence manifold on a subpicosecond time scale, with the 3s pi-Rydberg state decay rate being larger due to a stronger valence-Rydberg mixing. Finally, we investigated superexcited valence states that fragment or autoionize within 200 fs, likely without involving Rydberg states.

  • 21.
    Stockett, Mark H.
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Aarhus University, Denmark.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Chen, Tao
    Stockholm University, Faculty of Science, Department of Physics.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Threshold Energies for Single-Carbon Knockout from Polycyclic Aromatic Hydrocarbons2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 22, p. 4504-4509Article in journal (Refereed)
    Abstract [en]

    We have measured absolute cross sections for ultrafast (femtosecond) single-carbon knockout from polycyclic aromatic hydrocarbon (PAR) cations as functions of He-PAR center-of-mass collision energy in the 10-200 eV range. Classical molecular dynamics (MD) simulations cover this range and extend up to 105 eV. The shapes of the knockout cross sections are well-described by a simple analytical expression yielding experimental and MD threshold energies of E-th(Exp) = 32.5 +/- 0.4 eV and E-th(MD) = 41.0 +/- 0.3 eV, respectively. These are the first measurements of knockout threshold energies for molecules isolated in vacuo. We further deduce semiempirical (SE) and MD displacement energies, i.e., the energy transfers to the PAH molecules at the threshold energies for knockout, of T-disp(SE) = 23.3 +/- 0.3 eV and T-disp(MD) = 27.0 +/- 0.3 eV. The semiempirical results compare favorably with measured displacement energies for graphene (T-disp = 23.6 eV).

  • 22. Wang, Chunlei
    et al.
    Tissot, Heloise
    Halldin Stenlid, Joakim
    Stockholm University, Faculty of Science, Department of Physics. KTH Royal Institute of Technology, Sweden.
    Kaya, Sarp
    Weissenrieder, Jonas
    High-Density Isolated Fe1O3 Sites on a Single-Crystal Cu2O(100) Surface2019In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 23, p. 7318-7323Article in journal (Refereed)
    Abstract [en]

    Single-atom catalysts have recently been subject to considerable attention within applied catalysis. However, complications in the preparation of well-defined single-atom model systems have hampered efforts to determine the reaction mechanisms underpinning the reported activity. By means of an atomic layer deposition method utilizing the steric hindrance of the ligands, isolated Fe1O3 motifs were grown on a single-crystal Cu2O(100) surface at densities up to 0.21 sites per surface unit cell. Ambient pressure X-ray photoelectron spectroscopy shows a strong metal-support interaction with Fe in a chemical state close to 3+. Results from scanning tunneling microscopy and density functional calculations demonstrate that isolated Fe1O3 is exclusively formed and occupies a single site per surface unit cell, coordinating to two oxygen atoms from the Cu2O lattice and another through abstraction from O-2. The isolated Fe1O3 motif is active for CO oxidation at 473 K. The growth method holds promise for extension to other catalytic systems.

  • 23. Wernet, Philippe
    et al.
    Kunnus, Kristjan
    Schreck, Simon
    Quevedo, Wilson
    Kurian, Reshmi
    Techert, Simone
    de Groot, Frank M. F.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Föhlisch, Alexander
    Dissecting Local Atomic and Intermolecular Interactions of Transition-Metal Ions in Solution with Selective X-ray Spectroscopy2012In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 3, no 23, p. 3448-3453Article in journal (Refereed)
    Abstract [en]

    Determining covalent and charge-transfer contributions to bonding in solution has remained an experimental challenge. Here, the quenching of fluorescence decay channels as expressed in dips in the L-edge X-ray spectra of solvated 3d transition-metal ions and complexes was reported as a probe. With a full set of experimental and theoretical ab initio L-edge X-ray spectra of aqueous Cr3+, including resonant inelastic X-ray scattering, we address covalency and charge transfer for this prototypical transition-metal ion in solution. We dissect local atomic effects from intermolecular interactions and quantify X-ray optical effects. We find no evidence for the asserted ultrafast charge transfer to the solvent and show that the dips are readily explained by X-ray optical effects and local atomic state dependence of the fluorescence yield. Instead, we find, besides ionic interactions, a covalent contribution to the bonding in the aqueous complex of ligand-to-metal charge-transfer character

  • 24.
    Yu, Yang
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Direct Experimental Evidence for Abundant BO4–BO4 Motifs in Borosilicate Glasses From Double-Quantum 11B NMR Spectroscopy2018In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, no 21, p. 6372-6376Article in journal (Refereed)
    Abstract [en]

    By using double-quantum–single-quantum correlation 11B nuclear magnetic resonance (NMR) experiments and atomistic molecular dynamics (MD) simulations, we resolve the long-standing controversy of whether directly interlinked BO4–BO4 groups exist in the technologically ubiquitous class of alkali/alkaline-earth based borosilicate (BS) glasses. Most structural models of Na2O–B2O3–SiO2 glasses assume the absence of B[4]–O–B[4] linkages, whereas they have been suggested to exist in Ca-bearing BS analogs. Our results demonstrate that while B[4]–O–B[4] linkages are disfavored relative to their B[3]–O–B[3]/B[4] counterparts, they are nevertheless abundant motifs in Na2O–B2O3–SiO2 glasses over a large composition space, while the B[4]–O–B[4] contents are indeed elevated in Na2O–CaO–B2O3–SiO2 glasses. We discuss the compositional and structural parameters that control the degree of B[4]–O–B[4] bonding.

1 - 24 of 24
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