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  • 1. Achari, Muthuraaman Bhagavathi
    et al.
    Elumalai, Viswanathan
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Vlachopoulos, Nick
    Safdari, Majid
    Gao, Jiajia
    Gardner, James M.
    Kloo, Lars
    A quasi-liquid polymer-based cobalt redox mediator electrolyte for dye-sensitized solar cells2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 40, p. 17419-17425Article in journal (Refereed)
    Abstract [en]

    Recently, cobalt redox electrolyte mediators have emerged as a promising alternative to the commonly used iodide/triiodide redox shuttle in dye-sensitized solar cells (DSCs). Here, we report the successful use of a new quasi-liquid, polymer-based electrolyte containing the Co3+/Co2+ redox mediator in 3-methoxy propionitrile solvent in order to overcome the limitations of high cell resistance, low diffusion coefficient and rapid recombination losses. The performance of the solar cells containing the polymer based electrolytes increased by a factor of 1.2 with respect to an analogous electrolyte without the polymer. The performances of the fabricated DSCs have been investigated in detail by photovoltaic, transient electron measurements, EIS, Raman and UV-vis spectroscopy. This approach offers an effective way to make high-performance and long-lasting DSCs.

  • 2. Aidas, Kestutis
    et al.
    Agren, Hans
    Kongsted, Jacob
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. the case of na+ in aqueous solution2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 5, p. 1621-1631Article in journal (Refereed)
    Abstract [en]

    The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

  • 3.
    Aleksis, Rihards
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Nedumkandathil, Reji
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Papawassiliou, Wassilios
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Carvalho, José P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Jaworski, Aleksander
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Häussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Pell, Andrew J.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Université de Lyon, France.
    Probing the electronic structure and hydride occupancy in barium titanium oxyhydride through DFT-assisted solid-state NMR2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 46, p. 28164-28173Article in journal (Refereed)
    Abstract [en]

    Perovskite-type oxhydrides such as BaTiO3−xHy exhibit mixed hydride ion and electron conduction and are an attractive class of materials for developing energy storage devices. However, the underlying mechanism of electric conductivity and its relation to the composition of the material remains unclear. Here we report detailed insights into the hydride local environment, the electronic structure and hydride conduction dynamics of barium titanium oxyhydride. We demonstrate that DFT-assisted solid-state NMR is an excellent tool for differentiating between the different feasible electronic structures in these solids. Our results indicate that upon reduction of BaTiO3 the introduced electrons are delocalized among all Ti atoms forming a bandstate. Furthermore, each vacated anion site is reoccupied by at most a single hydride, or else remains vacant. This single occupied bandstate structure persists at different hydrogen concentrations (y = 0.13–0.31) and a wide range of temperatures (∼100–300 K).

  • 4. Andersson, Ove
    et al.
    B. Brant Carvalho, Paulo H.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Häussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hsu, Ying-Jui
    Evidence suggesting kinetic unfreezing of water mobility in two distinct processes in pressure-amorphized clathrate hydrates2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 34, p. 20064-20072Article in journal (Refereed)
    Abstract [en]

    Type II clathrate hydrates (CHs) with tetrahydrofuran (THF), cyclobutanone (CB) or 1,3-dioxolane (DXL) guest molecules collapse to an amorphous state near 1 GPa on pressurization below 140 K. On subsequent heating in the 0.2–0.7 GPa range, thermal conductivity and heat capacity results of the homogeneous amorphous solid show two glass transitions, first a thermally weak glass transition, GT1, near 130 K; thereafter a thermally strong glass transition, GT2, which implies a transformation to an ultraviscous liquid on heating. Here we compare the GTs of normal and deuterated samples and samples with different guest molecules. The results show that GT1 and GT2 are unaffected by deuteration of the THF guest and exchange of THF with CB or DXL, whereas the glass transition temperatures (Tgs) shift to higher temperatures on deuteration of water; Tg of GT2 increases by 2.5 K. These results imply that both GTs are associated with the water network. This is corroborated by the fact that GT2 is detected only in the state which is the amorphized CH's counterpart of expanded high density amorphous ice. The results suggest a rare transition sequence of an orientational glass transition followed by a glass to liquid transition, i.e., kinetic unfreezing of H2O reorientational and translational mobility in two distinct processes.

  • 5. Anniyev, Toyli
    et al.
    Ogasawara, Hirohito
    Ljungberg, Mathias
    Stockholm University, Faculty of Science, Department of Physics.
    Wikfeldt, Kjartan T.
    Stockholm University, Faculty of Science, Department of Physics.
    MacNaughton, Janay B.
    Näslund, Lars-Åke
    Bergmann, Uwe
    Koh, Shirlaine
    Strasser, Peter
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Complementarity between high-energy photoelectron and L-edge spectroscopy for probing the electronic structure of 5d transition metal catalysts2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 21, p. 5694-5700Article in journal (Refereed)
    Abstract [en]

    We demonstrate the successful use of hard X-ray photoelectron spectroscopy (HAXPES) for selectively probing the platinum partial d-density of states (DOS) in a Pt-Cu nanoparticle catalyst which shows activity superior to pure Pt towards the oxygen-reduction reaction (ORR). The information about occupied Pt d-band states was complemented by Pt L-2-edge X-ray absorption near-edge spectroscopy (XANES), which probes unoccupied valence states. We found a significant electronic perturbation of the Pt projected d-DOS which was narrowed and shifted to higher binding energy compared to pure platinum. The effect of this electronic structure perturbation on the chemical properties of the nanoparticle surface is discussed in terms of the d-band model. We have thereby demonstrated that the combination of L-edge spectroscopy and HAXPES allows for an experimental derivation of the valence electronic structure in an element-specific way for 5d metal catalysts.

  • 6.
    Arafa, Wael A. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Kärkäs, Markus D.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Lee, Bao-Lin
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Torbjörn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Berends, Hans-Martin
    Messinger, Johannes
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Åkermark, Björn
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Dinuclear manganese complexes for water oxidation: evaluation of electronic effects and catalytic activity2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 24, p. 11950-11964Article in journal (Refereed)
    Abstract [en]

    During recent years significant progress has been made towards the realization of a sustainable and carbon-neutral energy economy. One promising approach is photochemical splitting of H2O into O-2 and solar fuels, such as H-2. However, the bottleneck in such artificial photosynthetic schemes is the H2O oxidation half reaction where more efficient catalysts are required that lower the kinetic barrier for this process. In particular catalysts based on earth-abundant metals are highly attractive compared to catalysts comprised of noble metals. We have now synthesized a library of dinuclear Mn-2 (II,III) catalysts for H2O oxidation and studied how the incorporation of different substituents affected the electronics and catalytic efficiency. It was found that the incorporation of a distal carboxyl group into the ligand scaffold resulted in a catalyst with increased catalytic activity, most likely because of the fact that the distal group is able to promote proton-coupled electron transfer (PCET) from the high-valent Mn species, thus facilitating O-O bond formation.

  • 7. Ashworth, Eleanor K.
    et al.
    Dezalay, Jordan
    Stockholm University, Faculty of Science, Department of Physics.
    Ryan, Christopher R. M.
    Ieritano, Christian
    Hopkins, W. Scott
    Chambrier, Isabelle
    Cammidge, Andrew N.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Noble, Jennifer A.
    Bull, James N.
    Protomers of the green and cyan fluorescent protein chromophores investigated using action spectroscopy2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 25, no 30, p. 20405-20413Article in journal (Refereed)
    Abstract [en]

    The photophysics of biochromophore ions often depends on the isomeric or protomeric distribution, yet this distribution, and the individual isomer contributions to an action spectrum, can be difficult to quantify. Here, we use two separate photodissociation action spectroscopy instruments to record electronic spectra for protonated forms of the green (pHBDI(+)) and cyan (Cyan(+)) fluorescent protein chromophores. One instrument allows for cryogenic (T = 40 & PLUSMN; 10 K) cooling of the ions, while the other offers the ability to perform protomer-selective photodissociation spectroscopy. We show that both chromophores are generated as two protomers when using electrospray ionisation, and that the protomers have partially overlapping absorption profiles associated with the S-1 & LARR; S-0 transition. The action spectra for both species span the 340-460 nm range, although the spectral onset for the pHBDI(+) protomer with the proton residing on the carbonyl oxygen is red-shifted by & AP;40 nm relative to the lower-energy imine protomer. Similarly, the imine and carbonyl protomers are the lowest energy forms of Cyan(+), with the main band for the carbonyl protomer red-shifted by & AP;60 nm relative to the lower-energy imine protomer. The present strategy for investigating protomers can be applied to a wide range of other biochromophore ions.

  • 8.
    B. Brant Carvalho, Paulo H.
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Ivanov, Mikhail
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Andersson, Ove
    Loerting, Thomas
    Bauer, Marion
    Tulk, Chris A.
    Haberl, Bianca
    Daemen, Luke L.
    Molaison, Jamie J.
    Amann-Winkel, Katrin
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bull, Craig L.
    Funnell, Nicholas P.
    Häussermann, Ulrich
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Neutron scattering study of polyamorphic THF·17(H2O) – toward a generalized picture of amorphous states and structures derived from clathrate hydrates2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, no 21Article in journal (Refereed)
    Abstract [en]

    From crystalline tetrahydrofuran clathrate hydrate, THF–CH (THF·17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF–CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77–140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, VHDA, upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third form, recovered amorphous (RA). Results from neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF–CH and liquid THF·17H2O solution (∼2.5 M). Although fully amorphous, HDA is heterogeneous with two length scales for water–water correlations (less dense local water structure) and guest–water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest–host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ∼23H2O. The local water structure in HDA is reminiscent of pure HDA-ice featuring 5-coordinated H2O. In VHDA, the hydration structure of HDA is maintained but the local water structure is densified and resembles pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ∼18 H2O molecules and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous.

  • 9.
    Baronio, Cesare M.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Baldassarre, Maurizio
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Insight into the internal structure of amyloid-β oligomers by isotope-edited Fourier transform infrared spectroscopy2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 16, p. 8587-8597Article in journal (Refereed)
    Abstract [en]

    The internal structure of amyloid-β (Aβ) oligomers was investigated with isotope-edited Fourier transform infrared spectroscopy. Homo-oligomers of Aβ(40) and Aβ(42) were prepared from unlabeled and C-13, N-15-labeled monomeric Aβ and from mixtures of these. For the unlabeled peptides, two main bands were observed in (H2O)-H-2 at 1685 and 1622 cm(-1) for Aβ(40) and at 1685 and 1626 cm(-1) for Aβ(42). These band positions indicate that the number of strands per sheet is at least four. The obtained experimental amide I spectra were simulated using a number of structural models (antiparallel β-sheets, β-barrels and a dodecamer structure). According to experiments and calculations, the main C-13-band shifts down at increasing molar ratio of labeled peptides. This shift occurs when vibrational coupling becomes possible between C-13-amide groups in close-by strands. It is small, when intervening C-12-strands increase the distance between C-13-strands; it is large, when many neighboring strands are labeled. The shift depends on the internal structure of the peptides within the oligomers, i.e. on the building block that each peptide molecule contributes to the β-sheets of the oligomers. The shift is largest, when individual peptides contribute just a single strand surrounded by strands from other peptide molecules. It is smaller when each molecule forms two or three adjacent strands. As indicated by a comparison between experiment and computation, the number of adjacent β-strands per peptide molecule is two for Aβ(40) oligomers and two or more for Aβ(42) oligomers. Our results are well explained by regular, antiparallel β-sheets or β-barrels.

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  • 10.
    Baronio, Cesare M.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Refining protein amide I spectrum simulations with simple yet effective electrostatic models for local wavenumbers and dipole derivative magnitudes2024In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 2, p. 1166-1181Article in journal (Refereed)
    Abstract [en]

    Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures – α-helices, parallel and antiparallel β-sheets – with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the CO bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment.

  • 11. Barreiro-Lage, Darío
    et al.
    Chiarinelli, Jacopo
    Bolognesi, Paola
    Richter, Robert
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Stockett, Mark Hugo
    Stockholm University, Faculty of Science, Department of Physics.
    Díaz-Tendero, Sergio
    Avaldi, Lorenzo
    Photofragmentation specificity of photoionized cyclic amino acids (diketopiperazines) as precursors of peptide building blocks2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 25, no 23, p. 15635-15646Article in journal (Refereed)
    Abstract [en]

    The photoionisation and photofragmentation of the two cyclic dipetides cyclo(alanyl-glycine) cGA and cyclo(glycyl-glycine) cGG, have been studied combining experiments and simulations. State selected fragments from the ionized molecules are detected using photo-electron photo-ion coincidence (PEPICO) measurements and specific fragmentation paths are identified and characterized via the use of ion-neutral coincidence maps. The simulations, performed using Quantum Chemistry methods, allow us to infer the fragmentation mechanisms of the ionized and excited molecules. We show that ring opening is followed by emission of the neutral fragments CO and HNCO. In the case of cGG the emission of neutral CO leads to a metastable structure that breaks producing small cationic fragments. The studied cyclic dipeptides evolve under ionizing radiation generating different small aziridin moieties and oxazolidinones. These two species are key reactants to elongate producing peptide chains. The corresponding mechanisms have been computed and show that the reaction requires very low energy and may occur in the presence of ionizing radiation.

  • 12.
    Berkowicz, Sharon
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Perakis, Fivos
    Stockholm University, Faculty of Science, Department of Physics.
    Exploring the validity of the Stokes-Einstein relation in supercooled water using nanomolecular probes2021In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 23, no 45, p. 25490-25499Article in journal (Refereed)
    Abstract [en]

    The breakdown of Stokes–Einstein relation in liquid water is one of the many anomalies that take place upon cooling and indicates the decoupling of diffusion and viscosity. It is hypothesized that these anomalies manifest due to the appearance of nanometer-scale spatial fluctuations, which become increasingly pronounced in the supercooled regime. Here, we explore the validity of the Stokes–Einstein relation in supercooled water using nanomolecular probes. We capture the diffusive dynamics of the probes using dynamic light scattering and target dynamics at different length scales by varying the probe size, from ≈100 nm silica spheres to molecular-sized polyhydroxylated fullerenes (≈1 nm). We find that all the studied probes, independent of size, display similar diffusive dynamics with an Arrhenius activation energy of ≈23 kJ mol−1. Analysis of the diffusion coefficient further indicates that the probes, independent of their size, experience similar dynamic environment, which coincides with the macroscopic viscosity, while single water molecules effectively experience a comparatively lower viscosity. Finally, we conclude that our results indicate that the Stokes–Einstein relation is preserved for diffusion of probes in supercooled water T ≥ 260 K with size as small as ≈1 nm.

  • 13. Bernard, Jérôme
    et al.
    Ji, MingChao
    Stockholm University, Faculty of Science, Department of Physics.
    Indrajith, Suvasthika
    Stockholm University, Faculty of Science, Department of Physics.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Navarro-Navarrete, José E.
    Stockholm University, Faculty of Science, Department of Physics.
    Kono, Naoko
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Martin, Serge
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Efficient radiative cooling of tetracene cations C18H12+: absolute recurrent fluorescence rates as a function of internal energy2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 25, no 15, p. 10726-10740Article in journal (Refereed)
    Abstract [en]

    We have measured recurrent fluorescence (RF) cooling rates of internally hot tetracene cations, C18H12+, as functions of their storage times and internal energies in two different electrostatic ion-beam storage rings – the cryogenic ring DESIREE with a circumference of 8.6 meters in Stockholm and the much smaller room temperature ring Mini-Ring in Lyon, which has a circumference of 0.71 meters. The RF rates were measured to be as high as 150 to 1000 s−1 for internal energies in the 7 to 9.4 eV energy range, where we have probed the time evolution of the internal energy distribution with nanosecond laser pulses with a 1 kHz repetition rate. These RF rates are found to be significantly higher than those of previously investigated smaller PAHs such as e.g. anthracene and naphthalene, for which the lowest non-forbidden electronic excited state, the D2 state, is populated with a smaller probability by inverse internal conversion. Furthermore, the D2–D0 transition rate is smaller for these smaller molecules than for tetracene. The complementary features of the two storage rings allow for RF rate measurements in a broader internal energy range than has been possible before. The smaller sampling period of about 6 μs in Mini-Ring is ideal to study the cooling dynamics of the hotter ions that decay fast, whereas DESIREE with a sampling period of about 60 μs is better suited to study the colder ions that decay on longer timescales ranging up to hundreds of milliseconds. The excellent agreement between the two series of measurements in the region where they overlap demonstrates the complementarity of the two electrostatic ion-beam storage rings.

  • 14.
    Bin, Maddalena
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Yousif, Rafat
    Stockholm University, Faculty of Science, Department of Physics.
    Berkowicz, Sharon
    Stockholm University, Faculty of Science, Department of Physics.
    Das, Sudipta
    Stockholm University, Faculty of Science, Department of Physics.
    Schlesinger, Daniel
    Stockholm University, Faculty of Science, Department of Environmental Science.
    Perakis, Fivos
    Stockholm University, Faculty of Science, Department of Physics.
    Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water2021In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 23, no 34, p. 18308-18313Article in journal (Refereed)
    Abstract [en]

    Understanding the mechanism responsible for the protein low-temperature crossover observed at T approximate to 220 K can help us improve current cryopreservation technologies. This crossover is associated with changes in the dynamics of the system, such as in the mean-squared displacement, whereas experimental evidence of structural changes is sparse. Here we investigate hydrated lysozyme proteins by using a combination of wide-angle X-ray scattering and molecular dynamics (MD) simulations. Experimentally we suppress crystallization by accurate control of the protein hydration level, which allows access to temperatures down to T = 175 K. The experimental data indicate that the scattering intensity peak at Q = 1.54 angstrom(-1), attributed to interatomic distances, exhibits temperature-dependent changes upon cooling. In the MD simulations it is possible to decompose the water and protein contributions and we observe that, while the protein component is nearly temperature independent, the hydration water peak shifts in a fashion similar to that of bulk water. The observed trends are analysed by using the water-water and water-protein radial distribution functions, which indicate changes in the local probability density of hydration water.

  • 15.
    Boscolo Bibi, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    El-Zohry, Ahmed M.
    Stockholm University, Faculty of Science, Department of Physics.
    Davies, Bernadette
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Faculty of Science, Department of Physics.
    Grigorev, Vladimir
    Stockholm University, Faculty of Science, Department of Physics.
    Goodwin, Christopher M.
    Stockholm University, Faculty of Science, Department of Physics.
    Lömker, Patrick
    Stockholm University, Faculty of Science, Department of Physics.
    Holm, Alexander
    Stockholm University, Faculty of Science, Department of Physics.
    Ali-Löytty, Harri
    Garcia-Martinez, Fernando
    Schlueter, Christoph
    Soldemo, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Koroidov, Sergey
    Stockholm University, Faculty of Science, Department of Physics.
    Hansson, Tony
    Stockholm University, Faculty of Science, Department of Physics.
    Multi-spectroscopic study of electrochemically-formed oxide-derived gold electrodes2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    Oxide-derived metals are produced by reducing an oxide precursor. These materials, including gold, have shown improved catalytic performance over many native metals. The origin of this improvement for gold is not yet understood. In this study, operando non-resonant sum frequency generation (SFG) and ex situ high-pressure X-ray photoelectron spectroscopy (HP-XPS) have been employed to investigate electrochemically-formed oxide-derived gold (OD-Au) from polycrystalline gold surfaces. A range of different oxidizing conditions were used to form OD-Au in acidic aqueous medium (H3PO4, pH = 1). Our electrochemical data after OD-Au is generated suggest that the surface is metallic gold, however SFG signal variations indicate the presence of subsurface gold oxide remnants between the metallic gold surface layer and bulk gold. The HP-XPS results suggest that this subsurface gold oxide could be in the form of Au2O3 or Au(OH)3. Furthermore, the SFG measurements show that with reducing electrochemical treatments the original gold metallic state can be restored, meaning the subsurface gold oxide is released. This work demonstrates that remnants of gold oxide persist beneath the topmost gold layer when the OD-Au is created, potentially facilitating the understanding of the improved catalytic properties of OD-Au.

  • 16. Brinkmann, Andreas
    et al.
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Central-transition double-quantum sideband NMR spectroscopy of half-integer quadrupolar nuclei: estimating internuclear distances and probing clusters within multi-spin networks2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 15, p. 7037-7050Article in journal (Refereed)
    Abstract [en]

    We introduce a strategy to estimate the size of clusters of recoupled homonuclear half-integer quadrupolar nuclei under magic-angle spinning (MAS) conditions, by combining double-quantum (2Q) sideband NMR experiments with an approximate numerical analysis based on the summation of all spin-pairs present over a given radius of the structure. The experiment relies solely on the evolution of homonuclear 2Q coherences (2QC) among the central-transitions (CT) of half-integer spins and is suitable for probing clusters in network structures, such as those encountered in large groups of oxide-based materials. Experimental B-11, Na-23 and Al-27 NMR results are presented on bis(catecholato)diboron, Na2SO4 and Al2O3, respectively; in each case, the growth of the spin-cluster size was monitored from a series of experiments that employed progressively lengthened 2QC excitation intervals. Our new approach is the first option for probing larger constellations of half-integer spins; it provides similar information as the multiple-quantum spin counting experiment, which is well-established for spin-1/2 applications but has hitherto not been demonstrated for half-integer spins undergoing MAS. We also discuss various options for determining the internuclear distance within a (nearly) isolated pair of half-integer spins by comparing the experimental 2Q sideband NMR spectra with results from numerical simulations involving various degrees of approximation.

  • 17. Bull, James N.
    et al.
    Carrascosa, Eduardo
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Bieske, Evan J.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics. University of Melbourne, Australia.
    Ion mobility action spectroscopy of flavin dianions reveals deprotomer-dependent photochemistry2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 29, p. 19672-19681Article in journal (Refereed)
    Abstract [en]

    The intrinsic optical properties and photochemistry of flavin adenine dinucleotide (FAD) dianions are investigated using a combination of tandem ion mobility spectrometry and action spectroscopy. Two principal isomers are observed, the more stable form being deprotonated on the isoalloxazine group and a phosphate (N-3,PO4 deprotomer), and the other on the two phosphates (PO4,PO4 deprotomer). Ion mobility data and electronic action spectra suggest that photo-induced proton transfer occurs from the isoalloxazine group to a phosphate group, converting the PO4,PO4 deprotomer to the N-3,PO4 deprotomer. Comparisons of the isomer selective action spectra of FAD dianions and flavin monoanions with solution spectra and gas-phase photodissociation action spectra suggests that solvation shifts the electronic absorption of the deprotonated isoalloxazine group to higher energy. This is interpreted as evidence for significant charge transfer in the lowest optical transition of deprotonated isoalloxazine. Overall, this work demonstrates that the site of deprotonation of flavin anions strongly affects their electronic absorptions and photochemistry.

  • 18.
    C. Couto, Rafael
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Suppressing non-radiative decay of photochromic organic molecular systems in the strong coupling regime2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 32, p. 19199-19208Article in journal (Refereed)
    Abstract [en]

    The lifetimes of electronic excited states have a strong influence on the efficiency of organic solar cells. However, in some molecular systems a given excited state lifetime is reduced due to the non-radiative decay through conical intersections. Several strategies may be used to suppress this decay channel. The use of the strong light-matter coupling provided in optical nano-cavities is the focus of this paper. Here, we consider the meso–tert-butyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene molecule (meso–tert-butyl-BODIPY) as a showcase of how strong and ultrastrong coupling might help in the development of organic solar cells. The meso–tert-butyl-BODIPY is known for its low fluorescence yield caused by the non-radiative decay through a conical intersection. However, we show here that, by considering this system within a cavity, the strong coupling can lead to significant changes in the multidimensional landscape of the potential energy surfaces of meso–tert-butyl-BODIPY, suppressing almost completely the decay of the excited state wave packet back to the ground state. By means of multi configuration electronic structure calculations and nuclear wave packet dynamics, the coupling with the cavity is analyzed in-depth to provide further insight of the interaction. By fine-tuning the cavity field strength and resonance frequency, we show that one can change the nuclear dynamics in the excited state, and control the non-radiative decay. This may lead to a faster and more efficient population transfer or the suppression of it.

  • 19.
    Cavalleri, M.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Nordlund, D.
    Stockholm University, Faculty of Science, Department of Physics.
    Odelius, M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, A.
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, L.G.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Half or full core hole in density functional theory X-ray absorption spectrum calculations of water?2005In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 7, no 15, p. 2854-2858Article in journal (Refereed)
    Abstract [en]

    We analyze the performance of two different core-hole potentials in the theoretical modeling of XAS of ice, liquid and gas phase water; the use of a full core-hole (FCH) in the calculations, as suggested by Hetenyi et al. [B. Hetenyi, F. De Angelis, P. Giamozzi and R. Car, J. Chem. Phys., 2004, 120(18), 8632], gives poor agreement with experiment in terms of intensity distribution as well as transition energies, while the half core hole (HCH) potential, in the case of water, provides a better compromise between initial and final state effects, leading to good agreement with the experimental data.

  • 20. Chen, Chen
    et al.
    Huang, Congcong
    Waluyo, Iradwikanari
    Weiss, Thomas
    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, USA.
    Long-range ion-water and ion-ion interactions in aqueous solutions2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 13, p. 8427-8430Article in journal (Refereed)
    Abstract [en]

    Using small-angle X-ray scattering (SAXS), we obtained direct experimental evidence on the structure of hydrated polyatomic anions, with hydration effects starkly different from those of cations (J. Chem. Phys., 2011, 134, 064513). We propose that the size and charge density of the naked ions do not sufficiently account for the differences in the SAXS curves. For cations, the ion-ion contribution gives a prominent first-order diffraction peak, whereas for anions, the low-Q enhancement in the SAXS curves indicates density inhomogeneities as a result of ion-water interactions.

  • 21. Chen, Shi-Lu
    et al.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    An investigation of possible competing mechanisms for Ni-containing methyl-coenzyme M reductase2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 27, p. 14029-14035Article in journal (Refereed)
    Abstract [en]

    Ni-containing methyl-coenzyme M reductase (MCR) is capable of catalyzing methane formation from methyl-coenzyme M (CH3-SCoM) and coenzyme B (CoB-SH), and also its reverse reaction (methane oxidation). Based on extensive experimental and theoretical investigations, it has turned out that a mechanism including an organometallic methyl-Ni(III)F-430 intermediate is inaccessible, while another mechanism involving a methyl radical and a Ni(II)-SCoM species currently appears to be the most acceptable one for MCR. In the present paper, using hybrid density functional theory and an active-site model based on the X-ray crystal structure, two other mechanisms were studied and finally also ruled out. One of them, involving proton binding on the CH3-SCoM substrate, which should facilitate methyl-Ni(III)F-430 formation, is demonstrated to be quite unfavorable since the substrate has a much smaller proton affinity than the F-430 cofactor. Another one (oxidative addition mechanism) is also shown to be unfavorable for the MCR reaction, due to the large endothermicity for the formation of the ternary intermediate with side-on C-S (for CH3-SCoM) or C-H (for methane) coordination to Ni.

  • 22.
    Cheung, Ocean
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Uppsala University, Sweden .
    Wardecki, Dariusz
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Bacsik, Zoltan
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Vasiliev, Petr
    McCusker, Lynne B.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). ETH Zürich, Switzerland.
    Hedin, Niklas
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Highly selective uptake of carbon dioxide on the zeolite vertical bar Na10.2KCs0.8 vertical bar-LTA - a possible sorbent for biogas upgrading2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 24, p. 16080-16083Article in journal (Refereed)
    Abstract [en]

    The vertical bar Na10.2KCs0.8 vertical bar(8)[Al12Si12O48](8)(Fm3c)-LTA zeolite adsorbs CO2-over-CH4 with a high selectivity (over 1500). The uptake of carbon dioxide is also high (3.31 mmol g(-1), 293 K, 101 kPa). This form of zeolite A is a very promising adsorbent for applications such as biogas upgrading, where keeping the adsorption of methane to a minimum is crucial.

  • 23. Chiarinelli, Jacopo
    et al.
    Barreiro-Lage, Darío
    Bolognesi, Paola
    Richter, Robert
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Stockett, Mark H.
    Stockholm University, Faculty of Science, Department of Physics.
    Díaz-Tendero, Sergio
    Avaldi, Lorenzo
    Electron and ion spectroscopy of the cyclo-alanine–alanine dipeptide2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 10, p. 5855-5867Article in journal (Refereed)
    Abstract [en]

    The VUV photoionisation and photofragmentation of cyclo-alanine–alanine (cAA) has been studied in a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron–photoion coincidence (PEPICO) measurements, which enable control of the energy being deposited, combined with quantum chemistry calculations, provide direct insight into the cAA molecular stability after photoionisation. The analysis of the ion-neutral coincidence experiments with the molecular dynamics simulations and the exploration of the potential energy surface allows a complete identification of the fragmentation pathways. It has been found that the fragmentation always starts with the ring opening through the C–C bond cleavage, followed by release of neutral CO or HNCO moieties.

  • 24. Dahle, Pal
    et al.
    Helgaker, Trygve
    Jonsson, Dan
    Stockholm University, Faculty of Science, Department of Physics.
    Taylor, Peter R.
    Accurate quantum-chemical calculations using Gaussian-type geminal and Gaussian-type orbital basis sets: applications to atoms and diatomics2007In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 9, no 24, p. 3112-3126Article in journal (Refereed)
    Abstract [en]

    We have implemented the use of mixed basis sets of Gaussian one- and two-electron (geminal) functions for the calculation of second-order Moller-Plesset (MP2) correlation energies. In this paper, we describe some aspects of this implementation, including different forms chosen for the pair functions. Computational results are presented for some closed-shell atoms and diatomics. Our calculations indicate that the method presented is capable of yielding highly accurate second-order correlation energies with rather modest Gaussian orbital basis sets, providing an alternative route to highly accurate wave functions. For the neon atom, the hydrogen molecule, and the hydrogen fluoride molecule, our calculations yield the most accurate MP2 energies published so far. A critical comparison is made with established MP2-R12 methods, revealing an erratic behaviour of some of these methods, even in large basis sets.

  • 25.
    Danilo, Cecile
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Vallet, Valerie
    Flament, Jean-Pierre
    Wahlgren, Ulf
    Stockholm University, Faculty of Science, Department of Physics.
    Effects of the first hydration sphere and the bulk solvent on the spectra of the f(2) isoelectronic actinide compounds: U4+, NpO2+, and PuO22+2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 5, p. 1116-1130Article in journal (Refereed)
    Abstract [en]

    The electronic spectra of the 5f(2) isoelectronic actinide compounds U4+, NpO2+, and PuO22+ have been investigated theoretically both in gas phase and in solution. In the latter case the solvent was modelled by a saturated first hydration sphere, five water molecules for NpO2+, and PuO22+ and eight for U4+, and a continuum model describing the remaining solvent. The transition energies and oscillator strengths were obtained at the spin-orbit level using the relativistic wave function based multi-configuration methods CASPT2 (complete active space with second-order perturbation theory) and MRCI + DC (Davidson corrected multi-reference configuration interaction), followed by a spin-orbit CI based on a dressed effective spin-orbit Hamiltonian. This study is an attempt to contribute to an enhanced understanding of the electronic structure of tetravalent actinide ions and actinyl(V) and (VI) ions. The spin-orbit MRCI and spin-orbit CASPT2 transitions energies have been compared for the bare ions, leading us to the conclusion that the spin-orbit CASPT2 approach is reasonably accurate and can be used with confidence for the calculation of the hydrated species. The first hydration sphere and the bulk solvent lift degeneracies, but the effect on the transition energies is fairly small for the two actinyl ions, while it is larger, up to several thousands of wave numbers for U4+. The calculations allowed us to make assignments of the experimentally observed absorption spectra for all species. The computed transition energies and intensities compared favourably with experiment.

  • 26. Domaracka, Alicja
    et al.
    Delaunay, Rudy
    Mika, Arkadiusz
    Gatchell, Michael
    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.
    Rousseau, Patrick
    Huber, Bernd A.
    Ion collision-induced chemistry in pure and mixed loosely bound clusters of coronene and C-60 molecules2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 22, p. 15052-15060Article in journal (Refereed)
    Abstract [en]

    Ionization, fragmentation and molecular growth have been studied in collisions of 22.5 keV He2+-or 3 keV Ar+-projectiles with pure loosely bound clusters of coronene (C24H12) molecules or with loosely bound mixed C-60-C24H12 clusters by using mass spectrometry. The heavier and slower Ar+ projectiles induce prompt knockout-fragmentation - C- and/or H-losses - from individual molecules and highly efficient secondary molecular growth reactions before the clusters disintegrate on picosecond timescales. The lighter and faster He2+ projectiles have a higher charge and the main reactions are then ionization by ions that are not penetrating the clusters. This leads mostly to cluster fragmentation without molecular growth. However, here penetrating collisions may also lead to molecular growth but to a much smaller extent than with 3 keV Ar+. Here we present fragmentation and molecular growth mass distributions with 1 mass unit resolution, which reveals that the same numbers of C- and H-atoms often participate in the formation and breaking of covalent bonds inside the clusters. We find that masses close to those with integer numbers of intact coronene molecules, or with integer numbers of both intact coronene and C-60 molecules, are formed where often one or several H-atoms are missing or have been added on. We also find that super-hydrogenated coronene is formed inside the clusters.

  • 27. Eland, J. H. D.
    et al.
    Fink, R. F.
    Linusson, Per
    Stockholm University, Faculty of Science, Department of Physics.
    Hedin, L.
    Stockholm University, Faculty of Science, Department of Physics.
    Plogmaker, S.
    Stockholm University, Faculty of Science, Department of Physics.
    Feifel, Raimund
    Stockholm University, Faculty of Science, Department of Physics.
    Single and multiple photoionisation of H(2)S by 40-250 eV photons2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 41, p. 18428-18435Article in journal (Refereed)
    Abstract [en]

    Multi-electron coincidence measurements on photoionisation of H(2)S have been carried out at photon energies from 40 to 250 eV. They quantify molecular field effects on the Auger process in detail and are in good agreement with the existing theory. Spectra of core-valence double ionisation of H(2)S are presented and partially analysed. Auger decays from the core-valence states produce triply charged product spectra with unexplained and surprising intensity distributions. Triple ionisation by the double Auger process from 2p hole states shows little effect of the molecular field splitting, but includes a substantial contribution from cascade processes, some involving dissociation in intermediate states. The onset of triple ionisation at the molecular geometry is determined as 61 +/- 0.5 eV.

  • 28. Elm, Jonas
    et al.
    Myllys, Nanna
    Olenius, Tinja
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Halonen, Roope
    Kurtén, Theo
    Vehkamäki, Hanna
    Formation of atmospheric molecular clusters consisting of sulfuric acid and C8H12O6 tricarboxylic acid2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 6, p. 4877-4886Article in journal (Refereed)
    Abstract [en]

    Using computational methods, we investigate the formation of atmospheric clusters consisting of sulfuric acid (SA) and 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA), identified from a-pinene oxidation. The molecular structure of the clusters is obtained using three different DFT functionals (PW91, M06-2X and oB97X-D) with the 6-31++ G(d, p) basis set and the binding energies are calculated using a high level DLPNO-CCSD(T)/ Def2-QZVPP method. The stability of the clusters is evaluated based on the calculated formation free energies. The interaction between MBTCA and sulfuric acid is found to be thermodynamically favourable and clusters consisting of 2-3 MBTCA and 2-3 SA molecules are found to be particularly stable. There is a large stabilization of the cluster when the amount of sulfuric acid-carboxylic acid hydrogen bonded interactions is maximized. The reaction free energies for forming the (MBTCA) 2-3(SA) 2-3 clusters are found to be similar in magnitude to those of the formation of the sulfuric acid-dimethylamine cluster. Using cluster kinetics calculations we identify that the growth of the clusters is essentially limited by a weak formation of the largest clusters studied, implying that other stabilizing vapours are required for stable cluster formation and growth.

  • 29. Eriksson, Susanna K.
    et al.
    Josefsson, Ida
    Stockholm University, Faculty of Science, Department of Physics.
    Ellis, Hanna
    Amat, Anna
    Pastore, Mariachiara
    Oscarsson, Johan
    Lindblad, Rebecka
    Eriksson, Anna I. K.
    Johansson, Erik M. J.
    Boschloo, Gerrit
    Hagfeldt, Anders
    Fantacci, Simona
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Rensmo, Håkan
    Geometrical and energetical structural changes in organic dyes for dye-sensitized solar cells probed using photoelectron spectroscopy and DFT2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 1, p. 252-260Article in journal (Refereed)
    Abstract [en]

    The effects of alkoxy chain length in triarylamine based donor acceptor organic dyes are investigated with respect to the electronic and molecular surface structures on the performance of solar cells and the electron lifetime. The dyes were investigated when adsorbed on TiO2 in a configuration that can be used for dye sensitized solar cells (DSCs). Specifically, the two dyes D35 and D45 were compared using photoelectron spectroscopy (PES) and density functional theory (DFT) calculations. The differences in solar cell characteristics when longer alkoxy chains are introduced in the dye donor unit are attributed to geometrical changes in dye packing while only minor differences were observed in the electronic structure. A higher dye load was observed for D45 on TiO2. However, D35 based solar cells result in higher photocurrent although the dye load is lower. This is explained by different geometrical structures of the dyes on the surface.

  • 30.
    Ermilova, Inna
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Stenberg, Samuel
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Quantum chemical and molecular dynamics modelling of hydroxylated polybrominated diphenyl ethers2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 41, p. 28263-28274Article in journal (Refereed)
    Abstract [en]

    A series of 19 hydroxylated polybrominated diphenyl ethers (OH-PBDEs) have been studied using density functional theory (DFT) and molecular dynamics simulations with the purpose of investigating eventual correlations between their physicochemical properties and toxic action. Dissociation constants (pK(a)), solvation free energies and octanol-water partition coefficients (logP) have been computed. Additionally, metadynamics simulations of OH-PBDEs passing through a lipid bilayer have been carried out for four OH-PBDE species. No correlations between computed pKa values and toxicity data have been found. Medium correlations were found between partition coefficients and the ability of OH-PBDEs to alter membrane potential in cell cultures, which is attributed to higher uptake of molecules with larger log P parameters. It was also demonstrated that in lipid bilayers, OH-PBDE molecules differ in their orientational distributions and can adopt different conformations which can affect the uptake of these molecules and influence the pathways of their toxic action.

  • 31.
    Ertan, Emelie
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Savchenko, Viktoriia
    Ignatova, Nina
    da Cruz, Vinicius Vaz
    Couto, Rafael C.
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    Foelisch, Alexander
    Gel'mukhanov, Faris
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Kimberg, Victor
    Ultrafast dissociation features in RIXS spectra of the water molecule2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 21, p. 14384-14397Article in journal (Refereed)
    Abstract [en]

    In this combined theoretical and experimental study we report on an analysis of the resonant inelastic X-ray scattering (RIXS) spectra of gas phase water via the lowest dissociative core-excited state |1s-1O4a11. We focus on the spectral feature near the dissociation limit of the electronic ground state. We show that the narrow atomic-like peak consists of the overlapping contribution from the RIXS channels back to the ground state and to the first valence excited state |1b-114a11 of the molecule. The spectral feature has signatures of ultrafast dissociation (UFD) in the core-excited state, as we show by means of ab initio calculations and time-dependent nuclear wave packet simulations. We show that the electronically elastic RIXS channel gives substantial contribution to the atomic-like resonance due to the strong bond length dependence of the magnitude and orientation of the transition dipole moment. By studying the RIXS for an excitation energy scan over the core-excited state resonance, we can understand and single out the molecular and atomic-like contributions in the decay to the lowest valence-excited state. Our study is complemented by a theoretical discussion of RIXS in the case of isotopically substituted water (HDO and D2O) where the nuclear dynamics is significantly affected by the heavier fragments' mass.

  • 32. Fransson, Thomas
    et al.
    Zhovtobriukh, Iurii
    Stockholm University, Faculty of Science, Department of Physics.
    Coriani, Sonia
    Wikfeldt, Kjartan T.
    Stockholm University, Faculty of Science, Department of Physics. University of Iceland, Iceland .
    Norman, Patrick
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Requirements of first-principles calculations of X-ray absorption spectra of liquid water2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 1, p. 566-583Article in journal (Refereed)
    Abstract [en]

    A computational benchmark study on X-ray absorption spectra of water has been performed by means of transition-potential density functional theory (TP-DFT), damped time-dependent density functional theory (TDDFT), and damped coupled cluster (CC) linear response theory. For liquid water, using TDDFT with a tailored CAM-B3LYP functional and a polarizable embedding, we find that an embedding with over 2000 water molecules is required to fully converge spectral features for individual molecules, but a substantially smaller embedding can be used within averaging schemes. TP-DFT and TDDFT calculations on 100 MD structures demonstrate that TDDFT produces a spectrum with spectral features in good agreement with experiment, while it is more difficult to fully resolve the spectral features in the TP-DFT spectrum. Similar trends were also observed for calculations of bulk ice. In order to further establish the performance of these methods, small water clusters have been considered also at the CC2 and CCSD levels of theory. Issues regarding the basis set requirements for spectrum simulations of liquid water and the determination of gas-phase ionization potentials are also discussed.

  • 33. Friebel, Daniel
    et al.
    Miller, Daniel J.
    O'Grady, Christopher P.
    Anniyev, Toyli
    Bargar, John
    Bergmann, Uwe
    Ogasawara, Hirohito
    Wikfeldt, Kjartan Thor
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    In situ x-ray probing reveals the importance of surface platinum oxide formation in fuel cell catalysis2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 1, p. 262-266Article in journal (Refereed)
    Abstract [en]

    In situ X-ray absorption spectroscopy (XAS) at the Pt L3 edge is a useful probe for Pt–O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard X-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF code and complementary extended X-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

  • 34.
    Gatchell, Michael
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Delaunay, Rudy
    D'Angelo, Giovanna
    Stockholm University, Faculty of Science, Department of Physics. Universidade do Porto, Portugal; Universidad Autónoma de Madrid, Spain.
    Mika, Arkadiusz
    Kulyk, Kostiantyn
    Stockholm University, Faculty of Science, Department of Physics.
    Domaracka, Alicja
    Rousseau, Patrick
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Huber, Bernd A.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Ion-induced molecular growth in clusters of small hydrocarbon chains2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 30, p. 19665-19672Article in journal (Refereed)
    Abstract [en]

    We report on studies of collisions between 3 keV Ar+ projectile ions and neutral targets of isolated 1,3-butadiene (C4H6) molecules and cold, loosely bound clusters of these molecules. We identify molecular growth processes within the molecular clusters that appears to be driven by knockout processes and that could result in the formation of (aromatic) ring structures. These types of reactions are not unique to specific projectile ions and target molecules, but will occur whenever atoms or ions with suitable masses and kinetic energies collide with aggregates of matter, such as carbonaceous grains in the interstellar medium or aerosol nanoparticles in the atmosphere.

  • 35.
    Gatchell, Michael
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Universität Innsbruck, Austria.
    Goulart, Marcelo
    Kranabetter, Lorenz
    Kuhn, Martin
    Martini, Paul
    Rasul, Bilal
    Scheier, Paul
    Complexes of gold and imidazole formed in helium nanodroplets2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 11, p. 7739-7745Article in journal (Refereed)
    Abstract [en]

    We have studied complexes of gold atoms and imidazole (C3N2H4, abbreviated Im) produced in helium nanodroplets. Following the ionization of the doped droplets we detect a broad range of different Au(m)Im(n)(+) complexes, however we find that for specific values of m certain n are magic and thus particularly abundant. Our density functional theory calculations indicate that these abundant clusters sizes are partially the result of particularly stable complexes, e.g. AuIm(2)(+), and partially due to a transition in fragmentation patterns from the loss of neutral imidazole molecules for large systems to the loss of neutral gold atoms for smaller systems.

  • 36.
    Giacomozzi, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    D'Angelo, Giovanna
    Stockholm University, Faculty of Science, Department of Physics. Universidade do Porto, Portugal; Universidad Autónoma de Madrid, Spain.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Knockout driven fragmentation of porphyrins2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 30, p. 19750-19755Article in journal (Refereed)
    Abstract [en]

    We have studied collisions between tetraphenylporphyrin cations and He or Ne at center-of-mass energies in the range 50-110 eV. The experimental results were interpreted in view of density functional theory calculations of dissociation energies and classical molecular dynamics simulations of how the molecules respond to the He/Ne impact. We demonstrate that prompt atom knockout strongly contributes to the total destruction cross sections. Such impulse driven processes typically yield highly reactive fragments and are expected to be important for collisions with any molecular system in this collision energy range, but have earlier been very difficult to isolate for biomolecules.

  • 37.
    Golets, Mikhail
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Shimpi, M. R.
    Wang, Y. -L.
    Antzutkin, O. N.
    Glavatskih, S.
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stellenbosch University, South Africa.
    Understanding the thermal decomposition mechanism of a halogen-free chelated orthoborate-based ionic liquid: a combined computational and experimental study2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 32, p. 22458-22466Article in journal (Refereed)
    Abstract [en]

    In the last few decades, ionic liquids (ILs) have gained significant attention as lubricants and lubricant additives due to their polar nature, low vapour pressure and tunable physicochemical properties. In this work, quantum chemistry calculations and atomistic Molecular Dynamics (MD) simulations were employed to predict thermal degradation mechanisms of a potential lubricating agent - the tributyloctylphosphonium bis(oxalato) borate ([P-4,P-4,P-4,P-8][BOB]) IL. It was found that the onset of decomposition of the studied IL coincides with a cleavage of the B-O bonds in the [BOB](-) anion. Consequently, a series of chemical reactions of the [P-4,P-4,P-4,P-8](+) cation with the [BOB](-) anion was triggered yielding alkylboranes, alkenes, trialkylphosphines, CO and CO2. Another ionic system, consisting of [P-4,P-4,P-4,P-8][Cl], was also tested for a comparison. Thermogravimetric measurements have shown a higher thermal stability of [P-4,P-4,P-4,P-8][BOB] compared to that of [P-4,P-4,P-4,P-8][Cl] at least at the initial stage of decomposition, in accord with the presented calculations. Quantum chemical frequency calculations also agreed with the experimental Fourier Transform Infrared (FTIR) spectroscopy results.

  • 38. Goulart, Marcelo
    et al.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics. Universität Innsbruck, Austria .
    Kranabetter, Lorenz
    Kuhn, Martin
    Martini, Paul
    Gitzl, Norbert
    Rainer, Manuel
    Postler, Johannes
    Scheier, Paul
    Ellis, Andrew M.
    The adsorption of helium atoms on small cationic gold clusters2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 14, p. 9554-9560Article in journal (Refereed)
    Abstract [en]

    Adducts formed between small gold cluster cations and helium atoms are reported for the first time. These binary ions, Aun+Hem, were produced by electron ionization of helium nanodroplets doped with neutral gold clusters and were detected using mass spectrometry. For a given value of n, the distribution of ions as a function of the number of added helium atoms, m, has been recorded. Peaks with anomalously high intensities, corresponding to so-called magic number ions, are identified and interpreted in terms of the geometric structures of the underlying Au-n(+) ions. These features can be accounted for by planar structures for Au-n(+) ions with n <= 7, with the addition of helium having no significant effect on the structures of the underlying gold cluster ions. According to ion mobility studies and some theoretical predictions, a 3-D structure is expected for Au-8(+). However, the findings for Au-8(+) in this work are more consistent with a planar structure.

  • 39. Goulart, Marcelo
    et al.
    Kuhn, Martin
    Rasul, Bilal
    Postler, Johannes
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics. Universität Innsbruck, Austria.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Scheier, Paul
    Echt, Olof
    The structure of coronene cluster ions inferred from H-2 uptake in the gas phase2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 41, p. 27968-27973Article in journal (Refereed)
    Abstract [en]

    Mass spectra of helium nanodroplets doped with H-2 and coronene feature anomalies in the ion abundance that reveal anomalies in the energetics of adsorption sites. The coronene monomer ion strongly adsorbs up to n = 38 H-2 molecules indicating a commensurate solvation shell that preserves the D-6h symmetry of the substrate. No such feature is seen in the abundance of the coronene dimer through tetramer complexed with H-2; this observation rules out a vertical columnar structure. Instead we see evidence for a columnar structure in which adjacent coronenes are displaced in parallel, forming terraces that offer additional strong adsorption sites. The experimental value for the number of adsorption sites per terrace, approximately six, barely depends on the number of coronene molecules. The displacement estimated from this number exceeds the value reported in several theoretical studies of the bare, neutral coronene dimer.

  • 40.
    Grote, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Dvinskikh, Sergey V.
    Rinwa, Vibhu
    Holmbäck, Jan
    Phase equilibrium, dynamics and rheology of phospholipid–ethanol mixtures: a combined molecular dynamics, NMR and viscometry study2023In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 25, no 23, p. 15905-15915Article in journal (Refereed)
    Abstract [en]

    Binary mixtures of ethanol and phospholipids DOPC and DOPE have been investigated in a composition range relevant for topical drug delivery applications. This was done using a combined computer simulation and experimental approach where molecular dynamics simulations of ethanol–lipid mixtures with different compositions were performed. Several key properties including diffusion coefficients, longitudinal relaxation times, and shear viscosity were computed. In addition, diffusion coefficients, viscosities and NMR longitudinal relaxation times were measured experimentally for comparison and in order to validate the results from simulation. Diffusion coefficients and relaxation times obtained from simulations are in good agreement with results from NMR and computed viscosities are in reasonable agreement with viscometry experiments indicating that the simulations provide a realistic description of the ethanol–phospholipid mixtures. Structural changes in the simulated systems were investigated using an analysis based on radial distribution functions. This showed that the structure of ethanol–DOPC mixtures remains essentially unchanged in the investigated concentration range while ethanol–DOPE mixtures undergo structural rearrangements with the tendency for forming small aggregates on the 100 ns time scale consisting of less than 10 lipids. Although our simulations and experiments indicate that no larger aggregates form, they also show that DOPE has stronger aggregation tendency than DOPC. This highlights the importance of the character of the lipid headgroup for lipid aggregation in ethanol and gives new insights into phase equilibrium, dynamics and rheology that could be valuable for the development of advanced topical drug delivery formulations.

  • 41.
    Hahlin, Maria
    et al.
    Uppsala universitet.
    Johansson, Erik M J
    Uppsala universitet.
    Plogmaker, Stefan
    Uppsala universitet.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Hagberg, Daniel P
    Sun, Licheng
    KTH, Organisk kemi.
    Siegbahn, Hans
    Uppsala universitet.
    Rensmo, Håkan
    Uppsala universitet.
    Electronic and molecular structures of organic dye/TiO(2) interfaces for solar cell applications: a core level photoelectron spectroscopy study.2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 7, p. 1507-17Article in journal (Refereed)
    Abstract [en]

    The electronic and molecular properties of three organic dye molecules with the general structure donor-linker-anchor have been investigated using core level photoelectron spectroscopy (PES). The molecules contain a diphenylaniline donor unit, a thiophene linker unit, and cyanoacrylic acid or rhodanine-3-acetic acid anchor units. They have been investigated both in the form of a multilayer and adsorbed onto nanoporous TiO(2) and the experimental results were also compared with DFT calculations. The changes at the dye-sensitized TiO(2) surface due to the modification of either the donor unit or the anchor unit was investigated and the results showed important differences in coverage as well as in electronic and molecular surface properties. By measuring the core level binding energies, the sub-molecular properties were characterized and the result showed that the adsorption to the TiO(2) influences the energy levels of the sub-molecular units differently.

  • 42. Hahlin, Maria
    et al.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Magnuson, Martin
    Johansson, Erik M. J.
    Plogmaker, Stefan
    Hagberg, Daniel P.
    Sun, Licheng
    Siegbahn, Hans
    Rensmo, Håkan
    Mapping the frontier electronic structures of triphenylamine based organic dyes at TiO2 Interafaces2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, p. 3534--3546Article in journal (Refereed)
    Abstract [en]

    The frontier electronic structures of a series of organic dye molecules containing a triphenylamine moiety, a thiophene moiety and a cyanoacrylic acid moiety have been investigated by photoelectron spectroscopy (PES), X-ray absorption spectroscopy (XAS), X-ray emission spectroscopy (XES) and resonant photoelectron spectroscopy (RPES). The experimental results were compared to electronic structure calculations on the molecules, which are used to confirm and enrich the assignment of the spectra. The approach allows us to experimentally measure and interpret the basic valence energy level structure in the dye, including the highest occupied energy level and how it depends on the interaction between the different units. Based on N 1s X-ray absorption and emission spectra we also obtain insight into the structure of the excited states, the molecular orbital composition and dynamics. Together the results provide an experimentally determined energy level map useful in the design of these types of materials. Included are also results indicating femtosecond charge redistribution at the dye/TiO2 interface.

  • 43.
    Halldin Stenlid, Joakim
    et al.
    Stockholm University, Faculty of Science, Department of Physics. KTH Royal Institute of Technology, Sweden.
    Johansson, Adam Johannes
    Brinck, Tore
    The local electron attachment energy and the electrostatic potential as descriptors of surface-adsorbate interactions2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 31, p. 17001-17009Article in journal (Refereed)
    Abstract [en]

    Two local reactivity descriptors computed by Kohn-Sham density functional theory (DFT) are used to predict and rationalize interactions of nucleophilic molecules (exemplified by CO and H2O) with transition metal (TM) and oxide surfaces. The descriptors are the electrostatic potential, V-S(r), and the local electron attachment energy, E-S(r), evaluated on surfaces defined by the 0.001 e Bohr(-3) isodensity contour. These descriptors have previously shown excellent abilities to predict regioselectivity and rank molecular as well as nanoparticle reactivities and interaction affinities. In this study, we generalize the descriptors to fit into the framework of periodic DFT computations. We also demonstrate their capabilities to predict local surface propensity for interaction with Lewis bases. It is shown that E-S(r) and V-S(r) can rationalize the interaction behavior of TM oxides and of fcc TM surfaces, including low-index, stepped and kinked surfaces spanning a wide range of interaction sites with varied coordination environments. Broad future applicability in surface science is envisaged for the descriptors, including heterogeneous catalysis and electrochemistry.

  • 44. Hansen, Martin Hangaard
    et al.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Rossmeisl, Jan
    Modelling pH and potential in dynamic structures of the water/Pt(111) interface on the atomic scale2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 34, p. 23505-23514Article in journal (Refereed)
    Abstract [en]

    We present atomic-scale structures of the Pt(111)/water interface, by calculating distributions of atomic distances as functions of pH. The structure of the Pt(111)/water interface is a particularly interesting model system in electro-catalysis for proton exchange reactions, especially the oxygen reduction reaction in polymer electrolyte membrane fuel cells. Further insight into such reactions requires accurate simulations of the electrolyte structure in the interface. The study displays many interesting details in the behaviour of the electrolyte structure, e.g. that the electrolyte structure average responds to the presence of protons by a H-down water orientation and that hexagonal adsorbed water layers are present only when they are anchored at the surface by HO*. New adsorbate configurations were also found at 5/12 ML coverage of HO*, suggesting an explanation for reported cyclic voltammetry experiments. The present study is a step towards a more complete understanding of the structure of the electrochemical interface on the atomic scale.

  • 45.
    Holm, Anne I. S.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Nielsen, Lisbeth M.
    Kohler, Bern
    Hoffman, Soren Vronning
    Nielsen, Steen Brondsted
    Electronic coupling between cytosine bases in DNA single strands and i-motifs revealed from synchrotron radiation circular dichroism experiments2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 14, p. 3426-3430Article in journal (Refereed)
    Abstract [en]

    In this work we have recorded synchrotron radiation circular dichroism (SRCD) spectra from 180 nm to 360 nm of cytosine strands [(dC)(n), n = 1, 2,..., 10] in aqueous solution at different pH values to reveal electronic coupling between bases in different ionisation states. The geometry of the strands is determined by the pH value and the strand length and the local organisation of the cytosines will determine the base-to-base interaction that impacts on the CD signal. At low pH where all bases are protonated, there is no signature of electronic coupling between the bases, and the SRCD spectrum is simply n times that of the n = 1 spectrum. At higher pH where all bases are neutral, the spectra for n > 1 differ from the monomer spectrum, which implies electronic coupling between bases. The correlation between the CD signal and n is linear, and the spatial extent of the excited state wavefunction is therefore over just two stacked bases both in the UV and VUV. At intermediate pH, the low-n spectra are different from the high-n spectra, and a transition is seen to occur at n = 6-8. We ascribe this behavior to the formation of i-motif structures between four (dC)(n) strands for high n.

  • 46.
    Holm, Anne Ivalu Sander
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Nielsen, Lisbeth Munksgaard
    Hoffmann, Søren Vrønning
    Nielsen, Steen Brøndsted
    Vacuum-ultraviolet circular dichroism spectroscopy of DNA: a valuable tool to elucidate topology and electronic coupling in DNA2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 33, p. 9581-9596Article in journal (Refereed)
    Abstract [en]

    Circular dichroism (CD) is a powerful technique to obtain information on electronic transitions and has been used extensively for studies on DNA. Most experiments are done in the UV region but new information is often revealed from extending the wavelength region down into the vacuum ultraviolet (VUV) region. Such experiments are most easily carried out with synchrotron radiation (SR) light sources that provide large photon fluxes. Here we provide a summary of the SRCD data taken on different DNA strands with emphasis on results from our own laboratory within the last five years.(1-3) Signal intensities in the VUV are often significantly larger than those in the UV, and the electronic coupling between bases may increase with excitation energy. CD spectroscopy is particularly useful for investigating the extent of electronic coupling within a strand, i.e., the degree of delocalisation of the excited-state electronic wavefunction. The spatial extent of the wavefunction may be limited to just one base or it extends over two or more bases in a stack or between bases on different strands.(4,5) The actual character of the electronically excited state is linked to base composition and sequence as well as DNA folding motif (A-, B-, Z-DNA, triplexes, quadruplexes, etc.). The latter depends on experimental conditions such as solution acidity, temperature, ionic strength, and solvent.

  • 47. Huang, Congcong
    et al.
    Wikfeldt, Thor Kjartan
    Stockholm University, Faculty of Science, Department of Physics.
    Nordlund, D.
    Bergmann, U.
    McQueen, T.
    Sellberg, Jonas
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars G.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Wide-angle X-ray diffraction and molecular dynamics study of medium-range order in ambient and hot water2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 44, p. 19997-20007Article in journal (Refereed)
    Abstract [en]

    We have developed wide-angle X-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 degrees C) under normal pressure. Using a spherically curved Ge crystal an energy resolution better than 15 eV has been achieved which eliminates influence from Compton scattering. The high quality of the data allows for a reliable Fourier transform of the experimental data resolving shell structure out to similar to 12 angstrom, i.e. 5 hydration shells. Large-scale molecular dynamics (MD) simulations using the TIP4P/2005 force-field reproduce excellently the experimental shell-structure in the range 4-12 angstrom although less agreement is seen for the first peak in the intermolecular pair-correlation function (PCF). The Shiratani-Sasai Local Structure Index [J. Chem. Phys. 104, 7671 (1996)] identifies a tetrahedral minority giving the intermediate-range oscillations in the O-O PCF and a disordered majority providing a more featureless background in this range. The current study supports the proposal that the structure of liquid water, even at high temperatures, can be described in terms of a two-state fluctuation model involving local structures related to the high-density and low-density forms of liquid water postulated in the liquid-liquid phase transition hypothesis.

  • 48. Huse, Nils
    et al.
    Wen, Haidan
    Nordlund, Dennis
    Szilagyi, Erzsi
    Daranciang, Dan
    Miller, Timothy A.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Schoenlein, Robert W.
    Lindenberg, Aaron M.
    Probing the hydrogen-bond network of water via time-resolved soft X-ray spectroscopy2009In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, no 20, p. 3951-3957Article in journal (Refereed)
    Abstract [en]

    We report time-resolved studies of hydrogen bonding in liquid H2O, in response to direct excitation of the O-H stretch mode at 3 mm, probed via soft X-ray absorption spectroscopy at the oxygen K-edge. This approach employs a newly developed nanofluidic cell for transient soft X-ray spectroscopy in the liquid phase. Distinct changes in the near-edge spectral region (XANES) are observed, and are indicative of a transient temperature rise of 10 K following transient laser excitation and rapid thermalization of vibrational energy. The rapid heating occurs at constant volume and the associated increase in internal pressure, estimated to be 8 MPa, is manifested by distinct spectral changes that differ from those induced by temperature alone. We conclude that the near-edge spectral shape of the oxygen K-edge is a sensitive probe of internal pressure, opening new possibilities for testing the validity of water models and providing new insight into the nature of hydrogen bonding in water.

  • 49. Jain, Kalpna
    et al.
    Kaniyankandy, Sreejith
    Kishor, Shyam
    Josefsson, Ida
    Stockholm University, Faculty of Science, Department of Physics.
    Ghosh, Hirendra N.
    Singh, Khundrakpam S.
    Mookerjee, Sumit
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Ramaniah, Lavanya M.
    Density functional investigation and some optical experiments on dye-sensitized quantum dots2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 43, p. 28683-28696Article in journal (Refereed)
    Abstract [en]

    Dye-sensitized quantum dots (QDs) are promising candidates for dye-sensitized solar cells (DSSCs). Here, we report steady state (absorption and photoluminescence) optical measurements on several sizes of CdS QDs ligated with Coumarin 343 dye (C-343) and two different solvents, viz., chloroform and toluene. We further report detailed first principles density functional theory and time-dependent density functional theory studies of the geometric, electronic and optical (absorption and emission) properties of three different sized capped QDs, ligated with C-343 dye. The absorption spectrum shows a QD-size-independent peak, and another peak which shifts to blue with decrease in QD size. The first peak is found to arise from the dye molecule and the second one from the QD. Charge transfer using natural transition orbitals (NTOs) is found to occur from dye-to-QDs and is solvent-dependent. In the emission spectra, the luminescence intensity of the dye is quenched by the addition of the QD indicating a strong interaction between the QD and the dye.

  • 50. Jain, Kalpna
    et al.
    Kishor, Shyam
    Singh, Khundrakpam S.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Ramaniah, Lavanya M.
    Quantum dots as an electron or hole acceptor: on some factors affecting charge transfer in dye-quantum dot composites2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 42, p. 27036-27048Article in journal (Refereed)
    Abstract [en]

    We report a density functional theory (DFT)/time dependent DFT (TDDFT) computational investigation on some factors affecting the nature of charge transfer in CdS quantum dots (QDs) of two different sizes attached to one or two units of dyes among three species viz., coumarine (C343), fluorescein (FLU) and NKX-2388 (NKX). The direction and nature of charge transfers have been ascertained from natural transition orbital analysis. Factors affecting the charge transfer mechanism include the interaction of dyes with QDs, the interaction of a dye with another dye and the effect of solvation. The strength of interaction of the dye and QD depends on the orientation of the dye unit(s) and the type of anchoring group of the dyes and even the direction of charge transfer reverses for different orientation of the dye with respect to the QD in some systems. In addition, hybridized energy levels of the dye-QD composites are formed which leads to direct charge transfer. We observe both direct and indirect charge transfers for different excited states, which is indeed an interesting feature. Interestingly, when two dye molecules are attached to a QD, the direct charge transfer exists between dyes of the same species only. The energy levels, as well as corresponding absorption peaks, exhibit pronounced energy shifts in implicit solvation models.

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