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  • 1. Ai, Yue-jie
    et al.
    Tian, Guangjun
    Liao, Rong-zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Zhang, Qiong
    Fang, Wei-hai
    Luo, Yi
    Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States2011In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, no 16, p. 2899-2902Article in journal (Refereed)
  • 2.
    Brea, Oriana
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Luna, Alberto
    Diaz, Cristina
    Corral, Ines
    Molecular Modelling of the H-2-Adsorptive Properties of Tetrazolate-Based Metal-Organic Frameworks: From the Cluster Approach to Periodic Simulations2018In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, no 11, p. 1349-1357Article in journal (Refereed)
    Abstract [en]

    Hydrogen has been proposed as a long-term non-fossil fuel to be used in a future ideal carbon-neutral energetic economy. However, its low volumetric energy density hinders its storage and transportation. Metal-organic frameworks (MOFs) represent very promising materials for this purpose due to their very extended surface areas. Azolates, in particular tetrazolates, are - together with carboxylate functionalities - very common organic linkers connecting metallic secondary building units in MOFs. This study addresses, from a theoretical perspective, the H-2 adsorptive properties of tetrazolate linkers at the molecular level, following a size-progressive approach. Specifically, we have investigated how the physisorption energies and geometries are affected when changing the environment of the linker by considering the azolates in the gas phase, immersed in a finite cluster, or being part of an infinite extended crystal material. Furthermore, we also study the H-2 adsorptive capacity of these linkers within the cluster model.

  • 3. Chen, Shi-Lu
    et al.
    Liao, Rong-Zhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Phosphate Monoester Hydrolysis by Trinuclear Alkaline Phosphatase; DFT Study of Transition States and Reaction Mechanism2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 11, p. 2321-2330Article in journal (Refereed)
    Abstract [en]

    Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP-catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p-nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a ping-pong mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2-bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.

  • 4. Delesma, Francisco A.
    et al.
    Van den Bossche, Maxime
    Grönbeck, Henrik
    Calaminici, Patrizia
    Köster, Andreas M.
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    A Chemical View on X-ray Photoelectron Spectroscopy: the ESCA Molecule and Surface-to-Bulk XPS Shifts2018In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, no 2, p. 169-174Article in journal (Refereed)
    Abstract [en]

    In this paper we remind the reader of a simple, intuitive picture of chemical shifts in X-ray photoelectron spectroscopy (XPS) as the difference in chemical bonding between the probed atom and its neighbor to the right in the periodic table, the so called Z + 1 approximation. We use the classical ESCA molecule, ethyl trifluoroacetate, and 4d-transition metals to explicitly demonstrate agreement between core-level shifts computed as differences between final core-hole states and the approach where each core-ionized atom is replaced by a Z + 1 atom. In this final state, or total energy picture, the XPS shift arises due to the more or less unfavorable chemical bonding of the effective nitrogen in the carbon geometry for the ESCA molecule. Surface core level shifts in metals are determined by whether the Z + 1 atom as an alloy segregates to the surface or is more soluble in the bulk. As further illustration of this more chemical picture, we compare the geometry of C 1s and O 1s core-ionized CO with that of, respectively, NO+ and CF+. The scope is not to propose a new method to compute XPS shifts but rather to stress the validity of this simple interpretation.

  • 5. Kirketerp, Maj-Britt Suhr
    et al.
    Petersen, Michael Axman
    Wanko, Marius
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Rubio, Angel
    Nielsen, Mogens Brondsted
    Nielsen, Steen Brondsted
    Double-Bond versus Triple-Bond Bridges: Does it Matter for the Charge-Transfer Absorption by Donor-Acceptor Chromophores?2010In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 11, no 12, p. 2495-2498Article in journal (Refereed)
  • 6.
    Kulyk, Kostiantyn
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Palianytsia, Borys
    Alexander, John D.
    Stockholm University, Faculty of Science, Department of Physics.
    Azizova, Liana
    Borysenko, Mykola
    Kartel, Mykola
    Larsson, Mats
    Stockholm University, Faculty of Science, Department of Physics.
    Kulik, Tetiana
    Kinetics of Valeric Acid Ketonization and Ketenization in Catalytic Pyrolysis on Nanosized SiO2, gamma-Al2O3, CeO2/SiO2, Al2O3/SiO2 and TiO2/SiO22017In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 18, no 14, p. 1943-1955Article in journal (Refereed)
    Abstract [en]

    Valeric acid is an important renewable platform chemical that can be produced efficiently from lignocellulosic biomass. Upgrading of valeric acid by catalytic pyrolysis has the potential to produce value added biofuels and chemicals on an industrial scale. Understanding the different mechanisms involved in the thermal transformations of valeric acid on the surface of nanometer-sized oxides is important for the development of efficient heterogeneously catalyzed pyrolytic conversion techniques. In this work, the thermal decomposition of valeric acid on the surface of nanoscale SiO2, gamma-Al2O3, CeO2/SiO2, Al2O3/SiO2 and TiO2/SiO2 has been investigated by temperature-programmed desorption mass spectrometry (TPD MS). Fourier transform infrared spectroscopy (FTIR) has also been used to investigate the structure of valeric acid complexes on the oxide surfaces. Two main products of pyrolytic conversion were observed to be formed depending on the nano-catalyst used-dibutylketone and propylketene. Mechanisms of ketene and ketone formation from chemisorbed fragments of valeric acid are proposed and the kinetic parameters of the corresponding reactions were calculated. It was found that the activation energy of ketenization decreases in the order SiO2 > gamma-Al2O3 > TiO2/SiO2 > Al2O3/SiO2, and the activation energy of ketonization decreases in the order gamma-Al2O3 > CeO2/SiO2. Nanooxide CeO2/SiO2 was found to selectively catalyze the ketonization reaction.

  • 7. Mensch, Carl
    et al.
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Johannessen, Christian
    Studying the Glycan Moiety of RNase B by Means of Raman and Raman Optical Activity2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 11, p. 2252-2254Article in journal (Refereed)
    Abstract [en]

    Raman and Raman optical activity (ROA) spectroscopy are used to study the solution-phase structure of the glycan moiety of the protein ribonuclease B (RNase B). Spectral data of the intact glycan moiety of RNase B is obtained by subtracting high-quality spectral data of RNase A, the non-glycosylated form of the RNase, from the spectra of the glycoprotein. The remaining difference spectra are compared to spectra generated from Raman and ROA data of the constituent disaccharides of the RNase glycan, achieving convincing spectral overlap. The results show that ROA spectroscopy is able to extract detailed spectral data of the glycan moieties of proteins, provided that the non-glycosylated isoform is available. Furthermore, good comparison between the full glycan spectrum and the regenerated spectra based on the disaccharide data lends great promise to ROA as a tool for the solution-phase structural analysis of this structurally elusive class of biomolecules.

  • 8.
    Nyhlén, Jonas
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Boschloo, Gerrit
    Hagfeldt, Anders
    Kloo, Lars
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Regeneration of oxidized organic photo-sensitizers in Grätzel solar cells: quantum-chemical portrait of a general mechanism2010In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 11, no 9, p. 1858-1862Article in journal (Refereed)
  • 9. Park, Ji Hyun
    et al.
    Noh, JungHyun
    Schütz, Christina
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Royal Institute of Technology, Sweden.
    Salazar Alvarez, German
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Royal Institute of Technology, Sweden.
    Scalia, Giusy
    Bergström, Lennart
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lagerwall, Jan P. F.
    Macroscopic Control of Helix Orientation in Films Dried from Cholesteric Liquid-Crystalline Cellulose Nanocrystal Suspensions2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 7, p. 1477-1484Article in journal (Refereed)
    Abstract [en]

    The intrinsic ability of cellulose nanocrystals (CNCs) to self-organize into films and bulk materials with helical order in a cholesteric liquid crystal is scientifically intriguing and potentially important for the production of renewable multifunctional materials with attractive optical properties. A major obstacle, however, has been the lack of control of helix direction, which results in a defect-rich, mosaic-like domain structure. Herein, a method for guiding the helix during film formation is introduced, which yields dramatically improved uniformity, as confirmed by using polarizing optical and scanning electron microscopy. By raising the CNC concentration in the initial suspension to the fully liquid crystalline range, a vertical helix orientation is promoted, as directed by the macroscopic phase boundaries. Further control of the helix orientation is achieved by subjecting the suspension to a circular shear flow during drying.

  • 10.
    Pu, Maoping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ab Initio Molecular Dynamics Study of Hydrogen Cleavage by a Lewis Base [tBu(3)P] and a Lewis Acid [B(C6F5)(3)] at the Mesoscopic Level-Dynamics in the Solute-Solvent Molecular Clusters2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 17, p. 3714-3719Article in journal (Refereed)
    Abstract [en]

    With the help of state-of-the-art ab initio molecular dynamics methods, we investigated the reaction pathway of the {tBu(3)P + H-2 + B(C6F5)(3)} system at the mesoscopic level. It is shown that: i) the onset of H-2 activation is at much larger boronphosphorus distances than previously thought; ii) the system evolves to the product in a roaming-like fashion because of quasi-periodic nuclear motion along the asymmetric normal mode of PHHB fragment; iii) transient configurations of a certain type are present despite structural interference from the solvent; iv) transient-state configurations with sub-picosecond lifetime have potentially interesting infrared activity in the organic solvent (toluene) as well as in the gas phase. The presented results should be helpful for future experimental and theoretical studies of frustrated Lewis pair (FLP) activity.

  • 11.
    Pu, Maoping
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    How Frustrated Lewis Acid/Base Systems Pass through Transition-State Regions: H-2 Cleavage by [tBu(3)P/B(C6F5)(3)]2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 14, p. 2936-2944Article in journal (Refereed)
    Abstract [en]

    We investigate the transition-state (TS) region of the potential energy surface (PES) of the reaction tBu(3)P+H-2 +B(C6F5)(3)-> tBu(3)P-H(+)+H(-)-B(C6F5)(3) and the dynamics of the TS passage at room temperature. Owing to the conformational inertia of the phosphane center dot center dot center dot borane pocket involving heavy tBu(3)P and B(C6F5)(3) species and features of the PES E(P center dot center dot center dot H, B center dot center dot center dot H vertical bar B center dot center dot center dot P) as a function of P center dot center dot center dot H, B center dot center dot center dot H, and B center dot center dot center dot P distances, a typical reactive scenario for this reaction is a trajectory that is trapped in the TS region for a period of time (about 350 fs on average across all calculated trajectories) in a quasi-bound state (scattering resonance). The relationship between the timescale of the TS passage and the effective conformational inertia of the phosphane center dot center dot center dot borane pocket leads to a prediction that isotopically heavier Lewis base/Lewis acid pairs and normal counterparts could give measurably different reaction rates. Herein, the predicted quasi-bound state could be verified in molecular collision experiments involving femtosecond spectroscopy.

  • 12.
    Siegbahn, Per E. M.
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The Effect of Backbone Constraints: The Case of Water Oxidation by the Oxygen-Evolving Complex in PSII2011In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, no 17, p. 3274-3280Article in journal (Refereed)
    Abstract [en]

    The procedure for fixing atoms of amino acid residues in cluster model calculations on enzymes is reviewed. Examples from recent calculations on photosystem II (PSII) and Mo,Cu-dependent CO dehydrogenase are given. In this context, the cluster model work on finding a mechanism for O?O bond formation and a structure of the oxygen-evolving complex in PSII is also reviewed. In that work, fixing certain atoms played an important role. The main part of the present study concerns the mechanism in PSII using models based on the new high-resolution (1.9 angstrom) X-ray structure, which is compared to that using the old, theoretically suggested, structure. It is concluded that the mechanism remains the same, with a similar barrier height. Finally, a connection between the OEC structure and Mn,Ca-containing minerals is also briefly discussed.

  • 13. Tosner, Zdenek
    et al.
    Skoch, Antonin
    Kowalewski, Jozef
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Behavior of Two Almost Identical Spins during the CPMG Pulse Sequence2010In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 11, no 3, p. 638-645Article in journal (Refereed)
    Abstract [en]

    Multiple-spin-echo experiments have found wide use in nuclear magnetic resonance spectroscopy. In particular, the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence is used to determine transverse relaxation times T-2. Herein it is demonstrated, both theoretically and experimentally, that for a pair of almost identical spins-1/2 the experimental setup can have a profound effect on the observed spin dynamics. It is shown that, in the case of dipolar relaxation, the measured T-2 values can roughly vary between the limits of identical and unlike spins, just depending on the repetition rate of pi pulses with respect to chemical shift separation. Such an effect can, in the extreme narrowing regime, amount to a 50% difference.

  • 14.
    Zettergren, Henning
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Adoui, Lamri
    Bernigaud, Virgile
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Haag, Nicole
    Stockholm University, Faculty of Science, Department of Physics.
    Holm, Anne I. S.
    Stockholm University, Faculty of Science, Department of Physics.
    Huber, Bernd A.
    Hvelplund, Preben
    Johansson, Henrik A. B.
    Stockholm University, Faculty of Science, Department of Physics.
    Kadhane, Umesh
    Larsen, Mikkel Kofoed
    Liu, Bo
    Manil, Bruno
    Bröndsted Nielsen, Steen
    Panja, Subhasis
    Rangama, Jimmy
    Reinhed, Peter
    Stockholm University, Faculty of Science, Department of Physics.
    Schmidt, Henning T.
    Stockholm University, Faculty of Science, Department of Physics.
    Stöchkel, Kristian
    Electron-Capture-Induced Dissociation of Microsolvated Di- and > Tripeptide Monocations: Elucidation of Fragmentation Channels from > Measurements of Negative Ions2009In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 10, no 9-10, p. 1619-1623Article in journal (Refereed)
    Abstract [en]

    The branching ratio between ammonia loss and NCα bond cleavage of singly charged microsolvated peptides after electron capture from cesium depends on the solvent molecule attached. Density functional calculations reveal that for [GA+H]+(CE) (G=glycine, A=alanine, CE=crown ether), the singly occupied molecular orbital of the neutral radical is located mainly on the amide group (see picture).

    The results from an experimental study of bare and microsolvated peptide monocations in high-energy collisions with cesium vapor are reported. Neutral radicals form after electron capture from cesium, which decay by H loss, NH3 loss, or NCα bond cleavage into characteristic z. and c fragments. The neutral fragments are converted into negatively charged species in a second collision with cesium and are identified by means of mass spectrometry. For protonated GA (G=glycine, A=alanine), the branching ratio between NH3 loss and NCα bond cleavage is found to strongly depend on the molecule attached (H2O, CH3CN, CH3OH, and 18-crown-6 ether (CE)). Addition of H2O and CH3OH increases this ratio whereas CH3CN and CE decrease it. For protonated AAA ([AAA+H]+), a similar effect is observed with methanol, while the ratio between the z1 and z2 fragment peaks remains unchanged for the bare and microsolvated species. Density functional theory calculations reveal that in the case of [GA+H]+(CE), the singly occupied molecular orbital is located mainly on the amide group in accordance with the experimental results.

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