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  • 51. Guo, J. D.
    et al.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Himo, Fahmi
    KTH, Superseded Departments, Biotechnology.
    DNA repair by spore photoproduct lyase: A density functional theory study2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 40, p. 11188-11192Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations using the hybrid functional B3LYP have been performed to probe the energetics of the spore photoproduct lyase (SPL) reactions. This enzyme catalyzes the repair of a thymine dimer caused by UV irradiation of bacterial spore DNA. The calculations support the experimentally suggested mechanism, in which the reaction proceeds through hydrogen atom abstraction from the C6 position of the thymine dimer, followed by beta-scission of the C-C bond linking the two bases. The calculations propose, furthermore, that an inter-thymine hydrogen atom transfer step takes place before the back-transfer of the hydrogen atom from the adenosine cofactor. The last step is shown to be the rate-determining step in the reactions.

  • 52.
    Guo, Jingdong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Himo, Fahmi
    KTH, Superseded Departments, Biotechnology.
    Catalytic mechanism of pyruvate-formate lyase revisited2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 39, p. 15347-15354Article in journal (Refereed)
    Abstract [en]

    The catalytic mechanism of the glycyl-radical-containing enzyme pyruvate-formate lyase (PFL) is investigated using high-level quantum chemical methods. PFL catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetylated CoA. Large models are employed, based on a recent X-ray crystal structure of PFL in complex with the pyruvate substrate. The rate-limiting step is shown to be the homolytic C1-C2 bond cleavage of pyruvate, which occurs after the attack of the Cys418 radical on the carbonyl carbon of pyruvate. For the acetylation of CoA, we propose a new mechanism, in which the released formyl radical anion abstracts a hydrogen atom directly from CoA. This way, the acetyl group transfer from Cys418 becomes facile. The full potential energy curve for the PFL reactions is presented.

  • 53. Hantal, Gyorgy
    et al.
    Partay, Livia B.
    Varga, Imre
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Jedlovszky, Pal
    Gilanyi, Tibor
    Counterion and surface density dependence of the adsorption layer of ionic surfactants at the vapor-aqueous solution interface: A computer simulation study2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 7, p. 1769-1774Article in journal (Refereed)
    Abstract [en]

    To test the validity of currently used adsorption theories and understand the origin of the lack of their ability of adequately describing existing surface tension measurement data, we have performed a series of molecular dynamics simulations of the adsorption layer of alkali decyl sulfate at the vapor/aqueous solution interface. The simulations have been performed with five different cations (i.e., Li(+), Na(+), K(+), Rb(+), and Cs(+)) at two different surface concentrations (i.e., 2 mu mol/m(2) and 4 mu mol/m(2)). The obtained results clearly show that the thickness of the outer Helmholtz plate, a key quantity of the various adsorption theories, depends on two parameters, that is, the size of the cations and the surface density of the anionic surfactant. Namely, with increasing surface concentration, the electrostatic attraction between the two, oppositely charged, layers becomes stronger, leading to a considerable shrinking of the outer Helmholtz plate. Furthermore, this layer is found to be thicker in the presence of larger cations. The former effect could be important in understanding the anomalous shape of the adsorption isotherms of alkali alkyl sulfate surfactants, while the second effect seems to be essential in explaining the cation specificity of these isotherms.

  • 54.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Modeling Rayleigh Scattering of Aerosol Particles2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 18, p. 4296-4301Article in journal (Refereed)
    Abstract [en]

    Rayleigh scattering of naturally polarized lightwas studied for systems with atmospheric relevance represent-ing growing water clusters with adsorbed cis-pinonic acid. Thescattering intensity was computed from the static anddynamical polarizabilities of the clusters obtained by a recentlyderived methodology for classical polarizabilities, in whichApplequist equations for interacting polarizable dipoles areused together with point-dipoles and polarizabilities obtainedby quantum chemistry and decomposed into the atomicdomain by the so-called LoProp transformation generalized forfrequency dependence. The Applequist interaction was foundto yield scattering intensities 20% larger for a cluster consistingof 1000 water molecules, as compared to the method where allof the polarizabilities of molecules are added withoutinteractions. It was confirmed that scattering intensity depends quadratically on the number of water molecules in the cluster,and that it also increases quadratically with increase in the mass constituent of the foreign substance. The adsorption of the cis-pinonic acid increases the contribution to the scattering intensity stemming from the anisotropic polarizability, as compared tothe isotropic contribution. The ramifications of the method in predicting Rayleigh scattering and the earth’s albedo with respectto man-made and natural gas emission are briefly discussed.

  • 55. Hellman, A
    et al.
    Baerends, E.J.
    Biczysko, M
    Bligaard, T
    Christensen, C.H.
    Clary, D.C.
    Dahl, S
    van Harrevelt, R.
    Honkala, K.
    Jonsson, H.
    Kroes, G.J.
    Luppi, M.
    Manthe, U.
    Norskov, J.K.
    Olsen, R.A.
    Rossmeisl, J.
    Skulason, E.
    Tautermann, C.S.
    Varandas, A. J. C.
    Vincent, Jonathan
    Predicting catalysis: understanding ammonia synthesis from first-principles calculations2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, p. 17719-17735Article in journal (Refereed)
    Abstract [en]

    Here, we give a full account of a large collaborative effort toward an atomic-scale understanding of modern industrial ammonia production over ruthenium catalysts. We show that overall rates of ammonia production can be determined by applying various levels of theory (including transition state theory with or without tunneling corrections, and quantum dynamics) to a range of relevant elementary reaction steps, such as N(2) dissociation, H(2) dissociation, and hydrogenation of the intermediate reactants. A complete kinetic model based on the most relevant elementary steps can be established for any given point along an industrial reactor, and the kinetic results can be integrated over the catalyst bed to determine the industrial reactor yield. We find that, given the present uncertainties, the rate of ammonia production is well-determined directly from our atomic-scale calculations. Furthermore, our studies provide new insight into several related fields, for instance, gas-phase and electrochemical ammonia synthesis. The success of predicting the outcome of a catalytic reaction from first-principles calculations supports our point of view that, in the future, theory will be a fully integrated tool in the search for the next generation of catalysts.

  • 56. Herschend, B.
    et al.
    Baudin, M.
    Hermansson, Kersti
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Influence of substrate dynamics on CO-MgO(001) bonding-using molecular dynamics snapshots in quantum-chemical calculations2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 11, p. 5473-5479Article in journal (Refereed)
    Abstract [en]

    Combined molecular dynamics (MD) and quantum mechanics QM) calculations have been performed for CO adsorbed on MgO(001) at 50 K. The changes in the adsorption energy caused by the surface dynamics have been analyzed, and a clear correlation was found between the dynamic variation of the adsorption energy and the electrostatic field above the adsorption site. By separating the electrostatic contributions arising from the local structure at the adsorption site from those originating from the rest of the slab, a linear expression of these contributions could be fitted which closely reproduces the dynamic changes in the adsorption energy. Using this simple linear expression, the distribution of adsorption energies for CO above the Mg2+ sites on the MgO(001) surface at 50, 80, and 150 K have been predicted.

  • 57. Herschend, B.
    et al.
    Hermansson, Kersti
    KTH, Superseded Departments, Biotechnology.
    Alfredsson, M.
    Zhukovskii, Y. F.
    Kotomin, E. A.
    Jacobs, P. W. M.
    Characterization of the metal-ceramic bonding in the Ag/MgO(001) interface from ab initio calculations2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 43, p. 11893-11899Article in journal (Refereed)
    Abstract [en]

    The nature of the metal-ceramic interaction in the Ag/MgO(001) interface is studied using periodic Hartree-Fock calculations with density functional theory a posteriori correlation corrections. Different aspects of the Ag-MgO interaction have been studied by analysis of the electronic properties: total and projected density of states, multipole moments, bond population, and the difference electron density. By linking these properties to the adsorption energy and making a comparative analysis for interfaces with different degrees of coverage and different adsorption models (one- and two-sided adsorption), a detailed description of the Ag-MgO has been acquired.

  • 58. Hess, Berk
    et al.
    Harings, Jules A W
    Rastogi, Sanjay
    Vegt, Nico F A van der
    Interaction of water with N,N'-1,2-ethanediyl-bis(6-hydroxy-hexanamide) crystals: a simulation study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 3, p. 627-31Article in journal (Refereed)
    Abstract [en]

    Recently it has been shown, using a variety of experimental techniques, that water can be hosted in N,N'-1,2-ethanediyl-bis(6-hydroxy-hexanamide) crystals. It forms stable interactions with the hydroxyl groups at the ends of the molecule, as well as with the amide groups. However, with experimental techniques one can not observe the exact hydrogen bonding geometries of the physically bound water molecules. Here a series of molecular dynamics simulations is presented that provide an atomistically detailed picture of the interactions of water with different parts of the crystals.

  • 59. Hess, Berk
    et al.
    van der Vegt, Nico F A
    Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 35, p. 17616-17626Article in journal (Refereed)
    Abstract [en]

    We present an extensive study on hydration thermodynamic properties of analogues of 13 amino acid side chains at 298 K and 1 atm. The hydration free energies DeltaG, entropies DeltaS, enthalpies DeltaH, and heat capacities Deltac(P)() were determined for 10 combinations of force fields and water models. The statistical sampling was extended such that precisions of 0.3, 0.8, 0.8 kJ/mol and 25 J/(mol K) were reached for DeltaG, TDeltaS, DeltaH, and Deltac(P)(), respectively. The three force fields used in this study are AMBER99, GROMOS 53A6, and OPLS-AA; the five water models are SPC, SPC/E, TIP3P, TIP4P, and TIP4P-Ew. We found that the choice of water model strongly influences the accuracy of the calculated hydration entropies, enthalpies, and heat capacities, while differences in accuracy between the force fields are small. On the basis of an analysis of the hydrophobic analogues of the amino acid side chains, we discuss what properties of the water models are responsible for the observed discrepancies between computed and experimental values. The SPC/E water model performs best with all three biomolecular force fields.

  • 60.
    Hevekerl, Heike
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Spielmann, Thiemo
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Chmyrov, Andriy
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Forster Resonance Energy Transfer beyond 10 nm: Exploiting the Triplet State Kinetics of Organic Fluorophores2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 45, p. 13360-13370Article in journal (Refereed)
    Abstract [en]

    Inter- or intramolecular distances of biomolecules can be studied by Forster resonance energy transfer (FRET). For most FRET methods, the observable range of distances is limited to 1-10 nm, and the labeling efficiency has to be controlled carefully to obtain accurate distance determinations, especially for intensity-based methods. In this study, we exploit the triplet state of the acceptor fluorophore as a FRET readout using fluorescence correlation spectroscopy and transient state monitoring. The influence of donor fluorescence leaking into the acceptor channel is minimized by a novel suppression algorithm for spectral bleed-through, thereby tolerating a high excess (up to 100-fold) of donor-only labeled samples. The suppression algorithm and the high sensitivity of the triplet state to small changes in the fluorophore excitation rate make it possible to extend the observable range of FRET efficiencies by up to 50% in the presence of large donor-only populations. Given this increased range of FRET efficiencies, its compatibility with organic fluorophores, and the low requirements on the labeling efficiency and instrumentation, we foresee that this approach will be attractive for in vitro and in vivo FRET-based spectroscopy and imaging.

  • 61.
    Hevekerl, Heike
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Wigenius, Jens
    Persson, Gustav
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Inganäs, Olle
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Dark states in ionic oligothiophene bioprobes-evidence from fluorescence correlation spectroscopy and dynamic light scattering2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 22, p. 5924--5933Article in journal (Refereed)
    Abstract [en]

    Luminescent conjugated polyelectrolytes (LCPs) can upon interaction with biological macromolecules change their luminescent properties, and thereby serve as conformation- and interaction-sensitive biomolecular probes. However, to exploit this in a more quantitative manner, there is a need to better understand the photophysical processes involved. We report studies of the conjugated pentameric oligothiophene, derivative p-FTAA, which changes optical properties with different p-FTAA concentrations in aqueous buffers, and in a pH and oxygen saturation dependent manner. Using dynamic light scattering, luminescence spectroscopy and fluorescence correlation spectroscopy, we find evidence for a monomer dimer equilibrium, for the formation of large clusters of p-FTAA in aqueous environment, and can couple aggregation to changed emission properties of oligothiophenes. In addition, we observe the presence of at least two dark transient states, one presumably being a triplet state. Oxygen was found to statically quench the p-FTAA fluorescence but also to promote molecular fluorescence by quenching dark transient states of the p-FTAA molecules. Taken together, this study provides knowledge of fluorescence and photophysical features essential for applying p-FTAA and other oligothiophene derivatives for diagnostic purposes, including detection and staining of amyloid aggregates.

  • 62.
    Himo, Fahmi
    KTH, Superseded Departments, Biotechnology.
    Catalytic mechanism of benzylsuccinate synthase, a theoretical study2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 31, p. 7688-7692Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations using the hybrid functional B3LYP have been performed to study the catalytic mechanism of benzylsuccinate synthase. This enzyme catalyzes the novel addition of the methyl carbon of toluene to fumarate, forming benzylsuccinate and thereby initiating the anaerobic metabolism of toluene in denitrifying bacteria. Benzylsuccinate synthase was suggested to contain a stable glycyl radical, based on sequence similarity to the two known glycyl radical containing enzymes pyruvate-formate lyase and class III anaerobic ribonucleotide reductase. This suggestion was recently confirmed by electron paramagnetic resonance experiments. The calculations demonstrate that an overall homolytic radical mechanism is thermodynamic ally very plausible. The radical is transferred from the stable glycyl radical to toluene via a cysteinyl radical in two hydrogen atom transfer steps, The rate-limitin, step is shown to he the addition of benzyl radical to fumarate, forming a benzylsuccinyl radical intermediate. A full potential energy surface for the benzylsuccinate synthase reactions is presented.

  • 63.
    Himo, Fahmi
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Guo, J. D.
    Rinaldo-Matthis, A.
    Nordlund, P.
    Reaction mechanism of deoxyribonucleotidase: A theoretical study2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 42, p. 20004-20008Article in journal (Refereed)
    Abstract [en]

    The reaction mechanism of human deoxyribonucleotidase (dN) is studied using high-level quantum-chemical methods. dN catalyzes the dephosphorylation of deoxyribonucleoside monophosphates (dNMPs) to their nucleoside form in human cells. Large quantum models are employed (99 atoms) based on a recent X-ray crystal structure [Rinaldo-Matthis et al. Nat. Struct. Biol. 2002, 9, 779]. The calculations support the proposed mechanism in which Asp41 performs a nucleophilic attack on the phosphate to form a phospho-enzyme intermediate. Asp43 acts in the first step as an acid, protonating the leaving nucleoside, and in the second step as a base, deprotonating the lytic water. No pentacoordinated intermediates could be located.

  • 64.
    Holtmann, J.
    et al.
    Department of Chemie, University of Hamburg.
    Walczuk, E.
    Department of Chemie, University of Hamburg.
    Dede, M.
    Department of Chemie, University of Hamburg.
    Wittenburg, C.
    Department of Chemie, University of Hamburg.
    Heck, J.
    Department of Chemie, University of Hamburg.
    Archetti, G.
    Department of Chemistry - Physical Chemistry, Technische Universität Kaiserslautern.
    Wortmann, R.
    Department of Chemistry - Physical Chemistry, Technische Universität Kaiserslautern.
    Kuball, H.-G.
    Department of Chemistry - Physical Chemistry, Technische Universität Kaiserslautern.
    Wang, Yanhua
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Liu, Kai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Three-branched dendritic dipolar nonlinear optical chromophores, more than three times a single-strand chromophore?2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 47, p. 14751-14761Article in journal (Refereed)
    Abstract [en]

    To elucidate the dependence of the nonlinear optical (NLO) response on the conformation of triply branched derivatives, a new series of D-pi-A dendrimers has been synthesized. A combined approach of experiments (UV-vis and EOA measurements) and computational predictions (semiempirical and ab initio) was applied both on the dendrimers and on the corresponding single-strand chromophores. It has been shown that depending on the surrounding media the NLO activity of a flexible dendrimer can be very different. Two limiting cases are proposed: (i) the dendrimer resembles a solution of the corresponding single-strand chromophores with about 3-fold concentration, where the hyperpolarizability is the sum of the effect of three noninteracting single-strand subunits ("independent chromophores" limit); (ii) the dendrimers show nearly parallel or helical alignments of the single-strand subunits. Because of this change of conformation the NLO activity can be enhanced up to nine times the value of the "independent chromophores" limit and, thus, are more than a single strand chromophore. Conformers of dendrimers with interacting single-strand chromophores have been identified experimentally in nonpolar solutions by the EOA spectroscopy and possible structures have been revealed by numerical calculations, which could moreover show the tendency of the effects on the hyperpolarizability due to structural changes of the flexible dendritic architecture. Implications for future research developments are given to implement the "more than three times" concept.

  • 65.
    Hopmann, Kathrin H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Himo, Fahmi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Insights into the Reaction Mechanism of Soluble Epoxide Hydrolase from Theoretical Active Site Mutants2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 42, p. 21299-21310Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations of active site mutants are used to gain insights into the reaction mechanism of the soluble epoxide hydrolases (sEHs). The quantum chemical model is based on the X-ray crystal structure of the human soluble epoxide hydrolase. The role of two conserved active site tyrosines is explored through in silico single and double mutations to phenylalanine. Full potential energy curves for hydrolysis of (1S,2S)-beta-methylstyrene oxide are presented. The results indicate that the two active site tyrosines act in concert to lower the activation barrier for the alkylation step. For the wild-type and three different tyrosine mutant models, the regioselectivity of epoxide opening is compared for the substrates (1S,2S)-beta-methylstyrene oxide and (S)-styrene oxide. An additional part of our study focuses on the importance of the catalytic histidine for the alkylation half-reaction. Different models are presented to explore the protonation state of the catalytic histidine in the alkylation step and to evaluate the possibility of an interaction between the nucleophilic aspartate and the catalytic histidine.

  • 66. Hu, W. K.
    et al.
    Gao, X. P.
    Kiros, Yohannes
    KTH, Superseded Departments, Chemical Engineering and Technology.
    Middelman, E.
    Noreus, D.
    Zr-based AB(2)-type hydrogen storage alloys as dual catalysts of gas-diffusion electrodes in an alkaline fuel cell2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 26, p. 8756-8758Article in journal (Refereed)
    Abstract [en]

    Zr-based AB(2)-type hydrogen storage alloys as dual catalysts for hydrogen adsorption and oxidation reactions in alkaline fuel cells were investigated. A hydrogen-diffusion electrode composed of this hydride alloy was constructed, and its performance in terms of catalytic activities and durability was evaluated. Results demonstrated that the hydrogen-diffusion electrode had not only good activity but also excellent stability at a current density of 40-60 mA/cm(2) after surface treatments using a 1.0 M HF solution. XPS analyses showed that the improvement in catalytic activity is related to the formation of a nickel-rich layer and the removal of other oxides on the catalyst surface. The novel possible application of Zr-based hydride alloys could lead to an attempt to exploit new catalysts to lower material cost for hydrogen fuel cells.

  • 67. Hu, W. K.
    et al.
    Kiros, Yohannes
    KTH, Superseded Departments, Chemical Engineering and Technology.
    Noreus, D.
    AB(5)-type hydrogen storage alloys as catalysts in hydrogen-diffusion electrodes for novel H-2/hydride//perovskite/O-2 alkaline fuel cells2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 48, p. 18530-18534Article in journal (Refereed)
    Abstract [en]

    Development of a non-noble-metal catalyst electrode is an important issue in the research and development of fuel cells. The catalytic activity and durability of AB(5)-type hydrogen storage alloys used in hydrogen-diffusion electrodes for alkaline fuel cells are evaluated. The experiments demonstrate that the activity and stability for hydrogen oxidation is greatly improved if the particle size is decreased from 5-30 to 1-10 mum. This also improves the electrode stability. SEM and XRD analyses show that no disintegration of the smaller catalyst particles is observed in long-term tests. A novel H-2/hydride//perovskite/O-2 alkaline fuel cell was constructed as a non-noble-metal fuel cell concept. The results showed that both gas-diffusion electrodes had high catalytic activities and good stability. A maximum power density of 54 mW/cm(2) was achieved at 120 mA/cm(2) when using H-2/O-2 and 49 mW/cm(2) at 100 mA/cm(2) when using H-2/air.

  • 68.
    Hua, Weijie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gao, Bin
    Li, Shuhua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Refinement of DNA Structures through Near-Edge X-ray Absorption Fine Structure Analysis: Applications on Guanine and Cytosine Nucleobases, Nucleosides, and Nucleotides2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 41, p. 13214-13222Article in journal (Refereed)
    Abstract [en]

    In this work we highlight the potential of NEXAFS-near-edge X-ray absorption fine structure-analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out first-principle calculations of the N1s NEXAFS spectra of the guanine and cytosine nucleobases and their tautomers, nucleosides, and nucleotides in the gas phase, as well as for five crystal structures of guanine, cytosine, or guanosine. The spectra all clearly show imine (pi*(1)) and amine (pi*(2)) nitrogen absorption bands with a characteristic energy difference (Delta). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around +/- 0.4-0.5 eV change of Delta, to the spectra due to a switch of single-double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Delta, while the phosphate groups have nearly negligible effects on the spectra. Two kinds of intermolecule interactions are analyzed, the hydrogen bonds and the stacking effect, by comparing "compressed" and "expanded" models. or by comparing models including or excluding the nearest stacking molecules. The shortening of hydrogen-bond length by 0.2-0.3 angstrom can result in the reduction of Delta by 0.2-0.8 eV. This is because the hydrogen bonds make the electrons more delocalized, and the amine and imine nitrogens become less distinguishable. Moreover, the hydrogen bond has a different ability to influence the spectra of different crystals, with guanine crystals as the largest (change by 0.8 eV) and the guanosine crystal as the smallest (change by 0.2 eV). The stacking has negligible effects on the spectra in all studied systems. A comparison of guanosine to guanine crystals shows that the sugars in the crystal could create "blocks" in the pi-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens More distinguishable with a larger Delta. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.

  • 69.
    Hua, Weijie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Yamane, Hiroyuki
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Li, Shuhua
    Kato, Hiroyuki S.
    Kawai, Maki
    Hatsui, Takaki
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kosugi, Nobuhiro
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Systematic Study of Soft X-ray Spectra of Poly(Dg)center dot Poly(Dc) and Poly(Da)center dot Poly(Dt) DNA Duplexes2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 20, p. 7016-7021Article in journal (Refereed)
    Abstract [en]

    In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG)center dot poly(dC) and poly(dA)center dot poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.

  • 70.
    Håkansson, Karl M. O.
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Prahl-Wittberg, Lisa
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Söderberg, L. Daniel
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Nanofibril Alignment in Flow Focusing: Measurements and Calculations2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 27, p. 6674-6686Article in journal (Refereed)
    Abstract [en]

    Alignment of anisotropic supermolecular building blocks is crucial to control the properties of many novel materials. In this study, the alignment process of cellulose nanofibrils (CNFs) in a flow-focusing channel has been investigated using small-angle X-ray scattering (SAXS) and modeled using the Smoluchowski equation, which requires a known flow field as input. This flow field was investigated experimentally using microparticle-tracking velocimetry and by numerically applying the two-fluid level set method. A semidilute dispersion of CNFs was modeled as a continuous phase, with a higher viscosity as compared to that of water. Furthermore, implementation of the Smoluchowski equation also needed the rotational Brownian diffusion coefficient, which was experimentally determined in a shear viscosity measurement. The order of the nanofibrils was found to increase during extension in the flow-focusing channel, after which rotational diffusion acted on the orientation distribution, driving the orientation of the fibrils toward isotropy. The main features of the alignment and dealignment processes were well predicted by the numerical model, but the model overpredicted the alignment at higher rates of extension. The apparent rotational diffusion coefficient was seen to increase steeply as the degree of alignment increased. Thus, the combination of SAXS measurements and modeling provides the necessary framework for quantified studies of hydrodynamic alignment, followed by relaxation toward isotropy.

  • 71. Imberg, A.
    et al.
    Evertsson, H.
    Stilbs, Peter
    KTH, Superseded Departments, Chemistry.
    Kriechbaum, M.
    Engstrom, S.
    On the self-assembly of monoolein in mixtures of water and a polar aprotic solvent2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 10, p. 2311-2318Article in journal (Refereed)
    Abstract [en]

    Four different one-phase regions: two liquid phases (L and L-3) and two liquid crystalline phases (L-alpha and V-2) of the MO/NMP/water system, were studied by SAXS, PGSE-NMR, and rheology at 20 degreesC. The location of the dramatic increase in solubility of MO, in binary NMP/water mixtures, can be explained in terms of the presence or absence of free water, as a consequence of strong NMP(water)(2) complex formation in the binary NMP/water system. A direct effect of this complexation is aggregate formation at a certain region within the L, phase. The microstructure of the L-3 phase can be modeled as bicontinuous according to the theory of interconnected rods when formation of NMP(water)(2) complexes are taken into consideration. The swelling of the sponge phase correlates well to predicted swelling laws and characteristic lengths, as found in other sponge phases. The cubic phase region of the ternary system consists of at least two different cubic phases, with (Pn3m) over bar and (Ia3d) over bar symmetry of the space group, respectively. At higher NMP contents it seems as if the (Pn3m) over bar symmetry of the space group transforms into (Im3m) over bar.

  • 72.
    Ito, Mika
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosterbid Isomerase2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 46, p. 13050-13058Article in journal (Refereed)
    Abstract [en]

    We propose a computationally efficient approach for evaluating the individual contributions of many different residues to the catalytic efficiency of an enzymatic reaction. This approach is based on the fragment molecular orbital (FMO) method, and it defines the energy of a deletion form, i.e., the energy of the system when a particular residue is deleted. Using this approach, we found that, among 10 investigated residues, three, Tyr14, Asp99, and Tyr55, in this order, significantly reduce the activation energy of the proton abstraction from a substrate, cyclopent-2-enone, catalyzed by ketosteroid isomerase (KSI). The relative activation energies estimated in this study are in good agreement with available previous experimental and theoretical data obtained for the similar proton abstraction with a native substrate and substitution mutants of KSI. It was thus indicated that the new approach is efficient for rationally evaluating the catalytic effects of multiple residues on an enzymatic reaction.

  • 73. Jansik, Branislav
    et al.
    Rizzo, Antonio
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ab initio study of the two-photon circular dichroism in chiral natural amino acids2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 2, p. 446-460Article in journal (Refereed)
    Abstract [en]

    Two-photon circular dichroism spectra calculated within an origin-invariant density functional theory approximation in the absorption region where the lowest electronic excited states appear are presented for all 19 essential amino acids in the gas phase. A comparison of intensities and characteristic features is made with the corresponding two-photon absorption and one-photon circular dichroism spectra for each species. Also, the contributions of the electric dipole, magnetic dipole, and electric quadrupole transitions to the rotational strengths are analyzed in some detail. The remarkable fingerprinting capabilities of the two-photon circular dichroism spectroscopy are highlighted.

  • 74. Jaouen, F.
    et al.
    Marcotte, S.
    Dodelet, J. P.
    Lindbergh, Göran
    KTH, Superseded Departments, Chemical Engineering and Technology.
    Oxygen reduction catalysts for polymer electrolyte fuel cells from the pyrolysis of iron acetate adsorbed on various carbon supports2003In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, no 6, p. 1376-1386Article in journal (Refereed)
    Abstract [en]

    Nonnoble metal catalysts for the electrochemical reduction of oxygen in acidic medium have been produced by adsorbing iron(II) acetate on 19 carbon supports. These materials were then pyrolyzed in an atmosphere containing NH3. The 19 carbon supports are (i) six as-received commercial supports (Printex XE-2, Norit SX Ultra, Ketjenblack EC-600JD, acetylene black, Vulcan XC-72R, and Black Pearls 2000), (ii) three as-received developmental supports (Lonza HS300 and Sid Richardson RC1 and RC2), (iii) the same nine previous supports prepyrolyzed at 900degreesC in an atmosphere containing NH3 to increase their N content, and (iv) a synthetic carbon made by pyrolyzing perylene tetracarboxylic dianhydride at 900degreesC in an atmosphere containing NH3. The goal of this study is to determine the effect of the carbon support on the catalytic activity of the catalysts. The specific surface area, the pore size distribution, the N and O contents, and the electrocatalytic activities of the 19 types of catalysts were measured. It was found that the activity of the catalysts varies greatly from one carbon support to another, but neither the specific surface area of the catalysts nor the distribution of their macro- or mesopores is a determining factor for the catalytic activity. The most important factor is the N content of the materials; the higher it is, the higher is the density of the catalytic sites on their surface and the better is the electrocatalyst. Carbon supports that are devoid of N, however, display some lower catalytic activity, which is attributed to an iron oxide. The latter catalytic site occurs also in the other N-containing catalysts. In these materials there are, therefore, three catalytic sites at work: an iron oxide site and two N-containing sites labeled FeN4/C and FeN2/C, with the last site being the most active for oxygen electroreduction.

  • 75.
    Johansson, Anna C V
    et al.
    Stockholm University.
    Lindahl, Erik
    Stockholm University.
    Titratable amino acid solvation in lipid membranes as a function of protonation state.2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 1, p. 245-53Article in journal (Refereed)
    Abstract [en]

    Knowledge about the insertion and stabilization of membrane proteins is a key step toward understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic so as to efficiently insert into membranes, but there are many exceptions with polar or titratable residues. An obvious example is the S4 helices of voltage-gated ion channels with up to 4 arginines, leading to vivid discussion about whether such helices can insert spontaneously, and if so, what their conformation, protonation state, and cost of insertion really are. To address this question, we have determined geometric and energetic solvation properties for different protonation states of the titrateable amino acids, including hydration, side chain orientation, free energy profiles, and effects on the membrane thickness. As expected, charged states are significantly more expensive to insert (8-16 kcal/mol) than neutral variants (1-3 kcal/mol). Although both sets of values exhibit quite high relative correlation with experimental in vivo hydrophobicity scales, the magnitudes of the in vivo hydrophobicity scales are much lower and strikingly appears as a compressed version of the calculated values. This agrees well with computational studies on longer lipids but results in an obvious paradox: the differences between in vivo insertion and simulations cannot be explained by methodological differences in force fields, possible limited hydrophobic thickness of the endoplasmic reticulum (ER) membrane, or parameters; even anionic lipid head groups (PG) only have limited effect on charged side chains, and virtually none for hydrophobic ones. This leads us to propose a model for in vivo insertion that could reconcile these differences and explain the correlation: if there are considerable hydrophobic barriers inside the translocon, the experimental reference state for the solvation free energy when comparing insertion/translocation in vivo would be quite close to the bilayer environment rather than water.

  • 76.
    Johnson, Magnus
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Corrosion Science.
    Tyrode, Eric
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    Baldelli, Steve
    Rutland, Mark
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface Chemistry.
    Leygraf, Christofer
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Corrosion Science.
    A vibrational sum frequency spectroscopy study of the liquid-gas interface of acetic acid-water mixtures: 1: surface speciation2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 1, p. 321-328Article in journal (Refereed)
    Abstract [en]

    Aqueous acetic acid solutions have been studied by vibrational sum frequency spectroscopy (VSFS) in order to acquire molecular information about the liquid-gas interface. The concentration range 0-100% acetic acid has been studied in the CH/OH and the C-O/C=O regions, and in order to clarify peak assignments, experiments with deuterated acetic acid and water have also been performed. Throughout the whole concentration range, the acetic acid is proven to be protonated. It is explicitly shown that the structure of a water surface becomes disrupted even at small additions of acetic acid. Furthermore, the spectral evolution upon increasing the concentration of acetic acid is explained in terms of the different complexes of acetic acid molecules, such as the hydrated monomer, linear dimer, and cyclic dimer. In the C=O region, the hydrated monomer is concluded to give rise to the sum frequency (SF) signal, and in the CH region, the cyclic dimer contributes to the signal as well. The combination of results from the CH/OH and the C-O/C=O regions allows a thorough characterization of the behavior of the acetic acid molecules at the interface to be obtained.

  • 77. Kalinin, Stanislav
    et al.
    Sisamakis, Evangelos
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Magennis, Steven W.
    Felekyan, Suren
    Seidel, Claus A. M.
    On the Origin of Broadening of Single-Molecule FRET Efficiency Distributions beyond Shot Noise Limits2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 18, p. 6197-6206Article in journal (Refereed)
    Abstract [en]

    Single-molecule FRET experiments on freely diffusing rigid molecules frequently show FRET efficiency (E) distributions broader than those defined by photon statistics. It is often unclear whether the observed extra broadening can be attributed to a physical donor-acceptor distance (R-DA) distribution. Using double-stranded DNA (dsDNA) labeled with Alexa488 and Cy5 (or Alexa647) as a test system, we investigate various possible contributions to the E distribution width. On the basis of simultaneous analysis of donor and acceptor intensities and donor lifetimes, we conclude that dsDNA chain dynamics can be ruled out as a possible reason for the observed E distribution broadening. We applied a set of tools to demonstrate that complex acceptor dye photophysics can represent a major contribution to the E distribution width. Quantitative analysis of the correlation between FRET efficiency and donor fluorescence lifetime in 2D multiparameter histograms allows one to distinguish between broadening due to distinct FRET or dye species. Moreover, we derived a simple theory, which predicts that the apparent distance width due to acceptor fluorescence quantum yield variations increases linearly with physical donor-acceptor distance. This theory nicely explains the experimentally observed FRET broadening of a series of freely diffusing labeled dsDNA and dsRNA molecules. Accounting for multiple acceptor states allowed the fitting of experimental E distributions, assuming a single fixed donor-acceptor distance.

  • 78. Kapla, Jon
    et al.
    Wohlert, Jakob
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Stevensson, Baltzar
    Engström, Olof
    Widmalm, Göran
    Maliniak, Arnold
    Molecular Dynamics Simulations of Membrane-Sugar Interactions2013In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 22, p. 6667-6673Article in journal (Refereed)
    Abstract [en]

    It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range W-TRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane sugar interactions.

  • 79. Kashtanov, Stepan
    et al.
    Zhuang, Guorong V.
    Augustsson, Andreas
    Nordgren, Joseph
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ross, Philip N.
    Guo, Jinghua
    Structural conformation in a poly(ethylene oxide) film determined by X-ray emission spectroscopy2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 40, p. 11658-11661Article in journal (Refereed)
    Abstract [en]

    The electronic structure of pol(ethylene oxide) (PEO) in a thin (< 1 mu) film sample was experimentally probed by X-ray emission spectroscopy. Both nonresonant and resonant X-ray emission spectra were simulated by using density functional theory (DFT) applied to four different models representing different conformations in the polymer. Calculated spectra were compared with experimental results for the PEO film. It was found that the best fit was obtained with the polymer conformation in PEO electrolytes from which the salt (LiMF6, M = P, As, or Sb) had been removed. This conformation is different from the crystalline bulk polymer and implies that film casting, commonly used to form electrolytes for Li polymer batteries, induces the same conformation in the polymer not depending upon the presence of salt.

  • 80.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Nordberg, Agneta
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Investigation of the Binding Profiles of AZD2184 and Thioflavin T with Amyloid-beta(1-42) Fibril by Molecular Docking and Molecular Dynamics Methods2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 35, p. 11560-11567Article in journal (Refereed)
    Abstract [en]

    Detecting deposits of amyloid beta fibrils in the brain is of paramount importance for an early diagnosis of Alzheimer's disease. A number of PET tracers have been developed for amyloid imaging, but many suffer from poor specificity and large signal to background ratio. Design of tracers with specificity and improved binding affinity requires knowledge about various potential binding sites in the amyloid beta fibril available for the tracers and the nature of the local microenvironment of these sites. In this study we investigate the local structure of fibrils using two important probes, namely, thioflavin T (a fluorescent probe) and AZD2184 (a PET tracer). The target structures for amyloid-beta(1-42) fibril are based on reported NMR solution models. By explicitly considering the effect of fibril flexibility on the available binding sites for all these models, the binding affinity of these probes has been investigated. The binding profiles of AZD2184 and thioflavin T were studied by molecular docking and molecular dynamics simulation methods. The two compounds were found to bind at the same sites of the fibril: three of which are within the fibril, and one is on the two sides of the Met35 residue on the surface. The binding affinity of AZD2184 and thioflavin T is found to be higher at the core sites than on the surface due to more contact residues. The binding affinity of AZD2184 is much higher than that of thioflavin T at every site due to electrostatic interaction and spatial restriction, which is in good agreement with experimental observation. However, the structural change of thioflavin T is much more significant than that of AZD2184, which is the chemical basis for its usage as a fluorescent probe. The ramifications of these results for the design and optimization of PET radioligands and fluorescent probes are briefly discussed.

  • 81. Laksman, J.
    et al.
    Kooser, K.
    Levola, H.
    Itälä, E.
    Ha, D. T.
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Kukk, E.
    Dissociation Pathways in the Cysteine Dication after Site-Selective Core Ionization2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 40, p. 11688-11695Article in journal (Refereed)
    Abstract [en]

    A photoelectronionion coincidence experiment has been carried out on the amino acid molecule cysteine after core-ionization of the O 1s, N 1s, C 1s, and S 2p orbitals. A number of different dissociation channels have been identified. Some of them show strong site-selective dependence that can be attributed to a combination of nuclear motion in the core-ionized state and Auger processes that populate different final electronic states in the dication.

  • 82.
    Li, Hongbao
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hua, Weijie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lin, Zijing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    First-Principles Study on Core-Level Spectroscopy of Arginine in Gas and Solid Phases2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 42, p. 12641-12650Article in journal (Refereed)
    Abstract [en]

    First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra of neutral arginine at different K-edges in the solid phase as well as X-ray photoelectron spectra (XPS) of neutral, deprotonated, and protonated arginines in the gas phase. Influences of the intra- and intermolecular hydrogen bonds (HBs) and different charge states have been carefully examined to obtain useful structure-property relationships. Our calculations show a noticeable difference in the NEXAFS/XPS spectra of the canonical and zwitterionic species that can be used for unambiguously identifying the dominant form in the gas phase. It is found that the deprotonation/protonation always results in red/blue shifts of several electronvolts for the core binding energies (BEs) at all edges. The normal hydrogen bond Y-H center dot center dot center dot X (X, Y = N, O) can cause a blue/red shift of ca. 1 eV to the core BEs of the proton acceptor X/donor Y, while the weak C-H center dot center dot center dot Y hydrogen bond may also lead to a weak red shift (less than 1 eV) of the C1s BEs. Moreover, the influence of intermolecular interactions in the solid state is reflected as a broadening in the sigma* region of the NEXAFS spectra at each edge, while in the pi* region, these interactions lead to a strengthening or weakening of individual transitions from different carbons, although no evident visual change is found in the resolved total spectra. Our results provide a better understanding of the influences of the intra- and intermolecular forces on the electronic structure of arginine.

  • 83.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nuclear magnetic shielding of the Cd-113(II) ion in aqua solution: A combined molecular dynamics/density functional theory study2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 36, p. 11347-11352Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics simulation and density functional theory investigation of the nuclear magnetic shielding constant of the Cd-113(II) ion solvated in aqueous solution. Molecular dynamics simulations are carried out for the cadmium-water system in order to produce instantaneous geometries for subsequent determination of the nuclear magnetic shielding constant at the density functional theory level. The nuclear magnetic shielding constant is computed using a perturbation theory formalism, which includes nonrelativistic and leading order relativistic contributions to the nuclear magnetic Shielding tensor. Although the NMR shielding constant varies significantly with respect to simulation time, the value averaged over increasing number of snapshots remains almost constant. The paramagnetic nonrelativistic contribution is found to be most sensitive to dynamical changes in the system and is mainly responsible for the thermal and solvent effects in solution. The relativistic correction features very little sensitivity to the chemical environment, and can be disregarded in theoretical calculations when a Cd complex is used as reference compound in Cd-113 NMR experiments, due to the mutual cancelation between individual relativistic corrections.

  • 84.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2: A Theoretical Study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 31, p. 10916-10922Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics and density functional theory study of dioxygen-induced perturbation of the F-19 NMR chemical shifts in an aqueous solution of fluorinated cysteine under 100 atm of O-2 partial pressure. Molecular dynamics Simulations are carried out to determine the dominant structures of O-2 and the fluorinated cysteine complexes in water, and the collected structural information is exploited in computation of F-19 chemical shifts using density functional theory. The obtained results indicate that the density redistribution of the O-2 unpaired electrons between the dioxygen and fluorinated cysteine is responsible for the experimentally observed perturbation of the F-19 NMR chemical shifts, where the Fermi contact interaction plays the key role. The O-2-induced paramagnetic F-19 chemical shift, averaged over the simulation trajectory, is comparable with the reported experimental values, proving the availability of the developed strategy for modeling F-19 NMR chemical shifts in the presence of paramagnetic agents in ail aqueous solution. The applicability of the combined molecular dynamics/density functional theory approach for dioxygen NMR perturbation to all resonating nuclei including H-1, C-13, N-15, and F-19 is emphasized, and the ramification of this for investigations of membrane protein structures is discussed.

  • 85. Li, Xueqiang
    et al.
    Wang, Mei
    Zhang, Suping
    Pan, Jingxi
    Na, Yong
    Liu, Jianhui
    Akermark, Bjorn
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Noncovalent assembly of a metalloporphyrin and an iron hydrogenase active-site model: Photo-induced electron transfer and hydrogen generation2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 27, p. 8198-8202Article in journal (Refereed)
    Abstract [en]

    A noncovalent assembly of a pyridyl-functionalized hydrogenase active-site model complex and zinc tetraphenylporphyrin has been obtained and characterized. Upon light irradiation, fluorescence quenching by electron transfer was observed from the singlet excited state of the porphyrin to the diiron center, and the mechanism was verified by fluorescence lifetime and transient absorption spectroscopic measurements. In contrast to molecular dyads linked by covalent bonds, the assembled system was designed to avoid charge recombination via complex dissociation after photo-induced electron transfer. Visible light-driven hydrogen generation was observed from this self-assembled system. The assembling strategy employed in this study has the potential to be used for any other hydrogenase models in the future.

  • 86. Lin, Ke
    et al.
    Zhou, Xiaoguo
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liu, Shilin
    The Microscopic Structure of Liquid Methanol from Raman Spectroscopy2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 10, p. 3567-3573Article in journal (Refereed)
    Abstract [en]

    The microscopic Structure of liquid methanol has been systematically investigated with Raman spectroscopy in a temperature range of 15-55 degrees C. The unbonded free -OH stretching vibrational hand has been observed at similar to 3660 cm(-1) in pure liquid. With the aid of depolarization measurements and theoretical calculations, four featured spectral components have been unambiguously identified and assigned to four well-defined vibrational modes of Clusters in chain or ring forms. Furthermore, the Cluster size distribution and its temperature dependence have been derived from the spectral fittings for the first time, which lead to the conclusion that the trimer, tetramer, and pentamer are the dominant Clusters ill liquid methanol, taking Up more than 50% of total Clusters.

  • 87.
    Lin, Na
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Solvent Effects on the Three-Photon Absorption of a Symmetric Charge-Transfer Molecule2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, p. 4703-4710Article in journal (Refereed)
    Abstract [en]

    We present a theoretical study of the solvent-induced three-photon absorption cross section of a highly conjugated fluorene derivative, performed using density functional (DFT) cubic response theory in combination with the polarizable continuum model. The applicability of the often used two-state model is examined by comparison against the full DFT response theory results. It is found that the simplified model performs poorly for the three-photon absorption properties of our symmetric charge-transfer molecule. The dielectric medium enhances the three-photon absorption cross section remarkably. The effects of solvent polarity and geometrical distortions have been carefully examined. A detailed comparison with experiment is presented.

  • 88.
    Linares, Mathieu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Stafström, Sven
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Complex Polarization Propagator Approach in the Restricted Open-Shell, Self-Consistent Field Approximation: The Near K-Edge X-ray Absorption Fine Structure Spectra of Allyl and Copper Phthalocyanine2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 18, p. 5096-5102Article in journal (Refereed)
    Abstract [en]

    A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that makes it possible to directly calculate the X-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted X-ray spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assign-lent of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

  • 89. Liu, G. M.
    et al.
    Jaegermann, W.
    He, J. J.
    Sundstrom, V.
    Sun, Licheng C.
    XPS and UPS characterization of the TiO2/ZnPcGly heterointerface: Aligmment of energy levels2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 23, p. 5814-5819Article in journal (Refereed)
    Abstract [en]

    The electronic structure and the highest occupied molecular orbitals (HOMO)/the lowest unoccupied molecular orbitals (LUMO) alignment at the molecular semiconductor heterointerface of nanostructured TiO2/ZnPcGly dye sensitizer were characterized by X-ray and ultraviolet photoemission spectroscopy (XPS and UPS). The HOMO level of the dye ZnPcGly was determined to be located at 1.62 eV below the Fermi edge, and the corresponding LUMO level was estimated to be 0.10 eV above the conduction band of TiO2 based on the HOMO/LUMO gap (1.82 eV) of ZnPcGly determined by optical absorption measurements. This energy level matching between the orbitals of the dye and the bands of TiO2 can enable efficient electron transfer from photoexcited ZnPcGly to TiO2, which is very important in photoinduced charge-transfer reactions and for applications in dye-sensitized solar cells.

  • 90.
    Liu, Ji-Cai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Nicolas, Christophe
    Sun, Yu-Ping
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Flammini, Roberto
    O'Keeffe, Patrick
    Avaldi, Lorenzo
    Morin, Paul
    Kimberg, Victor
    Kosugi, Nobuhiro
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Miron, Catalin
    Multimode Resonant Auger Scattering from the Ethene Molecule2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 18, p. 5103-5112Article in journal (Refereed)
    Abstract [en]

    Resonant Auger spectra of ethene molecule have been measured with vibrational resolution at several excitation energies in the region of the C1s(-1)1b(2g)(π*) resonance. The main features observed in the experiment have been assigned and are accurately interpreted on the basis of ab initio multimode calculations. Theory explains the extended vibrational distribution of the resonant Auger spectra and its evolution as a function of the excitation energy by multimode excitation during the scattering process. As a result, the resonant Auger spectra display two qualitatively different spectral features following the Raman and non-Raman dispersion laws, respectively. Calculations show that two observed thresholds of formation of non-Raman spectral bands are related to the "double-edge" structure of the X-ray absorption spectrum.

  • 91.
    Liu, Kai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wang, Yanhua
    Department of Physics, Linyi Normal University.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Two-photon absorption of hydrogen-bonded octupolar molecule clusters2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 14, p. 4387-4392Article in journal (Refereed)
    Abstract [en]

    Charge-transfer octupolar molecules can form clusters in solution through intermolecular hydrogen bonds. In the present work we explore the role of such clustering on two-photon absorption (TPA) spectra assuming 1,3,5-triamino-2,4,6- trinitrobenzene (TATB) as a model system. Using density functional quadratic response theory we examine different cluster structures of TATB dimers, trimers, and tetramers taken from snapshots of molecular dynamics simulations. In comparison with the TPA spectrum of a monomer, significant red shifts of charge-transfer states are predicted for all chosen clusters, which mainly is the result of the distortion of the structures induced by the aggregation. The TPA spectra for dimers and trimers show strong conformation dependence, whereas they turn out to be more stable for tetramers. Enhancements of TPA absorption have also been found for clusters containing less distorted molecules connected by hydrogen bonds.

  • 92.
    Lundborg, Magnus
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Center for Biomembrane Research, Stockholm University, Sweden .
    Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 3, p. 810-823Article in journal (Refereed)
    Abstract [en]

    Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.

  • 93.
    Löytynoja, Tuomas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Oulu, Finland.
    Niskanen, J.
    Jankala, K.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Quantum Mechanics/Molecular Mechanics Modeling of Photoelectron Spectra: The Carbon 1s Core-Electron Binding Energies of Ethanol-Water Solutions2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 46, p. 13217-13225Article in journal (Refereed)
    Abstract [en]

    Using ethanolwater solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solutesolvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics modelelectrostatic, polarization, and van der Waalswith atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  • 94. Mahrov, B.
    et al.
    Boschloo, Gerrit
    Hagfeldt, A.
    Siegbahn, H.
    Rensmo, H.
    Photoelectron spectroscopy studies of Ru(dcbpyH(2))(2)(NCS)(2)/CuI and Ru(dcbpyH(2))(2)(NCS)(2)/CuSCN interfaces for solar cell applications2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 31, p. 11604-11610Article in journal (Refereed)
    Abstract [en]

    In this work, the electronic structure of the wide band gap hole conductors Cut and CuSCN in contact with an organic dye (Ru(dcbpyH(2))(2)(NCS)(2), cis-bis(4,4'-dicarboxy-2,2-bipyridine)bis(isothiocyanato)ruthenium(II)) were investigated by means of photoelectron spectroscopy. The experiments show specific interaction between the NCS groups of the dye molecules and the Cut and CuSCN surfaces. For Cut there are strong indications that the dye molecules interact with Cut through both NCS ligands. Also, one of the carboxylic groups is affected by the surface adsorption on the CuI substrate. For the CuSCN surface the results indicate that about half of the molecules interact with the surface through both NCS ligands, that about half of the molecules interact with the surface through one NCS ligand, and that there is no specific interaction with the carboxylic groups. The measurements also reveal changes in the electronic structure of the dye molecule when adsorbed onto the substrates. In particular, changes in the upper valence electronic structure, important for the function of this material combination in a solar cell device, are discussed.

  • 95. Matczyszyn, Katarzyna
    et al.
    Olesiak-Banska, Joanna
    Nakatani, Keitaro
    Yu, Pei
    Murugan, Natarajan Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zalesny, Robert
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Wrocław University of Technology, Poland .
    Roztoczynska, Agnieszka
    Bednarska, Joanna
    Bartkowiak, Wojciech
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Samoc, Marek
    One- and Two-Photon Absorption of a Spiropyran-Merocyanine System: Experimental and Theoretical Studies2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 4, p. 1515-1522Article in journal (Refereed)
    Abstract [en]

    We report on the nonlinear optical properties measurements and quantum-chemical calculations of a well-known photochromic system consisting of spiropyran and the merocyanine photoproduct. The study of nonlinear absorption and refraction properties of the molecules dissolved in chloroform were performed with the Z-scan technique, using femtosecond pulses in a wide range of wavelengths. Maxima in the two-photon absorption spectrum at 700 and 1050 nm were found for the merocyanine form, and the corresponding two-photon absorption cross section is 80 GM and 20 GM, respectively. The latter feature does not vanish completely in the nonlinear spectrum of the spiropyran form, possibly because of the existence of some photoconversion caused by the laser beam during the measurements. A nonlinear absorption peak at 900 nm is found in the spiropyran form with an effective cross section of about 20 GM; it is likely due to three-photon absorption or to absorption by some intermediate species. The experimental data are supported by calculations performed with the use of a hybrid quantum mechanics-molecular mechanics approach.

  • 96. Matthews, James F.
    et al.
    Bergenstråhle, Malin
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Biocomposites. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Beckham, Gregg T.
    Himmel, Michael E.
    Nimlos, Mark R.
    Brady, John W.
    Crowley, Michael F.
    High-Temperature Behavior of Cellulose I2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 10, p. 2155-2166Article in journal (Refereed)
    Abstract [en]

    molecular simulation to elucidate the structural behavior of small hydrated cellulose I beta microfibrils heated to 227 degrees C (500 K) with two carbohydrate force fields. In contrast to the characteristic two-dimensional hydrogen-bonded layer sheets present in the cellulose I beta crystal structure, we show that at high temperature a three-dimensional hydrogen bond network forms, made possible by hydroxymethyl groups changing conformation from trans-gauche (TG) to gauche-gauche (GG) in every second layer corresponding to "center" chains in cellulose I beta and from TG to gauche-trans (GT) in the "origin" layer. The presence of a regular three-dimensional hydrogen bond network between neighboring sheets eliminates the possibility of twist, whereas two-dimensional hydrogen bonding allows for microfibril twist to occur. Structural features of this high-temperature phase as determined by molecular simulation may explain several experimental observations for which no detailed structural basis has been offered. This includes an explanation for the observed temperature and crystal size dependence for the extent of hydrogen/deuterium exchange, and diffraction patterns of cellulose at high temperature.

  • 97. Meng, Xianle
    et al.
    Zhu, Weihong
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Feng, Yanli
    Tan, Wenjuan
    Tian, He
    Novel Bisthienylethenes Containing Naphthalimide as the Center Ethene Bridge: Photochromism and Solvatochromism for Combined NOR and INHIBIT Logic Gates2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 49, p. 15636-15645Article in journal (Refereed)
    Abstract [en]

    Two novel photochromic bisthienylethene derivatives BTE-NA1 and BTE-NA2 with a six-membered aryl ring of naphthalimide fluorescent moiety as the center ethene bridging unit were synthesized and fully characterized by H-1 NMR, C-13 NMR, and HRMS. They exhibit considerably high cyclization quantum yield and good fatigue resistance. Interestingly, the fluorescence of BTE-NA1 arising from the naphthalimide unit could be well modulated by photochromism and solvatochromism. Quantum chemical calculations were carried out to study their geometrical, electronic, and optical properties, which were in good accordance with the experimental data. Furthermore, a combined NOR and INHIBIT logic operation based on BTE-NA1 has been successfully mimicked with fluorescence changes as outputs.

  • 98. Molochnikov, L S
    et al.
    Kovalyova, E G
    Grigor'ev, I A
    Zagorodni, Andrei A.
    KTH, Superseded Departments, Materials Science and Engineering.
    Direct measurement of H+ activity inside cross-linked functional polymers using nitroxide spin probes2004In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, no 4, p. 1302-1313Article in journal (Refereed)
    Abstract [en]

    The lack of a direct method for measuring activity inside ion-exchamye resins was the main obstacle for strict thermodynamic investigations of such objects during the past decades. This paper proposes a method for the activity determination. The method is based on exploring the ESR response of stable nitroxide radicals introduced as probes into the resin phase. This method allows for the measurement of the hydrogen ion activity inside cross-linked polyelectrolytes. In addition to the method verification, the paper reports its application to the determination of ionization constants of functional groups and to the investigation of the hydrolysis and sorption of copper on different types of sorbents (weak cation and anion-exchange resins, functionalized and nonfunctionalized polymeric films). The applicability of known thermodynamic approaches developed for the investigation of micelles and biomembranes with nitroxide radicals is discussed. The paper also includes a critical analysis of the potentiometric method conventionally used for the investigation of ion-exchange equilibria.

  • 99. Morandeira, A.
    et al.
    Boschloo, Gerrit
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Hammarstrom, L.
    Photoinduced ultrafast dynamics of comnarin 343 sensitized p-type-nanostructured NiO films2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 41, p. 19403-19410Article in journal (Refereed)
    Abstract [en]

    Photoinduced electron transfer from the valence band of nanocrystalline NiO, a p-type semiconductor, to an excited bound dye, coumarin 343, and the subsequent recombination have been measured by femtosecond transient absorbance spectroscopy probing with white light. It was found that both processes are nonexponential. The photoinduced electron transfer from the semiconductor to the excited bound dye has an ultrafast component (similar to 200 fs), which is comparable to the time constants measured for photoinduced electron injection in C343-TiO2 colloid solutions. The process is very efficient and constitutes the main path of deactivation of the excited dye. Back electron transfer is also remarkably fast, with the main part of the recombination process happening with a time constant of similar to 20 ps. Dye-sensitized nanostructured p-type semiconductors are attractive materials due to their potential use as photocathodes in dye-sensitized solar cells and solid electrolytes in solid-state dye-sensitized solar cells. To our knowledge, this is the first time that the photoinduced electron-transfer kinetics of a sensitized p-type semiconductor has been studied.

  • 100.
    Mudedla, Sathish Kumar
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Natarajan Arul, Murugan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. AlbaNova Univ Ctr, Royal Inst Technol KTH, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden.;Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Free Energy Landscape for Alpha-Helix to Beta-Sheet Interconversion in Small Amyloid Forming Peptide under Nanoconfinement2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 42, p. 9654-9664Article in journal (Refereed)
    Abstract [en]

    Understanding the mechanism of fibrillization of amyloid forming peptides could be useful for the development of therapeutics for Alzheimer's disease (AD). Taking this standpoint, we have explored in this work the free energy profile for the interconversion of monomeric and dimeric forms of amyloid forming peptides into different secondary structures namely beta-sheet, helix, and random coil in aqueous solution using umbrella sampling simulations and density functional theory calculations. We show that the helical structures of amyloid peptides can form beta sheet rich aggregates through random coil conformations in aqueous condition. Recent experiments (Chem. Eur. J. 2018, 24, 3397-3402 and ACS Appl. Mater. Interfaces 2017, 9, 21116-21123) show that molybdenum disulfide nanosurface and nanoparticles can reduce the fibrillization process of amyloid beta peptides. We have unravelled the free energy profile for the interconversion of helical forms of amyloid forming peptides into beta-sheet and random coil in the presence of a two-dimensional nanosurface of MoS2. Results indicate that the monomer and dimeric forms of the peptides adopt the random coil conformation in the presence of MoS2 while the helical form is preferable for the monomeric form and that the beta-sheet and helix forms are the preferable forms for dimers in aqueous solution. This is due to strong interaction with MoS2 and intramolecular hydrogen bonds of random coil conformation. The stabilization of random coil conformation does not lead to a beta sheet like secondary structure for the aggregate. Thus, the confinement of MoS2 promotes deaggregation of amyloid beta peptides rather than aggregation, something that could be useful for the development of therapeutics for AD.

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