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  • 1101.
    T., Levitina and E. J. Brändas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics.
    Computational Techniques for Prolate Spheroidal Wave Functions in Signal Processing2001In: J. Comp. Meth. Sci. Eng., ISSN 1472-7978, Vol. 1, no 1, p. 287-Article in journal (Refereed)
  • 1102.
    Tal, Alexey
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Electronic and structural properties of nanoclusters2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Nanoclusters have gained a huge interest due to their unique properties. They represent an intermediate state between an atom and a solid, which manifests itself in their atomic configurations and electronic structure. The applications of nanoclusters require detailed understanding of their properties and strongly depend on the ability to control their synthesis process. Significant effort has been invested in modelling of nanoclusters properties. However, the complexity of these systems is such that many aspects of their growth process and properties are yet to be understood.

    My thesis focuses on describing structural and electronic properties of nanoclusters. In particular, the model for nanoparticles growth in plasma condition is developed and applied, allowing to describe the influence of the plasma conditions on the evaporation, growth and morphological transformation processes. The mechanism driving the morphology transition from icosahedral to decahedral phase is suggested based on force-fields models. Spectroscopic methods allow for precise characterization of nanoclusters and constitute an important tool for analysis of their electronic structure of valence band as well as core-states. The special attention in the thesis is paid to the core-states of nanoclusters and influences that affect them. In particular, the effects of local coordination, interatomic distances and confinement effects are investigated in metal nanoclusters by density functional theory methods. These effects and their contribution to spectroscopic features of nanoclusters in X-ray photoemission are modelled. The relation between the reactivity of nanoclusters and their spectroscopic features calculated in different approximations are revealed and explained. Ceria is a very important system for many applications due to the ability of cerium atoms to change their oxidation state depending on the environment. The shift of the oxidation state and its effects on the core-states is examined with X-ray absorption measurements and modelling allowing to build a rigid foundation for interpretation of the measured spectra and characterization of electronic structure of ceria nanoparticles.  

  • 1103.
    Tal, Alexey A.
    et al.
    Ecole Polytech Fed Lausanne, Switzerland.
    Posada-Borbon, Alvaro
    Chalmers Univ Technol, Sweden; Chalmers Univ Technol, Sweden.
    Gronbeck, Henrik J.
    Chalmers Univ Technol, Sweden; Chalmers Univ Technol, Sweden.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Natl Univ Sci and Technol MISIS, Russia.
    Correlation between Ethylene Adsorption Energies and Core-Level Shifts for Pd Nanoclusters2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 4, p. 2544-2548Article in journal (Refereed)
    Abstract [en]

    Density functional theory calculations have been used to investigate the adsorption of ethylene on Pd nanoclusters together with shifts in core-level binding energies of Pd atoms bonded to the adsorbate. The adsorption energy is found to correlate with the core-level shifts (CLS), which is consistent with the notion that the core-level binding energy is a measure of differences in cohesion. The correlation between adsorption energies and core-level shifts is found to be stronger than the correlation between adsorption energies and generalized coordination numbers, indicating that descriptors preferably should account for electronic effects explicitly. The advantages of CLS as a descriptor for the screening of adsorption properties is discussed.

    The full text will be freely available from 2019-12-24 10:57
  • 1104.
    Tal, Alexey
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. National University of Science and Technology MISIS, Russia.
    Olovsson, Weine
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Origin of the core-level binding energy shifts in Au nanoclusters2017In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 95, no 24, article id 245402Article in journal (Refereed)
    Abstract [en]

    We investigate the shifts of the core-level binding energies in small gold nanoclusters by using ab initio density-functional-theory calculations. The shift of the 4f states is calculated for magic-number nanoclusters in a wide range of sizes and morphologies. We find a nonmonotonous behavior of the core-level shift in nanoclusters depending on the size. We demonstrate that there are three main contributions to the Au 4f shifts, which depend sensitively on the interatomic distances, coordination, and quantum confinement. They are identified and explained by the change of the on-site electrostatic potential.

  • 1105.
    Tamayo-Mendoza, Teresa
    et al.
    Harvard Univ, Dept Chem & Chem Biol, 12 Oxford St, Cambridge, MA 02138 USA.
    Kreisbeck, Christoph
    Harvard Univ, Dept Chem & Chem Biol, 12 Oxford St, Cambridge, MA 02138 USA.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aspuru-Guzik, Alaprimen
    Harvard Univ, Dept Chem & Chem Biol, 12 Oxford St, Cambridge, MA 02138 USA;Canadian Inst Adv Res, Toronto, ON M5G 1Z8, Canada.
    Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock2018In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 5, p. 559-566Article in journal (Refereed)
    Abstract [en]

    Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult, a Hartree-Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

  • 1106. Tang, Y.
    et al.
    Ding, Y.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, T.
    Zhang, W.
    Xie, Y.
    Acylation of dipyrromethanes at the α and β positions and further development of fluorescent Zn2+ probes2014In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 206, p. 291-302Article in journal (Refereed)
    Abstract [en]

    The acylation of 5-aryl dipyrromethanes afforded products with interestingly rich substitution modes, i.e.; α- and β-monoacylated (modes a and b), and α, α′-, α, β′- and β, β′-diacylated (modes c-e). Especially, the β- and β, β′-acylation modes are unprecedented. And most of these products can be synthesized at a gram scale. The anisoyl substituted 5-(4-cyanophenyl) dipyrromethanes (1a-1e) were oxidized with DDQ. Thus, 1a and 1b afforded the corresponding dipyrrins 1a-DPR, and 1b-DPR. More interestingly, the diacylated ones 1c-1e could not be oxidized by DDQ. Instead, 1c-OH-1e-OH were obtained with a hydroxyl group attached to the 5-position. 1a-DPR-1e-OH were further developed as fluorescence turn-on Zn2+ probes. 1d-OH showed the highest sensitivity, with a detection limit of 1.5 × 10-8 M, and it was successfully applied in Zn2+ imaging in Hela cells. Furthermore, single crystals of two Zn2+ complexes were obtained and analyzed by X-ray diffraction.

  • 1107. Tejero, Ismael
    et al.
    Gonzalez-Lafont, Angels
    Lluch, José M.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical modeling of hydroxyl-radical-induced lipid peroxidation reactions2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 20, p. 5684-5693Article in journal (Refereed)
    Abstract [en]

    The OH-radical-induced mechanism of lipid peroxidation, involving hydrogen abstraction followed by O2 addition, is explored using the kinetically corrected hybrid density functional MPWB1K in conjunction with the MG3S basis set and a polarized continuum model to mimic the membrane interior. Using a small nonadiene model of linoleic acid, it is found that hydrogen abstraction preferentially occurs at the mono-allylic methylene groups at the ends of the conjugated segment rather than at the central bis-allylic carbon, in disagreement with experimental data. Using a full linoleic acid, however, abstraction is correctly predicted to occur at the central carbon, giving a pentadienyl radical. The Gibbs free energy for abstraction at the central C11 is 8 kcal/mol, compared to 9 kcal/mol at the end points (giving an allyl radical). Subsequent oxygen addition will occur at one of the terminal atoms of the pentadienyl radical fragment, giving a localized peroxy radical and a conjugated butadiene fragment, but is associated with rather high free energy barriers and low exergonicity at the CPCM-MPWB1K/MG3S level. The ZPE-corrected potential energy surfaces obtained without solvent effects, on the other hand, display considerably lower barriers and more exergonic reactions.

  • 1108. Tellgren, E.
    et al.
    Henriksson, J.
    Norman, Patrick
    Linköping University, Sweden.
    First-order excited state properties in the four-component Hartree-Fock approximation: The excited state electric dipole moments in CsAg and CsAu2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 126, no 6, article id 064313Article in journal (Refereed)
    Abstract [en]

    An implementation of the second-order residue of the quadratic response function is presented in the four-component Hartree-Fock approximation, and the calculation of first-order properties of electronically excited states can thereby be achieved. Results are presented for the excited state electric dipole moments of the valence excited states in CsAg and CsAu. For CsAg, and even more so for CsAu, nonscalar relativistic effects on this property may be substantial, e.g., at the four-component level of theory, the excited-to-ground state dipole moment difference Δμ ranges from 1.994 to 4.110 a.u. for the six components of the 1 Π3 state in CsAg, whereas, at the scalar relativistic level of theory, the common value of Δμ is 2.494 a.u.

  • 1109. Telyatnyk, L.
    et al.
    Oprea, Corneliu Ioan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Density functional theory for spin Hamiltonian parameters of azurin: ERP parametersManuscript (Other academic)
  • 1110. Tian, Bo-Xue
    et al.
    Erdtman, Edvin
    University of Borås, School of Engineering.
    Eriksson, Leif A.
    Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 40, p. 12105-12112Article in journal (Refereed)
    Abstract [en]

    Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation and cyclization of two 5-aminolevulinic acid (5-ALA) substrate molecules to give porphobilinogen (PBG). The chemical step of PBGS is herein revisited using QM/MM (ONIOM) calculations. Two different protonation states and several different mechanisms are considered. Previous mechanisms based on DFT-only calculations are shown unlikely to occur. According to these new calculations, the deprotonation step rather than ring closure is rate-limiting. Both the C–C bond formation first mechanism and the C–N bond formation first mechanism are possible, depending on how the A-site ALA binds to the enzyme. We furthermore propose that future work should focus on the substrate binding step rather than the enzymatic mechanism.

  • 1111.
    Tian, Bo-Xue
    et al.
    School of Chemistry, National University of Ireland – Galway, Galway, Ireland.
    Erdtman, Edvin
    Högskolan i Borås, Institutionen Ingenjörshögskolan, Borås, Sweden.
    Eriksson, Leif A.
    Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
    Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations2012In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 40, p. 12105-12112Article in journal (Refereed)
    Abstract [en]

    Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation and cyclization of two 5-aminolevulinic acid (5-ALA) substrate molecules to give porphobilinogen (PBG). The chemical step of PBGS is herein revisited using QM/MM (ONIOM) calculations. Two different protonation states and several different mechanisms are considered. Previous mechanisms based on DFT-only calculations are shown unlikely to occur. According to these new calculations, the deprotonation step rather than ring closure is rate-limiting. Both the C–C bond formation first mechanism and the C–N bond formation first mechanism are possible, depending on how the A-site ALA binds to the enzyme. We furthermore propose that future work should focus on the substrate binding step rather than the enzymatic mechanism.

  • 1112.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Electron-vibration coupling and its effects on optical and electronic properties of single molecules2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The thesis is devoted to theoretical investigations of electron-vibration coupling and its effects on optical and electronic properties of single molecules, especially for molecules confined between metallic electrodes.

    A density-matrix approach has been developed to describe the photon emission of single molecules confined in the scanning tunneling microscope (STM). With this new method electronic excitations induced by both the tunneling electron and the localized surface plasmon (LSP) can be treated on an equal footing. Model calculations for porphyrin derivatives have successfully reproduced and explained the experimentally observed unusual variation of the photon emission spectra. The method has also been extended to study the STM induced fluorescence and phosphorescence of C60 molecules in combination with the first principles calculations. In particularly, the non-Condon vibronic couplings have been exclusively included in the calculations. The experimental spectra have been nicely reproduced by our calculations, which also enable us to identify the unique spectral fingerprint and origin of the measured spectra. The observed rich spectral features have been finally correctly assigned.

    The electron transport properties of molecular junctions with bipyridine isomers have been studied in the sequential tunneling (SET) regime by assuming that the molecules are weakly coupled to metallic electrodes. It is shown that the strong electron-vibration coupling in the 2, 2’-bipyridine molecule and the 4,4’-bipyridine molecule can lead to observable Franck-Condon blockade. Taking advantage of such novel effect, a gate-controlled conductance switch with ideal on-off ratio has been proposed for a molecular junction with the 4, 4’-bipyridine molecule.

    The effect of the electron-vibration coupling on one-photon and two-photon absorption spectra of green fluorescent protein (GFP) has been systematically examined. The hydroxybenzylidene-2, 3-dimethylimidazolinone molecule in the deprotonated anion state (HBDI) is used to model the fluorescence chromophore of the GFP. Both Condon and non-Condon vibronic couplings have been considered in the calculations. The calculated spectra are in good agreement with the available experimental spectra. It confirms the notion that the observed blue-shift of the two-photon absorption spectrum with respect to its one-photon absorption counterpart is caused by the non-Condon vibronic coupling.

    All the calculations are carried out with our own software package, DynaVib. It is capable of modeling a variety of vibrational-resolved spectroscopies, such as absorption, emission, and resonant Raman scattering (RRS) spectra. In our package, the Duschinsky rotation and non-Condon effect have been fully taken into account. Both time-independent and time-dependent approaches have been implemented, allowing to simulate the spectra of very large molecules.

  • 1113.
    Tian, Guangjun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fluorescence and Phosphorescence of Single C60 Molecules as Stimulated by a Scanning Tunneling Microscope2013In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 52, no 18, p. 4814-4817Article in journal (Refereed)
    Abstract [en]

    Glow-in-the-dark buckyballs: Reproduction of the fluorescence and phosphorescence spectra of single C60 molecules in a scanning tunneling microscope by simulations according to first principles (see picture) revealed the underlying mechanisms and enabled the correct assignment of the spectra.

  • 1114.
    Tian, Guangjun
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Isomeric dependent Franck-Condon blockade in weakly coupled bipyridine molecular junctionsArticle in journal (Other academic)
  • 1115.
    Tian, Li-Yun
    et al.
    Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology, Stockholm, Sweden.
    Levämäki, Henrik
    Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology, Stockholm, Sweden.
    Eriksson, Olle
    Örebro University, School of Science and Technology. Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Uppsala, Sweden.
    Kokko, Kalevi
    Department of Physics and Astronomy, University of Turku, Turku, Finland; Turku University Centre for Materials and Surfaces (MatSurf), Turku, Finland.
    Nagy, Ágnes
    Department of Theoretical Physics, University of Debrecen, Debrecen, Hungary.
    Délczeg-Czirják, Erna Krisztina
    Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Uppsala, Sweden.
    Vitos, Levente
    Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology, Stockholm, Sweden; Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Uppsala, Sweden; Research Institute for Solid State Physics and Optics, Wigner Research Center for Physics, Budapest, Hungary.
    Density Functional Theory description of the order-disorder transformation in Fe-Ni2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, no 1, article id 8172Article in journal (Refereed)
    Abstract [en]

    The thermodynamic ordering transformation of tetragonal FeNi system is investigated by the Exact Muffin-Tin Orbitals (EMTO) method. The tetragonal distortion of the unit cell is taken into account and the free energy is calculated as a function of long-range order and includes the configurational, vibrational, electronic and magnetic contributions. We find that both configurational and vibrational effects are important and that the vibrational effect lowers the predicted transformation temperature by about 480 K compared to the value obtained merely from the configurational free energy. The predicted temperature is in excellent agreement with the experimental value when all contributions are taken into account. We also perform spin dynamics calculations for the magnetic transition temperature and find it to be in agreement with the experiments. The present research opens new opportunities for quantum-mechanical engineering of the chemical and magnetic ordering in tetrataenite.

  • 1116.
    Tian, Yuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Biomolecule Functionalization of Diamond Surfaces for Implant Applications - A Theoretical Study2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Diamond is a promising material with unique chemical properties. In this thesis, nano-scale diamond quantum size effects were investigated using several chemical property indicators. The results show that the chemical properties are strongly dependent on size for film thicknesses smaller than 1 nm (1D), and for nanodiamond particle diameters less than 2 nm (3D). When the sizes exceed these ranges there are no longer any quantum effects.

    The influence of surface termination coverage on the surface chemical properties has been calculated for the 2×1 reconstructed diamond (100) surface and for the diamond (111) surface. The terminating species included COOH and NH2 groups, which both are beneficial for the immobilization of biomolecules. The results of the calculations show that it is energetically possible to terminate the diamond surfaces up to 100% with NH2, while it is only possible to cover the surfaces up to 50% with COOH species. The reason for the latter result is most probably the larger sterical hindrance amongst the adsorbates. Both types of termination species were shown to influence the diamond surface electronic properties (e.g., HOMO/LUMO levels).

    In order to extend the diamond utility for biomedical applications, especially implant design, interactions of various growth factors with the diamond surfaces were also simulated. For non-solvent diamond-biomolecule systems, the results show that adhesion affinities are strongly dependent on biomolecule molecular weights. When including a water based solvent in the systems, the results show good physisorption affinities between proteins and diamond. Proteins structures, before and after physisorption, were visualized, and further investigated with respect to electrostatic properties and functional groups. By comparing the biomolecular structural changes during the adhesion processes, it can be concluded that both the general structures, as well as the binding pocket structures, were kept intact after the adhesion to the diamond surfaces (regardless of the adhesion affinities). In addition, the surface electronic potential distributions were maintained, which indicate preserved biomolecule functionalities.

  • 1117.
    Todde, Guido
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Exploring Protein Functions by Molecular Modelling2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Proteins are one of the most important families of biological macromolecules. Proteins can assume many different structures. This makes them perfect to serve a wide range of functions in all organisms. In the last decades, molecular modeling has become an important and powerful tool in the investigation of biological systems. Adopting different computational methods many protein functions and structure related problems can be explored.

    This thesis focuses on three different protein issues. The structural changes induced by high temperature on a large enzyme were investigated simulating the denaturation of glucose oxidase. Molecular dynamics (MD) simulations at different high temperatures were performed. The transition state of the denaturation process was found and the relative ensemble of structures characterized. Different protein properties were analyzed and found in agreement with experimental and theoretical data. Moreover the breaking points of the protein were localized and point mutations on the protein sequence were suggested.

    Antifreeze proteins (AFP) allow different organisms to survive in subzero environments. These proteins lower the freezing point of physiological fluids. MD simulations of the snow flea AFP (sfAFP) in water have shown partial instability of the protein structure. When attached to different ice planes at the ice/water interface, the sfAFP induces local ice melting. AFPs are divided into two categories: hyperactive and moderately active depending on their antifreeze power. The water diffusion profile of ice/water systems containing one protein from each family were compared. The ice/water interface width was found to be broadened to different extent by the two proteins, while a control protein (ubiquitin) did not affect the interface thickness.

    Hemoglobin is the oxygen carrier in all vertebrates. Mutation along the protein sequence can alter the protein functionality and its capability of binding molecular oxygen. Density Functional Theory methods were applied in the calculation of the oxygen binding energy of the wild type hemoglobin and four other variants. Evaluations on the electronic structures and on the binding energies of the different hemoglobin variants suggest that perhaps none of the mutated hemoglibins efficiently bind oxygen.

  • 1118.
    Todde, Guido
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Activation and Inactivation of the FLT3 Kinase: Pathway Intermediates and the Free Energy of Transition2019In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 123, no 26, p. 5385-5394Article in journal (Refereed)
    Abstract [en]

    The aberrant expression of kinases is often associated with pathologies such as cancer and autoimmune diseases. Like other types of enzymes, kinases can adopt active and inactive states, where a shift toward more stable active state often leads to disease. Dozens of kinase inhibitors are, therefore, used as drugs. Most of these bind to either the inactive or active state. In this work, we study the transitions between these two states in FLT3, an important drug target in leukemias. Kinases are composed of two lobes (N- and C-terminal lobes) with the catalytic site in-between. Through projection of the largest motions obtained through molecular dynamics (MD) simulations, we show that each of the end-states (active or inactive) already possess the ability for transition as the two lobes rotate which initiates the transition. A targeted simulation approach known as essential dynamics sampling (EDS) was used to speed up the transition between the two protein states. Coupling the EDS to implicit-solvent MD was performed to estimate the free energy barriers of the transitions. The activation energies were found in good agreement with previous estimates obtained for other kinases. Finally, we identified FLT3 intermediates that assumed configurations that resemble that of the c-Src nonreceptor tyrosine kinase. The intermediates show better binding to the drug ponatinib than c-Src and the inactive state of FLT3. This suggests that targeting intermediate states can be used to explain the drug-binding patterns of kinases and for rational drug design.

  • 1119.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). Wallenberg Research Centre at Stellenbosch University, South Africa.
    Influence of Antifreeze Protein on the Ice/Water Interface2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 8, p. 3407-3413Article in journal (Refereed)
    Abstract [en]

    Antifreeze proteins (AFP) are responsible for the survival of several species, ranging from bacteria to fish, that encounter subzero temperatures in their living environment. AFPs have been divided into two main families, moderately and hyperactive, depending on their thermal hysteresis activity. We have studied one protein from both families, the AFP from the snow flea (sfAFP) and from the winter flounder (wfAFP), which belong to the hyperactive and moderately active family, respectively. On the basis of molecular dynamics simulations, we have estimated the thickness of the water/ice interface for systems both with and without the AFPs attached onto the ice surface. The calculation of the diffusion profiles along the simulation box allowed us to measure the interface width for different ice planes. The obtained widths clearly show a different influence of the two AFPs on the ice/water interface. The different impact of the AFPs here studied on the interface thickness can be related to two AFPs properties: the protein hydrophobic surface and the number of hydrogen bonds that the two AFPs faces form with water molecules.

  • 1120.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    The Influence of Mutations at the Proximal Histidine Position on the Fe-O2 Bond in Hemoglobin from Density Functional TheoryManuscript (preprint) (Other academic)
  • 1121.
    Tomita, Kota
    et al.
    University of Tokyo, Japan.
    Miyata, Tomohiro
    University of Tokyo, Japan.
    Olovsson, Weine
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Mizoguchi, Teruyasu
    University of Tokyo, Japan.
    Core-Exciton Interaction in Sodium L-2,L-3 edge Structure Investigated Using the Bethe-Salpeter Equation2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 17, p. 9036-9042Article in journal (Refereed)
    Abstract [en]

    Despite the importance of sodium compounds for their application in sodium-ion rechargeable batteries, core-exciton interactions in sodium L-2,L-3 edge core-electron loss spectra are not well-understood. In this study, Bethe-Salpeter equation calculations of sodium L-2,L-3 edges of sodium compounds were performed to understand the relationships between the core-exciton interactions and the electronic structure of sodium compounds. It was revealed that the core-exciton interaction of sodium compounds is strongly dependent on the compounds. We found that neither band gap nor ionic charge can explain the trend; however, the transition energy shows a clear correlation to the magnitude of the core-exciton interaction. These results indicate that the magnitude of the core-exciton interaction is decided by the excited electronic structure of each compound.

  • 1122. Toriyama, Kazumi
    et al.
    Okazaki, Masaharu
    Jansson, Magnus
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Lund, Anders
    Lunell, Sten
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Isotope effect on the J-T distortion of partially deuteriated benzene cation radicals: an experimental EPR and theoretical DFT study2004In: Physical Chemistry and Chemical Physics: PCCP, Vol. 6, no 1658Article in journal (Refereed)
  • 1123.
    Tress, Wolfgang
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering. Swiss Federal Institute Technology EPFL, Switzerland.
    Beyer, Beatrice
    Fraunhofer Institute Electron Beam Plasma Technology and CO, Germany.
    Ashari Astani, Negar
    Ecole Polytech Federal Lausanne, Switzerland.
    Gao, Feng
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Meloni, Simone
    Ecole Polytech Federal Lausanne, Switzerland.
    Rothlisberger, Ursula
    Ecole Polytech Federal Lausanne, Switzerland.
    Extended Intermolecular Interactions Governing Photocurrent-Voltage Relations in Ternary Organic Solar Cells2016In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 19, p. 3936-3944Article in journal (Refereed)
    Abstract [en]

    Efficient organic solar cells are based on (electron) donor-acceptor heterojunctions. An optically generated excited molecular state (exciton) is dissociated at this junction, forming a charge-transfer (CT) state in an intermediate step before the electron and hole are completely separated. The observed highly efficient dissociation of this Coulombically bound state raises the question on the dissociation mechanism. Here, we show that the observed high quantum yields of charge carrier generation and CT state dissociation are due to extended (and consequently weakly bound) CT states visible in absorption and emission spectra and first-principles calculations. Identifying a new geminate-pair loss mechanism via donor excimers, we find that the hole on the small-molecule donor is not localized on a single molecule and charge separation is correlated with the energetic offset between excimer and CT states. Thus, the charges upon interface charge transfer and even in the case of back-transfer and recombination are less localized than commonly assumed.

  • 1124.
    Trobro, Stefan
    et al.
    Uppsala University.
    Åqvist, Johan
    Uppsala University.
    Mechanism of the translation termination reaction on the ribosome2009In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 47, p. 11296-303Article in journal (Refereed)
    Abstract [en]

    Ribosomal release factors (RFs) catalyze the termination of protein synthesis by triggering hydrolysis of the peptidyl-tRNA ester bond in the peptidyl transferase center of the ribosome. With new medium-resolution crystallographic structures of RF-ribosome complexes available, it has become possible to examine the detailed mechanism of this process to resolve the key factors responsible for catalysis of the termination reaction. Here, we report computer simulations of the termination reaction that utilize both the new RF complex structures and information from a high-resolution complex with a P-site substrate analogue. The calculations yield a consistent reaction mechanism that reproduces experimental rates and allows us to identify key interactions responsible for the catalytic efficiency. The results are also in general agreement with an earlier model based on molecular docking. The methylated glutamine residue of the universally conserved GGQ motif plays a key role in the hydrolysis reaction by orienting the water nucleophile and by stabilizing the transition state, and its side chain makes an entropic contribution to the lowering of the activation barrier. Two additional water molecules interacting with the P-site substrate are also found to be critically important. Furthermore, the 2'-OH group of the peptidyl-tRNA substrate is predicted to act as a proton shuttle for the leaving group in analogy with the consensus mechanism for peptidyl transfer. Thus, the ribosome's ability to catalyze both the termination (hydrolysis) and peptidyl transfer (aminolysis) reactions is largely explained by this type of unified mechanism, with similar transition states occurring in both processes.

  • 1125.
    Trzetrzelewski, Maciej
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.). KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Jagiellonian Univ, M Smoluchowski Inst Phys, Lojasiewicza St 11, PL-30348 Krakow, Poland.
    On the equivalence principle and electrodynamics of moving bodies2017In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 120, no 4, article id 40003Article in journal (Refereed)
    Abstract [en]

    We consider a certain extension of Einstein's elevator thought experiment by assuming that the elevator is charged and falls into an electromagnetic field. We argue, on grounds of the equivalence principle, that an observer-dependent metric should exist, for which the geodesics coincide with the trajectories of the charged body in the electromagnetic field. We give a solution to this problem by finding such a metric and hence we are able to recover the Lorentz force law. Recovery of the leading terms of the radiation reaction force is also possible with this approach.

  • 1126.
    Tu, Guangde
    KTH, School of Biotechnology (BIO).
    Studies of self-interaction corrections in density functional theory2007Licentiate thesis, comprehensive summary (Other scientific)
  • 1127.
    Tu, Guangde
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Studies of Self-interaction Corrections in Density Functional Theory2008Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    The self-interaction error (SIE) in density functional theory (DFT) appears from the fact that the residual self-interaction in the Coulomb part and that in the exchange part do not cancel each other exactly. This error is responsible for the unphysical orbital energies of DFT and the failure to reproduce the potential energy curves of several physical processes.

    The present thesis addresses several methods to solve the problem of SIE in DFT. A new algorithm is presented which is based on the Perdew-Zunger (PZ) energy correction and which includes the self-interaction correction (SIC) self-consistently (SC SIC PZ).

    When applied to the study of hydrogen abstraction reactions, for which conventional DFT can not describe the processes properly, SC PZ SIC DFT produces reasonable potential energy curves along the reaction coordinate and reasonable transition barriers.

    A semi-empirical SIC method is designed to correct the orbital energies. It is found that a potential coupling term is generally nonzero for all available approximate functionals. This coupling term also contributes to the self-interaction error. In this scheme, the potential coupling term is multiplied by an empirical parameter , introduced to indicate the strength of the potential coupling, and used to correct the PZ SIC DFT. Through a fitting scheme, we find that a unique can be used for C, N, O core orbitals in different molecules. Therefore this method is now used to correct the core orbital energies and relevant properties. This method is both efficient and accurate in predicting core ionization energies.

    A new approach has been designed to solve the problem of SIE. A functional is constructed based on electron-electron interactions, Coulomb and exchange-correlation parts, which are free of SIE. A post-SCF procedure for this method has been implemented. The orbital energies thus obtained are of higher quality than in conventional DFT. For a molecular system, the orbital energy of the highest occupied molecular orbital (HOMO) is comparable to the experimental first ionization potential energy.

  • 1128.
    Tu, Guangde
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Carravetta, Vincenzo
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Core ionization potentials from self-interaction corrected Kohn-Sham Orbital energies2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 17, p. 174110-Article in journal (Refereed)
    Abstract [en]

    We propose a simple self-interaction correction to Kohn-Sham orbital energies in order to apply ground state Kohn-Sham density functional theory to accurate predictions of core electron binding energies and chemical shifts. The proposition is explored through a series of calculations of organic compounds of different sizes and types. Comparison is made versus experiment and the " ΔKohn -Sham" method employing separate state optimizations of the ground and core hole states, with the use of the B3LYP functional and different basis sets. A parameter α is introduced for a best fitting of computed and experimental ionization potentials. It is found that internal parametrizations in terms of basis set expansions can be well controlled. With a unique α=0.72 and basis set larger than 6-31G, the core ionization energies (IPs) of the self-interaction corrected Kohn-Sham calculations fit quite well to the experimental values. Hence, self-interaction corrected Kohn-Sham calculations seem to provide a promising tool for core IPs that combines accuracy and efficiency.

  • 1129.
    Tu, Guangde
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    An alternative approach to the solution of the self-interaction error in density functional theory with applications to ionization potentialsManuscript (Other academic)
  • 1130.
    Tu, Guangde
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Perdew-Zunger self-interaction corrections in density functional calculations of transition barriers of hydrogen abstraction reactionsArticle in journal (Other academic)
  • 1131.
    Tu, Guangde
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ekström, Ulf
    Department of Physics, Chemistry and Biology, Linköping University.
    Norman, Patrick
    Department of Physics, Chemistry and Biology, Linköping University.
    Carravetta, Vincenzo
    Institute of Chemical-Physical Processes, C.N.R..
    Self-interaction-corrected time-dependent density-functional-theory calculations of x-ray-absorption spectra2007In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 76, no 2, p. 022506-Article in journal (Refereed)
    Abstract [en]

    We outline an approach within time-dependent density functional theory that predicts x-ray spectra on an absolute scale. The approach rests on a recent formulation of the resonant-convergent first-order polarization propagator [P. Norman , J. Chem. Phys. 123, 194103 (2005)] and corrects for the self-interaction energy of the core orbital. This polarization propagator approach makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited-state spectrum. The self-interaction correction for the employed density functional accounts for an energy shift of the spectrum, and fully correlated absolute-scale x-ray spectra are thereby obtained based solely on optimization of the electronic ground state. The procedure is benchmarked against experimental spectra of a set of small organic molecules at the carbon, nitrogen, and oxygen K edges.

  • 1132.
    Tu, Guangde
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    School of Science and Technology, Örebro University.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Core electron chemical shifts of hydrogen-bonded structures2009In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 468, no 4-6, p. 294-298Article in journal (Refereed)
    Abstract [en]

    We examine the possibility to study hydrogen-bonded structures through core ionization energies. We use a recently derived self-interaction corrected density functional theory method where the core ionization energies for all chemically shifted elements are obtained by a single calculation of the ground state of the structures. A direct dependency between the hydrogen atom to acceptor atom bond length and the chemical shift of the core ionization energy of the acceptor atom is found, something that has rami. cations for the possibility of effective predictions of hydrogen bond lengths in hydrogen-bonded systems. This observation is verified by the conventional, much more time-consuming, self-consistent field calculations based on density functional theory.

  • 1133. Tu, Y
    et al.
    Costa Felicissimo, Viviane
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Guimaraes, Freddy
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Selective decomposition of water clusters by strong infrared fields: Rextification of the Lorentz force as a novel mechanism of bond breakingManuscript (preprint) (Other academic)
  • 1134.
    Tu, Yaoquan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Can octupolar molecules be poled by an external electric field?2005In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 109, no 35, p. 16730-16735Article in journal (Refereed)
    Abstract [en]

    Octupolar molecules are generally believed to be of potential use in developing nonlinear optical materials owing to the fact that they do not easily form molecular aggregates. This is often put against the conjectured drawback that electric fields have no poling, or ordering, effect for this class of molecules because of the lack of a permanent ground state dipole moment. In this paper, we analyze this notion in some detail and present results from molecular dynamics computer simulations of an ensemble of a prototypical octupolar molecule, the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecule, dissolved in chloroform. It is found that TATB molecules indeed show rather significant dipole moments in solutions because of the dual action of the thermal motions of the atoms and the strong intermolecular interactions. Applied electric fields accordingly show significant effects on the orientations of the molecular dipole moments. We also find that TATB molecules can aggregate because of the strong hydrogen-bonding interactions between the molecules, though they lack a static permanent dipole moment. Thus, the simulation results for TATB molecules in solution present us with a totally different notion about the collective properties of octupolar molecules. Taking account of quantum chemistry results, we found that the collective molecular nonlinear optical (NLO) properties are enhanced after the onset of the electric field, showing significant anisotropic characteristics.

  • 1135.
    Tu, Yaoquan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Molecular dynamics simulations applied to electric field induced second harmonic generation in dipolar chromophore solutions2006In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, no 18, p. 8971-8977Article in journal (Refereed)
    Abstract [en]

    Electric field induced second harmonic generation (EFISH) is an important experimental technique in extracting the first hyperpolarizability of an organic chromophore molecule. Such experiments are carried out in solutions with chromophore molecules dissolved in some common solvents. A known fact is that the first hyperpolarizabilities extracted from EFISH experiments are subject to the use of local field factors. In this work, we apply simulations to study the EFISH properties of chromophore solutions. By combining quantum chemistry calculations with the results derived from molecular dynamics simulations, we show how macroscopic EFISH properties can be modeled, using 4-(dimethylamino)-4'-nitroazobenzene dissolved in chloroform as a demonstration case. The focus of the study is on deriving accurate local field factors. We find that the local field approach applies very well to dipolar solutions, such as the one studied here, but that the local field factors derived are much smaller than the commonly used Onsager or Lorentz local field factors. Our study indicates that many of the reported first hyperpolarizabilities for dipolar molecules from EFISH experiments are most probably underestimated because the Onsager/Lorentz approach, commonly used in extracting the molecular first hyperpolarizability, neglects the effects of the shapes of dipolar chromophore molecules on the local field factors.

  • 1136.
    Tu, Yaoquan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Nilsson, Lennart
    Laaksonen, Aatto
    A highly efficient Ab initio tight-binding-like approximate density-functional quantum mechanical method2007In: Applied Parallel Computing: State Of The Art In Scientific Computing / [ed] Kagstrom, B; Elmroth, E; Dongarra, J; Wasniewski, J, 2007, Vol. 4699, p. 100-108Conference paper (Refereed)
    Abstract [en]

    A highly efficient ab initio tight-binding-like approximate density-functional quantum mechanical method has recently been developed by us. In this method, the integrals related to the exchange-correlation part are obtained by higher order many-center expansions and all the integrals can be obtained by the interpolation of the look-up tables. The speed of the calculation is also enhanced by using a better way to choose the integrals in the look-up tables. It is shown that the calculated molecular equilibrium geometries and the reaction energies for hydrogenation reactions are very close to those from the usual density functional theory calculations.

  • 1137.
    Ueda, K.
    et al.
    KTH, School of Biotechnology (BIO).
    Liu, X.-J.
    Prumper, G.
    Lischke, T.
    Tanaka, T.
    Hoshino, M.
    Tanaka, H.
    Minkov, Ivaylo
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Kimberg, Victor
    KTH, School of Biotechnology (BIO).
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Role of the recoil effect on two-center interference in x-ray photoionization2006In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 329, no 1-3, p. 329-337Article in journal (Refereed)
    Abstract [en]

    X-ray photoelectron spectra of the N-2 molecule are studied both experimentally and theoretically in the extended energy region up to 1 keV. The ratio of the photoionization cross sections for the gerade and ungerade core levels displays a modulation in the high energy region caused by the two-center interference, as predicted by Cohen and Fano (CF) in 1966. The physical background of this CF effect is the same as in Young's double-slit experiment. We have found that the interference pattern deviates significantly from the CF prediction. The origin of such a breakdown of the CF formula is the scattering of the photoelectron inside the molecule and the momentum transfer from the emitted fast photoelectron to the nuclei. Usually the recoil effect is small. We show that the electron recoil strongly affects the two-center interference pattern. Both stationary and dynamical aspects of the recoil effect shed light on the role of the momentum exchange in the two-center interference.

  • 1138.
    Ugandi, Mihkel
    et al.
    Uppsala Univ, Dept Chem Angstrom, Theoret Chem Programme, Box 538, S-75121 Uppsala, Sweden..
    Galvan, Ignacio Fdez
    Uppsala Univ, Dept Chem Angstrom, Theoret Chem Programme, Box 538, S-75121 Uppsala, Sweden..
    Widmark, Per-Olof
    Lund Univ, Dept Theoret Chem, Lund, Sweden..
    Lindh, Roland
    Uppsala Univ, Dept Chem Angstrom, Theoret Chem Programme, Box 538, S-75121 Uppsala, Sweden..
    Uncontracted basis sets for ab initio calculations of muonic atoms and molecules2018In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 118, no 21, article id e25755Article in journal (Refereed)
    Abstract [en]

    In this work, we investigated muonic atoms and molecules from a quantum chemist's viewpoint by incorporating muons in the CASSCF model. With the aim of predicting muonic X-ray energies, primitive muonic basis sets were developed for a selection of elements. The basis sets were then used in CASSCF calculations of various atoms and molecules to calculate muonic excited states. We described the influence of nuclear charge distribution in predicting muonic X-ray energies. Effects of the electronic wave function on the muonic X-ray energies were also examined. We have computationally demonstrated how the muon can act as a probe for the nuclear charge distribution or electronic wave function by considering lower or higher muonic excited states, respectively.

  • 1139.
    Unge, Mikael
    Linköping University, Department of Physics, Measurement Technology, Biology and Chemistry. Linköping University, The Institute of Technology.
    Electronic properties of organic molecular materials2004Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the context of molecular based electronics, different molecular systems have been studied. In molecular crystals of pentacene, the conduction process has been reported to occur in a single layer in field-effect transistor applications. The electron localization length and its sensitivity to disorder of such two-dimensional disordered systems have been calculated. The electron localization in DNA has also been investigated. Our results show that DNA containing an approximately equal amount of the four basis is insulating. For instance, the human chromosome 22 is an insulator even though it has long-range correlation, which elsewhere has been suggested to give delocalized states.

    The on-site Coulomb interaction has been calculated for rubidium-doped tetracyanoethylene (TCNE). If the electronic state is localized to a small region, e.g., a single molecule, the on-site Coulomb interaction becomes important. The interaction is a measure of the work needed to add an extra electron to the system. When the electronic state is localized to a single molecule/site it becomes large. The result has been used to interpret the outcome of ultraviolet photoelectron spectroscopy (UPS) measurements.

  • 1140. Vaara, J.
    et al.
    Rizzo, A.
    Kauczor, J.
    Norman, Patrick
    Linköping University, Sweden.
    Coriani, S.
    Nuclear spin circular dichroism2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 13, article id 4869849Article in journal (Refereed)
    Abstract [en]

    Recent years have witnessed a growing interest in magneto-optic spectroscopy techniques that use nuclear magnetization as the source of the magnetic field. Here we present a formulation of magnetic circular dichroism (CD) due to magnetically polarized nuclei, nuclear spin-induced CD (NSCD), in molecules. The NSCD ellipticity and nuclear spin-induced optical rotation (NSOR) angle correspond to the real and imaginary parts, respectively, of (complex) quadratic response functions involving the dynamic second-order interaction of the electron system with the linearly polarized light beam, as well as the static magnetic hyperfine interaction. Using the complex polarization propagator framework, NSCD and NSOR signals are obtained at frequencies in the vicinity of optical excitations. Hartree-Fock and density-functional theory calculations on relatively small model systems, ethene, benzene, and 1,4-benzoquinone, demonstrate the feasibility of the method for obtaining relatively strong nuclear spin-induced ellipticity and optical rotation signals. Comparison of the proton and carbon-13 signals of ethanol reveals that these resonant phenomena facilitate chemical resolution between non-equivalent nuclei in magneto-optic spectra.

  • 1141.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Brakestad, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Dynamical Insights into the Decomposition of 1,2-Dioxetane2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 6, p. 2448-2457Article in journal (Refereed)
    Abstract [en]

    Chemiluminescence in 1,2-dioxetane occurs through a thermally activated decomposition reaction into two formaldehyde molecules. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction have been simulated, starting from the first O–O bond-breaking transition structure. The ground-state dissociation occurs between t = 30 fs and t = 140 fs. The so-called entropic trap leads to frustrated dissociations, postponing the decomposition reaction. Specific geometrical conditions are necessary for the trajectories to escape from the entropic trap and for dissociation to be possible. The singlet excited states participate as well in the trapping of the molecule: dissociation including the nonadiabatic transitions to singlet excited states now occurs from t = 30 fs to t = 250 fs and later. Specific regions of the seam of the So/S1 conical intersections that would "retain" the molecule for longer on the excited state have been identified.

  • 1142.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ding, Bo-Wen
    Schramm, Stefan
    Berraud-Pache, Romain
    Naumov, Pance
    Ferré, Nicolas
    Liu, Ya-Jun
    Navizet, Isabelle
    Roca-Sanjuán, Daniel
    Baader, Wilhelm J.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Chemi- and Bioluminescence of Cyclic Peroxides2018In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 118, no 15, p. 6927-6974Article, review/survey (Refereed)
    Abstract [en]

    Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.

  • 1143.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Brakestad, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Non-adabatic dynamics of the 1,2-dioxetane chemiluminescence2017In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 254Article in journal (Other academic)
  • 1144. Vahlberg, C.
    et al.
    Linares, M.
    Norman, Patrick
    Linköping University, Sweden.
    Uvdal, K.
    Phenylboronic ester- and phenylboronic acid-terminated alkanethiols on gold surfaces2012In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 116, no 1, p. 796-806Article in journal (Refereed)
    Abstract [en]

    In this work, it is shown that a well-organized monolayer of phenylboronic ester-terminated thiol (BOR-capped) on gold surfaces can be prepared. Our results also show that the BOR-capped molecular system can be cleaved directly on the surface, resulting in an unprotected BOR-uncapped monolayer with the boronic acid functional groups available for coordination to diol molecules in the ambient media. The monolayers of BOR-capped and BOR-uncapped were characterized using infrared spectroscopy, near edge X-ray absorption fine structure spectroscopy, X-ray photoelectron spectroscopy, ellipsometry, and contact angle goniometry. The X-ray photoelectron spectroscopy results showed that both BOR-capped and BOR-uncapped are chemically linked to the gold substrate. According to the infrared spectroscopy results, the main component of the C=O vibrational mode present in the amide moiety is perpendicular oriented relative to the gold surface normal for the BOR-capped molecular system. The near edge X-ray absorption fine structure spectroscopy resonance peak located at approximately 285 eV, assigned to π 1* transitions, was used to estimate the average tilt angle of the vector parallel to the π* orbitals of the aromatic ring relative to the gold surface normal. The average tilt angle is estimated to be approximately 63° for the BOR-capped monolayer on gold surfaces. The aromatic ring of the BOR-uncapped molecule has a more tilted orientation compared to the BOR-capped one. The experimental infrared spectroscopy and near edge X-ray absorption fine structure spectroscopy results were supported with theoretical modeling including calculations of vibrational modes and of excitation processes.

  • 1145. Vahlberg, C.
    et al.
    Linares, M.
    Villaume, S.
    Norman, Patrick
    Linköping University, Sweden.
    Uvdal, K.
    Noradrenaline and a thiol analogue on gold surfaces: An infrared reflection-absorption spectroscopy, X-ray photoelectron spectroscopy, and near-edge X-ray absorption fine structure spectroscopy study2011In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 115, no 1, p. 165-175Article in journal (Refereed)
    Abstract [en]

    Self-assembled monolayers and multilayers of a noradrenaline analogue (Nor-Pt) on gold substrates as well as multilayers of noradrenaline have been investigated by means of the molecular orientation, the molecule-surface interaction, the molecular composition and the functional group availability for further biointeraction processes, using X-ray photoelectron spectroscopy (XPS), infrared reflection-absorption spectroscopy (IRAS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. A chemical shift (1.7 eV) of the S 2p peak to lower binding energies is observed, in the XPS spectrum, indicating that the Nor-Pt molecules are chemisorbed onto the gold substrate. The IR results show that Nor-Pt adsorbate has the C=O stretching vibration modes parallel oriented relative to the gold substrate. The average tilt angle of the aromatic ring relative to the gold surface normal is determined to be approximately 51°, based on the NEXAFS measurements on Nor-Pt monolayers. The experimental results and assignments are supported with theoretical studies where we use the building block principle in the spectral analysis and compare with the measurements of noradrenaline and Nor-Pt. The theoretical calculations are shown to be useful; for angle dependence NEXAFS studies as resonances with fully φ* or σ* character are preferred for correct analysis.

  • 1146.
    Valiev, R. R.
    et al.
    Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia.;Univ Helsinki, Dept Chem, POB 55,AI Virtanens Plats 1, FIN-00014 Helsinki, Finland..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Tomsk State Univ, 36 Lenin Ave, Tomsk 634050, Russia.
    Sundholm, D.
    Univ Helsinki, Dept Chem, POB 55,AI Virtanens Plats 1, FIN-00014 Helsinki, Finland..
    Relations between the aromaticity and magnetic dipole transitions in the electronic spectra of hetero[8]circulenes2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 48, p. 30239-30246Article in journal (Refereed)
    Abstract [en]

    Magnetically induced current densities have been calculated at the second-order MOller-Plesset perturbation theory (MP2) level for seven hetero[8]circulenes and their dicationic and dianionic forms. Calculations of the magnetic dipole transition moments have also been carried out at the algebraic diagrammatic construction (ADC(2)) and the second-order approximate coupled-cluster (CC2) levels. The calculations show that the degree of aromaticity and the size of the magnetic dipole transition moment of the lowest magnetic-dipole allowed excited state are related. We show that neutral hetero[8]circulenes are weakly antiaromatic when the first excited state with a large magnetic dipole transition moment of 10-16 a.u. lies at high energies (approximate to 2.8-3.5 eV). For the dications, this transition often lies at much lower energies. Hetero[8]circulene dications with large magnetic dipole transition moments are strongly antiaromatic. The lowest excited states of the hetero[8]circulene dianions have very small magnetic dipole transition moments implying that they are aromatic.

  • 1147.
    Van der Spoel, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Ghahremanpour, Mohammad Mehdi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Lemkul, Justin A
    Small Molecule Thermochemistry: A Tool for Empirical Force Field Development2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Refereed)
  • 1148.
    Van Der Spoel, David
    et al.
    Uppsala University.
    Lindahl, Erik
    Stockholm University.
    Hess, Berk
    Max-Planck Institut Mainz.
    Groenhof, Gerrit
    Max-Planck Institut Göttingen.
    Mark, Alan E.
    Groningen University.
    Berendsen, Herman J. C.
    Groningen University.
    GROMACS: fast, flexible, and free2005In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 26, no 16, p. 1701-1718Article in journal (Refereed)
    Abstract [en]

    This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

  • 1149. Van Regemorter, Tanguy
    et al.
    Beljonne, D
    Cornil, J
    Edvinsson, T
    Electronic Structure of Self-Assembled Monolayerson ZnO Surfaces2011Conference paper (Other academic)
  • 1150. Van Regemorter, Tanguy
    et al.
    Jacobsson, Jesper
    Edvinsson, Tomas
    Beljonne, D
    Cornil, J
    Electronic Structure of Self-Assembled Monolayers on ZnO Surfaces2011Conference paper (Other academic)
    Abstract [en]

    Controlling the electronic properties at the interface between organic and inorganic materials is an issue of high interest since it is known to strongly affect the charge injection and the overall efficiency of opto-electronic devices. Self-assembled monolayers (SAMs) can be used to change the electronic properties of the underlying inorganic material and optimize the charge injection occurring at the interface. In this context, we aim here at a fundamental understanding of the electronic processes taking place when SAMs are deposited on ZnO. In particular, our theoretical investigations focus on the origin of the shift in the conduction band upon addition of SAMs on the ZnO surface. Calculations were performed within the framework of density functional theory (DFT) using periodic boundary conditions. The SAMs investigated here are 4-tertbutylpyridine (SAM1) and benzoic acid (SAM2), this latter with three different terminations. We show how the conduction band varies in the presence of SAMs on both polar and non-polar ZnO surfaces, in comparison to the bare surface. We find a shift in opposite direction for SAM1 and SAM2 for both surface orientations. A charge density analysis has been performed to identify the role of the surface orientation, bond dipole and dipole moment of the individual molecules in the observed effect. These theoretical observations have been confronted to preliminary experimental data for ZnO nano-particles with and without SAMs.

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