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  • 1.
    Abrikosov, Igor A.
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Alling, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Steneteg, Peter
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hultberg, Lasse
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Hellman, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Yu Mosyagin, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Department of Theoretical Physics and Quantum Technologies, National Research, Technological University MISiS, Moscow, Russia.
    Lugovskoy, Andrey V.
    Department of Theoretical Physics and Quantum Technologies, National Research, Technological University MISiS, Russia.
    Barannikova, Svetlana A.
    Institute of Strength Physics and Materials Science, Siberian Branch of Russian Academy of Science, Tomsk, Russia; Department of Physics and Engineering, Tomsk State University, Tomsk, Russia.
    Finite Temperature, Magnetic, and Many-Body Effects in Ab Initio Simulations of Alloy Thermodynamics2013In: TMS2013 Supplemental Proceedings, John Wiley & Sons, 2013, p. 617-626Chapter in book (Refereed)
    Abstract [en]

    Ab initio electronic structure theory is known as a useful tool for prediction of materials properties. However, majority of simulations still deal with calculations in the framework of density functional theory with local or semi-local functionals carried out at zero temperature. We present new methodological solution.s, which go beyond this approach and explicitly take finite temperature, magnetic, and many-body effects into account. Considering Ti-based alloys, we discuss !imitations of the quasiharmonic approximation for the treatment of lattice vibrations, and present an accurate and easily extendable method to calculate free ,energies of strongly anharmonic solids. We underline the necessity to going beyond the state-of-the-art techniques for the determination of effective cluster interactions in systems exhibiting mctal-to-insulator transition, and describe a unified cluster expansion approach developed for this class of materials. Finally, we outline a first-principles method, disordered local moments molecular dynamics, for calculations of thermodynamic properties of magnetic alloys, like Cr1-x,.AlxN, in their high-temperature paramagnetic state. Our results unambiguously demonstrate importance of finite temperature effects in theoretical calculations ofthermodynamic properties ofmaterials.

  • 2.
    Andres Cisneros, Gerardo
    et al.
    Wayne State University, MI 48202 USA.
    Thor Wikfeldt, Kjartan
    University of Iceland, Iceland; Stockholm University, Sweden.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Lu, Jibao
    University of Utah, USA.
    Xu, Yao
    Ruhr University of Bochum, Germany.
    Torabifard, Hedieh
    Wayne State University, USA.
    Bartok, Albert P.
    University of Cambridge, England.
    Csanyi, Gabor
    University of Cambridge, England.
    Molinero, Valeria
    University of Utah, USA.
    Paesani, Francesco
    University of Calif San Diego, USA.
    Modeling Molecular Interactions in Water: From Pairwise to Many Body Potential Energy Functions2016In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 116, no 13, p. 7501-7528Article, review/survey (Refereed)
    Abstract [en]

    Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

  • 3.
    Aschebrock, Thilo
    et al.
    University of Bayreuth, Germany.
    Armiento, Rickard
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Kuemmel, Stephan
    University of Bayreuth, Germany.
    Orbital nodal surfaces: Topological challenges for density functionals2017In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 95, no 24, article id 245118Article in journal (Refereed)
    Abstract [en]

    Nodal surfaces of orbitals, in particular of the highest occupied one, play a special role in Kohn-Sham density-functional theory. The exact Kohn-Sham exchange potential, for example, shows a protruding ridge along such nodal surfaces, leading to the counterintuitive feature of a potential that goes to different asymptotic limits in different directions. We show here that nodal surfaces can heavily affect the potential of semilocal density-functional approximations. For the functional derivatives of the Armiento-Kummel (AK13) [Phys. Rev. Lett. 111, 036402 (2013)] and Becke88 [Phys. Rev. A 38, 3098 (1988)] energy functionals, i.e., the corresponding semilocal exchange potentials, as well as the Becke-Johnson [J. Chem. Phys. 124, 221101 (2006)] and van Leeuwen-Baerends (LB94) [Phys. Rev. A 49, 2421 (1994)] model potentials, we explicitly demonstrate exponential divergences in the vicinity of nodal surfaces. We further point out that many other semilocal potentials have similar features. Such divergences pose a challenge for the convergence of numerical solutions of the Kohn-Sham equations. We prove that for exchange functionals of the generalized gradient approximation (GGA) form, enforcing correct asymptotic behavior of the potential or energy density necessarily leads to irregular behavior on or near orbital nodal surfaces. We formulate constraints on the GGA exchange enhancement factor for avoiding such divergences.

  • 4.
    Bengtsson, Katarina
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, Faculty of Science & Engineering. LunaMicro AB, Linkoping, Sweden.
    Robinson, Nathaniel D
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, Faculty of Science & Engineering. LunaMicro AB, Linkoping, Sweden.
    A large-area, all-plastic, flexible electroosmotic pump2017In: Microfluidics and Nanofluidics, ISSN 1613-4982, E-ISSN 1613-4990, Vol. 21, no 12, article id 178Article in journal (Refereed)
    Abstract [en]

    A large-area, fabric-like pump would potentially have applications, for example, in controlling water transport through a garment, such as a rain jacket, regardless of the external temperature and humidity. This paper presents an all-plastic, flexible electroosmotic pump, constructed from commercially available materials: A polycarbonate membrane combined with the electrochemically active polymer poly(3,4-ethylenedioxythiophene) polystyrene sulfonate that actively transports water using an electric potential that can be supplied by a small battery. By using electrochemically active polymer electrodes instead of metal electrodes, the electrochemical reaction that drives flow avoids the oxygen and hydrogen gas production or pH changes associated with water electrolysis. We observe a water mass flux up to 23 mg min(-1) per cm(2) polycarbonate membrane (porosity 10-15%), at an applied potential of 5 V, and a limiting operating pressure of 0.3 kPa V-1, similar to previously reported membrane-based electroosmotic pumps.

  • 5.
    Birke, Ronald L.
    et al.
    CUNY City Coll, NY 10031 USA; CUNY, NY 10016 USA.
    Lombardi, John R.
    CUNY City Coll, NY 10031 USA; CUNY, NY 10016 USA.
    Saidi, Wissam A.
    University of Pittsburgh, PA USA.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Surface-Enhanced Raman Scattering Due to Charge-Transfer Resonances: A Time-Dependent Density Functional Theory Study of Ag-13-4-Mercaptopyridine2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 37, p. 20721-20735Article in journal (Refereed)
    Abstract [en]

    We have used time-dependent density functional theory in conjunction with the CAM-B3LYP functional and MWB28/aug-cc-pVDZ basis set to determine non-, near-, and on-resonance Raman spectra for a complex formed by 4-mercaptopyridine (4-Mpy) binding with a Ag-13 cluster via the thiolate Ag-S bond. Geometry optimizations of the Ag-13-4-mpy complex showed an on-top structure directly bound to one Ag atom with the ring of the molecule almost flat with respect to two Ag atoms of the complex. The corresponding B3LYP/MWB28/aug-cc-pVDZ geometry is also an on-top structure directly bound to one Ag atom, but the molecule is directed away from the surface,. The near-resonance Raman calculations were carried out in the infinite lifetime approximation, while the on-resonant Raman excitation profiles were calculated with the complex polarization propagator (CPP) approach, introducing a half width at half-maximum spectral broadening of 0.2 eV. Calculation of the UV-vis spectra of the isolated 4-Mpy and of the Ag-13-4-Mpy complex showed that binding shifts the spectra from deep in the UV to the visible region. Calculation of the near-resonance Raman spectra of the two structures of the complex at 410 (3.025 eV) and 425 nm (2.918 eV) showed a strong enhancement. A very large variation across vibrational modes by a factor of at least 10(3) was found for both the static chemical enhancement and charge-transfer (CT) enhancement mechanisms. ThiS large variation in enhancement factor indicates that B-term Herzberg-Teller scattering is occurring because inactive or very low intensity modes in the static spectra of the molecule are much stronger in both the static and near-resonance spectra of the Complex. From the excitation profile using the CPP method, an overall surface enhancement on the order 10(3) or higher was found for individual modes on excitation into a CT excited state.

  • 6.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Formation mechanisms of covalent nanostructures from density functional theory2016In: Proceedings of International Workshop on On-Surface Synthesis, Cham: Springer, 2016, p. 269-287Conference paper (Refereed)
    Abstract [en]

    In this chapter, it is demonstrated how electronic structure calculations, with focus on density functional theory, can be used to gain insight about on-surface reactions. I first give a brief introduction to how density functional theory can be used to study reactions. The focus is then shifted to two different types of on-surface reactions, highlighting the theoretical work that has been performed to gain detailed atomistic insight into them. First, the state of the art of the theory behind on-surface Ullmann coupling is described. In this reaction, molecular building blocks dehalogenate, which enables them to covalently couple. The most crucial reaction parameters are identified—the diffusion and coupling barriers of surface-supported radicals—and the potential for theory to optimize these is discussed. We then concentrate on the homo-coupling between terminal alkynes, a rudimentarily different process where molecules initially couple before undergoing a dehydrogenation step. The theory of the mechanism behind this coupling strategy is less developed than that of the on-surface Ullmann coupling, where fundamental questions remain to be unraveled. For example, by the subtle change of substrate from Ag to Au, the on-surface alkyne chemistry is completely altered from the homo-coupling to a cyclodehydrogenation reaction for the same molecular building block, of which origin remains unknown. The main objective of the chapter is to give an impression of what kind of information theory can obtain about reaction on surface, as well as to motivate and inspire for future theoretical studies, which will be needed to turn on-surface synthesis into a more predictive discipline.

  • 7.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Reaction mechanisms for on-surface synthesis of covalent nanostructures2016In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 28, no 8, p. 083002-Article, review/survey (Refereed)
    Abstract [en]

    In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

  • 8.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Linköping University.
    Thermodynamics of an Electrocyclic Ring-Closure Reaction on Au(111)2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 38, p. 21716-21721Article in journal (Refereed)
    Abstract [en]

    We have computationally studied the effects of temperature on the reaction pathway of an electrocyclic ring-closure reaction on the Au(111) surface, particularly focusing on thermodynamic aspects of the reaction. The electrocyclic ring closure is accompanied by a series of dehydrogenation steps, and while it is found that temperature, in terms of vibrational entropy and enthalpy, has a reducing effect on most energy barriers, it does not alter the qualitative appreciation of the reaction kinetics. However, it is found that the way the abstracted hydrogen atoms are treated is crucial for the thermodynamics of the reaction. The overall reaction is highly endothermic but becomes thermodynamically favorable due to the entropy gain of the hydrogen byproducts, which desorb associatively from the surface as H2. The study provides new outlooks for the theoretical treatment of reactions related to on-surface synthesis, anticipated to be instructive for future studies.

  • 9.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Adsorption of large hydrocarbons on coinage metals: a van der Waals density functional study2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 13, p. 2851-2858Article in journal (Refereed)
    Abstract [en]

    The adsorption of organic molecules onto the close-packed facets of coinage metals is studied, and how accurately adsorption heights can be described by using recent advances of the van der Waals density functional (vdWDF), with optPBE/vdWDF, optB86b/vdWDF, vdWDF2, and rev/vdWDF2 functionals is illustrated. The adsorption of two prototypical aromatic hydrocarbons is investigated, and the calculated adsorption heights are compared to experimental literature values from normal incident X-ray standing wave absorption and a state-of-the-art semi-empirical method. It is shown that both the optB86b/vdWDF and rev/vdWDF2 functionals describe adsorption heights with an accuracy of 0.1 Å, compared to experimental values, and are concluded as reliable methods of choice for related systems.

  • 10.
    Bushnell, Eric A. C.
    et al.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Erdtman, Edvin
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Llano, Jorge
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    Örebro universitet, Akademin för naturvetenskap och teknik; School of Chemistry, National University of Ireland, Galway, Ireland.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed)
    Abstract [en]

    In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

  • 11.
    Börjesson, Anders
    et al.
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Erdtman, Edvin
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Ahlström, Peter
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Berlin, Mikael
    Tetra Pak Packaging Solutions AB, Ruben Rausings gata, Lund, Sweden.
    Andersson, Thorbjörn
    Tetra Pak Packaging Solutions AB, Ruben Rausings gata, Lund, Sweden.
    Bolton, Kim
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Molecular modelling of oxygen and water permeation in polyethylene2013In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 54, no 12, p. 2988-Article in journal (Refereed)
    Abstract [en]

    Monte Carlo and molecular dynamics simulations were performed to calculate solubility, S, and diffusion, D, coefficients of oxygen and water in polyethylene, and to obtain a molecular-level understanding of the diffusion mechanism. The permeation coefficient, P, was calculated from the product of S and D. The AMBER force field, which yields the correct polymer densities under the conditions studied, was used for the simulations, and it was observed that the results were not sensitive to the inclusion of atomic charges in the force field. The simulated S for oxygen and water are higher and lower than experimental data, respectively. The calculated diffusion coefficients are in good agreement with experimental data. Possible reasons for the discrepancy in the simulated and experimental solubilities, which results in discrepancies in the permeation coefficients, are discussed. The diffusion of both penetrants occurs mainly by large amplitude, infrequent jumps of the molecules through the polymer matrix.

  • 12.
    Ciobanu, C V
    et al.
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Shavitt, I
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.
    Singer, S J
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.
    Structure and vibrational spectra of H(+)(H(2)O)(8): Is the excess proton in a symmetrical hydrogen bond?2000In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 113, no 13, p. 5321-5330, article id PII [S0021-9606(00)30735-8]Article in journal (Refereed)
    Abstract [en]

    The energetics, structure, and vibrational spectra of a wide variety of H + (H 2 O) 8 structures are calculated using density functional theory and second-order Møller–Plesset ab initio methods. In these isomers of H + (H 2 O) 8 the local environment of the excess proton sometimes resembles a symmetric H 5 O + 2 structure and sometimes H 3 O + , but many structures are intermediate between these two limits. We introduce a quantitative measure of the degree to which the excess proton resembles H 5 O + 2 or H 3 O + . Other bond lengths and, perhaps most useful, the position of certain vibrational bands track this measure of the symmetry in the local structure surrounding the excess proton. The general trend is for the most compact structures to have the lowest energy. However, adding zero-point energy counteracts this trend, making prediction of the most stable isomer impossible at this time. At elevated temperatures corresponding to recent experiments and atmospheric conditions (150–200 K), calculated Gibbs free energies clearly favor the least compact structures, in agreement with recent thermal simulations [Singer, McDonald, and Ojamäe, J. Chem. Phys. 112, 710 (2000)]. © 2000 American Institute of Physics.

  • 13.
    Cirera, Borja
    et al.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain.
    Giménez-Agulló, Nelson
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Martínez-Peña, Francisco
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Martin-Jimenez, Alberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Rodriguez-Fernandez, Jonathan
    Departamento de F´ısica de la Materia Condensada, Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Pizarro, Ana M.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Otero, Roberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, 28049 Madrid, Spain,Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Gallego, José M.
    Instituto de Ciencia de Materiales de Madrid, c/ Sor Juana Ine´s de la Cruz 3, Cantoblanco,Madrid, Spain..
    Ballester, Pablo
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Galan-Mascaros, José R.
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Ecija, David
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, Madrid, Spain.
    Thermal selectivity of intermolecular versus intramolecular reactions on surfaces2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, no 11002Article in journal (Refereed)
    Abstract [en]

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  • 14.
    Dannetun, Per
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Lögdlund, Michael
    Université de Mons-Hainaut, Belgium.
    Spangler, C. W.
    Northen Illinois University, USA.
    Bredas, J. L.
    Université de Mons-Hainaut, Belgium.
    Salaneck, William R.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. william.r.salaneck@liu.se.
    Evolution of Charge-Induced Gap States in Short Diphenylpolyenes as Studied by Photoelectron Spectroscopy1994In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, The Journal of Physical Chemistry, Vol. 98, no 11, p. 2853-2858Article in journal (Refereed)
    Abstract [en]

    The evolution of doping-induced electronic states within the otherwise forbidden energy gap has been studied as a function of the polyene length in a series of diphenylpolyenes. The chemical and electronic structures ha ve been studied using both X-ray and ultraviolet photoelectron spectroscopies. The results are interpreted with the help of quantum chemical calculations, performed using the semiempirical Austin Model 1 and valence effective Hamiltonian methods. The molecules studied area series of diphenylpolyenes, DPx, with x = 1-7 C=C double bonds in the pol yene part of the molecule. Since the frontier or bitals of the diphenylpolyenes are localized on the polyene chain portion of the molecule, there is a high degree of separation of the phenyl and polyene parts of the 11"-systems. Hence, many chemical and electronic properties of diphenylpolyenes are expected to be similar to those of short-chain trans-polyacetylene. For the longer molecules, n = 6 or 7, the present results indicate the presence of doubly charged, interacting soliton-antisoliton pairs, which appear as two new energy levels in the otherwise forbidden energy gap. In diphenyldecaheptaene to stilbene, i.e. 1 ≤ x ≤ 5, however, a singly charged state is formed at intermediate doping levels, after which the soliton-antisoliton pairs appear for the fully doubly charged systems. These results show that, remarkably, even for very short polyene  segments, charges transferred are stored in the form of ( confined) solitons.

  • 15.
    Delange, Pascal
    et al.
    University of Paris Saclay, France.
    Ayral, Thomas
    CEA, France.
    Simak, Sergey
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Ferrero, Michel
    University of Paris Saclay, France; Coll France, France.
    Parcollet, Olivier
    CEA, France.
    Biermann, Silke
    University of Paris Saclay, France; Coll France, France.
    Pourovskii, Leonid
    University of Paris Saclay, France; Coll France, France; National University of Science and Technology MISIS, Russia.
    Large effects of subtle electronic correlations on the energetics of vacancies in alpha-Fe2016In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 94, no 10, p. 100102-Article in journal (Refereed)
    Abstract [en]

    We study the effect of electronic Coulomb correlations on the vacancy formation energy in paramagnetic alpha-Fe within ab initio dynamical mean-field theory. The calculated value for the formation energy is substantially lower than in standard density-functional calculations and in excellent agreement with experiment. The reduction is caused by an enhancement of electronic correlations at the nearest neighbors of the vacancy. This effect is explained by subtle changes in the corresponding spectral function of the d electrons. The local lattice relaxations around the vacancy are substantially increased by many-body effects.

  • 16.
    dos Santos, R. B.
    et al.
    University of Federal Bahia, Brazil.
    Rivelino, R.
    University of Federal Bahia, Brazil.
    de Brito Mota, F.
    University of Federal Bahia, Brazil.
    Kostov Gueorguiev, Gueorgui
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Kakanakova-Gueorguie, Anelia
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Dopant species with Al-Si and N-Si bonding in the MOCVD of AlN implementing trimethylaluminum, ammonia and silane2015In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 48, no 29, article id 295104Article in journal (Refereed)
    Abstract [en]

    We have investigated gas-phase reactions driven by silane (SiH4), which is the dopant precursor in the metalorganic chemical vapor deposition (MOCVD) of aluminum nitride (AlN) doped by silicon, with prime focus on determination of the associated energy barriers. Our theoretical strategy is based on combining density-functional methods with minimum energy path calculations. The outcome of these calculations is suggestive for kinetically plausible and chemically stable reaction species with Al-Si bonding such as (CH3)(2)AlSiH3 and N-Si bonding such as H2NSiH3. Within this theoretical perspective, we propose a view of these reaction species as relevant for the actual MOCVD of Si-doped AlN, which is otherwise known to be contributed by the reaction species (CH3)(2)AlNH2 with Al-N bonding. By reflecting on experimental evidence in the MOCVD of various doped semiconductor materials, it is anticipated that the availability of dopant species with Al-Si, and alternatively N-Si bonding near the hot deposition surface, can govern the incorporation of Si atoms, as well as other point defects, at the AlN surface.

  • 17.
    dos Santos, Renato B.
    et al.
    University of Federal Bahia, Brazil.
    Rivelino, R.
    University of Federal Bahia, Brazil.
    de Brito Mota, F.
    University of Federal Bahia, Brazil.
    Kakanakova-Gueorguie, Anelia
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Gueorguiev, Gueorgui Kostov
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Feasibility of novel (H3C)(n)X(SiH3)(3-n) compounds (X = B, Al, Ga, In): structure, stability, reactivity, and Raman characterization from ab initio calculations2015In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 44, no 7, p. 3356-3366Article in journal (Refereed)
    Abstract [en]

    We employ ab initio calculations to predict the equilibrium structure, stability, reactivity, and Raman scattering properties of sixteen different (H3C)(n)X(SiH3)(3-n) compounds (X = B, Al, Ga, In) with n = 0-3. Among this methylsilylmetal family, only the (H3C)(3)X members, i.e., trimethylboron (TMB), trimethylaluminum (TMA), trimethylgallium (TMG), and trimethylindium (TMI), are currently well-studied. The remaining twelve compounds proposed here open up a two-dimensional array of new possibilities for precursors in various deposition processes, and evoke potential applications in the chemical synthesis of other compounds. We infer that within the (H3C)(n)X(SiH3)(3-n) family, the compounds with fewer silyl groups (and consequently with more methyl groups) are less reactive and more stable. This trend is verified from the calculated cohesive energy, Gibbs free energy of formation, bond strength, and global chemical indices. Furthermore, we propose sequential reaction routes for the synthesis of (H3C)(n)X(SiH3)(3-n) by substitution of methyl by silyl groups, where the silicon source is the silane gas. The corresponding reaction barriers for these chemical transformations lie in the usual energy range typical for MOCVD processes. We also report the Raman spectra and light scattering properties of the newly proposed (H3C)(n)X(SiH3)(3-n) compounds, in comparison with available data of known members of this family. Thus, our computational experiment provides useful information for a systematic understanding of the stability/reactivity and for the identification of these compounds.

  • 18.
    Elinder, Fredrik
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Madeja, Michael
    University of Munster, Germany; Goethe University of Frankfurt, Germany.
    Zeberg, Hugo
    Karolinska Institute, Sweden.
    Arhem, Peter
    Karolinska Institute, Sweden.
    Extracellular Linkers Completely Transplant the Voltage Dependence from Kv1.2 Ion Channels to Kv2.12016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, no 8, p. 1679-1691Article in journal (Refereed)
    Abstract [en]

    The transmembrane voltage needed to open different voltage-gated K (Kv) channels differs by up to 50 mV from each other. In this study we test the hypothesis that the channels voltage dependences to a large extent are set by charged amino-acid residues of the extracellular linkers of the Kv channels, which electrostatically affect the charged amino-acid residues of the voltage sensor S4. Extracellular cations shift the conductance-versus-voltage curve, G(V), by interfering with these extracellular charges. We have explored these issues by analyzing the effects of the divalent strontium ion (Sr2+) on the voltage dependence of the G(V) curves of wild-type and chimeric Kv channels expressed in Xenopus oocytes, using the voltage-clamp technique. Out of seven Kv channels, Kv1.2 was found to be most sensitive to Sr2+ (50 mM shifted G(V) by +21.7 mV), and Kv2.1 to be the least sensitive (+7.8 mV). Experiments on 25 chimeras, constructed from Kv1.2 and Kv2.1, showed that the large Sr2+-induced G(V) shift of Kv1.2 can be transferred to Kv2.1 by exchanging the extracellular linker between S3 and S4 (L3/4) in combination with either the extracellular linker between S5 and the pore (L5/P) or that between the pore and S6 (LP/6). The effects of the linker substitutions were nonadditive, suggesting specific structural interactions. The free energy of these interactions was similar to 20 kJ/mol, suggesting involvement of hydrophobic interactions and/or hydrogen bonds. Using principles from double-layer theory we derived an approximate linear equation (relating the voltage shifts to altered ionic strength), which proved to well match experimental data, suggesting that Sr2+ acts on these channels mainly by screening surface charges. Taken together, these results highlight the extracellular surface potential at the voltage sensor as an important determinant of the channels voltage dependence, making the extracellular linkers essential targets for evolutionary selection.

  • 19.
    Elm, Jonas
    et al.
    University of Copenhagen, Denmark.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Mikkelsen, Kurt V.
    University of Copenhagen, Denmark.
    Rayleigh light scattering properties of atmospheric molecular clusters consisting of sulfuric acid and bases2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 24, p. 15701-15709Article in journal (Refereed)
    Abstract [en]

    The Rayleigh light scattering properties of (H2SO4)(a)(NH3)(b) and (H2SO4)(a)((CH3)(2)NH)(b) atmospheric molecular clusters have been investigated using a response theory approach. Using density functional theory the molecular structures and stepwise formation free energies of clusters with a and b up to 4 have been re-investigated. The Rayleigh scattering intensities are calculated from the dipole polarizability tensor a using the CAM-B3LYP functional by applying linear response methods. The intrinsic scattering properties of (H2SO4)(a)(NH3)(b) and (H2SO4)(a)((CH3)(2)NH)(b) indicate that amine containing clusters scatter light significantly more efficiently then their ammonia containing counterparts. Using the Atmospheric Cluster Dynamics Code (ACDC) the steady state cluster concentrations are estimated and the effective scattering is calculated. The effective scattering is shown to be highly dependent on the estimated concentrations and indicates that there exist competitive pathways, such as nucleation and coagulation, which influence the cluster distributions. The frequency dependence of the scattering is found to depend on the cluster composition and show increased responses when clusters contain more bases than acid molecules. Based on structures obtained using semi-empirical molecular dynamics simulations the Rayleigh scattering properties of clusters with up to 20 acid-base pairs are evaluated. This study represents the first step towards gaining a fundamental understanding of the scattering properties of small atmospheric clusters in the ambient atmosphere.

  • 20.
    Erdtman, Edvin
    Örebro universitet, Akademin för naturvetenskap och teknik.
    5-Aminolevulinic acid and derivatives thereof: properties, lipid permeability and enzymatic reactions2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.

    List of papers
    1. Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives
    Open this publication in new window or tab >>Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives
    2007 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 434, no 1-3, p. 101-106Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.

    Place, publisher, year, edition, pages
    Amsterdam: North-Holland Publishing Co, 2007
    Keywords
    5-aminolevulinic acid, 5ALA, B3LYP, DFT, Protonation states, Alkyl esters
    National Category
    Theoretical Chemistry Physical Chemistry
    Research subject
    Biochemistry; Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150073 (URN)10.1016/j.cplett.2006.11.084 (DOI)000243820100020 ()2-s2.0-33846018089 (Scopus ID)
    Available from: 2007-06-25 Created: 2018-08-09 Last updated: 2018-08-09
    2. Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism
    Open this publication in new window or tab >>Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism
    2008 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 18, p. 4367-4374Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.

    Place, publisher, year, edition, pages
    Washington DC: American Chemical Society, 2008
    Keywords
    Aminolevulinic Acid/*chemistry, Carboxylic Acids/chemistry, Catalysis, Isomerism, Protons, Quantum Theory, Thermodynamics, Water/chemistry
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150074 (URN)10.1021/jp7118197 (DOI)000255486400026 ()18416542 (PubMedID)2-s2.0-43949116597 (Scopus ID)
    Available from: 2008-10-13 Created: 2018-08-09 Last updated: 2018-08-09
    3. Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
    Open this publication in new window or tab >>Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer
    2008 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 463, no 1-3, p. 178-182Article in journal (Refereed) Published
    Abstract [en]

    5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

    Place, publisher, year, edition, pages
    Amsterdam: North-Holland Publishing Co, 2008
    Keywords
    Molecular-dynamics simulations, photodynamic therapy, adenocarcinoma cells, beta transporters, hydrated DPPC, derivates, permeation, protoporphyrin, transition, membranes
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Medicinal Chemistry Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150071 (URN)10.1016/j.cplett.2008.08.021 (DOI)000259150400035 ()2-s2.0-51349091343 (Scopus ID)
    Available from: 2008-10-13 Created: 2018-08-09 Last updated: 2018-08-09
    4. Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase
    Open this publication in new window or tab >>Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase
    2011 (English)In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2-3, p. 479-489Article in journal (Refereed) Published
    Abstract [en]

    Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

    Place, publisher, year, edition, pages
    Amsterdam: Elsevier, 2011
    Keywords
    Schiff base, 5-Aminolevulinic acid, Porphobilinogen synthase, Density functional theory, Catalysis
    National Category
    Natural Sciences Physical Chemistry Physical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150070 (URN)10.1016/j.comptc.2010.11.015 (DOI)000288834500036 ()2-s2.0-80054879916 (Scopus ID)
    Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-08-09
    5. Computational insights into the mechanism of porphobilinogen synthase
    Open this publication in new window or tab >>Computational insights into the mechanism of porphobilinogen synthase
    2010 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 50, p. 16860-16870Article in journal (Refereed) Published
    Abstract [en]

    Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersubstrateC-N and C-C bonds. The active site consists of several invariant residues, including two lysyl residues (Lys210 and Lys263; yeast numbering) that bind the two substrate moieties as Schiff bases. Based on experimental studies, various reaction mechanisms have been proposed for this enzyme that generally can be classified according to whether the intersubstrate C-C or C-N bond is formed first. However, the detailed catalytic mechanism of PBGS remains unclear. In the present study, we have employed density functional theory methods in combination with chemical models of the two key lysyl residues and two substrate moieties in order to investigate various proposed reaction steps and gain insight into the mechanism of PBGS. Importantly, it is found that mechanisms in which the intersubstrate C-N bond is formed first have a ratelimiting barrier (17.5 kcal/mol) that is lower than those in which the intersubstrate C-C bond is formed first (22.8 kcal/mol).

    Place, publisher, year, edition, pages
    Washington: American Chemical Society (ACS), 2010
    National Category
    Natural Sciences Physical Chemistry Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150069 (URN)10.1021/jp103590d (DOI)000285236700023 ()21090799 (PubMedID)2-s2.0-78650384685 (Scopus ID)
    Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-08-09
    6. The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
    Open this publication in new window or tab >>The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase
    Show others...
    2011 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed) Published
    Abstract [en]

    In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

    Place, publisher, year, edition, pages
    New York: John Wiley & Sons, 2011
    Keywords
    uroporphyrinogen decarboxylase III, uroporphyrinogen III, porphyrin biosynthesis, quantum mechanics/molecular mechanics and density functional theory
    National Category
    Natural Sciences Physical Chemistry Physical Chemistry Theoretical Chemistry Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-150066 (URN)10.1002/jcc.21661 (DOI)000288400600007 ()20941734 (PubMedID)2-s2.0-79951968121 (Scopus ID)
    Available from: 2011-01-14 Created: 2018-08-09 Last updated: 2018-08-09
  • 21.
    Erdtman, Edvin
    et al.
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    Bohlén, Martin
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    Ahlström, Peter
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    Gkourmpis, Thomas
    Innovation & Technology, Borealis AB, Stenungsund, Sweden.
    Berlin, Mikael
    Tetra Pak Packaging Solutions AB, Ruben Rausings Gata, Lund, Sweden.
    Andersson, Thorbjörn
    Tetra Pak Packaging Solutions AB, Ruben Rausings Gata, Lund, Sweden.
    Bolton, Kim
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    A molecular-level computational study of the diffusion and solubility of water and oxygen in carbonaceous polyethylene nanocomposites2016In: Journal of Polymer Science Part B: Polymer Physics, ISSN 0887-6266, E-ISSN 1099-0488, Vol. 54, no 5, p. 589-602Article in journal (Refereed)
    Abstract [en]

    Monte Carlo and molecular dynamics simulations were performed to investigate the effect on the solubility, diffusion, and permeability of water and oxygen when adding graphene or single-walled carbon nanotubes (SWCNTs) to polyethylene (PE). When compared with pure PE, addition of graphene lowered the solubility of water, whereas at lower temperatures, the oxygen solubility increased because of the oxygen–graphene interaction. Addition of SWCNTs lowered the solubility of both water and oxygen when compared with pure PE. A detailed analysis showed that an ordered structure of PE is induced near the additive surface, which leads to a decrease in the diffusion coefficient of both penetrants in this region. The addition of graphene does not change the permeation coefficient of oxygen (in the direction parallel to the filler) and, in fact, may even increase this coefficient when compared with pure PE. In contrast, the water permeability is decreased when graphene is added to PE. The addition of SWCNTs decreases the permeability of both penetrants. Graphene can consequently be added to selectively increase the solubility and permeation of oxygen over water, at least at lower temperatures. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 589–602

  • 22.
    Erdtman, Edvin
    et al.
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Bushnell, Eric A. C.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    School of Chemistry, National University of Ireland (NUI Galway), Galway, Ireland.
    Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase2011In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2-3, p. 479-489Article in journal (Refereed)
    Abstract [en]

    Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

  • 23.
    Erdtman, Edvin
    et al.
    Institutionen för naturvetenskap and Modelling and Simulation Research Center, Örebro University, Sweden.
    dos Santos, Daniel J. V. A.
    i. Med. UL/Institute for Medicine and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon. Av. Prof. Gama Pinto, Lisbon, Portugal.
    Löfgren, Lennart
    Head- and Neck Oncology Center, Örebro University Hospital, Örebro, Sweden.
    Eriksson, Leif A.
    Örebro universitet, Institutionen för naturvetenskap.
    Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 463, no 1-3, p. 178-182Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

  • 24.
    Erdtman, Edvin
    et al.
    Örebro universitet, Institutionen för naturvetenskap.
    Eriksson, Leif A.
    Örebro universitet, Institutionen för naturvetenskap.
    Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 434, no 1-3, p. 101-106Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.

  • 25.
    Erdtman, Edvin
    et al.
    Örebro universitet, Institutionen för naturvetenskap.
    Eriksson, Leif A.
    Örebro universitet, Institutionen för naturvetenskap.
    Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 18, p. 4367-4374Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.

  • 26.
    Eriksson, Emma S. E.
    et al.
    Department of Chemistry and Molecular Biology, University of Gothenburg.
    Erdtman, Edvin
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Eriksson, Leif A.
    Department of Chemistry and Molecular Biology, University of Gothenburg.
    Permeability of 5-aminolevulinic acid oxime derivatives in lipid membranes2016In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 135, no 1, p. 1-9Article in journal (Refereed)
    Abstract [en]

    The endogenous molecule 5-aminolevulinic acid (5ALA) and its methyl ester (Me-5ALA) have been used as prodrugs in photodynamic treatment of actinic keratosis and superficial non-melanoma skin cancers for over a decade. Recently, a novel set of 5ALA derivatives based on introducing a hydrolyzable oxime functionality was proposed and shown to generate considerably stronger onset of the photoactive molecule protoporphyrin IX (PpIX) in the cells. In the current work, we employ molecular dynamics simulation techniques to explore whether the higher intercellular concentration of PpIX caused by the oxime derivatives is related to enhanced membrane permeability, or whether other factors contribute to this. It is concluded that the oximes show overall similar accumulation at the membrane headgroup regions as the conventional derivatives and that the transmembrane permeabilities are in general close to that of 5ALA. The highest permeability of all compounds explored is found for Me-5ALA, which correlates with a considerably lower fee energy barrier at the hydrophobic bilayer center. The high PpIX concentration must hence be sought in other factors, where slow hydrolysis of the oxime functionality is a plausible reason, enabling stronger buildup of PpIX over time.

  • 27.
    Eriksson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Photoluminescence Characteristics of III-Nitride Quantum Dots and Films2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    III-Nitride semiconductors are very promising in both electronics and optical devices. The ability of the III-Nitride semiconductors as light emitters to span the electromagnetic spectrum from deep ultraviolet light, through the entire visible region, and into the infrared part of the spectrum, is a very important feature, making this material very important in the field of light emitting devices. In fact, the blue emission from Indium Gallium Nitride (InGaN), which was awarded the 2014 Nobel Prize in Physics, is the basis of the common and important white light emitting diode (LED).

    Quantum dots (QDs) have properties that make them very interesting for light emitting devices for a range of different applications, such as the possibility of increasing device efficiency. The spectrally well-defined emission from QDs also allows accurate color reproduction and high-performance communication devices. The small size of QDs, combined with selective area growth allows for an improved display resolution. By control of the polarization direction of QDs, they can be used in more efficient displays as well as in traditional communication devices. The possibility of sending out entangled photon pairs is another QD property of importance for quantum key distribution used for secure communication.

    QDs can hold different exciton complexes, such as the neutral single exciton, consisting of one electron and one hole, and the biexciton, consisting of two excitons. The integrated PL intensity of the biexciton exhibits a quadratic dependence with respect to the excitation power, as compared to the linear power dependence of the neutral single exciton. The lifetime of the neutral exciton is 880 ps, whereas the biexciton, consisting of twice the number of charge carriers and lacks a dark state, has a considerably shorter lifetime of only 500 ps. The ratio of the lifetimes is an indication that the size of the QD is in the order of the exciton Bohr radius of the InGaN crystal making up these QDs in the InGaN QW.

    A large part of the studies of this thesis has been focused on InGaN QDs on top of hexagonal Gallium Nitride (GaN) pyramids, selectively grown by Metal Organic Chemical Vapor Deposition (MOCVD). On top of the GaN pyramids, an InGaN layer and a GaN capping layer were grown. From structural and optical investigations, InGaN QDs have been characterized as growing on (0001) facets on truncated GaN pyramids. These QDs exhibit both narrow photoluminescence linewidths and are linearly polarized in directions following the symmetry of the pyramids.

    In this work, the neutral single exciton, and the more rare negatively charged exciton, have been investigated. At low excitation power, the integrated intensity of the PL peak of the neutral exciton increases linearly with the excitation power. The negatively charged exciton, on the other hand, exhibits a quadratic power dependence, just like that of the biexciton. Upon increasing the temperature, the power dependence of the negatively charged exciton changes to linear, just like the neutral exciton. This change in power dependence is explained in terms of electrons in potential traps close to the QD escaping by thermal excitation, leading to a surplus of electrons in the vicinity of the QD. Consequently, only a single exciton needs to be created by photoexcitation in order to form a negatively charged exciton, while the extra electron is supplied to the QD by thermal excitation.

    Upon a close inspection of the PL of the neutral exciton, a splitting of the peak of just below 0.4 meV is revealed. There is an observed competition in the integrated intensity between these two peaks, similar to that between an exciton and a biexciton. The high energy peak of this split exciton emission is explained in terms of a remotely charged exciton. This exciton state consists of a neutral single exciton in the QD with an extra electron or hole in close vicinity of the QD, which screens the built-in field in the QD.

    The InGaN QDs are very small; estimated to be on the order of the exciton Bohr radius of the InGaN crystal, or even smaller. The lifetimes of the neutral exciton and the negatively charged exciton are approximately 320 ps and 130 ps, respectively. The ratio of the lifetimes supports the claim of the QD size being on the order of the exciton Bohr radius or smaller, as is further supported by power dependence results. Under the assumption of a spherical QD, theoretical calculations predict an emission energy shift of 0.7 meV, for a peak at 3.09 eV, due to the built-in field for a QD with a diameter of 1.3 nm, in agreement with the experimental observations.

    Studying the InGaN QD PL from neutral and charged excitons at elevated temperatures (4 K to 166 K) has revealed that the QDs are surrounded by potential fluctuations that trap charge carriers with an energy of around 20 meV, to be compared with the exciton trapping energy in the QDs of approximately 50 meV. The confinement of electrons close to the QD is predicted to be smaller than for holes, which accounts for the negative charge of the charged exciton, and for the higher probability of capturing free electrons. We have estimated the lifetimes of free electrons and holes in the GaN barrier to be 45 ps and 60 ps, in consistence with excitons forming quickly in the barrier upon photoexcitation and that free electrons and holes get trapped quickly in local potential traps close to the QDs. This analysis also indicates that there is a probability of 35 % to have an electron in the QD between the photoexcitation pulses, in agreement with a lower than quadratic power dependence of the negatively charged exciton.

    InN is an attractive material due to its infrared emission, for applications such as light emitters for communication purposes, but it is more difficult to grow with high quality and low doping concentration as compared to GaN. QDs with a higher In-composition or even pure InN is an interesting prospect as being a route towards increased quantum confinement and room temperature device operation. For all optical devices, p-type doping is needed. Even nominally undoped InN samples tend to be heavily n-type doped, causing problems to make pn-junctions as needed for LEDs. In our work, we present Mg-doped p-type InN films, which when further increasing the Mg-concentration revert to n-type conductivity. We have focused on the effect of the Mg-doping on the light emission properties of these films. The low Mg doped InN film is inhomogeneous and is observed to contain areas with n-type conductivity, so called n-type pockets in the otherwise p-type InN film. A higher concentration of Mg results in a higher crystalline quality and the disappearance of the n-type pockets. The high crystalline quality has enabled us to determine the binding energy of the Mg dopants to 64 meV. Upon further increase of the Mg concentration, the film reverts to ntype conductivity. The highly Mg doped sample also exhibits a red-shifted emission with features that are interpreted as originating from Zinc-Blende inclusions in the Wurtzite InN crystal, acting as quantum wells. The Mg doping is an important factor in controlling the conductivity of InN, as well as its light emission properties, and ultimately construct InN-based devices.

    In summary, in this thesis, both pyramidal InGaN QDs and InGaN QDs in a QW have been investigated. Novel discoveries of exciton complexes in these QD systems have been reported. Knowledge has also been gained about the challenging material InN, including a study of the effect of the Mg-doping concentration on the semiconductor crystalline quality and its light emission properties. The outcome of this thesis enriches the knowledge of the III-Nitride semiconductor community, with the long-term objective to improve the device performance of III-Nitride based light emitting devices.

    List of papers
    1. InGaN quantum dot formation mechanism on hexagonal GaN/InGaN/GaN pyramids
    Open this publication in new window or tab >>InGaN quantum dot formation mechanism on hexagonal GaN/InGaN/GaN pyramids
    Show others...
    2012 (English)In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 23, no 30, p. 305708-Article in journal (Refereed) Published
    Abstract [en]

    Growing InGaN quantum dots (QDs) at the apex of hexagonal GaN pyramids is an elegant approach to achieve a deterministic positioning of QDs. Despite similar synthesis procedures by metal–organic chemical vapor deposition, the optical properties of the QDs reported in the literature vary drastically. The QDs tend to exhibit either narrow or broad emission lines in the micro-photoluminescence spectra. By coupled microstructural and optical investigations, the QDs giving rise to narrow emission lines were concluded to nucleate in association with a (0001) facet at the apex of the GaN pyramid.

    Place, publisher, year, edition, pages
    Institute of Physics (IOP), 2012
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:liu:diva-79321 (URN)10.1088/0957-4484/23/30/305708 (DOI)000306333500030 ()
    Available from: 2012-07-10 Created: 2012-07-10 Last updated: 2017-12-07Bibliographically approved
    2. Dynamic characteristics of the exciton and the biexciton in a single InGaN quantum dot
    Open this publication in new window or tab >>Dynamic characteristics of the exciton and the biexciton in a single InGaN quantum dot
    Show others...
    2012 (English)In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 101, no 6Article in journal (Refereed) Published
    Abstract [en]

    The dynamics of the exciton and the biexciton related emission from a single InGaN quantum dot (QD) have been measured by time-resolved microphotoluminescence spectroscopy. An exciton-biexciton pair of the same QD was identified by the combination of power dependence and polarization-resolved spectroscopy. Moreover, the spectral temperature evolution was utilized in order to distinguish the biexciton from a trion. Both the exciton and the biexciton related emission reveal mono-exponential decays corresponding to time constants of similar to 900 and similar to 500 ps, respectively. The obtained lifetime ratio of similar to 1.8 indicates that the QD is small, with a size comparable to the exciton Bohr radius.

    Place, publisher, year, edition, pages
    American Institute of Physics (AIP), 2012
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-84908 (URN)10.1063/1.4742343 (DOI)000307862400022 ()
    Note

    Funding Agencies|Thaksin University in Thailand||Swedish Research Council (VR)||Swedish Foundation for Strategic Research (SSF)||Knut and Alice Wallenberg Foundation||

    Available from: 2012-10-26 Created: 2012-10-26 Last updated: 2017-12-07
    3. The charged exciton in an InGaN quantum dot on a GaN pyramid
    Open this publication in new window or tab >>The charged exciton in an InGaN quantum dot on a GaN pyramid
    Show others...
    2013 (English)In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 103, no 1Article in journal (Refereed) Published
    Abstract [en]

    The emission of a charged exciton in an InGaN quantum dot (QD) on top of a GaN pyramid is identified experimentally. The intensity of the charged exciton exhibits the expected competition with that of the single exciton, as observed in temperature-dependent micro-photoluminescence measurements, performed with different excitation energies. The non-zero charge state of this complex is further supported by time resolved micro-photoluminescence measurements, which excludes neutral alternatives of biexciton. The potential fluctuations in the vicinity of the QD that localizes the charge carriers are proposed to be responsible for the unequal supply of electrons and holes into the QD.

    Place, publisher, year, edition, pages
    American Institute of Physics (AIP), 2013
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-95961 (URN)10.1063/1.4812984 (DOI)000321497200036 ()
    Note

    Funding Agencies|NANO-N consortium||Swedish Foundation for Strategic Research (SSF)||

    Available from: 2013-08-19 Created: 2013-08-12 Last updated: 2017-12-06
  • 28.
    Fahleson, Tobias
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Development and characterization of damped cubic response functions with application to two-photon absorption2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Molecular response to electromagnetic fields - static or optical - within a framework of perturbation theory diverges close to resonance with molecular transitionen energies, and need work-around solutions for real-valued response functions. This licentiate thesis deals with nonlinear response, with focus being on cubic polarizaibilities, and outlines the underlying mathematics for exact-state and approximatestate, complex-valued response functions applicable to quantum chemical computation. Such a complex-valued response theory is commonly known as dampedresponse theory, for which the response functions consists of a real and an imaginary component, each of them representing various spectroscopies in nature. In addition to the mathematics, the formulas have been implemented in the quantum chemical package DALTON, and several tests determining the integrity of the implementation has been conducted.

    The fourth and final major part of the thesis is concerned with applied nonlinear response theory, including not only cubic response functions, but also quadratic and linear response functions, some of which are of the more exotic character. Three spectroscopies have been investigated for small and medium-sized organic molecules and the neon atom: two-photon absorption (TPA), Jones birefringence (JB), and magnetic circular dichroism (MCD).

    The TPA part is a simple demonstration of capability of the damped cubic response code, for which neon is the example system. Perfect agreement is shown for the Ehrenfest approach and an independent implementation based on the quasienergy formalism.

    JB is an optical eect in which induced refractive anisotropy, by means of external electric and magnetic static elds, results in ellipticity of linearly polarized light beams. This part mainly discuss implications from a paper which the current author took part in. The paper ultimately attempts to indentify the general observable strength of the effect, and coincidentaly pin-point some particular system suitable for experiments. Among other finds, JB is found to be correlated to the electric dipole moment, and for monosubstituted benzenes, the para-Hammett constant.

    Finally, MCD is discussed based on three papers in which the present author is included. The elegant MCD solution to broad absorption peaks, for which it is desired to distinguish individual states, is demonstrated on adenine and three additional purine derivatives. A drawn out debate regarding relative stability of certain low-lying states could be settled by this method. Furthermore, appropriate description of solvation environment in conjunction with the exchange-correlation functionals B3LYP and CAM-B3LYP is investigated on purine and pyrimidine derivatives. CAM-B3LYP is found to be superior in terms of general prole shapes, while results regarding solvation model are rather inconclusive, although the results suggests some level of solvation model is appropriate, such as a polarizable continuum model or explicit solvation molecules.

    List of papers
    1. The magnetic circular dichroism spectrum of the C-60 fullerene
    Open this publication in new window or tab >>The magnetic circular dichroism spectrum of the C-60 fullerene
    2013 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, no 9-11, p. 1401-1404Article in journal (Refereed) Published
    Abstract [en]

    The magnetic circular dichroism spectrum of the C-60 fullerene has been determined with the use of Kohn-Sham density functional theory in conjunction with the CAM-B3LYP exchange-correlation functional. The experimental spectrum of Gasyna etal. [Chem. Phys. Lett. 183, 283 (1991)] covering the wavelength region above 200 nm is explained by the signal responses from the three lowest singlet states of T-1u symmetry.

    Place, publisher, year, edition, pages
    Taylor and Francis: STM, Behavioural Science and Public Health Titles, 2013
    Keywords
    magnetic circular dichroism, MCD, C60, fullerene, density functional theory, DFT, response theory
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-97674 (URN)10.1080/00268976.2013.779394 (DOI)000323409600035 ()
    Note

    Funding Agencies|Swedish Research Council|621-2010-5014|Italian PRIN funding scheme (project: Theoretical and Computational Simulations of Quantum Molecular Processes)||

    Available from: 2013-09-19 Created: 2013-09-19 Last updated: 2017-12-06
    2. A density functional theory study of magneto-electric Jones birefringence of noble gases, furan homologues, and mono-substituted benzenes
    Open this publication in new window or tab >>A density functional theory study of magneto-electric Jones birefringence of noble gases, furan homologues, and mono-substituted benzenes
    Show others...
    2013 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, no 19, p. 194311-Article in journal (Refereed) Published
    Abstract [en]

    We report on the results of a systematic ab initio study of the Jones birefringence of noble gases, of furan homologues, and of monosubstituted benzenes, in the gas phase, with the aim of analyzing the behavior and the trends within a list of systems of varying size and complexity, and of identifying candidates for a combined experimental/theoretical study of the effect. We resort here to analytic linear and nonlinear response functions in the framework of time-dependent density functional theory. A correlation is made between the observable (the Jones constant) and the atomic radius for noble gases, or the permanent electric dipole and a structure/chemical reactivity descriptor as the para Hammett constant for substituted benzenes.

    Place, publisher, year, edition, pages
    American Institute of Physics (AIP), 2013
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-102851 (URN)10.1063/1.4830412 (DOI)000327714900024 ()
    Note

    Funding Agencies|EuroMagNET II, under EU|228043|Swedish Research Council|621-2010-5014|Italian Ministero dellIstruzione, Universita e Ricerca|2009C28YBF_001|National Supercomputer Centre (NSC), Sweden||Italian CINECA||

    Available from: 2014-01-07 Created: 2014-01-02 Last updated: 2017-12-06
    3. Relative Stability of the L-a and L-b Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra
    Open this publication in new window or tab >>Relative Stability of the L-a and L-b Excited States in Adenine and Guanine: Direct Evidence from TD-DFT Calculations of MCD Spectra
    Show others...
    2014 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 5, no 11, p. 1806-1811Article in journal (Refereed) Published
    Abstract [en]

    The relative position of L-a and L-b pi pi* electronic states in purine nucleobases is a much debated topic, since it can strongly affect our understanding of their photoexcited dynamics. To assess this point, we calculated the absorption and magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides in gas-phase and aqueous solution,. exploiting recent developments in MCD computational technology within time-dependent density functional theory. MCD spectroscopy allows us to resolve the intense S-0 -greater than L-a transition from the weak S-0 -greater than L-b transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP functionals and describing solvent effect by cluster models and by the polarizable continuum model (PCM), are in very good agreement with the experimental counterparts, thus providing direct and unambiguous evidence that the energy ordering predicted by TD-DFT, L-a less than L-b, is the correct one.

    Place, publisher, year, edition, pages
    American Chemical Society, 2014
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-108796 (URN)10.1021/jz500633t (DOI)000337012500005 ()
    Available from: 2014-07-07 Created: 2014-07-06 Last updated: 2017-12-05
    4. TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids
    Open this publication in new window or tab >>TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids
    Show others...
    2015 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5476-5489Article in journal (Refereed) Published
    Abstract [en]

    We present a computational study of the Magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil,thymine, and cytosine, Using the B3LYP and CAM-B3LYP functionals. Solvent effects, are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In, general; the computed spectra are found to be in good agreement with the experimental ones, aprt from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine base are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to,that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific,but they do not in general alter the qualitative shape of the spectra. The bands are dominated the-bright pi -greater than pi* transitions; and our calculations in solution nicely reproduce theft energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n -greater than pi* excitations, but they are too weak to be observed in the. experiment.

    Place, publisher, year, edition, pages
    American Chemical Society, 2015
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-119800 (URN)10.1021/jp512468k (DOI)000355495100043 ()25648759 (PubMedID)
    Note

    Funding Agencies|PRIN [2010ERFKXL_008]; University of Trieste [CHIM02-Ricerca]

    Available from: 2015-06-26 Created: 2015-06-26 Last updated: 2017-12-04
    5. Resonant-convergent cubic response function in the random-phase approximation with application to two-photon absorption on neon in the ultraviolet-visible region
    Open this publication in new window or tab >>Resonant-convergent cubic response function in the random-phase approximation with application to two-photon absorption on neon in the ultraviolet-visible region
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Damped cubic response functions are presented for exact-state and approximate-state methods eligible for quantum chemical computational applications. Proof of proper implementation is given, accompanied by a two-photon absorption example on neon in the ultraviolet-visible spectral region. The method accurately distinguish one- and two-photon resonances and exhibits spot-on agreement with other approaches.

    Keywords
    Hyperpolarizability, damped response, cubic response
    National Category
    Theoretical Chemistry Chemical Sciences
    Identifiers
    urn:nbn:se:liu:diva-123971 (URN)
    Available from: 2016-01-15 Created: 2016-01-15 Last updated: 2016-01-15Bibliographically approved
  • 29.
    Fahleson, Tobias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Kauczor, Joanna
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Santoro, Fabrizio
    CNR, Italy.
    Improta, Roberto
    CNR, Italy.
    Coriani, Sonia
    University of Trieste, Italy; Aarhus University, Denmark.
    TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5476-5489Article in journal (Refereed)
    Abstract [en]

    We present a computational study of the Magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil,thymine, and cytosine, Using the B3LYP and CAM-B3LYP functionals. Solvent effects, are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In, general; the computed spectra are found to be in good agreement with the experimental ones, aprt from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine base are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to,that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific,but they do not in general alter the qualitative shape of the spectra. The bands are dominated the-bright pi -greater than pi* transitions; and our calculations in solution nicely reproduce theft energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n -greater than pi* excitations, but they are too weak to be observed in the. experiment.

  • 30.
    Fahleson, Tobias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Resonant-convergent cubic response function in the random-phase approximation with application to two-photon absorption on neon in the ultraviolet-visible regionManuscript (preprint) (Other academic)
    Abstract [en]

    Damped cubic response functions are presented for exact-state and approximate-state methods eligible for quantum chemical computational applications. Proof of proper implementation is given, accompanied by a two-photon absorption example on neon in the ultraviolet-visible spectral region. The method accurately distinguish one- and two-photon resonances and exhibits spot-on agreement with other approaches.

  • 31.
    Falklöf, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Computational Studies of Photobiological Keto-Enol Reactions and Chromophores2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents computational chemistry studies of keto-enol reactions and chromophores of photobiological signicance.

    The rst part of the thesis is concerned with two protein-bound chromophores that, depending on the chemical conditions, can exist in a number of dierent ketonic and enolic forms. The rst chromophore is astaxanthin, which occurs in the protein complex responsible for the deep-blue color of lobster carapace. By investigating how dierent forms of astaxanthin absorb UV-vis radiation of dierent wavelengths, a model is presented that explains the origin of the dramatic color change from deep-blue to red upon cooking of live lobsters.

    The second chromophore is the oxyluciferin light emitter of fireflies, which is formed in the catalytic center of the enzyme firefly luciferase. To date, there is no consensus regarding which of the possible ketonic and enolic forms is the key contributor to the light emission. In the thesis, the intrinsic tendency of oxyluciferin to prefer one particular form over other possible forms is established through calculation of keto-enol and acid-base excited-state equilibrium constants in aqueous solution.

    The second part of the thesis is concerned with two families of biological photoreceptors: the blue-light-absorbing LOV-domain proteins and the red-light-absorbing phytochromes. Based on the ambient light environment, these proteins regulate physiological and developmental processes by switching between inactive and active conformations. In both families, the conversion of the inactive into the active conformation is triggered by a chemical reaction of the respective chromophore.

    The LOV-domain proteins bind a LOV-domain proteins bidn in flavin chromophore and regulate processes such as chloroplast relocation and phototropism in plants. An important step in the activation of these photoreceptors is a singlet-triplet transition between two electronically excited states of the flavin chromophore. In the thesis, this transition is used as a prototype example for illustrating, for the rst time, the ability of rst-principles methods to calculate rate constants of inter-excited state phosphorescence events.

    Phytochromes, in turn, bind bilin chromophores and are active in the regulation of processes like seed germination and  flowering time in plants. Following two systematic studies identifying the best way to model the UV-vis absorption and fluorescence spectra of these photoreceptors, it is demonstrated that steric interactions between the chromophore and the apoprotein play a decisive role for how phytochromes are activated by light.

    List of papers
    1. On the origin and variation of colors in lobster carapace
    Open this publication in new window or tab >>On the origin and variation of colors in lobster carapace
    Show others...
    2015 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 26, p. 16723-16732Article in journal (Refereed) Published
    Abstract [en]

    The chemical basis of the blue-black to pink-orange color change on cooking of lobster, due to thermal denaturation of an astaxanthin-protein complex, alpha-crustacyanin, in the lobster carapace, has so far been elusive. Here, we investigate the relaxation of the astaxanthin pigment from its bound enolate form to its neutral hydroxyketone form, as origin of the spectral shift, by analyzing the response of UV-vis spectra of a water-soluble 3-hydroxy-4-oxo-beta-ionone model of astaxanthin to increases in pH, and by performing extensive quantum chemical calculations over a wide range of chemical conditions. The enolization of astaxanthin is consistent with the X-ray diffraction data of beta-crustacyanin (PDB code: 1GKA) whose crystals possess the distinct blue color. We find that enolate formation is possible within the protein environment and associated with a large bathochromic shift, thus offering a cogent explanation for the blue-black color and the response to thermal denaturation and revealing the chemistry of astaxanthin upon complex formation.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2015
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:liu:diva-120247 (URN)10.1039/c4cp06124a (DOI)000356874000010 ()25797168 (PubMedID)
    Note

    Funding Agencies|Bildungs- und Kultur-departement des Kantons Luzern, Switzerland; Swedish Research Council; Olle Engkvist Foundation; Nuffield Foundation; School of Chemistry, University of Manchester; European Molecular Biology Laboratory

    Available from: 2015-07-21 Created: 2015-07-20 Last updated: 2017-12-04
    2. Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants
    Open this publication in new window or tab >>Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants
    2014 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 30, p. 2184-2194Article in journal (Refereed) Published
    Abstract [en]

    Although recent years have seen much progress in the elucidation of the mechanisms underlying the bioluminescence of fireflies, there is to date no consensus on the precise contributions to the light emission from the different possible forms of the chemiexcited oxyluciferin (OxyLH(2)) cofactor. Here, this problem is investigated by the calculation of excited-state equilibrium constants in aqueous solution for keto-enol and acid-base reactions connecting six neutral, monoanionic and dianionic forms of OxyLH(2). Particularly, rather than relying on the standard Forster equation and the associated assumption that entropic effects are negligible, these equilibrium constants are for the first time calculated in terms of excited-state free energies of a Born-Haber cycle. Performing quantum chemical calculations with density functional theory methods and using a hybrid cluster-continuum approach to describe solvent effects, a suitable protocol for the modeling is first defined from benchmark calculations on phenol. Applying this protocol to the various OxyLH(2) species and verifying that available experimental data (absorption shifts and ground-state equilibrium constants) are accurately reproduced, it is then found that the phenolate-keto-OxyLH(-) monoanion is intrinsically the preferred form of OxyLH(2) in the excited state, which suggests a potential key role for this species in the bioluminescence of fireflies.

    Place, publisher, year, edition, pages
    Wiley: 12 months, 2014
    Keywords
    light emission; tautomerism; protonation state; Born-Haber cycle; density functional theory
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-112610 (URN)10.1002/jcc.23735 (DOI)000344173700003 ()25226816 (PubMedID)
    Note

    Funding Agencies|Linkoping University; Swedish Research Council; Olle Engkvist Foundation; Wenner-Gren Foundations

    Available from: 2014-12-10 Created: 2014-12-05 Last updated: 2017-12-05
    3. Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin
    Open this publication in new window or tab >>Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin
    2015 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 49, p. 11911-11921Article in journal (Refereed) Published
    Abstract [en]

    Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states, can be supplemented by the ability to also describe inter-excited state phosphorescence. Specifically, performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL*) singlet state of lumiflavin to the 3(πHπL*), 3(nN2πL*) and 3(πH–1πL*) triplet states, and subsequently compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically two to five orders of magnitude smaller than the nonradiative ones.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2015
    Keywords
    Inter-excited state transition dipole moments, Radiative transitions, Nonradiative transitions, Response theory, Time-dependent density functional theory, Flavin chromophores
    National Category
    Chemical Sciences Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-122743 (URN)10.1021/acs.jpca.5b08908 (DOI)000366339400016 ()
    Note

    Vid tiden för disputation förelåg publikationen som manuskript

    Available from: 2015-11-19 Created: 2015-11-19 Last updated: 2017-12-01Bibliographically approved
    4. Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
    Open this publication in new window or tab >>Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
    2013 (English)In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 19-28Article in journal (Refereed) Published
    Abstract [en]

    Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

    Place, publisher, year, edition, pages
    Elsevier, 2013
    Keywords
    bilin chromophores, photoreceptor proteins, fluorescent proteins, excited states, quantum chemistry
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-96694 (URN)10.1016/j.chemphys.2013.07.018 (DOI)000327443700003 ()
    Note

    Funding agencies|Linkoping University||Swedish Research Council||Olle Engkvist Foundation||Wenner-Gren Foundations||

    Available from: 2013-08-23 Created: 2013-08-23 Last updated: 2017-12-06Bibliographically approved
    5. Modeling of phytochrome absorption spectra
    Open this publication in new window or tab >>Modeling of phytochrome absorption spectra
    2013 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 16, p. 1363-1374Article in journal (Refereed) Published
    Abstract [en]

    Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2013
    Keywords
    photosensory proteins, bilin chromophores, QM/MM methods, time-dependent density functional theory
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-92393 (URN)10.1002/jcc.23265 (DOI)000318696800001 ()
    Available from: 2013-05-10 Created: 2013-05-10 Last updated: 2017-12-06Bibliographically approved
    6. QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome
    Open this publication in new window or tab >>QM/MM Modeling Highlights the Importance of Steric Effects in the Photoactivation of a Bacteriophytochrome
    2015 (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Phytochromes constitute a superfamily of photoreceptor proteins that exist in two forms that absorb red (Pr) and far-red (Pfr) light. The conversion of Pr into Pfr (the biologically active form) is triggered by a ZE photoisomerization of the bilin chromophore at the C15-C16 bond of the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on a highresolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions prevent photoisomerization at any other site than the C15-C16 bond. The tendency of phytochromes to always isomerize at this very bond would thus be explained by steric effects.

    National Category
    Chemical Sciences Physical Chemistry
    Identifiers
    urn:nbn:se:liu:diva-122744 (URN)
    Available from: 2015-11-19 Created: 2015-11-19 Last updated: 2015-11-26Bibliographically approved
  • 32.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    About the atomic shell structure in real space and the Pauli exclusion principle2016In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 135, no 6, p. 148-Article in journal (Refereed)
    Abstract [en]

    It is shown that any set of eigenfunctions (1s, 2s) of a bare Coulomb Hamiltonian exhibit the same atomic shell structure pattern for the real-space indicator a(1), which is defined as the ratio between the positive kinetic energy density and the electron density. Since this model Hamiltonian excludes all effects due to the electron-electron repulsion, the appearance of the atomic shell structure is attributed to the Pauli exclusion principle that arises from the requirements for a fermionic wavefunction. Since the derivation is independent of the nuclear charge and the energy of the system, reversely imposing proper atomic shell structure behavior in the design of kinetic energy functionals mimics the Pauli exclusion principle during a variational process.

  • 33.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    About the compatibility between ansatzes and constraints for a local formulation of orbital-free density functional theory2017In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 117, no 5, article id UNSP e25329Article in journal (Refereed)
    Abstract [en]

    Functional properties that are exact for the Hohenberg-Kohn functional may turn into mutually exclusive constraints at a given level of ansatz. This is exemplarily shown for the local density approximation. Nevertheless, it is possible to reach exactly the Kohn-Sham data from an orbital-free density functional framework based on simple one-point functionals by starting from the Levy-Perdew-Sahni formulation. The energy value is obtained from the density-potential pair, and therefore does not refer to the functional dependence of the potential expression. Consequently, the potential expression can be obtained from any suitable model and is not required to follow proper scaling behavior.

  • 34.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    About the Difference Between Density Functionals Defined by Energy Criterion and Density Functionals Defined by Density Criterion: Exchange Functionals2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, no 15, p. 1187-1189Article in journal (Refereed)
    Abstract [en]

    The difference between density functionals defined by energy criterion and density functionals defined by density criterion is studied for the exchange functional. It is shown that Slater potentials are exact exchange potentials in the sense that they yield the Hartree-Fock electron density if all operators are given by local expressions. (C) 2016 Wiley Periodicals, Inc.

  • 35.
    Finzel, Kati
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Approximating the Pauli Potential in Bound Coulomb Systems2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, no 16, p. 1261-1266Article in journal (Refereed)
    Abstract [en]

    It is shown that the Pauli potential in bound Coulomb systems can in good approximation be composed from the corresponding atomic fragments. This provides a simple and fast procedure how to generate the Pauli potential in bound systems, which is needed to perform an orbital-free density functional calculation. The method is applicable to molecules and solids. (c) 2016 Wiley Periodicals, Inc.

  • 36.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Ayers, Paul W.
    McMaster University, Canada.
    Functional constructions with specified functional derivatives2016In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 135, no 12, article id 255Article in journal (Refereed)
    Abstract [en]

    A bifunctional construction depending on a specified density-potential pair and an approximate guiding electron density functional is presented. The proposed bifunctional construction properly transforms under homogeneous coordinate scaling and yields the specified functional derivative, which determines the electron density. Whereas the method is general and applicable to all functional types, it will prove especially helpful in the context of orbital-free density functional theory, where most existing approximate density functionals predict inaccurate potentials.

  • 37.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Baranov, Alexey I.
    Max Planck Institute Chemistry Phys Solids, Germany.
    A simple model for the Slater exchange potential and its performance for solids2017In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 117, no 1, p. 40-47Article in journal (Refereed)
    Abstract [en]

    A simple local model for the Slater exchange potential is determined by least square fit procedure from Hartree-Fock (HF) atomic data. Since the Slater potential is the exact exchange potential yielding HF electron density from Levy-Perdew-Sahni density functional formalism (Levy et al., Phys. Rev. A 1984, 30, 2745), the derived local potential is significantly more negative than the conventional local density approximation. On the set of 22 ionic, covalent and van der Waals solids including strongly correlated transition metal oxides, it has been demonstrated, that this simple model potential is capable of reproducing the band gaps nearly as good as popular meta GGA potentials in close agreement with experimental values.

  • 38.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Davidsson, Joel
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Energy-Surfaces from the Upper Bound of the Pauli Kinetic Energy2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, no 18, p. 1337-1341Article in journal (Refereed)
    Abstract [en]

    Based on the Kohn-Sham Pauli potential and the Kohn-Sham electron density, the upper bound of the Pauli kinetic energy is tested as a suitable replacement for the exact Pauli kinetic energy for application in orbital-free density functional calculations. It is found that bond lengths for strong and moderately bound systems can be qualitatively predicted, but with a systematic shift toward larger bond distances with a relative error of 6% up to 30%. Angular dependence of the energy-surface cannot be modeled with the proposed functional. Therefore, the upper bound model is the first parameter-free functional expression for the kinetic energy that is able to qualitatively reproduce binding curves with respect to bond distortions. (C) 2016 Wiley Periodicals, Inc.

  • 39.
    Finzel, Kati
    et al.
    Linköping University, Department of Physics, Chemistry and Biology.
    Martin Pendas, Angel
    University of Oviedo, Spain.
    Francisco, Evelio
    University of Oviedo, Spain.
    Efficient algorithms for Hirshfeld-I charges2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 8, p. 084115-Article in journal (Refereed)
    Abstract [en]

    A new viewpoint on iterative Hirshfeld charges is presented, whereby the atomic populations obtained from such a scheme are interpreted as such populations which reproduce themselves. This viewpoint yields a self-consistent requirement for the Hirshfeld-I populations rather than being understood as the result of an iterative procedure. Based on this self-consistent requirement, much faster algorithms for Hirshfeld-I charges have been developed. In addition, new atomic reference densities for the Hirshfeld-I procedure are presented. The proposed reference densities are N-representable, display proper atomic shell structure and can be computed for any charged species.

  • 40.
    Fourre, Isabelle
    et al.
    University of Paris 06, France.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering. University of Limoges, France.
    Podloucka, Pavlina
    Palacky University, Czech Republic.
    Otyepka, Michal
    Palacky University, Czech Republic.
    Trouillas, Patrick
    University of Limoges, France; Palacky University, Czech Republic.
    Dimerization of quercetin, Diels-Alder vs. radical-coupling approach: a joint thermodynamics, kinetics, and topological study2016In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 22, no 8, p. 190-Article in journal (Refereed)
    Abstract [en]

    Quercetin is a prototypical antioxidant and prominent member of flavonoids, a large group of natural polyphenols. The oxidation of quercetin may lead to its dimerization, which is a paradigm of the more general polyphenol oligomerization. There exist two opposing mechanisms to describe the dimerization process, namely radical-coupling or Diels-Alder reactions. This work presents a comprehensive rationalization of this dimerization process, acquired from density functional theory (DFT) calculations. It is found that the two-step radical-coupling pathway is thermodynamically and kinetically preferred over the Diels-Alder reaction. This is in agreement with the experimental results showing the formation of only one isomer, whereas the Diels-Alder mechanism would yield two isomers. The evolution in bonding, occurring during these two processes, is investigated using the atoms in molecules (AIM) and electron localization function (ELF) topological approaches. It is shown that some electron density is accumulated between the fragments in the transition state of the radical-coupling reaction, but not in the transition state of the Diels-Alder process.

  • 41.
    Fransson, Thomas
    Linköping University, Department of Physics, Chemistry and Biology.
    X-ray absorption spectroscopy by means of Lanczos-chain driven damped coupled cluster response theory2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A novel method by which to calculate the near edge X-rayabsorption fine structure region of the X-ray absorption spectrum has been derived and implemented. By means of damped coupled cluster theory at coupled cluster levels CCS, CC2, CCSD and CCSDR(3), the spectra of neon and methane have been investigated. Using methods incorprating double excitations, the important relaxation effects maybe taken into account by simultaneous excitation of the core electron and relaxation of other electrons. An asymmetric Lanczos-chain driven approach has been utilized as a means to partially resolve the excitation space given by the coupled cluster Jacobian. The K-edge of the systems have been considered, and relativistic effects are estimated with use of the Douglas--Kroll scalar relativistic Hamiltonian. Comparisons have been made to results obtained with the four-component static-exchange approach and ionization potentials obtained by the {Delta}SCF-method.

    The appropriate basis sets by which to describe the core and excited states have been been determined.  The addition of core-polarizing functions and diffuse or Rydberg functions is important for this description. Scalar relativistic effects accounts for an increase in excitation energies due to the contraction of the 1s-orbital, and this increase is seen to be 0.88 eV for neon. The coupled cluster hierachy shows a trend of convergence towards the experimental spectrum, with an 1s -> 3p excitation energy for neon of an accuracy of 0.40 eV at a relativistic CCSDR(3) level of theory. Results obtained at the damped coupled cluster and STEX levels of theory, respectively, are seen to be in agreement, with a mere relative energy shift.

  • 42.
    Fransson, Thomas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Zhovtobriukh, Iurii
    Fysikum, Stockholm University, Albanova, Stockholm, Sweden.
    Coriani, Sonia
    Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy / Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark.
    Wikfeldt, Kjartan T.
    Fysikum, Stockholm University, Albanova, Stockholm, Sweden / Science Institute, University of Iceland, VR-III, Reykjavik, Iceland.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Pettersson, Lars G. M.
    Fysikum, Stockholm University, Albanova, Stockholm, Sweden.
    Requirements of first-principles calculations of X-ray absorption spectra of liquid water2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 1, p. 566-583Article in journal (Refereed)
    Abstract [en]

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

  • 43.
    Gällström, Andreas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Magnusson, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Leone, Stefano
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Kordina, Olof
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Son, Nguyen Tien
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Ivády, Viktor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Wigner Research Center for Physics, Hungarian Academy of Sciences, Hungary.
    Gali, Adam
    Wigner Research Center for Physics, Hungarian Academy of Sciences, Budapest Hungary; Department of Atomic Physics, Budapest University of Technology and Economics, Budapest, Hungary.
    Abrikosov, Igor A.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Materials Modeling and Development Laboratory, NUST “MISIS,” Moscow, Russia; LACOMAS Laboratory, Tomsk State University, Tomsk, Russia.
    Janzén, Erik
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Ivanov, Ivan G.
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Optical properties and Zeeman spectroscopy of niobium in silicon carbide2015In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, no 7, p. 1-14, article id 075207Article in journal (Refereed)
    Abstract [en]

    The optical signature of niobium in the low-temperature photoluminescence spectra of three common polytypes of SiC (4H, 6H, and 15R) is observed and confirms the previously suggested concept that Nb occupies preferably the Si-C divacancy with both Si and C at hexagonal sites. Using this concept we propose a model considering a Nb-bound exciton, the recombination of which is responsible for the observed luminescence. The exciton energy is estimated using first-principles calculation and the result is in very good agreement with the experimentally observed photon energy in 4H SiC at low temperature. The appearance of six Nb-related lines in the spectra of the hexagonal 4H and 6H polytypes at higher temperatures is tentatively explained on the grounds of the proposed model and the concept that the Nb center can exist in both C1h and C3v symmetries. The Zeeman splitting of the photoluminescence lines is also recorded in two different experimental geometries and the results are compared with theory based on phenomenological Hamiltonians. Our results show that Nb occupying the divacancy at the hexagonal site in the studied SiC polytypes behaves like a deep acceptor.

  • 44.
    Hagelin, Alexander
    Linköping University, Department of Physics, Chemistry and Biology.
    ZnO nanoparticles: synthesis of Ga-doped ZnO, oxygen gas sensing and quantum chemical investigation2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Doped ZnO nanoparticles were synthesized by three different methods – electrochemical deposition under oxidizing conditions (EDOC) , combustion method and wet chemical synthesis – for investigating the oxygen gas sensing response. Ga-doped ZnO was mostly synthesized but also In-doped ZnO was made. The samples were analyzed by XRD, SEM, EDX and TEM. Gas response curves are given alongside with Langmuir fitted curves and data for pure ZnO and Ga-doped ZnO.

    DFT quantum chemical investigation of cluster models ZnO nanoparticles were performed to evaluate defect effects and oxygen and nitrogen dioxide reactions with the ZnO surface. Defects were investigated by DOS and HOMO-LUMO plots , and are oxygen vacancy, zinc vacancy, zinc interstitial and gallium doping by replacing zinc with gallium. Oxygen and nitrogen dioxide reactions were investigated by computing Mulliken charges, bond lengths, DOS spectra and HOMO-LUMO plots.

  • 45.
    Ivády, Viktor
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Hungarian Academic Science, Hungary.
    Gali, Adam
    Hungarian Academic Science, Hungary; Budapest University of Technology and Econ, Hungary.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. National University of Science and Technology MISIS, Russia.
    Hybrid-DFT + V-w method for band structure calculation of semiconducting transition metal compounds: the case of cerium dioxide2017In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 29, no 45, article id 454002Article in journal (Refereed)
    Abstract [en]

    Hybrid functionals non-local exchange-correlation potential contains a derivative discontinuity that improves on standard semi-local density functional theory (DFT) band gaps. Moreover, by careful parameterization, hybrid functionals can provide self-interaction reduced description of selected states. On the other hand, the uniform description of all the electronic states of a given system is a known drawback of these functionals that causes varying accuracy in the description of states with different degrees of localization. This limitation can be remedied by the orbital dependent exact exchange extension of hybrid functionals; the hybrid-DFT + V-w method (Ivady et al 2014 Phys. Rev. B 90 035146). Based on the analogy of quasi-particle equations and hybrid-DFT single particle equations, here we demonstrate that parameters of hybrid-DFT + V-w functional can be determined from approximate theoretical quasi-particle spectra without any fitting to experiment. The proposed method is illustrated on the charge self-consistent electronic structure calculation for cerium dioxide where itinerant valence states interact with well-localized 4f atomic like states, making this system challenging for conventional methods, either hybrid-DFT or LDA + U, and therefore allowing for a demonstration of the advantages of the proposed scheme.

    The full text will be freely available from 2018-10-10 18:26
  • 46.
    Kalered, Emil
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Quantum chemical studies of deposition and catalytic surface reactions2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantum chemical calculations have been used to model chemical reactions in epitaxial growth of silicon carbide by chemical vapor deposition (CVD) processes and to study heterogeneous catalytic reactions for methanol synthesis. CVD is a common method to produce high-quality materials and e.g. thin films in the semiconductor industry, and one of the many usages of methanol is as a promising future renewable and sustainable energy carrier. To optimize the chemical processes it is essential to understand the reaction mechanisms. A comprehensive theoretical model for the process is therefore desired in order to be able to explore various variables that are difficult to investigate in situ. In this thesis reaction paths and reaction energies are computed using quantum chemical calculations. The quantum-chemical results can subsequently be used as input for thermodynamic, kinetic and computational fluid dynamics modelling in order to obtain data directly comparable with the experimental observations.

    For the CVD process, the effect of halogen addition to the gas mixture is studied by modelling the adsorption and diffusion of SiH2, SiCl2 and SiBr2 on the (0001̅) 4H-SiC surface. SiH2 was found to bind strongest to the surface and SiBr2 binds slightly stronger than the SiCl2 molecule. The diffusion barrier is shown to be lower for SiH2 than for SiBr2 and SiCl2 which have similar barriers. SiBr2 and SiCl2 are found to have similar physisorption energies and bind stronger than the SiH2 molecule. Gibbs free-energy calculations also indicate that the SiC surface is not fully hydrogen terminated at CVD conditions since missing-neighboring pair of surface hydrogens is found to be common. Calculations for the (0001) surface show that SiCl, SiCl2, SiHCl, SiH, and SiH2 likely adsorb on a methylene site, but the processes are thermodynamically less favorable than their reverse reactions. However, the adsorbed products may be stabilized by subsequent surface reactions to form a larger structure. The formation of these larger structures is found to be fast enough to compete with the desorption processes. Also the Gibbs free energies for adsorption of Si atoms, SiX, SiX2, and SiHX where X is F or Br are presented. Adsorption of Si atoms is shown to be the most thermodynamically favorable reaction followed by SiX, SiHX, and SiX2, X being a halide. The results in this study suggest that the major Si contributors in the SiC–CVD process are Si atoms, SiX and SiH.

    Methanol can be synthesized from gaseous carbon dioxide and hydrogen using solid metal-metal oxide mixtures acting as heterogeneous catalysts. Since a large surface area of the catalyst enhances the speed of the heterogeneous reaction, the use of nanoparticles (NP) is expected to be advantageous due to the NPs’ large area to surface ratio. The plasma-induced creation of copper NPs is investigated. One important element during particle growth is the charging process where the variation of the work function (W) with particle size is a key quantity, and the variation becomes increasingly pronounced at smaller NP sizes. The work functions are computed for a set of NP charge numbers, sizes and shapes, using copper as a case study. A derived analytical expression for W is shown to give quite accurate estimates provided that the diameter of the NP is larger than about a nanometer and that the NP has relaxed to close to a spherical shape. For smaller sizes W deviates from the approximative expression, and also depends on the charge number. Some consequences of these results for NP charging process are outlined.

    Key reaction steps in the methanol synthesis reaction mechanism using a Cu/ZrO2 nanoparticle catalyst is investigated. Two different reaction paths for conversion of CO2 to CO is studied. The two paths result in the same complete reaction 2 CO2 → 2 CO + O2 where ZrO2 (s) acts as a catalyst. The highest activation energies are significantly lower compared to that of the gas phase reaction. The presence of oxygen vacancies at the surface appear to be decisive for the catalytic process to be effective. Studies of the reaction kinetics show that when oxygen vacancies are present on the ZrO2 surface, carbon monoxide is produced within a microsecond. The IR spectra of CO2 and H2 interacting with ZrO2 and Cu under conditions that correspond to the catalyzed CH3OH production process is also studied experimentally and compared to results from the theoretical computations. Surface structures and gas-phase molecules are identified through the spectral lines by matching them to specific vibrational modes from the literature and from the new computational results. Several surface structures are verified and can be used to pin point surface structures in the reaction path. This gives important information that help decipher how the reaction mechanism of the CO2 conversion and ultimately may aid to improve the methanol synthesis process.

    List of papers
    1. Adsorption and surface diffusion of silicon growth species in silicon carbide chemical vapour deposition processes studied by quantum-chemical computations
    Open this publication in new window or tab >>Adsorption and surface diffusion of silicon growth species in silicon carbide chemical vapour deposition processes studied by quantum-chemical computations
    2013 (English)In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 132, no 12Article in journal (Refereed) Published
    Abstract [en]

    The effect chlorine addition to the gas mixture has on the surface chemistry in the chemical vapour deposition (CVD) process for silicon carbide (SiC) epitaxial layers is studied by quantum-chemical calculations of the adsorption and diffusion of SiH2 and SiCl2 on the (000-1) 4H–SiC surface. SiH2 was found to bind more strongly to the surface than SiCl2 by approximately 100 kJ mol−1 and to have a 50 kJ mol−1 lower energy barrier for diffusion on the fully hydrogen-terminated surface. On a bare SiC surface, without hydrogen termination, the SiCl2 molecule has a somewhat lower energy barrier for diffusion. SiCl2 is found to require a higher activation energy for desorption once chemisorbed, compared to the SiH2 molecule. Gibbs free energy calculations also indicate that the SiC surface may not be fully hydrogen terminated at CVD conditions since missing neighbouring pair of surface hydrogens is found to be a likely type of defect on a hydrogen-terminated SiC surface.

    Place, publisher, year, edition, pages
    Springer Verlag (Germany), 2013
    Keywords
    Quantum-chemical calculations, Density functional theory (DFT), B3LYP, Chemical vapour deposition (CVD), Silicon carbide (SiC), SiCl2, SiH2, Surface reactions, Adsorption, Reaction path, Activation energy, Diffusion, Hydrogen termination
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-100478 (URN)10.1007/s00214-013-1403-3 (DOI)000325724400001 ()
    Available from: 2013-11-08 Created: 2013-11-08 Last updated: 2018-06-19Bibliographically approved
    2. Brominated chemistry for chemical vapor deposition of electronic grade SiC
    Open this publication in new window or tab >>Brominated chemistry for chemical vapor deposition of electronic grade SiC
    Show others...
    2015 (English)In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 27, no 3, p. 793-801Article in journal (Refereed) Published
    Abstract [en]

    Chlorinated chemical vapor deposition (CVD) chemistry for growth of homoepitaxial layers of silicon carbide (SiC) has paved the way for very thick epitaxial layers in short deposition time as well as novel crystal growth processes for SiC. Here, we explore the possibility to also use a brominated chemistry for SiC CVD by using HBr as additive to the standard SiC CVD precursors. We find that brominated chemistry leads to the same high material quality and control of material properties during deposition as chlorinated chemistry and that the growth rate is on average 10 % higher for a brominated chemistry compared to chlorinated chemistry. Brominated and chlorinated SiC CVD also show very similar gas phase chemistries in thermochemical modelling. This study thus argues that brominated chemistry is a strong alternative for SiC CVD since the deposition rate can be increased with preserved material quality. The thermochemical modelling also suggest that the currently used chemical mechanism for halogenated SiC CVD might need to be revised.

    National Category
    Chemical Sciences Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-111075 (URN)10.1021/acs.chemmater.5b00074 (DOI)000349934500016 ()
    Available from: 2014-10-07 Created: 2014-10-07 Last updated: 2018-06-19Bibliographically approved
    3. Growth Mechanism of SiC Chemical Vapor Deposition: Adsorption and Surface Reactions of Active Si Species
    Open this publication in new window or tab >>Growth Mechanism of SiC Chemical Vapor Deposition: Adsorption and Surface Reactions of Active Si Species
    Show others...
    2018 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 1, p. 648-661Article in journal (Refereed) Published
    Abstract [en]

    Silicon carbide is a wide bandgap semiconductor ideally suitable for high temperature and high power applications. An active SiC layer is usually fabricated using halide-assisted chemical vapor deposition (CVD). In this work, we use quantum chemical density functional theory (B3LYP and M06-2X) and transition state theory to study adsorptions of active Si species in the CVD process on both the Si face and the C face of 4H-SiC. We show that adsorptions of SiCl, SiCl2, SiHCl, SiH, and SiH2 on the Si face likely occur on a methylene site, CH2(ads), but the processes are thermodynamically less favorable than their reverse or desorptions. Nevertheless, the adsorbed products become stabilized with the help of subsequent surface reactions to form a larger cluster. These cluster formation reactions happen with rates that are fast enough to compete with the desorption processes. On the C face, the adsorptions likely occur on a surface site terminated by a dangling bond, *(ads), and produce the products which are thermodynamically stable. Lastly, we present the Gibbs free energies of adsorptions of Si atoms, SiX, SiX2, and SiHX, for X being F and Br. Adsorptions of Si atoms are shown to be the most thermodynamically favorable among all the species in the study. Among the halide-containing species, the Gibbs free energies (ARG) from smallest to largest are observed in the adsorptions of SiX, SiHX, and SiX2, for X being the halides. The results in this study suggest that the major Si contributors in the SiC CVD process are Si atoms, SiX (for X being the halide) and SiH.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2018
    National Category
    Inorganic Chemistry
    Identifiers
    urn:nbn:se:liu:diva-144885 (URN)10.1021/acs.jpcc.7b10751 (DOI)000422814200069 ()
    Note

    Funding Agencies|Swedish Foundation for Strategic Research from Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University [2009 00971]; Swedish Research Council (VR) [2016-05137_4]

    Available from: 2018-02-09 Created: 2018-02-09 Last updated: 2018-06-19
    4. On the work function and the charging of small (r <= 5 nm) nanoparticles in plasmas
    Open this publication in new window or tab >>On the work function and the charging of small (r <= 5 nm) nanoparticles in plasmas
    Show others...
    2017 (English)In: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 24, no 1, article id 013702Article in journal (Refereed) Published
    Abstract [en]

    The growth of nanoparticles (NPs) in plasmas is an attractive technique where improved theoretical understanding is needed for quantitative modeling. The variation of the work function W with size for small NPs, r(NP) amp;lt;= 5 nm, is a key quantity for modeling of three NP charging processes that become increasingly important at a smaller size: electron field emission, thermionic electron emission, and electron impact detachment. Here we report the theoretical values of the work function in this size range. Density functional theory is used to calculate the work functions for a set of NP charge numbers, sizes, and shapes, using copper for a case study. An analytical approximation is shown to give quite accurate work functions provided that r(NP) amp;gt; 0.4 nm, i.e., consisting of about amp;gt; 20 atoms, and provided also that the NPs have relaxed close to spherical shape. For smaller sizes, W deviates from the approximation, and also depends on the charge number. Some consequences of these results for nanoparticle charging are outlined. In particular, a decrease in W for NP radius below about 1 nm has fundamental consequences for their charge in a plasma environment, and thereby on the important processes of NP nucleation, early growth, and agglomeration. Published by AIP Publishing.

    Place, publisher, year, edition, pages
    AMER INST PHYSICS, 2017
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:liu:diva-136218 (URN)10.1063/1.4973443 (DOI)000395395100092 ()
    Note

    Funding Agencies|Knut and Alice Wallenberg foundation (KAW) [2014.0276]; Swedish Research Council via the Linkoping Linneaus Environment LiLi-NFM [2008-6572]

    Available from: 2017-03-31 Created: 2017-03-31 Last updated: 2018-06-19
  • 47.
    Knippenberg, Stefan
    et al.
    KTH Royal Institute Technology, Sweden.
    Gieseking, Rebecca L.
    Georgia Institute Technology, GA 30332 USA; Georgia Institute Technology, GA 30332 USA; Northwestern University, IL 60208 USA.
    Rehn, Dirk
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Mukhopadhyay, Sukrit
    Georgia Institute Technology, GA 30332 USA; Georgia Institute Technology, GA 30332 USA; Dow Chemistry Co USA, MI 48674 USA.
    Dreuw, Andreas
    Heidelberg University, Germany.
    Bredas, Jean-Luc
    Georgia Institute Technology, GA 30332 USA; Georgia Institute Technology, GA 30332 USA; King Abdullah University of Science and Technology, Saudi Arabia.
    Benchmarking Post-Hartree-Fock Methods To Describe the Nonlinear Optical Properties of Polymethines: An Investigation of the Accuracy of Algebraic Diagrammatic Construction (ADC) Approaches2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 11, p. 5465-5476Article in journal (Refereed)
    Abstract [en]

    Third-order nonlinear optical (NLO) properties of polymethine dyes have been widely studied for applications such as all-optical switching. However, the limited accuracy of the current computational methodologies has prevented a comprehensive understanding of the nature of the lowest excited states and their influence on the molecular optical and NLO properties. Here, attention is paid to the lowest excited-state energies and their energetic ratio, as these characteristics impact the figure-of-merit for all-optical switching. For a series of model polymethines, we compare several algebraic diagrammatic construction (ADC) schemes for the polarization propagator with approximate second-order coupled cluster (CC2) theory, the widely used INDO/MRDCI approach and the symmetry adapted cluster configuration interaction (SAC-CI) algorithm incorporating singles and doubles linked excitation operators (SAC-CI SD-R). We focus in particular on the ground-to-excited state transition dipole moments and the corresponding state dipole moments, since these quantities are found to be of utmost importance for an effective description of the third-order polarizability gamma and two-photon absorption spectra. A sum-overstates expression has been used, which is, found to quickly converge. While ADC(3/2) has been found to be the most appropriate method to calculate these properties, CC2 performs poorly.

  • 48.
    Konig, Carolin
    et al.
    KTH Royal Inst Technol, Sweden.
    Skånberg, Robin
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Hotz, Ingrid
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Ynnerman, Anders
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    KTH Royal Inst Technol, Sweden.
    Linares, Mathieu
    KTH Royal Inst Technol, Sweden; KTH Royal Inst Technol, Sweden.
    Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations2018In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 24, p. 3030-3033Article in journal (Refereed)
    Abstract [en]

    A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

  • 49.
    Kuo, J. L.
    et al.
    Univ Penn, Dept Chem, Ctr Mol Modeling, Philadelphia, PA 19104 USA.
    Klein, M. L.
    Univ Penn, Dept Chem, Ctr Mol Modeling, Philadelphia, PA 19104 USA.
    Singer, S. J.
    Ohio State Univ, Dept Chem, Columbus, OH 43210 USA.
    Ojamäe, L.
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry .
    Ice lh-Ice XI phase transition: A quantum mechanical study2004Conference paper (Other academic)
  • 50.
    Kuo, Jer-Lai
    et al.
    Department of Chemistry, Ohio State University, Columbus, Ohio 43214.
    Coe, James V.
    Department of Chemistry, Ohio State University, Columbus, Ohio 43214.
    Singer, Sherwin J.
    Department of Chemistry, Ohio State University, Columbus, Ohio 43214.
    Band, Yehuda B.
    Departments of Chemistry and Physics, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry .
    On the use of graph invariants for efficiently generating hydrogen bond topologies and predicting physical properties of water clusters and ice2001In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 114, no 6, p. 2527-2540Article in journal (Refereed)
    Abstract [en]

    Water clusters and some phases of ice are characterized by many isomers with similar oxygen positions, but which differ in direction of hydrogen bonds. A relationship between physical properties, like energy or magnitude of the dipole moment, and hydrogen bond arrangements has long been conjectured. The topology of the hydrogen bond network can be summarized by oriented graphs. Since scalar physical properties like the energy are invariant to symmetry operations, graphical invariants are the proper features of the hydrogen bond network which can be used to discover the correlation with physical properties. We demonstrate how graph invariants are generated and illustrate some of their formal properties. It is shown that invariants can be used to change the enumeration of symmetry-distinct hydrogen bond topologies, nominally a task whose computational cost scales like N2, where N is the number of configurations, into an N ln N process. The utility of graph invariants is confirmed by considering two water clusters, the (H2O)6 cage and (H2O)20 dodecahedron, which, respectively, possess 27 and 30 026 symmetry-distinct hydrogen bond topologies associated with roughly the same oxygen atom arrangements. Physical properties of these clusters are successfully fit to a handful of graph invariants. Using a small number of isomers as a training set, the energy of other isomers of the (H2O)20 dodecahedron can even be estimated well enough to locate phase transitions. Some preliminary results for unit cells of ice-Ih are given to illustrate the application of our results to periodic systems.

     

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