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  • 1.
    Agback, M
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Lunell, S
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Hussenius, A
    Department of Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Matsson, O
    Department of Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Theoretical studies of proton transfer reactions in 1-methylindene1998In: ACTA CHEMICA SCANDINAVICA, ISSN 0904-213X, Vol. 52, no 5, p. 541-548Article in journal (Refereed)
    Abstract [en]

    The base-catalysed 1,3-proton transfer reactions in 1-methylindene have been studied theoretically in polar (water) and unpolar (cyclohexane) solvents, respectively, for two different choices of bases, namely ammonia and trimethylamine (TMA), using the SM

  • 2. Ajitha, D
    et al.
    Wierzbowska, M
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Malmqvist, P A
    Spin-orbit ab initio study of alkyl halide dissociation via electronic curve crossing2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 12, p. 5761-5766Article in journal (Refereed)
    Abstract [en]

    An ab initio study of the role of electronic curve crossing in the photodissociation dynamics of the alkyl halides is presented. Recent experimental studies show that curve crossing plays a deterministic role in deciding the channel of dissociation. Coupled repulsive potential energy curves of the low-lying n-sigma* states are studied including spin-orbit and relativistic effects. Basis set including effect of core correlation is used. Ab initio vertical excitation spectra of CH3I and CF3I are in agreement with the experimental observation. The curve crossing region is around 2.371 Angstrom for CH3I and CF3I. The potential curves of the repulsive excited states have larger slope for CF3I, suggesting a higher velocity and decreased intersystem crossing probability on fluorination. We also report the potential curves and the region of curve crossing for CH3Br and CH3Cl.

  • 3.
    Andersson, Ole
    et al.
    Dept. of Physics, Stockholm University, Sweden.
    Bengtsson, Ingemar
    Dept. of Physics, Stockholm University, Sweden.
    Ericsson, Marie
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Uppsala universitet.
    Geometric phases for mixed states of the Kitaev chain2016In: Philosophical Transactions. Series A: Mathematical, physical, and engineering science, ISSN 1364-503X, E-ISSN 1471-2962, Vol. 374, no 2069, article id 20150231Article in journal (Refereed)
    Abstract [en]

    The Berry phase has found applications in building topological order parameters for certain condensed matter systems. The question whether some geometric phase for mixed states can serve the same purpose has been raised, and proposals are on the table. We analyze the intricate behaviour of Uhlmann’s geometric phase in the Kitaev chain at finite temperature, and then argue that it captures quite different physics from that intended. We also analyze the behaviour of a geometric phase introduced in the context of interferometry. For the Kitaev chain, this phase closely mirrors that of the Berry phase, and we argue that it merits further investigation. 

  • 4. Aquilante, Francesco
    et al.
    Boman, Linus
    Boström, Jonas
    Koch, Henrik
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Sánchez de Merás, Alfredo
    Pedersen, Thomas Bondo
    Cholesky decomposition techniques in electronic structure theory2011In: Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications / [ed] R. Zalesny, P. Mezey, M. G. Papadopoulos and J. Leszczynski, Springer, 2011, p. 301-304Chapter in book (Other academic)
    Abstract [en]

    We review recently developed methods to efficiently utilize the Cholesky decomposition technique in electronic structure calculations. The review starts with a brief introduction to the basics of the Cholesky decomposition technique. Subsequently, examples of applications of the technique to ab inito procedures are presented. The technique is demonstrated to be a special type of a resolution-of-identity or density-fitting scheme. This is followed by explicit examples of the Cholesky techniques used in orbital localization, computation of the exchange contributionto the Fock matrix, in MP2, gradient calculations, and so-called method specific Cholesky decomposition. Subsequently, examples of calibration of the method with respect to computed total energies, excitation energies, and auxiliary basis set pruning are presented. In particular, it is demonstrated that the Cholesky method is an unbiased method to derive auxiliary basis sets. Furthermore, details of the implementational considerations are put forward and examples from a parallel Cholesky decomposition scheme is presented. Finally, an outlook and perspectives are presented, followed by a summary and conclusions section. We are of the opinion that the Cholesky decomposition method is a technique that has been overlooked for too long. We have just recently started to understand how to efficiently incorporate the method in existing ab initio programs. The full potential of the Cholesky technique has not yet been fully explored.

  • 5. Armour, EA
    et al.
    Bradbury, J
    Cohen, J
    Davies, J
    Froelich, Piotr
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Hartmann, FJ
    Marshall, GM
    Nagamine, K
    Petitjean, C
    Petrov, YV
    Schellenberg, L
    Semenchuk, GG
    Zinov, VG
    Perspectives for muCF - panel discussion1996In: Hyperfine Interactions, Vol. 101/102, p. 699-Article in journal (Refereed)
  • 6. Avery, John
    et al.
    Avery, James
    Goscinski, Osvaldo
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Natural Orbitals from Generalized Sturmian Calculations2003In: Advances in Quantum Chemistry, vol. 43, Elsevier Academic Press , 2003, p. 207-216Chapter in book (Refereed)
  • 7.
    Azimi Mousolou, Vahid
    et al.
    School of Computer Science, Physics and Mathematics, Linnaeus Univ., Sweden.
    Canali, Carlo M.
    School of Computer Science, Physics and Mathematics, Linnaeus Univ., Sweden.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Non-Abelian quantum holonomy of hydrogen-like atoms2011In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 84, no 3, article id 032111Article in journal (Refereed)
    Abstract [en]

    We study the Uhlmann holonomy [Rep. Math. Phys. 24, 229 (1986)] of quantum states for hydrogen-like atoms, where the intrinsic spin and orbital angular momentum are coupled by the spin-orbit interaction and subject to a slowly varying magnetic field. We show that the holonomy for the orbital angular momentum and spin subsystems is non-Abelian, while the holonomy of the whole system is Abelian. Quantum entanglement in the states of the whole system is crucially related to the non-Abelian gauge structure of the subsystems. We analyze the phase of the Wilson loop variable associated with the Uhlmann holonomy, and find a relation between the phase of the whole system with corresponding marginal phases. Based on the result for the model system we provide evidence that the phase of the Wilson loop variable and the mixed-state geometric phase [Phys. Rev. Lett. 85, 2845 (2000)] are in general inequivalent.

  • 8. Ban, FQ
    et al.
    Lundqvist, Maria J.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Boyd, Russel J.
    Eriksson, Leif A.
    Department of Biochemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine2002In: Journal of the American Chemical Society, Vol. 124, no 11, p. 2753-2761Article in journal (Refereed)
  • 9.
    Berggren, P.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Stegeby, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Voronin, A.
    Froelich, Piotr
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Impact of the strong force on the Coulombic decay of a hydrogen-antihydrogen molecule2008In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 41, no 15, p. 155202-Article in journal (Refereed)
    Abstract [en]

    The lifetime of the meta-stable hydrogen-antihydrogen molecule in various vibrational states is calculated. The partial lifetime with respect to the proton-antiproton annihilation is obtained from complex eigenvalues which arise upon inclusion of the strong force in the adiabatic formulation of the molecular decay problem. We study the influence of the strong force, which causes annihilation, on the transition probability for decay via Coulombic rearrangement to protonium and positronium.

  • 10.
    Borg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    A singlet mechanism for photodissociation of bromofluorobenzenes2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 436, no 1-3, p. 57-62Article in journal (Refereed)
    Abstract [en]

    The C-Br photo-fragmentation of bromo-3,5-difluorobenzene (Br-3,5-diFBz) has been investigated using ab initio methods. A reaction coordinate combining a carbon-bromine bond stretch and a bromine out-of-plane bending on the S1 surface has been found with an activation energy of 2.96 kcal/mol, compatible with the observed picosecond time scale.

  • 11.
    Borg, Anders
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Physics, Department of Quantum Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Photochemistry of Fluorinated Bromobenzenes and Phytochromobilin2006Licentiate thesis, monograph (Other scientific)
  • 12.
    Borg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Theoretical Photochemistry: Halogenated Arenes, Phytochromobilin, Ru(II)polypyridyl complexes and 6-4 photoadducts2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents Quantum Chemical calculations on the Photochemistry of Halogenated benzenes, Phytochromobilin, Ruthenium Polypyridyl complexes and 6-4 photoadducts in DNA. The work is focused on improving the understanding of a number of experimentally observed photochemical processes in these systems. New results regarding the mechanism of photodissociation of halogenated arenes, photointerconversion of phytochromobilin are presented, as well as of the photoprocesses of Ruthenium Polypyridyl complexes and new mechanistic insights in the repair of 6-4 photoadducts in DNA.

    List of papers
    1. Photochemistry of Bromofluorobenzenes
    Open this publication in new window or tab >>Photochemistry of Bromofluorobenzenes
    Show others...
    2006 (English)In: Journal of Physical Chemistry A, Vol. 110, p. 7045-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96758 (URN)
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
    2. A singlet mechanism for photodissociation of bromofluorobenzenes
    Open this publication in new window or tab >>A singlet mechanism for photodissociation of bromofluorobenzenes
    2007 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 436, no 1-3, p. 57-62Article in journal (Refereed) Published
    Abstract [en]

    The C-Br photo-fragmentation of bromo-3,5-difluorobenzene (Br-3,5-diFBz) has been investigated using ab initio methods. A reaction coordinate combining a carbon-bromine bond stretch and a bromine out-of-plane bending on the S1 surface has been found with an activation energy of 2.96 kcal/mol, compatible with the observed picosecond time scale.

    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-96759 (URN)10.1016/j.cplett.2007.01.035 (DOI)000244946400011 ()
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
    3. Experimental and theoretical study of the photodissociation of bromo-3-fluorobenzene
    Open this publication in new window or tab >>Experimental and theoretical study of the photodissociation of bromo-3-fluorobenzene
    Show others...
    2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 3, p. 034307-Article in journal (Refereed) Published
    Abstract [en]

    The UV photodissociation of bromo-3-fluorobenzene under collisionless conditions has been studied as a function of the excitation wavelength between 255 and 265 nm. The experiments were performed using ultrafast pump-probe laser spectroscopy. To aid in the interpretation of the results, it was necessary to extend the theoretical framework substantially compared to previous studies, to also include quantum dynamical simulations employing a two-dimensional nuclear Hamiltonian. The nonadiabatic potential energy surfaces (PES) were parameterized against high-level MS-CASTP2 quantum chemical calculations, using both the C–Br distance and the out-of-plane bending of the bromine as nuclear parameters. We show that the wavelength dependence of the photodissociation via the S01ππ*1πσ* channel, accessible with a ∼ 260 nm pulse, is captured in this model. We thereby present the first correlation between experiments and theory within the quantitative regime.

    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-96760 (URN)10.1063/1.2819093 (DOI)000252471100017 ()
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
    4. The mechanism for Photodissociation of Chlorobenzene - Beyond the pseudo-diatomic level
    Open this publication in new window or tab >>The mechanism for Photodissociation of Chlorobenzene - Beyond the pseudo-diatomic level
    Show others...
    (English)In: Chemical Physics LettersArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-96761 (URN)
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
    5. Phytochromobilin C15-Z,syn -> C15-E,anti isomerization: concerted or stepwise?
    Open this publication in new window or tab >>Phytochromobilin C15-Z,syn -> C15-E,anti isomerization: concerted or stepwise?
    2004 (English)In: Physical Chemistry Chemical Physics, Vol. 6, p. 5066-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96762 (URN)
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
    6. Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome
    Open this publication in new window or tab >>Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome
    2005 (English)In: Chemical Physics Letters, Vol. 416, p. 83-Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96763 (URN)
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2009-03-26Bibliographically approved
    7. Relative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational StudyRelative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational Study
    Open this publication in new window or tab >>Relative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational StudyRelative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational Study
    2007 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 39, p. 11554-11565Article in journal (Refereed) Published
    Abstract [en]

    The conversion of the plant photoreceptor phytochrome from an inactive (Pr) to an active form (Pfr) is accomplished by a red-light induced Z→ E photoisomerization of its phytochromobilin chromophore. In recent years, the question whether the photoactivation involves a change in chromophore protonation state has been the subject of many experimental studies. Here, we have used quantum chemical methods to calculate relative ground and excited-state pKa values of the different pyrrole moieties of phytochromobilin in a protein-like environment. Assuming (based on experimental data) a Pr ZaZsZa chromophore and considering isomerizations at C15 and C5, it is found that moieties B and C are the strongest acids both in the ground state and in the bright first singlet excited state, which is rationalized in simple geometric and electronic terms. It is also shown that neither light absorption nor isomerization increases the acidity of phytochromobilin relative to the reference Pr state with all pyrrolenic nitrogens protonated. Hence, provided that the subset of chromophore geometries under investigation is biologically relevant, there appears to be no intrinsic driving force for a proton-transfer event. In a series of benchmark calculations, the performance of ab initio and time-dependent density functional theory methods for excited-state studies of phytochromobilin is evaluated in light of available experimental data.

    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-96764 (URN)10.1021/jp0727953 (DOI)000249838600031 ()
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
    8. Which Factors Determine the Acidity of the Phytochromobilin Chromophore of Plant Phytochrome?
    Open this publication in new window or tab >>Which Factors Determine the Acidity of the Phytochromobilin Chromophore of Plant Phytochrome?
    2008 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 18, p. 2528-2537Article in journal (Refereed) Published
    Abstract [en]

    Quantum chemical calculations aimed at identifying the factors controlling the acidity of phytochromobilin, the tetrapyrrole chromophore of the plant photoreceptor phytochrome, are reported. Phytochrome is converted from an inactive (Pr) to an active form (Pfr) through a series of events initiated by a Z --> E photoisomerization of phytochromobilin, forming the Lumi-R intermediate, and much controversy exists as to whether the protonation state of the chromophore (cationic in Pr with all nitrogens protonated) changes during the photoactivation. Here, relative ground (S0) and excited-state (S1) pKa s of all four pyrrole moieties of phytochromobilin in all 64 possible configurations with respect to the three methine bridges are calculated in a protein-like environment, using a recently benchmarked level of theory. Accordingly, the relationships between acidity and chromophore geometry and charge distribution, hydrogen bonding, and light absorption are investigated in some detail, and discussed in terms of possible mechanisms making a proton transfer reaction more probable along the Pr --> Pfr reaction than in the parent cationic Pr state. It is found that charge distribution in the cationic species, intra-molecular hydrogen bonding in the neutral, and hydrogen bonding with two highly conserved aspartate and histidine residues have a significant effect on the acidity, while overall chromophore geometry and electronic state are less important factors. Furthermore, based on the calculations, two processes that may facilitate a proton transfer by substantially lowering the pKa s relative to their Pr values are identified: (i) a thermal Z,anti --> Z,syn isomerization at C5, occurring after formation of Lumi-R; (ii) a perturbation of the hydrogen bonding network which in Pr comprises the nitrogens of pyrroles A, B and C and the two aspartate and histidine residues.

    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-96765 (URN)10.1039/b719190a (DOI)000255449200011 ()18446253 (PubMedID)
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
    9. A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis
    Open this publication in new window or tab >>A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis
    Show others...
    2008 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 19, p. 4470-4476Article in journal (Refereed) Published
    Abstract [en]

    The potential energy surfaces of the first excited triplet state of some ruthenium polypyridyl complexes were investigated by means of density functional theory. Focus was placed on the interaction between the geometrical changes accompanying the photoactivity of these complexes when used as antenna complexes in artificial photosynthesis and dye-sensitized solar cells and the accompanying changes in electronic structure. The loss process (3)MLCT --> (3)MC can be understood by means of ligand-field splitting, traced down to the coordination of the central ruthenium atom.

    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-96766 (URN)10.1021/jp8000702 (DOI)000255649300011 ()18426189 (PubMedID)
    Available from: 2008-02-26 Created: 2008-02-26 Last updated: 2017-12-14Bibliographically approved
    10. Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study
    Open this publication in new window or tab >>Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study
    2007 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 12, p. 2351-2361Article in journal (Refereed) Published
    Abstract [en]

    The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C−N and C−C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-92096 (URN)10.1021/jp0676383 (DOI)000245083600013 ()17388321 (PubMedID)
    Available from: 2004-09-03 Created: 2004-09-03 Last updated: 2017-12-14Bibliographically approved
  • 13.
    Borg, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Durbeej, Bo
    Which Factors Determine the Acidity of the Phytochromobilin Chromophore of Plant Phytochrome?2008In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 18, p. 2528-2537Article in journal (Refereed)
    Abstract [en]

    Quantum chemical calculations aimed at identifying the factors controlling the acidity of phytochromobilin, the tetrapyrrole chromophore of the plant photoreceptor phytochrome, are reported. Phytochrome is converted from an inactive (Pr) to an active form (Pfr) through a series of events initiated by a Z --> E photoisomerization of phytochromobilin, forming the Lumi-R intermediate, and much controversy exists as to whether the protonation state of the chromophore (cationic in Pr with all nitrogens protonated) changes during the photoactivation. Here, relative ground (S0) and excited-state (S1) pKa s of all four pyrrole moieties of phytochromobilin in all 64 possible configurations with respect to the three methine bridges are calculated in a protein-like environment, using a recently benchmarked level of theory. Accordingly, the relationships between acidity and chromophore geometry and charge distribution, hydrogen bonding, and light absorption are investigated in some detail, and discussed in terms of possible mechanisms making a proton transfer reaction more probable along the Pr --> Pfr reaction than in the parent cationic Pr state. It is found that charge distribution in the cationic species, intra-molecular hydrogen bonding in the neutral, and hydrogen bonding with two highly conserved aspartate and histidine residues have a significant effect on the acidity, while overall chromophore geometry and electronic state are less important factors. Furthermore, based on the calculations, two processes that may facilitate a proton transfer by substantially lowering the pKa s relative to their Pr values are identified: (i) a thermal Z,anti --> Z,syn isomerization at C5, occurring after formation of Lumi-R; (ii) a perturbation of the hydrogen bonding network which in Pr comprises the nitrogens of pyrroles A, B and C and the two aspartate and histidine residues.

  • 14.
    Borg, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Eriksson, Leif
    Durbeej, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 12, p. 2351-2361Article in journal (Refereed)
    Abstract [en]

    The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C−N and C−C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

  • 15.
    Borg, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Karlsson, Daniel
    Isomäki-Krondahl, Magnus
    Davidsson, Jan
    Lunell, Sten
    The mechanism for Photodissociation of Chlorobenzene - Beyond the pseudo-diatomic levelIn: Chemical Physics LettersArticle in journal (Refereed)
  • 16.
    Borg, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Liu, Ya-Jun
    Persson, Petter
    Lunell, Sten
    Karlsson, Daniel
    Kadi, Malin
    Davidsson, Jan
    Photochemistry of Bromofluorobenzenes2006In: Journal of Physical Chemistry A, Vol. 110, p. 7045-Article in journal (Refereed)
  • 17.
    Borg, O. Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Godinho, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Lundqvist, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Persson, Petter
    A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 19, p. 4470-4476Article in journal (Refereed)
    Abstract [en]

    The potential energy surfaces of the first excited triplet state of some ruthenium polypyridyl complexes were investigated by means of density functional theory. Focus was placed on the interaction between the geometrical changes accompanying the photoactivity of these complexes when used as antenna complexes in artificial photosynthesis and dye-sensitized solar cells and the accompanying changes in electronic structure. The loss process (3)MLCT --> (3)MC can be understood by means of ligand-field splitting, traced down to the coordination of the central ruthenium atom.

  • 18.
    Borg, O. Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Karlsson, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Isomäki-Krondahl, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Davidsson, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Predissociation of Chlorobenzene, beyond the pseudo-diatomic model2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 456, no 4-6, p. 123-126Article in journal (Refereed)
    Abstract [en]

    Dissociation of chlorobenzene via the lowest singlet excited state has been investigated by means of pump-probe femtosecond spectroscopy and spin-orbit corrected ab initio quantum chemistry. We have found that the so far accepted model with a (1)pi pi* -> (3)pi/n sigma* reaction mechanism has to be amended. We suggest that the mechanism goes via a transition from (1)pi pi* to a pi sigma* state that is to 90% a singlet. Further, three nuclear degrees of freedom required to describe the dissociation have been defined.

  • 19.
    Borg, O Anders
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Avdelningen för kvantkemi.
    Liu, Ya-Jun
    Persson, Petter
    Lunell, Sten
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Avdelningen för kvantkemi.
    Karlsson, Daniel
    Department of Photochemistry and Molecular Science. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics.
    Kadi, Malin
    Davidsson, Jan
    Department of Photochemistry and Molecular Science. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics.
    Photochemistry of bromofluorobenzenes.2006In: J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory, ISSN 1089-5639, Vol. 110, no 22, p. 7045-56Article in journal (Refereed)
  • 20.
    Brandas, Erkki
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Decoherence and the Appearance of a Classical World in Quantum Theory: E. Joos, H. D. Zeh, C. Kiefer, D. Giulini, J. Kupsch and I.-O Stamatescu, Springer-Verlag, New York, 20032004In: International Journal of Quantum Chemistry, ISSN 0020-7608, Vol. 99, p. 115-116Article, book review (Other (popular scientific, debate etc.))
  • 21.
    Br�ndas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. kvantkemi.
    Sabin, John R.
    Advances in Quantum Chemistry: Theory of the Interaction of Radiation with Biomolecules2007In: Advances in Quantum Chemistry: Preface, ISSN 0065-3276, Vol. 52, p. xi-xiiArticle, review/survey (Other (popular scientific, debate etc.))
    Abstract [en]

    This thematic issue of Advances in Quantum Chemistry is devoted to the theory of the interaction of radiation with biological systems. The subject is timely, as knowledge of the fundamental physics and chemistry of the interaction is critical to understanding problems as critical as radiation therapy of tumors and radiation protection in space. A true understanding of the interaction of radiation with a biological entity requires study of phenomena ranging over many orders of magnitude in size and time. In this volume, however, we concentrate on the individual collision processes between an ion or photon and a single biomolecule. The volume is composed of thirteen contributions from specialists in the field.

    As most of the theory used in this volume is based in quantum mechanics, the size of target systems under consideration is generally small: There are calculations on nucleobases, on DNA radicals, on transient negative ions (TNI), and on the most common biomolecule - water. All are important for the understanding of the primary ion-biomolecule interactions. However, the volume does not go to larger clusters such as double strands, nor to longer timescales where the chemical phase of radiation damage becomes important.

    It is very easy for a theorist to carry out complex calculations on a system thought to be both interesting and relevant to the biological problem, only to discover at some later time that the interest remains but that these is no biological relevance to the problem. To put this problem in perspective, the first paper, after a short introduction, is by an experimentalist, Clemens von Sonntag who discusses the calculation of ion-molecule reactive collisions with particular emphasis on the types of problems where quantum calculations on biomolecules would be of use to experimentalists.

    Von Sonntag�s paper is followed by a series of contributions describing various aspects of radiation damage.

    The first a contribution by Mu�oz et al. concerning high accuracy quantum mechanical modeling of energy deposition by electrons in biologically important molecules. These calculations are used to determine parameters used as input to a Monte Carlo scheme to simulate energy deposition.

    Radicals, and their importance to radiobiological processes are the subject of the next two papers. Li and Sevilla discuss electrons and holes produced in DNA models by ionizing radiation and the effect of these radicals on the subsequent chemical reactions of the biomolecules, while Tur_ek addresses structures and energetics of nucleobase and carbohydrate radical reactions using density functional methods.

    The next contribution, authored by Stolterfoht et al., treats one of the most ubiquitous processes in radiation damage studies: Namely electron capture and fragmentation of water by swift ions. High levels of dynamical theory are used to calculate appropriate cross sections, which are compared to experimental results.

    As much of the radiation damage in biological systems arises from secondary, or delta, electrons coming from ionization of water by the incoming radiation, the interaction of these electrons with biological molecules is of utmost importance in the overall understanding of radiation damage. In the next paper, Jack Simons uses high level quantum mechanical theory to discuss the formation of a transient negative ion (TNI) in a DNA fragment and the mechanism that leads to a subsequent strand break. This paper is followed by a contribution by Baccarelli et al., which also deals with TNI�s, but in this case, their formation from biological molecules in the gas phase. Continuing with the theme of electron attachment to biomolecules, Jalbout and Adamowicz present ab initio quantum mechanical studies of electron attachment to DNA base complexes. Following that paper, Sulik and T_k�si address the problem of the Fermi shuttle acceleration of secondary electrons using classical trajectory Monte Carlo methods.

    The last two contributions in this volume with energy deposition or stopping power. Akar et al. discuss the stopping power of electrons by biological molecules, while Paul et al. consider the effects of stopping power on dosimetry.

    All in all, we find this an informative and useful collection of papers, and we hope that you enjoy reading it as much as we enjoyed putting it together. Finally, we wish to thank all the authors for their help in producing this volume.

    Erkki Br�ndas and John R. Sabin

    Editors

  • 22.
    Brändas, Erkki
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    A Tribute to Ilya Prigogine: (1917-2003)2004In: International Journal of Quantum Chemistry, ISSN 0020-7608, Vol. 98, p. 59-Article in journal (Other scientific)
  • 23.
    Brändas, Erkki
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Advanced instrumentation and measurements: a graduate research education programme in science and engineering2004In: Computational and Mathematical Methods in Science and Engineering: Proceedings of CMMSE 2004, 2004, p. 350-Conference paper (Other (popular scientific, debate etc.))
  • 24.
    Brändas, Erkki
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Are Jordan Blocks Necessary for the Interpretation of Dynamical Processes in Nature?2004In: Advances in Quantum Chemistry, ISSN 0065-3276, Vol. 47, p. 93-108Article in journal (Refereed)
  • 25.
    Brändas, Erkki
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Quantum Mechanics: F. Schwabl, Springer-Verlag, New York, 20022004In: International Journal of Quantum Chemistry, ISSN 0020-7608, Vol. 99, p. 59-Article, book review (Other (popular scientific, debate etc.))
  • 26.
    Brändas, Erkki
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical Chemistry. Department of Physical and Analytical Chemistry, Quantum Chemistry. Avdelningen för kvantkemi.
    The reduced partitioning procedure revisited2005In: Molecular Physics, Vol. 103, no 15-16, p. 2073-2080Article in journal (Refereed)
    Abstract [en]

    A review. The present article reports on the inherent connections between perturbation and variation theories known as the Reduced Partitioning Procedure. The topic formed the basis for the PhD thesis of Rodney J. Bartlett. In this work he analyzed the interrelations between current (at the time) perturbation and variational theories, with particular ref. to the Lanczos algorithm, the Krylov vectors, Hankel determinants as well as inferences from the Pade-Stieltjes moment problem and assocd. Lippman-Schwinger-type principles. Numerical computations for small mol. systems displayed rapid convergence, in excellent agreement with the deduced optimal properties of the method.

  • 27.
    Brändas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Anderberg, Bengt
    The importance of competence-driven research2004In: InPhase: Bridging the Gap between Academia and Industry, ISSN 1652-7593, Vol. 2, no 2Article in journal (Other (popular scientific, debate etc.))
  • 28.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Complex Symmetric Forms and the Emergence of Jordan Blocks in Analytically Extended Quantum Theory2009In: International Journal of Computer Mathematics, ISSN 0020-7160, E-ISSN 1029-0265, Vol. 86, no 2, p. 315-319Article in journal (Refereed)
    Abstract [en]

    The justification and rationale for analytically continuing quantum mechanics into the complex plane are recognized and briefly discussed. This extension is described by a complex symmetric representation, which is derived and demonstrated to include general Jordan block forms of Segre characteristics larger than one. Various applications in physics and chemistry, in which this extension appears necessary, are pointed out.

  • 29.
    Brändas, Erkki J
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Complex Symmetry, Jordan Blocks and Microscopic Selforganization: An Examination of the Limits of Quantum Theory. Based on Nonself-adjoint Extensions with Illustrations from Chemistry and Physics2009In: Self-Organization of Molecular Systems: From Molecules and Clusters to nanotubes and Proteins / [ed] N. Russo, V. Ya. Antonchenko, E. Kryachko, Springer , 2009, p. 49-87Chapter in book (Refereed)
    Abstract [en]

    The basis and motivation for extending quantum mechanics beyond its traditional domain are recognized and examined. The mathematical details are briefly discussed and a convenient compact complex symmetric representation derived. An original formula is proved and demonstrated to incorporate general Jordan block configurations characterized by Segrè characteristics larger than one. It is verified that these triangular forms can portray realistic evolutions via maps established both within fundamental quantum mechanics as well as within a generalized thermodynamic formulation displaying features that are reminiscent of self-organization on a microscopic level. Various applications of these so-called coherent dissipative structures in physics and chemistry are pointed out, and discussed with possible inferences also made to the biological domain.

  • 30.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Godelian Structures and Self-Organization in Biological Systems2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 7-8, p. 1321-1332Article in journal (Refereed)
    Abstract [en]

    In 1986, Seel and Ladik asked, which role Godel's incompleteness theorem should have in a basic theory of biology. Recently, the author has tried to collect the conditions, which such a meta-theory must fulfill. A further argument concerned the deeper connection between classical canonical forms of so-called (triangular) Jordan blocks in the description of open quantal systems far from equilibrium and those of self-referential contradictions and paradoxes in philosophy and mathematical logic. Related examples were quoted from the emergence of self-organization in so-called dissipative structures with applications to both fundamental-and of higher order levels of organization. To bring this analogy closer together, we have developed a quantum logical formalism, describing such a Godelian situation, via the characterization of a well-defined "truth matrix." In this setting, the modus operandi of exploiting self-referential traits and paradoxical inconsistencies emphasize the possibility of a meta-code in complicated enough (biological) systems. In conclusion, we will revisit situations were the aforementioned self-referential property, together with the laws of physics and chemistry will guide our understanding of biology. We will finally consider subsequent implications on the various positions on artificial intelligence.

  • 31.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Partitioning technique for open systems2010In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 108, no 21-23, p. 3259-3272Article in journal (Refereed)
    Abstract [en]

    The focus of the present contribution is essentially confined to three research areas carried out during the author's turns as visiting (assistant, associate and full) professor at the University of Florida's Quantum Theory Project, QTP. The first two topics relate to perturbation theory and spectral theory for self-adjoint operators in Hilbert space. The third subject concerns analytic extensions to non-self-adjoint problems, where particular consequences of the occurrence of continuous energy spectra are measured. In these studies general partitioning methods serve as general cover for perturbation-, variational- and general matrix theory. In addition we follow up associated inferences for the time dependent problem as well as recent results and conclusions of a rather general yet surprising character. Although the author spent most of his times at QTP during visits in the 1970s and 1980s, collaborations with department members and shorter stays continued through later decades. Nevertheless the impact must be somewhat fragmentary, yet it is hoped that the present account is sufficiently self-contained to be realistic and constructive.

  • 32.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Quantum mechanics and the special and general theory of relativity2008In: Advances in Quantum Chemistry, Vol 54: DV-X Alpha for Industrial-Academic Cooperation, 2008, p. 115-132Conference paper (Refereed)
    Abstract [en]

    The old dilemma of quantum mechanics versus the theory of relativity is reconsidered. A first principles relativistically invariant theory will be provided through a model, which is basically quantum mechanical. Moreover, by analytically extending quantum mechanics into the complex plane, it is possible to include dynamical features such as time-, length-, and temperature-scales into the theory. The flexibility of including complex symmetric interactions will in the same way support a transition from firmly quantum mechanical non-local behaviour to a decidedly classical-local appearance. Furthermore, the extended formulation gives rise to so-called Jordan blocks. They will be shown to appear logically in the present generalized dynamical picture and a compelling interpretation is microscopic self-organization (MSO). Not only have the manifestation of quantum-thermal correlations, and the emergence of generic time scales been established, but the present viewpoint also appears to throw new light on the age-old problem of quantum mechanics versus relativity. To bring all these ideas together, we will demonstrate that our model (i) displays the simple occurrence of such a degenerate unit, (ii) demonstrates the link with the Klein-Gordon-Dirac relativistic theory and (iii) provides dynamical features of both special and general relativity theory.

  • 33.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Some Comments on the Problem of Decoherence2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 2, p. 215-224Article in journal (Refereed)
    Abstract [en]

    We consider a universally valid superposition principle derived from a general complex symmetric ansatz. The approach concerns open, dissipative systems and its significance for the examination and analysis of system-environment correlations. In particular, we discuss the concept of decoherence in the ensuing fundamental operator equations, incorporating simultaneously holistic and classical regimes. Despite its reductionist character, the theory applies to both micro-and macroscopic systems. Examples are drawn from general relativity, for example, the law of light deflection, the gravitational redshift, the time delay and the perihelion motion of Mercury, and from the macroscopic domain, for example, the emergence of selforganization in complicated enough systems. The preceding portrayal commends autonomicity and provides legitimate concepts of central importance in biological organization and artificial intelligence.

  • 34.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    The equivalence principle from a quantum mechanical perspective2009In: Advances in the theory of atomic and molecular systems / [ed] P. Piecuch, J. Maruani, G. Delgado-Barrio, S. Wilson, Springer Netherlands, 2009, p. 73-92Chapter in book (Other academic)
  • 35.
    Brändas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Kryachko, Eugene
    Preface: A Tribute Volume in Honour of Professor Osvaldo Goscinski2004In: Advances in Quantum Chemistry, ISSN 0065-3276, Vol. 47, p. xvii-xviiiArticle in journal (Other scientific)
  • 36.
    Brändas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Kryachko, Eugene
    Preface, Fundamental World of Quantum Chemistry, Vol III: A Tribute to the Memory of Per-Olov Löwdin2004Other (Other (popular scientific, debate etc.))
  • 37.
    Brändas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Vigo-Aguiar, Jesus
    Computational and Mathematical Methods on Science and Engineering: Proceedings of CMMSE-20042004Conference proceedings (editor) (Refereed)
  • 38.
    Burmeister, F. ,..Feifel,.R., Karlsson, L. and Svensson, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Physics II.
    Andersson, L. Mauritz
    Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Physics II.
    Karlsson, Hans
    Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Physics II.
    Goscinski, Osvaldo
    Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Physics II.
    Confirmation of non adiabatic vibrational progression in the inner valence 4sigmaminus photoionization band of DCl and HCl2002In: Phys Rev AArticle in journal (Refereed)
  • 39. Chen, Shu-Feng
    et al.
    Liu, Ya-Jun
    Navizet, Isabelle
    Ferré, Nicolas
    Fang, Wei-Hai
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Systematic theoretical investigation on the light emitter of firefly2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 3, p. 798-803Article in journal (Refereed)
    Abstract [en]

    This is a systematic theoretical investigation on all the possible light emitters of firefly using multireference method. Six chemical forms of oxyluciferin (OxyLH2) molecules/anions were studied by a multi-state complete active space second order perturbation (MS-CASPT2) method in vacuum and DMSO. The calculated results and subsequent analysis excluded enol-OxyLH2, keto-OxyLH2 and enolate-OxyLH- as possible light emitters. The remaining three candidates, phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2-, were further investigated in protein by a MS-CASPT2/molecular mechanics (MM) study to explain the natural bioluminescence of firefly. By comparison of the MS-CASPT2/MM calculated results of phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2- with the experimental observation and detailed analysis, we concluded that the direct decomposition excited-state product of firefly dioxetanone in vivo and the only light emitter of firefly in natural bioluminescence is the first singlet exited state (S1) of phenolate-keto-OxyLH-.

  • 40. Chen, Shu-Feng
    et al.
    Yue, Ling
    Liu, Ya-Jun
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Multireference theoretical studies on the solvent effect of firefly multicolor bioluminescence2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 13, p. 3371-3377Article in journal (Refereed)
    Abstract [en]

    In concert with the recent spectroscopic studies of the light-color modulation mechanism of firefly (Hirano et al., J Am Chem Soc 2009, 131, 2385), quantum chemical calculations using complete active space SCF (CASSCF), multistate complete active space second order perturbation (MS-CASPT2) theory as well as a time-dependent density functional theory (TD-DFT) approach with the Coulomb attenuated hybrid exchange-correlation functional (CAM-B3LYP) were performed on the excited state (S1) of the keto-form oxyluciferin (keto-OxyLH2). Benzene, DMSO, CH3CN, and H2O were chosen as polar solvents. The polarization effect of less polar solvent was considered by a simple model, complex of keto-OxyLH2, and NH3 with different covalent character. The calculated results supported the experimental conclusion: (1) the light emitter of bioluminescence is the S1 state of keto-OxyLH2 anion [(keto-1)*], and (2) light emission from (keto-1)* is modulated by the polarity of surrounding environment and the degree of covalent character of hydrogen bond between (keto-1)* and a protonated basic moiety. The mechanism of the multicolor bioluminescence was discussed from the theoretical viewpoint.

  • 41. Dalgarno, Alex
    et al.
    Froelich, Piotr
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Jonsell, Svante
    Saenz, Alejandro
    Zygelman, Bernard
    Collisions of H and Hbar2001In: New Directions in Antimatter Chemistry and Physics, Kluwer Academic Publishers, 2001, p. 47-52Chapter in book (Refereed)
  • 42. de Jong, Wibe A
    et al.
    Bylaska, Eric
    Govind, Niranjan
    Janssen, Curtis L
    Kowalski, Karol
    Müller, Thomas
    Nielsen, Ida M B
    van Dam, Hubertus J J
    Veryazov, Valera
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Utilizing high performance computing for chemistry: parallel computational chemistry2010In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, no 26, p. 6896-6920Article in journal (Refereed)
    Abstract [en]

    Parallel hardware has become readily available to the computational chemistry research community. This perspective will review the current state of parallel computational chemistry software utilizing high-performance parallel computing platforms. Hardware and software trends and their effect on quantum chemistry methodologies, algorithms, and software development will also be discussed.

  • 43. Delgado-Barrio, Gerardo
    et al.
    Maruani, Jean
    Piecuch, Piotr
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Special Issue: Proceedings from the Fourteenth European Workshop on Quantum Systems in Chemistry and Physics Preface2011In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, no 2, p. 203-204Article in journal (Other academic)
  • 44. Dunne, Lawrence J.
    et al.
    Brändas, Erkki J.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Two-fluid Model of Superconducting Condensates and Spin Gaps in dx2-dy2 Wave High Tc Cuprates from Repulsive Electronic Correlations2004In: International Journal of Quantum Chemistry, ISSN 0020-7608, Vol. 99, p. 798-804Article in journal (Refereed)
  • 45.
    Durbeej, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    On the primary event of phytochrome: quantum chemical comparison of photoreactions at C4, C10 and C152009In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, no 9, p. 1354-1361Article in journal (Refereed)
    Abstract [en]

    Phytochromes are widespread photoreceptors responsive to red and far-red light that exist in two photochromic forms Pr (inactive) and Pfr (active). The Pr → Pfr conversion proceeds through a series of events initiated by ZE photoisomerization of the tetrapyrrole chromophore, believed to occur at C15 of the methine bridge between rings C and D. Recent crystal structures show that ring D in Pr is less tightly packed by the protein than rings A, B and C, which should favor the C15 reaction over reactions at C4 (AB methine bridge) and C10 (BC). In the present work, quantum chemical methods are used to establish the intrinsic reactivity of the chromophore towards all three possible ZE isomerization events in the absence of steric effects and specific interactions with the protein. Using a level of theory that reproduces spectroscopic data with an accuracy of 0.2 eV, it is demonstrated that isolated conditions allow the C10 photoreaction to substantially dominate. This finding suggests that the different degrees of ring-packing observed in the protein are crucial not only to facilitate a reaction at C15, but also to prevent an intrinsically more favorable reaction at C10 from taking place.

  • 46. Durbeej, Bo
    et al.
    Borg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Eriksson, Leif
    Computational evidence in favor of a protonated chromophore in the photoactivation of phytochrome2005In: Chemica