uu.seUppsala University Publications
Change search
Refine search result
123456 1 - 50 of 261
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the 'Create feeds' function.
  • 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, 541-548 p.Article 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.
    Ahlstrand, Emma
    et al.
    Linnæus University Centre for Biomaterials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Friedman, Ran
    Interaction Energies Between Metal Ions (Zn2+ and Cd2+) and Biologically Relevant Ligands2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 23, 2554-2562 p.Article in journal (Refereed)
    Abstract [en]

    Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.

  • 3.
    Almquist, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Mattsson, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Edvinsson, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    High-fidelity numerical solution of the time-dependent Dirac equation2014In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 262, 86-103 p.Article in journal (Refereed)
  • 4.
    Almquist, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Mattsson, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Edvinsson, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Stable and accurate simulation of phenomena in relativistic quantum mechanics2013In: Proc. 11th International Conference on Mathematical and Numerical Aspects of Waves, Tunisia: ENIT , 2013, 213-214 p.Conference paper (Other academic)
  • 5.
    Amrein, Beat Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Extending the Reach of Computational Approaches to Model Enzyme Catalysis2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Recent years have seen tremendous developments in methods for computational modeling of (bio-) molecular systems. Ever larger reactive systems are being studied with high accuracy approaches, and high-level QM/MM calculations are being routinely performed. However, applying high-accuracy methods to large biological systems is computationally expensive and becomes problematic when conformational sampling is needed. To address this challenge, classical force field based approaches such as free energy perturbation (FEP) and empirical valence bond calculations (EVB) have been employed in this work. Specifically:

    1. Force-field independent metal parameters have been developed for a range of alkaline earth and transition metal ions, which successfully reproduce experimental solvation free energies, metal-oxygen distances, and coordination numbers. These are valuable for the computational study of biological systems.

    2. Experimental studies have shown that the epoxide hydrolase from Solanum tuberosum (StEH1) is not only an enantioselective enzyme, but for smaller substrates, displays enantioconvergent behavior. For StEH1, two detailed studies, involving combined experimental and computational efforts have been performed: We first used trans-stilbene oxide to establish the basic reaction mechanism of this enzyme. Importantly, a highly conserved and earlier ignored histidine was identified to be important for catalysis. Following from this, EVB and experiment have been used to investigate the enantioconvergence of the StEH1-catalyzed hydrolysis of styrene oxide. This combined approach involved wildtype StEH1 and an engineered enzyme variant, and established a molecular understanding of enantioconvergent behavior of StEH1.

    3. A novel framework was developed for the Computer-Aided Directed Evolution of Enzymes (CADEE), in order to be able to quickly prepare, simulate, and analyze hundreds of enzyme variants. CADEE’s easy applicability is demonstrated in the form of an educational example.

    In conclusion, classical approaches are a computationally economical means to achieve extensive conformational sampling. Using the EVB approach has enabled me to obtain a molecular understanding of complex enzymatic systems. I have also increased the reach of the EVB approach, through the implementation of CADEE, which enables efficient and highly parallel in silico testing of hundreds-to-thousands of individual enzyme variants.

    List of papers
    1. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
    Open this publication in new window or tab >>Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
    Show others...
    2014 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 16, 4351-4362 p.Article in journal (Refereed) Published
    Abstract [en]

    The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase 1 as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.

    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-225523 (URN)10.1021/jp501737x (DOI)000335113600010 ()
    Funder
    Swedish National Infrastructure for Computing (SNIC), 2013/26-1
    Available from: 2014-06-23 Created: 2014-06-04 Last updated: 2017-12-05
    2. Expanding the catalytic triad in epoxide hydrolases and related enzymes
    Open this publication in new window or tab >>Expanding the catalytic triad in epoxide hydrolases and related enzymes
    Show others...
    2015 (English)In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 5, no 10, 5702-5713 p.Article in journal (Refereed) Published
    Abstract [en]

    Potato epoxide hydrolase 1 exhibits rich enantio- and regioselectivity in the hydrolysis of a broadrange of substrates. The enzyme can be engineered to increase the yield of optically pureproducts, as a result of changes in both enantio- and regioselectivity. It is thus highly attractive inbiocatalysis, particularly for the generation of enantiopure fine chemicals and pharmaceuticals.The present work aims to establish the principles underlying the activity and selectivity of theenzyme through a combined computational, structural, and kinetic study, using the substratetrans-stilbene oxide as a model system. Extensive empirical valence bond simulations have beenperformed on the wild-type enzyme together with several experimentally characterized mutants.We are able to computationally reproduce the differences in activities between differentstereoisomers of the substrate, and the effects of mutations in several active-site residues. Inaddition, our results indicate the involvement of a previously neglected residue, H104, which iselectrostatically linked to the general base, H300. We find that this residue, which is highlyconserved in epoxide hydrolases and related hydrolytic enzymes, needs to be in its protonatedform in order to provide charge balance in an otherwise negatively-charged active site. Our datashow that unless the active-site charge balance is correctly treated in simulations, it is notpossible to generate a physically meaningful model for the enzyme that can accurately reproduceactivity and selectivity trends. We also expand our understanding of other catalytic residues,demonstrating in particular the role of a non-canonical residue, E35, as a “backup-base” in theabsence of H300. Our results provide a detailed view of the main factors driving catalysis andregioselectivity in this enzyme, and identify targets for subsequent enzyme design efforts.

    National Category
    Biochemistry and Molecular Biology
    Research subject
    Biochemistry
    Identifiers
    urn:nbn:se:uu:diva-260232 (URN)10.1021/acscatal.5b01639 (DOI)000362391500006 ()
    Funder
    EU, FP7, Seventh Framework Programme, 306474Swedish Research Council, 621-2011-6055, 621-2010-5145Swedish National Infrastructure for Computing (SNIC), 2015/16-12
    Available from: 2015-08-18 Created: 2015-08-18 Last updated: 2017-12-04Bibliographically approved
    3. Conformational Diversity and Enantioconvergence in Potato Epoxide Hydrolase 1
    Open this publication in new window or tab >>Conformational Diversity and Enantioconvergence in Potato Epoxide Hydrolase 1
    Show others...
    2016 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 14, no 24, 5639-5651 p.Article in journal (Refereed) Published
    Abstract [en]

    Potato epoxide hydrolase 1 (StEH1) is a biocatalytically important enzyme that exhibits rich enantio-and regioselectivity in the hydrolysis of chiral epoxide substrates. In particular, StEH1 has been demonstrated to enantioconvergently hydrolyze racemic mixes of styrene oxide (SO) to yield (R)-1-phenylethanediol. This work combines computational, crystallographic and biochemical analyses to understand both the origins of the enantioconvergent behavior of the wild-type enzyme, as well as shifts in activities and substrate binding preferences in an engineered StEH1 variant, R-C1B1, which contains four active site substitutions (W106L, L109Y, V141K and I155V). Our calculations are able to reproduce both the enantio-and regioselectivities of StEH1, and demonstrate a clear link between different substrate binding modes and the corresponding selectivity, with the preferred binding modes being shifted between the wild-type enzyme and the R-C1B1 variant. Additionally, we demonstrate that the observed changes in selectivity and the corresponding enantioconvergent behavior are due to a combination of steric and electrostatic effects that modulate both the accessibility of the different carbon atoms to the nucleophilic side chain of D105, as well as the interactions between the substrate and protein amino acid side chains and active site water molecules. Being able to computationally predict such subtle effects for different substrate enantiomers, as well as to understand their origin and how they are affected by mutations, is an important advance towards the computational design of improved biocatalysts for enantioselective synthesis.

    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-282015 (URN)10.1039/C6OB00060F (DOI)000378933400042 ()27049844 (PubMedID)
    Funder
    Swedish National Infrastructure for Computing (SNIC), 25/2-10EU, European Research Council, 306474;283570Swedish Research Council, 621-2011-6055Carl Tryggers foundation , CTS13:104
    Available from: 2016-04-01 Created: 2016-04-01 Last updated: 2017-11-30Bibliographically approved
    4. CADEE: Computer-Aided Directed Evolution of Enzymes
    Open this publication in new window or tab >>CADEE: Computer-Aided Directed Evolution of Enzymes
    Show others...
    2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, no 1, 50-64 p.Article in journal (Refereed) Published
    Abstract [en]

    The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.

    Keyword
    computational directed evolution, computational enzyme design, distributed computing, empirical valence bond, triosephosphate isomerase
    National Category
    Structural Biology Bioinformatics (Computational Biology) Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-314218 (URN)10.1107/S2052252516018017 (DOI)000392925800007 ()
    Funder
    EU, FP7, Seventh Framework Programme, 306474Knut and Alice Wallenberg FoundationThe Royal Swedish Academy of SciencesSwedish Research Council, 2015-04928Swedish National Infrastructure for Computing (SNIC), 2015/16-12
    Available from: 2017-01-31 Created: 2017-01-31 Last updated: 2018-01-13Bibliographically approved
  • 6.
    Amrein, Beat Anton
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Steffen-Munsberg, Fabian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Szeler, Ireneusz
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Purg, Miha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kulkarni, Yashraj
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    CADEE: Computer-Aided Directed Evolution of Enzymes2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, no 1, 50-64 p.Article in journal (Refereed)
    Abstract [en]

    The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.

  • 7.
    Anders, Brakestad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ab Initio Characterization of Conical Intersections Related to Chemiluminescence in Methylated 1,2-Dioxetanes2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 8.
    Andersson, Mauritz
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Quantum Dynamics of Molecular Systems and Guided Matter Waves2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantum dynamics is the study of time-dependent phenomena in fundamental processes of atomic and molecular systems. This thesis focuses on systems where nature reveals its quantum aspect; e.g. in vibrational resonance structures, in wave packet revivals and in matter wave interferometry. Grid based numerical methods for solving the time-dependent Schrödinger equation are implemented for simulating time resolved molecular vibrations and to compute photo-electron spectra, without the necessity of diagonalizing a large matrix to find eigenvalues and eigenvectors.

    Pump-probe femtosecond laser spectroscopy on the sodium potassium molecule, showing a vibrational period of 450 fs, is theoretically simulated. We find agreement with experiment by inclusion of the finite length laser pulse and finite temperature effects.

    Complicated resonance structures observed experimentally in photo-electron spectra of hydrogen- and deuterium chloride is analyzed by a numerical computation of the spectra. The dramatic difference in the two spectra arises from non-adiabatic interactions, i.e. the interplay between nuclear and electron dynamics. We suggest new potential curves for the 32Σ+ and 42Σ+ states in HCI+.

    It is possible to guide slow atoms along magnetic potentials like light is guided in optical fibers. Quantum mechanics dictates that matter can show wave properties. A proposal for a multi mode matter wave interferometer on an atom chip is studied by solving the time-dependent Schrödinger equation in two dimensions. The results verifies a possible route for an experimental realization.

    An improved representation for wave functions using a discrete set of coherent states is presented. We develop a practical method for computing the expansion coefficients in this non-orthogonal set. It is built on the concept of frames, and introduces an iterative method for computing a representation of the identity operator. The phase-space localization property of the coherent states gives adaptability and better sampling efficiency.

  • 9.
    Aquilante, Francesco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Carlson, Rebecca K.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Delcey, Mickael G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    De Vico, Luca
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen O, Denmark..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ferre, Nicolas
    Univ Aix Marseille, CNRS, Inst Chim Radicalaire, Campus Etoile St Jerome Case 521,Ave Esc, F-13397 Marseille 20, France..
    Frutos, Luis Manuel
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Gagliardi, Laura
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy.;Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Giussani, Angelo
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Hoyer, Chad E.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Li Manni, Giovanni
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Lischka, Hans
    Texas Tech Univ, Dept Chem & Biochem, Mem Circle & Boston, Lubbock, TX 79409 USA.;Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Ma, Dongxia
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Malmqvist, Per Ake
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Mueller, Thomas
    Forschungszentrum Julich, IAS, JSC, Wilhelm Johnen Str, D-52425 Julich, Germany..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, 141 Overman Hall, Bowling Green, OH 43403 USA.;Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam, IL-91904 Jerusalem, Israel..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, POB 1033 Blindern, N-0315 Oslo, Norway..
    Peng, Daoling
    S China Normal Univ, Coll Chem & Environm, Guangzhou 510006, Guangdong, Peoples R China..
    Plasser, Felix
    Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Pritchard, Ben
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Reiher, Markus
    ETH, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Rivalta, Ivan
    Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Schapiro, Igor
    Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France..
    Segarra-Marti, Javier
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Truhlar, Donald G.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Ungur, Liviu
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Valentini, Alessio
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Vancoillie, Steven
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Veryazov, Valera
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Vysotskiy, Victor P.
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Weingart, Oliver
    Univ Dusseldorf, Inst Theoret Chem & Computerchem, Univ Str 1, D-40225 Dusseldorf, Germany..
    Zapata, Felipe
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, 506-541 p.Article in journal (Refereed)
    Abstract [en]

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

  • 10.
    Aquilante, Francesco
    et al.
    Univ Bologna, Dipartimento Chim G Ciamician, Bologna, Italy..
    Delcey, Mickael G.
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA USA.;Univ Calif Berkeley, Dept Chem, Kenneth S Pitzer Ctr Theoret Chem, Berkeley, CA 94720 USA..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, Oslo, Norway..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala Univ, Dept Chem Angstrom, Theoret Chem Programme, Uppsala, Sweden..
    Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, 2052-2064 p.Article in journal (Refereed)
    Abstract [en]

    The density-fitting technique for approximating electron-repulsion integrals relies on the quality of auxiliary basis sets. These are commonly obtained through data fitting, an approach that presents some shortcomings. On the other hand, it is possible to derive auxiliary basis sets by removing elements from the product space of both contracted and primitive orbitals by means of a particular form of inner projection technique that has come to be known as Cholesky decomposition (CD). This procedure allows for on-the-fly construction of auxiliary basis sets that may be used in conjunction with any quantum chemical method, i.e. unbiased auxiliary basis sets. One key feature of these sets is that they represent the electron-repulsion integral matrix in atomic orbital basis with an accuracy that can be systematically improved. Another key feature is represented by the fact that locality of fitting coefficients is obtained even with the long-ranged Coulomb metric, as result of integral accuracy. Here we report on recent advances in the development of the CD-based density fitting technology. In particular, the implementation of analytical gradients algorithms is reviewed and the present status of local formulations - potentially linear scaling - is analysed in detail.

  • 11.
    Aquilante, Francesco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pedersen, Thomas Bondo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Veryazov, Valera
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    MOLCAS—a software for multiconfigurational quantum chemistry calculations2013In: Wiley Interdisciplinary Reviews: Computational Molecular Science, ISSN 1759-0876, Vol. 3, no 2, 143-149 p.Article in journal (Refereed)
    Abstract [en]

    At variance, with most of the quantum chemistry software presently available, MOLCAS is a package that is specialized in multiconfigurational wave function theory (MC-WFT) rather than density functional theory (DFT). Given the much higher algorithmic complexity of MC-WFT versus DFT, an extraordinary effort needs to be made from the programming point of view to achieve state-of-the-art performance for large-scale calculations. In particular, a robust and efficient implementation of the Cholesky decomposition techniques for handling two-electron integrals has been developed which is unique to MOLCAS. Together with this 'Cholesky infrastructure', a powerful and multilayer graphical and scripting user interface is available, which is an essential ingredient for the setup of MC-WFT calculations. These two aspects of the MOLCAS software constitute the focus of the present report.

  • 12.
    Banerjee, Paramita
    et al.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    Pathak, Biswarup
    Indian Inst Technol, Discipline Chem, Indore 452020, India..
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Das, G. P.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    First principles design of Li functionalized hydrogenated h-BN nanosheet for hydrogen storage2016In: International journal of hydrogen energy, ISSN 0360-3199, E-ISSN 1879-3487, Vol. 41, no 32, 14437-14446 p.Article in journal (Refereed)
    Abstract [en]

    Employing first principles density functional theory (DFT) based approach, the structure, stability and hydrogen storage efficiency of a hydrogenated hexagonal boron nitride sheet (BHNH chair conformer) functionalized by the lightest alkali metal atom Li has been explored here in details. Substituting one hydrogen atom from both B and N sides of BHNH sheet by a Li atom, we have found that Li becomes cationic and acts as a binding site to adsorb hydrogen molecules. The stability of this Li-substituted BHNH sheet has been indicated via Ab-initio Molecular Dynamics (AIMD) simulation upto 400 K. The binding energy (similar to 0.18-0.3 eV/H-2 molecule) and gravimetric density (similar to 6 wt %) (upto similar to 200 K) of the hydrogen molecules fall in the required window for practical hydrogen storage. AIMD simulation indicates complete dehydrogenation from this system occurs at similar to 400 K, thereby predicting the suitability of this system from the point of view of efficient hydrogen storage.

  • 13. Behzadi, Hadi
    et al.
    Manzetti, Sergio
    Darghai, Mayram
    Payman, Roonasi
    Khalilnia, Zahra
    Application of calculated NMR parameters, aromaticity indices and wavefunction properties for evaluation of corrosion inhibition efficiency of pyrazine inhibitors2017In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 1151, 34-40 p.Article in journal (Refereed)
  • 14. Beinik, Igor
    et al.
    Hellström, Matti
    Jensen, Thomas
    Broqvist, Peter
    Lauritsen, Jeppe
    Cu wets the polar ZnO(0001)-Zn surface because of interaction with subsurface defectsArticle in journal (Refereed)
  • 15.
    Bengtson, Charlotta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Quantum nonlocality in the excitation energy transfer in the Fenna-Matthews-Olson complex2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, 1763-1771 p.Article in journal (Refereed)
    Abstract [en]

    The Fenna-Matthews-Olson (FMO) complex - a pigment protein complex involved in photosynthesis in green sulfur bacteria - is remarkably efficient in transferring excitation energy from light harvesting antenna molecules to a reaction center. Recent experimental and theoretical studies suggest that quantum coherence and entanglement may play a role in this excitation energy transfer (EET). We examine whether bipartite quantum nonlocality, a property that expresses a stronger-than-entanglement form of correlation, exists between different pairs of chromophores in the FMO complex when modeling the EET by the hierarchically coupled equations of motion method. We compare the results for nonlocality with the amount of bipartite entanglement in the system. In particular, we analyze in what way these correlation properties are affected by different initial conditions. It is found that bipartite nonlocality only exists when the initial conditions are chosen in an unphysiological manner and probably is absent when considering the EET in the FMO complex in its natural habitat. It is also seen that nonlocality and entanglement behave quite differently in this system. In particular, for localized initial states, nonlocality only exists on a very short time scale and then drops to zero in an abrupt manner. As already known from previous studies, quantum entanglement between chromophore pairs on the other hand is oscillating and exponentially decaying and follow thereby a pattern more similar to the chromophore population dynamics. The abrupt disappearance of nonlocality in the presence of nonvanishing entanglement is a phenomenon we call nonlocality sudden death; a striking manifestation of the difference between these two types of correlations in quantum systems. 

  • 16. Bondesson, Laban
    et al.
    Rudberg, Elias
    Luo, Yi
    Salek, Pawel
    A linear scaling study of solvent-solute interaction energy of drug molecules in aqua solution2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 34, 10320-10328 p.Article in journal (Refereed)
  • 17. Bondesson, Laban
    et al.
    Rudberg, Elias
    Luo, Yi
    Salek, Pawel
    Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, 1725-1732 p.Article in journal (Refereed)
  • 18.
    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, 7045- p.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, 57-62 p.Article 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, 034307- p.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, 5066- p.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, 83- p.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, 11554-11565 p.Article 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, 2528-2537 p.Article 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, 4470-4476 p.Article 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, 2351-2361 p.Article 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
  • 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, 7045-56 p.Article in journal (Refereed)
  • 20. Boström, Jonas
    et al.
    Aquilante, Francesco
    Pedersen, Thomas Bondo
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical gradients of Hartree-Fock exchange with density fitting approximations2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 1, 204-212 p.Article in journal (Refereed)
    Abstract [en]

    We extend the local exchange (LK) algorithm [Aquilante, F.; Pedersen, T. B.; Lindh, R. J. Chem. Phys.2007, 126, 194106] to the calculation of analytical gradients with density fitting. We discuss the features of the screening procedure and demonstrate the possible advantages of using this formulation, which is easily interfaced to a standard integral-direct gradient code. With auxiliary basis sets obtained from Cholesky decomposition of atomic or molecular integral blocks with a decomposition threshold of 10-4Eh, typical errors due to the density fitting in bond lengths, bond angles, and dihedral angles are 0.1 pm, 0.1°, and 0.5°, respectively. The overall speedup of geometry optimizations is about 1 order of magnitude for atomic natural-orbital-type basis sets but much less pronounced for correlation-consistent basis sets.

  • 21. Boström, Jonas
    et al.
    Veryazov, Valera
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Bondo Pedersen, Thomas
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical gradients of the second-order Møller–Plesset energy using Cholesky decompositions2014In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 114, no 5, 321-327 p.Article in journal (Refereed)
    Abstract [en]

    An algorithm for computing analytical gradients of the second-order Møller–Plesset (MP2) energy using density fitting (DF) is presented. The algorithm assumes that the underlying canonical Hartree–Fock reference is obtained with the same auxiliary basis set, which we obtain by Cholesky decomposition (CD) of atomic electron repulsion integrals. CD is also used for the negative semidefinite MP2 amplitude matrix. Test calculations on the weakly interacting dimers of the S22 test set (Jurečka et al., Phys. Chem. Chem. Phys. 2006, 8, 1985) show that the geometry errors due to the auxiliary basis set are negligible. With double-zeta basis sets, the error due to the DF approximation in intermolecular bond lengths is better than 0.1 pm. The computational time is typically reduced by a factor of 6–7.

  • 22.
    Boukharta, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods.

    We report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 G-protein coupled receptor and a series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Site-directed mutagenesis, homology modelling and docking were further used to characterize agonist binding to the human neuropeptide Y2 receptor, which is important in feeding behavior and an obesity drug target.  In a separate project, homology modelling was also used for rationalization of mutagenesis data for an integron integrase involved in antibiotic resistance.

    Blockade of the hERG potassium channel by various drug-like compounds, potentially causing serious cardiac side effects, is a major problem in drug development. We have used a homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations are in good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships with implications for design of new compounds. Docking, scoring, molecular dynamics, and the linear interaction energy method were also used to predict binding modes and affinities for a large set of inhibitors to HIV-1 reverse transcriptase. Good agreement with experiment was found and the work provides a validation of the methodology as a powerful tool in structure-based drug design. It is also easily scalable for higher throughput of compounds.

    List of papers
    1. Mutagenesis of human neuropeptide Y/peptide YY receptor Y2 reveals additional differences to Y1 in interactions with highly conserved ligand positions
    Open this publication in new window or tab >>Mutagenesis of human neuropeptide Y/peptide YY receptor Y2 reveals additional differences to Y1 in interactions with highly conserved ligand positions
    Show others...
    2010 (English)In: Regulatory Peptides, ISSN 0167-0115, E-ISSN 1873-1686, Vol. 163, no 1-3, 120-129 p.Article in journal (Refereed) Published
    Abstract [en]

    Neuropeptide Y (NPY) and peptide YY (PYY) share similar to 70% of their 36 amino acids and bind to the same three human receptor subtypes, Y1, Y2 and Y5, even though these receptors only share similar to 30% sequence identity Based on our previous investigation of human Y1 we describe here a mutagenesis study of three corresponding positions in human Y2, i e Tyr(2 64), Val(6 58) and Tyr(7 31) Pharmacological characterization was performed with the four peptide agonists PYY, NPY, PYY(3-36) and NPY(13-36) as well as the non-peptide antagonist BIIE0246 Results from mutants where Tyr(2 64) has been substituted by Ala suggest that Tyr(2 64) is involved in the interaction with all investigated ligands whereas position Tyr(7 31) seems to be more important for interaction with the truncated peptide PYY(3-36) than with intact NPY Surprisingly, substitution of Tyr(7 31) with His, the corresponding residue in Y1, resulted in total loss of binding of iodinated porcine PYY The third position. Val(6 58), did not influence binding of any of the ligands. These findings differ from those obtained for Y1 where Ala substitution resulted in lost or changed binding for each of the three positions. Although Tyr(2 64) and Tyr(7 31) in Y2 are involved in ligand binding, their interactions with the peptide ligands seem to be different from the corresponding positions in Y1 This suggests that the receptor-ligand interactions have changed during evolution after Y1 and Y2 arose from a common ancestral receptor.

    Keyword
    Site-directed mutagenesis, G-protein coupled receptor, Three dimensional model, Evolution
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-135756 (URN)10.1016/j.regpep.2010.04.011 (DOI)000280050000018 ()
    Note

    Manuscript title: Investigation of receptor-ligand interactions of the human neuropeptide Y receptor Y2 by site-directed mutagenesis: comparison with the structurally divergent Y1 subtype

    Available from: 2010-12-08 Created: 2010-12-08 Last updated: 2017-12-11Bibliographically approved
    2. Mutagenesis and Computational Modeling of Human G‑Protein-Coupled Receptor Y2 for Neuropeptide Y and Peptide YY
    Open this publication in new window or tab >>Mutagenesis and Computational Modeling of Human G‑Protein-Coupled Receptor Y2 for Neuropeptide Y and Peptide YY
    Show others...
    2013 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 52, no 45, 7987-7998 p.Article in journal (Refereed) Published
    Abstract [en]

    Neuropeptide Y and peptide YY receptor type 2 (Y2) is involved in appetite regulation and several other physiological processes. We have investigated the structure of the human Y2 receptor. Computational modeling of receptor–agonist interactions was used as a guide to design a series of receptor mutants, followed by binding assays using full-length and truncated peptide agonists and the Y2-specific antagonist BIIE0246. Our model suggested a hydrogen bond network among highly conserved residues Thr2.61, Gln3.32, and His7.39, which could play roles in ligand binding and/or receptor structure. In addition, the C-terminus of the peptide could make contact with residues Tyr5.38 and Leu6.51. Mutagenesis of all these positions, followed by binding assays, provides experimental support for our computational model: most of the mutants for the residues forming the proposed hydrogen bond network displayed reduced peptide agonist affinities as well as reduced hPYY3-36 potency in a functional assay. The Ala and Leu mutants of Gln3.32 and His7.39 disrupted membrane expression of the receptor. Combined with the modeling, the experimental results support roles for these hydrogen bond network residues in peptide binding as well as receptor architecture. The reduced agonist affinity for mutants of Tyr5.38 and Leu6.51 supports their role in a binding pocket surrounding the invariant tyrosine at position 36 of the peptide ligands. The results for antagonist BIIE0246 suggest several differences in interactions compared to those of the peptides. Our results lead to a new structural model for NPY family receptors and peptide binding.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2013
    National Category
    Natural Sciences Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-154994 (URN)10.1021/bi400830c (DOI)000330017700012 ()
    Available from: 2011-08-04 Created: 2011-06-14 Last updated: 2017-12-08Bibliographically approved
    3. Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors
    Open this publication in new window or tab >>Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors
    2014 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 10, no 4, e1003585- p.Article in journal (Refereed) Published
    Abstract [en]

    Site-directed mutagenesis combined with binding affinity measurements is widely used to probe the nature of ligand interactions with GPCRs. Such experiments, as well as structure-activity relationships for series of ligands, are usually interpreted with computationally derived models of ligand binding modes. However, systematic approaches for accurate calculations of the corresponding binding free energies are still lacking. Here, we report a computational strategy to quantitatively predict the effects of alanine scanning and ligand modifications based on molecular dynamics free energy simulations. A smooth stepwise scheme for free energy perturbation calculations is derived and applied to a series of thirteen alanine mutations of the human neuropeptide Y1 receptor and series of eight analogous antagonists. The robustness and accuracy of the method enables univocal interpretation of existing mutagenesis and binding data. We show how these calculations can be used to validate structural models and demonstrate their ability to discriminate against suboptimal ones. Author Summary G-protein coupled receptors constitute a family of drug targets of outstanding interest, with more than 30% of the marketed drugs targeting a GPCR. The combination of site-directed mutagenesis, biochemical experiments and computationally generated 3D structural models has traditionally been used to investigate these receptors. The increasing number of GPCR crystal structures now paves the way for detailed characterization of receptor-ligand interactions and energetics using advanced computer simulations. Here, we present an accurate computational scheme to predict and interpret the effects of alanine scanning experiments, based on molecular dynamics free energy simulations. We apply the technique to antagonist binding to the neuropeptide Y receptor Y1, the structure of which is still unknown. A structural model of a Y1-antagonist complex was derived and used as starting point for computational characterization of the effects on binding of alanine substitutions at thirteen different receptor positions. Further, we used the model and computational scheme to predict the binding of a series of seven antagonist analogs. The results are in excellent agreement with available experimental data and provide validation of both the methodology and structural models of the complexes.

    National Category
    Bioinformatics (Computational Biology) Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-212102 (URN)10.1371/journal.pcbi.1003585 (DOI)000336507500014 ()
    Available from: 2013-12-05 Created: 2013-12-05 Last updated: 2018-01-11Bibliographically approved
    4. Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers
    Open this publication in new window or tab >>Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers
    Show others...
    2011 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 50, no 27, 6146-6156 p.Article in journal (Refereed) Published
    Abstract [en]

    The hERG potassium channel is of major pharmaceutical importance, and its blockade by various compounds, potentially causing serious cardiac side effects, is a major problem in drug development. Despite the large amounts of existing biochemical data on blockade of hERG by drugs and druglike compounds, relatively little is known regarding the structural basis of binding of blockers to the channel. Here, we have used a recently developed homology model of hERG to conduct molecular docking experiments with a series of channel blockers, followed by molecular dynamics simulations of the complexes and evaluation of binding free energies with the linear interaction energy method. The calculations yield a remarkably good agreement with experimental binding affinities and allow for a rationalization of three-dimensional structure-activity relationships in terms of a number of key interactions. Two main interaction regions of the channel are thus identified with implications for further mutagenesis experiments and design of new compounds.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-156474 (URN)10.1021/bi200173n (DOI)000292430600018 ()
    Available from: 2011-07-27 Created: 2011-07-25 Last updated: 2017-12-08Bibliographically approved
    5. Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase
    Open this publication in new window or tab >>Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase
    2008 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 51, no 9, 2648-56 p.Article in journal (Refereed) Published
    Abstract [en]

    Docking, scoring, molecular dynamics (MD), and the linear interaction energy (LIE) method are used here to predict binding modes and affinities for a set of 43 non-nucleoside inhibitors to HIV-1 reverse transcriptase. Starting from a crystallographic structure, the binding modes of 43 inhibitors are predicted using automated docking. The Goldscore scoring function and the LIE method are then used to determine the relative binding free energies for the inhibitors. The Goldscore scoring function does not reproduce the relative binding affinities for the inhibitors, while the standard parametrization of the LIE method reproduces the experimental binding free energies for 39 inhibitors with an R (2) = 0.70 and an unsigned average error of 0.8 kcal/mol. The present calculations provide a validation of the combination of docking, MD, and LIE as a powerful tool in structure-based drug design, and the methodology is easily scalable for attaining a higher throughput of compounds.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-97214 (URN)10.1021/jm7012198 (DOI)000255500000010 ()18410085 (PubMedID)
    Available from: 2008-04-29 Created: 2008-04-29 Last updated: 2017-12-14Bibliographically approved
    6. Mutagenesis and homology modelling of the Tn21 integron integrase IntI1
    Open this publication in new window or tab >>Mutagenesis and homology modelling of the Tn21 integron integrase IntI1
    Show others...
    2009 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 8, 1743-1753 p.Article in journal (Refereed) Published
    Abstract [en]

    Horizontal DNA transfer between bacteria is widespread and a major cause of antibiotic resistance. For logistic reasons, single or combined genes are shuttled between vectors such as plasmids and   bacterial chromosomes. Special elements termed integrons operate in such shuttling and are therefore vital for horizontal gene transfer. Shorter elements carrying genes, cassettes, are integrated in the integrons, or excised from them, by virtue of a recombination site, attC, positioned in the 3' end of each unit. It is a remarkable and   possibly restricting elementary feature of attC that it must be single-stranded while the partner target site, attI, may be double-stranded. The integron integrases belong to the tyrosine recombinase family, and this work reports mutations of the integrase IntI1 from transposon Tn21, chosen within a well-conserved region characteristic of the integron integrases. The mutated proteins were  tested for binding to a bottom strand of an attC substrate, by using an electrophoresis mobility shift assay. To aid in interpreting the   results, a homology model was constructed on the basis of the crystal structure of integron integrase VchIntIA from Vibrio cholerae bound to its cognate attC substrate VCRbs. The local stability and hydrogen bonding network of key domains of the modeled structure were further examined using molecular dynamics simulations. The homology model allowed us to interpret the roles of several amino acid residues, four of which were clearly binding assay responsive upon mutagenesis. Notably, we also observed features indicating that IntI1 may be more prone to base-specific contacts with VCRbs than VchIntIA.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95309 (URN)10.1021/bi8020235 (DOI)000263697300009 ()
    Available from: 2007-01-02 Created: 2007-01-02 Last updated: 2017-12-14Bibliographically approved
  • 23. Brandt, Peter
    et al.
    Norrby, Per-Ola
    Daly, Adrian M
    Gilheany, Declan G
    Chromium-salen-mediated alkene epoxidation: a theoretical and experimental study indicates the importance of spin-surface crossing and the presence of a discrete intermediate.2002In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 8, no 18, 4299-307 p.Article in journal (Refereed)
    Abstract [en]

    The mechanism of alkene epoxidation by chromium(v) oxo salen complexes has been studied by DFT and experimental methods. The reaction is compared to the closely related Mn-catalyzed process in an attempt to understand the dramatic difference in selectivity between the two systems. Overall, the studies show that the reactions have many similarities, but also a few critical differences. In agreement with experiment, the chromium system requires a change from low- to high-spin in the catalytic cycle, whereas the manganese system can proceed either with spin inversion or entirely on the high-spin surface. The low-spin addition of metal oxo species to an alkene leads to an intermediate which forms epoxide either with a barrier on the low-spin surface or without a barrier after spin inversion. Supporting evidence for this intermediate was obtained by using vinylcyclopropane traps. The chromium(v) oxo complexes can adopt a stepped shape or form a more concave surface, analogous to previous results on manganese salen complexes.

  • 24.
    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, xi-xii p.Article, 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

  • 25.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Multiscale modelling: the spiral staircase from theory to experiment2017Conference paper (Refereed)
    Abstract [en]

    Multiscale modelling has become a catch phrase in modern e-science, and is widely (and rather broadly) used in many different research fields. From Wikipedia, one can read the following definition of the phrase:

    In engineering, mathematics, physics, chemistry, bioinformatics, computational biology, meteorology and computer science, multiscale modelling or multiscale mathematics is the field of solving problems which have important features at multiple scales of time and/or space.”

    The materials science community often deals with just such multiscale problems, i.e. problems that at the same time concern macroscale properties such as hardness, colour and ductility, which in turn heavily relies on the microscale (electrons and atoms). In this community, multiscale modelling is often referred to as a solution to bridge existing gaps between “first-principles” theoretical approaches and experiments. The strategy, or aim, of multiscale materials modelling is to connect data from different distinguishable levels of models, either in a sequential or a concurrent manner. Generally, these levels are i) quantum mechanical models, which concern electrons, ii) molecular dynamics models, which concern the movement of atoms and molecules, iii) coarse graining models, which concerns groups of atoms/molecules, iv) continuum models, and finally, v) the level of device modelling. Each of these levels is capable of describing a certain time- and length scale, and multiscale materials modelling is thereby often visualized schematically in the form of a “multiscale ladder” or a “multiscale staircase”.

    One of the key obstacles in multiscale materials modelling is to link and harmonize the different models. In some cases, the link between different levels of models can be obvious and made using empirical approaches. Here, constitutive relations, often based on very simplistic ideas such as linearization, or symmetry, plays an important role. However, extending these simple empirical approaches to be used for more complex systems, where discrete and finite size effects are of importance, has been proven difficult.

    In this talk, I will present and discuss common methods used in materials chemistry to link the various levels of models. Both simple (linearized) models and more complex multi-dimensional approaches will be discussed, as well as how this emerging field opens up new opportunities for research collaboration with other disciplines, such as computer science.

  • 26.
    Brumboiu, Iulia Emilia
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    The Electronic Structure of Organic Molecular Materials: Theoretical and Spectroscopic Investigations2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the present thesis the electronic properties of two organic molecules were studied by means of density functional theory (DFT) in connection to their possible applications in organic photovoltaics and molecular spintronics respectively.

    The first analysed system is the C60 derivative PCBM extensively used in polymer solar cells for the charge separation process. Since fullerenes have been shown to undergo modifications as a result of light exposure, investigating their electronic structure is the first step in elucidating the photodegradation process. The electronic excitations from core levels to unoccupied molecular orbitals reveal not only the empty level structure of the molecule, but provide additional information related to the chemical bonds involving a specific atom type. In this way, they represent a means of determining the chemical changes that the molecule might withstand. The electronic transitions from carbon 1s core levels to unoccupied states are explained for the unmodified PCBM by a joint theoretical (DFT) and experimental study using the near edge x-ray absorption fine structure (NEXAFS) spectroscopy.

    The second investigated system is the transition metal phthalocyanine with a manganese atom as the metal center. Manganese phthalocyanine (MnPc) is a single molecular magnet in which the spin switch process can be triggered by various methods. It has been shown, for instance, that the adsorption of hydrogen to the Mn center changes the spin state of the molecule from 3/2 to 1. More interestingly, the process is reversible and can be controlled, opening up the possibility of using MnPc as a quantum bit in magnetic memory devices. Up to this date, the d orbital occupation in MnPc has been under a long debate, both theoretical and experimental studies revealing different configurations. In this thesis the electronic structure of the phthalocyanine is thoroughly analysed by means of DFT and the calculated results are compared to photoelectron spectroscopy measurements. The combination of theoretical and experimental tools reveals that in gas phase at high temepratures the molecule exhibits a mixed electronic configuration. In this light, the possible control of the specific electronic state of the central metal represents an interesting prospect for molecular spintronics.

    List of papers
    1. Near-edge X-ray absorption fine structure study of the C-60-derivative PCBM
    Open this publication in new window or tab >>Near-edge X-ray absorption fine structure study of the C-60-derivative PCBM
    Show others...
    2013 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 568, 130-134 p.Article in journal (Refereed) Published
    Abstract [en]

    The fullerene derivative [6,6]-phenyl-C-61-butyric acid methyl ester plays a key role for electron transport in polymer solar cells. We have studied the unoccupied molecular orbitals of PCBM by near edge X-ray absorption fine structure spectroscopy and were able to assign the main resonances to molecular moieties by comparison with calculated sum spectra of individual carbons. We analyzed specifically the origin of the high-energy shoulder to the first pi*-resonance and identified contributions from the lowest-energy transition of a specific carbon in the phenyl and from transitions to higher unoccupied orbitals of the unmodified carbons in the C-60-cage. 

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-201237 (URN)10.1016/j.cplett.2013.03.031 (DOI)000318320300025 ()
    Available from: 2013-06-10 Created: 2013-06-10 Last updated: 2017-12-06Bibliographically approved
    2. Elucidating the 3d Electronic Configuration in Manganese Phthalocyanine
    Open this publication in new window or tab >>Elucidating the 3d Electronic Configuration in Manganese Phthalocyanine
    Show others...
    2014 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 5, 927-932 p.Article in journal (Refereed) Published
    Abstract [en]

    To shed light on the metal 3d electronic structure of manganese phthalocyanine, so far controversial, we performed photoelectron measurements both in the gas phase and as thin film. With the purpose of explaining the experimental results, three different electronic configurations close in energy to one another were studied by means of density functional theory. The comparison between the calculated valence band density of states and the measured spectra revealed that in the gas phase the molecules exhibit a mixed electronic configuration, while in the thin film, manganese phthalocyanine finds itself in the theoretically computed ground state, namely, the b2g1eg3a1g1b1g0 electronic configuration.

    Keyword
    MnPc, photoelectron spectroscopy, density functional theory
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-218224 (URN)10.1021/jp4100747 (DOI)000331153400015 ()
    Available from: 2014-02-10 Created: 2014-02-10 Last updated: 2017-12-06Bibliographically approved
  • 27.
    Brändas, E., and Goscinski O.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. QUANTUM CHEMISTRY.
    Preface: New Perspectives in Quantum Systems in Chemistry and Physics2001In: Advances in Quantum Chemistry, Vol. 39 and 40, xxv-xxvi p.Other (Other scientific)
  • 28.
    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, 59- p.Article in journal (Other scientific)
  • 29.
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Chapter 1: The Relativistic Kepler Problem and Gödel’s Paradox2012In: Progress in Theoretical Chemistry and Physics 26. Progress in Methods and Applications: Quantum Systems in Chemistry and / [ed] K. Nishikawa et al., Heidelberg: Springer, 2012, 3-22 p.Chapter in book (Refereed)
    Abstract [en]

    Employing a characteristic functional model that conscripts arrays ofoperators in terms of energy and momentum adjoined with their conjugate operatorsof time and position, we have recently derived an extended superposition principlecompatible both with quantum mechanics and Einstein’s laws of relativity.We havelikewise derived a global, universal superposition principle with the autonomouschoice to implement, when required, classical or quantum representations. Thepresent viewpoint amalgamates the microscopic and the macroscopic domainsvia abstract complex symmetric forms through suitable operator classificationsincluding appropriate boundary conditions. An important case in point comes fromthe theory of general relativity, i.e. the demand for the proper limiting order at theSchwarzschild radius. In this example, one obtains a surprising relation betweenG¨odel’s incompleteness theorem and the proper limiting behaviour of the presenttheory at the Schwarzschild singularity. In the present study, we will apply ourtheoretical formulation to the relativistic Kepler problem, recovering the celebratedresult from the theory of general relativity in the calculation of the perihelionmovement of Mercury.

  • 30.
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Per-Olov Löwdin - father of quantum chemistry2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, 1995-2024 p.Article in journal (Other academic)
    Abstract [en]

    During 2016, we celebrate the 100th anniversary of the birth of Per-Olov Lowdin. He was appointed to the first Lehrstuhl in quantum chemistry at Uppsala University in 1960. Lowdin introduced quantum chemistry as a field in its own right by formulating its goals, establishing fundamental concepts, like the correlation energy, the method of configuration interaction, reduced density matrices, natural spin orbitals, charge and bond order matrices, symmetric orthogonalisation, and generalised self-consistent fields. His exposition of partitioning technique and perturbation theory, wave and reaction operators and associated non-linear summation techniques, introduced mathematical rigour and deductive order in the interpretative organisation of the new field. He brought the first computer to Uppsala University and pioneered the initiation of electronic brains' and anticipated their significance for quantum chemistry. Perhaps his single most influential contribution to the field was his education of two generations of future faculty in quantum chemistry through Summer Schools in the Scandinavian Mountains, Winter Institutes at Sanibel Island in the Gulf of Mexico. Per-Olov Lowdin founded the book series Advances in Quantum Chemistry and the International Journal of Quantum Chemistry. The evolution of quantum chemistry is appraised, starting from a collection of cross-disciplinary applications of quantum mechanics to the technologically advanced and predominant field of today, virtually used in all branches of chemistry. The scientific work of Per-Olov Lowdin has been crucial for the development of this new important province of science. [GRAPHICS] .

  • 31.
    Brändas, Erkki
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics.
    Prolate Spheroidal wavefunctions for signal processing2002In: Third International Workshop on the Dv-Xa Method, held at RIKEN, Wako, Japan, 2002Conference paper (Refereed)
  • 32.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    A Zero Energy Universe Scenario: From Unstable Chemical States to Biological Evolution and Cosmological Order2015In: Frontiers In Quantum Methods And Applications In Chemistry And Physics / [ed] Nascimento, MAC; Maruani, J; Brandas, EJ; DelgadoBarrio, G, Heidelberg: Springer, 2015, Vol. A29, 247-284 p.Conference paper (Refereed)
    Abstract [en]

     A Zero-Energy Universe Scenario (ZEUS) is portrayed and its implications are examined and clarified. The formulation is based on the algebra of observables, e.g. the momentum-energy and their canonical conjugate partner space-time. Operators represent them in quantum theory and classical canonical variables in nonquantum applications. Conjugate operator/variable arrays impart a united edifice for a zero-energy universe scenario, which corresponds to using a non-positive definite metric for the manifestation of unstable states as recently employed in the field of chemical physics. Analogous formulations within a general complex symmetric setting provide a compelling analogy between Einstein s theory of general gravity and Gödel s first incompleteness theorem. This scenario brings together up-to-date theories in chemical physics with modern research in biology, physics, and astronomy. This unification establishes an edifice for the various arrows of time as well as authenticates Darwin s Paradigm of Evolution from the microscopic realm to the cosmological domain.

  • 33.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Arrows of Time and Fundamental Symmetries in Chemical Physics2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 3, 173-184 p.Article in journal (Refereed)
    Abstract [en]

    The field of chemical and physical processes, using principal microscopic techniques, should today allegedly be identified as a fundamental branch of physics. The discipline, by tradition known as chemical physics, is undergoing rapid progress. This assessment, illustrated by the advances presented at this Congress, is characterized by modern developments and novel trends with a concrete bearing on original theoretical understanding, with the possibility to go beyond traditional interpretations and explanations. In this vein, we do not only consider nonrelativistic treatments of various types of molecules including interactions between these and polymers, theoretical examinations of chemical reactions, surface states and interface states, disordered phenomena etc., but also recent progress together with non-Hermitian extensions to quantum mechanics and statistical mechanics. The latter leads to a united edifice of theoretical constructions including the law of self-reference, which emerges in analogy with the illustrious Gödel theorem(s) of mathematical logic, that is, the assertion of the inherent limitations of all nontrivial axiomatic systems. The current development begets the foundation of temporal processes and associated invariance principles including the valuation of the various arrows of time. The present conjugate operator array formulation supports the possible gravitational origin of molecular chirality and other principal symmetry violations.

  • 34.
    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, 315-319 p.Article 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.

  • 35.
    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, 49-87 p.Chapter 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.

  • 36.
    Brändas, Erkki J.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics.
    Dissipative Systems and Microscopic Selforganization2002In: Advances in Quantum Chemistry, ISSN 0-12-034841-1, Vol. 41, 121- p.Article in journal (Refereed)
  • 37.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Frontiers in Quantum Methods and Applications in Chemistry and Physics: Selected Proceedings of QSCP-XVIII (Paraty, Brazil, December, 2013)2015 (ed. A29)Book (Refereed)
    Abstract [en]

    This volume collects 15 selected papers from the scientific contributions presented at the Eighteenth International Workshop on Quantum Systems in Chemistry, Physics, and Biology (QSCP-XVIII), which was organized by Prof. M.A.C. Nascimento at the Casa da Cultura in Paraty (Rio de Janeiro), Brazil, from December 1 to 7, 2013. Over 100 scientists from 25 countries attended this meeting. Participants of the QSCP-XVIII workshop discussed the state of the art, new trends, and future evolution of methods in molecular quantum mechanics, and their applications to a wide variety of problems in chemistry, physics, and biology. The high-level attendance attained in this conference was particularly gratifying. It is the renowned interdisciplinary nature and friendly feeling of QSCP meetings that make them such successful discussion forums. Paraty is located in the south coast of Brazil, 250 km from Rio de Janeiro, the state capital. This historical town, nestled on the Costa Verde, is a living memory of the Gold Cycle: gold extracted from the mines of the state of Minas Gerais was transported by mule along the Estrada Real down to Paraty and from there shipped to Rio de Janeiro. The area of Paraty is probably the only place on the planet that brings together a native forest about 80 % preserved, a bay protected from the open sea by over a hundred islands, and a seventeenth-century town which is regarded by UNESCO as the most harmonious baroque location in the world. From this past originate the relics and traditions that so enchant the visitors: a wonderful wealth of cultural and ecological attractions, as well as a tourist infrastructure consisting of cosy inns and picturesque restaurants. Details of the Paraty meeting, including the scientific program, can be found on the web site: http://www.qscp2013.iq.ufrj.br. Altogether, there were 18 morning and afternoon sessions, where 55 plenary talks were given, and two evening poster sessions, with 18 fl ash presentations for a total of 38 displayed posters. We are grateful to all participants for making the QSCP-XVIII workshop a stimulating experience and a great success. QSCP-XVIII followed the traditions established at previous workshops:

     QSCP-I, organized by Roy McWeeny in 1996 at San Miniato (Pisa, Italy);

    QSCP-II, by Stephen Wilson in 1997 at Oxford (England);

    QSCP-III, by Alfonso Hernandez-Laguna in 1998 at Granada (Spain);

    QSCP-IV, by Jean Maruani in 1999 at Marly-le-Roi (Paris, France);

    QSCP-V, by Erkki Brä ndas in 2000 at Uppsala (Sweden);

    QSCP-VI, by Alia Tadjer in 2001 at Sofi a (Bulgaria);

    QSCP-VII, by Ivan Hubac in 2002 near Bratislava (Slovakia);

    QSCP-VIII, by Aristides Mavridis in 2003 at Spetses (Athens, Greece);

    QSCP-IX, by Jean-Pierre Julien in 2004 at Les Houches (Grenoble, France);

    QSCP-X, by Souad Lahmar in 2005 at Carthage (Tunisia);

    QSCP-XI, by Oleg Vasyutinskii in 2006 at Pushkin (St Petersburg, Russia);

    QSCP-XII, by Stephen Wilson in 2007 near Windsor (London, England);

    QSCP-XIII, by Piotr Piecuch in 2008 at East Lansing (Michigan, USA);

    QSCP-XIV, by Gerardo Delgado-Barrio in 2009 at El Escorial (Madrid, Spain);

    QSCP-XV, by Philip Hoggan in 2010 at Cambridge (England);

    QSCP-XVI, by Kiyoshi Nishikawa in 2011 at Kanazawa (Japan);

    QSCP-XVII, by Matti Hotokka in 2012 at Turku (Finland).

    The lectures presented at QSCP-XVIII were grouped into nine areas in the field of Quantum Systems in Chemistry, Physics, and Biology , ranging from Concepts and Methods in Quantum Chemistry and Physics through Molecular Structure and Dynamics, Reactive Collisions and Chemical Reactions, to Computational Chemistry, Physics, and Biology. The width and depth of the topics discussed at QSCP-XVIII are refl ected in the contents of this volume of proceedings in the book series Progress in Theoretical Chemistry and Physics, which includes four sections:

    I. Quantum Methodology (3 papers);

    II. Structure and Properties (4 papers);

    III. Molecular Dynamics (4 papers);

    IV. Fundamental Theory (3 papers).

    In addition to the scientifi c program, the workshop had its usual share of cultural events. There was a boat cruise in the Paraty bay and a show by the internationally known group Contador de Estórias . The award ceremony of the CMOA Prize and Medal took place during the congress banquet in the most traditional restaurant of Paraty, Margarida Café. The CMOA Prize was shared between two selected nominees: Jer-Lai Kuo and Yuan-Chung Cheng, both from Taiwan. Two other nominees, Jhih-Wei Chu (from Taiwan) and Andriy Loboda (from Ukraine) received a certifi cate of nomination and a gift. The prestigious CMOA Medal for senior scientists was awarded to Prof. Lorentz Cederbaum (University of Heidelberg, Germany). According to a custom of QSCP meetings, the venue of the next yearly workshop was announced to be in Odessa, Ukraine, in 2015, followed by one in Taipei, Taiwan, in 2016. However, due to the political events, the dates of the two meetings were later reversed. We are pleased to acknowledge the generous support given to the QSCP-XVIII conference by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), the City of Paraty Convention Bureau and Casa da Cultura  of Paraty. We are most grateful to all members of the Local Organizing Committee for their work and dedication, which made the stay and work of participants both pleasant and fruitful. We also thank the members of the International Scientifi c Committee and the Honorary Committee for their invaluable expertise and advice. We hope the readers will fi nd as much interest in consulting these proceedings as the participants in attending the meeting.

    M.A.C. Nascimento

    Jean Maruani

    Erkki J. Brändas

    Gerardo Delgado-Barrio

  • 38.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Quantum Chemistry.
    Microscopic self-organization and self-referential systems: a progress report.2009In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 109, no 14, 3500-3504 p.Article in journal (Refereed)
    Abstract [en]

    It is contended that (the classical canonical form of) Jordan blocks, play a role analogous to those of paradoxes and self-referential contradictions in philosophy and mathematical logic. As examples we will briefly discuss the occurrence of such triangular units in appropriately generalized quantum theory of microscopic as well as open dissipative systems with structures appearing on both the fundamental as well as in higher order levels of organization. The mathematical structure centers on specific transformations within coherent-dissipative ensembles that exhibit certain factorization properties allowing prime number algorithms, cf. the Godel encoding system used to derive the celebrated incompleteness theorem. This prompts the suggestion that an additional meta-code, cf. the genetic code, might be a-scripted for the mapping between the genotype and phenotype spaces.

  • 39.
    Brändas, Erkki J.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Department of Quantum Chemistry. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    New Perspectives in Theoretical Chemical Physics2003In: Advances in Quantum Chemistry, ISSN ISBN: 0-12-034843-8, Vol. 42, 383-398 p.Article in journal (Refereed)
  • 40.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Preface2015Book (Other academic)
    Abstract [en]

    PREFACE

     

    Advances in Quantum Chemistry provides researchers in quantum chemistry, physical chemistry and chemical physics with up-to-date surveys, invited reviews and highlights of recent achievements. Although the field of quantum chemistry has emerged as a subject of its own it overlaps fundamentally with other fields like applied mathematics, theoretical biology, signal processing including applications in medicine.

    In the present volume, the readers are presented with an exciting combination of themes, i.e. a description of anti-ferromagnetism in copper oxide, proton-conducting mechanism in solid oxide fuel cells, time-dependent processes in molecular processes, the essence of chemical bonding, biological models for repair of cellular radiation damage, momentum space methods for accurate molecular electronic structure calculations and functional theoretic models for hydrogen bonding networks and proton wires in water oxidation reactions.

     

    The first chapter in this volume Chapter, by Kimichika Fukushima, deals with the description of antiferromagaetism in copper oxides using density functional theory.  This is a longstanding problem, and the solution is discussed in terms of the variational method based SIWB (surrounding or solid Coulomb-potential-induced well for basis set) scheme.  The characteristics of the well stabilizing the O2- ion and making antiferromagaetism possible are discussed.

     

    In the second chapter Taku Onishi investigates proton-conducting mechanisms in solid electrolyte oxide fuel cells. Specifically LaAlO3 perovskite is allegedly proposed and compared with conventional perovskite-type conductors. The analysis, based on hybrid Kohn-Sham density functional theory, characterizing the proton conducting pathways, confronts mechanism elucidation and material design, including safety aspects regarding the conflicts with oxide ion conduction. In particular as the oxygen vacancy, doped to incorporate the proton, may conflict with oxide ion conduction, it was concluded, when utilizing LaAlO3 that the temperature strictly regulates the prevention of coincident oxide ion conduction.

     

    In Chapter 3, Yngve Öhrn presents and discusses a time dependent treatment of molecular processes.  The scheme, known as electron nuclear dynamics (END), is described in formal detail wich includes the choice of coordinate system and its effect on the molecular Hamiltonian, the choice of molecular wave function and the particular role of the time-dependent parameters that originates in a coherent state representation is discussed.  References are given to some of the work done with ENDYNE.

     

    Chapter 4 concerns chemical bonding. In the present contribution, Elena Sheka describes her experiences of chemical bonds in various investigations of structural chemistry. The investigations comprise a rich selection of chemical compounds from single, double and triple bonds, involving carbon, to provoking the main issues of modern chemistry devoted to fullerenes and recently graphene, the famous nobeliated 2D solid. The structures investigated permit a rather simple methodology based on the odd electron strategy, predominantly advocated by the author.

     

    In chapter 5, Dževad and Karen Belkić, advance their notable input to a far-reaching and across-the-board biophysical and chemical analysis of surviving fractions of irradiate cells and their new mechanistic repair-based Padé linear-quadratic model, PLQ. As current dose planning systems in radiotherapy, based on linear-quadratic models (LQ), is satisfactory only at low doses and inadequate for treatment modalities, or hyperfractionation, it is demonstrated that PLQ significantly outperforms LQ models regarding cell survival fractions including saturation effects.

     

    Although Gaussian technology has greatly simplified mainstream quantum chemistry, it is a cognizant fact that exponential-type orbitals, ETO’s, are better suited for molecular electronic structure calculations. In chapter 6, James and John Avery contribute to new progress in quantum chemistry by using Fock’s projection of 3D momentum space to 4D hyperspherical harmonics. The authors exploit their extraordinary competence in treating so-called Coulomb Sturmians to derive a general mathematical theorem including elegant, rapid and accurate evaluations of appropriate quantum mechanical molecular integrals. The ensuing closed form expression is illustrated by adequate examples.

     

    The final contribution to this volume, Chapter 7 by Yamaguchi et al., uses a QM/MM method to calculate complicated properties of water oxidation in the biosystem known as photosystem II (PSII).  Water oxidation in the oxygen evolving complex of PSII is dependent on the hydrogen-bonding networks.  The QM/MM computations elucidate the network structures: hydrogen–bonding O…. O(N) and O…H distances and O(N)-H…O angles in PRP, together with the Cl-O(N) and Cl…H distances and O(N)-H…Cl angles for chloride anions.  The results are compared with experiment.

     

    As advertised, the contents of this volume are multifarious as regards both fundamental theory and innovative applications. The contributing authors have made great strides to share their insights with the reader of the Advances. As series editors, we hope that the present volume will impart the same pleasure and enjoyment as we faced during the preparation of this volume.

     John R. Sabin and Erkki J. Brändas

  • 41.
    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, 73-92 p.Chapter in book (Other academic)
  • 42.
    Brändas, Erkki J
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Kryachko, Eugene S.
    Fundamental World of Quantum Chemistry: A Tribute to the Memory of Per-Olov Löwdin: Foreword to Volume I2003In: Fundamental World of Quantum Chemistry, Vol. I, vii-viii p.Other (Other scientific)
  • 43.
    Brändas, Erkki J
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Department of Quantum Chemistry. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Kryachko, Eugene S.
    Fundamental World of Quantum Chemistry: A Tribute to the Memory of Per-Olov Löwdin: Foreword to Volume II2003In: Fundamental World of Quantum Chemistry, Vol. II, vii-viii p.Other (Other scientific)
  • 44.
    Brändas, Erkki J
    et al.
    Uppsala University.
    Kryachko, Eugene S.
    Uppsala University.
    Fundamental World of Quantum Chemistry: A Tribute to the Memory of Per-Olov Löwdin: Volume I2003In: Fundamental World of Quantum Chemistry, Vol. I, 1-677 p.Book (Refereed)
  • 45.
    Brändas, Erkki J
    et al.
    Uppsala University.
    Kryachko, Eugene S.
    Uppsala University.
    Fundamental World of Quantum Chemistry: A Tribute to the Memory of Per-Olov Löwdin: Volume II2003In: Fundamental World of Quantum Chemistry, Vol. II, 1-696 p.Book (Refereed)
  • 46.
    Brändas, Erkki J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Levitina, Tatiana
    Filter Diagonalization: filtering and postprocessing with prolates.2009In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 180, no 9, 1448-1457 p.Article in journal (Refereed)
    Abstract [en]

    A detailed account is given of a recent modification of the Filter Diagonalization technique that serves to analyze a signal spectrum within a selected energy range. Our approach employs for filtering the eigenfunctions of the Finite Fourier Transform, or prolates, which are superior to other filters due to their special properties. In particular, prolates are simultaneously band-limited and highly concentrated at a finite time-interval, producing filters with optimal accuracy. In addition both features are acquired by the convolution of a band-limited function with a prolate, that permits the latter to be interpolated via the Walter and Shen sampling formula, which essentially simplifies the supplementary computations. Rigorous filtering error estimates are obtained. Test calculations illustrate the facilities of the presented modification.

  • 47.
    Brändas, Erkki J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Obituary: Osvaldo Goscinski (1938–2013)2015Other (Other academic)
  • 48.
    Brändas, Erkki J
    et al.
    Uppsala University.
    Öhrn, Yngve
    Uppsala University.
    International Journal of Quantum Chemistry2003In: International Journal of Quantum Chemistry, Vol. 91-95, no 1-6, 1-4000 p.Other (Other scientific)
  • 49.
    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, xvii-xviii p.Article in journal (Other scientific)
  • 50.
    Brändas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Sabin John R.,
    Advances in Quantum Chemistry: Preface2003In: Advances in Quantum Chemistry, Vol. 43, xi-xii p.Other (Other scientific)
123456 1 - 50 of 261
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf