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  • 1.
    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, p. 506-541Article 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.

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  • 2.
    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, p. 2052-2064Article 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.

  • 3.
    Augusto, Felipe A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, Av Prof Lineu Prestes 748, Sao Paulo, Brazil..
    Francés-Monerris, Antonio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    Fdez. Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuán, Daniel
    Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    Bastos, Erick L.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, Av Prof Lineu Prestes 748, Sao Paulo, Brazil..
    Baader, Wilhelm J.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, Av Prof Lineu Prestes 748, Sao Paulo, Brazil..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Mechanism of activated chemiluminescence of cyclic peroxides: 1,2-dioxetanes and 1,2-dioxetanones2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 19, no 5, p. 3955-3962Article in journal (Refereed)
    Abstract [en]

    Almost all chemiluminescent and bioluminescent reactions involve cyclic peroxides. The structure of the peroxide and reaction conditions determine the quantum efficiency of light emission. Oxidizable fluorophores, the so-called activators, react with 1,2-dioxetanones promoting the former to their first singlet excited state. This transformation is inefficient and does not occur with 1,2-dioxetanes; however, they have been used as models for the efficient firefly bioluminescence. In this work, we use the SA-CASSCF/CASPT2 method to investigate the activated chemiexcitation of the parent 1,2-dioxetane and 1,2-dioxetanone. Our findings suggest that ground state decomposition of the peroxide competes efficiently with the chemiexcitation pathway, in agreement with the available experimental data. The formation of non-emissive triplet excited species is proposed to explain the low emission efficiency of the activated decomposition of 1,2-dioxetanone. Chemiexcitation is rationalized considering a peroxide/activator supermolecule undergoing an electron-transfer reaction followed by internal conversion.

  • 4. Barata-Morgado, Rute
    et al.
    Luz Sanchez, M.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Corchado, Jose C.
    Elena Martin, M.
    Munoz-Losa, Aurora
    Aguilar, Manuel A.
    Theoretical study of the conformational equilibrium of 1,4-dioxane in gas phase, neat liquid, and dilute aqueous solutions2013In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 132, no 10, p. 1390-Article in journal (Refereed)
    Abstract [en]

    The conformational equilibrium of 1,4-dioxane in the gas phase, in the pure liquid, and in aqueous solution has been studied by means of the Average Solvent Electrostatic Potential from Molecular Dynamics (ASEP/MD) method and the Integral Equation Formalism for the Polarizable Continuum Model (IEF-PCM). The dioxane molecule was described at the DFT(B3LYP)/aug-cc-pVTZ level. In the three phases, the equilibrium is almost completely shifted toward the chair conformer, with populations of the twist-boat conformers lower than 0.01 %. The equilibrium is dominated by the internal energy of the molecule, as the solute-solvent interaction free energies are very similar in the three conformers considered (chair, 1,4 twist-boat, and 2,5 twist-boat). In the pure liquid, where the dioxane-dioxane interaction is dominated by the Lennard-Jones term, the structure is characteristic of a van der Waals liquid. However, the decrease in the C-H distance from gas phase to solution, the increase in the C-H vibrational frequencies, and the presence of a shoulder in the O-Haxial pair radial distribution function point to the presence of a weak C-H-O hydrogen bond. The analysis of the occupancy maps of water oxygen and hydrogen atoms around the 1,4-dioxane molecule confirms this conclusion. Contrary to what is found in small water-dioxane clusters, in the liquid, there is a preference for oxygen atoms to interact with axial hydrogen atoms to form C-H-O hydrogen bonds. Comparison of ASEP/MD and IEF-PCM results indicates that including specific interactions is very important for an adequate description of the solute-solvent interaction; however, the influence of these interactions does not translate in changes in the relative stability of the conformers because it cancels out when energy differences are calculated.

  • 5. Corchado, José C.
    et al.
    Sánchez, M. Luz
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Martín, M. Elena
    Muñoz-Losa, Aurora
    Barata-Morgado, Rute
    Aguilar, Manuel A.
    Theoretical Study of Solvent Effects on the Ground and Low-Lying Excited Free Energy Surfaces of a Push–Pull Substituted Azobenzene2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 43, p. 12518-12530Article in journal (Refereed)
    Abstract [en]

    The ground and low-lying excited free energy surfaces of 4-amino-4'-cyano azobenzene, a molecule that has been proposed as building block for chiroptical switches, are studied in gas phase and a variety of solvents (benzene, chloroform, acetone, and water). Solvent effects on the absorption and emission spectra and on the cistrans thermal and photo isomerizations are analyzed using two levels of calculation: TD-DFT and CASPT2/CASSCF. The solvent effects are introduced using a polarizable continuum model and a QM/MM method, which permits one to highlight the role played by specific interactions. We found that, in gas phase and in agreement with the results found for other azobenzenes, the thermal cistrans isomerization follows a rotation-assisted inversion mechanism where the inversion angle must reach values close to 180 degrees but where the rotation angle can take almost any value. On the contrary, in polar solvents the mechanism is controlled by the rotation of the CN=NC angle. The change in the mechanism is mainly related to a better solvation of the nitrogen atoms of the azo group in the rotational transition state. The photoisomerization follows a rotational pathway both in gas phase and in polar and nonpolar solvents. The solvent introduces only small modifications in the n pi* free energy surface (S-1), but it has a larger effect on the pi pi* surface (S-2) that, in polar solvents, gets closer to S-1. In fact, the S-2 band of the absorption spectrum is red-shifted 0.27 eV for the trans isomer and 0.17 eV for the cis. In the emission spectrum the trend is similar: only S-2 is appreciably affected by the solvent, but in this case a blue shift is found.

  • 6.
    Farahani, Pooria
    et al.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, BR-05508000 Sao Paulo, SP, Brazil..
    Oliveira, Marcelo A.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, BR-05508000 Sao Paulo, SP, Brazil..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Baader, Wilhelm J.
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, BR-05508000 Sao Paulo, SP, Brazil..
    A combined theoretical and experimental study on the mechanism of spiro-adamantyl-1,2-dioxetanone decomposition2017In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 28, p. 17462-17472Article in journal (Refereed)
    Abstract [en]

    1, 2-Dioxetanones have been considered as model compounds for bioluminescence processes. The unimolecular decomposition of these prototypes leads mainly to the formation of triplet excited states whereas in the catalysed decomposition of these peroxides singlet states are formed preferentially. Notwithstanding, these cyclic peroxides are important models to understand the general principles of chemiexcitation as they can be synthesised, purified and characterised. We report here results of experimental and theoretical approaches to investigating the decomposition mechanism of spiro-adamantyl- 1,2-dioxetanone. The activation parameters in the unimolecular decomposition of this derivative have been determined by isothermal kinetic measurements (30-70 degrees C) and the chemiluminescence activation energy calculated from the correlation of emission intensities. The activation energy for peroxide decomposition proved to be considerably lower than the chemiluminescence activation energy indicating the existence of different reaction pathways for ground and excited state formation. These experimental results are compared with the calculations at the complete active space second-order perturbation theory (CASPT2), which reveal a two-step biradical mechanism starting by weak peroxide bond breakage followed by carbon-carbon elongation. The theoretical findings also indicate different transition state energies on the excited and ground state surfaces during the C-C bond cleavage in agreement with the experimental activation parameters.

  • 7.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Gustafsson, Hannes
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Chemiexcitation without the Peroxide Bond?: Replacing oxygen with other heteroatoms2019In: ChemPhotoChem, ISSN 2367-0932, Vol. 3, no 9, p. 957-967Article in journal (Refereed)
    Abstract [en]

    Chemiexcitation is the population of electronic excited states from the electronic ground state via radiationless non-adiabatic transitions upon thermal activation. The subsequent emission of the excess of energy in the form of light is called chemiluminescence or bioluminescence when occurring in living organisms. Key intermediates in these reactions have been shown to contain a high-energy (often cyclic) peroxide which decomposes. The simplest molecules, 1,2-dioxetane and 1,2-dioxetanone, have thus been used extensively both theoretically and experimentally as model systems to understand the underlying mechanisms of chemiexcitation. An outstanding question remains whether the peroxide bond is a necessity and whether equivalent processes could happen in other simple molecules not containing an OO bond. In the present work, the decomposition reactions of four analogs of 1,2-dioxetane not containing a peroxide bond, the 1,2-oxazetidine anion, the 1,2-diazetidine anion, (neutral) 1,2-oxazetidine and 1,2-dithietane, have been studied theoretically using ab initio multicongurational methods. In particular, the reaction energy barriers and spin-orbit coupling strengths were calculated; the electronic degeneracy was studied and compared to the case of 1,2-dioxetane to assess the potentiality of chemiexcitation in the analog molecules.

  • 8.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Stenrup, Michael
    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.
    Quantum dynamics simulations of model chemiluminescence systems2014In: Luminescence (Chichester, England Print), ISSN 1522-7235, E-ISSN 1522-7243, Vol. 29, no S1, p. 67-67Article in journal (Other academic)
  • 9.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ugandi, Mihkel
    Uncontracted basis sets for ab initio calculations of muonic atoms and molecules2018In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, E-ISSN 1097-461X, Vol. 118, no 21, article id e25755Article in journal (Refereed)
    Abstract [en]

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

  • 10.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Alavi, Ali
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Angeli, Celestino
    Univ Ferrara, Dipartimento Sci Chim & Farmaceut, Via Luigi Borsari 46, I-44121 Ferrara, Italy.
    Aquilante, Francesco
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Bao, Jie J.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Bokarev, Sergey I.
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Bogdanov, Nikolay A.
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Carlson, Rebecca K.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Chibotaru, Liviu F.
    Univ Leuven, Theory Nanomat Grp, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Creutzberg, Joel
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden;Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Dattani, Nike
    Harvard Smithsonian Ctr Astrophys, 60 Garden St, Cambridge, MA 02138 USA.
    Delcey, Mickael G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Dong, Sijia S.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Dreuw, Andreas
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany.
    Freitag, Leon
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Manuel Frutos, Luis
    Univ Alcala De Henares, Dept Quim Analit Quim Fis & Ingn Quim, E-28871 Madrid, Spain;Univ Alcala De Henares, Inst Invest Quim Andres M del Rio, E-28871 Madrid, Spain.
    Gagliardi, Laura
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Gendron, Frederic
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.
    Giussani, Angelo
    UCL, Dept Chem, 20 Gordon St, London WC1H 0AJ, England;Univ Valencia, Inst Ciencia Mol, Apartado 22085, ES-46071 Valencia, Spain.
    Gonzalez, Leticia
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Grell, Gilbert
    Univ Rostock, Inst Phys, Albert Einstein Str 23-24, D-18059 Rostock, Germany.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Hoyer, Chad E.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Johansson, Marcus
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Keller, Sebastian
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Knecht, Stefan
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Kovacevic, Goran
    Rudjer Boskovic Inst, Div Mat Phys, POB 180,Bijenicka 54, HR-10002 Zagreb, Croatia.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Li Manni, Giovanni
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ma, Yingjin
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Mai, Sebastian
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Malhado, Joao Pedro
    Imperial Coll London, Dept Chem, London SW7 2AZ, England.
    Malmqvist, Per Ake
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Marquetand, Philipp
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Mewes, Stefanie A.
    Heidelberg Univ, Interdisciplinary Ctr Sci Comp, Neuenheimer Feld 205 A, D-69120 Heidelberg, Germany;Massey Univ Albany, Ctr Theoret Chem & Phys, NZLAS, Private Bag 102904, Auckland 0632, New Zealand.
    Norell, Jesper
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden.
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via A Moro 2, I-53100 Siena, Italy;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA;Univ Strasbourg, CNRS, USIAS, F-67034 Strasbourg, France;Univ Strasbourg, CNRS, Inst Phys & Chim Mat Strasbourg, F-67034 Strasbourg, France.
    Oppel, Markus
    Univ Vienna, Inst Theoret Chem, Fac Chem, Wahringer Str 17, A-1090 Vienna, Austria.
    Phung, Quan Manh
    Pierloot, Kristine
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
    Plasser, Felix
    Loughborough Univ, Dept Chem, Loughborough LE11 3TU, Leics, England.
    Reiher, Markus
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sand, Andrew M.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, Jerusalem, Israel.
    Sharma, Prachi
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Stein, Christopher J.
    Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland.
    Sörensen, Lasse Kragh
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Truhlar, Donald G.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, Minneapolis, MN 55455 USA;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.
    Ugandi, Mihkel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, Singapore 117543, Singapore.
    Valentini, Alessio
    Res Unit MolSys, Theoret Phys Chem, Allee 6 Aout 11, B-4000 Liege, Belgium.
    Vancoillie, Steven
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Weser, Oskar
    Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany.
    Wesolowski, Tomasz A.
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Widmark, Per-Olof
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Wouters, Sebastian
    Brantsandpatents, Pauline van Pottelsberghelaan 24, B-9051 Sint Denijs Westrem, Belgium.
    Zech, Alexander
    Univ Geneva, Dept Chim Phys, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland.
    Zobel, J. Patrick
    Lund Univ, Div Theoret Chem, Kemictr, POB 124, SE-22100 Lund, Sweden.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Uppsala Center for Computational Chemistry (UC3), Uppsala University, P.O. Box 596, SE-751 24 Uppsala, Sweden.
    OpenMolcas: From Source Code to Insight2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 11, p. 5925-5964Article in journal (Refereed)
    Abstract [en]

    In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.

  • 11.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Xiao, Hong-Yan
    Navizet, Isabelle
    Liu, Ya-Jun
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    S0 → S3 transition in recombination products of photodissociated dihalomethanes2014In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 112, no 5-6, p. 575-582Article in journal (Refereed)
    Abstract [en]

    Species of the form CH2X–Y (X, Y = Br, I) have been proposed and identified as recombination products of the photodissociation of the parent dihalomethanes. Second-order complete active space perturbation theory (CASPT2) calculations of the vertical absorption energies considerably overestimate the experimental transient absorption band maxima, while the computationally cheaper time-dependent density functional theory (TD-DFT) method yields results with a reasonable agreement. In this work, we try to find the reason for this unexpected performance difference. In an initial study of the I2 molecule, we establish that CASPT2 is capable of providing quantitatively accurate results and that the TD-DFT values are only valid at first sight, but are qualitatively flawed. In the CASPT2 calculations for the CH2X–Y molecules, we include relativistic corrections, spin–orbit coupling, vibrational and thermal effects, and the solvent polarisation. Unfortunately, the results do not improve appreciably compared to the experimental measurements. We conclude that the good agreement of TD-DFT results is very likely fortuitous in this case as well, and that further theoretical and experimental investigations are probably needed to resolve the current discrepancy between CASPT2 and experiments.

  • 12. Fernández García-Prieto, F.
    et al.
    Aguilar, M. A.
    Fdez. Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Muñoz-Losa, A.
    Olivares del Valle, F. J.
    Sánchez, M. L.
    Martín, M. E.
    Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5504-5514Article in journal (Refereed)
    Abstract [en]

    Solvent effects on the UV–vis absorption spectra and molecular properties of four models of the photoactive yellow protein (PYP) chromophore have been studied with ASEP/MD, a sequential quantum mechanics/molecular mechanics method. The anionic trans-p-coumaric acid (pCA), thioacid (pCTA), methyl ester (pCMe), and methyl thioester (pCTMe) derivatives have been studied in gas phase and in water solution. We analyze the modifications introduced by the substitution of sulfur by oxygen atoms and hydrogen by methyl in the coumaryl tail. We have found some differences in the absorption spectra of oxy and thio derivatives that could shed light on the different photoisomerization paths followed by these compounds. In solution, the spectrum substantially changes with respect to that obtained in the gas phase. The n → π1* state is destabilized by a polar solvent like water, and it becomes the third excited state in solution displaying an important blue shift. Now, the π → π1* and π → π2* states mix, and we find contributions from both transitions in S1 and S2. The presence of the sulfur atom modulates the solvent effect and the first two excited states become practically degenerate for pCA and pCMe but moderately well-separated for pCTA and pCTMe.

  • 13.
    Frances-Monerris, Antonio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Roca-Sanjuan, Daniel
    Fernandez Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Towards the Understanding of the Larger Phosphorescence Quantum Yield than Fluorescence in Dioxetanone2014In: Luminescence (Chichester, England Print), ISSN 1522-7235, E-ISSN 1522-7243, Vol. 29, p. 67-68Article in journal (Other academic)
  • 14.
    Francés-Monerris, Antonio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    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.
    Roca-Sanjuan, Daniel
    Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia 46071, Spain..
    Triplet versus singlet chemiexcitation mechanism in dioxetanone: a CASSCF/CASPT2 study2017In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 136, no 6, article id 70Article in journal (Refereed)
    Abstract [en]

    Chemiluminescence is a fundamental process of chemistry consisting in the conversion of chemical energy stored in chemical bonds into light. It is used by nature and by man-made technology, being especially relevant in chemical analysis. The understanding of the phenomenon strongly relies in the study of peroxide models such as 1,2-dioxetanones. In the present contribution, the singlet S2 and the triplet T2 potential energy surfaces of the unimolecular decomposition of 1,2-dioxetanone have been mapped along the O-O and C-C bond coordinates on the grounds of the multiconfigurational CASPT2//CASSCF approach. Results confirm the energy degeneracy between T2, T1, S1, and S0 at the TS region, whereas S2 is unambiguously predicted at higher energies. Triplet-state population is also supported by the spin-orbit couplings between the singlet and triplet states partaking in the process. In particular, the first-principle calculations show that decomposition along the T2 state is a competitive process, having a small (similar to 3 kcal/mol) energy barrier from the ground-state TS structure. The present findings can explain the higher quantum yield of triplet-state population with respect to the excited singlet states recorded experimentally for the uni-molecular decomposition of 1,2-dioxetanone models.

  • 15. Garcia-Prieto, Francisco F.
    et al.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Munoz-Losa, Aurora
    Aguilar, Manuel A.
    Elena Martin, M.
    Solvent Effects on the Absorption Spectra of the para-Coumaric Acid Chromophore in Its Different Protonation Forms2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 10, p. 4481-4494Article in journal (Refereed)
    Abstract [en]

    The effects of the solvent and protonation state on the electronic absorption spectrum of the para-coumaric acid (pCA), a model of the photoactive yellow protein (PYP), have been studied using the ASEP/MD (averaged solvent electrostatic potential from molecular dynamics) method. Even though, in the protein, the chromophore is assumed to be in its phenolate monoanionic form, when it is found in water solution pH control can favor neutral, monoanionic, and dianionic species. As the pCA has two hydrogens susceptible of deprotonation, both carboxylate and phenolate monoanions are possible. Their relative stabilities are strongly dependent on the medium. In gas phase, the most stable isomer is the phenolate while in aqueous solution it is the carboxylate, although the population of the phenolate form is not negligible. The s-cis, s-trans, syn, and anti conformers have also been included in the study. Electronic excited states of the chromophore have been characterized by SA-CAS(14,12)-PT2/cc-pVDZ level of theory. The bright state corresponds, in all the cases, to a pi -> pi* transition involving a charge displacement in the system. The magnitude and direction of this displacement depends on the protonation state and on the environment (gas phase or solution). In the same way, the calculated solvatochromic shift of the absorption maximum depends on the studied form, being a red shift for the neutral, carboxylate monoanion, and dianionic chromophores and a blue shift for the phenolate monoanion. Finally, the contribution that the solvent electronic polarizability has on the solvent shift was analyzed. It represents a very important part of the total solvent shift in the neutral form, but its contribution is completly negligible in the mono- and dianionic forms.

  • 16.
    Garcia-Prieto, Francisco F.
    et al.
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Muñoz-Losa, Aurora
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Fdez. Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sanchez, M. Luz
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Aguilar, Manuel A.
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    Martin, M. Elena
    Univ Extremadura, Area Quim Fis, Avda Elvas S-N, Badajoz 06006, Spain..
    QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 2, p. 737-748Article in journal (Refereed)
    Abstract [en]

    Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the transcis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.

  • 17. Häse, Florian
    et al.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aspuru-Guzik, Alan
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    How machine learning can assist the interpretation of ab initio molecular dynamics simulations and conceptual understanding of chemistry2019In: Chemical Science, ISSN 2041-6520, Vol. 10, no 8, p. 2298-2307Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations are often key to the understanding of the mechanism, rate and yield of chemical reactions. One current challenge is the in-depth analysis of the large amount of data produced by the simulations, in order to produce valuable insight and general trends. In the present study, we propose to employ recent machine learning analysis tools to extract relevant information from simulation data without a priori knowledge on chemical reactions. This is demonstrated by training machine learning models to predict directly a specific outcome quantity of ab initio molecular dynamics simulations - the timescale of the decomposition of 1,2-dioxetane. The machine learning models accurately reproduce the dissociation time of the compound. Keeping the aim of gaining physical insight, it is demonstrated that, in order to make accurate predictions, the models evidence empirical rules that are, today, part of the common chemical knowledge. This opens the way for conceptual breakthroughs in chemistry where machine analysis would provide a source of inspiration to humans.

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  • 18.
    Jorner, Kjell
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Dreos, Ambra
    Chalmers, Dept Chem & Chem Engn, Kemigarden 4, SE-41296 Gothenburg, Sweden..
    Emanuelsson, Rikard
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Nanotechnology and Functional Materials.
    El Bakouri, Ouissam
    Univ Girona, Dept Quim, IQCC, Campus Montilivi, Girona 17003, Spain..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala Univ, UC3, Box 523, SE-75120 Uppsala, Sweden..
    Borjesson, Karl
    Chalmers, Dept Chem & Chem Engn, Kemigarden 4, SE-41296 Gothenburg, Sweden.;Univ Gothenburg, Dept Chem & Mol Biol, Kemigarden 4, SE-41296 Gothenburg, Sweden..
    Feixas, Ferran
    Univ Girona, Dept Quim, IQCC, Campus Montilivi, Girona 17003, Spain..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala Univ, UC3, Box 523, SE-75120 Uppsala, Sweden..
    Zietz, Burkhard
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Moth-Poulsen, Kasper
    Chalmers, Dept Chem & Chem Engn, Kemigarden 4, SE-41296 Gothenburg, Sweden..
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Unraveling factors leading to efficient norbornadiene-quadricyclane molecular solar-thermal energy storage systems2017In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 5, no 24, p. 12369-12378Article in journal (Refereed)
    Abstract [en]

    Developing norbornadiene-quadricyclane (NBD-QC) systems for molecular solar-thermal (MOST) energy storage is often a process of trial and error. By studying a series of norbornadienes (NBD-R-2) doubly substituted at the C7-position with R = H, Me, and iPr, we untangle the interrelated factors affecting MOST performance through a combination of experiment and theory. Increasing the steric bulk along the NBD-R-2 series gave higher quantum yields, slightly red-shifted absorptions, and longer thermal lifetimes of the energy-rich QC isomer. However, these advantages are counterbalanced by lower energy storage capacities, and overall R = Me appears most promising for short-term MOST applications. Computationally we find that it is the destabilization of the NBD isomer over the QC isomer with increasing steric bulk that is responsible for most of the observed trends and we can also predict the relative quantum yields by characterizing the S-1/S-0 conical intersections. The significantly increased thermal half-life of NBD-iPr(2) is caused by a higher activation entropy, highlighting a novel strategy to improve thermal half-lives of MOST compounds and other photo-switchable molecules without affecting their electronic properties. The potential of the NBD-R-2 compounds in devices is also explored, demonstrating a solar energy storage efficiency of up to 0.2%. Finally, we show how the insights gained in this study can be used to identify strategies to improve already existing NBD-QC systems.

  • 19.
    Khamesian, Marjan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Delcey, Mickael G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sørensen, Lasse Kragh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology, Stockholm, Sweden.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Uppsala Center of Computational Chemistry–UC3, Uppsala University, Uppsala, Sweden.
    Spectroscopy of linear and circular polarized ligth with the exact semiclassical light–matter interaction2019In: Annual Reports in Computational Chemistry: Volume 15 / [ed] David A. Dixon, Elsevier, 2019, p. 39-76Chapter in book (Refereed)
    Abstract [en]

    We present the theory and the analytical and numerical solution for the calculation of the oscillator and rotatory strengths of molecular systems using a state-specific formalism. For a start, this is done in the context of the exact semiclassical light–matter interaction in association with electronic wave functions expanded in a Gaussian basis. The reader is guided through the standard approximations of the field, e.g., the use of commutators, truncation of Taylor expansions, and the implications of these are discussed in parallel. Expressions for the isotropically averaged values are derived, recovering the isotropic oscillator strength in terms of the transition electric-dipole moment, and the isotropic rotatory strength in terms of the transition electric-dipole and magnetic-dipole moments. This chapter gives a detailed description of the computation of the integrals over the plane wave in association with Gaussian one-particle basis sets. Finally, a brief description is given of how the computed oscillator and rotatory strengths are related to the quantities commonly used and discussed in experimental studies.

  • 20.
    Martín, M. Elena
    et al.
    University of Extremadura.
    Sánchez, M. Luz
    University of Extremadura.
    Muñoz-Losa, Aurora
    University of Extremadura.
    Fdez. Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aguilar, Manuel A.
    University of Extremadura.
    Accelerating QM/MM Calculations by Using the Mean Field Approximation2015In: Quantum Modeling of Complex Molecular Systems / [ed] Jean-Louis Rivail, Manuel Ruiz-Lopez, Xavier Assfeld, Springer, 2015, p. 135-152Chapter in book (Other academic)
    Abstract [en]

    It is well known that solvents can modify the frequency and intensity of the solute spectral bands, the thermodynamics and kinetics of chemical reactions, the strength of molecular interactions or the fate of solute excited states. The theoretical study of solvent effects is quite complicated since the presence of the solvent introduces additional difficulties with respect to the study of analogous problems in gas phase. The mean field approximation (MFA) is used for many of the most employed solvent effect theories as it permits to reduce the computational cost associated to the study of processes in solution. In this chapter we revise the performance of ASEP/MD, a quantum mechanics/molecular mechanics method developed in our laboratory that makes use of this approximation. It permits to combine state of the art calculations of the solute electron distribution with a detailed, microscopic, description of the solvent. As examples of application of the method we study solvent effects on the absorption spectra of some molecules involved in photoisomerization processes of biological systems.

  • 21. Roca-Sanjuán, Daniel
    et al.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Giussani, Angelo
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    A Theoretical Analysis of the Intrinsic Light-Harvesting Properties of Xanthopterin2014In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 1040-1041, p. 230-236Article in journal (Refereed)
    Abstract [en]

    Belonging to the family of pterins, which are common chromophores in several bio-organisms, xanthopterin has been shown experimentally (Plotkin et al., 2010) to have the ability of acting as a light-harvesting molecule. In the present study, multiconfigurational second-order perturbation theory is used to determine the stability of distinct amino/imino and lactam/lactim tautomers and the absorption and emission spectroscopic characteristics, electron donor and acceptor properties and the electron and charge transfer efficiencies via π-stacking. The lactam–lactam form 3H5H (and in a lesser extent 1H5H) is predicted to have the most appropriate intrinsic characteristics for the light-harvesting properties of xanthopterin, since it is the most stable isomer predicted for the gas phase and estimated for polar environments, absorbs solar light at longer wave lengths, has relatively low donor properties and the presence of the keto groups, instead of enol, increases the efficiency for energy transfer through excimer-like interactions.

  • 22. Roca-Sanjuán, Daniel
    et al.
    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.
    Liu, Ya-Jun
    Recent method developments and applications in computational photochemistry, chemiluminescence and bioluminescence2015In: Photochemistry: Volume 42 / [ed] Elisa Fasani, Angelo Albini, Royal Society of Chemistry, 2015, p. 11-42Chapter in book (Other academic)
    Abstract [en]

    This review summarises and discusses the advances of computational photochemistry in 2012 and 2013 in both methodology and applications fields. The methodological developments of models and tools used to study and simulate non-adiabatic processes are highlighted. These developments can be summarised as assessment studies, new methods to locate conical intersections, tools for representation, interpretation and visualisation, new computational approaches and studies introducing simpler models to rationalise the quantum dynamics near and in the conical intersection. The applied works on the topics of photodissociation, photostability, photoisomerisations, proton/charge transfer, chemiluminescence and bioluminescence are summarised, and some illustrative examples of studies are analysed in more detail, particularly with reference to photostability and chemi/bioluminescence. In addition, theoretical studies analysing solvent effects are also considered. We finish this review with conclusions and an outlook on the future.

  • 23. Roca-Sanjuán, Daniel
    et al.
    Francés-Monerris, Antonio
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Farahani, Pooria
    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.
    Liu, Ya-Jun
    Advances in computational photochemistry and chemiluminescence of biological and nanotechnological molecules2017In: Photochemistry: Volume 44 / [ed] Angelo Albini, Elisa Fasani, Cambridge, UK: Royal Society of Chemistry, 2017, p. 16-60Chapter in book (Other academic)
    Abstract [en]

    Recent advances (2014–2015) in computational photochemistry and chemiluminescence derive from the development of theory and from the application of state-of-the-art and new methodology to challenging electronic-structure problems. Method developments have mainly focused, first, on the improvement of approximate and cheap methods to provide a better description of non-adiabatic processes, second, on the modification of accurate methods in order to decrease the computation time and, finally, on dynamics approaches able to provide information that can be directly compared with experimental data, such as yields and lifetimes. Applications of the ab initio quantum-chemistry methods have given rise to relevant findings in distinct fields of the excited-state chemistry. We briefly summarise, in this chapter, the achievements on photochemical mechanisms and chemically-induced excited-state phenomena of interest in biology and nanotechnology.

  • 24.
    Sanchez, M. Luz
    et al.
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Corchado, Jose C.
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Martin, M. Elena
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Fdez. Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Barata-Morgado, Rute
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    Aguilar, Manuel A.
    Univ Extremadura, Area Quim Fis, Planta Badajoz 06006, Spain..
    A new QM/MM method oriented to the study of ionic liquids2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 25, p. 1893-1901Article in journal (Refereed)
    Abstract [en]

    The interest on room temperature ionic liquids has grown in the last decades because of their use as all-purpose solvent and their low environmental impact. In the present work, a new theoretical procedure is developed to study pure ionic liquids within the framework of the quantum mechanics/molecular mechanics method. Each type of ion (cation or anion) is considered as an independent entity quantum mechanically described that follows a differentiated path in the liquid. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1-ethyl-3-methylimidazolium tetrafluoroborate. It was found that, similar to non-polar liquids and as a consequence of the low value of the reaction field, the cation and anion charge distributions are hardly polarized by the rest of molecules in the liquid. Their structure is characterized by an alternance between anion and cation shells as evidenced by the coincidence of the first maximum of the anion-anion and cation-cation radial distribution functions with the first minimum of the anion-cation. Some degree of stacking between the cations is also found.

  • 25. Sankari, Anna
    et al.
    Stråhlman, Christian
    Sankari, Rami
    Partanen, Leena
    Laksman, Joakim
    Kettunen, J. Antti
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Malmqvist, Per-Åke
    Sorensen, Stacey L.
    Non-radiative decay and fragmentation in water molecules after 1a1-14a1 excitation and core ionization studied by electron-energy-resolved electron–ion coincidence spectroscopy2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 7, article id 074302Article in journal (Refereed)
    Abstract [en]

    In this paper, we examine decay and fragmentation of core-excited and core-ionized water molecules combining quantum chemical calculations and electron-energy-resolved electron–ion coincidence spectroscopy. The experimental technique allows us to connect electronic decay from core-excited states, electronic transitions between ionic states, and dissociation of the molecular ion. To this end, we calculate the minimum energy dissociation path of the core-excited molecule and the potential energy surfaces of the molecular ion. Our measurements highlight the role of ultra-fast nuclear motion in the 1a1-14a1 core-excited molecule in the production of fragment ions. OH+ fragments dominate for spectator Auger decay. Complete atomization after sequential fragmentation is also evident through detection of slow H+ fragments. Additional measurements of the non-resonant Auger decay of the core-ionized molecule (1a1-1) to the lower-energy dication states show that the formation of the OH+ + H+ ion pair dominates, whereas sequential fragmentation OH+ + H+ → O + H+ + H+ is observed for transitions to higher dication states, supporting previous theoretical investigations.

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  • 26.
    Schalk, Oliver
    et al.
    Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden; Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
    Galiana, Joachim
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Department of Chemistry, École normale supérieure de Lyon, 69342 Lyon, France.
    Geng, Ting
    Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden.
    Larsson, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Thomas, Richard
    Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Hansson, Tony
    Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 44300 Nantes, France.
    Competition between ring-puckering and ring-opening excited state reactions exemplified on 5H-furan-2-one and derivatives2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 6, article id 064301Article in journal (Refereed)
    Abstract [en]

    The influence of ring-puckering on the light-induced ring-opening dynamics of heterocyclic compounds was studied on the sample 5-membered ring molecules γ-valerolactone and 5H-furan-2-one using time-resolved photoelectron spectroscopy and ab initio molecular dynamics simulations. In γ-valerolactone, ring-puckering is not a viable relaxation channel and the only available reaction pathway is ring-opening, which occurs within one vibrational period along the C—O bond. In 5H-furan-2-one, the C=C double bond in the ring allows for ring-puckering which slows down the ring-opening process by about 150 fs while only marginally reducing its quantum yield. This demonstrates that ring-puckering is an ultrafast process, which is directly accessible upon excitation and which spreads the excited state wave packet quickly enough to influence even the outcome of an otherwise expectedly direct ring-opening reaction.

  • 27.
    Stenrup, Michael
    et al.
    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.
    Galvan, Ignacio Fdez.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Constrained numerical gradients and composite gradients: Practical tools for geometry optimization and potential energy surface navigation2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 22, p. 1698-1708Article in journal (Refereed)
    Abstract [en]

    A method is proposed to easily reduce the number of energy evaluations required to compute numerical gradients when constraints are imposed on the system, especially in connection with rigid fragment optimization. The method is based on the separation of the coordinate space into a constrained and an unconstrained space, and the numerical differentiation is done exclusively in the unconstrained space. The decrease in the number of energy calculations can be very important if the system is significantly constrained. The performance of the method is tested on systems that can be considered as composed of several rigid groups or molecules, and the results show that the error with respect to conventional optimizations is of the order of the convergence criteria. Comparison with another method designed for rigid fragment optimization proves the present method to be competitive. The proposed method can also be applied to combine numerical and analytical gradients computed at different theory levels, allowing an unconstrained optimization with numerical differentiation restricted to the most significant degrees of freedom. This approach can be a practical alternative when analytical gradients are not available at the desired computational level and full numerical differentiation is not affordable. (c) 2015 Wiley Periodicals, Inc.

  • 28.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Brakestad, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Dynamical Insights into the Decomposition of 1,2-Dioxetane2017In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 6, p. 2448-2457Article in journal (Refereed)
    Abstract [en]

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

  • 29.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Farahani, Pooria
    Univ Sao Paulo, Inst Quim, Dept Quim Fundamental, BR-05508000 Sao Paulo, Brazil..
    Valentini, Alessio
    Univ Liege, Dept Chim, Allee 6 Aout 11, B-4000 Liege, Belgium..
    Frutos, Luis Manuel
    Univ Alcala De Henares, Dept Quim Fis, E-28871 Madrid, Spain..
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    How Do Methyl Groups Enhance the Triplet Chemiexcitation Yield of Dioxetane?2017In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, no 16, p. 3790-3794Article in journal (Refereed)
    Abstract [en]

    Chemiluminescence is the emission of light as a result of a nonadiabatic chemical reaction. The present work is concerned with understanding the yield of chemiluminescence, in particular how it dramatically increases upon methylation of 1,2-dioxetane. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction of various methyl-substituted dioxetanes have been simulated. Methyl-substitution leads to a significant increase in the dissociation time scale. The rotation around the O-C-C-O dihedral angle is slowed; thus, the molecular system stays longer in the "entropic trap" region. A simple kinetic model is proposed to explain how this leads to a higher chemiluminescence yield. These results have important implications for the design of efficient chemiluminescent systems in medical, environmental, and industrial applications.

  • 30.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ding, Bo-Wen
    Schramm, Stefan
    Berraud-Pache, Romain
    Naumov, Pance
    Ferré, Nicolas
    Liu, Ya-Jun
    Navizet, Isabelle
    Roca-Sanjuán, Daniel
    Baader, Wilhelm J.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Chemi- and Bioluminescence of Cyclic Peroxides2018In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 118, no 15, p. 6927-6974Article, review/survey (Refereed)
    Abstract [en]

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

  • 31.
    Vacher, Morgane
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Brakestad, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Non-adabatic dynamics of the 1,2-dioxetane chemiluminescence2017In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 254Article in journal (Other academic)
  • 32.
    Valentini, Alessio
    et al.
    Univ Alcala De Henares, Dept Analyt Chem Phys Chem & Chem Engn, Ctra A2 Km 33,6, Alcala De Henares 28871, Spain.;Univ Siena, Dept Biotechnol Chem & Pharm, Via A Moro 2, I-53100 Siena, Italy..
    Rivero, Daniel
    Univ Alcala De Henares, Dept Analyt Chem Phys Chem & Chem Engn, Ctra A2 Km 33,6, Alcala De Henares 28871, Spain..
    Zapata, Felipe
    Univ Alcala De Henares, Dept Analyt Chem Phys Chem & Chem Engn, Ctra A2 Km 33,6, Alcala De Henares 28871, Spain..
    García-Iriepa, Cristina
    Univ Alcala De Henares, Dept Analyt Chem Phys Chem & Chem Engn, Ctra A2 Km 33,6, Alcala De Henares 28871, Spain.;Univ La Rioja, CISQ, Dept Quim, Madre Dios 53, Logrono 26006, Spain..
    Marazzi, Marco
    Univ Lorraine Nancy, Theory Modeling Simulat SRSMC, Nancy, France.;CNRS, Theory Modeling Simulat SRSMC, SRSMC Blvd Aiguillettes, Vandoeuvre Les Nancy, France..
    Palmeiro, Raúl
    Univ Alcala De Henares, Dept Analyt Chem Phys Chem & Chem Engn, Ctra A2 Km 33,6, Alcala De Henares 28871, Spain..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sampedro, Diego
    Univ La Rioja, CISQ, Dept Quim, Madre Dios 53, Logrono 26006, Spain..
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via A Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA.;Univ Strasbourg, CNRS, USIAS, F-67034 Strasbourg, France.;Univ Strasbourg, CNRS, Inst Phys & Chim Mat Strasbourg, F-67034 Strasbourg, France..
    Frutos, Luis Manuel
    Univ Alcala De Henares, Dept Analyt Chem Phys Chem & Chem Engn, Ctra A2 Km 33,6, Alcala De Henares 28871, Spain..
    Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model2017In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 56, no 14, p. 3842-3846Article in journal (Refereed)
    Abstract [en]

    The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans-to-cis photoisomerization quantum yield in a counter-intuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.

1 - 32 of 32
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