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  • 51.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Revisiting the Nonadiabatic Process in 1,2-Dioxetane2013In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, no 12, p. 5404-5411Article in journal (Refereed)
    Abstract [en]

    Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.; Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111, 8013-8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O-O' and C-C' bond dissociations. New high-level multistate multi configurational reference second-order perturbation theory calculations and ab initio molecular dynamics simulations at constant temperature are performed in the present study, which provide further details on the mechanisms and allow to rationalize further experimental observations. In particular, the new results explain the high ratio of triplet to singlet dissociation products.

  • 52.
    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)
  • 53.
    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.

  • 54.
    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.

  • 55. Ferre, Nicolas
    et al.
    Huix-Rotllant, Miquel
    Filatov, Michael
    Gozem, Samer
    Schapiro, Igor
    Olivucci, Massimo
    Chen, Shufeng
    Navizet, Isabelle
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Liu, Yajun
    Approximate density functional theory for complex photoreactions in biological systems2014In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 247, article id 475-PHYSArticle in journal (Other academic)
  • 56.
    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)
  • 57.
    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.

  • 58. Freitag, Leon
    et al.
    Knecht, Stefan
    Keller, Sebastian F.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pedersen, Thomas Bondo
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Reiher, Markus
    Gonzalez, Leticia
    Orbital entanglement and CASSCF analysis of the Ru-NO bond in a Ruthenium nitrosyl complex2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 22, p. 14383-14392Article in journal (Refereed)
    Abstract [en]

    Complete active space self-consistent field (CASSCF) wavefunctions and an orbital entanglement analysis obtained from a density-matrix renormalisation group (DMRG) calculation are used to understand the electronic structure, and, in particular, the Ru-NO bond of a Ru nitrosyl complex. Based on the configurations and orbital occupation numbers obtained for the CASSCF wavefunction and on the orbital entropy measurements evaluated for the DMRG wavefunction, we unravel electron correlation effects in the Ru coordination sphere of the complex. It is shown that Ru-NO pi bonds show static and dynamic correlation, while other Ru-ligand bonds feature predominantly dynamic correlation. The presence of static correlation requires the use of multiconfigurational methods to describe the Ru-NO bond. Subsequently, the CASSCF wavefunction is analysed in terms of configuration state functions based on localised orbitals. The analysis of the wavefunctions in the electronic singlet ground state and the first triplet state provides a picture of the Ru-NO moiety beyond the standard representation based on formal oxidation states. A distinct description of the Ru and NO fragments is advocated. The electron configuration of Ru is an equally weighted superposition of Ru-II and Ru-III configurations, with the Ru-III configuration originating from charge donation mostly from Cl ligands. However, and contrary to what is typically assumed, the electronic configuration of the NO ligand is best described as electroneutral.

  • 59. Gaenko, Alexander
    et al.
    Devarajan, Ajitha
    Lindh, Roland
    Hoffmann, Mark R.
    PHYS 611-Macroconfiguration based approach for heavy element compounds: Implementation of relativistic generalized van Vleck perturbation theory (GVVPT3)2008Conference paper (Other academic)
  • 60. Gaenko, Alexander V
    et al.
    Devarajan, Ajitha
    Gagliardi, Laura
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Orlandi, Giorgio
    Ab initio DFT study of Z-E isomerization pathways of N-benzylideneaniline2007In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 118, no 1, p. 271-279Article in journal (Refereed)
    Abstract [en]

    The ground state properties and absorption spectra of N-benzylideneaniline (NBA) have been studied at the density functional (DFT) and at the time-dependent density functional (TD-DFT) level of the theory. The equilibrium geometries of the E and Z isomers in the ground state and their vibrational frequencies have been computed. Furthermore, the excitation energies of the lowest excited singlet and triplet states and the potential energy curves along the torsion and the inversion isomerization coordinates were evaluated. The results are discussed in light of the available experimental data.

  • 61. Gagliardi, Laura
    et al.
    Evangelisti, Stefano
    Bernhardsson, Anders
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn O
    Dissociation reaction of N-8 azapentalene to 4N(2): A theoretical study2000In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 77, no 1, p. 311-315Article in journal (Refereed)
    Abstract [en]

    We present a theoretical study on the dissociation reaction of Ng azapantalene to four N-2 molecules. The process proceeds via isomerization of Ns azapentalene to N-8 azidopentazole, which then dissociates directly into four nitrogen molecules. The calculations have determined the relative energies of the two isomers and the two transition states involved in the dissociation process. The results show azidopentazole to be 13 kcal/mol more stable than azapentalene. The barrier to dissociation into four N-2 molecules is computed to be 19 kcal/mol. It is concluded that Ns is not stable enough to be considered as a candidate for a high-energy density material. The calculations have been carried out using multiconfigurational self-consistent field and second-order perturbation theory.

  • 62. Gagliardi, Laura
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Karlström, Gunnar
    Local properties of quantum chemical systems: The LoProp approach2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 10, p. 4494-4500Article in journal (Refereed)
    Abstract [en]

    A new method is presented, which makes it possible to partition molecular properties like multipole moments and polarizabilities, into atomic and interatomic contributions. The method requires a subdivision of the atomic basis set into occupied and virtual basis functions for each atom in the molecular system. The localization procedure is organized into a series of orthogonalizations of the original basis set, which will have as a final result a localized orthonormal basis set. The new localization procedure is demonstrated to be stable with various basis sets, and to provide physically meaningful localized properties. Transferability of the methyl properties for the alkane series and of the carbon and hydrogen properties for the benzene, naphtalene, and anthracene series is demonstrated.

  • 63.
    Ghahremanpour, Mohammad Mehdi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    van Maaren, Paul J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Ditz, Jonas C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145Article in journal (Refereed)
    Abstract [en]

    Large scale quantum calculations for molar enthalpy of formation (ΔfH0), standard entropy (S0), and heat capacity (CV) are presented. A large data set may help to evaluate quantum thermochemistry tools in order to uncover possible hidden shortcomings and also to find experimental data that might need to be reinvestigated, indeed we list and annotate approximately 200 problematic thermochemistry measurements. Quantum methods systematically underestimate S0 for flexible molecules in the gas phase if only a single (minimum energy) conformation is taken into account. This problem can be tackled in principle by performing thermochemistry calculations for all stable conformations [Zheng et al., Phys. Chem. Chem. Phys. 13, 10885–10907 (2011)], but this is not practical for large molecules. We observe that the deviation of composite quantum thermochemistry recipes from experimental S0 corresponds roughly to the Boltzmann equation (S = RlnΩ), where R is the gas constant and Ω the number of possible conformations. This allows an empirical correction of the calculated entropy for molecules with multiple conformations. With the correction we find an RMSD from experiment of ≈13 J/mol K for 1273 compounds. This paper also provides predictions of ΔfH0, S0, and CV for well over 700 compounds for which no experimental data could be found in the literature. Finally, in order to facilitate the analysis of thermodynamics properties by others we have implemented a new tool obthermo in the OpenBabel program suite [O’Boyle et al., J. Cheminf. 3, 33 (2011)] including a table of reference atomization energy values for popular thermochemistry methods.

  • 64. Giussani, Angelo
    et al.
    Farahani, Pooria
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Martinez-Munoz, Daniel
    Lundberg, Marcus
    Lindh, Roland
    Roca-Sanjuan, Daniel
    Molecular Basis of the Chemiluminescence Mechanism of Luminol2019In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, no 20, p. 5202-5213Article in journal (Refereed)
    Abstract [en]

    Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.

  • 65.
    Giussani, Angelo
    et al.
    Univ Valencia, Inst Ciencia Mol, POB 22085, Valencia, Spain.
    Farahani, Pooria
    KTH Royal Inst Technol, Dept Theoret Chem & Biol, Sch Engn Sci Chem Biotechnol & Hlth CBH, S-10691 Stockholm, Sweden.
    Martinez-Muñoz, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Lundberg, Marcus
    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, Spain.
    Molecular Basis of the Chemiluminescence Mechanism of Luminol2019In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, no 20, p. 5202-5213Article in journal (Refereed)
    Abstract [en]

    Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.

  • 66. Giussani, Angelo
    et al.
    Merchan, Manuela
    Roca-Sanjuan, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    Essential on the Photophysics and Photochemistry of the lndole Chromophore by Using a Totally Unconstrained Theoretical Approach2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 12, p. 4088-4096Article in journal (Refereed)
    Abstract [en]

    Indole is a chromophore present in many different molecules of biological interest, such as the essential amino acid tryptophan and the neurotransmitter serotonin. On the basis of CASPT2//CASSCF quantum chemical calculations, the photophysical properties of the system after UV irradiation have been studied through the exploration of the potential energy hypersurfaces of the singlet and triplet low-lying valence excited states. In contrast to previous studies, the present work has been carried out without imposing any restriction to the geometry of the molecule (C(1) symmetry) and by performing minimum energy path calculations, which is the only instrument able to provide the lowest-energy evolution of the system. Relevant findings to the photophysics of bare indole have been obtained, which compete with the currently accepted mechanism for the energy decay in the molecule. The results show the presence of a conical intersection (CI) between the initially populated (1)(L(a) pi pi*) and the (1)(L(b) pi pi*) state, easily accessible through a barrierless pathway from the Franck Condon region. At this CI region, part of the population is switched from the bright (1)(L(a) pi pi*) state to the (1)(L(b) pi pi*) state, and the system evolves toward a minimum structure from which the expected fluorescence takes place. The reported low values of the fluorescence quantum yield are explained by means of a new nonracliative mechanism specific for the (1)(L(b) pi pi*) state, in which the presence of an ethene-like CI between the (1)(L(b) pi pi*) and ground states is the main feature.

  • 67. Gozem, Samer
    et al.
    Huntress, Mark
    Schapiro, Igor
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Granovsky, Alexander A.
    Angeli, Celestino
    Olivucci, Massimo
    Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4069-4080Article in journal (Refereed)
    Abstract [en]

    The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.

  • 68. Gozem, Samer
    et al.
    Melaccio, Federico
    Valentini, Alessio
    Filatov, Michael
    Huix-Rotllant, Miquel
    Ferre, Nicolas
    Manuel Frutos, Luis
    Angeli, Celestino
    Krylov, Anna I.
    Granovsky, Alexander A.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Olivucci, Massimo
    Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 8, p. 3074-3084Article in journal (Refereed)
    Abstract [en]

    We report and characterize ground-state and excited-state potential energy profiles using a variety of electronic structure methods along a loop lying on the branching plane associated with a conical intersection (Cl) of a reduced retinal model, the penta-2,4-dieniminium cation (PSB3). Whereas the performance of the equation-of-motion coupled-duster, density functional theory, and multireference methods had been tested along the excited- and ground-state paths of PSB3 in our earlier work, the ability of these methods to correctly describe the potential energy surface shape along a CI branching plane has not yet been investigated. This is the focus of the present contribution. We find, in agreement with earlier studies by others, that standard time-dependent DFT (TDDFT) does not yield the correct two-dimensional (i.e., conical) crossing along the branching plane but rather a one-dimensional (i.e., linear) crossing along the same plane. The same type of behavior is found for SS-CASPT2(IPEA=0), SS-CASPT2(IPEA=0.25), spin-projected SF-TDDFT, EOM-SF-CCSD, and, finally, for the reference MRCISD+Q method. In contrast, we found that MRCISD, CASSCF, MS-CASPT2(IPEA=0), MS-CASPT2(IPEA=0.25), XMCQDPT2, QD-NEVPT2, non-spin-projected SF-TDDFT, and SI-SA-REKS yield the expected conical crossing. To assess the effect of the different crossing topologies (i.e., linear or conical) on the PSB3 photoisomerization efficiency, we discuss the results of 100 semiclassical trajectories computed by CASSCF and SS-CASPT2(IPEA=0.25) for a PSB3 derivative. We show that for the same initial conditions, the two methods yield similar dynamics leading to isomerization quantum yields that differ by only a few percent.

  • 69.
    Guo, Meiyuan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Southwest Univ, Dept Chem & Chem Engn, Chongqing, Peoples R China.
    Källman, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pinjari, Rahul V.
    Swami Ramanand Teerth Marathwada Univ, Sch Chem Sci, Nanded, Maharashtra, India.
    Couto, Rafael Carvalho
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sörensen, Lasse Kragh
    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.
    Pierloot, Kristine
    Univ Leuven, Dept Chem, Heverlee, Belgium.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Siena, Dept Biotechnol Chem & Pharm, Siena, Italy.
    Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra2019In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 1, p. 477-489Article in journal (Refereed)
    Abstract [en]

    The capability of the multiconfigurational restricted active space approach to identify electronic structure from spectral fingerprints is explored by applying it to iron L-edge X-ray absorption spectroscopy (XAS) of three heme systems that represent the limiting descriptions of iron in the Fe-O-2 bond, ferrous and ferric [Fe(P)(ImH)(2)](0/1+) (P = porphine, ImH = imidazole), and Fe-II(P). The level of agreement between experimental and simulated spectral shapes is calculated using the cosine similarity, which gives a quantitative and unbiased assignment. Further dimensions in fingerprinting are obtained from the L-edge branching ratio, the integrated absorption intensity, and the edge position. The results show how accurate ab initio simulations of metal L-edge XAS can complement calculations of relative energies to identify unknown species in chemical reactions.

  • 70. Gusarov, Sergey
    et al.
    Malmqvist, Per-Åke
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Using on-top pair density for construction of correlation functionals for multideterminant wave functions2004In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 102, no 21-22, p. 2207-2216Article in journal (Refereed)
    Abstract [en]

    The value of the two-particle density function at coalescence P-2(ontop)(r) = rho(2)(r, r) is frequently used as an additional variable for formulating approximate exchange-correlation or correlation functionals. Here, its applications as one of the key variables for the construction of new DFT (preferably multi-determinant) functionals is investigated. The basic formalism is presented and it is shown that this replacement avoids some difficulty to construct a Fock matrix in a ROKS (restricted open-shell Kohn-Sham) method and also to reduce the ‘double counting’ of correlation energy in CASDFT (complete active space density functional theory) calculations. Calculations of excitation energies for transition metals and dissociation curves for diatomic molecules are presented as an example.

  • 71. Gusarov, Sergey
    et al.
    Malmqvist, Per-Åke
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Roos, Björn O
    Correlation potentials for a multiconfigurational-based density functional theory with exact exchange2004In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 112, no 2, p. 84-94Article in journal (Refereed)
    Abstract [en]

    A density functional theory based on a complete active space self consistent field (CASSCF) reference function with exact exchange is discussed. It is first shown that such a theory may be formulated with a correlation potential dependent on the density function and on the active space used. Auxiliary functions, such as the on-top two-particle density, are used to define uniquely the potential for different active spaces. The paper also analyses the correlation functional for some atomic and molecular cases. Large ab initio calculations are performed to obtain accurate density functions. A correlation potential is then fitted such that the reference CASSCF function gives the same density. The correlation potential values are saved in a data base for future analysis.

  • 72.
    Head-Gordon, Martin
    et al.
    Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    A celebration of the Swedish school2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 1993-1994Article in journal (Other academic)
  • 73. Hermida-Ramón, Jose Manuel
    et al.
    Karlström, Gunnar
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Analysis of the relative stability of cis-urocanic acid in condensed phase: The use of Langevin dipoles2002In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 106, no 28, p. 7115-7120Article in journal (Refereed)
    Abstract [en]

    A series of ab initio calculations employing a modified Langevin dipoles method to model neutral, cationic, and anionic cis-urocanic acid in human skin is presented. A comparison between the stability of the conformers in gas phase and in a condensed phase is performed. In particular, the energy barrier and transition state of the isomerization reaction of the anionic forms of cis-urocanic acid have been characterized. The modifications of the Langevin dipoles method, a procedure to obtain the required model parameters, and model verifications are presented. The latter include computing the water solvation energy and the free energy of the water dissociation.

  • 74.
    Hoffmann, Inga
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Hamberg, Mats
    Karolinska institutet.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Oliw, Ernst H.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Novel insights into cyclooxygenases, linoleate diol synthases, and lipoxygenases from deuterium kinetic isotope effects and oxidation of substrate analogs2012In: Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, ISSN 1388-1981, E-ISSN 1879-2618, Vol. 1821, no 12, p. 1508-1517Article in journal (Refereed)
    Abstract [en]

    Cyclooxygenases (COX) and 8R-dioxygenase (8R-DOX) activities of linoleate diol synthases (LDS) are homologous heme-dependent enzymes that oxygenate fatty acids by a tyrosyl radical-mediated hydrogen abstraction and antarafacial insertion of O2. Soybean lipoxygenase-1 (sLOX-1) contains non-heme iron and oxidizes 18:2n-6 with a large deuterium kinetic isotope effect (D-KIE). The aim of the present work was to obtain further mechanistic insight into the action of these enzymes by using a series of n-6 and n-9 fatty acids and by analysis of D-KIE. COX-1 oxidized C20 and C18 fatty acids in the following order of rates: 20:2n-6 > 20:1n-6 > 20:3n-9 > 20:1n-9 and 18:3n-3 ≥ 18:2n-6 > 18:1n-6. 18:2n-6 and its geometrical isomer (9E,12Z)18:2 were both mainly oxygenated at C-9 by COX-1, but the 9Z,12E isomer was mostly oxygenated at C-13. A cis-configured double bond in the n-6 position therefore seems important for substrate positioning. 8R-DOX oxidized (9Z,12E)18:2 at C-8 in analogy with 18:2n-6, but the 9E,12Z isomer was only subject to hydrogen abstraction at C-11 and oxygen insertion at C-9 by 8R-DOX of 5,8-LDS. sLOX-1 and 13R-MnLOX oxidized [11S-2H]18:2n-6 with similar D-KIE (~53), which implies that the catalytic metals did not alter the D-KIE. Oxygenation of 18:2n-6 by COX-1 and COX-2 took place with a D-KIE of 3-5 as probed by incubations of [11,11-2H2]- and [11S-2H]18:2n-6. In contrast, the more energetically demanding hydrogen abstractions of the allylic carbons of 20:1n-6 by COX-1 and 18:1n-9 by 8R-DOX were both accompanied by large D-KIE (>20).

  • 75. Holt, Asbjorn
    et al.
    Boström, Jonas
    Karlström, Gunnar
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    A NEMO potential that includes the dipole-quadrupole and quadrupole-quadrupole polarizability2010In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 31, no 8, p. 1583-1591Article in journal (Refereed)
    Abstract [en]

    To increase the accuracy of molecular force fields a systematical and balanced improvement of the various terms included is needed. In this work, we have followed this strategy to improve the quality of the NEMO potential for the formaldehyde dimer by introducing local quadrupole moments and higher-order polarizabilities. It is found that inclusion of the quadrupole moment significantly improves the interaction potential. Furthermore, the inclusion of higher-order polarizabilities up to quadrupole-quadrupole polarizability is shown to give a better description of the intermolecular interaction. In addition, it is demonstrated that localized properties based on MP2 densities reproduces the BSSE corrected MP2 interaction energy at large intermolecular separations. This is not the case for HF-SCF based properties.

  • 76. Holt, Asbjorn
    et al.
    Karlström, Gunnar
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    The charge capacity of the chemical bond2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 436, no 1-3, p. 297-301Article in journal (Refereed)
    Abstract [en]

    A bond capacitance is introduced via the LoProp formalism, and the calculated bond capacitances reflects the properties of the corresponding chemical bond remarkably well. It is clearly possible to characterize the properties of the chemical bond with the help of the calculated bond capacitances.

  • 77. 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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  • 78.
    Jeong, WooSeok
    et al.
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Stoneburner, Samuel J.
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    King, Daniel
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Li, Ruye
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Walker, Andrew
    Univ Minnesota, Dept Comp Sci & Engn, Minneapolis, MN 55455 USA..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Uppsala Univ, Uppsala Center for Computational Chemistry, S-75123 Uppsala, Sweden..
    Gagliardi, Laura
    Univ Minnesota, Dept Chem, Nanoporous Mat Genome Ctr, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Automation of Active Space Selection for Multireference Methods via Machine Learning on Chemical Bond Dissociation2020In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 16, no 4, p. 2389-2399Article in journal (Refereed)
    Abstract [en]

    Predicting and understanding the chemical bond is one of the major challenges of computational quantum chemistry. Kohn-Sham density functional theory (KS-DFT) is the most common method, but approximate density functionals may not be able to describe systems where multiple electronic configurations are equally important. Multiconfigurational wave functions, on the other hand, can provide a detailed understanding of the electronic structures and chemical bonds of such systems. In the complete active space self-consistent field (CASSCF) method, one performs a full configuration interaction calculation in an active space consisting of active electrons and active orbitals. However, CASSCF and its variants require the selection of these active spaces. This choice is not black box; it requires significant experience and testing by the user, and thus active space methods are not considered particularly user-friendly and are employed only by a minority of quantum chemists. Our goal is to popularize these methods by making it easier to make good active space choices. We present a machine learning protocol that performs an automated selection of active spaces for chemical bond dissociation calculations of main group diatomic molecules. The protocol shows high prediction performance for a given target system as long as a properly correlated system is chosen for training. Good active spaces are correctly predicted with a considerably better success rate than random guess (larger than 80% precision for most systems studied). Our automated machine learning protocol shows that a "black-box" mode is possible for facilitating and accelerating the large-scale calculations on multireference systems where single-reference methods such as KS-DFT cannot be applied.

  • 79.
    Johnstone, Erik V.
    et al.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA.;Univ Sheffield, Dept Mat Sci & Engn, Sheffield S1 3JD, S Yorkshire, England..
    Poineau, Frederic
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA..
    Todorova, Tanya K.
    UPMC, CNRS, Coll France, Lab Chim Proc Biol,UMR 8229, 11 Pl Marcelin Berthelot, F-75231 Paris 05, France..
    Forster, Paul M.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA..
    Sørensen, Lasse K.
    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.
    Czerwinski, Kenneth R.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA..
    Sattelberger, Alfred P.
    Univ Nevada, Dept Chem, Las Vegas, NV 89154 USA.;Argonne Natl Lab, Argonne, IL 60439 USA..
    Molecular and Electronic Structure of Re2Br4(PMe3)(4)2016In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 55, no 14, p. 7111-7116Article in journal (Refereed)
    Abstract [en]

    The dinuclear rhenium(II) complex Re2Br4(PMe3)(4) was prepared from the reduction of [Re2Br8](2-) with (n-Bu4N)BH4 in the presence of PMe3 in propanol. The complex was characterized by single-crystal X-ray diffraction (SCXRD) and UV-visible spectroscopy. It crystallizes in the monoclinic C2/c space group and is isostructural with its molybdenum and technetium analogues. The Re-Re distance (2.2521(3) angstrom) is slightly longer than the one in Re2Cl4(PMe3)(4) (2.247(1) angstrom). The molecular and electronic structure of Re2X4(PMe3)(4) (X = Cl, Br) were studied by multiconfigurational quantum chemical methods. The computed ground-state geometry is in excellent agreement with the experimental structure determined by SCXRD. The calculated total bond order (2.75) is consistent with the presence of an electron-rich triple bond and is similar to the one found for Re2Cl4(PMe3)(4). The electronic absorption spectrum of Re2Br4(PMe3)(4) was recorded in benzene and shows a series of low-intensity bands in the range 10 000-26 000 cm(-1). The absorption bands were assigned based on calculations of the excitation energies with the multireference wave functions followed by second-order perturbation theory using the CASSCF/CASPT2 method. Calculations predict that the lowest energy band corresponds to the delta* -> sigma* transition, while the next higher energy bands were attributed to the delta* -> pi*, delta -> sigma*, and delta -> pi* transitions.

  • 80.
    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.

  • 81.
    Jorner, Kjell
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Feixas, Ferran
    Univ Girona, IQCC, Campus Montilivi S-N, Girona 17071, Catalonia, Spain.;Univ Girona, Dept Quim, Campus Montilivi S-N, Girona 17071, Catalonia, Spain..
    Ayub, Rabia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala Univ, Uppsala Ctr Computat Chem UC3, Box 518, S-75120 Uppsala, Sweden..
    Sola, Miquel
    Univ Girona, IQCC, Campus Montilivi S-N, Girona 17071, Catalonia, Spain.;Univ Girona, Dept Quim, Campus Montilivi S-N, Girona 17071, Catalonia, Spain..
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Analysis of a Compound Class with Triplet States Stabilized by Potentially Baird Aromatic [10]Annulenyl Dicationic Rings2016In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 22, no 8, p. 2793-2800Article in journal (Refereed)
    Abstract [en]

    The low-lying triplet state of a recently published compound (TMTQ) was analyzed quantum chemically in light of suggestions that it is influenced by Baird aromaticity. Two mesomeric structures describe this state: 1)a zwitterionic Baird aromatic structure with a triplet diradical 8-electron methano[10]annulene (M10A) dicationic ring and 2)a Huckel aromatic with a neutral closed-shell 10-electron ring. According to charge and spin density distributions, the Huckel aromatic structure dominates the triplet state (the Baird aromatic contributes at most 12%), and separation of the aromatic fluctuation index (FLU) into and electron contributions emphasizes this finding. The small singlet-triplet energy gap is due to Huckel aromaticity of the M10A ring, clarified by comparison to the smaller analogues of TMTQ. Yet, TMTQ and its analogues are Huckel-Baird hybrids allowing for tuning between closed-shell 4n+2 Huckel aromaticity and open-shell 4n Baird aromaticity.

  • 82. Karlström, Gunnar
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per-Åke
    Roos, Björn O
    Ryde, Ulf
    Veryazov, Valera
    Widmark, Per-Olof
    Cossi, Maurizio
    Schimmelpfennig, Bernd
    Neogrady, Pavel
    Seijo, Luis
    MOLCAS: a program package for computational chemistry2003In: Computational materials science, ISSN 0927-0256, E-ISSN 1879-0801, Vol. 28, no 2, p. 222-239Article in journal (Refereed)
    Abstract [en]

    The program system MOLCAS is a package for calculations of electronic and structural properties of molecular systems in gas, liquid, or solid phase. It contains a number of modern quantum chemical methods for studies of the electronic structure in ground and excited electronic states. A macromolecular environment can be modeled by a combination of quantum chemistry and molecular mechanics. It is further possible to describe a crystalline material using model potentials. Solvent effects can be treated using continuum models or by combining quantum chemical calculations with molecular dynamics or Monte-Carlo simulations. MOLCAS is especially adapted to treat systems with a complex electronic structure, where the simplest quantum chemical models do not work. These features together with the inclusion of relativistic effects makes it possible to treat with good accuracy systems including atoms from the entire periodic system. MOLCAS has effective methods for geometry optimization of equilibria, transition states, conical intersections, etc. This facilitates studies of excited state energy surfaces, spectroscopy, and photochemical processes.

  • 83.
    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.

  • 84. Krogh, J W
    et al.
    Barone, G
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    The prediction of the nuclear quadrupole splitting of Sn-119 Mossbauer spectroscopy data by scalar relativistic DFT calculations2006In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 12, no 19, p. 5116-5121Article in journal (Refereed)
    Abstract [en]

    The electric field gradient components for the tin nucleus of 34 tin compounds of experimentally known structures and Sn-119 Mossbauer spectroscopy parameters were computed at the scalar relativistic density functional theory level of approximation. The theoretical values of the electric field gradient components were used to determine a quantity, V, which is proportional to the nuclear quadrupole splitting parameter (Delta E). In a subsequent linear regression analysis the effective nuclear quadrupole moment, Q, was evaluated. The value of (11.9 +/- 0.1) fm(2) is a significant improvement over the non-relativistic result of (15.2 +/- 4.4) fm(2) and is in agreement with the experimental value of (10.9 +/- 0.8) fm(2). The average mean square error Delta E-calcd-Delta E-exptl = +/- 0.3 mm s(-1) is a factor of two smaller than in the non-relativistic case. Thus, the approach has a quality which provides accurate support for the structure interpretation by Sn-119 spectroscopy. It was noted that geometry optimization at the relativistic level does not significantly increase the quality of the results compared with non-relativistic optimized structures. The accuracy in the approach called on us to consider the singlet-triplet state nature of the electronic structure of one of the investigated compounds.

  • 85. Krylov, Anna I.
    et al.
    Herbert, John M.
    Furche, Filipp
    Head-Gordon, Martin
    Knowles, Peter J.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Manby, Frederick R.
    Pulay, Peter
    Skylaris, Chris-Kriton
    Werner, Hans-Joachim
    What Is the Price of Open-Source Software?2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 14, p. 2751-2754Article in journal (Other academic)
  • 86.
    Li, Chenyang
    et al.
    Emory Univ, Dept Chem, Atlanta, GA 30322 USA;Emory Univ, Cherry Emerson Ctr Sci Computat, Atlanta, GA 30322 USA.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Evangelista, Francesco A.
    Emory Univ, Dept Chem, Atlanta, GA 30322 USA;Emory Univ, Cherry Emerson Ctr Sci Computat, Atlanta, GA 30322 USA.
    Dynamically weighted multireference perturbation theory: Combining the advantages of multi-state and state-averaged methods2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 14, article id 144107Article in journal (Refereed)
    Abstract [en]

    We introduce two new approaches to compute near-degenerate electronic states based on the driven similarity renormalization group (DSRG) framework. The first approach is a unitary multi-state formalism based on the DSRG (MS-DSRG), whereby an effective Hamiltonian is built from a set of state-specific solutions. The second approach employs a dynamic weighting parameter to smoothly interpolate between the multi-state and the state-averaged DSRG schemes. The resulting dynamically weighted DSRG (DW-DSRG) theory incorporates the most desirable features of both multi-state approaches (ability to accurately treat many states) and state-averaged methods (correct description of avoided crossings and conical intersections). We formulate second-order perturbation theories (PT2) based on the MS-and DW-DSRG and study the potential energy curves of LiF, the conical intersection of the two lowest singlet states of NH3, and several low-lying excited states of benzene, naphthalene, and anthracene. The DW-DSRG-PT2 predicts the correct avoided crossing of LiF and avoids artifacts produced by the corresponding state-specific and multi-state theories. Excitation energies of the acenes computed with the DW-DSRG-PT2 are found to be more accurate than the corresponding state-averaged values, showing a small dependence on the number of states computed.

  • 87.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Cholesky Decomposition of the two-electron integrals: A reliable tool for linear scaling methods?2006In: RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B, 2006, Vol. 7A-BConference paper (Other academic)
  • 88. Lindh, Roland
    Integrals of Electron Repulsion2002In: Encyclopedia of Computational Chemistry / [ed] Paul von Ragué Schleyer, John Wiley & Sons, 2002Chapter in book (Other academic)
  • 89.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    THE REDUCED MULTIPLICATION SCHEME OF THE RYS-GAUSS QUADRATURE FOR 1ST-ORDER INTEGRAL DERIVATIVES1993In: THEORETICA CHIMICA ACTA, ISSN 0040-5744, Vol. 85, no 6, p. 423-440Article in journal (Refereed)
    Abstract [en]

    An implementation of the reduced multiplication scheme of the Rys-Gauss quadrature to compute the gradients of electron repulsion integrals is discussed. The study demonstrates that the Rys-Gauss quadrature is very suitable for efficient utilization of simplifications as offered by the direct computation of symmetry adapted gradients and the use of the translational invariance of the integrals. The introduction of the so-called intermediate products is also demonstrated to further reduce the floating point operation count. Two prescreening techniques based on the 2nd order density matrix in the basis of the uncontracted Gaussian functions is proposed and investigated in the paper. This investigation gives on hand that it is not necessary to employ the Cauchy-Schwarz inequality to achieve efficient prescreening. All the features mentioned above were demonstrated by their implementation into the gradient program ALASKA. The paper offers a theoretical and practical assessment of the modified Rys-Gauss quadrature in comparison with other methods and implementations and a detailed analysis of the behavior of the method as suggested above as a function of changes with respect to symmetry, basis set quality, molecular size, and prescreening threshold.

  • 90.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Barnes, Leslie A
    The fraternal twins of quartet O+41994In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 100, no 1, p. 224-237Article in journal (Refereed)
    Abstract [en]

    Eleven stationary geometries of quartet O4+ have been studied by ab initio methods. The geometries were optimized at the complete active space self-consistent field (CASSCF) level of theory and the energies were calculated by the multiconfigurational second order pertubation method (CASPT2), using double-zeta plus polarization (DZP), triple-zeta plus double polarization (TZ2P), average atomic natural orbital (ANO) [5s4p2d] and average ANO [6s5p3d2f] basis sets. The rectangular and trans-planar structures are found to be the most stable, with an energy barrier to conversion between the two at the threshold of dissociation. Both have a delocalized hole and are stable relative to separated O2 and O2+ by 11.0 and 11. 5 kcal/mol for the rectangular and the trans-planar structure, respectively, compared with the experimentally deduced energy in the range of 9.2 to 10.8 kcal/mol. The adiabatic ionization potentials of O4 and O2 are computed to be 11.67 and 12.21 eV, while experimental values are 11.66 and 12.07 eV, respectively. The vibrational frequencies have been computed for all degrees of freedom at the CASSCF level of theory. Symmetry breaking is found to be a particular problem in the computation of the antisymmetric stretch frequency for the delocalized structures at the CASSCF level of theory. Attempts to rectify these problems using the restricted active space self-consistent field (RASSCF) method leads to additional difficulties, but further analysis yields insight into the symmetry breaking and problems with earlier calculations. Finally, a nonorthogonal configuration interaction (CI) calculation based on the interaction of localized CASSCF wave functions using the complete active space state interation (CASSI) method leads to a balanced treatment of the antisymmetric stretch which is free from symmetry breaking. The study explains the four most prominent absorption frequencies observed in the partially unassigned IR spectrum of 04+ isolated in solid neon as the antisymmetric OO stretch, and the combination band of the symmetric and antisymmetric OO stretch of both the rectangular and trans-planar structures.

  • 91.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Bernhardsson, Anders
    Karlström, Gunnar
    Mamlqvist, Per-Åke
    On the use of a Hessian model function in molecular geometry optimizations1995In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 241, no 4, p. 423-428Article in journal (Refereed)
    Abstract [en]

    When a molecular equilibrium geometry is determined by minimizing the energy by a quasi-Newton-Raphson method, the number of iterations required depends critically on the choice of an approximate molecular Hessian matrix. We find that a simple 15-parameter function of the nuclear positions gives a good choice for any molecule with atoms from the first three rows of the periodic table. This Hessian is used for ah initio geometry optimizations with the quasi-Newton-Raphson method, with or without update. The equilibrium geometries of 30 molecules, with a variety of sizes and symmetries, is obtained with the new scheme, which is shown to converge significantly faster than other methods.

  • 92.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Bernhardsson, Anders
    Schütz, Martin
    Benzyne thermochemistry: A benchmark ab initio study1999In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, no 48, p. 9913-9920Article in journal (Refereed)
    Abstract [en]

    The thermochemistry of the benzynes has been reinvestigated in a set of benchmark calculations including, e.g., multireference perturbation theory in combination with large basis sets up to correlation consistent polarized valence quadruple xi followed by basis set extrapolation procedures. The vibrational corrections have been deduced from multiconfiguration self-consistent field (MCSCF) calculations employing average atomic natural orbital basis sets. The quality of the isodesmic reactions has been investigated by analyzing the errors of the utilized methods in predicting the CH bond strengths and energies of the related molecules. It turns out that multireference third order perturbation theory, although occasionally better than second order, suffers from less systematic errors and thus is not as well suited for use in isodesmic reactions as the corresponding second order theory. The present extended calculations show that all the isodesmic reactions used in previous studies of the thermochemistry of the benzynes are adequate. Furthermore, it is demonstrated that multireference second order perturbation theory accurately reproduces the singlet-triplet energy splittings of the benzynes.

  • 93.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Bernhardsson, Anders
    Schütz, Martin
    Force-constant weighted redundant coordinates in molecular geometry optimizations1999In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 303, no 5-6, p. 567-575Article in journal (Refereed)
    Abstract [en]

    A novel procedure to select internal coordinates for molecular geometry optimizations is presented. The procedure has features in common with other so-called redundant internal coordinates schemes. It is a black-box method which automatically selects an appropriate set of internal coordinates in which the geometry optimization is performed. The method is explicitly expressed in the non-redundant parameter space, thus avoiding the need for projections from the redundant internal coordinate space. The new procedure introduces a weighting in which the redundancy is modified prior to the generation of the non-redundant internal coordinates. The new method favors those redundant internal coordinates which are the most significant. It has favorable properties for the automatic generation of molecular coordinates in van der Waals complexes and transition state optimizations.

  • 94.
    Lindh, Roland
    et al.
    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.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Non-adiabatic process in 1,2-dioxetane2014In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 247Article in journal (Other academic)
  • 95.
    Lindh, Roland
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Galvan, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Liu, Ya-Jun
    Roca-Sanjuan, Daniel
    Recent method developments and applications in computational photochemistry, chemiluminescene and bioluminescence2015In: Photochemistry: Volume 42 / [ed] Elisa Fasani, Angelo Albini, Royal Society of Chemistry, 2015, 42, 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.

  • 96.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Kraemer, Wolfgang P
    Kamper, Manfred
    On the thermodynamic stability of ArO41999In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, no 41, p. 8295-8302Article in journal (Refereed)
    Abstract [en]

    The argon tetroxide molecule, ArO4, and the isoelectronically associated perchlorate, ClO4-, and sulfate, SO42-, ions are investigated on different levels of ab initio theory. The equilibrium structures, harmonic vibrational frequencies, and heats of formation are computed applying density functional theory, second order Moller-Plesset perturbation, singles and doubles coupled-cluster with triples corrections, and Bruekner’s doubles coupled-cluster with triples corrections methods in conjunction with various one-particle basis sets. The calculations demonstrate that the description of the bond characteristics in argon tetroxide is sensitive to the applied level of theory. A careful analysis of the global potential energy surface shows that a stationary point exists for the ArO4 complex corresponding to a local mininium. The calculated equilibrium Ar-O bond distance of 1.48 Angstrom for this structure is slightly longer than the corresponding bond length of the perchlorate ion. Harmonic frequencies for ArO4 obtained using Bruekner’s doubles coupled-cluster with triples corrections are found to have a similar pattern like those obtained for the isoelectronic series of ions SiO44-, PO43-, SO42-, ClO4-. Using the concept of an isodesmic reaction, the enthalpy of formation of ArO4 is determined to be endothermic by as much as 1236 kJ/mol. The present theoretically predicted strong endothermicity and the large Ar-O bond distance are in conflict with the monotonic trends obtained for the isoelectronic ions, but can be supported by other chemical extrapolation schemes.

  • 97.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Lee, Timothy J
    Bernhardsson, Anders
    Persson, B Joakim
    Karlström, Gunnar
    Research Article Extended ab Initio and Theoretical Thermodynamics Studies of the Bergman Reaction and the Energy Splitting of the Singlet o-, m-, and p-Benzynes1995In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 117, no 27, p. 7186-7194Article in journal (Refereed)
    Abstract [en]

    The autoaromatization of (Z)-hex-3-ene-1,5-diyne to the singlet biradical p-benzyne has been reinvestigated by state of the art ab initio methods. Previous CCSD(T)/6-31G(d,p) and CASPT2[0]/ANO[C(5s4p2dlf)/H(3s2p)] calculations estimated the reaction heat at 298 K to be 8-10 and 3.9 +/- 3.2 kcal/mol, respectively. Recent NO- and oxygen-dependent trapping experiments and collision-induced dissociation threshold energy experiments estimate the heat of reaction to be 8.5 +/- 1.0 kcal/mol at 470 K (corrected to 9.5 +/- 1.0 kcal/mol at 298 K) and 8.4 +/- 3.0 kcal/mol at 298 K, respectively. New theoretical estimates at 298 K predict the values at the basis set Limit for the CCSD(T) and CASPT2[gl] methods to be 12.7 +/- 2.0 and 5.4 +/- 2.0 kcal/mol, respectively. The experimentally predicted electronic contribution to the heat of activation is 28.6 kcal/mol. This can be compared with 25.5 and 29.8 kcal/mol from the CASPT2[gl] and the CCSD(T) methods, respectively. The new study has a much larger one-particle basis set for the CCSD(T) method as compared to earlier studies. For the CASPT2 investigation the better suited CASPT2[gl] approximation is utilized. The original CASPT2 method, CASPT2[0], systematically favors open-shell systems relative to closed-shell systems. This was previously corrected empirically. The current study shows that the energy difference between CCSD(T) and CASPT2[gl] at the basis set limit is estimated to be 7 +/- 2 kcal/mol. The study also demonstrates that the estimated heat of reaction is very sensitive to the quality of the basis set. In particular CCSD(T)/6-31G(d,p) approach underestimates the basis set limit of the enthalpy by approximately 5 kcal/mol. Furthermore, the relative energies of the p-, m-, and o-benzynes are computed at the CASPT2[gl] and CCSD(T) levels of theory. These results help to explain the discrepancy between the two methods in the case of the Bergman reaction. The deficiency of the CASPT2 method is mainly attributed to the approximate way in which the dynamic correlation is included by perturbation theory. A similar sized error is attributed to the CCSD(T) method due to the approximate way in which near degeneracy effects are included. This combined CCSD(T) and CASPT2[gl] study indicates that the most recent experimental value of the p-benzyne-o-benzyne energy splitting is overestimated.

  • 98.
    Lindh, Roland
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    LIU, B
    Accurate abinitio calculations of the quadrupole-moment of acetylene: a combined study of basis set, correlation, and vibrational effects1991In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 94, no 6, p. 4356-4368Article in journal (Refereed)
    Abstract [en]

    The quadrupole moment of acetylene has been studied at the multiconfiguration self-consistent field (MCSCF) and multireference single and double configuration interaction (MRSDCI) level of theory. At the MCSCF level the pi-CI complete active space SCF (CASSCF) and the valence-CI CASSCF were employed. The subsequent MRSDCI calculations were continued until the reference space included all configuration state functions (CSFs) of the MCSCF wave function with a coefficient larger than 0.01 [MRSDCI(0.01)]. The higher level basis sets in this study were all based on van Duijneveldt’s C(13s 8p) and H(6s) and extensions of that basis set. The study shows in a consistent way that both the one- and n-particle spaces are saturated at the highest level of theory. The study has revealed that in addition to the well known increase of the quadrupole moment due to the inclusion of polarizing functions in the basis (typically 0.20 a.u.), the inclusion of electronic correlation in the model wave function as well as vibrational corrections will decrease the quadrupole moment significantly more, -0.66, -0.49, and -0.36 a.u., for the correlation correction and zero-point correction for HCCH and DCCD, respectively. The most accurate computations predict the quadrupole moment of HCCH, including zero-point correction, to be 4.29 +/- 0.12 a.u., which discriminates the experimental estimates of 4.03 +/- 0.30, 4.28 +/- 0.30, and 4.57 +/- 0.30 a.u. (the first being the favored value). The quadrupole moment of DCCD is computed to 4.42 +/- 0.10 a.u. In the study it was observed that in contradiction to previous experiences the use of the model equilibrium geometries rather than the experimental geometry gives a smoother convergence as the level of theory is increased. The effects of basis set quality and electron correlation on the quadrupole moment are studied in detail. These effects are analyzed with reference to the redistribution of the electronic charge.

  • 99.
    Lindh, Roland
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Liu, Ya-Jun
    Roca-Sanjuan, Daniel
    Computational Photochemistry and Photophysics: the state of the art2012In: Photochemistry: Volume 40 / [ed] Angelo Albini, Elisa Fasani, Royal Society of Chemistry, 2012, 40, p. 42-72-Chapter in book (Other academic)
    Abstract [en]

    This review starts with the most basic concepts in photochemistry and photophysics, followed by a chronological introduction of theoretical methods and relevant applications in the history of computational photochemistry, along with the authors’ comments on the methodologies currently available for photochemical studies. Recent advances in the field are next summarized and discussed, focusing separately on methodology and computational techniques and some highlighted applied works carried out during the last two years on the topics of photodissociations, photostability, photodimerizations, photoisomerizations, proton/hydrogen transfer, photodecarboxylations, charge transport, bioexcimers, chemiluminescence and bioluminescence. We finish this review by conclusions and an outlook of the future.

  • 100.
    Lindh, Roland
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Malmquist, PA
    A submatrix algorithm for the matrix-vector multiplication of very large matrices1989In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 10, no 3, p. 344-345Article in journal (Refereed)
    Abstract [en]

    In self-consistent field (SCF) calculations the construction of the Fock matrix is most time-consuming step. The Fock matrix construction may formally be seen as a matrix-vector multiplication, where the matrix is the supermatrix,��ijkl, and the vector is the first-order density matrix, γij. This formalism should be optimal for vector machines. This is not, however, fully utilized in most programs running on computers with small core memory. The size of the �� matrix, typically in the order of 106–108 elements, has forced programmers to implement other nonvectorizable methods. We will present a submatrixbased algorithm which will partition the supermatrix so that vectorizable methods can be employed. The method will also reduce the input/output.

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