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  • 51.
    Caldwell, Dennis
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Conundrums in Chemical Physics2013In: Advances in Quantum Chemistry, Elsevier, 2013, p. 31-111Chapter in book (Refereed)
    Abstract [en]

    In this review, we identify several fundamental concepts and models that have been challenging to students and teachers: (1) the Marcus theory of electron transfer reactions; (2) the Landau-Zener model for diabatic transitions; (3) the concept of reaction path curvature as illustrated by the affine transformation; and (4) a progression of stochastic models: the Langevin equation, the Fokker-Planck equation, and Kramers' theory of phase space diffusion as embodied in the Klein-Kramers equation. The gravamen of the work is the connection between Kramers' version of Transition State theory in the context of phase space diffusion. These classical concepts are then transferred to the realm of quantum chemistry, where we outline a program for tracking ensembles of time-dependent wave functions in analogy with their classical counterparts by means of a superoperator space and a Trace Algebra.

  • 52.
    Caldwell, Dennis
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Conundrums in Chemical Physics2013In: Advances in Quantum Chemistry, ISSN 0065-3276, E-ISSN 2162-8815, Vol. 66, p. 31-111Article in journal (Refereed)
    Abstract [en]

    In this review, we identify several fundamental concepts and models that have been challenging to students and teachers: (1) the Marcus theory of electron transfer reactions; (2) the Landau–Zener model for diabatic transitions; (3) the concept of reaction path curvature as illustrated by the affine transformation; and (4) a progression of stochastic models: the Langevin equation, the Fokker–Planck equation, and Kramers’ theory of phase space diffusion as embodied in the Klein–Kramers equation.

    The gravamen of the work is the connection between Kramers’ version of Transition State theory in the context of phase space diffusion. These classical concepts are then transferred to the realm of quantum chemistry, where we outline a program for tracking ensembles of time-dependent wave functions in analogy with their classical counterparts by means of a superoperator space and a Trace Algebra.

  • 53. Chaudret, Robin
    et al.
    Contreras-Garcia, Julia
    Delcey, Mickaël
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Parisel, Olivier
    Yang, Weitao
    Piquemal, Jean-Philip
    Revisiting H2O Nucleation around Au+ and Hg2+: The Peculiar "Pseudo-Soft" Character of the Gold Cation2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 5, p. 1900-1909Article in journal (Refereed)
    Abstract [en]

    In this contribution, we propose a deeper understanding of the electronic effects affecting the nucleation of water around the Au+ and Hg2+ metal cations using quantum chemistry. To do so, and in order to go beyond usual energetical studies, we make extensive use of state of the art quantum interpretative techniques combining ELF/NCI/QTAIM/EDA computations to capture all ranges of interactions stabilizing the well characterized microhydrated structures. The Electron Localization Function (ELF) topological analysis reveals the peculiar role of the Au+ outer-shell core electrons (subvalence) that appear already spatially preorganized once the addition of the first water molecule occurs. Thus, despite the addition of other water molecules, the electronic structure of Au(H2O)(+) appears frozen due to relativistic effects leading to a maximal acceptation of only two waters in gold's first hydration shell. As the values of the QTAIM (Quantum Theory of Atoms in Molecules) cations's charge is discussed, the Non Covalent Interactions (NCI) analysis showed that Au+ appears still able to interact through longer range van der Waals interaction with the third or fourth hydration shell water molecules. As these types of interaction are not characteristic of either a hard or soft metal cation, we introduced the concept of a "pseudo-soft" cation to define Au+ behavior. Then, extending the study, we performed the same computations replacing Au+ with Hg2+, an isoelectronic cation. If Hg2+ behaves like Au+ for small water clusters, a topological, geometrical, and energetical transition appears when the number of water molecules increases. Regarding the HSAB theory, this transition is characteristic of a shift of Hg2+ from a pseudosoft form to a soft ion and appears to be due to a competition between the relativistic and correlation effects. Indeed, if relativistic effects are predominant, then mercury will behave like gold and have a similar subvalence/geometry; otherwise when correlation effects are predominant, Hg2+ behaves like a soft cation.

  • 54. Chen, Shufeng
    et al.
    Navizet, Isabelle
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Liu, Yajun
    Ferre, Nicolas
    Hybrid QM/MM Simulations of the Obelin Bioluminescence and Fluorescence Reveal an Unexpected Light Emitter2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 11, p. 2896-2903Article in journal (Refereed)
    Abstract [en]

    Obelia longissima, a tiny hydrozoan living in temperate and cold seas, features the Obelin photoprotein, which emits blue light. The Obelin bioluminescence and the Ca2+-discharged Obelin fluorescence spectra show multimodal characteristics that are currently interpreted by the concomitant participation of several light emitters. Up to now, the coelenteramide luminophore is thought to exist in different protonation states, one of them engaged in an ion-pair with the nearby residue, His22. Using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, we demonstrate that such an ion-pair cannot exist as a stable light emitter. However, when His22 electric neutrality is maintained by means of another proton transfer, the phenolate state of coelenteramide exhibits emission properties in agreement with experiment. Finally, an alternative nonradiative decay pathway, involving the formation of a diradical excited state, is postulated for the first time.

  • 55. Chen, Shu-Feng
    et al.
    Navizet, Isabelle
    Roca-Sanjuán, Daniel
    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
    Ferre, Nicolas
    Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide: A Systematic Theoretical Study2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 8, p. 2796-2807Article in journal (Refereed)
    Abstract [en]

    A systematic investigation of the structural and spectroscopic properties of coelenteramide has been performed at the TD-CAM-B3LYP/6-31+G(d,p) level of theory, including various fluorescence and chemiluminescence states. The influence of geometric conformations, solvent polarity, protonation state, and the covalent character of the O-H bond of the hydroxyphenyl moiety were carefully studied. Striking differences in geometries and electronic structures among the states responsible for light emission were characterized. All fluorescence states can be described as a limited charge transfer process for a planar amide moiety. However, the chemiluminescence state is characterized by a much larger charge transfer that takes place over a longer distance. Moreover, the chemiluminescent coelenteramide structure exhibits an amide moiety that is no longer planar, in agreement with recent, more accurate ab initio results [Roca-Sanjuan et al J. Chem. Theory Comput. 2011, 7, 4060] Because the chemiluminescence state appears to be completely dark, a new mechanism is tentatively introduced for this process.

  • 56. 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.

  • 57. Daku, Latevi Max Lawson
    et al.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Robinson, Timothy W.
    Hauser, Andreas
    Accurate Spin-State Energetics of Transition Metal Complexes. 1. CCSD(T), CASPT2, and DFT Study of [M(NCH)(6)](2+) (M = Fe, Co)2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4216-4231Article in journal (Refereed)
    Abstract [en]

    Highly accurate estimates of the high-spin/low-spin energy, difference Delta E-HL(el) in the high-spin complexes [Fe(NCH)(6)](2+) and [Co(NCH)(6)](2+) have been obtained from the results of CCSD(T) calculations extrapolated to the complete basis set limit. These estimates are shown to be strongly influenced by scalar relativistic effects. They have been used to assess the performances of the CASPT2 method and 30 density functionals of the GGA, meta-GGA, global hybrid, RSH, and double-hybrid types. For the CASPT2 method, the results of the assessment support the proposal [Kepenekian, M.; Robert, V.; Le Guennic, B. J. Chem. Phys. 2009, 131, 114702] that the ionization potential-electron affinity (IPEA) shift defining the zeroth-order Hamiltonian be raised from its standard value of 0.25 au to 0.50-0.70 au for the determination of Delta E-HL(el) in Fe(II) complexes with a [FeN6] core. At the DFT level, some of the assessed functionals proved to perform within chemical accuracy (+/- 350 cm(-1)) for the spin-state energetics of [Fe(NCH)(6)](2+), others for that of [Co(NCH)(6)](2+), but none of them simultaneously for both complexes. As demonstrated through a reparametrization of the CAM-PBEO range-separated hybrid, which led to a functional that performs within chemical accuracy for the spin-state energetics of both complexes, performing density functionals of broad applicability may be devised by including in their training sets highly accurate data like those reported here for [Fe(NCH)(6)](2+) and [Co(NCH)(6)](2+).

  • 58.
    Delcey, Mickael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Aquilante, Francesco
    Pedersen, Thomas B.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical CD/RI-SA-CASSCF gradients: Implementation and performance2014In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 248Article in journal (Other academic)
  • 59.
    Delcey, Mickael G
    et al.
    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.
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Couto, Rafael Carvalho
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions2019In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, no 19, p. 1789-1799Article in journal (Refereed)
    Abstract [en]

    Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies.

  • 60.
    Delcey, Mickaël G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Extending the Reach of Accurate Wavefunction Methods2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Multiconfigurational quantum chemistry methods, and especially the multiconfigurational self-consistent field (MCSCF) and multireference perturbation theory (MRPT2), are powerful tools, particularly suited to the accurate modeling of photochemical processes and transition metal catalysis. However, they are limited by their high computational cost compared to other methods, especially density functional theory. Moreover, there are areas where they would be expected to perform well, but where they are not applied due to lack of experience.

    This thesis addresses those issues. First, the efficiency of the Cholesky decomposition approximation to reduce the cost of MCSCF and MRPT2 without sacrificing their accuracy is demonstrated. This then motivates the extension of the Cholesky approximation to the computation of MCSCF nuclear gradients, thus strongly improving the ability to perform MCSCF non-adiabatic molecular dynamics. Typically, a tenfold speed-up is observed allowing dynamic simulation of larger systems or over longer times.

    Finally, multiconfigurational methods are applied to the computation of X-ray spectra of transition metal complexes. The importance of the different parameters in the calculation is systematically investigated, laying the base for wider applications of those accurate methods in the modeling of X-ray spectroscopy. A tool to analyze the resulting spectrum in terms of molecular orbitals is also presented, strengthening the interplay between theory and experiments.

    With these developments and other significant ones that have happened in recent years, multiconfigurational methods can now reach new grounds and contribute to important new discoveries

    List of papers
    1. Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies
    Open this publication in new window or tab >>Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies
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    2010 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 3, p. 747-754Article in journal (Refereed) Published
    Abstract [en]

    The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.

    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-141205 (URN)10.1021/ct900612k (DOI)
    Available from: 2011-01-11 Created: 2011-01-11 Last updated: 2017-12-11Bibliographically approved
    2. Analytical gradients of complete active space self-consistent field energies using Cholesky decomposition: Geometry optimization and spin-state energetics of a ruthenium nitrosyl complex
    Open this publication in new window or tab >>Analytical gradients of complete active space self-consistent field energies using Cholesky decomposition: Geometry optimization and spin-state energetics of a ruthenium nitrosyl complex
    Show others...
    2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 17, p. 174103-Article in journal (Refereed) Published
    Abstract [en]

    We present a formulation of analytical energy gradients at the complete active space self-consistent field (CASSCF) level of theory employing density fitting (DF) techniques to enable efficient geometry optimizations of large systems. As an example, the ground and lowest triplet state geometries of a ruthenium nitrosyl complex are computed at the DF-CASSCF level of theory and compared with structures obtained from density functional theory (DFT) using the B3LYP, BP86, and M06L functionals. The average deviation of all bond lengths compared to the crystal structure is 0.042 angstrom at the DF-CASSCF level of theory, which is slightly larger but still comparable with the deviations obtained by the tested DFT functionals, e. g., 0.032 angstrom with M06L. Specifically, the root-mean-square deviation between the DF-CASSCF and best DFT coordinates, delivered by BP86, is only 0.08 angstrom for S-0 and 0.11 angstrom for T-1, indicating that the geometries are very similar. While keeping the mean energy gradient errors below 0.25%, the DF technique results in a 13-fold speedup compared to the conventional CASSCF geometry optimization algorithm. Additionally, we assess the singlet-triplet energy vertical and adiabatic differences with multiconfigurational second-order perturbation theory (CASPT2) using the DF-CASSCF and DFT optimized geometries. It is found that the vertical CASPT2 energies are relatively similar regardless of the geometry employed whereas the adiabatic singlet-triplet gaps are more sensitive to the chosen triplet geometry. (C) 2014 AIP Publishing LLC.

    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-227732 (URN)10.1063/1.4873349 (DOI)000336048000005 ()
    Available from: 2014-06-30 Created: 2014-06-30 Last updated: 2017-12-05Bibliographically approved
    3. Analytical gradients of the state-average complete active space self-consistent field method with density fitting
    Open this publication in new window or tab >>Analytical gradients of the state-average complete active space self-consistent field method with density fitting
    2015 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 4, article id 044110Article in journal (Refereed) Published
    Abstract [en]

    An efficient implementation of the state-averaged complete active space self-consistent field (SA-CASSCF) gradients employing density fitting (DF) is presented. The DF allows a reduction both in scaling and prefactors of the different steps involved. The performance of the algorithm is demonstrated on a set of molecules ranging up to an iron-Heme b complex which with its 79 atoms and 811 basis functions is to our knowledge the largest SA-CASSCF gradient computed. For smaller systems where the conventional code could still be used as a reference, both the linear response calculation and the gradient formation showed a clear timing reduction and the overall cost of a geometry optimization is typically reduced by more than one order of magnitude while the accuracy loss is negligible.

    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243572 (URN)10.1063/1.4927228 (DOI)000358929100016 ()26233110 (PubMedID)
    Funder
    Swedish Research CouncileSSENCE - An eScience Collaboration
    Available from: 2015-02-10 Created: 2015-02-10 Last updated: 2017-12-04Bibliographically approved
    4. Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states
    Open this publication in new window or tab >>Restricted active space calculations of L-edge X-ray absorption spectra: From molecular orbitals to multiplet states
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    2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 12, article id 124116Article in journal (Refereed) Published
    Abstract [en]

    The metal L-edge (2p -> 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe3+, high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)(6)](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-236075 (URN)10.1063/1.4896373 (DOI)000342844100021 ()25273421 (PubMedID)
    Note

    Correction in: Journal of Chemical Physics, vol. 141, issue 4, article number: 149905, DOI: 10.1063/1.4908043 ISI: 000349847000064

    Available from: 2014-11-12 Created: 2014-11-12 Last updated: 2017-12-05Bibliographically approved
    5. Cost and stability core restricted active space calculations of L-edge X-ray absorption spectra.
    Open this publication in new window or tab >>Cost and stability core restricted active space calculations of L-edge X-ray absorption spectra.
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243570 (URN)
    Available from: 2015-02-10 Created: 2015-02-10 Last updated: 2015-03-13
    6. Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method
    Open this publication in new window or tab >>Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method
    Show others...
    2016 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 4, p. 3250-3259Article in journal (Refereed) Published
    Abstract [en]

    The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.

    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Quantum Chemistry
    Identifiers
    urn:nbn:se:uu:diva-243571 (URN)10.1039/c5cp07487h (DOI)000369506000108 ()26742851 (PubMedID)
    Funder
    Marcus and Amalia Wallenberg FoundationSwedish Research CouncilCarl Tryggers foundation Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish National Infrastructure for Computing (SNIC), snic2013-1-317Swedish National Infrastructure for Computing (SNIC), snic2014-5-36
    Available from: 2015-02-10 Created: 2015-02-10 Last updated: 2018-08-13Bibliographically approved
  • 61.
    Delcey, Mickaël G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Freitag, Leon
    Pedersen, Thomas Bondo
    Aquilante, Francesco
    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.
    Gonzalez, Leticia
    Analytical gradients of complete active space self-consistent field energies using Cholesky decomposition: Geometry optimization and spin-state energetics of a ruthenium nitrosyl complex2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 17, p. 174103-Article in journal (Refereed)
    Abstract [en]

    We present a formulation of analytical energy gradients at the complete active space self-consistent field (CASSCF) level of theory employing density fitting (DF) techniques to enable efficient geometry optimizations of large systems. As an example, the ground and lowest triplet state geometries of a ruthenium nitrosyl complex are computed at the DF-CASSCF level of theory and compared with structures obtained from density functional theory (DFT) using the B3LYP, BP86, and M06L functionals. The average deviation of all bond lengths compared to the crystal structure is 0.042 angstrom at the DF-CASSCF level of theory, which is slightly larger but still comparable with the deviations obtained by the tested DFT functionals, e. g., 0.032 angstrom with M06L. Specifically, the root-mean-square deviation between the DF-CASSCF and best DFT coordinates, delivered by BP86, is only 0.08 angstrom for S-0 and 0.11 angstrom for T-1, indicating that the geometries are very similar. While keeping the mean energy gradient errors below 0.25%, the DF technique results in a 13-fold speedup compared to the conventional CASSCF geometry optimization algorithm. Additionally, we assess the singlet-triplet energy vertical and adiabatic differences with multiconfigurational second-order perturbation theory (CASPT2) using the DF-CASSCF and DFT optimized geometries. It is found that the vertical CASPT2 energies are relatively similar regardless of the geometry employed whereas the adiabatic singlet-triplet gaps are more sensitive to the chosen triplet geometry. (C) 2014 AIP Publishing LLC.

  • 62.
    Delcey, Mickaël G.
    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.
    Linguerri, R.
    Hochlaf, M.
    Francisco, J. S.
    Communication: Theoretical prediction of the structure and spectroscopic properties of the X∼ and A∼ states of hydroxymethyl peroxy (HOCH2OO) radical2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, no 2, p. 021105-Article in journal (Refereed)
    Abstract [en]

    The hydroxymethyl peroxy (HMOO) radical is a radical product from the oxidation of non-methane hydrocarbons. The present study provides theoretical prediction of critical spectroscopic features of this radical that should aid in its experimental characterization. Structure, rotational constants, and harmonic frequencies are presented for the ground and first excited electronic states of HMOO. The adiabatic transition energy for the A←X process is 7360 cm-1, suggesting that this transition, occurring in the mid to near infrared, is the most promising candidate for observing the radical spectroscopically. The band origin of the A←X transition of HMOO is calibrated and benchmarked with the corresponding state of the HOO radical, which is experimentally and theoretically well characterized.

  • 63.
    Delcey, Mickaël G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pedersen, Thomas Bondo
    University of Oslo.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Università di Bologna.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical gradients of the state-average complete active space self-consistent field method with density fitting2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 4, article id 044110Article in journal (Refereed)
    Abstract [en]

    An efficient implementation of the state-averaged complete active space self-consistent field (SA-CASSCF) gradients employing density fitting (DF) is presented. The DF allows a reduction both in scaling and prefactors of the different steps involved. The performance of the algorithm is demonstrated on a set of molecules ranging up to an iron-Heme b complex which with its 79 atoms and 811 basis functions is to our knowledge the largest SA-CASSCF gradient computed. For smaller systems where the conventional code could still be used as a reference, both the linear response calculation and the gradient formation showed a clear timing reduction and the overall cost of a geometry optimization is typically reduced by more than one order of magnitude while the accuracy loss is negligible.

  • 64.
    Delcey, Mickaël G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pierloot, Kristine
    Phung, Quan M.
    Vancoillie, Steven
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ryde, Ulf
    Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 17, p. 7927-7938Article in journal (Refereed)
    Abstract [en]

    We have studied the geometry and singlet-triplet energy difference of two mono-nuclear Ni2+ models related to the active site in [NiFe] hydrogenase. Multiconfigurational second-order perturbation theory based on a complete active-space wavefunction with an active space of 12 electrons in 12 orbitals, CASPT2(12,12), reproduces experimental bond lengths to within 1 pm. Calculated singlet-triplet energy differences agree with those obtained from coupled-cluster calculations with single, double and (perturbatively treated) triple excitations (CCSD(T)) to within 12 kJ mol(-1). For a bimetallic model of the active site of [NiFe] hydrogenase, the CASPT2(12,12) results were compared with the results obtained with an extended active space of 22 electrons in 22 orbitals. This is so large that we need to use restricted active-space theory (RASPT2). The calculations predict that the singlet state is 48-57 kJ mol(-1) more stable than the triplet state for this model of the Ni-Sl(a) state. However, in the [NiFe] hydrogenase protein, the structure around the Ni ion is far from the square-planar structure preferred by the singlet state. This destabilises the singlet state so that it is only similar to 24 kJ mol(-1) more stable than the triplet state. Finally, we have studied how various density functional theory methods compare to the experimental, CCSD(T), CASPT2, and RASPT2 results. Semi-local functionals predict the best singlet-triplet energy differences, with BP86, TPSS, and PBE giving mean unsigned errors of 12-13 kJ mol(-1) (maximum errors of 25-31 kJ mol(-1)) compared to CCSD(T). For bond lengths, several methods give good results, e. g. TPSS, BP86, and M06, with mean unsigned errors of 2 pm for the bond lengths if relativistic effects are considered.

  • 65. Dong, Hua
    et al.
    Chen, Bo-Zhen
    Huang, Ming-Bao
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theortical Chemistry.
    The bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 5, p. 537-549Article in journal (Refereed)
    Abstract [en]

    The Bergman cyclizations of the enediyne and its four N-substituted analogs [(Z)-pent-2-en-4-ynenitrile, 3-azahex-3-en-1,5-diyne, malenotrile, and 3,4-azahex-3-en-1,5-diyne] have been studied using the complete active space self-consistent field and multiconfigurational second-order perturbation theory methods in conjunction with the atomic natural orbital basis sets. The geometries and energies of the reactants, transition states, and products along both the S0 (the ground state) and T1 (the lowest-lying triplet state) potential energy surfaces (PESs) were calculated. The calculated geometries are in good agreement with the available experimental data. The distance between two terminal carbons in enediyne, which was considered as an important parameter governing the Bergman cyclization, was predicted to be 4.319 angstrom, in agreement with the experimental value of 4.321 angstrom. Our calculations indicate that the replacements of the terminal C atom(s) or the middle C atom(s) in the C-C bond by the N atom(s) increase or decrease the energy barrier values, respectively. There exist stable ring biradical products on the T1 PESs for the five reactions. However, on the S0 PESs the ring biradical products exist only for the reactions of enediyne, (Z)-pent-2-en-4-ynenitrile, and 3-azahex-3-en-1,5-diyne.

  • 66. Dunne, Lawrence J.
    et al.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Review of Off-Diagonal Long-Range Order and High-Temperature Superconductivity from Repulsive Electronic Correlations2013In: Advances in Quantum Chemistry / [ed] Sabin, JR; Brandas, EJ, Elsevier, 2013, p. 1-30Chapter in book (Refereed)
    Abstract [en]

    The question as to how off-diagonal long-range order (ODLRO) might arise from repulsive electron correlations in high-temperature superconductors is investigated. The review makes a fuller explanation of our recent work on this topic which is currently a central issue in the theory of high-temperature superconductivity. Particularly, we study the issue as to whether ODLRO can arise from repulsive electronic correlations. Pairs of electrons on Cuprate and the iron-based pnictide and chalcogenide alternant lattices may have a weak long-range attractive tail and much stronger short-range repulsive Coulomb interaction. The long-range attractive tail may find its origin in one of the many proposals for high-T-C superconductor and thus has an uncertain origin. Some possibilities arise from Friedel-type oscillations or polarization of the background but ultimately these must reflect the alternant nature of the lattice structure. Here, we make it plausible that such interacting electrons can cooperate to produce a superconducting state in which time-reversed pairs of electrons effectively avoid the repulsive part but dwell on average in the attractive region of the potential. The alternant lattice structure is thus central to the occurrence of most stable high-temperature superconductivity with d(x2-y2) or sign alternating s-wave or s +/- condensate symmetries.

  • 67.
    Dunne, Lawrence J.
    et al.
    Imperial College London.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Review of Off-Diagonal Long-Range Order and High-Temperature Superconductivity from Repulsive Electronic Correlations2013In: Advances in Quantum Chemistry, ISSN 0065-3276, E-ISSN 2162-8815, Vol. 66, p. 1-30Article in journal (Refereed)
    Abstract [en]

    The question as to how off-diagonal long-range order (ODLRO) might arise from repulsive electron correlations in high-temperature superconductors is investigated. The review makes a fuller explanation of our recent work on this topic which is currently a central issue in the theory of high-temperature superconductivity. Particularly, we study the issue as to whether ODLRO can arise from repulsive electronic correlations. Pairs of electrons on Cuprate and the iron-based pnictide and chalcogenide alternant lattices may have a weak long-range attractive tail and much stronger short-range repulsive Coulomb interaction. The long-range attractive tail may find its origin in one of the many proposals for high-Tc superconductor and thus has an uncertain origin. Some possibilities arise from Friedel-type oscillations or polarization of the background but ultimately these must reflect the alternant nature of the lattice structure. Here, we make it plausible that such interacting electrons can cooperate to produce a superconducting state in which time-reversed pairs of electrons effectively avoid the repulsive part but dwell on average in the attractive region of the potential. The alternant lattice structure is thus central to the occurrence of most stable high-temperature superconductivity with dx2-y2 or sign alternating s-wave or s± condensate symmetries.

  • 68.
    Dunne, Lawrence J.
    et al.
    Imperial College London.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Superconductivity from Repulsive Electronic Correlations on Alternant Cuprate and Iron-Based Lattices2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 17, p. 2053-2059Article in journal (Refereed)
    Abstract [en]

    A key question in the theory of high-temperature superconductivityis whether off-diagonal long-range order can beinduced wholly or in large part by repulsive electronic correlations. Electron pairs on cuprate and the iron-based pnictide and chalcogenide alternant lattices may interact with a strong shortrange Coulomb repulsion and much weaker longer range attractive tail. Here, we show that such interacting electrons can cooperate to produce a superconducting state in which time reversed electron pairs effectively avoid the repulsive part but reside predominantly in the attractive region of the potential. The alternant lattice structure is a key feature of such a stabilization mechanism leading to the occurrence of high-temperature superconductivity with dx2y2 or sign alternating s-wave or s-condensate symmetries

  • 69. Dunne, Lawrence J.
    et al.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Superconductivity from repulsive electronic correlations on alternant cuprate and iron-based lattices2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 17, p. 2053-2059Article in journal (Refereed)
    Abstract [en]

    A key question in the theory of high-temperature superconductivity is whether off-diagonal long-range order can be induced wholly or in large part by repulsive electronic correlations. Electron pairs on cuprate and the iron-based pnictide and chalcogenide alternant lattices may interact with a strong short-range Coulomb repulsion and much weaker longer range attractive tail. Here, we show that such interacting electrons can cooperate to produce a superconducting state in which time-reversed electron pairs effectively avoid the repulsive part but reside predominantly in the attractive region of the potential. The alternant lattice structure is a key feature of such a stabilization mechanism leading to the occurrence of high-temperature superconductivity with d(x2-y2) or sign alternating s-wave or s +/- condensate symmetries. 

  • 70.
    Dunne, Lawrence J.
    et al.
    London South Bank University, UK.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Cox, Hazel
    University of Sussex, UK.
    High Temperature Superconductivity in Strongly Correlated Electronic Systems2017In: Advances in Quantum Chemistry: Löwdin Volume / [ed] John R. Sabin, Erkki J. Brändas, Elsevier, 2017, Vol. 74, p. 183-208Chapter in book (Refereed)
    Abstract [en]

    In this chapter we give a selective review of our work on the role of electron correlation in the theory of high-temperature superconductivity (HTSC). The question of how electronic repulsions might give rise to off-diagonal long-range order (ODLRO) in high-temperature superconductors is currently one of the key questions in the theory of condensed matter. This chapter argues that the key to understanding the occurrence of HTSC in cuprates is to be found in the Bohm-Pines Hamiltonian, modified to include a polarizable dielectric background. The approach uses reduced electronic density matrices and discusses how these can be used to understand whether ODLRO giving rise to superconductivity might arise from a Bohm-Pines-type potential which is comprised of a weak long-range attractive tail and a much stronger short-range repulsive Coulomb interaction. This allows time-reversed electron pairs to undergo a superconducting condensation on alternant cuprate lattices. Thus, a detailed summary is given of the arguments that such interacting electrons can cooperate to produce a superconducting state in which time-reversed pairs of electrons effectively avoid the repulsive hard-core of the interelectronic Coulomb interaction but reside on average in the attractive well of the effective potential. In a superconductor the plasma wave function becomes the longitudinal component of a massive photon by the Anderson-Higgs mechanism. The alternant cuprate lattice structure is the key to achieving HTSC in cuprates with d(x2) - (y2) symmetry condensate symmetry.

  • 71.
    Ericsson, Marie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Comment on `Detecting non-Abelian geometric phases with three-level Λ systems'2013In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 87, no 3, p. 036101-Article in journal (Refereed)
    Abstract [en]

    In their recent paper, Yan-Xiong Du {\it et al.} [Phys. Rev. A {\bf 84}, 034103 (2011)] claim to have found a non-Abelian adiabatic geometric phase associated with the energy eigenstates of a large-detuned $\Lambda$ three-level system. They further propose a test to detect the non-commutative feature of this geometric phase. On the contrary, we show that the non-Abelian geometric phase picked up by the energy eigenstates of a $\Lambda$ system is trivial in the adiabatic approximation, while, in the exact treatment of the time evolution, this phase is very small and cannot be separated from the non-Abelian dynamical phase acquired along the path in parameter space.

  • 72.
    Esmieu, Charlene
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. CNRS, LCC, 205 Route Narbonne,BP 44099, F-31077 Toulouse 4, France.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Redman, Holly J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Berggren, Gustav
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Synthesis of a miniaturized [FeFe] hydrogenase model system2019In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 48, no 7, p. 2280-2284Article in journal (Refereed)
    Abstract [en]

    The reaction occurring during artificial maturation of [FeFe] hydrogenase has been recreated using molecular systems. The formation of a miniaturized [FeFe] hydrogenase model system, generated through the combination of a [4Fe4S] cluster binding oligopeptide and an organometallic Fe complex, has been monitored by a range of spectroscopic techniques. A structure of the final assembly is suggested based on EPR and FTIR spectroscopy in combination with DFT calculations. The capacity of this novel H-cluster model to catalyze H-2 production in aqueous media at mild potentials is verified in chemical assays.

  • 73.
    Farahani, Pooria
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Theoretical Studies of Seemingly Simple Chemical Reactions2013Licentiate thesis, comprehensive summary (Other academic)
    List of papers
    1. Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals
    Open this publication in new window or tab >>Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals
    2015 (English)In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, no 1, p. 181-190Article in journal (Refereed) Published
    Abstract [en]

    One route to break down halomethanes is through reactions with radical species. The capability of the artificial force-induced reaction algorithm to efficiently explore a large number of radical reaction pathways has been illustrated for reactions between haloalkanes (CX3Y; X=H, F; Y=Cl, Br) and ground-state (2Σ+) cyano radicals (CN). For CH3Cl+CN, 71 stationary points in eight different pathways have been located and, in agreement with experiment, the highest rate constant (108 s−1 M−1 at 298 K) is obtained for hydrogen abstraction. For CH3Br, the rate constants for hydrogen and halogen abstraction are similar (109 s−1 M−1), whereas replacing hydrogen with fluorine eliminates the hydrogen-abstraction route and decreases the rate constants for halogen abstraction by 2–3 orders of magnitude. The detailed mapping of stationary points allows accurate calculations of product distributions, and the encouraging rate constants should motivate future studies with other radicals.

    Keywords
    gas-phase reactions; quantum chemistry; radical reactions; reaction mechanisms; transition states
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-228448 (URN)10.1002/cphc.201402601 (DOI)000347239200018 ()25263486 (PubMedID)
    Funder
    Marcus and Amalia Wallenberg FoundationSwedish Research CouncilSwedish National Infrastructure for Computing (SNIC), p2011004
    Available from: 2014-07-15 Created: 2014-07-15 Last updated: 2017-12-05Bibliographically approved
    2. Ab initio quantum mechanical calculation of the reaction probability for the Cl- + PH2Cl -> ClPH2 + Cl- reaction
    Open this publication in new window or tab >>Ab initio quantum mechanical calculation of the reaction probability for the Cl- + PH2Cl -> ClPH2 + Cl- reaction
    2013 (English)In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 134-140Article in journal (Refereed) Published
    Abstract [en]

    The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2ClClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

    Place, publisher, year, edition, pages
    Amsterdam: Elsevier, 2013
    Keywords
    Nucleophilic substitution (S(N)2); Reaction probability; Quantum dynamics
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-210368 (URN)10.1016/j.chemphys.2013.08.011 (DOI)000327443700016 ()
    Funder
    Marcus and Amalia Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC), p2011004
    Available from: 2013-11-06 Created: 2013-11-06 Last updated: 2017-12-06Bibliographically approved
  • 74.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lundberg, Marcus
    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.
    Ab initio quantum mechanical calculation of the reaction probability for the Cl- + PH2Cl -> ClPH2 + Cl- reaction2013In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 134-140Article in journal (Refereed)
    Abstract [en]

    The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2ClClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

  • 75.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    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, ES-46071 Valencia, Spain.
    Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 28, p. 18653-18664Article in journal (Refereed)
    Abstract [en]

    Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference multiconfigurational quantum chemistry methods and accurate reaction-path computational strategies were used to determine the reaction coordinate of three successive processes: decomposition of the dioxetane moiety, non-adiabatic energy transfer from the ground to the excited state, and finally non-radiative decay of the 1,3-butadiene group. With the present study, we open a new area of research within computational photochemistry to study chemically-induced excited-state chemistry that is difficult to tackle experimentally due to the short-lived character of the species involved in the process. The findings shall be of relevance to unveil "dark'' photochemistry mechanisms, which might operate in biological systems under conditions of lack of light. These mechanisms might allow reactions that are typical of photo-induced phenomena.

  • 76.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Maeda, Satoshi
    Hokkaido Univ, Dept Chem, Fac Sci, Kita Ku, Sapporo, Hokkaido 0600810, Japan.
    Fancisco, Joseph S.
    Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals2015In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, no 1, p. 181-190Article in journal (Refereed)
    Abstract [en]

    One route to break down halomethanes is through reactions with radical species. The capability of the artificial force-induced reaction algorithm to efficiently explore a large number of radical reaction pathways has been illustrated for reactions between haloalkanes (CX3Y; X=H, F; Y=Cl, Br) and ground-state (2Σ+) cyano radicals (CN). For CH3Cl+CN, 71 stationary points in eight different pathways have been located and, in agreement with experiment, the highest rate constant (108 s−1 M−1 at 298 K) is obtained for hydrogen abstraction. For CH3Br, the rate constants for hydrogen and halogen abstraction are similar (109 s−1 M−1), whereas replacing hydrogen with fluorine eliminates the hydrogen-abstraction route and decreases the rate constants for halogen abstraction by 2–3 orders of magnitude. The detailed mapping of stationary points allows accurate calculations of product distributions, and the encouraging rate constants should motivate future studies with other radicals.

  • 77.
    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.

  • 78.
    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.

  • 79.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuán, Daniel
    Universitat de València, Spain.
    Aquilante, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Università di Bologna, Italy.
    A Two-Scale Approach to Electron Correlation in Multiconfigurational Perturbation Theory2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 22, p. 1609-1617Article, review/survey (Refereed)
    Abstract [en]

    We present a new approach for the calculation of dynamicelectron correlation effects in large molecular systems usingmulticonfigurational second-order perturbation theory(CASPT2). The method is restricted to cases where partitioningof the molecular system into an active site and an environment is meaningful. Only dynamic correlation effects derivedfrom orbitals extending over the active site are included at theCASPT2 level of theory, whereas the correlation effects of theenvironment are retrieved at lower computational costs. Forsufficiently large systems, the small errors introduced by thisapproximation are contrasted by the substantial savings inboth storage and computational demands compared to thefull CASPT2 calculation. Provided that static correlation effectsare correctly taken into account for the whole system, the proposed scheme represent a hierarchical approach to the electron correlation problem, where two molecular scales aretreated each by means of the most suitable level of theory.

  • 80.
    Fernández Galván, Ignacio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Delcey, Mickael G.
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 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, POB 1033 Blindern, N-0315 Oslo, Norway..
    Aquilante, Francesco
    Univ Bologna, Dipartimento Chim G Ciamician, Via F Selmi 2, IT-40126 Bologna, Italy..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Analytical State-Average Complete-Active-Space Self-Consistent Field Nonadiabatic Coupling Vectors: Implementation with Density-Fitted Two-Electron Integrals and Application to Conical Intersections2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 8, p. 3636-3653Article in journal (Refereed)
    Abstract [en]

    Analytical state-average complete-active-space self-consistent field derivative (nonadiabatic) coupling vectors are implemented. Existing formulations are modified such that the implementation is compatible with Cholesky-based density fitting of two-electron integrals, which results in efficient calculations especially with large basis sets. Using analytical nonadiabatic coupling vectors, the optimization of conical intersections is implemented within the projected constrained optimization method. The standard description and characterization of conical intersections is reviewed and clarified, and a practical and unambiguous system for their classification and interpretation is put forward. These new tools are subsequently tested and benchmarked for 19 different conical intersections. The accuracy of the derivative coupling vectors is validated, and the information that can be drawn from the proposed characterization is discussed, demonstrating its usefulness.

  • 81.
    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.

  • 82.
    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)
  • 83.
    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.

  • 84.
    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.

  • 85. Fernández García-Prieto, F.
    et al.