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  • 201.
    da Cruz, Vinicius Vaz
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Lab Nonlinear Opt & Spect, Krasnoyarsk 660041, Russia.
    Eckert, Sebastian
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Iannuzzi, Marcella
    Univ Zurich, Phys Chem Inst, CH-8057 Zurich, Switzerland..
    Ertan, Emelie
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Niskanen, Johannes
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany.;Univ Turku, Dept Phys & Astron, FI-20014 Turunyliopisto, Finland..
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Dantz, Marcus
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Schmitt, Thorsten
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Lu, Xingye
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    McNally, Daniel
    Paul Scherrer Inst, Photon Sci Div, CH-5232 Villigen, Switzerland..
    Jay, Raphael M.
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany..
    Kimberg, Victor
    Foehlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Odelius, Michael
    Stockholm Univ, Dept Phys, AlbaNova Univ Ctr, S-10691 Stockholm, Sweden..
    Probing hydrogen bond strength in liquid water by resonant inelastic X-ray scattering2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 1013Article in journal (Refereed)
    Abstract [en]

    Local probes of the electronic ground state are essential for understanding hydrogen bonding in aqueous environments. When tuned to the dissociative core-excited state at the O1s pre-edge of water, resonant inelastic X-ray scattering back to the electronic ground state exhibits a long vibrational progression due to ultrafast nuclear dynamics. We show how the coherent evolution of the OH bonds around the core-excited oxygen provides access to high vibrational levels in liquid water. The OH bonds stretch into the long-range part of the potential energy curve, which makes the X-ray probe more sensitive than infra-red spectroscopy to the local environment. We exploit this property to effectively probe hydrogen bond strength via the distribution of intramolecular OH potentials derived from measurements. In contrast, the dynamical splitting in the spectral feature of the lowest valence-excited state arises from the short-range part of the OH potential curve and is rather insensitive to hydrogen bonding.

  • 202.
    Dahlstrand, Christian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Jahn, Burkhard
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Grigoriev, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Villaume, Sebastien
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Physical Organic Chemistry.
    Tuning the Band Gap of Polyfulvenes by Use of “Handles”: On the Effects of Exocyclic Substitution, Benzannulation, and Ring Methylation.Manuscript (preprint) (Other academic)
  • 203.
    Dannetun, Per
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Lögdlund, Michael
    Université de Mons-Hainaut, Belgium.
    Spangler, C. W.
    Northen Illinois University, USA.
    Bredas, J. L.
    Université de Mons-Hainaut, Belgium.
    Salaneck, William R.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. william.r.salaneck@liu.se.
    Evolution of Charge-Induced Gap States in Short Diphenylpolyenes as Studied by Photoelectron Spectroscopy1994In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, The Journal of Physical Chemistry, Vol. 98, no 11, p. 2853-2858Article in journal (Refereed)
    Abstract [en]

    The evolution of doping-induced electronic states within the otherwise forbidden energy gap has been studied as a function of the polyene length in a series of diphenylpolyenes. The chemical and electronic structures ha ve been studied using both X-ray and ultraviolet photoelectron spectroscopies. The results are interpreted with the help of quantum chemical calculations, performed using the semiempirical Austin Model 1 and valence effective Hamiltonian methods. The molecules studied area series of diphenylpolyenes, DPx, with x = 1-7 C=C double bonds in the pol yene part of the molecule. Since the frontier or bitals of the diphenylpolyenes are localized on the polyene chain portion of the molecule, there is a high degree of separation of the phenyl and polyene parts of the 11"-systems. Hence, many chemical and electronic properties of diphenylpolyenes are expected to be similar to those of short-chain trans-polyacetylene. For the longer molecules, n = 6 or 7, the present results indicate the presence of doubly charged, interacting soliton-antisoliton pairs, which appear as two new energy levels in the otherwise forbidden energy gap. In diphenyldecaheptaene to stilbene, i.e. 1 ≤ x ≤ 5, however, a singly charged state is formed at intermediate doping levels, after which the soliton-antisoliton pairs appear for the fully doubly charged systems. These results show that, remarkably, even for very short polyene  segments, charges transferred are stored in the form of ( confined) solitons.

  • 204. Das, Susanta
    et al.
    Nam, Kwangho
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, University of Texas at Arlington, United States.
    Major, Dan Thomas
    Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA2018In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 3, p. 1695-1705Article in journal (Refereed)
    Abstract [en]

    In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. +/- 1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

  • 205.
    Das, Tisita
    et al.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    Chakraborty, Sudip
    Uppsala Univ, Condensed Matter Theory Grp, Dept Phys & Astron, Box 516, S-75120 Uppsala, Sweden..
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Das, Gour P.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    TiS2 Monolayer as an Emerging Ultrathin Bifunctional Catalyst: Influence of Defects and Functionalization2019In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 20, no 4, p. 608-617Article in journal (Refereed)
    Abstract [en]

    We have envisaged the hydrogen evolution and oxygen evolution reactions (HER and OER) on a two-dimensional (2D) noble-metal-free titanium disulfide (TiS2) monolayer, which belongs to the exciting family of transition metal dichalcogenides (TMDCs). Our theoretical investigation to probe the HER and OER on both the H and T phases of 2D TiS2 is based on electronic-structure calculations witihin the framework of density functional theory (DFT). Since TiS2 is the lightest compound among the group-IV TMDCs, it is worth exploring the catalytic activity of a TiS2 monolayer through the functionalization at the anion (S) site, substituting with P, N, and C dopants as well as by incorporating single sulfur vacancy defects. We have investigated the effect of functionalization and vacancy defects on the structural, electronic, and optical response of a TiS2 monolayer by determining the density of states, work-function, and optical absorption spectra. We have determined the HER and OER activities for the functionalized and defective TiS2 monolayers based on the reaction coordinate, which can be constructed from the adsorption free energies of the intermediates (H*, O*, OH* and OOH*, where * denotes the adosrbed state) in the HER and OER mechanisms. Finally, we have shown that TiS2 monolayers are emerging as a promising material for the HER and OER mechanisms under the influence of functionalization and defects.

  • 206.
    Das, Tisita
    et al.
    Indian Assoc Cultivat Sci, Dept Mat Sci, India.
    Chakraborty, Sudip
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Royal Inst Technol KTH, Dept Mat & Engn, Appl Mat Phys, Stockholm, Sweden.
    Das, Gour P.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata, India.
    TiS2 Monolayer as an Emerging Ultrathin Bifunctional Catalyst: Influence of Defects and Functionalization2019In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 20, no 4, p. 608-617Article in journal (Refereed)
    Abstract [en]

    We have envisaged the hydrogen evolution and oxygen evolution reactions (HER and OER) on a two‐dimensional (2D) noble‐metal‐free titanium disulfide (TiS2) monolayer, which belongs to the exciting family of transition metal dichalcogenides (TMDCs). Our theoretical investigation to probe the HER and OER on both the H and T phases of 2D TiS2 is based on electronic‐structure calculations witihin the framework of density functional theory (DFT). Since TiS2 is the lightest compound among the group‐IV TMDCs, it is worth exploring the catalytic activity of a TiS2 monolayer through the functionalization at the anion (S) site, substituting with P, N, and C dopants as well as by incorporating single sulfur vacancy defects. We have investigated the effect of functionalization and vacancy defects on the structural, electronic, and optical response of a TiS2 monolayer by determining the density of states, work‐function, and optical absorption spectra. We have determined the HER and OER activities for the functionalized and defective TiS2 monolayers based on the reaction coordinate, which can be constructed from the adsorption free energies of the intermediates (H*, O*, OH* and OOH*, where * denotes the adosrbed state) in the HER and OER mechanisms. Finally, we have shown that TiS2 monolayers are emerging as a promising material for the HER and OER mechanisms under the influence of functionalization and defects.

  • 207. De Backer, A.
    et al.
    Sand, A.
    Ortiz, C. J.
    Domain, C.
    Olsson, Pär
    KTH, School of Engineering Sciences (SCI), Physics, Reactor Physics.
    Berthod, E.
    Becquart, C. S.
    Primary damage in tungsten using the binary collision approximation, molecular dynamic simulations and the density functional theory2016In: Physica Scripta, ISSN 0031-8949, E-ISSN 1402-4896, Vol. T167, article id 014018Article in journal (Refereed)
    Abstract [en]

    The damage produced by primary knock-on atoms (PKA) in W has been investigated from the threshold displacement energy (TDE) where it produces one self interstitial atom-vacancy pair to larger energies, up to 100 keV, where a large molten volume is formed. The TDE has been determined in different crystal directions using the Born-Oppenheimer density functional molecular dynamics (DFT-MD). A significant difference has been observed without and with the semi-core electrons. Classical MD has been used with two different empirical potentials characterized as 'soft' and 'hard' to obtain statistics on TDEs. Cascades of larger energy have been calculated, with these potentials, using a model that accounts for electronic losses (Sand et al 2013 Europhys. Lett. 103 46003). Two other sets of cascades have been produced using the binary collision approximation (BCA): a Monte Carlo BCA using SDTrimSP (Eckstein et al 2011 SDTrimSP: Version 5.00. Report IPP 12/8) (similar to SRIM www.srim.org) and MARLOWE (RSICC Home Page. (https://rsicc.ornl.gov/codes/psr/psr1/psr-137.html) (accessed May, 2014)). The comparison of these sets of cascades gave a recombination distance equal to 12 angstrom which is significantly larger from the one we reported in Hou et al (2010 J. Nucl. Mater. 403 89) because, here, we used bulk cascades rather than surface cascades which produce more defects (Stoller 2002 J. Nucl. Mater. 307 935, Nordlund et al 1999 Nature 398 49). Investigations on the defect clustering aspect showed that the difference between BCA and MD cascades is considerably reduced after the annealing of the cascade debris at 473 K using our Object Kinetic Monte Carlo model, LAKIMOCA.

  • 208. Deiana, Luca
    et al.
    Zhao, Gui-Ling
    Lin, Shuangzheng
    Dziedzic, Pawel
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Leijonmarck, Hans
    Cordova, Armando
    Organocatalytic Enantioselective Aziridination of alpha-Substituted alpha,beta-Unsaturated Aldehydes: Asymmetric Synthesis of Terminal Aziridines2010In: Advanced Synthesis and Catalysis, ISSN 1615-4150, E-ISSN 1615-4169, Vol. 352, no 18, p. 3201-3207Article in journal (Refereed)
    Abstract [en]

    The first example of a highly enantioselective organocatalytic aziridination of alpha-substituted alpha,beta-unsaturated aldehydes is presented. The reaction is catalyzed by simple chiral amines and gives access to highly functional terminal azirdines containing an alpha-tertiary amine stereocenter in high yields and enantiomeric ratios (95.5:4.5-98:2).

  • 209.
    Delange, Pascal
    et al.
    University of Paris Saclay, France.
    Ayral, Thomas
    CEA, France.
    Simak, Sergey
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Ferrero, Michel
    University of Paris Saclay, France; Coll France, France.
    Parcollet, Olivier
    CEA, France.
    Biermann, Silke
    University of Paris Saclay, France; Coll France, France.
    Pourovskii, Leonid
    University of Paris Saclay, France; Coll France, France; National University of Science and Technology MISIS, Russia.
    Large effects of subtle electronic correlations on the energetics of vacancies in alpha-Fe2016In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 94, no 10, p. 100102-Article in journal (Refereed)
    Abstract [en]

    We study the effect of electronic Coulomb correlations on the vacancy formation energy in paramagnetic alpha-Fe within ab initio dynamical mean-field theory. The calculated value for the formation energy is substantially lower than in standard density-functional calculations and in excellent agreement with experiment. The reduction is caused by an enhancement of electronic correlations at the nearest neighbors of the vacancy. This effect is explained by subtle changes in the corresponding spectral function of the d electrons. The local lattice relaxations around the vacancy are substantially increased by many-body effects.

  • 210.
    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.

  • 211.
    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

  • 212.
    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.

  • 213.
    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.

  • 214.
    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.

  • 215. Di Meo, F.
    et al.
    Pedersen, M. N.
    Rubio-Magnieto, J.
    Surin, M.
    Linares, M.
    Norman, P.
    DNA electronic circular dichroism on the inter-base pair scale: An experimental-theoretical case study of the at homo-oligonucleotide2015In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 6, no 3, p. 355-359Article in journal (Refereed)
    Abstract [en]

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. (Chemical Equation Presented). © 2015 American Chemical Society.

  • 216. Diller, Katharina
    et al.
    Ma, Yong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Allegretti, Francesco
    Liu, Jianzhao
    Tang, Ben Zhong
    Lin, Nian
    Barth, Johannes V.
    Klappenberger, Florian
    Polyphenylsilole multilayers - an insight from X-ray electron spectroscopy and density functional theory2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 46, p. 31117-31124Article in journal (Refereed)
    Abstract [en]

    We present a combined investigation by means of X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy of condensed multilayers of two polyphenylsiloles, namely hexaphenylsilole (HPS) and tetraphenylsilole (TPS). Both compounds exhibit very similar spectroscopic signatures, whose interpretation is aided by density functional theory (DFT) calculations. High-resolution XPS spectra of the Si 2p and C 1s core levels of these multilayers indicate a positively charged silicon ion flanked by two negatively charged adjacent carbon atoms in the silole core of both molecules. This result is corroborated quantitatively by DFT calculations on isolated HPS (TPS) molecules, which show a natural bond orbital partial charge of + 1.67 e (+1.58 e) on the silicon and -0.34 e (-0.58 e) on the two neighbouring carbon atoms in the silole ring. These charges are conserved in direct contact with a Cu(111) substrate for films of submonolayer coverage, as evidenced by the Si 2p XPS data. The C K-edge NEXAFS spectra of HPS and TPS multilayers exhibit distinct and differing features. Their main characteristics reappear in the simulated spectra and are assigned to the different inequivalent carbon species in the molecule. The angle-dependent measurements hardly reveal any dichroism, i.e., the molecular p-systems are not uniformly oriented parallel or perpendicular with respect to the surface. Changes in the growth conditions of TPS, i.e., a reduction of the substrate temperature from 240 K to 80 K during deposition, lead to a broadening of both XPS and NEXAFS signatures, as well as an upward shift of the Si 2p and C 1s binding energies, indicative of a less ordered growth mode at low temperature.

  • 217. Ding, Yubin
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hill, Jonathan P.
    Ariga, Katsuhiko
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Andreasson, Joakim
    Zhu, Weihong
    Tian, He
    Xie, Yongshu
    Acid/Base Switching of the Tautomerism and Conformation of a Dioxoporphyrin for Integrated Binary Subtraction2014In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, no 40, p. 12910-12916Article in journal (Refereed)
    Abstract [en]

    Compared with most of the reported logic devices based on the supramolecular approach, systems based on individual molecules can avoid challenging construction requirements. Herein, a novel dioxoporphyrin DPH22 was synthesized and two of its tautomers were characterized by single-crystal X-ray diffraction studies. Compound DPH22 exhibits multichannel controllable stepwise tautomerization, protonation, and deprotonation processes through interactions with H and F- ions. By using the addition of H+ and F- ions as inputs and UVNis absorption values at.1=412, 510, 562, and 603 nm as outputs, the controlled tautomerism of DPH22 has been successfully used for the construction of an integrated molecular level half-subtractor and comparator. In addition, this acid/base-switched tautomerism is reversible, thus endowing the system with ease of reset and recycling; consequently, there is no need to modulate complicated intermolecular interactions and electron-/chargetransfer processes.

  • 218.
    Dinér, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Superacid-Promoted Ionization of Alkanes Without Carbonium Ion Formation: A Density Functional Theory Study2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 40, p. 9979-9984Article in journal (Refereed)
    Abstract [en]

    The carbonium ion has been suggested to be the intermediate in superacid-promoted reactions (SbF5-HF) such as hydrogen-deuterium exchange and in the electrophilic C-H cleavage into hydrogen and the carbenium ion. In this study, the superacid-promoted C-H cleavage into hydrogen and the carbenium ion was studied using density functional theory (B3LYP and M062X) and ab initio methods (MP2 and CCSD). The calculations suggest that the superacid-promoted C-H cleavage proceeds via a concerted transition state leading to hydrogen (H-2) and the carbenium ion without the formation of the elusive carbonium ion. The reactivity for the superacid promoted C-H cleavage decreases upon going from isobutane (tertiary) > propane (secondary) > isobutane (primary) > propane (primary) > ethane >> methane.

  • 219.
    dos Santos, R. B.
    et al.
    University of Federal Bahia, Brazil.
    Rivelino, R.
    University of Federal Bahia, Brazil.
    de Brito Mota, F.
    University of Federal Bahia, Brazil.
    Kostov Gueorguiev, Gueorgui
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Kakanakova-Gueorguie, Anelia
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Dopant species with Al-Si and N-Si bonding in the MOCVD of AlN implementing trimethylaluminum, ammonia and silane2015In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 48, no 29, article id 295104Article in journal (Refereed)
    Abstract [en]

    We have investigated gas-phase reactions driven by silane (SiH4), which is the dopant precursor in the metalorganic chemical vapor deposition (MOCVD) of aluminum nitride (AlN) doped by silicon, with prime focus on determination of the associated energy barriers. Our theoretical strategy is based on combining density-functional methods with minimum energy path calculations. The outcome of these calculations is suggestive for kinetically plausible and chemically stable reaction species with Al-Si bonding such as (CH3)(2)AlSiH3 and N-Si bonding such as H2NSiH3. Within this theoretical perspective, we propose a view of these reaction species as relevant for the actual MOCVD of Si-doped AlN, which is otherwise known to be contributed by the reaction species (CH3)(2)AlNH2 with Al-N bonding. By reflecting on experimental evidence in the MOCVD of various doped semiconductor materials, it is anticipated that the availability of dopant species with Al-Si, and alternatively N-Si bonding near the hot deposition surface, can govern the incorporation of Si atoms, as well as other point defects, at the AlN surface.

  • 220.
    dos Santos, Renato B.
    et al.
    University of Federal Bahia, Brazil.
    Rivelino, R.
    University of Federal Bahia, Brazil.
    de Brito Mota, F.
    University of Federal Bahia, Brazil.
    Kakanakova-Gueorguie, Anelia
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, The Institute of Technology.
    Gueorguiev, Gueorgui Kostov
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Feasibility of novel (H3C)(n)X(SiH3)(3-n) compounds (X = B, Al, Ga, In): structure, stability, reactivity, and Raman characterization from ab initio calculations2015In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 44, no 7, p. 3356-3366Article in journal (Refereed)
    Abstract [en]

    We employ ab initio calculations to predict the equilibrium structure, stability, reactivity, and Raman scattering properties of sixteen different (H3C)(n)X(SiH3)(3-n) compounds (X = B, Al, Ga, In) with n = 0-3. Among this methylsilylmetal family, only the (H3C)(3)X members, i.e., trimethylboron (TMB), trimethylaluminum (TMA), trimethylgallium (TMG), and trimethylindium (TMI), are currently well-studied. The remaining twelve compounds proposed here open up a two-dimensional array of new possibilities for precursors in various deposition processes, and evoke potential applications in the chemical synthesis of other compounds. We infer that within the (H3C)(n)X(SiH3)(3-n) family, the compounds with fewer silyl groups (and consequently with more methyl groups) are less reactive and more stable. This trend is verified from the calculated cohesive energy, Gibbs free energy of formation, bond strength, and global chemical indices. Furthermore, we propose sequential reaction routes for the synthesis of (H3C)(n)X(SiH3)(3-n) by substitution of methyl by silyl groups, where the silicon source is the silane gas. The corresponding reaction barriers for these chemical transformations lie in the usual energy range typical for MOCVD processes. We also report the Raman spectra and light scattering properties of the newly proposed (H3C)(n)X(SiH3)(3-n) compounds, in comparison with available data of known members of this family. Thus, our computational experiment provides useful information for a systematic understanding of the stability/reactivity and for the identification of these compounds.

  • 221.
    Doverstål, Mats
    Stockholm University, Faculty of Science.
    Experimental studies of dimers and clusters1994Doctoral thesis, comprehensive summary (Other academic)
  • 222.
    Dreos, Ambra
    et al.
    Chalmers Univ Technol, Gothenburg, Sweden.
    Jorner, Kjell
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Borjesson, Karl
    Gothenburg Univ, Gothenburg, Sweden.
    Wang, Zhihang
    Chalmers Univ Technol, Gothenburg, Sweden.
    Ottosson, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Uppsala Univ, Uppsala, Sweden.
    Moth-Poulsen, Kasper
    Chalmers Univ Technol, Gothenburg, Sweden.
    Norbornadiene-quadricyclane photochromic systems for solar energy storage applications and testing in devices2018In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 255Article in journal (Other academic)
  • 223.
    Dsouza, Raison
    et al.
    Max Planck Inst Struct and Dynam Matter, Germany.
    Cheng, Xinxin
    Max Planck Inst Struct and Dynam Matter, Germany; Univ Hamburg, Germany.
    Li, Zheng
    Max Planck Inst Struct and Dynam Matter, Germany.
    Miller, R. J. Dwayne
    Max Planck Inst Struct and Dynam Matter, Germany; Univ Hamburg, Germany; Univ Toronto, Canada.
    Kochman, Michal
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Oscillatory Photoelectron Signal of N-Methylmorpholine as a Test Case for the Algebraic-Diagrammatic Construction Method of Second Order2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 50, p. 9688-9700Article in journal (Refereed)
    Abstract [en]

    Motivated by recent progress in the application of time-resolved photoelectron spectroscopy (TRPES) to molecular Rydberg states, we report herein a detailed assessment of the performance of the second-order algebraic diagrammatic construction (ADC(2)) method in the simulation of their TRPES spectra. As the test case, we employ the tertiary aliphatic amine N-methylmorpholine (NMM), which is notable for the fact that the signal of its 3s state exhibits long-lived oscillations along the electron binding energy axis. The relaxation process of photoexcited NMM is simulated via the Born-Oppenheimer molecular dynamics method, and the resulting TRPES spectrum is generated on the basis of ionization energies and approximate Dyson orbital norms calculated with the continuum orbital technique. On the whole, the simulated TRPES spectrum achieves satisfactory agreement with experiment, which suggests that the ADC(2) method provides a realistic description of the potential energy surfaces of the relevant excited and ionized states. In particular, the simulations reproduce the fine oscillatory structure of the signal of the 3s state, and provide evidence to the effect that it results from a coherent vibrational wavepacket evolving along the deformation modes of the six-membered ring. However, it is found that ADC(2) underestimates electron binding energies by up to a few tenths of an electronvolt. The case of NMM demonstrates the usefulness of ADC(2) as a tool to aid the interpretation of the TRPES spectra of large organic molecules.

  • 224.
    Du, Dou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Simulated temperature programmed reduction by H2 — a key to understanding OSC on nanoceriaManuscript (preprint) (Other academic)
  • 225.
    Du, Dou
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry. Uppsala Univ, Dept Chem, Angstrom Lab, Box 538, S-75121 Uppsala, Sweden.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Broqvist, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    From Ceria Clusters to Nanoparticles: Superoxides and Supercharging2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 3, p. 1742-1750Article in journal (Refereed)
    Abstract [en]

    Several studies have reported a dramatically increased oxygen storage capacity (OSC) for small ceria nanoparticles (∼5 nm). Both experiments and theory have correlated this effect with superoxide ion formation. In previous studies, density functional theory (DFT) calculations with the PBE+U density functional have been used, and the obtained results were only in qualitative agreement with the experimental observations. One severe problem is the underbinding of the O2 molecule upon superoxide ion formation, which suggests that such species should not exist above room temperature. In this work, we use hybrid DFT functional to resolve this problem. We find that the discrepancy between theory and experiment originates from an incorrect estimate of the energy associated with the localized f-electrons with respect to the oxygen p-levels. By using average O2 adsorption energies from hybrid DFT calculations, extrapolated to large nanoparticles (3−10 nm), in conjunction with first-order desorption kinetics, we find that superoxide ions are indeed stable on nanosized ceria well above room temperature, in accordance with experiments.

  • 226.
    Duarte, Fernanda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Amrein, Beat Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Kamerlin, Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Modeling catalytic promiscuity in the alkaline phosphatase superfamily2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 27, p. 11160-11177Article in journal (Refereed)
    Abstract [en]

    In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution.

  • 227. Duarte, Fernanda
    et al.
    Barrozo, Alexandre
    Åqvist, Johan
    H. Williams, Nicholas
    Kamerlin, Shina Caroline Lynn
    Mechanistic Shifts Along the Linear Free Energy Relationship for Aryl Phosphate Monoester HydrolysisManuscript (preprint) (Other academic)
  • 228. Duarte, Fernanda
    et al.
    Barrozo, Alexandre
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Åqvist, Johan
    Williams, Nicholas
    Kamerlin, Shina
    Mechanistic Shifts Along the Linear Free Energy Relationship for ArylPhosphate Monoester Hydrolysis.Manuscript (preprint) (Other academic)
  • 229. Dunne, L. J.
    et al.
    Brändas, Erkki
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Quantum Chemistry.
    D-wave Bipolaronic Condensate with Short Range Repulsive Electronic Correlations in an Extended Hubbard Model of High Tc Cuprate Superconductors2001In: Advances in Quantum Chemistry, ISSN 0065-3276, E-ISSN 2162-8815, Vol. 40, p. 225-247Article in journal (Refereed)
    Abstract [en]

    Abstract

    The question as to whether Fermion pairs interacting with a short range Coulomb repulsion and longer range attractive tail can form a Condensate is a key question for High Temperature Superconductivity [1–30]. If such a form of interaction can support a bound state it is commonly suggested that Bose-Einstein condensation of such pairs may occur, as in widely discussed Bipolaron models of High Temperature Cuprate superconductivity where the paired Fermions are holes. On the other hand it is frequently stated that strongly overlapping real-space pairing with a strong short range Coulomb repulsion is a priori implausible [4]. In this paper a review is made of our work on D-wave pairing [7–19] in real-space between electrons on a Cuprate lattice due to any effective interaction with a short range repulsive part and a longer range attractive tail such as might arise from Bipolaronic coupling.

  • 230.
    Dunne, Lawrence J
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Brändas, Erkki J.
    Superconducting and Spin Gaps in dx2-y2-Wave High Tc Cuprates2003In: Fundamental World of Quantum Chemistry, ISSN ISBN: 1-4020-1291-8, Vol. II, p. 257-270Article in journal (Refereed)
  • 231.
    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.

  • 232.
    Durbeej, B. and Eriksson, L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    A density functional theory study of coniferyl alcohol intermonomeric cross linkages in lignin - Three-dimensional structures, stabilities and the thermodynamic control hypothesis2003In: Holzforschung, Vol. 57, no 2, p. 150-164Article in journal (Refereed)
  • 233.
    Durbeej, B. and Eriksson, L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Formation of beta-O4 lignin models - A theoretical study2003In: Holzforschung, Vol. 57, no 5, p. 466-Article in journal (Refereed)
  • 234.
    Durbeej, B. and Eriksson, L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    On the bathochromic shift of the absorption by astaxanthin in crustacyanin: A quantum chemical study2003In: Chem. Phys. Lett., Vol. 375, p. 30-38Article in journal (Refereed)
  • 235.
    Durbeej, B. and Eriksson, L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    On the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: Why are thymines more reactive?2003In: Photochem. Photobiol., Vol. 78, no 2, p. 159-167Article in journal (Refereed)
  • 236.
    Durbeej, B. and Eriksson, L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Reaction mechanism of thymine dimer formation in DNA induced by UV light2002In: J. Photochem. Photobio. A, Vol. 152, p. 95-101Article in journal (Refereed)
  • 237.
    Durbeej, B. and Eriksson, L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Spin distribution in dehydrogenated coniferyl alcohol and associated dilignol radicals2003In: Holzforschung, Vol. 57, no 1, p. 59-61Article in journal (Refereed)
  • 238.
    Durbeej, B., Wang, Y.-N., and Eriksson, L. A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Lignin biosynthesis and degradation - a major challenge for computational chemistry2003In: Lect. Notes Comput. Sc., Vol. 2565, p. 137-165Article, book review (Other scientific)
  • 239.
    Durbeej, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    On the primary event of phytochrome: quantum chemical comparison of photoreactions at C4, C10 and C152009In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, no 9, p. 1354-1361Article in journal (Refereed)
    Abstract [en]

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

  • 240.
    Durbeej, Bo
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical Chemistry, Quantum Chemistry.
    Quantum Chemical Studies of Protein-Bound Chromophores, UV-Light Induced DNA Damages, and Lignin Formation2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantum chemical methods have been used to provide a better understanding of the photochemistry of astaxanthin and phytochromobilin; the photoenzymic repair of UV-light induced DNA damages; and the formation of lignin.

    The carotenoid astaxanthin (AXT) is responsible for the colouration of lobster shell. In solution, the electronic absorption spectra of AXT peak in the 470-490 nm region, corresponding to an orange-red colouration. Upon binding to the lobster-shell protein-complex α-crustacyanin, the absorption maximum is shifted to 632 nm, yielding a slate-blue colouration. Herein, the structural origin of this bathochromic shift is investigated on the basis of recent experimental work.

    The tetrapyrrole phytochromobilin (PΦB) underlies the photoactivation of the plant photoreceptor phytochrome. Upon absorption of 660-nm light, PΦB isomerizes from a C15-Z,syn configuration (in the inactive form of the protein) to C15-E,anti (in the active form). In this work, a reaction mechanism for this isomerization is proposed.

    DNA photolyases are enzymes that repair DNA damages resulting from far-UV-light induced [2+2] cycloaddition reactions involving pyrimidine nucleobases. The catalytic activity of these enzymes is initiated by near-UV and visible light, and is governed by electron transfer processes between a catalytic cofactor of the enzyme and the DNA lesions. Herein, an explanation for the experimental observation that the repair of cyclobutane pyrimidine dimers (CPD) – the major type of lesion – proceeds by electron transfer from the enzyme to the dimer is presented. Furthermore, the formation of CPD is studied.

    Lignin is formed by dehydrogenative polymerization of hydroxycinnamyl alcohols. A detailed understanding of the polymerization mechanism and the factors controlling the outcome of the polymerization is, however, largely missing. Quantum chemical calculations on the initial dimerization step have been performed in order to gain some insight into these issues.

  • 241.
    Eckert, Sebastian
    et al.
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    da Cruz, Vinicius Vaz
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia.
    Ertan, Emelie
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Polyutov, Sergey
    Siberian Fed Univ, Inst Nanotechnol Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
    Couto, Rafael C.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fondell, Mattis
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Dantz, Marcus
    PSI, Res Dept Synchrotron Radiat & Nanotechnol, CH-5232 Villigen, Switzerland..
    Kennedy, Brian
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Schmitt, Thorsten
    PSI, Res Dept Synchrotron Radiat & Nanotechnol, CH-5232 Villigen, Switzerland..
    Pietzsch, Annette
    Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, S-10691 Stockholm, Sweden..
    Foehlisch, Alexander
    Univ Potsdam, Inst Phys & Astron, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.;Helmholtz Zentrum Berlin Mat & Energie, Inst Methods & Instrumentat Synchrotron Radiat Re, Albert Einstein Str 15, D-12489 Berlin, Germany..
    One-dimensional cuts through multidimensional potential-energy surfaces by tunable x rays2018In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 97, no 5, article id 053410Article in journal (Refereed)
    Abstract [en]

    The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of our description of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.

  • 242. Eckert, Sebastian
    et al.
    Vaz da Cruz, Vinicius
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Polyutov, Sergey
    Carvalho Couto, Rafael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    Odelius, Michael
    Föhlisch, Alexander
    One-dimensional cuts through multidimensional potential energy surfaces by tunable X-rays2018Manuscript (preprint) (Other academic)
    Abstract [en]

    The concept of the potential-energy surface (PES) and directional reaction coordinates is the backbone of ourdescription of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to (near) degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close-lying vibrational levels. We show here that resonant inelastic x-ray scattering (RIXS) constitutes an ideal probe for revealing one-dimensional cuts through the ground-state PES of molecular systems, even far away from the equilibrium geometry, where the independent-mode picture is broken. We strictly link the center of gravity of close-lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one-dimensional Hamiltonian along the propagation coordinate of the core-excited wave packet. This concept, combined with directional and site selectivity of the core-excited states, allows us to experimentally extract cuts through the ground-state PES along three complementary directions for the showcase H2O molecule.

  • 243.
    Edvardsson, David
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. QUANTUM CHEMISTRY.
    Lunell, Sten
    Marian, Christel M.
    Calculation of potential energy curves for Rb2 including relativistic effects2003In: Molecular Physics, Vol. 101, no 15, p. 2381-2389Article in journal (Refereed)
  • 244.
    Edvinsson, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Elvingson, Christer
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Arteca, Gustavo
    Effect of compression on the molecular shape of polymer mushrooms with variable stiffness2002In: Journal of chemical physics, Vol. 116, p. 9510-Article in journal (Refereed)
  • 245.
    Ekholm, Marcus
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Gambino, Davide
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Jönsson, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Tasnadi, Ferenc
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Alling, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Max Planck Inst Eisenforsch GmbH, Germany.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Natl Univ Sci and Technol MISIS, Russia.
    Assessing the SCAN functional for itinerant electron ferromagnets2018In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 98, no 9, article id 094413Article in journal (Refereed)
    Abstract [en]

    Density functional theory is a standard model for condensed-matter theory and computational material science. The accuracy of density functional theory is limited by the accuracy of the employed approximation to the exchange-correlation functional. Recently, the so-called strongly constrained appropriately normed (SCAN) [Sun, Ruzsinszky, and Perdew, Phys. Rev. Lett. 115, 036402 (2015)] functional has received a lot of attention due to promising results for covalent, metallic, ionic, as well as hydrogen- and van der Waals-bonded systems alike. In this work, we focus on assessing the performance of the SCAN functional for itinerant magnets by calculating basic structural and magnetic properties of the transition metals Fe, Co, and Ni. We find that although structural properties of bcc-Fe seem to be in good agreement with experiment, SCAN performs worse than standard local and semilocal functionals for fcc-Ni and hcp-Co. In all three cases, the magnetic moment is significantly overestimated by SCAN, and the 3d states are shifted to lower energies, as compared to experiments.

  • 246. Ekström, U.
    et al.
    Norman, Patrick
    Linköping University, Sweden.
    X-ray absorption spectra from the resonant-convergent first-order polarization propagator approach2006In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 74, no 4, article id 042722Article in journal (Refereed)
    Abstract [en]

    The one-photon absorption cross sections of molecular systems have been determined in the high-energy region from the imaginary part of the electric dipole polarizability tensor. In contrast to commonly adopted state-specific methodologies, the complex polarization propagator approach does not require explicit consideration of the excited states and it is open-ended towards multiphoton absorption. It is shown that the electronic relaxation in the core-hole state is well accounted for in the present approach with use of standard density-functional based electronic structure methods. Sample calculations are presented of the K -edge x-ray absorption spectra for H2 O, CO, C4 H4 N, and C6 H6.

  • 247. Ekström, U.
    et al.
    Norman, Patrick
    Linkoping University, Sweden.
    Carravetta, V.
    Relativistic four-component static-exchange approximation for core-excitation processes in molecules2006In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 73, no 2, article id 022501Article in journal (Refereed)
    Abstract [en]

    A generalization of the static-exchange approximation for core-electron spectroscopies to the relativistic four-component realm is presented. The initial state is a Kramers restricted Hartree-Fock state and the final state is formed as the configuration-interaction single excited state, based on the average of configurations for (n-1) electrons in n near-degenerate core orbitals for the reference ionic state. It is demonstrated that the static-exchange Hamiltonian can be made real by considering a set of time-reversal symmetric electron excitation operators. The static-exchange Hamiltonian is constructed at a cost that parallels a single Fock matrix construction in a quaternion framework that fully exploits time-reversal and spatial symmetries for the D2h point group and subgroups. The K - and L -edge absorption spectra of H2 S are used to illustrate the methodology. The calculations adopt the Dirac-Coulomb Hamiltonian, but the theory is open ended toward improvements in the electron-electron interaction operator. It is demonstrated that relativistic effects are substantial for the L -edge spectrum of sulfur, and substantial deviations from the statistical 2:1 spin-orbit splitting of the intensity distribution are found. The average ratio in the mixed region is 1.54 at the present level of theory.

  • 248. Ekström, U.
    et al.
    Norman, Patrick
    Linköping University, Sweden.
    Rizzo, A.
    Four-component Hartree-Fock calculations of magnetic-field induced circular birefringence - Faraday effect - In noble gases and dihalogens2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 7, article id 074321Article in journal (Refereed)
    Abstract [en]

    The effects of relativity on the magnetic-field induced circular birefringence, or Faraday effect, in He, Ne, Ar, Xe, Rn, F 2, Cl 2, Br 2, and I 2 have been determined at the four-component Hartree-Fock level of theory. A measure of the birefringence is given by the Verdet constant, which is a third-order molecular property and thus relates to quadratic response functions. A fully analytical nonlinear polarization propagator approach is employed. The results are gauge invariant as a consequence of the spatial symmetries in the molecular systems. The calculations include electronic as well as vibrational contributions to the property. Comparison with experiment is made for He, Ne, Ar, Xe, and Cl 2, and, apart from neon, the theoretical values of the Verdet constant are within 10% of the experimental ones. The inclusion of nonrelativistically spin-forbidden excitations in the propagator parametrization has significant effects on the dispersion in general, but such effects are in the general case largely explained by the use of a resonant-divergent propagator theory. In the present work we do, however, observe noticeable relativistic corrections to the Verdet constant in the off-resonant regions for systems with light elements (F 2 and Cl 2), and nonrelativistic results for the Verdet constant of Br 2 are in error by 25% in the low-frequency region.

  • 249. Ekström, U.
    et al.
    Ottosson, H.
    Norman, Patrick
    Linköping University, Sweden.
    Characterization of the chemisorption of methylsilane on a au(1,1,1) surface from the silicon K- And L-edge spectra: A theoretical study using the four-component static exchange approximation2007In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 111, no 37, p. 13846-13850Article in journal (Refereed)
    Abstract [en]

    X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectra (NEXAFS) of methylsilane, isolated and chemisorbed to a Au(1,1,1) surface, are determined in the fully relativistic four-component static exchange approximation - both the K- and the L-edge of silicon are addressed in this investigation. In the fully chemisorbed structure, three H(Si) atoms have been cleaved off when Si binds in the hollow site of Au forming three Si - Au bonds of normal length. As due to die tri-coordinated chemisorption, the onsets of the K- and L-edge NEXAFS absorption bands occur some 2.0 and 2.5 eV lower in energy, respectively. The spin-orbit splittings in the silicon 2p-shell are not significantly changed due to adsorption. A partly chemisorbed methylsilane with only one H(Si) bond cleaved was also studied, and it is shown that the polarization dependence in the surface spectra contains details that can be used experimentally to identify the surface coordination of silicon. The red-shifts in the XPS silicon 1s (2p) spectra upon surface binding are 0.95 (0.65) and 1.15 (0.83) eV for the mono- and tricoordinated system, respectively.

  • 250. Ekström, Ulf
    et al.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH.
    Carravetta, Vincenzo
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Polarization propagator for X-ray spectra2006In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 97, no 14Article in journal (Refereed)
    Abstract [en]

    A polarization propagator for x-ray spectra is outlined and implemented in density functional theory. It rests on a formulation of a resonant-convergent first-order polarization propagator approach which makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted x-ray spectrum relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects.

2345678 201 - 250 of 1248
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