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  • 1.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gimenez, Judit
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Scalability analysis of Dalton, a molecular structure program2013In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, no 8, p. 2197-2204Article in journal (Refereed)
    Abstract [en]

    Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.

  • 2.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Gimenez, Judit
    Barcelona Supercomputing Center, Universitat Politecnica de Catalunya, Barcelona, Spain.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Scaling Dalton, a molecular electronic structure program2011In: Seventh International Conference on e-Science, e-Science 2011, 5-8 December 2011, Stockholm, Sweden, IEEE conference proceedings, 2011, p. 256-262Conference paper (Refereed)
    Abstract [en]

    Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a characterization and performance optimization of Dalton that increases the scalability and parallel efficiency of the application. We also propose asolution that helps to avoid the master/worker design of Daltonto become a performance bottleneck for larger process numbers and increase the parallel efficiency.

  • 3. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    The Dalton quantum chemistry program system2014In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, no 3, p. 269-284Article in journal (Refereed)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 4. Carravetta, V.
    et al.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Jensen, H. J. A.
    Ab initio calculations of molecular resonant photoemission spectra2000In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 113, no 18, p. 7790-7798Article in journal (Refereed)
    Abstract [en]

    An ab initio method for calculations of molecular resonant photoemission (RPE) spectra is described. The method includes a multicenter expansion of both the dipole matrix element-direct emission-and the Hamiltonian matrix element between the resonant state and the autoionizing states-resonant emission. These quantities are relevant for the description of the process both in the two-step model, where the spectrum is computed at the resonance energy only, and in the one-step model where, by a K-matrix approach, the direct-to-resonant interference is taken into account and the electronic line profile is fully described. The resonant two-electron matrix elements are evaluated over the core-excited relaxed orbitals with the outgoing Auger electron orbital expanded on an augmented multicentered Gaussian basis set. Stieltjes imaging is shown to work excellently for such Gaussian basis sets giving correct continuum normalization matrix elements even for RPE electron energies as high as 100-1000 eV. A numerical investigation is carried out for the participator decay of the C 1s --> pi* and O 1s --> pi* states of CO.

  • 5.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Spectral character of intermediate state in solid-state photoarrangement of alpha-santonin2012In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 405, p. 40-45Article in journal (Refereed)
    Abstract [en]

    The vibronically resolved spectra of an intermediate and a product involved in the photoreaction of alpha-santonin have been explored by the density functional theory and the post-SCF methodologies, and a detailed comparison of theory with experiment was conducted to obtain reliable assignments to the observed spectra. The predicted emission energies of photosantonic acid and a topochemical product are found to match with the experimental values reasonably. The further calculations manifest that the absorption spectrum of photosantonic acid exhibits vibrationally resolved features, while the absorption band of topochemical product without vibrational resolution is opposite to the experimental observation. These new computational findings lead to a revised assignment to the observed bands and provide a basis for experimentalists to draw a convinced reaction mechanism for the alpha-santonin photorearrangement.

  • 6.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ying, Fuming
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wu, Wei
    Department of Chemsitry, Center for Theoretical Chemistry, and the State Kay Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China.
    Cao, Zexing
    Department of Chemistry, Center for Theoretical Chemsitry, and the State Key Laboratory for Physical Chemsitry of Solid Surfaces, Xiamen University, Xiamen 361005, China.
    Restricted-unrestricted density functional theory for hyperfine coupling constants: vanadium complexesManuscript (preprint) (Other academic)
  • 7.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Wei-Wei
    Department of Chemistry, Xiamen University.
    Liao, Rong-Zhen
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yi
    Department of Chemistry, Xiamen University.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on reaction of cofactor-free enzyme with triplet oxygen moleculeManuscript (preprint) (Other academic)
  • 8. de Almeida, K. J.
    et al.
    Ramalho, T. C.
    Alves, M. C.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical insights into the visible near-infrared absorption spectra of Bis(hexafluoroacetylacetonate) copper(II) in pyridine2012In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, no 13, p. 2571-2577Article in journal (Refereed)
    Abstract [en]

    The density functional theory calculations were performed to investigate the specific solvent effects on the optical absorption spectrum of copper(II) hexafluoroacetylacetonate complex in pyridine. The effects of single and double coordination of pyridine molecules at axial position of bis(hexafluoroacetylacetonate) copper(II) indicate that both positions and intensities of 3d3d electronic transitions are strongly dependent on the coordination environment around the copper(II) complex. The results indicate that the nature of the electron-acceptor atoms in the equatorial ligands plays an important role in the number of solvent molecules in the first solvation shell of copper(II) acac systems.

  • 9.
    de Almeida, Katia Júlia
    et al.
    Univ Fed Minas Gerais, Dept Quim.
    Cesar, Amary
    Univ Fed Minas Gerais, Dept Quim.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Modelling the visible absorption spectra of copper(II) acetylacetonate by density functional theory2010In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 492, no 1-3, p. 14-18Article in journal (Refereed)
    Abstract [en]

    Spin restricted open-shell Density Functional Theory calculations have been carried out by means of linear response theory to investigate the visible absorption spectrum of copper(II) acetylacetonate complex, Cu(acac)(2). The 3d -> 3d transition energies and the influence of molecular structure and non-coordinating solvent on the spectra have been investigated. The obtained four 3d -> 3d transition energies accord well with the experimental data in the crystal phase. The presented results indicate that the experimentally observed four band structure of Cu(acac)(2) is of molecular nature, and not caused by factor-group splitting in the crystal environment as previously suggested.

  • 10.
    de Almeida, Katia Júlia
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Hugosson, Håkan Wilhelm
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cesar, Amary
    Universidade Federal de Minas Gerais, Departamento de Química.
    Conformations, structural transitions and visible near-infrared absorption spectra of four-, five- and six-coordinated Cu(II) aqua complexes2009In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, no 3, p. 508-519Article in journal (Refereed)
    Abstract [en]

    We have performed Car-Parrinello molecular dynamics simulations at ambient conditions for four-, five- and six-coordinated Cu(II) aqua complexes. The molecular geometry has been investigated in terms of Cu-O, Cu-H bond lengths and O-Cu-O bond angles and compared with earlier experimental measurement results and theoretical calculations. We find that the average Cu-O and Cu-H bond lengths increase with increasing coordination number. We have also observed relatively faster structural transition in the case of five- coordinated complex between trigonal bipyramidal and square pyramidal geometry. This result deviates from the findings of the earlier report (A. Pasquarello et al., Science, 2001, 291, 856) on copper( II) in aqueous solution and we attribute these differences to the neglect of solvent environment in our calculations. The averaged absorption spectra for the copper( II) aqua complexes have been computed using spin-restricted density functional linear response formalism taking 100 snap shots from a trajectory of 0.48 ps. We find that the calculated spectra are significantly different, showing clear features that distinguish each coordination model. Comparison with the experimentally reported absorption spectra is made wherever it is possible and the results obtained favor the distorted fivefold-coordination arrangement for the molecular structure of the Cu(II) ion in aqueous solution.

  • 11. de Almeida, Katia Júlia
    et al.
    Ramalho, T. C.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cesar, Amary
    Theoretical Study of Specific Solvent Effects on the Optical and Magnetic Properties of Copper(II) Acetylacetonate2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 8, p. 1331-1339Article in journal (Refereed)
    Abstract [en]

    Specific and basicity solvent effects on the visible near-infrared electronic transitions and the electron paramagnetic resonance (EPR) parameters of the copper(II) acetylacetonate complex, Cu(acac)(2), have been investigated at the density functional theory level. The computed absorption transitions as well as the EPR parameters show a strong dependence on the direct coordination environment around the Cu(II) complex. High solvatocromic shifts are observed for 3d-3d transitions, with the highest effect observed for the d(z2)-->d(xy) transition, which is red-shifted by 6000 cm(-1) and 9000 cm(-1) in water and pyridine solvent models, respectively. Compared to the electronic g-tensors, the hyperfine coupling constants of the Cu(acac)(2) complex show a more pronounced dependence on the effect of base strength of solvent. Overall, the present methodology satisfactorily models the solvent effect on the optical and magnetic properties of the Cu(acac)(2) complex, and theory and experiment agree sufficiently well to warrant the use of the computed optical and EPR parameters to elucidate the coordination environment of the Cu(II) systems in basic solutions.

  • 12.
    de Almeida, Katia Júlia
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Cesar, Amary
    Universidade Federal de Minas Gerais, Departamento de Química.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Theoretical study of specific solvent effects on the optical and magnetic properties of copper(II) acetylacetonateManuscript (Other academic)
  • 13. Engstrom, M.
    et al.
    Himo, Fahmi
    KTH, Superseded Departments, Biotechnology.
    Graslund, A.
    Minaev, B.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Hydrogen bonding to tyrosyl radical analyzed by ab initio g-tensor calculations2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 21, p. 5149-5153Article in journal (Refereed)
    Abstract [en]

    Hydrogen bonding to the tyrosyl radical in ribonucleotide reductase (RNR) has been simulated by a complex between the phenoxyl radical and a water molecule. Multiconfigurational self-consistent field linear response theory was used to calculate the g-tensor of the isolated phenoxyl radical and of the phenoxyl-water model. The relevance of the model was motivated by the fact that spin density distributions and electron paramagnetic resonance (EPR) spectra of the phenoxyl and tyrosyl radicals are very similar. The calculated g-tensor anisotropy of the phenoxyl radical was comparable with experimental findings for tyrosyl in those RNRs where the H-bond is absent: g(x) = 2.0087(2.0087), g(y) = 2.0050(2.0042), and g(z) = 2.0025(2.0020), where the tyrosyl radical EPR data from Escherichia coli RNR are given in parentheses. The hydrogen bonding models reproduced a shift toward a lower g(x) value that was observed experimentally for mouse and herpes simplex virus RNR where the H-bond was detected by electron-nuclear double resonance after deuterium exchange. This decrease could be traced to lower angular momentum and spin-orbit coupling matrix elements between the ground B-2(1) and the first excited B-2(2) states (oxygen lone-pair n to pi(SOMO) excitation) upon hydrogen bonding in a linear configuration. The g(x) value was further decreased by hydrogen bonding in bent configurations due to a blue shift of this excitation.

  • 14. Engstrom, M.
    et al.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    MCSCF and DFT calculations of EPR parameters of sulfur centered radicals2000In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 328, no 06-apr, p. 483-491Article in journal (Refereed)
    Abstract [en]

    The EPR parameters of sulfur centered radicals are different depending on the radical structure, charge and solvent. That is, the g- and A-tensor components provide significant patterns which may distinguish sulfur radical structures from each other. In the present work, these EPR parameters were calculated for monosulfide radicals (RS'), disulfide radicals (RSS.), radical cations ((RSSR+)-S-.) and anions ((RSSR-)-S-.), with R = CH3, using the MCSCF linear response and DFT/B3LYP methods. Results were in agreement with experimental data for the cases when well-resolved EPR spectra are available. Especially, the assignment of the disulfide anion in ribonucleotide reductase was confirmed. The results indicate that investigations with the present computational methods on refined structures and solvent modeling may provide interpretations of experimental data on unassigned radical species.

  • 15. Engström, M.
    et al.
    Owenius, R.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ab initio g-tensor calculations of hydrogen bond effects on a nitroxide spin label2001In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 338, no 06-apr, p. 407-413Article in journal (Refereed)
    Abstract [en]

    Hydrogen bonding effects on the electron paramagnetic resonance (EPR) g-tensor of a nitroxide spin label was investigated by quantum chemical calculations. The restricted open-shell Hartree-Fock (ROHF) linear response method with the atomic mean field approximation (AMFI) was used in the calculations. The results show that hydrogen bonding reduces the g-tensor component directed along the NO bond, g(xx). This decrease is traced to higher excitation energy and lower spin-orbit coupling and angular momentum matrix elements for the n-pi* excitation. The calculations show that the g-tensor is practically invariable when hydrogen bonding was modeled with methanol instead of water.

  • 16.
    Frecus, Bogdan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 7, p. 2427-2434Article in journal (Refereed)
    Abstract [en]

    Encapsulation of spin-labels into "host'' compounds, like cucurbit[n]urils or cyclodextrins, in solutions has profound effects on the EPR spin Hamiltonian parameters of the spin-labels. In this work we study the microscopic origin of the EPR spin Hamiltonian parameters of spin-labels enclosed in hydrophobic cavities. We focus on the dependence of the EPR properties of encapsulated spin-labels on the hydrogen bonding topologies that occur upon encapsulation, and quantize various contributions to these parameters according to specific hydrogen bonding patterns. The obtained results provide refined insight into the role of the hydrogen bonding induced encapsulation shifts of EPR spin Hamiltonian parameters in solvated "spin-label@host compound'' complexes.

  • 17.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Agren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 8, p. 3492-3502Article in journal (Refereed)
    Abstract [en]

    The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environment electronic embedding and polarizable electronic embedding accounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed.

  • 18.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    First hyperpolarizability of collagen using the point dipole approximationManuscript (preprint) (Other academic)
    Abstract [en]

    The application of localized hyperpolarizabilities to predict a total protein hyperpolariz-ability is presented for the first time, using rat-tail collagen as a demonstration example. Weemploy a model comprising the quadratic Applequist point-dipole approach, the so-calledLoProp transformation and a procedure with molecular fractionation using conjugate capsin order to determine the atomic and bond contributions to the net β tensor of the collagen[(PPG)3 ]10 triple-helix. By using Tholes exponential damping modification to the dyadic ten-sor in the Applequist equations, a correct qualitative agreement with experiment is found. Theintensity of the βHRS signal and the depolarization ratios are best reproduced by decomposingthe LoProp properties into the atomic positions, and using Tholes exponential damping withthe original damping parameter. Some ramifications of the model for general protein propertyoptimization are briefly discussed.

  • 19.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    First Hyperpolarizability of Collagen Using the Point Dipole Approximation2016In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 11, p. 2132-2138Article in journal (Refereed)
    Abstract [en]

    The application of localized hyperpolarizabilities to predict a total protein hyperpolarizability is presented for the first time, using rat-tail collagen as a demonstration example. We employ a model comprising the quadratic Applequist point-dipole approach, the so-called LoProp transformation, and a procedure with molecular fractionation using conjugate caps to determine the atomic and bond contributions to the net beta tensor of the collagen [(PPG)(10)](3) triple-helix. By using Tholes exponential damping modification to the dyadic tensor in the Applequist equations, a correct qualitative agreement with experiment is found. The intensity of the beta(HRS) signal and the depolarization ratios are best reproduced by decomposing the LoProp properties into the atomic positions and using Tholes exponential damping with the original damping parameter. Some ramifications of the model for general protein property optimization are briefly discussed.

  • 20.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Frequency-dependent force fields for QMMM calculations2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 12, p. 7800-7812Article in journal (Refereed)
    Abstract [en]

    We outline the construction of frequency-dependent polarizable force fields. The force fields are derived from analytic response theory for different frequencies using a generalization of the LoProp algorithm giving a decomposition of a molecular dynamical polarizability to localized atomic dynamical polarizabilities. These force fields can enter in a variety of applications - we focus on two such applications in this work: firstly, they can be incorporated in a physical, straightforward, way for current existing methods that use polarizable embeddings, and we can show, for the first time, the effect of the frequency dispersion within the classical environment of a quantum mechanics-molecular mechanics (QMMM) method. Our methodology is here evaluated for some test cases comprising water clusters and organic residues. Secondly, together with a modified Silberstein-Applequist procedure for interacting inducible point-dipoles, these frequency-dependent polarizable force fields can be used for a classical determination of frequency-dependent cluster polarizabilities. We evaluate this methodology by comparing with the corresponding results obtained from quantum mechanics or QMMM where the absolute mean (alpha) over bar is determined with respect to the size of the QM and MM parts of the total system.

  • 21.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hyperpolarizabilities of extended molecular mechanical systems2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 12, p. 8710-8722Article in journal (Refereed)
    Abstract [en]

    We propose and evaluate algorithms for the calculation of molecular polarizabilities and hyperpolarizabilities of extended chemical systems. These algorithms are generalizations of the Silberstein-Applequist procedure involving interacting induced classical dipoles through the localized polarizabilities and hyperpolarizabilities. The models are evaluated in terms of interacting molecular units as well as interacting atomic units that result from the atomic decomposition scheme known as the LoProp transformation. We introduce a generalized LoProp scheme which applies to hyperpolarizabilities as well as to polarizabilities. The accuracy of the second-order Applequist method is tested for the first hyperpolarizability for the TIP3P water model using both Hartree-Fock and density functional theory evaluated with different basis sets. Possible applications and ramifications of the scheme are discussed.

  • 22.
    Harczuk, Ignat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Modeling Rayleigh Scattering of Aerosol Particles2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 18, p. 4296-4301Article in journal (Refereed)
    Abstract [en]

    Rayleigh scattering of naturally polarized lightwas studied for systems with atmospheric relevance represent-ing growing water clusters with adsorbed cis-pinonic acid. Thescattering intensity was computed from the static anddynamical polarizabilities of the clusters obtained by a recentlyderived methodology for classical polarizabilities, in whichApplequist equations for interacting polarizable dipoles areused together with point-dipoles and polarizabilities obtainedby quantum chemistry and decomposed into the atomicdomain by the so-called LoProp transformation generalized forfrequency dependence. The Applequist interaction was foundto yield scattering intensities 20% larger for a cluster consistingof 1000 water molecules, as compared to the method where allof the polarizabilities of molecules are added withoutinteractions. It was confirmed that scattering intensity depends quadratically on the number of water molecules in the cluster,and that it also increases quadratically with increase in the mass constituent of the foreign substance. The adsorption of the cis-pinonic acid increases the contribution to the scattering intensity stemming from the anisotropic polarizability, as compared tothe isotropic contribution. The ramifications of the method in predicting Rayleigh scattering and the earth’s albedo with respectto man-made and natural gas emission are briefly discussed.

  • 23. Jansik, B.
    et al.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Jonsson, D.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cubic response functions in time-dependent density functional theory2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 5Article in journal (Refereed)
    Abstract [en]

    We present density-functional theory for time-dependent response functions up to and including cubic response. The working expressions are derived from an explicit exponential parametrization of the density operator and the Ehrenfest principle, alternatively, the quasienergy ansatz. While the theory retains the adiabatic approximation, implying that the time-dependency of the functional is obtained only implicitly-through the time dependence of the density itself rather than through the form of the exchange-correlation functionals-it generalizes previous time-dependent implementations in that arbitrary functionals can be chosen for the perturbed densities (energy derivatives or response functions). In particular, general density functionals beyond the local density approximation can be applied, such as hybrid functionals with exchange correlation at the generalized-gradient approximation level and fractional exact Hartree-Fock exchange. With our implementation the response of the density can always be obtained using the stated density functional, or optionally different functionals can be applied for the unperturbed and perturbed densities, even different functionals for different response order. As illustration we explore the use of various combinations of functionals for applications of nonlinear optical hyperpolarizabilities of a few centrosymmetric systems; molecular nitrogen, benzene, and the C-60 fullerene. Considering that vibrational, solvent, and local field factors effects are left out, we find in general that very good experimental agreement can be obtained for the second dynamic hyperpolarizability of these systems. It is shown that a treatment of the response of the density beyond the local density approximation gives a significant effect. The use of different functional combinations are motivated and discussed, and it is concluded that the choice of higher order kernels can be of similar importance as the choice of the potential which governs the Kohn-Sham orbitals.

  • 24. Jonsson, Dan
    et al.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Jansik, Branislav
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Kohn–Sham Time-Dependent Density Functional Theory with Applications to Linear and Nonlinear Properties2006In: Nonlinear optical properties of matter: From molecules to condensed phases / [ed] Manthos G. Papadopoulos, Andrzej J. Sadlej, Jerzy Leszczynski., Springer Netherlands, 2006, p. 151-209Chapter in book (Refereed)
    Abstract [en]

    We review Kohn–Sham density-functional theory for time-dependent response functionsup to and including cubic response. The working expressions are derived from anexplicit exponential parametrization of the density operator and the Ehrenfest principle,alternatively the quasi-energy ansatz. While the theory retains the adiabatic approximation,implying that the time-dependency of the functional is obtained only implicitly—through the time-dependency of the density itself rather than through the form ofthe exchange-correlation functionals—our implementation generalizes previous timedependentapproaches in that arbitrary functionals can be chosen for the perturbed densities(energy derivatives or response functions). Thus, the response of the density canalways be obtained using the stated density functional, or optionally different functionalscan be applied for the unperturbed and perturbed densities, even different functionals fordifferent response order. In particular, general density functionals beyond the local densityapproximation can be applied, such as hybrid functionals with exchange–correlation atthe generalized gradient-approximation level and fractional exact Hartree–Fock exchange.We also review some recent progress in time-dependent density functional theory foropen-shell systems, in particular spin-restricted and spin restricted-unrestricted formalismsfor property calculations. We highlight a sample of applications of the theory

  • 25. Kaznacheyev, K.
    et al.
    Osanna, A.
    Jacobsen, C.
    Plashkevych, O.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Innershell absorption Spectroscopy of amino acids2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 13, p. 3153-3168Article in journal (Refereed)
    Abstract [en]

    We present comprehensive measurements of the C (carbon) K edge near-edge X-ray absorption (NEXAFS) spectra of all 20 amino acids commonly occurring in nature. Qualitative trends among the spectra of amino acids with similar chemical character are identified and spectral features are compared with extensive ab initio calculations. The contributions of individual units and substitutional groups have been determined to explore their fingerprinting character using the building block concept. Several such units are found. Two that give particularly clear features in the C Is NEXAFS spectra are the carboxyl group (which can be clearly identified by a pronounced structure due to the C 1s-->pi*c-o transition with maximum at 288.65(5) eV) and modified phenol rings in aromatic amino acids (which give sharp C 1s-->pi*c=o structures). The latter transitions are located around 285 cV, and their shape is specific for each aromatic amino acid. Other building blocks, such as the CNHn group and the CH, CC, CO, CN pair bonds, are also identified, although their characteristic features are less pronounced in the C K edge spectra than the carboxylic and aromatic structures. This study provides the basis for rigorous assignment of the NEXAFS spectra of the amino acids, and will be helpful in developing X-ray absorption spectroscopy for quantitative analysis of proteins.

  • 26. Loboda, O.
    et al.
    Minaev, B.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ruud, K.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Ab initio study of nonhomogeneous broadening of the zero-field splitting of triplet guest molecules in diluted glasses2003In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 119, no 6, p. 3120-3129Article in journal (Refereed)
    Abstract [en]

    Nonhomogeneous broadening of phosphorescence lines and microwave signals in optical detection of magnetic resonance (ODMR) has been calculated using multiconfigurational self-consistent field wave functions and the polarized continuum model. The solvent effects on the zero-field splitting (ZFS) parameters in the low-lying triplet states of aza-aromatic molecules are found to be linearly dependent on the solvent-induced shifts in the phosphorescence frequency in agreement with experimental data. The main contribution to the ZFS originates in the dipolar interaction of the two electron spins, the spin-spin coupling. The spin-orbit coupling (SOC) contribution to the ZFS parameter is much larger for the (3)npi(*) state of pyrazine compared to the (3)pipi(*) states of quinoline. The second-order SOC contribution to the splitting of the (3)npi(*) state in the pyrazine molecule does not show any appreciable dependence on the dielectric constant of the solvent. This raises doubts about earlier theories for explaining the inhomogeneous broadening in triplet-state spectra based exclusively on the SOC-induced mixing of the singlet and triplet states. We complete the interpretation of the ODMR spectrum of pyrazine by calculating the hyperfine coupling (HFC) tensors in the lowest triplet state using the UB3LYP hybrid functional. An appreciable solvent-induced rotation of the anisotropic HFC tensor axes has been obtained for the (3)npi(*) state of pyrazine, in particular for C-13 and N-14 nuclei. This produces additional nonhomogeneous broadening not only in electron-nuclear double resonance spectra, but also in electron paramagnetic resonance signals because the anisotropic HFC perturbation results in an intensity redistribution among the magnetic transitions between the spin sublevels. A small in-plane rotation of the ZFS tensor axes upon solvation has been predicted for quinoline. Rotation of the magnetic axes induced by the interaction with isotropic solvents can provide a new mechanism for spin-lattice relaxation in the triplet state.

  • 27. Loboda, O.
    et al.
    Minaev, B.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Schimmelpfennig, B.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Ruud, K.
    Jonsson, D.
    Ab initio calculations of zero-field splitting parameters in linear polyacenes2003In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 286, no 1, p. 127-137Article in journal (Refereed)
    Abstract [en]

    The results of ab initio calculations of zero-field splitting (ZFS) parameters are presented for the linear polyacenes from benzene to pentacene. We show how the electron spin-spin (SS) parameters can be efficiently obtained from restricted high-spin open-shell wave functions (ROHF), and present calculations of these, comparing with the results of a recent multi-configurational self-consistent field approach. The SS parameters are obtained from electron SS coupling strengths evaluated as expectation values over the wave functions and from state-to-state spin-orbit (SO) interactions. The results for the two lowest triplet states of naphthalene demonstrate that excellent values can be obtained even using moderate basis sets in the wave function, indicating that this technique can be used to obtain reliable ZFS parameters of aromatic compounds. Electron correlation is, however, not negligible; by accounting for full pi-electron correlation the ZFS parameters are in considerably better agreement with experiment than the ROHF results. The ROHF method still reproduced the qualitative trend in the polyacene series in which the ZFS parameters are reduced with increasing size of the pi-conjugation. We confirm that the SS coupling contributions completely determine the D and E parameters for the lowest triplet state of the linear polyacenes and that the SO coupling contributions are small. Geometry optimization of the lowest triplet state was found to be fairly significant for the calculated D and E values; these were reduced by about 30% and 40%, respectively, when the geometry was changed from the ground-state singlet to the triplet-excited state optimized geometry, with the latter values being in better agreement with experiment. The present calculations predict that the second triplet state of naphthalene is very unusual, as it has a negative zero-field splitting, implying an altered ordering of the spin sublevels compared to what is common in aromatic systems.

  • 28. Löytynoja, T.
    et al.
    Harczuk, Ignat
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Jankala, K.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Quantum-classical calculations of X-ray photoelectron spectra of polymers-Polymethyl methacrylate revisited2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 12, article id 124902Article in journal (Refereed)
    Abstract [en]

    In this work, we apply quantum mechanics/molecular mechanics (QM/MM) approach to predict core-electron binding energies and chemical shifts of polymers, obtainable via X-ray photoelectron spectroscopy (XPS), using polymethyl methacrylate as a demonstration example. The results indicate that standard parametrizations of the quantum part (basis sets, level of correlation) and the molecular mechanics parts (decomposed charges, polarizabilities, and capping technique) are sufficient for the QM/MM model to be predictive for XPS of polymers. It is found that the polymer environment produces contributions to the XPS binding energies that are close to monotonous with the number of monomer units, totally amounting to approximately an eV decrease in binding energies. In most of the cases, the order of the shifts is maintained, and even the relative size of the differential shifts is largely preserved. The coupling of the internal core-hole relaxation to the polymer environment is found to be weak in each case, amounting only to one or two tenths of an eV. The main polymeric effect is actually well estimated already at the frozen orbital level of theory, which in turn implies a substantial computational simplification. These conclusions are best represented by the cases where the ionized monomer and its immediate surrounding are treated quantum mechanically. If the QM region includes only a single monomer, a couple of anomalies are spotted, which are referred to the QM/MM interface itself and to the neglect of a possible charge transfer.

  • 29. Löytynoja, Tuomas
    et al.
    Harczuk, Ignat
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Jänkälä, Kari
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Quantum-classical calculations of X-ray photoelectron spectra of polymers –polymethyl methacrylate revisitedManuscript (preprint) (Other academic)
  • 30.
    Löytynoja, Tuomas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Oulu, Finland.
    Niskanen, J.
    Jankala, K.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Quantum Mechanics/Molecular Mechanics Modeling of Photoelectron Spectra: The Carbon 1s Core-Electron Binding Energies of Ethanol-Water Solutions2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 46, p. 13217-13225Article in journal (Refereed)
    Abstract [en]

    Using ethanolwater solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solutesolvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics modelelectrostatic, polarization, and van der Waalswith atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  • 31. Minaev, B.
    et al.
    Loboda, O.
    Rinkevicius, Zilvinas
    KTH, Superseded Departments, Biotechnology.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Fine and hyperfine structure in three low-lying (3)Sigma(+) states of molecular hydrogen2003In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 101, no 15, p. 2335-2346Article in journal (Refereed)
    Abstract [en]

    The fine structure constant (electron spin-spin coupling) and the hyperfine structure parameters (electron-nuclear spin coupling, including spin-rotation and electron-nuclear quadrupole coupling) in the low-lying triplet states b (3)Sigma(u)(+), a (3)Sigma(g)(+) and e (3)Sigma(u)(+) of molecular hydrogen and deuterium are calculated using a recently developed technique with full configu-ration interaction and multiconfiguration self-consistent field wave functions. The second-order spin-orbit coupling contribution to the (3)Sigma(+) states splitting is negligible, and the calculations therefore provide a good estimate of the zero-field splitting based only on the electron spin-spin coupling values. For the bound state a (3)Sigma(g)(+) negligible zero-field splitting is found, in qualitative agreement with the e-a spectrum. The zero-field splitting parameter is considerable for the repulsive b (3)Sigma(u)(+) state (similar or equal to1 cm(-1) ) and of intermediate size for the bound e (3)Sigma(u)(+) state. The isotropic hyperfine coupling constant is very large not only for the valence b (3)Sigma(u)(+) state (1580 MHz) but also for the Rydberg a and e triplet states (similar or equal to1400 MHz). The quadrupole coupling constants for the deuterium isotopes are negligible (0.04-0.07 MHz) for all studied triplet states. The electric dipole activity of the spin sublevels in the triplet-singlet transitions to the ground state is estimated by means of the quadratic response technique.

  • 32. Minaev, B.
    et al.
    Loboda, O.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Bilan, E.
    Physical properties and spectra of IO, IO- and HOI studied by ab initio methods2002In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 58, no 5, p. 1039-1053Article in journal (Refereed)
    Abstract [en]

    Structure and properties of the IO, IO- and HOI species, which are of potential importance for the ozone destruction catalytic cycle in the troposphere, have been calculated together with the EPR, NMR and UV-visible spectra by ab initio methodology with account of spin-orbit coupling (SOC) effects. Multi-configuration self-consistent field calculations with linear and quadratic response techniques and the multi-reference configuration interaction method have been employed. Photodissociation of these species, crucial for the catalytic ozone-destruction cycle, is critically reviewed and analyzed. Calculations predict that the singlet-triplet (S-T) transition to the lowest triplet state (X(1)A' --> (3)A) should be responsible for the weak long-wavelength tail absorption ( similar to450-560 nm) and photodissociation of the HOI molecule. The second, more intense, band around 400 nm is produced by two overlapping S-S and S-T transitions. In order to check this assignement of the HOI photodissociation the isoelectronic IO- anion and IO radical have been studied by the same methods. Comparison with the EPR spectrum of the 10 radical indicates that the methods are reliable which gives credit to the accuracy of the HOI spectral interpretation. NMR spectra of HOI and IO- molecules,and some other properties are calculated for the first time.

  • 33.
    Minaev, Boris
    et al.
    KTH, Superseded Departments, Biotechnology.
    Loboda, Oleksandr
    KTH, Superseded Departments, Biotechnology.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ruud, K.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Solvent effects on optically detected magnetic resonance in triplet spin labels2004In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 111, no 2-6, p. 168-175Article in journal (Refereed)
    Abstract [en]

    We have calculated solvent effects on the zero-field splitting (ZFS) constants induced by electron spin-spin coupling (SSC) in the low-lying triplet states of azaaromatic molecules in solutions using multiconfiguration self-consistent-field wave functions and the polarizable continuum model. The second-order spin-orbit coupling (SOC) contribution to the splitting of the (3)pipi(*) states is found to be almost negligible, and the calculations therefore provide a good estimate of the ZFS parameters and their solvent dependence based only on the electron spin-spin coupling expectation values. The correlation between the shift in the ZFS and the phosphorescence frequency that has been observed in optically detected magnetic resonance experiments in low-temperature glasses is supported by our direct SSC calculations without taking SOC into account. This makes it possible to distinguish between the two theories that earlier were proposed to explain the inhomogeneous broadening of triplet state spectra, and discard the one that is exclusively based on the SOC-induced mixing of the singlet and triplet states.

  • 34.
    Minaev, Boris
    et al.
    KTH, Superseded Departments, Biotechnology.
    Tunell, Ingvar
    KTH, Superseded Departments, Biotechnology.
    Salek, Pawel
    KTH, Superseded Departments, Biotechnology.
    Loboda, Oleksandr
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Singlet-triplet transitions in three-atomic molecules studied by time-dependent MCSCF and density functional theory2004In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 102, no 13, p. 1391-1406Article in journal (Refereed)
    Abstract [en]

    Singlet-triplet transition moments and phosphorescence lifetimes have been calculated for the three-atomic molecules HCN, O-3, H2O, H2S, GeF2, GeCl2 and GeBr2 by time-dependent density functional theory (DFT) utilizing quadratic response functions in order to qualify DFT which recently has become available for studies of this kind [TUNELL, I., RINKEVIVIUS, Z., VAHTRAS, O., SALEK, P., HELGAKER, T., and AGREN, H., 2003, J. chem. phys., 119, 11024]. Comparison with ab initio and experimental data indicates that DFT exhibit results of similar quality as explicitly correlated methods which indicates that it indeed is a viable approach for singlet-triplet transitions. O-3 provides an intriguing example in that a systematic investigation of the singlet-triplet transition moment of its Wulf band indicates a clear advantage of the DFT technique despite the multiconfigurational character of the electronic structure of this molecule. The electronic spin-spin coupling and the hyperfine nuclear coupling constants have also been calculated in order to further characterize the triplet state in the spectra of the investigated systems.

  • 35.
    Niskanen, Johannes
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Andersson, E.
    Eland, J. H. D.
    Linusson, P.
    Hedin, L.
    Karlsson, L.
    Feifel, R.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Symmetry breaking in core-valence double photoionization of SO22012In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 85, no 2, p. 023408-Article in journal (Refereed)
    Abstract [en]

    Core-valence double photoionization electron spectra of the SO2 molecule involving the S 2p and O 1s inner shells have been measured using a time-of-flight multiparticle coincidence technique. The experimental spectra are compared with quantum-chemical calculations based on density functional theory by which several core-valence dicationic states are identified. Assignments conform with a picture where the formation of a O 1s-valence dicationic state is associated with a physical, "pseudo-Jahn-Teller," symmetry breaking and core-hole localization. It is shown that while density functional theory gives very good transition energies in the symmetry-broken case, it gives a poor representation in the symmetry-restricted case, and an incomplete account of the Hartree-Fock localization energy.

  • 36.
    Niskanen, Johannes
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Carravetta, V.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Aksela, H.
    Andersson, E.
    Hedin, L.
    Linusson, P.
    Eland, J. H. D.
    Karlsson, L.
    Rubensson, J. -E
    Feifel, R.
    Experimental and theoretical study of core-valence double photoionization of OCS2010In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 82, no 4, p. 043436-Article in journal (Refereed)
    Abstract [en]

    O 1s, C 1s, and S 2p core-valence double ionization electron spectra of the OCS molecule have been obtained experimentally by a time-of-flight photoelectron-photoelectron coincidence spectroscopy technique. In order to analyze and assign the spectral features observed, we present a protocol for computing core-valence ionization energies of such systems. The protocol is based on a restricted active space multiconfigurational self-consistent field (MCSCF) methodology with a freeze-relax procedure to guarantee a correct core-valence state root index without variational collapse. Corrections for extended dynamical correlation and core-core correlation, respectively, are made by multiconfigurational perturbation theory and by uncontracted basis set Moller-Plesset theory. Envisioning applications to larger molecules, a spin-restricted open-shell density functional method is also applied for the lowest core-valence energies. Furthermore, cross sections through a scheme for computing multiatom Auger transitions generating core-valence holes are presented. We find that the procedure outlined is capable of deriving the energy onset of core-valence ionization within a fraction of an eV and that assignments can be made of the most salient spectral features.

  • 37.
    Niskanen, Johannes
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, Cui
    Monti, Susanna
    Carravetta, Vincenzo
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hybrid density functional-molecular mechanics calculations for core-electron binding energies of glycine in water solution2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 1, p. 244-254Article in journal (Refereed)
    Abstract [en]

    We report hybrid density functional theory-molecular mechanics (DFT/MM) calculations performed for glycine in water solution at different pH values. In this paper, we discuss several aspects of the quantum mechanics-molecular mechanics (QM/MM) simulations where the dynamics and spectral binding energy shifts are computed sequentially, and where the latter are evaluated over a set of configurations generated by molecular or Car-Parrinello dynamics simulations. In the used model, core ionization takes place in glycine as a quantum mechanical (QM) system modeled with DFT, and the solution is described with expedient force fields in a large molecular mechanical (MM) volume of water molecules. The contribution to the core electronic binding energy from all interactions within and between the two (DFT and MM) parts is accounted for, except charge transfer and dispersion. While the obtained results were found to be in qualitative agreement with experiment, their precision must be qualified with respect to the problem of counter ions, charge transfer and optimal division of QM and MM parts of the system. Results are compared to those of a recent study [Ottoson et al., J. Am. Chem. Soc., 2011, 133, 3120].

  • 38. Nørby, M. S.
    et al.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden .
    Kongsted, J.
    Assessing frequency-dependent site polarisabilities in linear response polarisable embedding2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, p. 39-47Article in journal (Refereed)
    Abstract [en]

    In this paper, we discuss the impact of using a frequency-dependent embedding potential in quantum chemical embedding calculations of response properties. We show that the introduction of a frequency-dependent embedding potential leads to further model complications upon solving the central equations defining specific molecular properties. On the other hand, we also show from a numerical point of view that the consequences of using such a frequency-dependent embedding potential is almost negligible. Thus, for the kind of systems and processes studied in this paper the general recommendation is to use frequency-independent embedding potentials since this leads to less complicated model issues. However, larger effects are expected if the absorption bands of the environment are closer to that of the region treated using quantum mechanics.

  • 39. Oprea, C
    et al.
    Rinkevicius, Zilvinas
    KTH, Superseded Departments, Biotechnology.
    Ruud, K
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Relativistic nuclear shielding obtained by linear and quadratic density functional response theoryManuscript (preprint) (Other academic)
  • 40. Oprea, C
    et al.
    Rinkevicius, Zilvinas
    KTH, Superseded Departments, Biotechnology.
    Ruud, K
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Relativistic nuclear shieldings obtained by linear and quadratic density functional response theoryManuscript (Other academic)
  • 41.
    Oprea, Corneliu Ioan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ruud, K.
    Relativistic nuclear shieldings with linear and quadratic density functional response theoryManuscript (Other academic)
  • 42.
    Oprea, Corneliu Ioan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ruud, K.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Restricted density functional quadratic response theory of electronic g-tensorsIn: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed)
  • 43.
    Oprea, Corneliu Ioan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ruud, K.
    Department of Chemistry, University of Tromsø.
    Density functional theory study of indirect nuclear spin-spin coupling constants with spin-orbit corrections2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 1, p. 014101-1-014101-10Article in journal (Refereed)
    Abstract [en]

    This work outlines the calculation of indirect nuclear spin-spin coupling constants with spin-orbit corrections using density functional response theory. The nonrelativistic indirect nuclear spin-spin couplings are evaluated using the linear response method, whereas the relativistic spin-orbit corrections are computed using quadratic response theory. The formalism is applied to the homologous systems H2X (X= O, S, Se, Te) and XH4 (X= C, Si, Ge, Sn, Pb) to calculate the indirect nuclear spin-spin coupling constants between the protons. The results confirm that spin-orbit corrections are important for compounds of the H2X series, for which the electronic structure allows for an efficient coupling between the nuclei mediated by the spin-orbit interaction, whereas in the case of the XH4 series the opposite situation is encountered and the spin-orbit corrections are negligible for all compounds of this series. In addition we analyze the performance of the density functional theory in the calculations of nonrelativistic indirect nuclear spin-spin coupling constants.

  • 44.
    Oprea, Corneliu Ioan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Telyatnyk, Lyudmyla
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Time-dependent density functional theory with the generalized restricted-unrestricted approach2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, no 17, p. 174103-Article in journal (Refereed)
    Abstract [en]

    This work presents the derivation, implementation, and first applications of the generalized restricted-unrestricted method based on the density functional Kohn-Sham formalism. By using a spin-restricted Kohn-Sham representation for the reference state the well-known spin contamination problem is avoided, while the unrestricted representation of the perturbation response retains a proper description of spin polarization. The formulation is a generalization of our previous implementation of the restricted-unrestricted method [Z. Rinkevicius , J. Chem. Phys. 121, 7614 (2004)], as it accounts for the full unrestricted response instead of describing the spin polarization in terms of triplet operators only. The purpose of this paper is to investigate the role of the generalization employed and demonstrate its numerical performance. For this purpose we focus on isotropic hyperfine coupling constants of a set of organic radicals and transition metal compounds. For both classes of molecules we observe that the effect of neglecting singlet excitation operators in the response part of restricted-unrestricted formalism changes the calculated hyperfine coupling parameters by a few MHz. The obtained results confirm the validity of the approximation used in the simplified restricted-unrestricted approach, i.e. spin polarization can, in most cases, be adequately described by an account of only triplet operators in the response term.

  • 45.
    Oprea, Corneliu
    et al.
    KTH, School of Biotechnology (BIO).
    Rinkevicius, Zilvinas
    KTH, Superseded Departments, Biotechnology.
    Telyatnyk, Lydumyla
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Density functional theory for spin Hamiltonian parameters of azurin: Part I. EPR parametersManuscript (Other academic)
  • 46.
    Perumal, Sathya S. R. R.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Minaev, Boris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olov
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Spin-spin coupling in (3)b(2) state of oxyallyl - A comparative study with trimethylenemethane2011In: Computational and Theoretical Chemistry, ISSN 2210-271X, Vol. 963, no 1, p. 51-54Article in journal (Refereed)
    Abstract [en]

    Internal splittings in the spectra are due to quantized angular momentum field of the molecule or atom, which couples through spin–spin and spin–orbit operators. These operators are subjected to recently observed close lying states of oxyallyl biradical and compared with the iso-electronic structure trimethylenemethane. With the multiconfigurational treatment of spin–spin coupling operator we predict reversal of the splitting parameter Dss of oxyallyl with reference to isoelectronic TMM spectra.

     

  • 47.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    de Almeida, Katia Júlia
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Oprea, Corneliu I.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ruud, Kenneth
    Univ Tromso, Dept Chem, Ctr Theoret & Computat Chem.
    Degenerate perturbation theory for electronic g tensors: leading-order relativistic effects2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 11, p. 1810-1828Article in journal (Refereed)
    Abstract [en]

    A new approach for the evaluation of the leading-order relativistic corrections to the electronic g tensors of molecules with a doublet ground state is presented. The methodology is based on degenerate perturbation theory and includes all relevant contributions to the g tensor shift up to order theta(alpha(4)) originating from the one-electron part of the Breit-Pauli Hamiltonian-that is, it allows for the treatment of scalar relativistic, spin-orbit, and mixed corrections to the spin and orbital Zeeman effects. This approach has been implemented in the framework of spin-restricted density functional theory and is in the present paper, as a first illustration of the theory, applied to study relativistic effects on electronic g tensors of dihalogen anion radicals X-2(-) (X = F, Cl, Br, I). The results indicate that the spin-orbit interaction is responsible for the large parallel component of the g tensor shift of Br-2(-) and I-2(-), and furthermore that both the leading-order scalar relativistic and spin-orbit corrections are of minor importance for the perpendicular component of the g tensor in these molecules since they effectively cancel each other. In addition to investigating the g tensors of dihalogen anion radicals, we also critically examine the importance of various relativistic corrections to the electronic g tensor of linear molecules with Sigma-type ground states and present a two-state model suitable for an approximate estimation of the g tensor in such molecules.

  • 48.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    de Almeida, Katia Júlia
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Density functional restricted-unrestricted approach for nonlinear properties: Application to electron paramagnetic resonance parameters of square planar copper complexes2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 6, p. 064109-1-064109-17Article in journal (Refereed)
    Abstract [en]

    The density functional restricted-unrestricted approach for treatments of spin polarization effects in molecular properties using spin restricted Kohn-Sham theory has been extended from linear to nonlinear properties. It is shown that the spin polarization contribution to a nonlinear property has the form of a quadratic response function that includes the zero-order Kohn-Sham operator, in analogy to the lower order case where the spin polarization correction to an expectation value has the form of a linear response function. The developed approach is used to formulate new schemes for computation of electronic g-tensors and hyperfine coupling constants, which include spin polarization effects within the framework of spin restricted Kohn-Sham theory. The proposed computational schemes are in the present work employed to study the spin polarization effects on electron paramagnetic resonance spin Hamiltonian parameters of square planar copper complexes. The obtained results indicate that spin polarization gives rise to sizable contributions to the hyperfine coupling tensor of copper in all investigated complexes, while the electronic g-tensors of these complexes are only marginally affected by spin polarization and other factors, such as choice of exchange-correlation functional or molecular structures, will have more pronounced impact on the accuracy of the results.

  • 49.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Frecus, Bogdan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Encapsulation Influence on EPR Parameters of Spin-Labels: 2,2,6,6-Tetramethyl-4-methoxypiperidine-1-oxyl in Cucurbit[8]uril2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 1, p. 257-263Article in journal (Refereed)
    Abstract [en]

    Encapsulation of a nitroxide spin label into a host cavity can prolong the lifetime of the spin label in biological tissues and other environments. Although such paramagnetic supramolecular complexes have been extensively studied experimentally, there is yet little understanding of the role of the encapsulation on the magnetic properties of the spin labels and their performance at the atomistic level. In this work, we approach this problem by modeling encapsulation induced changes of the magnetic properties of spin labels for a prototypical paramagnetic guest host complex, 2,2,6,6-tetramethyl-4-methoxypiperidine-1-oxyl, enclosed in the hydrophobic cavity of cucurbit[8]uril, using state-of-the-art hybrid quantum mechanics/molecular mechanics methodology. The results allow a decomposition of the encapsulation shift of the electronic g-tensor and the nitrogen isotropic hyperfine coupling constant of nitroxide radical into a set of distinct contributions associated with the host cavity confinement and with changes of the local solvent environment of the spin label upon encapsulation. It is found that the hydrophobic cavity of cucurbit[8]uril only weakly influences the electronic g-tensor of the 2,2,6,6-tetramethyl-4-methoxypiperidine-1-oxyl but induces a significant encapsulation shift of the nitrogen hyperfine coupling constant. The latter is caused by the change of topology of the hydrogen bonding network and the nature of the hydrogen bonds around the spin label induced by the hydrophobic cavity of the inclusion host. This indirect effect is found to be more important than the direct influence of the cavity exerted on the radical. The ramification of this finding for the use of approximate methods for computing electron paramagnetic resonance spectra of spin labels and for designing optimal spin labels based on guest-host templates is discussed.

  • 50.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Jha, Prakash Chandra
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Oprea, Corneliu Ioan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Time-dependent density functional theory for non-linear properties of open-shell systems2007In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 127, no 11, p. 114101-Article in journal (Refereed)
    Abstract [en]

    This paper presents response theory based on a spin-restricted Kohn-Sham formalism for computation of time-dependent and time-independent nonlinear properties of molecules with a high spin ground state. The developed approach is capable to handle arbitrary perturbations and constitutes an efficient procedure for evaluation of electric, magnetic, and mixed properties. Apart from presenting the derivation of the proposed approach, we show results from illustrating calculations of static and dynamic hyperpolarizabilities of small Si(3n+1)H(6n+3) (n=0,1,2) clusters which mimic Si(111) surfaces with dangling bond defects. The results indicate that the first hyperpolarizability tensor components of Si(3n+1)H(6n+3) have an ordering compatible with the measurements of second harmonic generation in SiO2/Si(111) interfaces and, therefore, support the hypothesis that silicon surface defects with dangling bonds are responsible for this phenomenon. The results exhibit a strong dependence on the quality of basis set and exchange-correlation functional, showing that an appropriate set of diffuse functions is required for reliable predictions of the first hyperpolarizability of open-shell compounds.

12 1 - 50 of 80
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