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  • 1. 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.

  • 2. Berman, G. P.
    et al.
    Borgonovi, F.
    Rinkevicius, Zilvinas
    KTH, Superseded Departments, Biotechnology.
    Tsifrinovich, V. I.
    Single-spin measurements for quantum computation using magnetic resonance force microscopy2003In: Superlattices and Microstructures, ISSN 0749-6036, E-ISSN 1096-3677, Vol. 34, no 06-mar, p. 509-511Article in journal (Refereed)
    Abstract [en]

    The quantum theory of a single-spin measurement using magnetic resonance force microscopy is presented. We use an oscillating cantilever-driven adiabatic reversal technique. The frequency shift of the cantilever vibrations is estimated. We show that the frequency shift causes the formation of a Schrodinger cat state for the cantilever. The interaction between the cantilever and the environment quickly destroys the coherence between the two cantilever trajectories. It is shown that using partial adiabatic reversals one can obtain a significant increase in the frequency shift. We discuss the possibility of sub-magneton spin density detection in molecules using magnetic resonance force microscopy.

  • 3.
    Chattopadhyaya, Mausumi
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    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.
    Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 36, p. 7175-7182Article in journal (Refereed)
    Abstract [en]

    We study the linear and nonlinear optical properties of a well-known acid base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral double right arrow anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral double right arrow anionic and open neutral double right arrow dianionic, can contribute to the pH- dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe.

  • 4.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cao, Zexing
    Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, China .
    Ruud, Kenneth
    Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsö, Norway.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zero-point vibrational corrections to isotropic hyperfine coupling constants in polyatomic molecules2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 2, p. 696-707Article in journal (Refereed)
    Abstract [en]

    The present work addresses isotropic hyperfine coupling constants in polyatomic systems with a particular emphasis on a largely neglected, but a posteriori significant, effect, namely zero-point vibrational corrections. Using the density functional restricted-unrestricted approach, the zero-point vibrational corrections are evaluated for the allyl radical and four of its derivatives. In addition for establishing the numerical size of the zero-point vibrational corrections to the isotropic hyperfine coupling constants, we present simple guidelines useful for identifying hydrogens for which such corrections are significant. Based on our findings, we critically re-examine the computational procedures used for the determination of hyperfine coupling constants in general as well as the practice of using experimental hyperfine coupling constants as reference data when benchmarking and optimizing exchange-correlation functionals and basis sets for such calculations.

  • 5.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Role of the 3(ππ*) state in photolysis of lumisantonin: insight from ab initio studies2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 26, p. 7815-7822Article in journal (Refereed)
    Abstract [en]

    The CASSCF and CASPT2 methodologies have been used to explore the potential energy surfaces of lumisantonin in the ground and low-lying triplet states along the photoisomerization pathways. Calculations indicate that the (n pi*) state is the accessible low-lying singlet state with a notable oscillator strength under an excitation wavelength of 320 nm and that it can effectively decay to the (3)(pi pi*) state through intersystem crossing in the region of minimum surface crossings with a notable spin-orbital coupling constant. The 3(pi pi*) state, derived from the promotion of an electron from the pi-type orbital mixed with the sigma orbital localized on the C-C bond in the three-membered alkyl ring to the pi* orbital of conjugation carbon atoms, plays a critical role in C-C bond cleavage. Based on the different C-C bond rupture patterns, the reaction pathways can be divided into paths A and B. Photolysis along path A arising from C1-C5 bond rupture is favorable because of the dynamic and thermodynamic preferences on the triplet excited-state PES. Path B is derived from the cleavage of the C5-C6 bond, leading first to a relatively stable species, compared to intermediate A-INT formed on the ground state PES. path B is relatively facile for the pyrolytic reaction. The present results provide a basis to interpret the experimental observations.

  • 6.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Theoretical studies on the mechanism of α-santonin photo-induced rearrangement2012In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 13, no 1, p. 353-362Article in journal (Refereed)
    Abstract [en]

    α-Santonin is the first organic compound observed to feature a photoinduced rearrangement and is now known to undergo a series of photochemical processes under UV irradiation. On the basis of the considerable interest of this system as a prototype, and of the yet limited insights reached for the basic photo mechanisms, we calculate the high-level electronic structures and explore the potential energy surfaces (PES) of α-santonin in the ground and lowest-lying excited states, their couplings, and the possible photoinduced isomerization pathways. The calculations identify the low-lying singlet excited state 1(nπ*) accessible under light irradiation, which decays to the low-energy 3(ππ*) state through an intersystem crossing in the Franck–Condon region to initiate the photoinduced rearrangement. The initial reaction from the C3C5 bond coupling, which takes place on the 3(ππ*) state potential energy surface, leads to a three-membered alkyl-ring compound intermediate state INT. The following photochemical reactions have the possibility to arise from two distinct CC bond cleavages, C4C5 and C3C4, denoted as path A and path B. Path A is favored both dynamically on the excited-state PES and thermodynamically on the ground-state PES in vacuo. Experiments show that it also becomes the dominant photoinduced rearrangement process in the crystal, which can be explained by considering the requirement for less space and the stacking effect under the confined environment. Path B is dynamical advantaged both on the ground- and excited-state PESs in a weak polar solvent, such as dioxane. Once the biradical intermediate B-INT is accessible on the ground-state PES, the formation of the product B-P is almost barrier free.

  • 7.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ruud, K.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Role of zero-point vibrational corrections to carbon hyperfine coupling constants in organic pi radicals2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 138, no 5, p. 054310-Article in journal (Refereed)
    Abstract [en]

    By analyzing a set of organic pi radicals, we demonstrate that zero-point vibrational corrections give significant contributions to carbon hyperfine coupling constants, in one case even inducing a sign reversal for the coupling constant. We discuss the implications of these findings for the computational analysis of electron paramagnetic spectra based on hyperfine coupling constants evaluated at the equilibrium geometry of radicals. In particular, we note that a dynamical description that involves the nuclear motion is in many cases necessary in order to achieve a semi-quantitatively predictive theory for carbon hyperfine coupling constants. In addition, we discuss the implications of the strong dependence of the carbon hyperfine coupling constants on the zero-point vibrational corrections for the selection of exchange-correlation functionals in density functional theory studies of these constants.

  • 8.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ruud, Kenneth
    Centre ofTheoretical and computational Chemistry, Department of Chemistry, University of Tromsø.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vibrationally induced carbon hyperfine coupling constants: a reinterpretation of the McConnell relationManuscript (preprint) (Other academic)
  • 9.
    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.

  • 10.
    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)
  • 11.
    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)
  • 12. Cronstrand, P.
    et al.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Time-dependent density-functional theory calculations of triplet-triplet absorption2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 22Article in journal (Refereed)
    Abstract [en]

    We present density-functional theory calculations of triplet-triplet absorption by three different approaches based on time-dependent density-functional theory (DFT): unrestricted DFT linear response, open-shell restricted DFT linear response applied to the triplet state, and quadratic response with triplet excitations applied to the ground state. Comparison is also made with corresponding results obtained by Hartree-Fock and multiconfiguration self-consistent-field response theory. Two main conclusions concerning triplet-triplet transitions are drawn in this study: First, the very good agreement between unrestricted and restricted DFT results indicates that spin contamination of the triplet state is not a serious problem when computing triplet-triplet spectra of common organic molecules. Second, DFT response calculations of triplet-triplet transitions can be affected by triplet instability problems, especially for the combination of DFT quadratic response with functionals containing fractional exact Hartree-Fock exchange.

  • 13.
    Daniel, Quentin
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Huang, Ping
    Fan, Ting
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wang, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Duan, Lele
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Wang, Lei
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Li, Fusheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mamedov, Fikret
    Styring, Stenbjörn
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Rearranging from 6-to 7-coordination initiates the catalytic activity: An EPR study on a Ru-bda water oxidation catalyst2017In: Coordination chemistry reviews, ISSN 0010-8545, E-ISSN 1873-3840, Vol. 346, p. 206-215Article in journal (Refereed)
    Abstract [en]

    The coordination of a substrate water molecule on a metal centered catalyst for water oxidation is a crucial step involving the reorganization of the ligand sphere. This process can occur by substituting a coordinated ligand with a water molecule or via a direct coordination of water onto an open site. In 2009, we reported an efficient ruthenium-based molecular catalyst, Ru-bda, for water oxidation. Despite the impressive improvement in catalytic activity of this type of catalyst over the past years, a lack of understanding of the water coordination still remains. Herein, we report our EPR and DFT studies on Ru-bda (triethylammonium 3-pyridine sulfonate)(2) (1) at its Ru-III oxidation state, which is the initial state in the catalytic cycle for the O-O bond formation. Our investigation suggests that at this III-state, there is already a rearrangement in the ligand sphere where the coordination of a water molecule at the 7th position (open site) takes place under acidic conditions (pH = 1.0) to form a rare 7-coordinated Ru-III species.

  • 14.
    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.

  • 15.
    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.

  • 16. 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.

  • 17.
    de Almeida, Katia Júlia
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hugosson, Håkan Wilhelm
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Cesar, Amary
    Univ Fed Minas Gerais, Dept Quim.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Modeling of EPR parameters of copper(II) aqua complexes2007In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 332, no 2-3, p. 176-187Article in journal (Refereed)
    Abstract [en]

    In this paper we report density functional theory calculations of the electronic g-tensor and hyperfine coupling constants of the copper dication in sixfold- and fivefold-coordination models of the first aqueous solvation sphere. The obtained results indicate that the electronic g-tensor of these copper complexes in combination with hyperfine coupling constants of copper in principle can be used to elucidate the coordination environment of the hydrated copper dication. In addition to these results, we have designed a methodology for accurate evaluation of electronic g-tensors and hyperfine coupling tensors in copper complexes, and demonstrate the applicability of this approach to copper dication aqua complexes.

  • 18.
    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)
  • 19.
    Duan, Sai
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Synerget Innovat Ctr Quantum Informat & Quantum P, Hefei 230026, Anhui, Peoples R China..
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre. Kaunas Univ Technol, Dept Phys, LT-51368 Kaunas, Lithuania..
    Tian, Guangjun
    Yanshan Univ, Sch Sci, Key Lab Microstruct Mat Phys Hebei Prov, Qinhuangdao 066004, Hebei, Peoples R China..
    Luo, Yi
    Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Synerget Innovat Ctr Quantum Informat & Quantum P, Hefei 230026, Anhui, Peoples R China..
    Optomagnetic Effect Induced by Magnetized Nanocavity Plasmon2019In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 141, no 35, p. 13795-13798Article in journal (Refereed)
    Abstract [en]

    We propose a new type of optomagnetic effect induced by a highly confined plasmonic field in a nanocavity. It is shown that a very large dynamic magnetic field can be generated as the result of the inhomogeneity of nanocavity plasmons, which can directly activate spin-forbidden transitions in molecules. The dynamic optomagnetic effects on optical transitions between states of different spin multiplicities are illustrated by first-principles calculations for C-60. Remarkably, the intensity of spin forbidden singlet-to-triplet transitions can even be stronger than that of singlet-to-singlet transitions when the spatial distribution of plasmon is comparable with the molecular size. This approach not only offers a powerful optomagnetic means to rationally fabricate molecular excited states with different multiplicities but also provides a groundbreaking concept of the light-matter interaction that could lead to the observation of new physical phenomena and the development of new techniques.

  • 20.
    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.

  • 21.
    Frecus, Bogdan
    et al.
    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.
    π –stacking effects on the EPR parameters of a prototypical DNA spin label2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 25, p. 10466-10471Article in journal (Refereed)
    Abstract [en]

    The character and value of spin labels for probing environments like double-stranded DNA depends on the degree of changeof the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoreticalinvestigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusingon the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporatingthe spin label into selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label is onlynegligibly affected by its incorporation into DNA, when compared to the its free form. This result gives theoretical ground forthe common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurementsof distance between spin labels incorporated into DNA.

  • 22. Frediani, L.
    et al.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Two-photon absorption in solution by means of time-dependent density-functional theory and the polarizable continuum model2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 24Article in journal (Refereed)
    Abstract [en]

    We present the first study of two-photon absorption (TPA) of solvated molecules based on direct evaluation of TPA cross sections from the quadratic response of time-dependent perturbations. A set of prototypical two-photon (TP) chromophores has been selected and analyzed: a pure pi system (t-stilbene) and its substituted homologs obtained employing a donor (D) and an acceptor (A) group to probe the solvent effects along the series pi, D-pi-D, A-pi-D, and A-pi-A. For the selected systems we have calculated the TPA cross sections in different environments by means of the polarizable continuum model. The data have been analyzed to evaluate how the structural and environmental parameters contribute to the final two-photon absorption cross section. These include molecular structure, geometry relaxation in solution, polarity, and refractive index of the solvent. The performances of the three common functionals SVWN, BLYP, and B3LYP have been compared. The results show a significant solvent dependence of the TPA cross section and an unusual trend when passing from cyclohexane to water. The data have also been rationalized in terms of the main orbital excitations leading to the transitions. Finally, trends along the series have been described and comparison with experiments and previous calculations has been drawn.

  • 23.
    Gavrilyuk, Sergey
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Polyutov, Sergey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jha, Prakash Chandra
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Many-photon dynamics of photobleaching2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, p. 11961-11975Article in journal (Refereed)
    Abstract [en]

    A detailed dynamical theory of photobleaching by periodical sequences of laser pulses is presented. The theory is used for interpretation of recent experiments with pyrylium salts. Our simulations are based on first-principles simulations of photoabsorption cross-sections and on empirical rate constants. Two competitive channels of photobleaching, namely, photobleaching from the lowest excited singlet and triplet states and from higher excited states, are found to explain different intensity dependences of the photobleaching rates in different samples. The process includes two-photon excitation from the ground state to the first or second excited singlet states and one-photon excitation from the first singlet or triplet states to higher excited states. The fluorescence follows double-exponential dynamics with two characteristic times. The first and the shorter one is the equilibrium settling time between the ground and the lowest triplet states. The second characteristic time, the time of photobleaching, is responsible for the long-term dynamics. The effective rate of photobleaching from the first excited singlet and lowest triplet states depends differently on the irradiance in comparison with the photobleaching in higher states. The first channel is characterized by a quadratic intensity dependence in contrast to the second channel that shows a cubic dependence. The competition between these photobleaching channels is very sensitive to the rate constants as well as to the repetition rate, the pulse duration, and the peak intensity. The double-exponential decay of the fluorescence is explained by the spatial inhomogeneity C of the light beam. The findings in this work are discussed in terms of the possibility of using many-photon-induced photobleaching for new three-dimensional read-write devices.

  • 24.
    Jha, Prakash Chandra
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Modeling two photon absorption cross sections of open-shell systems2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 1Article in journal (Refereed)
    Abstract [en]

    We demonstrate the prospects of computing two photon absorption cross sections of open-shell systems by applying recently developed spin-restricted time-dependent density functional response theory using the pyrrole radical as an example. The spin multiplicity effects on two photon absorption cross sections of this species are investigated for the doublet, quartet, and sextet states. It is found that irrespective of the exchange-correlation functional employed, the two photon cross sections increase with the increase in spin multiplicity. This result indicates that two photon cross sections of paramagnetic compounds can be controlled by manipulating their spin states and this opens new possibilities for design of hybrid magneto-optical materials.

  • 25.
    Jha, Prakash Chandra
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Spin Multiplicity Dependence of Nonlinear Optical Properties2009In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 10, no 5, p. 817-823Article in journal (Refereed)
    Abstract [en]

    Open-shell spin-restricted time-dependent density functional theory is applied to explore the spin multiplicity dependence of linear and nonlinear optical properties. An open-shell neutral conjugated system, the CAN radical in the doublet X(2)A(2), quartet X(4)A(2), and sextet X(6)A(1) states, is chosen as a model system to illustrate various aspects of the theory. It is found that irrespective of the exchange-correlation functional employed, the components of the polarizability alpha(-omega,omega) and first hyperpolarizability beta(-2(omega,omega,omega) show very different dependency with respect to the multiplicity, with an increasing trend for higher spin states. This is rationalized by the decrease in conjugation and stability of the system with increasing multiplicity, and by the way the interaction between unpaired electrons and the external field is shielded by remaining electrons of the molecule. The study suggests the applicability of open-shell systems for frequency-dependent nonlinear optical properties and for the possibility of spin control for such properties.

  • 26. Jha, Prakash Chandra
    et al.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Seal, Prasenjit
    Chakrabarti, Swapan
    Searching of potential energy curves for the benzene dimer using dispersion-corrected density functional theory2008In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 19, p. 2715-2721Article in journal (Refereed)
    Abstract [en]

    The present work aims to establish the utility of dispersion-corrected density functional theory for potential energy curves of the benzene dimer, a problem that has received significant attention for a long time. The interaction energies of parallel-stacked, T-shaped and parallel-displaced benzene dimer configurations have been evaluated using both dispersion- and normal gradient-corrected Perdew-Burke-Ernzerhof functionals along with Dunning's augmented correlation-consistent polarized valence triple-zeta (aug-cc-pVTZ) basis functions and compared with explicit correlation methods. The potential energy curves for the parallel-stacked and parallel-displaced benzene dimers are in excellent agreement with highly accurate coupled cluster (CCSD( T)) results, while for the T-shaped benzene dimer the dispersion- corrected results show a distinct deviation, being closer in that case to the MP2 level of results. The overestimation of interaction energy in the T-shaped dimer may be attributed to the presence of a permanent dipole moment in this configuration and indicates a structural dependence of the dispersion- corrected density functional method.

  • 27. 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

  • 28.
    Li, Cui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Institute of Chemical and Physical Processes, Italy.
    Monti, Susanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Institute of Chemistry of Organometallic Compounds, Italy.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Carravetta, V.
    Theoretical study of para-nitro-aniline adsorption on the Au(111) surface2016In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 649, p. 124-132Article in journal (Refereed)
    Abstract [en]

    The electronic structure, bonding properties and dynamics of para-nitro-aniline (PNA) adsorbed on the Au(111) surface for a sub-monolayer coverge have been investigated by density-functional theory (DFT) static calculations and quantum molecular dynamics simulations. Four main adsorption geometries have been identified by DFT energy optimization with the gradient corrected PBE functional and accounting for the role of the van del Waals (vdW) interaction. Quantum dynamics calculations starting from the four different structures have been performed at room temperature to estimate the relative stability of the adsorbates and the presence of barriers for their interconversion. Quantum simulations suggest that the most stable adsorption geometry at room temperature is that of PNA with a slightly distorted molecular plane almost parallel to the Au(111) surface. In a second less populated configuration the PNA molecule interacts with the substrate by its NO2 group while the molecular plane is orthogonal to the surface. The N 1s electron photoemission spectrum has been simulated for the identified adsorbate geometries and a measurable variation of the absolute and relative chemical shift for the two nitrogen atoms in comparison with the known values for PNA in gas phase is predicted.

  • 29.
    Li, Junfeng
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China .
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    A time-dependent density-functional theory and complete active space self-consistent field method study of vibronic absorption and emission spectra of coumarin2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 1, p. 014306-Article in journal (Refereed)
    Abstract [en]

    Time-dependent density-functional theory (TD-DFT) and complete active space multiconfiguration self-consistent field (CASSCF) calculations have been used to determine equilibrium structures and vibrational frequencies of the ground state and several singlet low-lying excited states of coumarin. Vertical and adiabatic transition energies of S-1, S-2, and S-3 have been estimated by TD-B3LYP and CASSCF/PT2. Calculations predict that the dipole-allowed S-1 and S-3 states have a character of (1)(pi pi*), while the dipole-forbidden (1)(n pi*) state is responsible for S-2. The vibronic absorption and emission spectra of coumarin have been simulated by TD-B3LYP and CASSCF calculations within the Franck-Condon approximation, respectively. The simulated vibronic spectra show good agreement with the experimental observations available, which allow us to reasonably interpret vibronic features in the S-0 -> S-1 and S-0 -> S-3 absorption and the S-0 <- S-1 emission spectra. Based on the calculated results, activity, intensity, and density of the vibronic transitions and their contribution to the experimental spectrum profile have been discussed.

  • 30.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Carravetta, Vincenzo
    Li, Cui
    Monti, Susanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. CNR-ICCOM, Italy .
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Optical Properties of Gold Nanoclusters Functionalized with a Small Organic Compound: Modeling by an Integrated Quantum-Classical Approach2016In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, no 7, p. 3325-3339Article in journal (Refereed)
    Abstract [en]

    Motivated by the growing importance of organometallic nanostructured materials and nanoparticles as microscopic devices for diagnostic and sensing applications, and by the recent considerable development in the simulation of such materials, we here choose a prototype system para-nitroaniline (pNA) on gold nanoparticles to demonstrate effective strategies for designing metal nanoparticles with organic conjugates from fundamental principles. We investigated the motion, adsorption mode, and physical chemistry properties of gold-pNA particles, increasing in size, through classical molecular dynamics (MD) simulations in connection with quantum chemistry (QC) calculations. We apply the quantum mechanics-capacitance molecular mechanics method [Z. Rinkevicius et al. J. Chem. Theory Comput. 2014, 10, 989] for calculations of the properties of the conjugate nanoparticles, where time dependent density functional theory is used for the QM part and a capacitance-polarizability parametrization of the MM part, where induced dipoles and charges by metallic charge transfer are considered. Dispersion and short-range repulsion forces are included as well. The scheme is applied to one- and two-photon absorption of gold-pNA clusters increasing in size toward the nanometer scale. Charge imaging of the surface introduces red-shifts both because of altered excitation energy dependence and variation of the relative intensity of the inherent states making up for the total band profile. For the smaller nanoparticles the difference in the crystal facets are important for the spectral outcome which is also influenced by the surrounding MM environment.

  • 31.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Binding Mechanism and Magnetic Properties of a Multifunctional Spin Label for Targeted EPR Imaging of Amyloid Proteins: Insight from Atomistic Simulations and First-Principles Calculations2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4766-4774Article in journal (Refereed)
    Abstract [en]

    Electron paramagnetic resonance (EPR) imaging techniques provide a promising approach to detect amyloid structures which are of paramount importance in early-stage diagnosis of conformational diseases. Here, we report a combined molecular dynamics and density functional theory/molecular mechanics computational scheme for evaluation of the binding mechanism between a multifunctional spin label and the target amyloid protein. In addition, we consider evaluation of EPR spin Hamiltonian parameters with the aim of providing a better microscopic understanding and interpretation of EPR spectroscopy. The results from molecular dynamics simulations suggest that the oligothiophene conjugate part of the spin label interacts with hydrophobic residues of the amyloid protein through hydrophobic attraction and that both the N-O bond length and the N-O out-of-plane tilt angle in the nitroxide group are slightly diminished after, complexation with the protein. The translational and rotational motions of the protein bound spin label are considerably slowed compared to those of the free spin label in aqueous solution, but interestingly, hydrogen bonds formed between the nitroxide oxygen group and the surrounding water molecules are hardly affected by the presence Of the amyloid protein. First principles calculation's suggest that EPR spin Hamiltonian parameters including the nitroxide nitrogen hyperfine coupling tensor A(N) and electronic g tensor suffer noticeable changes upon complexation with the protein. The magnitude of the A(N) tensor is found,to:be. closely related to the nitroxide N-O out tilt angle, while the g tensor is affected by both the nitroxide N-O bond length as well as the interaction between the spin label and the amyloid protein With this work we show that state-of-the-art simulation techniques represent a promising way of providing a detailed understanding of the microscopic mechanisms responsible for the formation and stability of a spin label complexed with amyloid structures as well as the magnetic properties of the free and protein-bound spin label.

  • 32.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nuclear magnetic shielding of the Cd-113(II) ion in aqua solution: A combined molecular dynamics/density functional theory study2008In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 112, no 36, p. 11347-11352Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics simulation and density functional theory investigation of the nuclear magnetic shielding constant of the Cd-113(II) ion solvated in aqueous solution. Molecular dynamics simulations are carried out for the cadmium-water system in order to produce instantaneous geometries for subsequent determination of the nuclear magnetic shielding constant at the density functional theory level. The nuclear magnetic shielding constant is computed using a perturbation theory formalism, which includes nonrelativistic and leading order relativistic contributions to the nuclear magnetic Shielding tensor. Although the NMR shielding constant varies significantly with respect to simulation time, the value averaged over increasing number of snapshots remains almost constant. The paramagnetic nonrelativistic contribution is found to be most sensitive to dynamical changes in the system and is mainly responsible for the thermal and solvent effects in solution. The relativistic correction features very little sensitivity to the chemical environment, and can be disregarded in theoretical calculations when a Cd complex is used as reference compound in Cd-113 NMR experiments, due to the mutual cancelation between individual relativistic corrections.

  • 33.
    Li, Xin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Tu, Yaoquan
    Tian, He
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Paramagnetic Perturbation of the F-19 NMR Chemical Shift in Fluorinated Cysteine by O-2: A Theoretical Study2009In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 113, no 31, p. 10916-10922Article in journal (Refereed)
    Abstract [en]

    We present a combined molecular dynamics and density functional theory study of dioxygen-induced perturbation of the F-19 NMR chemical shifts in an aqueous solution of fluorinated cysteine under 100 atm of O-2 partial pressure. Molecular dynamics Simulations are carried out to determine the dominant structures of O-2 and the fluorinated cysteine complexes in water, and the collected structural information is exploited in computation of F-19 chemical shifts using density functional theory. The obtained results indicate that the density redistribution of the O-2 unpaired electrons between the dioxygen and fluorinated cysteine is responsible for the experimentally observed perturbation of the F-19 NMR chemical shifts, where the Fermi contact interaction plays the key role. The O-2-induced paramagnetic F-19 chemical shift, averaged over the simulation trajectory, is comparable with the reported experimental values, proving the availability of the developed strategy for modeling F-19 NMR chemical shifts in the presence of paramagnetic agents in ail aqueous solution. The applicability of the combined molecular dynamics/density functional theory approach for dioxygen NMR perturbation to all resonating nuclei including H-1, C-13, N-15, and F-19 is emphasized, and the ramification of this for investigations of membrane protein structures is discussed.

  • 34.
    Li, Xin
    et al.
    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.
    Electronic Circular Dichroism of Surface-Adsorbed Molecules by Means of Quantum Mechanics Capacitance Molecular Mechanics2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 11, p. 5833-5840Article in journal (Refereed)
    Abstract [en]

    To promote a more comprehensive understanding of the influence of metal-adsorbate interaction for molecules at metallo surfaces or metallo nanoparticles in solvent environments on their electronic circular dichroism (ECD) spectra, we evaluate the application of a recently derived quantum mechanics capacitance molecular mechanics (QMCMM) model for ECD. Using helicene absorbed on gold surfaces in protic and aprotic solvents as illustration, we elucidate the detailed effects on excitation energies, transition moments, rotatory strengths, orientation dependence of ECD spectra, and the different roles of aprotic and protic solvents and the induced charge distribution patterns on the surface. These changes are decomposed in terms of surface alone, solvent alone, and combined surface solvent influence, and furthermore into the indirect contributions by the surface-induced restructuring of the helicene. Much of the salient changes of the ECD can be rationalized to the substantial redistribution of charge at the gold surface induced by the presence of the helicene. The study indicates that through the QMCMNI model the effects of a metallic surface on the circular dichroism spectra of adsorbed organic molecules can be tackled by extended QM calculations coupled to polarizability-capacitance force fields for large metallic clusters representing surfaces or nanoparticles.

  • 35.
    Li, Xin
    et al.
    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.
    Two-Photon Absorption of Metal-Assisted Chromophores2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 12, p. 5630-5639Article in journal (Refereed)
    Abstract [en]

    Aiming to understand the effect of a metal surface on nonlinear optical properties and the combined effects of surface and solvent environments on such properties, we present a multiscale response theory study, integrated with dynamics of the two-photon absorption of 4-nitro-4'-amino-trans-stilbene physisorbed on noble metal surfaces, considering two such surfaces, Ag(111) and Au(111), and two solvents, cyclohexane and water, as cases for demonstration. A few conclusions of general character could be drawn: While the geometrical change of the chromophore induced by the environment was found to notably alter (diminish) the two-photon absorption cross section in the polar medium, the effects of the metal surface and solvent on the electronic structure of the chromophore surpasses the geometrical effects and leads to a considerably enhanced two-photon absorption cross section in the polar solvent. This enhancement of two-photon absorption arises essentially from the metal charge image induced enlargement of the difference between the dipole moment of the excited state and the ground state. The orientation-dependence of the two-photon absorption is found to connect with the lateral rotation of the chromophore, where the two-photon absorption reaches its maximum when the polarization of the incident light coincides with the long-axis of the chromophore. Our results demonstrate a distinct enhancement of the two-photon absorption by a metal surface and a polar medium and envisage the employment of metal-chromophore composite materials for future development of nonlinear optical materials with desirable properties.

  • 36.
    Linares, Mathieu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Stafström, Sven
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Complex Polarization Propagator Approach in the Restricted Open-Shell, Self-Consistent Field Approximation: The Near K-Edge X-ray Absorption Fine Structure Spectra of Allyl and Copper Phthalocyanine2011In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 18, p. 5096-5102Article in journal (Refereed)
    Abstract [en]

    A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that 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 spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assign-lent of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

  • 37.
    Liu, Ji-Cai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Velkov, Yasen
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Resonant inelastic X-ray Raman scattering induced by Rabi flopping of core holes 2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 453, no 1-3, p. 117-121Article in journal (Refereed)
    Abstract [en]

    A new scheme of X-ray pump-probe experiment is suggested in this Letter, namely resonant inelastic X-ray scattering accompanied by core-hole hopping induced by a strong laser field. In particular, we study the dynamics of X-ray Raman scattering of N-2 molecules in a strong IR field. The laser-induced mixing of the core holes of opposite parities opens symmetry forbidden scattering channels. The strength of the symmetry forbidden channels strongly depends on the interrelationship between the time of Rabi flopping of the core holes and the scattering duration or the duration of the X-ray pulse.

  • 38.
    Liu, Ji-Cai
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Velkov, Yasen
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gel`mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Symmetry-forbidden x-ray Raman scattering induced by a strong infrared-laser field2008In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 77, no 4, p. 043405-Article in journal (Refereed)
    Abstract [en]

    Resonant inelastic x-ray scattering accompanied by core-hole hopping induced by a strong infrared-laser field is studied for the nitrogen molecule. This process involves a strong laser-field-induced promotion of ungerade core holes created by a weak x-ray pulse to a gerade core level, which opens symmetry-forbidden scattering channels and gives rise to new features in the x-ray scattering spectrum. The core-hole hopping within the short lifetime of the core-excited state required for observation of the described process can be achieved at moderate intensities of the infrared field (similar to 10(12) W/cm(2)) because of the large transition dipole moment between the relevant core levels. The dynamics of resonant inelastic x-ray scattering assisted by change of core-hole parity is studied in detail versus the intensity, detuning, phase, and duration of the incident infrared-laser and x-ray pulses.

  • 39. Loytynoja, T.
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Jankala, K.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Quantum mechanics capacitance molecular mechanics modeling of core-electron binding energies of methanol and methyl nitrite on Ag(111) surface2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145, no 2, article id 024703Article in journal (Refereed)
    Abstract [en]

    We study a newly devised quantum mechanics capacitance molecular mechanics ( QMCMM) method for the calculation of core-electron binding energies in the case of molecules adsorbed on metal surfaces. This yet untested methodology is applied to systems with monolayer of methanol/methyl nitrite on an Ag(111) surface at 100 K temperature. It was found out that the studied C, N, and O 1s core-hole energies converge very slowly as a function of the radius of the metallic cluster, which was ascribed to build up of positive charge on the edge of the Ag slab. Further analysis revealed that an extrapolation process can be used to obtain binding energies that deviated less than 0.5 eV against experiments, except in the case of methanol O 1s where the difference was as large as 1.8 eV. Additional QM-cluster calculations suggest that the latter error can be connected to the lack of charge transfer over the QM-CMM boundary. Thus, the results indicate that the QMCMM and QM-cluster methods can complement each other in a holistic picture of molecule-adsorbate core-ionization studies, where all types of intermolecular interactions are considered.

  • 40.
    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.

  • 41.
    Marcos, Rocio
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bertini, Federica
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Peruzzini, Maurizio
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Gonsalvi, Luca
    CNR, Inst Chim Composti Organometallici ICCOM, Via Madonna Piano 10, I-50019 Florence, Italy..
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Mechanistic Studies on NaHCO3 Hydrogenation and HCOOH Dehydrogenation Reactions Catalysed by a Fe-II Linear Tetraphosphine Complex2018In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 24, no 20, p. 5366-5372Article in journal (Refereed)
    Abstract [en]

    We present a theoretical extension of the previously published bicarbonate hydrogenation to formate and formic acid dehydrogenation catalysed by Fe-II complexes bearing the linear tetraphosphine ligand tetraphos-1. The hydrogenation reaction was found to proceed at the singlet surface with two competing pathways: A)H-2 association to the Fe-H species followed by deprotonation to give a Fe(H)(2) intermediate, which then reacts with CO2 to give formate. B)CO2 insertion into the Fe-H bond, followed by H-2 association and subsequent deprotonation. B was found to be slightly preferred with an activation energy of 22.8kcalmol(-1), compared to 25.3 for A. Further we have reassigned the Fe-H complex, as a Fe(H)(H-2), which undergoes extremely rapid hydrogen exchange.

  • 42.
    Masys, S.
    et al.
    Vilnius Univ, Fac Phys, Inst Theoret Phys & Astron, LT-10257 Vilnius, Lithuania..
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Theoret Chem & Biol, SE-10691 Stockholm, Sweden.;Kaunas Univ Technol, Fac Math & Nat Sci, Dept Phys, LT-51369 Kaunas, Lithuania..
    Tamuliene, J.
    Vilnius Univ, Fac Phys, Inst Theoret Phys & Astron, LT-10257 Vilnius, Lithuania..
    On the magnetic properties of nanodiamonds: Electronic g-tensor calculations2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 4, article id 044305Article in journal (Refereed)
    Abstract [en]

    The electronic g-tensor calculations are carried out for various paramagnetic defects introduced into hydrogenated diamond nanocrystal C35H36, showing that such a system can be successfully used to model magnetic properties of nanodiamonds (NDs) with paramagnetic centers containing no vacancies. In addition, it is revealed that, depending on the geometric positions in ND, paramagnetic centers of the same type produce noticeable variations of the g-tensor values. A side-by-side comparison of the performance of effective nuclear charge and spin-orbit mean field (SOMF) approaches indicates that the latter is more sensitive to the quality of basis sets, especially concerning diffuse functions, the inclusion of which is found to be nonbeneficial. What is more, the SOMF method also exhibits a much more pronounced gauge-origin dependence. Compared to electronic charge centroid, spin centers (SCs) demonstrate a superior suitability as gauge origins, providing a better agreement with diamagnetic and paramagnetic contributions of g-tensor obtained employing gauge-including atomic orbitals (GIAOs). Therefore, SCs can be recommended for the g-tensor calculations of NDs whenever GIAOs are not available.

  • 43. 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.

  • 44.
    Murugan, N Arul
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, J
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mikkelsen, K V
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution2011In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 13, no 27, p. 12506-12516Article in journal (Refereed)
    Abstract [en]

    The dimethylamino nitro stilbene (DANS) molecule is studied for exploring solvent effects on two-photon absorption using the quantum mechanical/molecular mechanical (QM/MM) response theory approach, where the quantum part is represented by density functional theory. We have explored the role of geometrical change of the chromophore in solution, the importance of taking a dynamical average over the sampled structures and the role of a granular representation of the polarization and electrostatic interactions with the classically described medium. The line shape function was simulated by the QM/MM technique thereby allowing for non-empirical prediction of the absolute two-photon cross section. We report a maximum in the TPA cross section for a medium of intermediate solvent polarity (i.e. in chloroform) and provide the grounds for an explanation of this effect which recently has been experimentally observed for a series of charge transfer species in solvents of different polarity. The calculations of absorption energies reproduce well the positive solvatochromic behavior of DANS and are in good agreement with experimental spectra available for the chloroform and DMSO solvents. In line with recent development of the QM/MM response technique for color modeling, we find this methodology to offer a versatile tool to predict and analyze two-photon absorption phenomena taking place within a medium.

  • 45.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    NMR Spin-Spin Coupling Constants in Polymethine Dyes as Polarity Indicators2012In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 18, no 37, p. 11677-11684Article in journal (Refereed)
    Abstract [en]

    Herein, we explore the use of spinspin coupling constants (SSCCs) in merocyanine (MCYNE) dyes as indicators of polarity. For this purpose, we use CarParrinello hybrid quantum mechanics/molecular mechanics (QM/MM) to determine the structures of MCYNE in solvents of different polarity, followed by computations of the SSCCs by using QM/MM linear-response theory. The molecular geometry of MCYNE switches between neutral, cyanine-like, and zwitterionic depending on the polarity of the solvent. This structural variation is clearly reflected in the proton SSCCs in the polymethine backbone, which are highly sensitive to the dielectric nature of the environment; this mechanism can be used as a polarity indicator for different microenvironments. This result is highlighted by computing the SSCCs of the MCYNE probe in the cavity of the beta-lactoglobulin protein. The computed SSCCs clearly indicate a non-polar hydrophobic dielectric nature of this cavity.

  • 46.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Apostolov, Rossen Pavlov
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    epartment of Physics, Chemistry and Pharmacy, University of Southern Denmark.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane2013In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, no 36, p. 13590-13597Article in journal (Refereed)
    Abstract [en]

    Along with the growing evidence that relates membrane abnormalities to various diseases, biological membranes have been acknowledged as targets for therapy. Any such abnormality in the membrane structure alters the membrane potential which in principle can be captured by measuring properties of specific optical probes. There exists by now many molecular probes with absorption and fluorescence properties that are sensitive to local membrane structure and to the membrane potential. To suggest new high-performance optical probes for membrane-potential imaging it is important to understand in detail the membrane-induced structural changes in the probe, the membrane association dynamics of the probe, and its membrane-specific optical properties. To contribute to this effort, we here study an optical probe, N-acetylaladanamide (NAAA), in the presence of a POPC lipid bilayer using a multiscale integrated approach to assess the probe structure, dynamics, and optical properties in its membrane-bound status and in water solvent. We find that the probe eventually assimilates into the membrane with a specific orientation where the hydrophobic part of the probe is buried inside the lipid bilayer, while the hydrophilic part is exposed to the water solvent. The computed absorption maximum is red-shifted when compared to the gas phase. The computations of the two-photon absorption and second harmonic generation cross sections of the NAAA probe in its membrane-bound state which is of its first kind in the literature suggest that this probe can be used for imaging the membrane potential using nonlinear optical microscopy.

  • 47.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Jha, Prakash Chandra
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ruud, Kenneth
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Solvatochromic shift of phenol blue in water from a combined Car-Parrinello molecular dynamics hybrid quantum mechanics-molecular mechanics and ZINDO approach2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 132, no 23, p. 234508-Article in journal (Refereed)
    Abstract [en]

    The present work addresses the solvatochromic shift of phenol blue (PB) dye. For this purpose the results of Car-Parrinello molecular dynamics (CPMD) simulations for PB in gas phase are compared with results obtained for PB in water from CPMD hybrid quantum mechanics-molecular mechanics (CPMD-QM/MM) calculations. The absorption spectra were obtained using the intermediate neglect of differential overlap/spectroscopic-configuration interaction (INDO/CIS) method and were calculated for a multitude of configurations of the trajectory. The calculated lambda(max) for PB in gas phase was found to be about 535 nm, which is considerably lower than the lambda(max) reported for PB in nonpolar solvents. Different solvation shells for PB in water have been defined based on the solute-all-atoms and solvent center of mass radial distribution function (g(r(X-O))). The electronic excitation energies for PB computed in the presence of solvent molecules in an increasing number of solvation shells were calculated in a systematic way to evaluate their contributions to the solvatochrmic shift. The inclusion of solvent molecules in the hydration shell yields a lambda(max) of 640 nm, which contributes to almost 78% of the solvatochromic shift. The inclusion of solvent molecules up to 10 angstrom in the g(r(X-O)) rdf yields a lambda(max) of 670 nm which is in good agreement with the experimentally reported value of 654-684 nm. Overall, the present study suggests that the combined CPMD-QM/MM and INDO-CIS approach can be used successfully to model solvatochromic shifts of organic dye molecules. (C) 2010 American Institute of Physics. [doi:10.1063/1.3436516]

  • 48.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Kongsted, Jacob
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Agren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Modeling the Structure and Absorption Spectra of Stilbazolium Merocyanine in Polar and Nonpolar Solvents Using Hybrid QM/MM Techniques2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 42, p. 13349-13357Article in journal (Refereed)
    Abstract [en]

    We have performed Car-Parrinello mixed quantum mechanics/molecular mechanics (CP-QM/MM) calculations for stilbazolium merocyanine (SM) in polar and nonpolar solvents in order to explore the role of solute molecular geometry, solvation shell structure, and different interaction mechanisms on the absorption spectra and its dependence on solvent polarity. On the basis of the average bond length values and group charge distributions, we find that the SM molecule remains in a neutral quinonoid form in chloroform (a nonpolar solvent) while it transforms to a charge-separated benzenoid form in water (a polar solvent). Based on a quantum mechanical/molecular mechanical response technique, with different MM descriptions for the water environment, absorption spectra were obtained as averages over configurations derived from the CP-QM/MM simulations. We show that for SM in water the solute polarization plays a major role in predictions of the lambda(max) and solvatochromic shift and that once this effect is included the contributions from solvent polarization and intermolecular charge transfer become less important. For SM in chloroform and water solvents, we have also performed absorption spectra calculations using a polarizable continuum model in order to address its relative performance compared to the QM/MM response technique. In the case of SM in water, our study supports the notion that, in order to predict accurate absorption spectra and solvatochromic shifts, it is important to use a discrete description of the solvent when it, as in water, is involved in site-specific interaction with the solute molecule. The technique is thus shown to outperform the more conventional polarizable continuum model in predicting the solvatochromic shift.

  • 49.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Kongsted, Jacob
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Breakdown of the first hyperpolarizability/bond-length alternation parameter relationship2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 38, p. 16453-16458Article in journal (Refereed)
    Abstract [en]

    We have investigated the dependence of the static first hyperpolarizability on the bond-length alternation (BLA) parameter. Our analysis indicates that the validity of the first hyperpolarizability/BLA parameter relationship is restricted to the no-field, vacuum, limit, while it successively breaks down along with increasing polarity of a surrounding medium, becoming invalid, for instance, in an aqueous solution. This contention is based on a series of TD-DFT, TD-DFT/PCM and hybrid TD-DFT/MM calculations of the first hyperpolarizability for a set of molecular configurations generated from Car-Parrinello hybrid QM/MM simulations of the stilbazolium merocyanine chromophore in chloroform and water solvents, and on a rationalization by means of the two-state model for the first hyperpolarizability. The BLA dependence of the three parameters entering the two-state model is shown to be qualitatively different in vacuum and in solvents. Particularly, in the vacuum case, the difference between ground and excited state dipole moments goes to zero for a vanishing BLA, which is not true in the presence of an aqueous medium. In the aqueous medium, an opposing behavior of the parameters involved in the two-state model results in an almost constant first hyperpolarizability with varying BLA parameter.

  • 50.
    Natarajan Arul, Murugan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Color modeling of protein optical probes2012In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, no 3, p. 1107-1112Article in journal (Refereed)
    Abstract [en]

    We present a strategy for modeling optical probes within heterogeneous environments of restricted dimension. The method is based on a multiphysics approach comprising sequential structure modeling by means of hybrid Car-Parrinello molecular dynamics and property modeling by means of quantum mechanics/molecular mechanics response theory. For demonstration we address the structural and optical properties of nile red within the beta-lacto globulin protein. We consider the cases with the probe situated on the surface or within the cavity of the protein, or embedded in a water solvent. We find the absorption properties of the probe to be highly dependent on its position relative to the protein. Structural rearrangements of the optical probe are found to contribute significantly to these environmental effects.

123 1 - 50 of 110
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