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  • 51. Baev, A.
    et al.
    Gelmukhanov, Faris
    KTH, Superseded Departments, Chemistry.
    Kimberg, Viktor
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Nonlinear propagation of strong multi-mode fields2003In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 36, p. 3761-3774Article in journal (Refereed)
    Abstract [en]

    We develop a strict theory of nonlinear propagation of few interacting stronglight beams. The key idea of our approach is a self-consistent solution ofthe nonlinear wave equation and the density matrix equations of the materialbeyond the rotatory wave approximation. We assume a Fourier expansion ofthe density matrixwhich goes beyond the conventionalTaylor expansions of thepolarization over the field amplitudeswhich is inadequate for the field strengthsthat we are interested in. Two qualitatively different situations are considered,with and without phase matching. Unlike in our previous paper (Baev et al2003 J. Opt. Soc. Am. B at press) devoted to the three-photon (TP) absorptioninduced upconverted lasing, we obtain here a strict solution for the nonlinearinteraction between different light beams. The general theory is applied to anumerical study of the role of saturation in TP photoabsorption by an organicchromophore in solution.

  • 52. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A quantum mechanical - Electrodynamical approach to nonlinear properties: Application to optical power limiting with platinum-organic compounds2007In: Journal of nonlinear optical physics and materials, ISSN 0218-8635, Vol. 16, no 2, p. 157-169Article in journal (Refereed)
    Abstract [en]

    Light propagation in a medium is sensitively dependent on the shape and intensity of the optical pulse as well as on the electronic and vibrational structure of the basic molecular units. We review in this paper the results of systematic studies of this problem for isotropic media. Our theoretical approach - the quantum mechanical-electrodynamical (QMED) approach - is based on a quantum mechanical account of the many-level electron-nuclear medium coupled to a numerical solution of the density matrix and Maxwell's equations. This allows us to accommodate a variety of nonlinear effects which accomplish the propagation of strong light pulses. Particular attention is paid to the understanding of the role of coherent and sequential excitations of electron-nuclear degrees of freedom. The QMED combination of quantum chemistry with classical pulse propagation enables us to estimate the optical transmission from cross sections of multi-photon absorption processes and from considerations of propagation effects, saturation and pulse effects. Results of the theory suggest that in the nonlinear regime, it is often necessary to simultaneously account for coherent one-step and incoherent step-wise multi-photon absorption, as well as for off-resonant excitations even when resonance conditions prevail. The dynamic theory of nonlinear propagation of a few interacting intense light pulses is highlighted here in a study of the optical power limiting with platinum-organic molecular compounds. © World Scientific Publishing Company.

  • 53. Baev, A.
    et al.
    Welinder, P.
    Erlandsson, R.
    Henriksson, J.
    Norman, P.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Light-matter interaction of strong laser pulses in the micro-, nano-, and picosecond regimes2007In: Materials Research Society Symposium Proceedings, 2007, p. 12-29Conference paper (Refereed)
    Abstract [en]

    Light propagation in a medium is sensitively dependent on the shape and intensity of the optical pulse as well as on the electronic and vibrational structure of the basic molecular units. We review in this paper results of systematic studies of this problem for isotropic media. Our theoretical approach-the quantum mechanical-electrodynamical (QMED) approach-is based on a quantum mechanical account of the many-level electron-nuclear medium coupled to a numerical solution of the density matrix and Maxwell s equations. This allows to accommodate a variety of nonlinear effects which accomplish the propagation of strong light pulses. Particular attention is paid to the understanding of the role of coherent and sequential excitations of electron-nuclear degrees of freedom. The QMED combination of quantum chemistry with classical pulse propagation allows to estimate the optical transmission from cross sections of multi-photon absorption processes and from considerations of propagation effects, saturation and pulse effects. Results of the theory suggest that in the nonlinear regime it is often necessary to account simultaneously for coherent one-step and incoherent step-wise multi-photon absorption, as well as for off-resonant excitations even when resonance conditions prevail. The dynamic theory of nonlinear propagation of a few interacting intense light pulses is here highlighted in a study of the optical power limiting with platinum-organic molecular compounds. © 2007 Materials Research Society.

  • 54.
    Baev, Alexander
    et al.
    KTH, Superseded Departments, Biotechnology.
    Gel'mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments, Biotechnology.
    Cronstrand, Peter
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Upconverted lasing based on many-photon absorption: an all dynamic description2004In: Journal of the Optical Society of America. B, Optical physics, ISSN 0740-3224, E-ISSN 1520-8540, Vol. 21, no 2, p. 384-396Article in journal (Refereed)
    Abstract [en]

    A theory is developed for the propagation through a nonlinear medium of strong pump and amplifiedspontaneous-emission pulses. The theory is based on a solution of the density matrix equations that aims at providing an adequate treatment of the nonlinear polarization of the material without addressing the Taylor expansion over the powers of intensity. The theory has been applied for modeling of three-photon absorption induced upconverted stimulated emission of organic molecules in solvents. Numerical results are presented for the organic chromophore 4-[N-(2-hydroxyethyl)-N-(methyl)amino phenyl]-4'-(6-hydroxyhexyl sulfonyl) stilbene dissolved in dimethyl sulfoxide. The results are in good agreement with available experimental results.

  • 55.
    Baev, Alexander
    et al.
    KTH, Superseded Departments, Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments, Biotechnology.
    Gel'Mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Optical limiting properties of Zinc- and Platinum-based organometallic compounds2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 36, p. 7406-7416Article in journal (Refereed)
    Abstract [en]

    Optical power limiting is theoretically studied using an approach that combines quantum electronic structure calculations of multiphoton excitations and classical calculations of dynamical wave propagation. We illustrate the capability of such a combined approach by presenting results for a couple of organometallic compounds; basic metal-base porphyrins, vinylphenylamine porhyrin, and the so-called type IVc platinum compound. A comparative analysis of their electronic properties related to nonlinear absorption of electromagnetic radiation and their optical limiting capability has been performed based on dynamical simulations of the nonlinear pulse propagation taking account of resonant as well as off-resonant effects. Several key features and rate-limiting steps in the transmission have been examined in relation to various characteristics of the pulse. It is found that the resonant vs off-resonant conditions, the saturation conditions and the dephasing play critical roles for the nonlinear transmission. The saturation effects are sensitive to the pulse duration, the inter-system crossing rate and the quenching of the higher triplet state. The inter-system crossing rate has to be comparable with the inverse pulse duration in order to boost the stepwise two-photon channel associated with singlet-singlet followed by triplet-triplet transitions. It is illustrated that structure-to-property relations of the rate-limiting steps serve as important criteria for choices of compounds suitable for the application of interest.

  • 56.
    Ballante, Flavio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection2018In: Rational Drug Design: Methods and Protocols / [ed] Thomas Mavromoustakos; Tahsin F. Kellici, New York, NY: Humana Press, 2018, p. 67-88Chapter in book (Refereed)
    Abstract [en]

    Main goal in drug discovery is the identification of drug-like compounds capable to modulate specific biological targets. Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key step to be pursued in structure-based drug design (SBDD). Since the increasing number of resolved three-dimensional ligand-protein structures, together with the expansion of computational power and software development, the comprehensive and systematic use of experimental data can be proficiently employed to validate the docking performance. This allows to select and refine the protocol to adopt when predicting the binding pose of trial compounds in a target. Given the availability of multiple docking software, a comparative docking assessment in an early research stage represents a must-use step to minimize fails in molecular modeling. This chapter describes how to perform a docking assessment, using freely available tools, in a semiautomated fashion.

  • 57.
    Banerjee, Paramita
    et al.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    Pathak, Biswarup
    Indian Inst Technol, Discipline Chem, Indore 452020, India..
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Das, G. P.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    First principles design of Li functionalized hydrogenated h-BN nanosheet for hydrogen storage2016In: International journal of hydrogen energy, ISSN 0360-3199, E-ISSN 1879-3487, Vol. 41, no 32, p. 14437-14446Article in journal (Refereed)
    Abstract [en]

    Employing first principles density functional theory (DFT) based approach, the structure, stability and hydrogen storage efficiency of a hydrogenated hexagonal boron nitride sheet (BHNH chair conformer) functionalized by the lightest alkali metal atom Li has been explored here in details. Substituting one hydrogen atom from both B and N sides of BHNH sheet by a Li atom, we have found that Li becomes cationic and acts as a binding site to adsorb hydrogen molecules. The stability of this Li-substituted BHNH sheet has been indicated via Ab-initio Molecular Dynamics (AIMD) simulation upto 400 K. The binding energy (similar to 0.18-0.3 eV/H-2 molecule) and gravimetric density (similar to 6 wt %) (upto similar to 200 K) of the hydrogen molecules fall in the required window for practical hydrogen storage. AIMD simulation indicates complete dehydrogenation from this system occurs at similar to 400 K, thereby predicting the suitability of this system from the point of view of efficient hydrogen storage.

  • 58.
    Banerjee, Saikat
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Institute for Materials Science, Los Alamos National Laboratory, USA.
    Fransson, J.
    Black-Schaffer, A. M.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Balatsky, A. V.
    Granular superconductor in a honeycomb lattice as a realization of bosonic Dirac material2016In: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, no 13, article id 134502Article in journal (Refereed)
    Abstract [en]

    We examine the low-energy effective theory of phase oscillations in a two-dimensional granular superconducting sheet where the grains are arranged in a honeycomb lattice structure. Using the example of graphene, we present evidence for the engineered Dirac nodes in the bosonic excitations: the spectra of the collective bosonic modes cross at the K and K' points in the Brillouin zone and form Dirac nodes. We show how two different types of collective phase oscillations are obtained and that they are analogous to the Leggett and the Bogoliubov-Anderson-Gorkov modes in a two-band superconductor. We show that the Dirac node is preserved in the presence of an intergrain interaction, despite induced changes of the qualitative features of the two collective modes. Finally, breaking the sublattice symmetry by choosing different on-site potentials for the two sublattices leads to a gap opening near the Dirac node, in analogy with fermionic Dirac materials. The Dirac node dispersion of bosonic excitations is thus expanding the discussion of the conventional Dirac cone excitations to the case of bosons. We call this case as a representative of bosonic Dirac materials (BDM), similar to the case of Fermionic Dirac materials extensively discussed in the literature.

  • 59.
    Barzegar, Hamid Reza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Gracia-Espino, Eduardo
    Umeå University, Faculty of Science and Technology, Department of Physics. Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sharifi, Tiva
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Nitze, Florian
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Nitrogen Doping Mechanism in Small Diameter Single-Walled Carbon Nanotubes: Impact on Electronic Properties and Growth Selectivity2013In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, no 48, p. 25805-25816Article in journal (Refereed)
    Abstract [en]

    Nitrogen doping in carbon nanostructures has attracted interest for more than a decade, and recent implementation of such structures in energy conversion systems has boosted the interest even more. Despite numerous studies, the structural conformation and stability of nitrogen functionalities in small diameter single-walled carbon nanotubes (SWNTs), and the impact of these functionalities on the electronic and mechanical properties of the SWNTs, are incomplete. Here we report a detailed study on nitrogen doping in SWNTs with diameters in the range of 0.8?1.0 nm, with well-defined chirality. We show that the introduction of nitrogen in the carbon framework significantly alters the stability of certain tubes, opening for the possibility to selectively grow nitrogen-doped SWNTs with certain chirality and diameter. At low nitrogen concentration, pyridinic functionalities are readily incorporated and the tubular structure is well pertained. At higher concentrations, pyrrolic functionalities are formed, which leads to significant structural deformation of the nanotubes and hence a stop in growth of crystalline SWNTs. Raman spectroscopy is an important tool to understand guest atom doping and electronic charge transfer in SWNTs. By correlating the influence of defined nitrogen functionalities on the electronic properties of SWNTs with different chirality, we make precise interpretation of experimental Raman data. We show that the previous interpretation of the double-resonance G?-peak in many aspects is wrong and instead can be well-correlated to the type of nitrogen doping of SWNTs originating from the p- or n-doping nature of the nitrogen incorporation. Our results are supported by experimental and theoretical data.

  • 60.
    Bassan, Arianna
    Stockholm University, Faculty of Science, Department of Physics.
    Theoretical studies of mononuclear non-heme iron active sites2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The quantum chemical investigations presented in this thesis use hybrid density functional theory to shed light on the catalytic mechanisms of mononuclear non-heme iron oxygenases, accommodating a ferrous ion in their active sites. More specifically, the dioxygen activation process and the subsequent oxidative reactions in the following enzymes were studied: tetrahydrobiopterin-dependent hydroxylases, naphthalene 1,2-dioxygenase and α-ketoglutarate-dependent enzymes. In light of many experimental efforts devoted to the functional mimics of non-heme iron oxygenases, the reactivity of functional analogues was also examined.

    The computed energetics and the available experimental data served to assess the feasibility of the reaction mechanisms investigated. Dioxygen activation in tetrahydrobiopterin- and α-ketoglutarate-dependent enzymes were found to involve a high-valent iron-oxo species, which was then capable of substrate hydroxylation. In the case of naphthalene 1,2-dioxygenase, the reactivity of an iron(III)-hydroxperoxo species toward the substrate was investigated and compared to the biomimetic counterpart.

  • 61. Bast, R.
    et al.
    Saue, T.
    Henriksson, J.
    Norman, P.
    Role of noncollinear magnetization for the first-order electric-dipole hyperpolarizability at the four-component Kohn-Sham density functional theory level2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 2, article id 024109Article in journal (Refereed)
    Abstract [en]

    The quadratic response function has been derived and implemented at the adiabatic four-component Kohn-Sham density functional theory level with inclusion of noncollinear spin magnetization and gradient corrections in the exchange-correlation functional-a work that is an extension of our previous report where magnetization dependencies in the exchange-correlation functional were ignored [J. Henriksson, T. Saue, and P. Norman, J. Chem. Phys. 128, 024105 (2008)]. The electric-field induced second-harmonic generation experiments on CF3 Cl and CF3 Br are addressed by a determination of Β- (-2ω;ω,ω) for a wavelength of 694.3 nm, and the same property is also determined for CF3 I. The relativistic effects on the static hyperpolarizability for the series of molecules amount to 1%, 5%, and 9%, respectively. At the experimental wavelength, the contributions to Β due to the magnetization dependence in the exchange-correlation functional are negligible for CF3 Cl and CF3 Br and small for CF 3 I. The noticeable effect of magnetization in the latter case is attributed to a near two-photon resonance with the excited state 1 E3 (nonrelativistic notation). It is emphasized, however, that the effect of magnetization on Β for CF3 I is negligible both in comparison to the total relativistic correction as well as to the effects of electron correlation. It is concluded that, in calculations of hyperpolarizabilities under nonresonant conditions, the magnetization dependence in the exchange-correlation functional may be ignored. © 2009 American Institute of Physics.

  • 62.
    Bazooyar, Faranak
    et al.
    University of Borås, Faculty of Textiles, Engineering and Business.
    Bohlén, Martin
    University of Borås, Faculty of Textiles, Engineering and Business.
    Bolton, Kim
    University of Borås, Faculty of Textiles, Engineering and Business.
    Computational Studies of Water and Carbon Dioxide Interactions with Cellobiose2015In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 21, p. 2553-Article in journal (Refereed)
    Abstract [en]

    B3LYP/6-311++G** with dispersion correction (DFT-D) was used to study local and global minimum energy structures of water (H2O) or carbon dioxide (CO2) bonding with a pair of cellobiose molecules. The calculations showed that neither the H2O nor the CO2 prefer to be between the cellobiose molecules, and that the minimum energy structures occur when these molecules bond to the outer surface of the cellobiose pair. The calculations also showed that the low energy structures have a larger number of inter-cellobiose hydrogen bonds than the high energy structures. These results indicate that penetration of H2O or CO2 between adjacent cellobiose pairs, which would assist steam or supercritical CO2 (SC-CO2) explosion of cellulose, is not energetically favored. Comparison of the energies obtained with DFT-D and DFT (the same method but without dispersion correction) show that both hydrogen bonds and van der Waals interactions play an important role in cellobiose-cellobiose interactions.

  • 63.
    Bazooyar, Faranak
    et al.
    University of Borås, School of Engineering.
    Bolton, Kim
    University of Borås, School of Engineering.
    Molecular-level Simulations of Cellulose Dissolution by Steam and SC-CO2 Explosion2014Conference paper (Refereed)
    Abstract [en]

    Dissolution of cellulose is an important but tough step in biofuel production from lignocellulosic materials. Steam and supercritical carbon dioxide (SC-CO2) explosion are two effective methods for dissolution of some lignocellulosic materials. Loading and explosion are the major processes of these methods. Studies of these processes were performed using grand canonical Monte Carlo and molecular dynamics simulations at different pressure/ temperature conditions on the crystalline structure of cellulose. The COMPASS force field was used for both methods. The validity of the COMPASS force field for the calculations was confirmed by comparing the energy and structures obtained from molecular mechanics simulations of cellobiose (the repeat unit of cellulose), water–cellobiose, water-cellobiose pair and CO2-cellobiose pair systems with those obtained from first principle calculations with and without dispersion correction. A larger disruption of the cellulose crystal structure was seen during loading than that during the explosion process. This is seen by an increased separation of the cellulose chains from the centre of mass of the crystal during the initial stages of the loading, especially for chains in the outer shell of the crystalline structure. Reducing and non-reducing ends of the cellulose crystal show larger disruption than the central core; this leads to increasing susceptibility to enzymatic attack in these end regions. There was also change from the syn to the anti torsion angle conformations, especially for chains in the outer cellulose shell. Increasing the temperature increases the disruption of the crystalline structure during loading and explosion.

  • 64.
    Bazooyar, Faranak
    et al.
    University of Borås, Faculty of Textiles, Engineering and Business.
    Bolton, Kim
    University of Borås, Faculty of Textiles, Engineering and Business.
    Molecular-level Simulations of Cellulose Steam Explosion2015In: Quantum Matter, ISSN 2164-7615, Vol. 4, no 2, p. 115-122Article in journal (Refereed)
    Abstract [en]

    Grand canonical Monte Carlo and molecular dynamics simulations are used to study steam explosion of crystalline cellulose using 100, 160, 210 and 250 °C saturated steam. The simulations are based on the COMPASS force field, which provides a valid description of the cellulose crystal structure and water-cellobiose interactions. Disruption of the crystal structure during steaming is typically larger than that during the explosion stage and the restructuring is larger at increased temperature and pressure. This is seen by an increased separation of the cellulose chains from the center of mass of the crystal during the initial stages of the steaming, especially for chains in the outer shell of the elementary fibril. There is a large change in the radius of gyration and fraction of anti torsion angle conformers for chains in the outer shell of the elementary fibril. In addition, the disruption at the reducing and non-reducing ends of the cellulose crystal is larger than in the central core, increasing susceptibility to enzymatic attack in these end regions.

  • 65.
    Becconi, Olga
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. University of Cagliari, Italy.
    Ahlstrand, Emma
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Salis, Andrea
    University of Cagliari, Italy.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Protein-ion Interactions: Simulations of Bovine Serum Albumin in Physiological Solutions of NaCl, KCl and LiCl2017In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 57, no 5, p. 403-412Article in journal (Refereed)
    Abstract [en]

    Specific interactions that depend on the nature of electrolytes are observed when proteins and other molecules are studied by potentiometric, spectroscopic and theoretical methods at high salt concentrations. More recently, it became clear that such interactions may also be observed in solutions that can be described by the Debye-Hückel theory, i.e., at physiological (0.1 mol dm−3) and lower concentrations. We carried out molecular dynamics simulations of bovine serum albumin in physiological solutions at T=300 and 350 K. Analysis of the simulations revealed some differences between LiCl solutions and those of NaCl and KCl. The binding of Li+ ions to the protein was associated with a negative free energy of interaction whereas much fewer Na+ and K+ ions were associated with the protein surface. Interestingly, unlike other proteins BSA does not show a preference to Na+ over K+. Quantum chemical calculations identified a significant contribution from polarisation to the hydration of Li+ and (to a lesser degree) Na+, which may indicate that polarisable force-fields will provide more accurate results for such systems.

  • 66. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 34, p. 9067-9075Article in journal (Refereed)
    Abstract [en]

    In this work, we examine, by means of computational methods, the mechanism of Zn2+ sensing by a bipyridine-centered, D-pi-A-pi-D-type-ratiometric molecular probe. According to recently published experimental data [Divya, K. P.; Sreejith, S.; Ashokkumar, P.; Yuzhan, K.; Peng, Q; Maji, S. K.; Tong, Y.; Yu, H.; Zhao, Y.; Ramamurthy, P.; Ajayaghosh, A. A ratiometric fluorescent molecular -probe with enhanced two-photon response upon Zn2+ binding for in vitro and in vivo: bioimaging.= Chem. Sci. 2014, S, 3469-3474], after coordination to zinc ions the -probe exhibits a large enhancement of the two -photon absorption cross section. The goal of our investigation was to elucidate the mechanism behind this phenomenon. For this purpose, linear and nonlinear optical properties of -the unbound (cation-free) and bound probe were calculated, including the influence of solute Solvent interactions, implicitly using a polarizable continuum model and exp-licitely employing the QM/MM approach. Because the results of the calculations indicate that many conformers of the probe are energetically accessible at room temperature in solution and hence contribute to the Signal, structurepteperty relationships were also taken into account. Results of our simulations-demonstrate that the one-photon absorption bands for both the unbound -and bound forms correspond to the bright pi -> pi* transition to the first excited state; which, on the other hand,. exhibits negligible two-photon activity. On the basis of the results of the quadratic respOnse calculations, we put forward-notion that it is the second excited state that gives the strong signal in the experimental nonlinear spectrum. To explain the differenCes in the two-photon absorption activity for the two lowest-lying excited states and nonlinear response enhancement upon binding, we employed the generalized few -state model including the ground, first, and- second excited states. The analysis of the optical channel suggests that the large two-photon response is due to the coordination -induced increase of the, transition- moment from the first to the second excited state.

  • 67.
    Behzadi, Hadi
    et al.
    Department of Physical Chemistry, Faculty of Chemistry, Kharazmi University, 15719-14911, Tehran, Iran.
    Manzetti, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Fjordforsk AS, N-6894 Midtun, Vangsnes, Norway.
    Darghai, Mayram
    Department of Chemistry, Faculty of Science, Imam Khomeini International University, Qazvin, Iran.
    Roonasi, Payman
    Department of Physical Chemistry, Faculty of Chemistry, Kharazmi University, 15719-14911, Tehran, Iran.
    Khalilnia, Zahra
    Department of Physical Chemistry, Faculty of Chemistry, Kharazmi University, 15719-14911, Tehran, Iran.
    Application of calculated NMR parameters, aromaticity indices and wavefunction properties for evaluation of corrosion inhibition efficiency of pyrazine inhibitors2018In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 1151, p. 34-40Article in journal (Refereed)
  • 68. Beinik, Igor
    et al.
    Hellström, Matti
    Jensen, Thomas
    Broqvist, Peter
    Lauritsen, Jeppe
    Cu wets the polar ZnO(0001)-Zn surface because of interaction with subsurface defectsArticle in journal (Refereed)
  • 69.
    Benatto, L.
    et al.
    Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    Marchiori, Cleber
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    da Luz, M. G. E.
    Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    Koehler, M.
    Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    Electronic and structural properties of fluorene-thiophene copolymers as function of the composition ratio between the moieties: a theoretical study2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 31, p. 20447-20458Article in journal (Refereed)
    Abstract [en]

    Through theoretical analysis, we study relevant properties of some molecular structures formed by oligothiophenes (T) and dioctylfluorenes (F) units, commonly employed in the fabrication of different kinds of optical and electronic devices. For so, we first consider F-(T)(n)-F molecules with different numbers of thiophene rings (n). Among other characteristics, we calculate the dipole moment change between the ground and excited state ((ge)), a quantity that greatly influences the exciton dissociation and charge carrier mobility. We show that the planarity of the ground state geometry correlates (ge) to the exciton binding energy (E-b), with higher (ge)'s corresponding to lower E-b's when n > 3. We also unveil a relevant dependence of (ge) with the odd-even parity of n and that (ge) assumes higher values when the molecule is composed by bithiophene (instead of simple thiophenes) moieties in the syn-conformation (with the two heteroatoms pointing in the same direction). From molecules results, we then address larger systems, formed by different oligomers of F-T copolymers containing blocks of dioctylfluorenes and bithiophenes (T2). We systematic investigate their electronic and structural properties as function of the composition ratio between the T2 and F moieties. Similar to the molecules, we deduce that the magnitude of (ge) is higher for the syn conformer of the T2 unit. Moreover, the highest values of (ge) are achieved when the number of the T2 increases relative to a fixed number of the F units in the mer. Such behaviors are in agreement and actually can qualitative explain measurements in the literature on the quantum efficiency of charge carrier generation in F-T copolymers. The present findings can be helpful in designing novel materials with improved photoelectric responses.

  • 70.
    Bengtson, Charlotta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Quantum nonlocality in the excitation energy transfer in the Fenna-Matthews-Olson complex2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, p. 1763-1771Article in journal (Refereed)
    Abstract [en]

    The Fenna-Matthews-Olson (FMO) complex - a pigment protein complex involved in photosynthesis in green sulfur bacteria - is remarkably efficient in transferring excitation energy from light harvesting antenna molecules to a reaction center. Recent experimental and theoretical studies suggest that quantum coherence and entanglement may play a role in this excitation energy transfer (EET). We examine whether bipartite quantum nonlocality, a property that expresses a stronger-than-entanglement form of correlation, exists between different pairs of chromophores in the FMO complex when modeling the EET by the hierarchically coupled equations of motion method. We compare the results for nonlocality with the amount of bipartite entanglement in the system. In particular, we analyze in what way these correlation properties are affected by different initial conditions. It is found that bipartite nonlocality only exists when the initial conditions are chosen in an unphysiological manner and probably is absent when considering the EET in the FMO complex in its natural habitat. It is also seen that nonlocality and entanglement behave quite differently in this system. In particular, for localized initial states, nonlocality only exists on a very short time scale and then drops to zero in an abrupt manner. As already known from previous studies, quantum entanglement between chromophore pairs on the other hand is oscillating and exponentially decaying and follow thereby a pattern more similar to the chromophore population dynamics. The abrupt disappearance of nonlocality in the presence of nonvanishing entanglement is a phenomenon we call nonlocality sudden death; a striking manifestation of the difference between these two types of correlations in quantum systems. 

  • 71.
    Bengtsson, Katarina
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, Faculty of Science & Engineering. LunaMicro AB, Linkoping, Sweden.
    Robinson, Nathaniel D
    Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry. Linköping University, Faculty of Science & Engineering. LunaMicro AB, Linkoping, Sweden.
    A large-area, all-plastic, flexible electroosmotic pump2017In: Microfluidics and Nanofluidics, ISSN 1613-4982, E-ISSN 1613-4990, Vol. 21, no 12, article id 178Article in journal (Refereed)
    Abstract [en]

    A large-area, fabric-like pump would potentially have applications, for example, in controlling water transport through a garment, such as a rain jacket, regardless of the external temperature and humidity. This paper presents an all-plastic, flexible electroosmotic pump, constructed from commercially available materials: A polycarbonate membrane combined with the electrochemically active polymer poly(3,4-ethylenedioxythiophene) polystyrene sulfonate that actively transports water using an electric potential that can be supplied by a small battery. By using electrochemically active polymer electrodes instead of metal electrodes, the electrochemical reaction that drives flow avoids the oxygen and hydrogen gas production or pH changes associated with water electrolysis. We observe a water mass flux up to 23 mg min(-1) per cm(2) polycarbonate membrane (porosity 10-15%), at an applied potential of 5 V, and a limiting operating pressure of 0.3 kPa V-1, similar to previously reported membrane-based electroosmotic pumps.

  • 72.
    Berraud-Pache, Romain
    et al.
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Navizet, Isabelle
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 20, p. 5173-5182Article in journal (Refereed)
    Abstract [en]

    The bioluminescence emission from fireflies is an astounding tool to mark and view cells. However, the bioluminescent mechanism is not completely deciphered, limiting the comprehension of key processes. We use a theoretical approach to study for the first time the arrival of a dioxygen molecule inside the fireflies protein and one path of the formation of the dioxetanone ring, the high-energy intermediate precursor of the bioluminescence. To describe this reaction step, a joint approach combining classical molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations is used. The formation of the dioxetanone ring has been studied for both singlet and triplet states with the help of MS-CASPT2 calculations. We also emphasize the role played by the proteinic environment in the formation of the dioxetanone ring. The results obtained shed some light on an important reaction step and give new insights concerning the bioluminescence in fireflies.

  • 73.
    Bertaccini, Edward J.
    et al.
    Stanford University.
    Lindahl, Erik
    Stockholm University.
    Sixma, Titia
    Netherlands Cancer Institute.
    Trudell, James R.
    Stanford University.
    Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein2008In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 48, no 4, p. 855-860Article in journal (Refereed)
    Abstract [en]

    Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.

  • 74.
    Bertaccini, Edward J
    et al.
    Stanford University.
    Lindahl, Erik
    Stanford University.
    Titia, Sixma
    Netherlands Cancer Institute.
    Trudell, James R
    Stanford University.
    Toxin Binding Serves as an Initial Model for Studying the Effects of Anesthetics on Ion Channels2007Conference paper (Refereed)
    Abstract [en]

    Introduction: We have previously used molecular modeling techniques combined with experimental data to visualize a plausible model of an anesthetic binding site within a LGIC complex.We have also previously shown a computational mechanism by which these ion channels may open and close and postulated how this motion may be affected by the presence of anesthetics.2 The difficulties with these methods, however, lay in their inability to account for the modest effects of a separate anesthetic ligand or small mutation on ion channel motion. Here we show the successful application of an elastic network calculation on a homologue of the extracellular component of LGIC's, the acetycholine binding protein (AChBP), in the presence and absence of large cobratoxin ligands. These calculations demonstrate a clear alteration in the native symmetric motion of a protein due to the presence of multiple ligands, as may occur with anesthetics and muscle relaxants.

    Methods: Coordinates of the AChBP with (1YI5)3 and without (1I9B)4 cobratoxin were obtained from the Research Collaboratory for Structural Biology (RCSB). Hydrogens were added using DSViewer 5.0 (Accelrys, San Diego, CA). Normal mode analysis was performed using an all atom elastic network model developed by Lindahl. Root-mean-square deviations (RMSD) of each residue were produced from the application of the RMSD analysis utility within the GROMACS software suite to the coordinate trajectory output files. The RMSD data was then imported into Microsoft Excel for plotting and further comparison of protein backbone motions between the two different normal mode trajectories.

    Results: Normal mode analysis reveals that ligand binding to this protein alters its natural harmonic vibration. In this case, the axially symmetric motion of the AChBP, that may be associated with channel gating in the full nAChR, is highly dampened by the presence of bound cobratoxin. A large proportion of the kinetic energy within this mode seems to be absorbed by the cobratoxin, leaving the channel motion significantly decreased.

    Conclusions: This is among the first descriptions of the effect of bound ligand on large scale protein dynamics, especially as it relates to ion channel gating. This analysis was possible using an elastic network approximation due to the large protein nature of the cobratoxin ligand. For nonpeptide drugs such as anesthetics which contain far fewer atoms, using the effects of bound ligand on protein motion as additional criteria for future drug design may require a more robust molecular mechanics treatment of the ligand-receptor complex.

  • 75.
    Bertaccini, Edward J
    et al.
    Stanford University.
    Wallner, Björn
    Stockholm University.
    Trudell, James R
    Stanford University.
    Lindahl, Erik
    Stockholm University.
    Modeling anesthetic binding sites within the glycine alpha one receptor based on prokaryotic ion channel templates: the problem with TM42010In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 50, no 12, p. 2248-2255Article in journal (Refereed)
    Abstract [en]

    Ligand-gated ion channels (LGICs) significantly modulate anesthetic effects. Their exact molecular structure remains unknown. This has led to ambiguity regarding the proper amino acid alignment within their 3D structure and, in turn, the location of any anesthetic binding sites. Current controversies suggest that such a site could be located in either an intra- or intersubunit locale within the transmembrane domain of the protein. Here, we built a model of the glycine alpha one receptor (GlyRa1) based on the open-state structures of two new high-resolution ion channel templates from the prokaryote, Gloebacter violaceus (GLIC). Sequence scoring suggests reasonable homology between GlyRa1 and GLIC. Three of the residues notable for modulating anesthetic action are on transmembrane segments 1-3 (TM1-3): (ILE229, SER 267, and ALA 288). They line an intersubunit interface, in contrast to previous models. However, residues from the fourth transmembrane domain (TM4) that are known to modulate a variety of anesthetic effects are quite distant from this putative anesthetic binding site. While this model can account for a large proportion of the physicochemical data regarding such proteins, it cannot readily account for the alterations on anesthetic effects that are due to mutations within TM4.

  • 76. Birke, R. L.
    et al.
    Lombardi, J. R.
    Saidi, W. A.
    Norman, P.
    Surface-Enhanced Raman Scattering Due to Charge-Transfer Resonances: A Time-Dependent Density Functional Theory Study of Ag13-4-Mercaptopyridine2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 37, p. 20721-20735Article in journal (Refereed)
    Abstract [en]

    We have used time-dependent density functional theory in conjunction with the CAM-B3LYP functional and MWB28/aug-cc-pVDZ basis set to determine non-, near-, and on-resonance Raman spectra for a complex formed by 4-mercaptopyridine (4-Mpy) binding with a Ag13 cluster via the thiolate Ag-S bond. Geometry optimizations of the Ag13-4-Mpy complex showed an on-top structure directly bound to one Ag atom with the ring of the molecule almost flat with respect to two Ag atoms of the complex. The corresponding B3LYP/MWB28/aug-cc-pVDZ geometry is also an on-top structure directly bound to one Ag atom, but the molecule is directed away from the surface. The near-resonance Raman calculations were carried out in the infinite lifetime approximation, while the on-resonant Raman excitation profiles were calculated with the complex polarization propagator (CPP) approach, introducing a half width at half-maximum spectral broadening of 0.2 eV. Calculation of the UV-vis spectra of the isolated 4-Mpy and of the Ag13-4-Mpy complex showed that binding shifts the spectra from deep in the UV to the visible region. Calculation of the near-resonance Raman spectra of the two structures of the complex at 410 (3.025 eV) and 425 nm (2.918 eV) showed a strong enhancement. A very large variation across vibrational modes by a factor of at least 103 was found for both the static chemical enhancement and charge-transfer (CT) enhancement mechanisms. This large variation in enhancement factor indicates that B-term Herzberg-Teller scattering is occurring because inactive or very low intensity modes in the static spectra of the molecule are much stronger in both the static and near-resonance spectra of the complex. From the excitation profile using the CPP method, an overall surface enhancement on the order 103 or higher was found for individual modes on excitation into a CT excited state. © 2016 American Chemical Society.

  • 77.
    Birke, Ronald L.
    et al.
    CUNY City Coll, NY 10031 USA; CUNY, NY 10016 USA.
    Lombardi, John R.
    CUNY City Coll, NY 10031 USA; CUNY, NY 10016 USA.
    Saidi, Wissam A.
    University of Pittsburgh, PA USA.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Surface-Enhanced Raman Scattering Due to Charge-Transfer Resonances: A Time-Dependent Density Functional Theory Study of Ag-13-4-Mercaptopyridine2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 37, p. 20721-20735Article in journal (Refereed)
    Abstract [en]

    We have used time-dependent density functional theory in conjunction with the CAM-B3LYP functional and MWB28/aug-cc-pVDZ basis set to determine non-, near-, and on-resonance Raman spectra for a complex formed by 4-mercaptopyridine (4-Mpy) binding with a Ag-13 cluster via the thiolate Ag-S bond. Geometry optimizations of the Ag-13-4-mpy complex showed an on-top structure directly bound to one Ag atom with the ring of the molecule almost flat with respect to two Ag atoms of the complex. The corresponding B3LYP/MWB28/aug-cc-pVDZ geometry is also an on-top structure directly bound to one Ag atom, but the molecule is directed away from the surface,. The near-resonance Raman calculations were carried out in the infinite lifetime approximation, while the on-resonant Raman excitation profiles were calculated with the complex polarization propagator (CPP) approach, introducing a half width at half-maximum spectral broadening of 0.2 eV. Calculation of the UV-vis spectra of the isolated 4-Mpy and of the Ag-13-4-Mpy complex showed that binding shifts the spectra from deep in the UV to the visible region. Calculation of the near-resonance Raman spectra of the two structures of the complex at 410 (3.025 eV) and 425 nm (2.918 eV) showed a strong enhancement. A very large variation across vibrational modes by a factor of at least 10(3) was found for both the static chemical enhancement and charge-transfer (CT) enhancement mechanisms. ThiS large variation in enhancement factor indicates that B-term Herzberg-Teller scattering is occurring because inactive or very low intensity modes in the static spectra of the molecule are much stronger in both the static and near-resonance spectra of the Complex. From the excitation profile using the CPP method, an overall surface enhancement on the order 10(3) or higher was found for individual modes on excitation into a CT excited state.

  • 78. Bishop, D. M.
    et al.
    Norman, P.
    Effects of vibration on the polarizability and the first and second hyperpolarizabilities of HF, HCl, and HBr1999In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 111, no 7, p. 3042-3050Article in journal (Refereed)
    Abstract [en]

    We report calculations, using electron uncorrelated and correlated wave functions, of the electronic and vibrational properties which pertain to certain nonlinear optical properties for HF, HCl, and HBr. Our main focus is on vibrational effects (zero-point-vibrational averaging and pure vibration). Analysis of the results obtained at various levels of approximation indicates that first-order perturbation theory is generally adequate for finding the zero-point-vibrational-averaging corrections for these molecules and that complete second-order perturbation theory nearly always gives reliable results for the pure vibrational corrections. Attention is drawn to some differences with previously published results for these properties. © 1999 American Institute of Physics.

  • 79. Bishop, David M.
    et al.
    Norman, Patrick
    Calculations of dynamic hyperpolarizabilities for small and medium sized molecules2001In: Handbook of Advanced Electronic and Photonic Materials / [ed] H. S. Nalwa, San Diego: Academic Press, 2001Chapter in book (Refereed)
  • 80.
    Bjelkmar, Pär
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Modeling of voltage-gated ion channels2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity.

    Starting from the open crystal structures, we have studied the gating mechanism of these channels by molecular modeling techniques. Firstly, by applying a membrane potential, initial stages of the closing of the channel were captured, manifested in a secondary-structure change in the voltage-sensor. In a follow-up study, we found that the energetic cost of translocating this 310-helix conformation was significantly lower than in the original conformation. Thirdly, collaborators of ours identified new molecular constraints for different states along the gating pathway. We used those to build new protein models that were evaluated by simulations. All these results point to a gating mechanism where the S4 helix undergoes a secondary structure transformation during gating.

    These simulations also provide information about how the protein interacts with the surrounding membrane. In particular, we found that lipid molecules close to the protein diffuse together with it, forming a large dynamic lipid-protein cluster. This has important consequences for the understanding of protein-membrane interactions and for the theories of lateral diffusion of membrane proteins.

    Further, simulations of the simple ion channel antiamoebin were performed where different molecular models of the channel were evaluated by calculating ion conduction rates, which were compared to experimentally measured values. One of the models had a conductance consistent with the experimental data and was proposed to represent the biological active state of the channel.

    Finally, the underlying methods for simulating molecular systems were probed by implementing the CHARMM force field into the GROMACS simulation package. The implementation was verified and specific GROMACS-features were combined with CHARMM and evaluated on long timescales. The CHARMM interaction potential was found to sample relevant protein conformations indifferently of the model of solvent used.

  • 81.
    Bjelkmar, Pär
    et al.
    Stockholm University.
    Larsson, Per
    Cuendet, Michel
    EPFL Lausanne.
    Lindahl, Erik
    Stockholm University.
    Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models2010In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 6, no 2, p. 459-466Article in journal (Refereed)
    Abstract [en]

    CHARMM27 is a widespread and popular force field for biomolecular simulation, and several recent algorithms such as implicit solvent models have been developed specifically for it. We have here implemented the CHARMM force field and all necessary extended functional forms in the GROMACS molecular simulation package, to make CHARMM-specific features available and to test them in combination with techniques for extended time steps, to make all major force fields available for comparison studies in GROMACS, and to test various solvent model optimizations, in particular the effect of Lennard-Jones interactions on hydrogens. The implementation has full support both for CHARMM-specific features such as multiple potentials over the same dihedral angle and the grid-based energy correction map on the phi, psi protein backbone dihedrals, as well as all GROMACS features such as virtual hydrogen interaction sites that enable 5 fs time steps. The medium-to-long time effects of both the correction maps and virtual sites have been tested by performing a series of 100 ns simulations using different models for water representation, including comparisons between CHARMM and traditional TIP3P. Including the correction maps improves sampling of near native-state conformations in our systems, and to some extent it is even able to refine distorted protein conformations. Finally, we show that this accuracy is largely maintained with a new implicit solvent implementation that works with virtual interaction sites, which enables performance in excess of 250 ns/day for a 900-atom protein on a quad-core desktop computer.

  • 82.
    Bjelkmar, Pär
    et al.
    Stockholm University.
    Niemelä, Perttu S
    Helsinki University of Technology.
    Vattulainen, Ilpo
    Helsinki University of Technology.
    Lindahl, Erik
    Stockholm University.
    Conformational changes and slow dynamics through microsecond polarized atomistic molecular simulation of an integral Kv1.2 ion channel2009In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 5, no 2, p. e1000289-Article in journal (Refereed)
    Abstract [en]

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins-not to mention numerous applications in drug design. Here, we present a full 1 micros atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120 degrees rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation ( approximately 35 degrees ) of the extracellular end of all S4 segments is present also in a reference 0.5 micros simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 3(10) helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4-lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5-1 micros). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations.

  • 83.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Formation mechanisms of covalent nanostructures from density functional theory2016In: Proceedings of International Workshop on On-Surface Synthesis, Cham: Springer, 2016, p. 269-287Conference paper (Refereed)
    Abstract [en]

    In this chapter, it is demonstrated how electronic structure calculations, with focus on density functional theory, can be used to gain insight about on-surface reactions. I first give a brief introduction to how density functional theory can be used to study reactions. The focus is then shifted to two different types of on-surface reactions, highlighting the theoretical work that has been performed to gain detailed atomistic insight into them. First, the state of the art of the theory behind on-surface Ullmann coupling is described. In this reaction, molecular building blocks dehalogenate, which enables them to covalently couple. The most crucial reaction parameters are identified—the diffusion and coupling barriers of surface-supported radicals—and the potential for theory to optimize these is discussed. We then concentrate on the homo-coupling between terminal alkynes, a rudimentarily different process where molecules initially couple before undergoing a dehydrogenation step. The theory of the mechanism behind this coupling strategy is less developed than that of the on-surface Ullmann coupling, where fundamental questions remain to be unraveled. For example, by the subtle change of substrate from Ag to Au, the on-surface alkyne chemistry is completely altered from the homo-coupling to a cyclodehydrogenation reaction for the same molecular building block, of which origin remains unknown. The main objective of the chapter is to give an impression of what kind of information theory can obtain about reaction on surface, as well as to motivate and inspire for future theoretical studies, which will be needed to turn on-surface synthesis into a more predictive discipline.

  • 84.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Reaction mechanisms for on-surface synthesis of covalent nanostructures2016In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 28, no 8, p. 083002-Article, review/survey (Refereed)
    Abstract [en]

    In recent years, on-surface synthesis has become an increasingly popular strategy to form covalent nanostructures. The approach has great prospects for facilitating the manufacture of a range of fascinating materials with atomic precision. However, the on-surface reactions are enigmatic to control, currently restricting its bright perspectives and there is a great need to explore how the reactions are governed. The objective of this topical review is to summarize theoretical work that has focused on comprehending on-surface synthesis protocols through studies of reaction mechanisms.

  • 85.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Linköping University.
    Thermodynamics of an Electrocyclic Ring-Closure Reaction on Au(111)2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 38, p. 21716-21721Article in journal (Refereed)
    Abstract [en]

    We have computationally studied the effects of temperature on the reaction pathway of an electrocyclic ring-closure reaction on the Au(111) surface, particularly focusing on thermodynamic aspects of the reaction. The electrocyclic ring closure is accompanied by a series of dehydrogenation steps, and while it is found that temperature, in terms of vibrational entropy and enthalpy, has a reducing effect on most energy barriers, it does not alter the qualitative appreciation of the reaction kinetics. However, it is found that the way the abstracted hydrogen atoms are treated is crucial for the thermodynamics of the reaction. The overall reaction is highly endothermic but becomes thermodynamically favorable due to the entropy gain of the hydrogen byproducts, which desorb associatively from the surface as H2. The study provides new outlooks for the theoretical treatment of reactions related to on-surface synthesis, anticipated to be instructive for future studies.

  • 86.
    Björk, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Stafström, Sven
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Adsorption of large hydrocarbons on coinage metals: a van der Waals density functional study2014In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 15, no 13, p. 2851-2858Article in journal (Refereed)
    Abstract [en]

    The adsorption of organic molecules onto the close-packed facets of coinage metals is studied, and how accurately adsorption heights can be described by using recent advances of the van der Waals density functional (vdWDF), with optPBE/vdWDF, optB86b/vdWDF, vdWDF2, and rev/vdWDF2 functionals is illustrated. The adsorption of two prototypical aromatic hydrocarbons is investigated, and the calculated adsorption heights are compared to experimental literature values from normal incident X-ray standing wave absorption and a state-of-the-art semi-empirical method. It is shown that both the optB86b/vdWDF and rev/vdWDF2 functionals describe adsorption heights with an accuracy of 0.1 Å, compared to experimental values, and are concluded as reliable methods of choice for related systems.

  • 87. Blomberg, Margareta R. A.
    et al.
    Johansson, Adam Johannes
    Stockholm University.
    Siegbahn, Per E. M.
    O-O bond cleavage in dinuclear peroxo complexes of iron porphyrins: a quantum chemical study2007In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, no 19, p. 7992-7997Article in journal (Refereed)
    Abstract [en]

    To gain insight into the mechanisms of O-2 activation and cleavage in metalloenzymes, biomimetic metal complexes have been constructed and experimentally characterized. One such model complex is the dinuclear peroxo complex of iron porphyrins observed at low temperature in a noncoordinating solvent. The present theoretical study examines the O-O bond cleavage in these complexes, experimentally observed to occur either at increased temperature or when a strongly coordinating base is added. Using hybrid density functional theory, it is shown that the O-O bond cleavage always occurs in a state where two low-spin irons (S = +/- 1/2) are antiferromagnetically coupled to a diamagnetic state. This state is the ground state when the strong base is present and forms an axial ligand to the free iron positions. In contrast, without the axial ligands, the ground state of the clinuclear peroxo complex has two high-spin irons (S = +/- 5/2) coupled antiferromagnetically. Thus, the activation barrier for O-O bond cleavage is higher without the base because it includes also the promotion energy from the ground state to the reacting state. It is further found that this excitation energy, going from 10 unpaired electrons in the high-spin case to 2 in the low-spin case, is unusually difficult to determine accurately from density functional theory because it is extremely sensitive to the amount of exact exchange included in the functional.

  • 88. Bochkarev, A. S.
    et al.
    Zamulko, S. O.
    Gorbatov, O. I.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Sidorenko, S. I.
    Puschnig, P.
    Ruban, Andrei V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    A single-volume approach for vacancy formation thermodynamics calculations2016In: Europhysics letters, ISSN 0295-5075, E-ISSN 1286-4854, Vol. 116, no 1, article id 16001Article in journal (Refereed)
    Abstract [en]

    The vacancy formation Gibbs free energy, enthalpy and entropy in fcc Al, Ag, Pd, Cu, and bcc Mo are determined by first-principles calculations using the quasi-harmonic approximation to account for vibrational contributions. We show that the Gibbs free energy can be determined with sufficient accuracy in a single-volume approach using the fixed equilibrium volume of the defect-free supercell. Although the partial contributions to the Gibbs free energy, namely, the formation enthalpy and entropy exhibit substantial errors when obtained directly in this approach, they can be computed from the Gibbs free energy using the proper thermodynamic relations. Compared to experimental data, the temperature dependence of the vacancy formation Gibbs free energy is accounted for at low temperatures, while it overestimates the measurements at high temperature, which is attributed to the neglect of anharmonic effects.

  • 89.
    Bohlén, Martin
    et al.
    University of Borås, School of Engineering.
    Bolton, Kim
    University of Borås, School of Engineering.
    Conformational studies of poly(vinylidene fluoride), poly(trifluoroethylene) and poly(vinylidene fluoride-co-trifluoroethylene) using density functional theory2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 25, p. 12929-12939Article in journal (Refereed)
    Abstract [en]

    Different conformations of systems consisting of poly(vinylidene fluoride) (PVDF), poly(trifluoroethylene) (PTrFE) and poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)) were investigated using density functional theory with dispersion correction. It was found that the trans-gauche-trans-gauche´ (TGTG´) conformation of a single PVDF chain is the lowest energy conformer. Crystals of PVDF were modelled using between two to five chains with up to 12 repeat units in each chain and, in agreement with experiment, structures comprised partly or completely of chains with the TGTG´ conformation are more stable than structures built up from chains with all-trans (TTTT) conformation. This indicates that an all-trans segment or chain will not induce the growth of a larger crystal with the same chain conformations. In contrast, the energetically preferred structure of PTrFE chains is an all-trans (TTTT) conformation, and the results indicate that copolymerization of vinylidene fluoride with trifluoroethylene can facilitate the formation of the all-trans PVDF conformations. This is probably due to increased intramolecular repulsion between the fluorine atoms and an increased intermolecular attraction in the crystal structure.

  • 90.
    Bohlén, Martin
    et al.
    University of Borås, School of Engineering.
    Bolton, Kim
    University of Borås, School of Engineering.
    Inducing the piezoelectric β-phase of PVDF: a DFT study2014Conference paper (Refereed)
  • 91.
    Bohlén, Martin
    et al.
    University of Borås, School of Engineering.
    Bolton, Kim
    University of Borås, School of Engineering.
    Inducing the β-phase of poly(vinylidene fluoride): a review2014In: Annual Review of Nanoscience and Nanotechnology, ISSN 2159-9688, Vol. 1, no 1Article in journal (Refereed)
    Abstract [en]

    Poly(vinylidene fluoride) (PVDF) is a versatile material with numerous applications in many fields of industry and science. The extent of applications, ranging from approved contact materials in the food industry to monitors for respiration and heart-rate in medicine, drives the research and development by the materials science community. The largest limiting factor when using PVDF in applications where its piezo- and pyroelectricity is important, is the amount of the highly polar crystalline β-phase in the material. PVDF is polymorphic and usually crystallizes from melt or solution into the non-polar α-phase, which is of little use in piezoelectric applications. Many studies have therefore aimed at increasing the amount of the β-phase crystal structure in the material. Cold drawing of α-phase PVDF, poling in high electric fields, copolymerization with trifluoroethylene, and inclusion of different types of additives to PVDF have been studied using both experimental and computational techniques. This review presents the current status and understanding of these processes, and summarizes results from previous studies. © Global Scientific Publishers 2015.

  • 92. Bondarchuk, Sergey V.
    et al.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bogdan Khmelnitsky Cherkasy Natl Univ, Ukraine.
    DFT design of polyguanidine - a unique two-dimensional material with high-energy density2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 19, p. 2423-2430Article in journal (Refereed)
    Abstract [en]

    We report herein a theoretical prediction and characterisation of a new two-dimensional (2D) material based on energetic polyguanidine. The structure represents a hexagonal type lattice of the P6/m space group. The material is dynamically and mechanically stable. Highly accurate band structure calculation with hybrid functional HSE06 reveals a tiny direct band gap being equal to 0.181 eV. We provide an additional spectral characterisation of the 2D polyguanidine substance including UV-vis, nuclear magnetic resonance and nuclear quadrupolar resonance parameters. The electron transport properties of a 26.6 angstrom wide polyguanidine ribbon are calculated in terms of tight-binding density functional theory approach. The predicted 2D material is also analysed by means of Quantum Theory of Atoms in Molecules and the aromatic character of the formed rings is estimated using nucleus-independent chemical shifts quantities.

  • 93. Bondarenko, N.
    et al.
    Eriksson, O.
    Skorodumova, Natalia V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling.
    Polaron mobility in oxygen-deficient and lithium-doped tungsten trioxide2015In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, no 16, article id 165119Article in journal (Refereed)
    Abstract [en]

    Electron localization and polaron mobility in oxygen-deficient as well as Li-doped monoclinic tungsten trioxide have been studied in the adiabatic limit in the framework of density functional theory. We show that small polarons formed in the presence of oxygen vacancy prefer the bipolaronicW(5+)-W5+ configuration, whereas the W6+-W4+ configuration is found to be metastable. Our calculations suggest that bipolarons are tightly bound by the vacancy and therefore largely immobile. On the contrary, polarons formed as a result of Li intercalation can be mobile; the activation energy for polaron jumping in this case varies between 98 and 124 meV depending on the crystallographic direction. The formation of W5+-W5+ bipolarons in Li-WO3 is possible. When situated along [001] the bipolaronic configuration is 8 meV lower in energy than two separate W5+ polarons.

  • 94. Bondesson, Laban
    et al.
    Rudberg, Elias
    Luo, Yi
    Salek, Pawel
    A linear scaling study of solvent-solute interaction energy of drug molecules in aqua solution2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 34, p. 10320-10328Article in journal (Refereed)
  • 95. Bondesson, Laban
    et al.
    Rudberg, Elias
    Luo, Yi
    Salek, Pawel
    Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, p. 1725-1732Article in journal (Refereed)
  • 96.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Basis set dependence of solute-solvent interaction energy of benzene in water: a HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, p. 1725-1732Article in journal (Refereed)
    Abstract [en]

    Solute-solvent interaction energies for the benzene molecule dissolved in water are computed using Hartree-Fock and B3LYP density functional theories. Explicit solvent molecules up to 14-angstrom away from the dissolved benzene molecule are included in the calculation of interaction energies. Both basis set dependence and basis Set Superposition errors are carefully examined. It is found that the use of a larger basis set for the region near the solute together with a smaller basis set for the outer region gives results very close to what would have been obtained if the larger basis set had been used for the whole system. It is also shown that a correction for the basis Set superposition error is a necessary component in this kind of calculations. With this correction, results obtained with different tested basis sets converge to within 1 kcal/mol.

  • 97.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Erratum to: Basis set dependence of solute-solvent interaction energy of benzene in waterA HF/DFT study (vol 29, pg 1725, 2008)2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 3, p. 354-354Article in journal (Refereed)
  • 98.
    Borg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Theoretical Photochemistry: Halogenated Arenes, Phytochromobilin, Ru(II)polypyridyl complexes and 6-4 photoadducts2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents Quantum Chemical calculations on the Photochemistry of Halogenated benzenes, Phytochromobilin, Ruthenium Polypyridyl complexes and 6-4 photoadducts in DNA. The work is focused on improving the understanding of a number of experimentally observed photochemical processes in these systems. New results regarding the mechanism of photodissociation of halogenated arenes, photointerconversion of phytochromobilin are presented, as well as of the photoprocesses of Ruthenium Polypyridyl complexes and new mechanistic insights in the repair of 6-4 photoadducts in DNA.

  • 99. Borg, O. Anders
    et al.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Durbeej, Bo
    Electron-transfer induced repair of 6-4 photoproducts in DNA: a computational study.2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 12, p. 2351-2361Article in journal (Refereed)
    Abstract [en]

    The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C−N and C−C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

  • 100.
    Borg, O Anders
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Avdelningen för kvantkemi.
    Liu, Ya-Jun
    Persson, Petter
    Lunell, Sten
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Chemistry, Department of Physical and Analytical Chemistry. Avdelningen för kvantkemi.
    Karlsson, Daniel
    Department of Photochemistry and Molecular Science. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics.
    Kadi, Malin
    Davidsson, Jan
    Department of Photochemistry and Molecular Science. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Department of Physics and Materials Science, Chemical Physics.
    Photochemistry of bromofluorobenzenes.2006In: J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory, ISSN 1089-5639, Vol. 110, no 22, p. 7045-56Article in journal (Refereed)
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