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  • 1. Atzori, Alessio
    et al.
    Liggi, Sonia
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). University of Cagliari, Italy.
    Porcu, Massimiliano
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Università di Cagliari, Italy.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Saba, Giuseppe
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stockholm University, Science for Life Laboratory (SciLifeLab). Università di Cagliari, Italy.
    Base sequence specificity of counterion binding to DNA: what can MD simulations tell us?2016In: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 94, no 12, 1181-1188 p.Article in journal (Refereed)
    Abstract [en]

    Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan-Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the A. qvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted.

  • 2. Brinkmann, Andreas
    et al.
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Estimating internuclear distances between half-integer quadrupolar nuclei by central-transition double-quantum sideband NMR spectroscopy2011In: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 89, no 7, 892-899 p.Article in journal (Refereed)
    Abstract [en]

    We demonstrate the estimation of homonuclear dipolar couplings, and thereby internuclear distances, between half-integer spin quadrupolar nuclei by central-transition (CT) double-quantum (2Q) sideband nuclear magnetic resonance (NMR) spectroscopy. It is shown that the rotor-encoded sideband amplitudes from CT 2Q coherences in the indirect dimension of the two-dimensional NMR spectrum are sensitive probes of the magnitude of the homonuclear dipolar coupling, but are significantly less affected by other NMR parameters such as the magnitudes and orientations of the electric field gradient tensors. Experimental results of employing the R2(2)(1)R2(2)(-1) recoupling sequence to the (11)B spin pair of bis(catecholato)diboron resulted in an estimation of the internuclear B-B distance as (169.6 +/- 3) pm, i.e., with a relative uncertainty of +/- 2%, and in excellent agreement with the distance of 167.8 pm determined by single-crystal X-ray diffraction.

  • 3.
    Samec, Joseph S M
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Mony, Laetitia
    Bäckvall, Jan-E
    Efficient Ruthenium-Catalyzed Transfer Hydrogenation of Functionalized Imines by Isopropanol under Controlled Microwave Heating2005In: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 83, no 6, 909-916 p.Article in journal (Refereed)
    Abstract [en]

    Transfer hydrogenation of various functionalized imines by isopropanol catalyzed by [Ru(CO)(2)(Ph4C4CO)](2) (3) has been studied. The use of either an oil bath or controlled microwave heating in toluene led to an efficient procedure with high turnover frequencies and the product amines were obtained in high yields. An advantage with catalyst 3 over the conventional [Ru-2(CO)(4)(mu-H)(Ph4C4COHOCC4Ph4)] (1) is the absence of an initiation period, which results in a faster reaction with 3 as compared to 1.

  • 4. Shaw, Dawn M.
    et al.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Tse, John S.
    Theoretical X-ray absorption investigation of the uniaxial compression of hexagonal graphite2007In: Canadian journal of chemistry (Print), ISSN 0008-4042, E-ISSN 1480-3291, Vol. 85, no 10, 837-842 p.Article in journal (Refereed)
    Abstract [en]

    The X-ray absorption (XAS) and powder X-ray diffraction (XRD) spectra for the intermediate structures along uniaxial c-axis compression of hexagonal graphite are studied with the first-principles pseudopotential plane wave method. Comparison with experiment is made whenever results are available. A transformation from graphite to a new carbon phase was observed in the simulation. The new phase consists of alternating linkages of the graphite layers via the formation of C-C sigma bonds. The calculated XAS and XRD reproduced most but not all of the features observed in a recent experiment. Comments are made on the reliability of the computational procedures to reproduce the XAS of these structures.

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