Browsing by Subject "SOLVATION"

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  • Lassfolk, Robert; Rahkila, Jani; Johansson, Mikael Peter; Ekholm, Filip Sebastian; Wärnå, Johan; Leino, Reko (2019)
    Acetylated oligosaccharides are common in nature. While they are involved in several biochemical and biological processes, the role of the acetyl groups and the complexity of their migration has largely gone unnoticed. In this work, by combination of organic synthesis, NMR spectroscopy and quantum chemical modeling, we show that acetyl group migration is a much more complex phenomenon than previously known. By use of synthetic oligomannoside model compounds, we demonstrate, for the first time, that the migration of acetyl groups in oligosaccharides and polysaccharides may not be limited to transfer within a single monosaccharide moiety, but may also involve migration over a glycosidic bond between two different saccharide units. The observed phenomenon is not only interesting from the chemical point of view, but it also raises new questions about the potential biological role of acylated carbohydrates in nature.
  • Timr, Stepan; Kadlec, Jan; Srb, Pavel; Ollila, O. H. Samuli; Jungwirth, Pavel (2018)
    The detailed functional mechanism of recoverin, which acts as a myristoyl switch at the rod outer-segment disk membrane, is elucidated by direct and replica-exchange molecular dynamics. In accord with NMR structural evidence and calcium binding assays, simulations point to the key role of enhanced calcium binding to the EF3 loop of the semiopen state of recoverin as compared to the closed state. This 2-4-order decrease in calcium dissociation constant stabilizes the semiopen state in response to the increase of cytosolic calcium concentration in the vicinity of recoverin. A second calcium ion then binds to the EF2 loop and, consequently, the structure of the protein changes from the semiopen to the open state. The latter has the myristoyl chain extruded to the cytosol, ready to act as a membrane anchor of recoverin.
  • Canaval, Eva; Hyttinen, Noora; Schmidbauer, Benjamin; Fischer, Lukas; Hansel, Armin (2019)
    In this study, we present reactions of NH4+ with a series of analytes (A): acetone (C3H6O), methyl vinyl ketone (C4H6O), methyl ethyl ketone (C4H8O) and eight monoterpene isomers (C10H16) using a Selective Reagent Ionization Time-of-Flight Mass Spectrometer (SRI-ToF-MS). We studied the ion-molecule reactions at collision energies of 55 meV and 80 meV. The ketones, having a substantially lower proton affinity than NH3, produce only cluster ions NH4+(A) in detectable amounts at 55 meV. At 80 meV, no cluster ions were detected meaning that these adduct ions are formed by strongly temperature dependent association reactions. Bond energies of cluster ions and proton affinities for most monoterpenes are not known and were estimated by high level quantum chemical calculations. The calculations reveal monoterpene proton affinities, which range from slightly smaller to substantially higher than the proton affinity of NH3. Proton affinities and cluster bond energies allow to group the monoterpenes as a function of the enthalpy for the dissociation reaction . We find that this enthalpy can be used to predict the NH4+-A cluster ion yield. The present study explains product ion formation involving NH4+ ion chemistry. This is of importance for chemical ionization mass spectrometry (CIMS) utilizing NH4+ as well as NH4+(H2O) as reagent ions to quantitatively detect atmospherically important organic compounds in real-time.
  • Lattouf, Elie; Anttalainen, Osmo Antero; Kotiaho, Tapio; Hakulinen, Hanna Idamaria; Vanninen, Paula; Eiceman, Gary Alan (2021)
    Gas phase reactions between hydrated protons H+(H2O)(n) and a substance M, as seen in atmospheric pressure chemical ionization (APCI) with mass spectrometry (MS) and ion mobility spectrometry (IMS), were modeled computationally using initial amounts of [M] and [H+(H2O)(n)], rate constants k(1) to form protonated monomer (MH+(H2O)(x)) and k(2) to form proton bound dimer (M2H+(H2O)(z)), and diffusion constants. At 1 x 10(10) cm(-3) (0.4 ppb) for [H+(H2O)(n)] and vapor concentrations for M from 10 ppb to 10 ppm, a maximum signal was reached at 4.5 mu s to 4.6 ms for MH+(H2O)(x) and 7.8 mu s to 46 ms for M2H+(H2O)(z). Maximum yield for protonated monomer for a reaction time of 1 ms was similar to 40% for k(1) from 10(-11) to 10(-8) cm(3).s(-1), for k(2)/k(1) = 0.8, and specific values of [M]. This model demonstrates that ion distributions could be shifted from [M2H+(H2O)(z)] to [MH+(H2O)(x)] using excessive levels of [H+(H2O)(n)], even for [M] > 10 ppb, as commonly found in APCI MS and IMS measurements. Ion losses by collisions on surfaces were insignificant with losses of
  • Miyazawa, Keisuke; Tracey, John; Reischl, Bernhard; Spijker, Peter; Foster, Adam S.; Rohl, Andrew L.; Fukuma, Takeshi (2020)
    In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite-water interfaces by experiments and simulations. We calculated 3D force images by simulations with the solvent tip approximation (STA), Ca, CO(3)and OH tip models. For all the 3D images, thezprofiles at the surface Ca and CO(3)sites alternately show oscillatory peaks corresponding to the hydration layers. However, the peak heights and spacings become larger when the mechanical stability of the tip becomes higher. For analyzing thexyslices of the 3D force images, we developed the extended STA (E-STA) model which allowed us to reveal the strong correlation between the hydration structure just under the tip and the atomic-scale force contrasts. Based on these understandings on the image features showing the strong tip dependence, we developed a method for objectively estimating the similarity between 3D force images. With this method, we compared the simulated images with the three experimentally obtained ones. Among them, two images showed a relatively high similarity with the image obtained by the simulation with the Ca or the CO(3)tip model. Based on these agreements, we characterized the hydration structure and mechanical stability of the experimentally used tips. The understanding and methodology presented here should help us to derive accurate information on the tip and the interfacial structure from experimentally obtained 3D-SFM images.