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  • 1.
    Ahlstrand, Emma
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Hermansson, Kersti
    Uppsala University.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, no 13, p. 2643-2654Article in journal (Refereed)
    Abstract [en]

    Zinc plays important roles in structural stabilization of proteins, eniyine catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynainics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Diode polarizable force field agreed better with the ab initio results,:although the deviations between QM and MM were still rather large (40-96 kcallmol). In order to gain further insight into Zn ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand ligand interactions did not play a significant role in the binding of Zn. Finally) analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn:binding dynamics. An exchange between earboxylate (Asp/Glii) and imidazole (His) is less likely.

  • 2.
    Medel, Victor M.
    et al.
    Virginia Commonwealth University, USA.
    Reveles, Ulises
    Virginia Commonwealth University, USA.
    Islam, Fhokrul
    Virginia Commonwealth University, USA.
    Khanna, Shiv
    Virginia Commonwealth University, USA.
    Robust Magnetic Moments on Impurities in Metallic Clusters: Localized Magnetic States in Superatoms2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 20, p. 4297-4303Article in journal (Refereed)
    Abstract [en]

    Introducing magnetic impurities into clusters of simplemetals can create localized states for higher angular momentum quantumnumbers (l = 2 or 3) that can breed magnetism analogous to that invirtual bound states in metallic hosts, offering a new recipe for magneticsuperatoms. In this work, we demonstrate that MnCan clusterscontaining 6−15 Ca atoms show a spin magnetic moment of 5.0 μBirrespective of the cluster size. Theoretical analysis reveals that the Mn dstates hybridize only partially with superatomic states and introduce extramajority and minority d states, largely localized at the Mn site, with alarge gap. Successive addition of Ca atoms introduces superatomic statesof varying angular momentum that are embedded in this gap, allowingcontrol over the stability of the motifs without altering the moment. Assemblies of such clusters can offer novel electronic features due to theformation of localized magnetic “quasibound states” in a confined nearlyfree electron gas.

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