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  • 1.
    Bazooyar, Faranak
    et al.
    University of Borås, School of Engineering.
    Momany, Frank A.
    Bolton, Kim
    University of Borås, School of Engineering.
    Validating Empirical Force Fields for Molecular-level Simulation of Cellulose Dissolution2012In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 984, p. 119-127Article in journal (Refereed)
    Abstract [en]

    The calculations presented here, which include dynamics simulations using molecular mechanics forcefields and first principles studies, indicate that the COMPASS forcefield is preferred over the Dreiding and Universal forcefields for studying dissolution of large cellulose structures. The validity of these forcefields was assessed by comparing structures and energies of cellobiose, which is the shortest cellulose chain, obtained from the forcefields with those obtained from MP2 and DFT methods. In agreement with the first principles methods, COMPASS is the only forcefield of the three studied here that favors the anti form of cellobiose in the vacuum. This forcefield was also used to compare changes in energies when hydrating cellobiose with 1–4 water molecules. Although the COMPASS forcefield does not yield the change from anti to syn minimum energy structure when hydrating with more than two water molecules – as predicted by DFT – it does predict that the syn conformer is preferred when simulating cellobiose in bulk liquid water and at temperatures relevant to cellulosedissolution. This indicates that the COMPASS forcefield yields valid structures of cellulose under these conditions. Simulations based on the COMPASS forcefield show that, due to entropic effects, the syn form of cellobiose is energetically preferred at elevated temperature, both in vacuum and in bulk water. This is also in agreement with DFT calculations.

  • 2.
    Erdtman, E
    et al.
    University of Borås, School of Engineering.
    Bushnell, EAC
    Eriksson, LA
    Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase2011In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2, p. 479-489Article in journal (Refereed)
    Abstract [en]

    Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however, is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogen synthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for the formation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to 14.0 kcal mol(-1). We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

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