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  • 1. Aidas, Kestutis
    et al.
    Agren, Hans
    Kongsted, Jacob
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. the case of na+ in aqueous solution2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 5, p. 1621-1631Article in journal (Refereed)
    Abstract [en]

    The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

  • 2.
    Jämbeck, Joakim P. M.
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Partial Atomic Charges and Their Impact on the Free Energy of Solvation2013In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 3, p. 187-197Article in journal (Refereed)
    Abstract [en]

    Free energies of solvation (Delta G) in water and n-octanol have been computed for common drug molecules by molecular dynamics simulations with an additive fixed-charge force field. The impact of the electrostatic interactions was investigated by computing the partial atomic charges with four methods that all fit the charges from the quantum mechanically determined electrostatic potential (ESP). Due to the redistribution of electron density that occurs when molecules are transferred from gas phase to condensed phase, the polarization impact was also investigated. By computing the partial atomic charges with the solutes placed in a conductor-like continuum, the charges were effectively polarized to take the polarization effects into account. No polarization correction term or similar was considered, only the partial atomic charges. Results show that free energies are very sensitive to the choice of atomic charges and that Delta G can differ by several k(B)T depending on the charge computing method. Inclusion of polarization effects makes the solutes too hydrophilic with most methods and in vacuo charges make the solutes too hydrophobic. The restrained-ESP methods together with effectively polarized charges perform well in our test set and also when applied to a larger set of molecules. The effect of water models is also highlighted and shows that the conclusions drawn are valid for different three-point models. Partitioning between an aqueous and a hydrophobic phase is also described better if the two environment's polarization is taken into account, but again the results are sensitive to the charge calculation method. Overall, the results presented here show that effectively polarized charges can improve the description of solvating a drug-like molecule in a solvent and that the choice of partial atomic charges is crucial to ensure that molecular simulations produce reliable results.

  • 3.
    Mocci, Francesca
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is worth its salt2012In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 8, no 36, p. 9268-9284Article, review/survey (Refereed)
    Abstract [en]

    Nucleic acids are highly charged polyelectrolytes. Their interactions with counterions are of great importance for their structural stability, conformational behaviour and biological functions. Molecular modelling and simulation techniques, particularly molecular dynamics, have been highly useful for studies of interactions between DNA, water and ions at the molecular level, allowing us to explain many experimental observations, or to obtain information not accessible experimentally. In this review we focus on both atomistic and coarse-grained molecular simulation studies concerning the interactions of DNA with different types of counterions, with emphasis on recent studies, still open questions, limits of the method and possible further developments.

  • 4. Rebic, Matus
    et al.
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Cagliari, Italy.
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Stellenbosch University, South Africa.
    Ulicny, Jozef
    Multiscale Simulations of Human Telomeric G-Quadruplex DNA2015In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, no 1, p. 105-113Article in journal (Refereed)
    Abstract [en]

    We present a coarse-grain (CG) model of human telomeric G-quadruplex, obtained using the inverse Monte Carlo (IMC) and iterative Boltzmann inversion (IBI) techniques implemented within the software package called MagiC. As a starting point, the 2HY9 human telomeric [3 + 1] hybrid, a 26-nucleobase sequence, was modeled performing a 1 mu s long atomistic molecular dynamics (MD) simulation. The chosen quadruplex includes two kinds of loops and all possible combinations of relative orientations of guanine strands that can be found in quadruplexes. The effective CG potential for a one bead per nucleotide model has been developed from the radial distribution functions of this reference system. The obtained potentials take into account explicitly the interaction with counterions, while the effect of the solvent is included implicitly. The structural properties of the obtained CG model of the quadruplex provided a perfect match to those resulting from the reference atomistic MD simulation. The same set of interaction potentials was then used to simulate at the CG level another quadruplex topology (PDB id 1KF1) that can be formed by the human telomeric DNA sequence. This quadruplex differs from 2HY9 in the loop topology and G-strand relative orientation. The results of the CG MD simulations of 1KF1 are very encouraging and suggest that the CG model based on 2HY9 can be used to simulate quadruplexes with different topologies. The CG model was further applied to a higher order human telomeric quadruplex formed by the repetition, 20 times, of the 1KF1 quadruplex structure. In all cases, the developed model, which to the best of our knowledge is the first model of quadruplexes at the CG level presented in the literature, reproduces the main structural features remarkably well.

  • 5.
    Todde, Guido
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Hovmöller, Sven
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Cagliari, Italy; Stellenbosch University, South Africa.
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Cagliari, Italy.
    Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations2014In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 82, no 10, p. 2353-2363Article in journal (Refereed)
    Abstract [en]

    Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification.

  • 6. Usula, M.
    et al.
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Cagliari .
    Marincola, F. Cesare
    Porcedda, S.
    Gontrani, L.
    Caminiti, R.
    The structural organization of N-methyl-2-pyrrolidone plus water mixtures: A densitometry, x-ray diffraction, and molecular dynamics study2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 140, no 12, p. 124503-Article in journal (Refereed)
    Abstract [en]

    A combined approach of molecular dynamics simulations, wide angle X-ray scattering experiments, and density measurements was employed to study the structural properties of N-methyl-2-pyrrolidone (NMP) + water mixtures over the whole concentration range. Remarkably, a very good agreement between computed and experimental densities and diffraction patterns was achieved, especially if the effect of the mixture composition on NMP charges is taken into account. Analysis of the intermolecular organization, as revealed by the radial and spatial distribution functions of relevant solvent atoms, nicely explained the density maximum observed experimentally.

  • 7. Usula, Marianna
    et al.
    Matteoli, Enrico
    Leonelli, Francesca
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). University of Cagliari, Italy.
    Marincola, Flaminia Cesare
    Gontrani, Lorenzo
    Porcedda, Silvia
    Thermo-physical properties of ammonium-based ionic liquid plus N-methyl-2-pyrrolidone mixtures at 298.15 K2014In: Fluid Phase Equilibria, ISSN 0378-3812, E-ISSN 1879-0224, Vol. 383, p. 49-54Article in journal (Refereed)
    Abstract [en]

    A systematic study of a series of room-temperature ionic liquids, belonging to the alkylammonium nitrate family (XAN), was carried out at 298.15 K and 0.1 MPa with the aim of investigating the effect of the cationic chain length on some thermo-physical properties and their behavior in the organic solvent N-methyl-2-pyrrolidone (NMP), over the whole concentration range. Experimental densities were used to calculate molar volumes, V-m, and excess molar volumes, V-E. Complementary information was obtained by isothermal titration calorimetry that provided the values of the heat of mixing, H-E, and the excess partial molar enthalpies of each component, (H) over bar (E)(1) and (H) over bar (E)(2). The density values of neat XAN samples decreased as the alkyl chain length of the cation increases, whereas, the addition of the methoxy group to the considered smaller alkyl chain resulted in an increase of density. Negative V-E and H-E values were found for each XAN + NMP system, indicating the presence of strong attracting interactions between the constituents.

  • 8. Usula, Marianna
    et al.
    Porcedda, Silvia
    Mocci, Francesca
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Gontrani, Lorenzo
    Caminiti, Ruggero
    Marincola, Flaminia Cesare
    NMR, Calorimetry, and Computational Studies of Aqueous Solutions of N-Methyl-2-pyrrolidone2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 35, p. 10493-10502Article in journal (Refereed)
    Abstract [en]

    N-Methyl-2-pyrrolidone (NMP) is a solvent with applications in different industrial fields. Although largely employed in aqueous mixtures, little is known on the structural and dynamic properties of this system. In order to improve the knowledge on NMP aqueous solutions, useful to the development of their applications, NMR spectroscopy, calorimetric titration, and puckering analysis of molecular dynamics (MD) simulations were employed in this work. Our calorimetric study evidenced the presence of strong interactions between NMP and water and revealed that, under comparable conditions, the solvation of NMP by water results in an interaction stronger than the solvation of water by NMP. Overall, the changes of H-1 and C-13 chemical shifts and 2D ROESY spectra upon dilution suggested a preferential location of water nearby the carbonyl group of NMP and the formation of hydrogen bonding between these two molecules. In parallel, observation of correlation times by C-13 NMR spectroscopy evidenced a different dynamic behavior moving from the NMP-rich region to the water-rich region, characterized by a maximum value at about 0.7 water mole fraction. MD simulations showed that the NMP conformation remains the same over the whole concentration range. Our results were discussed in terms of changes in the NMP assembling upon dilution.

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