References of "Fresch, Barbara"
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See detailAtomistic account of structural and dynamical changes induced by small binders in the double helix of a short DNA
Fresch, Barbara ULg; Remacle, Françoise ULg

in Physical Chemistry Chemical Physics [=PCCP] (in press)

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See detailAn atomistic view of DNA dynamics and its interaction with small binders: insights from Molecular Dynamics and Principal Component Analysis
Fresch, Barbara ULg; Remacle, Françoise ULg

in Joachim, Christian (Ed.) Advances in Atom and Single Molecule Machines (in press)

DNA oligomers are promising building blocks for the development of bottom-up nano-devices and molecular logic machines. To control and exploit their unique capabilities of self-assembling and molecular ... [more ▼]

DNA oligomers are promising building blocks for the development of bottom-up nano-devices and molecular logic machines. To control and exploit their unique capabilities of self-assembling and molecular recognition a deep understanding of their dynamical properties is essential. We theoretically investigate the dynamics of a DNA dodecamer and its complexes with two common ligands, Hoechst33258 and the ethidium cation, by means of classical Molecular Dynamics (MD) simulations and Principal Component Analysis (PCA). We study the structural relation between the flexibility of the double helix and the binding process. The dynamics of a terminal base pair unbinding is also analysed as an example of process that involves multiple energy minima in the underlying free energy landscape. [less ▲]

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See detailTailoring the Properties of Metallic Clusters by Ligand Coatings
Fresch, Barbara ULg

Conference (2014, January 23)

Tuning the properties of metallic clusters using different protecting ligand shells is an important step toward the application-orientated design of nanoparticles for nano-electronics and catalysis. An ... [more ▼]

Tuning the properties of metallic clusters using different protecting ligand shells is an important step toward the application-orientated design of nanoparticles for nano-electronics and catalysis. An attractive property of these materials is the ability to engineer ligand shells composed of different molecules that influence the electronic structure of the system due to their chemical interaction with the metal core. Sometimes properties are not simply additive, and cooperative effects emerge so that the presence of more than one ligand type in the ligand shell imparts novel properties to the nanoparticles. We theoretically investigate at the DFT level palladium and gold metal cores interacting with only-thiol, only-phosphine and mixed phosphine-thiol ligand shells. In this talk, we present some examples of how these capping systems affect structural, optical, magnetic and charging properties of metallic clusters. For Au11 and Au13, we show that ligation stabilizes structural isomers characterized by a flake geometry of the metal core, and they show different optical properties than isomers with a compact gold core. The magnetic ground state of small bare Pd13 clusters is a high spin state, nonet or septet depending on the structural isomer. We demonstrate that interaction with thiols and phosphines differently affect structure and magnetic ground state in these systems. The mixed ligand species Pd13(SCH3)6(PH3)6 shows multiple energetically accessible spin states and consequently an unusual thermal behaviour of the average magnetic moment. The charge transfer character of the metal-ligand interaction is studied in small Pd13 and truly nano-sized Pd55 ligand protected metal cores. We discuss cooperative effects in the ligand induced charge redistribution and demonstrate that the electron donor or acceptor character of the ligand molecules affects the energetics of charging processes [less ▲]

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See detailTuning the Properties of Pd Nanoclusters by Ligand Coatings: Electronic Structure Computations on Phosphine, Thiol, and Mixed PhosphineThiol Ligand Shells
Fresch, Barbara ULg; Remacle, Françoise ULg

in Journal of Physical Chemistry C (2014)

Tuning the properties of Palladium nanoparticles using different protecting ligand shells is an important step toward the application-orientated design of nanoparticles for nano-electronics and catalysis ... [more ▼]

Tuning the properties of Palladium nanoparticles using different protecting ligand shells is an important step toward the application-orientated design of nanoparticles for nano-electronics and catalysis. We present a density functional theoretical characterization of Pd13 and Pd55 metal cores protected by only-thiol, only-phosphine and mixed phosphine-thiol ligand shells. We analyze the ligand contributions to the frontier orbitals and the charge redistribution between the ligand shell and the metal core and show that these properties control the values of the charging energy and the catalytic activity. The charge transfer character of the metal-ligand interaction is influenced by the presence of other ligands in the capping system indicating a cooperative effect in the ligand induced charge redistribution. Because of the interplay between the stabilization of the frontier orbital due to the contribution of the sulfur and the charge donation by the phosphine, the charging energy of the mixed phosphine-thiol protected cluster is larger than that of the only-phosphine and the only-thiol systems. The complementary point of view is adopted for rationalizing the catalytic properties of the clusters by analyzing the effect of the interaction with the metallic core on the properties of the ligand. The impact of solvation on the electronic structure of the ligand capped Pd13 cluster is investigated by including explicitly a layer of water molecules in the model system. [less ▲]

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See detailLigand and solvation effects on the structural and electronic properties of small gold clusters
Dufour, F.; Fresch, Barbara ULg; Durupthy, O. et al

in Journal of Physical Chemistry C: Nanomaterials, Interfaces, and Hard Matter (2014), 118(8), 4362

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See detailDynamical properties of DNA-ligand complexes under shear stress: insights from classical molecular dynamics
Fresch, Barbara ULg

Conference (2013, June 19)

Nucleic acids are flexible molecules: their dynamical properties play an essential role in molecular recognition and self-assembly. In the biological environment, because of mechanical forces acting at ... [more ▼]

Nucleic acids are flexible molecules: their dynamical properties play an essential role in molecular recognition and self-assembly. In the biological environment, because of mechanical forces acting at the molecular level, DNA is transiently deformed, cut and resealed, damaged and repaired, and the strands pulled apart and then re-annealed. These unique features make short DNA oligonucleotides promising building blocks in the development of “bottom-up” nano-devices and molecular logic machines. Single molecule manipulation techniques (Atomic Force Microscopy/ Optical Tweezers) allow detailed investigation of nucleic acids response to the application of controlled mechanical stress. Interpretations of these data in terms of molecular structural changes and dynamical properties call for a collaborative effort between experiments and theoretical/computational modeling. We have theoretically investigated the dynamical properties a DNA dodecamer and its complex with two different binders (Hoechst 33258 and Ethidium cation) by performing fully atomistic classical Molecular Dynamics (MD) simulations. We focused on the modeling of the so-called overstretching transition occurring when double stranded DNA is subjected to a shear stress until separation of the two strands occurs. The results of our analysis reveal the molecular details of the overstretching dynamics and point out the effects of the binders on the structure and the dynamics of the oligonucleotide under stress. The minor groove binder Hoechst 33258 acts as a zip between the two strands enhancing the lifetime of some base-pairs during the pulling experiment while ethidium cation, which is an intercalator, facilitates the separation of the double helix at high elongations. The understanding of the interactions between the binders and the helix at the molecular level gives insights into the unbinding pathways probed by Single Molecule Force Spectroscopy (SMFS). [less ▲]

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See detailReactivity of auranofin with selenols and thiols: implications for the anticancer activity of gold(I) compounds
Di Sarra, Francesca; Fresch, Barbara ULg; Bini, Riccardo et al

in European Journal of Inorganic Chemistry [=EurJIC] (2013), 2013(15), 2718

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See detailTypical response of quantum pure states
Fresch, Barbara ULg; Moro, Giorgio J.

in European Physical Journal B -- Condensed Matter (2013), 86

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See detailMolecular decision trees realized by ultrafast electronic spectroscopy
Fresch, Barbara ULg; Hiluf, Dawit; Collini, Elisabetta et al

in Proceedings of the National Academy of Sciences (2013), 110(43), 17183-17188

The outcome of a light–matter interaction depends on both the state of matter and the state of light. It is thus a natural setting for implementing bilinear classical logic. A description of the state of ... [more ▼]

The outcome of a light–matter interaction depends on both the state of matter and the state of light. It is thus a natural setting for implementing bilinear classical logic. A description of the state of a time-varying system requires measuring an (ideally complete) set of time-dependent observables. Typically, this is prohibitive, but in weak-field spectroscopy we can move toward this goal because only a finite number of levels are accessible. Recent progress in nonlinear spectroscopies means that nontrivial measurements can be implemented and thereby give rise to interesting logic schemes where the outputs are functions of the observables. Lie algebra offers a natural tool for generating the outcome of the bilinear light–matter interaction. We show how to synthesize these ideas by explicitly discussing three-photon spectroscopy of a bichromophoric molecule for which there are four accessible states. Switching logic would use the on–off occupancies of these four states as outcomes. Here, we explore the use of all 16 observables that define the time-evolving state of the bichromophoric system. The bilinear laser–system interaction with the three pulses of the setup of a 2D photon echo spectroscopy experiment can be used to generate a rich parallel logic that corresponds to the implementation of a molecular decision tree. Our simulations allow relaxation by weak coupling to the environment, which adds to the complexity of the logic operations. [less ▲]

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See detailQuerying a quasi-classical Oracle: one bit function identification problem implemented in a single atom transistor
Fresch, Barbara ULg; Verduijn, J.; Mol, J. A. et al

in Europhysics Letters [=EPL] (2012), 99(2), 28004

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See detailModeling of ligand induced changes in the magneto-structural properties of Pd13 cluster
Fresch, Barbara ULg; Remacle, Françoise ULg

Poster (2012)

Palladium nanostructures are widely used as catalyst of many organic reactions1 and present intriguing and controversial magnetic properties. Since the direct experimental determination of ground state ... [more ▼]

Palladium nanostructures are widely used as catalyst of many organic reactions1 and present intriguing and controversial magnetic properties. Since the direct experimental determination of ground state structure for small transition metal clusters is difficult, theory and first-principles calculations, such as density functional theory (DFT), have been used extensively to reveal the interplay between geometric and electronic structure. We present a theoretical study at the DFT/B3LYP level on three selected geometric arrangements for the Pd13 cluster with particular emphasis on the effects of thiolate and phosphine based ligands on their magneto-structural properties. The results point out that the interactions with ligands can change the relative stability of different structures of the metallic core, leading to the stabilization of the more compact icosahedral shape with respect to other bi-layer structures which are more stable in the free standing cluster. Beyond this structural evolution, the interactions with the ligand shell strongly modify also the electronic and magnetic properties of the metal core. In particular, both thiolate and phosphine ligands quench the high spin state that characterized the magnetic ground state of the bare Pd13 cluster, but while the interaction with phosphine quench the magnetic moment completely, the thiol-capped particles retain a permanent magnetic moment even when they are saturated by the ligand molecules. Our study suggests that different ligands can be effectively used to tune electronic and magnetic properties of Pd nanoparticles in view of the design and experimental realization of logic nano devices and intelligent sensors. [less ▲]

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See detailMagnetostructural effects in ligand stabilized Pd13 clusters: a density functional theory study
Fresch, Barbara ULg; Boyen, H.-G.; Remacle, Françoise ULg

in Nanoscale (2012), 4(14), 4138-4147

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See detailInterplay of structural and electronic stabilizing factors in neutral and cationic phosphine protected Au13 clusters
Fresch, Barbara ULg; Hanozin, Emeline ULg; Dufour, Fabien ULg et al

in European Physical Journal D -- Atoms, Molecules, Clusters & Optical Physics (2012), 66(12),

Detailed reference viewed: 38 (12 ULg)