References of "Remacle, Françoise"
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See detailLogic Circuit
Remacle, Françoise ULiege; Levine, Raphael; Klymenko, Mikhailo et al

Patent (2017)

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See detailWhere Ion Mobility and Molecular Dynamics Meet to Unravel the (Un)Folding Mechanisms of an Oligorotaxane Molecular Switch
Hanozin, Emeline ULiege; Mignolet, Benoît ULiege; Morsa, Denis ULiege et al

in ACS Nano (2017), 11(10), 10253-10263

At the interface between foldamers and mechanically interlocked molecules, oligorotaxanes exhibit a spring-like folded secondary structure with remarkable mechanical and physicochemical properties. Among ... [more ▼]

At the interface between foldamers and mechanically interlocked molecules, oligorotaxanes exhibit a spring-like folded secondary structure with remarkable mechanical and physicochemical properties. Among these properties, the ability of oligorotaxanes to act as molecular switches through controlled modulations of their spatial extension over (un)folding dynamics is of particular interest. The present study aims to assess and further characterize this remarkable feature in the gas phase using mass spectrometry tools. In this context, we focused on the [4]5NPR+12 oligorotaxane molecule complexed with PF6 - counterion and probed its co-conformational states as a function of the in-source-generated charge states. Data were interpreted in light of electronic secondary structure computations at the PM6 and DFT levels. Our results highlight two major co-conformational groups associated either with folded compact structures, notably stabilized by intramolecular π-π interactions and predominant for low charge states or with fully stretched structures resulting from significant Coulombic repulsions at high charge states. Between, the oligorotaxane adopts intermediate folded co-conformations, suggesting a stepwise unfolding pathway under increasing repulsive Coulombic constraints. The reversibility of this superstructural transition was next interrogated under electron-driven (nondissociative electron transfer) and heat-driven (collision-induced unfolding) activation stimuli. The outcomes support the feasibility to either unfold or (partially) refold the oligorotaxane foldamer on purpose in the gas phase. Our results show that the balance between the stabilizing π-π interactions and the versatile Coulomb interactions dictates the elongation state of the foldamer in the gas phase and emphasizes the adequacy of mass spectrometry tools for the superstructural characterization of desolvated prototypical artificial molecular machines. © 2017 American Chemical Society. [less ▲]

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See detailCoulombic driven multi-conformational aspects of oligorotaxane switches studied by ion mobility mass spectrometry and molecular dynamics
Hanozin, Emeline ULiege; Mignolet, Benoît ULiege; Morsa, Denis ULiege et al

Conference (2017, June)

Introduction Artificial Molecular Machines (AMMs), such as Mechanically Interlocked Molecules (MIMs) and foldamers, have recently raised tremendous interest due to their unique properties. Under the ... [more ▼]

Introduction Artificial Molecular Machines (AMMs), such as Mechanically Interlocked Molecules (MIMs) and foldamers, have recently raised tremendous interest due to their unique properties. Under the influence of an appropriate stimuli (pH, redox potential, light…), such molecules are able to reversibly switch between distinct conformational states. Scientists may capitalize on such exclusive properties to get a better understanding of the biomacromolecular level or to design innovative “smart” materials. At the interface between foldamers and MIMs, oligorotaxanes exhibit a spring-like folded secondary structure with remarkable mechanical and physicochemical properties. In the present study, we use ion mobility coupled with mass spectrometry (IM-MS) to probe the conformational states of differentially charged oligorotaxanes in the gas phase. Method Oligorotaxanes are donor-acceptor polymers composed of a π electron-donating dumbbell over which a discrete number of π electron-accepting tetracationic cyclophanes are threaded. The numerous intra-molecular interactions provide them a highly-stabilized rigid rod-like structure in solution. We use IM-MS as implemented in the Synapt G2 HDMS (Waters, Manchester, UK) to investigate the structure of the ionized oligorotaxanes. Our purposes are to probe (i) the different populations of stable conformers generated according to the charge state z and (ii) the reversibility of an electron-driven or thermal-driven conformational change in the gas phase implemented via an electron transfer or collisional activation process prior to the mobility separation. Our experimental observations are supported by electronic structure optimizations at the PM6 and DFT levels coupled with Born-Oppenheimer Molecular Dynamics simulations. Preliminary data Our results highlight a progressive elongation of the oligorotaxane structure with increasing charge numbers until it reaches a maximum extension state. Matching the experimental data with theoretical simulations, we find that the oligorotaxanes adopt an entropically-favored globular shape at low z. As z increases, coulombic repulsions occurring between the cyclophanes gradually outweigh the stabilizing π-stacking interactions and force the structure to elongate. This process occurs in a multistep fashion, each corresponding to a distinct group of helical-shaped conformers, before it eventually results in a fully stretched structure. On the other hand, our results also highlight that a charge reduction driven by a non-dissociative electron transfer process leads to a refolding of the structure so that it adopts a size similar to its electrospray-generated counterpart when the appropriate number of electrons is added. This observation may be imparted to the gradual decrease of the Coulomb repulsions between the cyclophanes mediated through increasing numbers of transferred electrons. These results suggests that the transition from one conformer to another is reversible so that the electrostatic balance between the cyclophanes may be used to further tune the structural state adopted by this artificial molecular switch. The second stimulus relied on collisional activation whose inelastic component provides a way to build up energy into the accessible vibrational degrees of freedom. The conformational landscapes of such-activated oligorotaxanes ions were found unchanged in term of collision cross section position but the repartition of population was altered with a promotion of the most elongated conformer, provided the absence of selective fragmentation. Altogether, these results highlight the feasibility of handling the elongation state of oligorotaxanes in the gas phase through appropriate inputs and underline its conformational reversibility properties. Novel aspect Stimuli-induced reversible conformational rearrangements of innovative AMMs studied by IM-MS and molecular dynamics in the gas phase. [less ▲]

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See detailThe Role of Super-Atom Molecular Orbitals in Doped Fullerenes in a Femtosecond Intense Laser Field
Xiong, Hui; Mignolet, Benoît ULiege; Fang, Li et al

in Scientific Reports (2017), 7

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See detailControlling coherent quantum nuclear dynamics in LiH by ultra short IR atto pulses
Nikodem, Astrid ULiege; Levine, R. D.; Remacle, Françoise ULiege

in Springer Series in Chemical Physics (2017), (9783319648392), 41-65

We examine computationally how ultrashort polarized strong one cycle IR pulses can be used for steering coherent nuclear dynamics in LiH. The nuclear motion is described using the time-dependent ... [more ▼]

We examine computationally how ultrashort polarized strong one cycle IR pulses can be used for steering coherent nuclear dynamics in LiH. The nuclear motion is described using the time-dependent Schrödinger equation on a grid for several coupled electronic states. The coupling to the strong field of the pump and probe pulses is included in the Hamiltonian as well as the non adiabatic coupling between the different electronic states. LiH possesses low lying Σ and Π states that can be selectively accessed by controlling the polarization of the pump pulse along the bond or perpendicularly to it. In addition, when using a one cycle pulse, controlling the carrier envelope phase (CEP) allows to select the states that will be coherently excited according to their polarity. Since some of the excited Σ states and all the Π states are repulsive, polarization and CEP control of the pump pulse leads to controlling the dissociation yields. In particular, our quantum dynamics simulations show that the ratio of the fragmentation yields of the Σ2 and Σ3 states can be changed by a factor 10 when the CEP of a one cycle IR pulse polarized along the bond is switched from 0 to π. In addition to probing the dynamics by following the fragmentation, we also report on probing the coherent vibronic wave packet using transient absorption spectra that results from the interaction of the molecular transition dipole with the electric fields of the pump and the probe pulses. The emission spectrum retrieves the different time scales of the vibronic dynamics and probes the time evolution of the coherences. © Springer International Publishing AG 2017. [less ▲]

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See detailCoherent electronic and nuclear dynamics in a rhodamine heterodimer-DNA supramolecular complex
Cipolloni, M.; Fresch, B.; Occhiuto, I. et al

in Physical Chemistry Chemical Physics [=PCCP] (2017), 19(34), 23043-23051

Elucidating the role of quantum coherences in energy migration within biological and artificial multichromophoric antenna systems is the subject of an intense debate. It is also a practical matter because ... [more ▼]

Elucidating the role of quantum coherences in energy migration within biological and artificial multichromophoric antenna systems is the subject of an intense debate. It is also a practical matter because of the decisive implications for understanding the biological processes and engineering artificial materials for solar energy harvesting. A supramolecular rhodamine heterodimer on a DNA scaffold was suitably engineered to mimic the basic donor-acceptor unit of light-harvesting antennas. Ultrafast 2D electronic spectroscopic measurements allowed identifying clear features attributable to a coherent superposition of dimer electronic and vibrational states contributing to the coherent electronic charge beating between the donor and the acceptor. The frequency of electronic charge beating is found to be 970 cm-1 (34 fs) and can be observed for 150 fs. Through the support of high level ab initio TD-DFT computations of the entire dimer, we established that the vibrational modes preferentially optically accessed do not drive subsequent coupling between the electronic states on the 600 fs of the experiment. It was thereby possible to characterize the time scales of the early time femtosecond dynamics of the electronic coherence built by the optical excitation in a large rigid supramolecular system at a room temperature in solution. © 2017 the Owner Societies. [less ▲]

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See detailPhotoinduced Ultrafast Charge Transfer and Charge Migration in Small Gold Clusters Passivated by a Chromophoric Ligand
Schwanen, Valérie ULiege; Remacle, Françoise ULiege

in Nano Letters (2017), 17(9), 5672-5681

Because the development of attopulses, charge migration induced by short optical pulses has been extensively investigated. We report a computational purely electronic dynamical study of ultrafast few ... [more ▼]

Because the development of attopulses, charge migration induced by short optical pulses has been extensively investigated. We report a computational purely electronic dynamical study of ultrafast few femtoseconds (fs) charge transfer and charge migration in realistic passivated stoichiometric Au11 and Au20 gold nanoclusters functionalized by a bipyridine ligand. We show that a net significant amount of electronic charge (0.1 to 0.4 |e| where |e| is the electron charge) is permanently transferred from the bipyridine chromophore to the gold cluster during the short 5-6 fs UV-vis strong pulse. This electron transfer to the metallic core is induced by the optical excitation of electronic states with a partial charge transfer character involving the chromophore before the onset of nuclei motion. In addition, the photoexcitation by the strong fs pulse builds a nonequilibrium electronic density that beats between the chromophore and the metallic core around the average of the transferred value. Modular systems made of a donor chromophore that can be photoexcited in the UV-vis range coupled to an efficient acceptor that could trap the charge are of interest for applications to nanodevices. Our study provides understanding on the very early, purely electronic dynamics built by the fs optical excitation and the initial charge separation step. © 2017 American Chemical Society. [less ▲]

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See detailOptical activity of the super-atom molecular orbital (SAMO) states in Li@C60+ conformers
Mignolet, Benoît ULiege; Campbell, Eleanor; Remacle, Françoise ULiege

in AIP Conference Proceedings (2017)

Super Atom Molecular Orbitals (SAMOs) are electronic excited states found in fullerenes in which an electron is excited to one or, more generally, several virtual orbitals with hydrogen like character ... [more ▼]

Super Atom Molecular Orbitals (SAMOs) are electronic excited states found in fullerenes in which an electron is excited to one or, more generally, several virtual orbitals with hydrogen like character. The photoexcitation mechanism of the SAMO states strongly depends on the symmetry of the fullerene. For instance the SAMOs of the spherical C60 fullerene are not optically active while breaking the symmetry by adding a dopant can make the SAMO states optically active. In this proceeding we investigate the optical activity of the SAMO states in several conformers of the Li@C60+ fullerene and we show that the position of the lithium atom inside the fullerene cage strongly affects the computed oscillator strengths and transition dipole moments of the SAMO states. [less ▲]

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See detailUltrafast 25-fs relaxation in highly excited states of methyl azide mediated by strong nonadiabatic coupling
Peters, William K.; Couch, David E.; Mignolet, Benoît ULiege et al

in Proceedings of the National Academy of Sciences of the United States of America (2017)

Highly excited states of neutral molecules behave qualitatively differently than the lower excited states that are commonly studied in photochemistry. Such states are involved in ionospheric and ... [more ▼]

Highly excited states of neutral molecules behave qualitatively differently than the lower excited states that are commonly studied in photochemistry. Such states are involved in ionospheric and astrochemical phenomena, as well as in detonation processes. However, highly excited states are poorly understood due to experimental and theoretical challenges in probing their complex dynamics. Here, we apply vacuum-UV femtosecond laser sources and an imaging photoelectron–photoion coincidence spectrometer to directly probe the surprisingly fast 25-fs reaction pathway of the energetic molecule methyl azide. Combined with advanced calculations, we conclude that the electronic relaxation is driven by strong nonadiabatic coupling and that population transfer occurs along a seam well above the minimum energy conical intersection. [less ▲]

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See detailLow-lying, Rydberg states of polycyclic aromatic hydrocarbons (PAHs) and cyclic alkanes
Bohl, E.; Mignolet, Benoît ULiege; Johansson, J. O. et al

in Physical Chemistry Chemical Physics [=PCCP] (2017), 19(35), 24090-24099

TD-DFT calculations of low-lying, Rydberg states of a series of polycyclic hydrocarbons and cyclic alkanes are presented. Systematic variations in binding energies and photoelectron angular distributions ... [more ▼]

TD-DFT calculations of low-lying, Rydberg states of a series of polycyclic hydrocarbons and cyclic alkanes are presented. Systematic variations in binding energies and photoelectron angular distributions for the first members of the s, p and d Rydberg series are predicted for increasing molecular complexity. Calculated binding energies are found to be in very good agreement with literature values where they exist for comparison. Experimental angle-resolved photoelectron spectroscopy results are presented for coronene, again showing very good agreement with theoretical predictions of binding energies and also for photoelectron angular distributions. The Dyson orbitals for the small "hollow" carbon structures, cubane, adamantane and dodecahedrane, are shown to have close similarities to atomic s, p and d orbitals, similar to the superatom molecular orbitals (SAMOs) reported for fullerenes, indicating that these low-lying, diffuse states are not restricted to π-conjugated molecules. © 2017 the Owner Societies. [less ▲]

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See detailPumping and probing vibrational modulated coupled electronic coherence in HCN using short UV fs laser pulses: A 2D quantum nuclear dynamical study
van den Wildenberg, Stéphan ULiege; Mignolet, Benoît ULiege; Levine, R. D. et al

in Physical Chemistry Chemical Physics [=PCCP] (2017), 19(30), 19837-19846

The coupled electronic-nuclear coherent dynamics induced by a short strong VUV fs pulse in the low excited electronic states of HCN is probed by transient absorption spectroscopy with a second weaker fs ... [more ▼]

The coupled electronic-nuclear coherent dynamics induced by a short strong VUV fs pulse in the low excited electronic states of HCN is probed by transient absorption spectroscopy with a second weaker fs UV pulse. The nuclear time-dependent Schrodinger equation is solved on a 2D nuclear grid with several electronic states with a Hamiltonian including the dipole coupling to the pump and the probe electric fields. The two internal nuclear coordinates describe the motion of the light H atom. There is a band of several excited electronic states at about 8 eV above the ground state (GS) that is transiently accessed by the pump pulse. We tailored the pump so as to selectively populate the lowest 1A′′ electronic state thereby the pulse creates an electronic coherence with the GS. Our simulations show that this electronic coherence is modulated by the nuclear motion and persists all the way to dissociation on the 1A′′ state. Transient absorption spectra computed as a function of the delay time between the pump and the probe pulses provide a detailed probe of the electronic amplitude and its phase, as well as of the modulation of the electronic coherence by the nuclear motion, both bound and dissociative. © the Owner Societies 2017. [less ▲]

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See detailElectronic states and valley-orbit coupling in linear and planar molecules formed by coupled P donors in silicon
Klymenko, M. V.; Rogge, S.; Remacle, Françoise ULiege

in Physical Review. B : Condensed Matter (2017), 95(20), 205301

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See detailImplementation of probabilistic algorithms by multi-chromophoric molecular networks with application to multiple travelling pathways
Fresch, B.; Remacle, Françoise ULiege; Levine, R. D.

in Chemphyschem : A European Journal of Chemical Physics and Physical Chemistry (2017), 18

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See detailImplementation of multivariable logic functions in parallel by electrical addressing a molecule of three dopants in Silicon
Fresch, B.; Bocquel, J.; Rogge, S. et al

in Chemphyschem : A European Journal of Chemical Physics and Physical Chemistry (2017), 18

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See detailSpatial and temporal control of populations, branching ratios, and electronic coherences in LiH by a single one-cycle infrared pulse
Nikodem, Astrid ULiege; Levine, R. D.; Remacle, Françoise ULiege

in Physical Review. A : General Physics (2017), 95(5), 053404

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See detailA new electron-ion coincidence 3D momentum-imaging method and its application in probing strong field dynamics of 2-phenylethyl-N, N-dimethylamine
Fan, Lin; Lee, Suk Kyoung; Tu, Yi-Jung et al

in Journal of Chemical Physics (2017), 147

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See detailMultivariate Surprisal Analysis of Gene Expression Levels
Remacle, Françoise ULiege; Goldstein, S. Andrew; Levine, D. Raphael

in Entropy (2017), 18(12), 445

We consider here multivariate data which we understand as the problem where each data point i is measured for two or more distinct variables. In a typical situation there are many data points i while the ... [more ▼]

We consider here multivariate data which we understand as the problem where each data point i is measured for two or more distinct variables. In a typical situation there are many data points i while the range of the different variables is more limited. If there is only one variable then the data can be arranged as a rectangular matrix where i is the index of the rows while the values of the variable label the columns. We begin here with this case, but then proceed to the more general case with special emphasis on two variables when the data can be organized as a tensor. An analysis of such multivariate data by a maximal entropy approach is discussed and illustrated for gene expressions in four different cell types of six different patients. The different genes are indexed by i, and there are 24 (4 by 6) entries for each i. We used an unbiased thermodynamic maximal-entropy based approach (surprisal analysis) to analyze the multivariate transcriptional profiles. The measured microarray experimental data is organized as a tensor array where the two minor orthogonal directions are the different patients and the different cell types. The entries are the transcription levels on a logarithmic scale. We identify a disease signature of prostate cancer and determine the degree of variability between individual patients. Surprisal analysis determined a baseline expression level common for all cells and patients. We identify the transcripts in the baseline as the “housekeeping” genes that insure the cell stability. The baseline and two surprisal patterns satisfactorily recover (99.8%) the multivariate data. The two patterns characterize the individuality of the patients and, to a lesser extent, the commonality of the disease. The immune response was identified as the most significant pathway contributing to the cancer disease pattern. Delineating patient variability is a central issue in personalized diagnostics and it remains to be seen if additional data will confirm the power of multivariate analysis to address this key point. The collapsed limits where the data is compacted into two dimensional arrays are contained within the proposed formalism. [less ▲]

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See detailNuclear Motion Driven Ultrafast Photodissociative Charge Transfer of the PENNA Cation: An Experimental and Computational Study
Sun, Shoutian; Mignolet, Benoît ULiege; Fan, lin et al

in Journal of Physical Chemistry A (2017), 121(7), 1442

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See detailA Probabilistic Finite State Logic Machine Realized Experimentally on a Single Dopant Atom
Fresch, Barbara; Bocquel, Juanita; Rogge, Sven et al

in Nano Letters (2017), 17

Exploiting the potential of nanoscale devices for logic processing requires the implementation of computing functionalities departing from the conventional switching paradigm. We report on the design and ... [more ▼]

Exploiting the potential of nanoscale devices for logic processing requires the implementation of computing functionalities departing from the conventional switching paradigm. We report on the design and the experimental realisation of a probabilistic finite state machine in a single phosphorus donor atom placed in a silicon matrix electrically addressed and probed by Scanning Tunneling Spectroscopy (STS). The single atom logic unit simulates the flow of visitors in a maze whose topology is determined by the dynamics of the electronic transport through the states of the dopant. By considering the simplest case of a unique charge state for which three electronic states can be resolved, we demonstrate an efficient solution of the following problem: in a maze of four connected rooms, what is the optimal combination of door opening rates in order to maximize the time that visitors spend in one specific chamber? The implementation takes advantage of the stochastic nature of electron tunneling while the output remains the macroscopic current whose reading can be realized with standard techniques and does not require single electron sensitivity. [less ▲]

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See detailContinuous variables logic via coupled automata using a DNAzyme cascade with feedback
Lilienthal, Sivan; Orbach, Ron; Willner, Itamar et al

in Chemical Science (2017), 8

The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To ... [more ▼]

The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To enable reactive chemical systems to compute we show how, using the Cox interpretation of probability theory, one can transcribe the equations of chemical kinetics as a sequence of coupled logic gates operating on continuous variables. It is discussed how the distinct chemical identity of a molecule allows us to create a common language for chemical kinetics and Boolean logic. Specifically, the logic AND operation is shown to be equivalent to a bimolecular process. The logic XOR operation represents chemical processes that take place concurrently. The values of the rate constants enter the logic scheme as inputs. By designing a reaction scheme with a feedback we endow the logic gates with a built in memory because their output then depends on the input and also on the present state of the system. Technically such a logic machine is an automaton. We report an experimental realization of three such coupled automata using a DNAzyme multilayer signaling cascade. A simple model verifies analytically that our experimental scheme provides an integrator generating a power series that is third order in time. The model identifies two parameters that govern the kinetics and shows how the initial concentrations of the substrates are the coefficients in the power series. [less ▲]

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