References of "Journal of Physical Chemistry A"
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See detailPump and probe of ultrafast charge reorganization in small peptides: A computational study through sudden ionizations
Kus, Tomasz ULg; Mignolet, Benoît ULg; Levine, R. D. et al

in Journal of Physical Chemistry A (2013), 117(40), 10513-10525

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See detailPhotodissociation and radiative association ofHeH+ in the metastable triplet state
Loreau, Jerôme; Vranckx, Stéphane; Desouter-Lecomte, Michèle ULg et al

in Journal of Physical Chemistry A (2013), 117

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See detailUV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase
Rosu, Frédéric ULg; Gabelica, Valérie ULg; De Pauw, Edwin ULg et al

in Journal of Physical Chemistry A (2012), 116

UV absorption spectroscopy is one of the most widely used methods to monitor nucleic acid folding in solution, but the absorption readout is the weighted average contribution of all species present in ... [more ▼]

UV absorption spectroscopy is one of the most widely used methods to monitor nucleic acid folding in solution, but the absorption readout is the weighted average contribution of all species present in solution. Mass spectrometry, on the other hand, is able to separate constituents of the solution based on their mass, but methods to probe the structure of each constituent are needed. Here, we explored whether gas-phase UV spectroscopy can give an indication of DNA folding in ions isolated by electrospray mass spectrometry. Model DNA single strands, duplexes, and G-quadruplexes were extracted from solution by electrospray; the anions were stored in a quadrupole ion trap and irradiated by a tunable laser to obtain the UV action spectra of each complex. We found that the duplex and quadruplex spectra are significantly different from the spectra of single strands, thereby suggesting that electronic spectroscopy can be used to probe the DNA gas-phase structure and obtain information about the intrinsic properties of high-order DNA structure. [less ▲]

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See detailControl in a dissipative environment: the example of a Cope rearrangement
Chenel, Aurélie; Dive, Georges ULg; Meier, Christopher et al

in Journal of Physical Chemistry A (2012), 116

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See detailThe Elimination of Redundant Constraints in Surprisal Analysis of Unimolecular Dissociation and Other Endothermic Processes
Remacle, Françoise ULg; Levine, R. D.

in Journal of Physical Chemistry A (2009), 113(16), 4658-4664

It is well understood that energy rich polyatomic molecules do not dissociate promptly because the number, P, of their energy states far exceeds the number, N, of the decay channels. In the simplest RRK ... [more ▼]

It is well understood that energy rich polyatomic molecules do not dissociate promptly because the number, P, of their energy states far exceeds the number, N, of the decay channels. In the simplest RRK theory, the fraction N/P is the probability of dissociation. We discuss the distribution of the decay rates of maximal entropy and conclude that it is governed by at most N linearly independent constraints, N < P, or, more typically, N << P. This mathematical requirement already severely restricts the number of constraints. Beyond it however, on physical grounds, one constraint, or at most a few, may be dominant. We discuss why just one constraint, or a few but less than N, can be sufficient to describe the product state distribution. [less ▲]

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See detailTypicality in Ensembles of Quantum States: Monte Carlo Sampling versus Analytical Approximations
Fresch, Barbara ULg; Moro, Giorgio J.

in Journal of Physical Chemistry A (2009), 113

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See detailThe Role of Long-Range Forces in the Determination of Translational Kinetic Energy Release. Loss of C4H4+ from Benzene and Pyridine Cations.
Gridelet, E.; Locht, Robert ULg; Lorquet, Andrée ULg et al

in Journal of Physical Chemistry A (2008), 112

Kinetic energy release distributions (KERDs) for the benzene ion fragmenting into C4H4+ and C2H2 have been recorded by double-focussing mass spectrometry in the metastable energy window and by a retarding ... [more ▼]

Kinetic energy release distributions (KERDs) for the benzene ion fragmenting into C4H4+ and C2H2 have been recorded by double-focussing mass spectrometry in the metastable energy window and by a retarding field experiment up to an energy of 5 eV above the fragmentation threshold. They are compared with those resulting from the HCN loss reaction from the pyridine ion. Both reactions display a similar variation of the kinetic energy release as a function of the internal energy: the average release is smaller than statistically expected, with a further restriction of the phase-space sampling for the C5H5N+ dissociation. Ab initio calculations of the potential-energy profile have been carried out. They reveal a complicated reaction mechanism, the last step of which consists in the dissociation of a weakly bound ion-quadrupole or ion-dipole complex. The KERDs have been analyzed by the maximum entropy method. The fraction of phase-space effectively sampled by the pair of fragments has been determined and is similar for both dissociations. Both reactions are constrained by the square root of the released kinetic energy, epsilon1/2. This indicates that in the latter stage of the dissociation process, the reaction coordinate is adiabatically decoupled from the bath of the bound degrees of freedom. For the C6H6+ fragmentation, the analysis of the experimental results strongly suggests that, just as for the symmetric interaction potential, the translational motion is confined to a two-dimensional subspace. This dimensionality reduction of the translational phase space is due to the fact that the Hamiltonian of both weakly bound complexes contains a cyclic coordinate. [less ▲]

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See detailCharge transfer study through the determination of the ionization energies of tetrapeptides X3-Tyr, X = Gly, Ala, or Leu. Influence of the inclusion of one glycine in alanine and leucine containing peptides
Dehareng, Dominique ULg; Dive, Georges ULg

in Journal of Physical Chemistry A (2006), 110(43), 11975-11987

The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the ... [more ▼]

The energies of the fundamental and several excited states of tetrapeptide radical cations were determined at the outer valence Green's function (OVGF) level, at three geometries corresponding to the lowest energy conformations: two for the neutral and one for the cation. The conformations were optimized at the density functional theory level within the B3LYP framework. It was found that, from a purely energetic point of view, a charge initially created on the tyrosine chromophore could migrate without any geometrical change and without further activation once the excited electronic state of the ionized chromophore was formed. This migration could reach the NH2 terminus for the neutral conformations but should stop at the adjacent peptide link for the cation conformation. These results stress the probable influence of the electronic coupling between the states rather than the existence of a barrier on the charge pathway to explain the difference between the peptides in the charge-transfer process leading to the loss of an iminium [NH2 = CHR](+) cation. The dissociation energy of the asymptote related to the formation of this NH2 terminus iminium cation was calculated for few species and it appears that the excess energy available for dissociation is significant when starting from the lowest energy conformations of the neutral or the cation, provided that the charge transfer is effective. It was also found that the amino acids did not conserve their energetic properties and their zero order energy levels turned to a complete new energetic scheme corresponding to the conformation of the peptide. [less ▲]

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See detailAb initio study of the ionization of the DNA bases: Ionization potentials and excited states of the cations
Cauët, Emilie; Dehareng, Dominique ULg; Lievin, Jacques

in Journal of Physical Chemistry A (2006), 110(29), 9200-9211

The ionization of the four DNA bases is investigated by means of ab initio calculations. Accurate values of the gas-phase vertical and adiabatic ionization potentials (IP) are obtained at the MP2/6-31G(2d ... [more ▼]

The ionization of the four DNA bases is investigated by means of ab initio calculations. Accurate values of the gas-phase vertical and adiabatic ionization potentials (IP) are obtained at the MP2/6-31G(2d(0.8, alpha(d)), p) level of theory. The need of introducing extra polarization to the standard 6-31G(d, p) basis set is demonstrated by test calculations and an optimal value of alpha(d) = 0.1 is obtained. Ionization to electronically excited radical cations is also considered. The low-lying excited states of the cations are characterized for the first time. The topology of the corresponding potential energy surfaces is qualitatively described in terms of the stationary points ( minima and saddle points) located on these surfaces. A conical intersection is characterized for the first time on the ground-state potential energy surface of all cations. It arises from the crossing of the adiabatic surfaces of the ground and first excited state at planar geometries. A nonplanar minimum is observed for the cytosine cation only. The geometry and electronic changes occurring along these surfaces are analyzed, leading to a comparison between the different nucleobase cations. The study of larger ionized systems related to DNA is rendered possible thanks to the optimized medium size basis set proposed in this work, as exemplified by the calculation of the IP of a stacked dimer of guanines. [less ▲]

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See detailHydrogen atom loss from the benzene cation. Why is the kinetic energy release so large?
Gridelet, E.; Lorquet, Andrée ULg; Locht, Robert ULg et al

in Journal of Physical Chemistry A (2006), 110(27), 8519-8527

The kinetic energy release distributions (KERDs) associated with the hydrogen loss from the benzene cation and the deuterium loss from the perdeuteriobenzene cation have been remeasured on the metastable ... [more ▼]

The kinetic energy release distributions (KERDs) associated with the hydrogen loss from the benzene cation and the deuterium loss from the perdeuteriobenzene cation have been remeasured on the metastable time scale and analyzed by the maximum entropy method. The experimental kinetic energy releases are larger than expected statistically, in contradistinction to what has been observed for the C-X fragmentations of the halogenobenzene cations. H(D) loss from C6H6+ (C6D6+) occurs via a conical intersection connecting the (2)A(2) and (2)A(1) electronic states. Two models are proposed to account for the experimental data: (i) a modified orbiting transition state theory (OTST) approach incorporating electronic nonadiabaticity; (ii) an electronically nonadiabatic version of the statistical adiabatic channel model ( SACM) of Quack and Troe. The latter approach is found to be preferable. It leads to the conclusion that the larger the energy stored in the transitional modes, which partly convert to the relative interfragment motion, the shorter the value of the reaction coordinate at which the adiabatic channels cross, and the larger the probability of undergoing the (2)A(2) -> (2)A(1) transition required for hydrogen loss. [less ▲]

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See detailMolecule-based photonically switched half and full adder
Remacle, Françoise ULg; Weinkauf, R.; Levine, R. D.

in Journal of Physical Chemistry A (2006), 110(1), 177-184

A single molecule logic gate using electronically excited states and ionization/fragmentation can take advantage of the differences in cross-sections for one and two photon absorption. Fault tolerant ... [more ▼]

A single molecule logic gate using electronically excited states and ionization/fragmentation can take advantage of the differences in cross-sections for one and two photon absorption. Fault tolerant optically pumped half adder and full adder are discussed as applications. A full adder requires two separate additions, and the logic concatenation that is required to implement this is physically achieved by an intramolecular transfer along the side chain of 2-phenylethyl-N,N-dimethylamine (PENNA). Solutions of the kinetic equations for the temporal evolution of the concentration of different states in the presence of time-varying laser fields are used to illustrate the high contrast ratios that are potentially possible for such devices. [less ▲]

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See detailGround and Excited State Dissociation Dynamics of Ionized 1,1-Difluoroethene
Gridelet, Evelyne; Dehareng, Dominique ULg; Locht, Robert ULg et al

in Journal of Physical Chemistry A (2005), 109(37), 8225-8235

The kinetic energy release distributions (KERDs) for the fluorine atom loss from the 1,1-difluoroethene cation have been recorded with two spectrometers in two different energy ranges. A first experiment ... [more ▼]

The kinetic energy release distributions (KERDs) for the fluorine atom loss from the 1,1-difluoroethene cation have been recorded with two spectrometers in two different energy ranges. A first experiment uses dissociative photoionization with the He(I) and Ne(I) resonance lines, providing the ions with a broad internal energy range, up to 7 eV above the dissociation threshold. The second experiment samples the metastable range, and the average ion internal energy is limited to about 0.2 eV above the threshold. In both energy domains, KERDs are found to be bimodal. Each component has been analyzed by the maximum entropy method. The narrow, low kinetic energy components display for both experiments the characteristics of a statistical, simple bond cleavage reaction: constraint equal to the square root of the fragment kinetic energy and ergodicity index higher than 90%. Furthermore, this component is satisfactorily accounted for in the metastable time scale by the orbiting transition state theory. Potential energy surfaces corresponding to the five lowest electronic states of the dissociating 1,1-C2H2F2+ ion have been investigated by ab initio calculations at various levels. The equilibrium geometry of these states, their dissociation energies, and their vibrational wavenumbers have been calculated, and a few conical intersections between these surfaces have been identified. It comes out that the ionic ground state (X) over tilde B-2(1) is adiabatically correlated with the lowest dissociation asymptote. Its potential energy curve increases in a monotonic way along the reaction coordinate, giving rise to the narrow KERD component. Two states embedded in the third photoelectron band ( (B) over tilde (2)A(1), at 15.95 eV and (C) over tilde B-2(2) at 16.17 eV) also correlate with the lowest asymptote at 14.24 eV. We suggest that their repulsive behavior along the reaction coordinate be responsible for the KERD high kinetic energy contribution. [less ▲]

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See detailKinetic Energy Release Distributions for Tropylium and Benzylium Ion Formation from the Toluene Cation.
Fati, D.; Lorquet, Andrée ULg; Locht, Robert ULg et al

in Journal of Physical Chemistry A (2004), 108

Hydrogen loss from the toluene molecular ion generates benzylium (Bz(+)) and tropylium (Tr+) ions via two competitive and independent pathways. The corresponding kinetic energy release distributions ... [more ▼]

Hydrogen loss from the toluene molecular ion generates benzylium (Bz(+)) and tropylium (Tr+) ions via two competitive and independent pathways. The corresponding kinetic energy release distributions (KERDs) have been determined under various conditions in the metastable time window for toluene and perdeuterated toluene and have been analyzed by the maximum entropy method (MEM). The isomeric fraction Tr+/Bz(+) is found to be equal to 0.9 +/- 0.3, in good agreement with the values obtained using photodissociation and charge exchange experiments. It is, however, in disagreement with the value 5 +/- 2 deduced by Moon, Choe, and Kim (J. Phys. Cheln. A 2000, 104, 458) from KERD measurements. The origin of the discrepancy is suggested to be the inadequacy of the orbiting transition state theory (OTST) for the calculation of KERDs in hydrogen loss reactions. For both channels, more translational energy is released in the reaction coordinate than would be expected on statistical grounds because of the presence of a barrier along the reaction path. For the Bz(+) channel, the barrier entirely results from centrifugal effects. Rotational energy is converted into translation as a result of angular momentum conservation. Deuteration is observed to reduce the importance of the rotational energy flow in the reaction coordinate. The Tr+ channel is characterized by the presence of a reverse activation energy barrier of electronic origin. The energy in excess of the dissociation asymptote can be partitioned into two components: the reverse barrier plus a nonfixed energy contribution. About 40% of the reverse barrier is converted into relative translational motion of the fragments. Here again, a lower fraction of the nonfixed energy flows into translation for the deuterated isotopomer. [less ▲]

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See detailESR Investigation of Chemical Exchange in Geminally Diphosphorylated Linear Nitroxide Radicals
Rockenbauer, Antal; Olive, Gilles ULg; Rozanska, Xavier et al

in Journal of Physical Chemistry A (2004), 108(25), 5484-5489

For geminally diphosphorylated linear nitroxide radicals, a marked line width alternation (LWA) can be observed. The LWA appears irrespectively whether the investigated radicals R¢¢N(O¥)C(P(O)(OEt)2)2R¢ ... [more ▼]

For geminally diphosphorylated linear nitroxide radicals, a marked line width alternation (LWA) can be observed. The LWA appears irrespectively whether the investigated radicals R¢¢N(O¥)C(P(O)(OEt)2)2R¢ contain any chiral group or not. If R¢¢ ) tert-butyl and R¢ ) H, the small â-hydrogen coupling indicates a completely blocked rotation around the N-C ó-bond and the LWA can be assigned to a chemical exchange between conformations in which the phosphoryl groups have a symmetric and a nonsymmetric geometry. The conformational change is accompanied by the deformation of the CP2 bonding angle and the rate of exchange is slowed in pentane for which the solvent molecules can be trapped by the chelating phosphoryl groups. If R¢¢ ) benzyl, both the proton hyperfine lines of the CH2 group and the phosphorus lines of the CP2 group produce a LWA; two coalescences can be observed. In the case of a chiral R¢¢ group (R¢¢ ) secondary butyl, R¢ ) methyl) a tentative four-site model can explain the highly complex LWA. [less ▲]

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See detailLarge phosphorus hyperfine coupling as a sensitive tool for studying molecular dynamics : ESR and Molecular Mechanics studies of ring interconversion in cis-2,5-diphosphoryl-2,5-dimethyl-pyrrolidinoxyl radical
Rockenbauer, Antal; Gaudel-Siri, Anouk; Siri, Didier et al

in Journal of Physical Chemistry A (2003), 107(19), 3851-3857

ESR spectra of cis- and trans-â-diphosphorylated pyrrolidine-N-oxyl radicals, c-1 and t-1, were studied in liquid and frozen solution. The expected 1:2:1 triplet (aP (2)) of the 1:1:1 triplet (aN) was ... [more ▼]

ESR spectra of cis- and trans-â-diphosphorylated pyrrolidine-N-oxyl radicals, c-1 and t-1, were studied in liquid and frozen solution. The expected 1:2:1 triplet (aP (2)) of the 1:1:1 triplet (aN) was observed for t-1; however, for c-1, the inner lines of the 1:2:1 triplet showed a dramatic broadening characteristic of chemical exchange between two equivalent conformations. Owing to the large difference in the hyperfine splitting constants (hfsc) of the exchanging phosphorus (¢aP 21 G), the coalescence temperature was unusually high (193 K, in n-pentane), and the potential barrier for ring interconversion (10.5 kJ mol-1) was easily obtained from the temperature dependence of the exchange rate. This value was in very good agreement with the value obtained for an empirical pseudorotational potential (11 kJ mol-1) that was adjusted to fit the temperature dependence of the phosphorus hfsc. For c-1, molecular mechanics calculations gave similar characteristics for the pseudorotational potential and indicated the existence of two identical minima with distorted geometries lying between 3T4 and 3E or 4T3 and E3. For t-1, only the 3T4 conformer was found to be significantly populated. Frozen solution spectra showed that the phosphorus hfsc anisotropy is higher when the C-P bond is pseudoaxial; this result can be explained by a geometry-dependent delocalization of the unpaired electron into the phosphorus 3p orbitals. [less ▲]

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See detailMechanism of Collisional Heating in Electrospray Mass Spectrometry: Ion Trajectory Calculations
Hoxha, Antuan; Collette, Caroline ULg; De Pauw, Edwin ULg et al

in Journal of Physical Chemistry A (2001), 105

To simulate the multicollisional heating process taking place in the intermediate pressure region of an electrospray source, ion trajectory calculations have been preformed by introducing in the SIMION ... [more ▼]

To simulate the multicollisional heating process taking place in the intermediate pressure region of an electrospray source, ion trajectory calculations have been preformed by introducing in the SIMION program a subroutine for handling the collision dynamics. The simulated internal energy distributions are compared with already available experimental distributions obtained by the "survival ion yield" method. [less ▲]

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See detailKinetic Energy Release Distributions in the Dissociation of Energy-Selected Fluoroethene and 1,1-Difluoroethene Ions.
Güthe, F.; Locht, Robert ULg; Leyh, Bernard ULg et al

in Journal of Physical Chemistry A (1999), 103

The unimolecular dissociation of energy-selected fluoroethene and 1,1-difluoroethene ions has been investigated by threshold photoelectron photoion coincidence TPEPICO) technique. The breakdown diagrams ... [more ▼]

The unimolecular dissociation of energy-selected fluoroethene and 1,1-difluoroethene ions has been investigated by threshold photoelectron photoion coincidence TPEPICO) technique. The breakdown diagrams of the 1,1-difluorethene and fluoroethene have been recorded between 13-22 eV. From time-of-flight (TOF) spectra, complete distributions of the kinetic energy released (KERD) in the dissociation of these energy-selected ions have been derived. For the HF-loss reaction channel, the KERD peaks at about 200 meV for low excitation energies but becomes thermal at higher excitation energies. For the F-loss channel, the KERD peaks at zero kinetic energy for low excitation energies but at about 200 meV for high excitation energy. The analysis of the KERD provides evidence that consecutive fragmentation takes place for the 1,1-difluoroethene at energies above 19 eV. [less ▲]

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See detailCombined Ring Inversion and Side Group Rotation in Geminal Diphosphoryl Substituted Pyrrolinoxyl Radicals: ESR Analysis of Chemical Exchange between Four Nonequivalent Sites
Rockenbauer, Antal; Mercier, Anne; Le Moigne, François et al

in Journal of Physical Chemistry A (1997), 101(43), 7965-7970

The ESR spectra of three diphosphorylated pyrrolidinoxyl radicals have been studied over a large temperature range. While for the trans 2,5-disubstituted compound 1 no line width alternation was found ... [more ▼]

The ESR spectra of three diphosphorylated pyrrolidinoxyl radicals have been studied over a large temperature range. While for the trans 2,5-disubstituted compound 1 no line width alternation was found, for the 2,2-disubstituted compounds 2 and 3, dramatic changes in the spectra were observed as a function of the temperature. These changes were explained by a four-site chemical exchange model including both ring inversion and hindered rotation around the carbon-phosphorus bonds. For radical 3, the presence of additional 5,5-dimethyl substitution can completely block rotations around carbon-phosphorus bonds for certain ring geometries, while for other ring conformations chemical exchange still occurs through combined inversionrotation processes. An effective two-site model composed of nonequivalent sites and a superposition model composed of a pair of exchanging conformers and a pair of nonexchanging conformers were used to simulate spectrum variations. A satisfactory fit was obtained over the entire temperature range investigated. From the temperature dependence of the exchange frequencies the potential barriers for ring inversion (27 kJ/mol), for combined inversion-rotation (11 kJ/mol), and for rotation around the carbon-phosphorus bonds (14 kJ/mol) were estimated. [less ▲]

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