ABIDIN-CSIC group
[1] Basis Set Convergence of Potential Energy Surfaces: Ground Electronic State of H2 and H3+
Velilla, L.; Paniagua, M.; Aguado, A.
International Journal of Quantum Chemistry (Special Issue: Proceedings from the Fourteenth European Workshop on Quantum Systems in Chemistry and Physics)
111; 387-399; 02/2011
1.302
In this work, we studied one of the many CBS extrapolation formula that has best performance to predict the total energies of the global potential energy surfaces for two-electron molecular systems, H2 and H3+. The vibrational energies calculated from the PEC for H2 or surface for the H3+ agree with the “exact values” to within a few tenths of a cm−1.
[2]Quantum stereodynamics of Li + HF reactive collisions: the role of reactants polarization on the differential cross section
González-Sánchez, L; Vasyutinskii, O; Zanchet, A; Sanz-Sanz, C; Roncero, O
Physical Chemistry Chemical Physics
13; 13656-69; 08/2011
3.453
A complete quantum study for the state-to-state Li + HF(v,j,m) → LiF(v′,j′,Ω′) + H reactive collisions has been performed using a wave packet method, for different initial rotational states and helicity states of the reactants. The state-to-state differential cross section has been simulated, and the polarization of products extracted. It is found that the reactivity is enhanced for nearly collinear collisions, which produces a vibrational excitation of HF, needed to overcome the late barrier.
[3]Ortho-Para H2 Conversion by Proton Exchange at Low Temperature: An Accurate Quantum Mechanical Study
Honvault, P.; Jorfi, M.; González-Lezana, T.; Faure, A.; Pagani, L.
Physical Review Letters
107; 023201-05; 07/2011
7.621
We report extensive, accurate fully quantum, time-independent calculations of cross sections at low collision energies, and rate coefficients at low temperatures for the H++H2(v=0,j)→H++H2(v=0,j′) reaction. Different transitions are considered, especially the ortho-para conversion (j=1→j′=0) which is of key importance in astrophysics.
[4]Quantum mechanical study of the proton exchange in the ortho–para H2 conversion reaction at low temperature
Honvault, P.; Jorfi, M.; González-Lezana, T.; Faure, A.; Pagani, L.
Physical Chemistry Chemical Physics
13; 19089–19100; 10/2011
3.453
Ortho–para H2 conversion reactions mediated by the exchange of a H+ proton have been investigated at very low energy for the first time by means of a time independent quantum mechanical (TIQM) approach. The relaxation ortho–para process j = 1 → j′ = 0 is found to be more efficient than the j = 0 → j′ = 1 conversion at low temperatures, in line with the extremely small ratio between the ortho and para species of molecular hydrogen predicted at the temperature of interstellar cold molecular clouds.
[5]Communication: Theoretical exploration of Au++H2, D2, and HD reactive collisions
Dorta-Urra, A.; Zanchet, A.; Roncero, O.; Aguado, A.; Armentrout, P. B.
Journal of Chemical Physics
135; 091102-06; 09/2011
2.920
A quasi-classical study of the endoergic Au+(1S) + H2(X1Σg+) → AuH+ (2Σ+) + H(2S) reaction, and isotopic variants, is performed to compare with recent experimental results. For this purpose, a new global potential energy surface has been developed based on multi-reference configuration interaction ab initio calculations. The quasi-classical trajectory results show a very good agreement with the experiments, showing the same trends for the different isotopic variants of the hydrogen molecule.
[6]Accurate time dependent wave packet calculations for the N + OH reaction
Bulut, N.; Roncero, O.; Jorfi, M.; Honvault, P.
Journal of Chemical Physics
135; 104307-15; 09/2011
2.920
Total reaction cross sections, state-specific rate constants, opacity functions, and product state-resolved integral cross-sections have been obtained by means of the wave packet method for several collision energies and compared with recent quasi-classical trajectory results obtained with the same potential energy surface. The rate constant for OH(v = 0, j = 0) is in good agreement with the previous theoretical values, but in disagreement with the experimental data, except at 300 K.
[7]Infrared spectrum of H5+ and D5+: The simplest shared-proton model
Sanz-Sanz, C.; Roncero, O.; Valdés, A.; Prosmiti, R.; Delgado-Barrio, G.; Villarreal, P.; Barragán, P.; Aguado, A.
Physical Review A
12/2011; DOI:10.1103/PhysRevA.84.060502
2.861
We present a two-dimensional collinear, adiabatic model to describe the motion of a proton in between two hydrogen molecules which adjust their elongation to trace a minimum-energy path. Together with bound states, the predissociative, vibrationally excited states involved in the electric dipole transitions are characterized. The main qualitative features of the infrared spectra of H5+ and its deuterated variant are discussed, and the effect of the temperature of the clusters is analyzed.
ABIDIN-CSIC in coll. with DINQUIM-UCM group
[8]Accurate Time-Dependent Wave Packet Study of the Li + H2+ Reaction and Its Isotopic Variants
Aslan, E.; Bulut, N.; Castillo, J.F.; Bañares, L.; Roncero, O.; Aoiz, F.J.
The Journal of Physical Chemistry A
12/2011; DOI: 10.1021/jp210254t
2.732
The dynamics and kinetics of the Li + H2+ reaction and its isotopic variants (D2+ and T2+) have been studied by using a time-dependent wave packet (TDWP) coupled-channel (CC) method. Integral cross sections have been evaluated from the reaction probabilities at collision energies from threshold (≈0.2 eV) up to 1.0 eV collision. The TDWP-CC results are in overall good agreement with those obtained applying the TDWP Centrifugal-Sudden (CS) approximation, showing that the CS approximation is rather accurate for the title reaction.
GFM-CSIC group
[9]Large effects of small pressure changes in the kinetics of low pressure glow discharges
Tanarro, I; Herrero, V. J.
Plasma Sources Science and Technology
20; 024006-13; 04/2011
2.218
The effect of comparatively small pressure changes on the composition of low pressure hollow cathode dc discharges is investigated with a combination of experimental diagnostic techniques and simple models of the plasma kinetics. The plasma precursors considered are H2, Ar/H2 mixtures, and air. In all cases, sudden characteristic composition changes are observed in the pressure interval between ≈0.5 and 3 Pa.
[10]Communication: observation of homonuclear propensity in collisional relaxation of the 13C12CD2 (v2=1) isotopologue of acetylene by stimulated Raman spectroscopy
Martínez, R. Z.; Doménech, J. L.; Bermejo, D.; Di Lonardo, G.; Fusina, L.
Journal of Chemical Physics
134; 231102-06; 06/2011
2.920
We report the first experimental observation of homonuclear propensity in collisional relaxation of a polyatomic molecule. A pump-probe stimulated Raman setup is used to pump population to a single rotational level of the v(2) = 1 vibrationally excited state in (13)C(12)CD(2) and then monitor the redistribution of the rotational population that has taken place after a fixed delay. The Q-branch of the 2ν(2)-ν(2) band shows a pattern of intensity alternation between the even and the odd rotational components. The effect can be explained by the existence of a propensity rule that favors collisional relaxation between rovibrational levels of the same parity.
GFM-CSIC in coll. with ABIDIN-CSIC group
[11]Inelastic collisions in molecular oxygen at low temperature (4 < T < 34). Close coupling calculations versus experiment
Pérez-Ríos, J.; Tejeda, G.; Fernández, J. M.; Hernández, M. I.; Montero, S.
Journal of Chemical Physics
134; 174307-18; 05/2011
2.920
Our results provide an experimental validation of state-to-state rates for O2:O2 inelastic collisions calculated in the close-coupling approach and, indirectly, of the anisotropy of the O2-O2 intermolecular potential employed in the calculation for energies up to 300 cm−1.
[12]Isotopic exchange processes in cold plasmas of H2/D2 mixtures
Jiménez-Redondo, M.; Carrasco, E.; Herrero, V. J.; Tanarro, I.
Physical Chemistry Chemical Physics
13; 9655-9666; 04/2011
3.453
Isotope exchange in low pressure cold plasmas of H2/D2 mixtures has been investigated by means of mass spectrometric measurements of neutrals and ions, and kinetic model calculations. The good global agreement between measurements and simulations over the wide range of conditions sampled indicates that the model and the associated set of rate coefficients (mostly from bibliographic sources) provide a consistent picture of the kinetics and can be used for the identification of the basic processes determining the observed discharge compositions.
[13]Neutral and ion chemistry in low pressure DC plasmas of H2/N2 mixtures: Routes for the efficient production of NH3 and NH4+
Carrasco, E.; Jiménez-Redondo, M.; Tanarro, I.; Herrero, V. J.
Physical Chemistry Chemical Physics
13(43); 19561-19572; 10/2011
3.453
The chemistry in low pressure (0.8–8 Pa) plasmas of H2 + 10% N2 mixtures has been experimentally investigated in a hollow cathode dc reactor using electrical probes for the estimation of electron temperatures and densities, and mass spectrometry to determine the concentration of ions and stable neutral species. At the lowest pressure, products from the protonation of the precursor molecules (H3+, N2H+ and NH4+) and others from direct ionization (H2+ and NH3+) are found in comparable amounts. At the higher pressures, the ionic distribution is largely dominated by ammonium. It is found that collisions of H3+, NH3+ and N2H+ with the minor neutral component NH3 are to a great extent responsible for the final prevalence of NH4+
DINQUIM-UCM group
in coll. with GFM-CSIC group
[14]Can quasiclassical trajectory calculations reproduce the extreme kinetic isotope effect observed in the muonic isotopologues of the H + H2 reaction?
Jambrina, P. G.; García, E.; Herrero, V. J.; Sáez-Rábanos, V.; Aoiz, F. J.
Journal of Chemical Physics
135; 034310-16 ;07/2011
2,920
Rate coefficients for the mass extreme isotopologues of the H + H(2) reaction, namely, Mu + H(2), where Mu is muonium, and Heμ + H(2), where Heμ is a He atom in which one of the electrons has been replaced by a negative muon, have been calculated in the 200-1000 K temperature range by means of accurate quantum mechanical (QM) and quasiclassical trajectory (QCT) calculations and compared with the experimental and theoretical results recently reported by Fleming et al. [Science 331, 448 (2011)]. The analysis of the results shows that the large zero point energy of the MuH product is the key factor for the large KIE observed.
in coll. with GFM-CSIC group
[15]Dynamics of the D+ + H2 and H+ + D2 reactions: a detailed comparison between theory and experiment
Jambrina, P. G.; Alvariño, J.M.; Gerlich, D.; Hankel, M.; Herrero, V. J.; Sáez-Rábanos, V.; Aoiz, F. J.
Physical Chemistry Chemical Physics
12/2011; DOI: 10.1039/c2cp23479c
3,453
An extensive set of experimental measurements on the dynamics of the H+ + D2 and D+ + H2 ion–molecule reactions is compared with the results of quantum mechanical (QM), quasiclassical trajectory (QCT), and statistical quasiclassical trajectory (SQCT) calculations. The dynamical observables considered include specific rate coefficients as a function of the translational energy, thermal rate coefficients in the 100–500 K temperature range. For the two reactions, the best global agreement between experiment and theory over the whole energy range corresponds to the QCT calculations. The comparison between theory and experiment also suggests that the most reliable rate coefficient measurements are those obtained with the merged beams technique.
[16]Dynamical regimes on the Cl + H2 collisions: Inelastic rainbow scattering
González-Sánchez, L.; Aldegunde, J.; Jambrina, P. G.; Aoiz, F. J.
Journal of Chemical Physics
135; 064301-11; 08/2011
2.920
Extensive quantum mechanical calculations covering the 0.5–1.5 eV total energy range and various initial rovibrational states have been carried out and used to perform a joint study of inelastic and reactive Cl + H2 collisions. The analysis of the inelastic transition probabilities has revealed the existence of two distinct dynamical regimes that correlate with low and high impact parameters, b, and are neatly separated by glory scattering.
[17]The k-j-j´ vector correlation in inelastic and reactive scattering
Brouard, M; Chadwick, H; Eyles, C. J.; Aoiz, F. J.; Kłos, J.
Journal of Chemical Physics
135; 084305-18; 09/2011
2.920
Quasi-classical trajectory (QCT) methods are presented which allow characterization of the angular momentum depolarization of the products of inelastic and reactive scattering. The classical j-j´ two-vector correlation results are compared with quantum mechanical calculations, and are shown to be in good agreement. Furthermore, it is shown that the projection of j along the kinematic apse is nearly conserved for this system under thermal collision energy conditions.
[18]Collisional angular momentum depolarization of OH(A) and NO(A) by Ar: a comparison of mechanisms
Brouard, M.; Chadwick, H.; Chang, Y. P.; Eyles, C. J.; Aoiz, F. J.; Kłos, J.
Journal of Chemical Physics
135; 084306(1) – (17); 09/2011
2.920
This paper discusses the contrasting mechanisms of collisional angular momentum depolarization of OH(A2Σ+) and NO(A2Σ+) by Ar. New experimental results are presented for the collisional depolarization of OH(A) + Ar under both thermal and superthermal collision conditions, including cross sections for loss of both angular momentum orientation and alignment. Experimental and theoretical results reveal that, as the collision energy is raised, the depolarization of OH(A) by Ar becomes more impulsive-like in nature.
[19]Interference structures in the differential cross-sections for inelastic scattering of NO by Ar
Eyles, C. J.; Brouard, M.; Yang, C. H.; Kłos, J.; Aoiz, F. J.; Gijsbertsen, A.; Wiskerke, A. E.; Stolte, S.
Nature Chemistry
3; 597–602; 06/2011
17.927
Inelastic scattering is a fundamental collisional process that plays an important role in many areas of chemistry, and its detailed study can provide valuable insight into more complex chemical systems. Here, we report the measurement of differential cross-sections for the rotationally inelastic scattering of NO(X2Π1/2, v=0, j=0.5, f) by Ar at a collision energy of 530 cm(-1) in unprecedented detail, with full Λ-doublet (hence total NO parity) resolution in both the initial and final rotational quantum states. The experimental data agree remarkably well with rigorous quantum-mechanical scattering calculations, and reveal the role played by total parity in acting as a potential energy landscape filter.
[20]Product rotational alignment in NO(X) + Kr collisions
Marinakis, S.; Howard, B. J.; Aoiz, F. J.; Kłos, J.
Chemical Physics Letters
512; 161-166; 08/2011
2.280
Quantum mechanical (QM) close-coupling calculations have been used to study fully quantum state-resolved product differential rotational alignment in collisions of NO(X 2Π1/2, v = 0, j = 0.5, f) + Kr at a collision energy of 500 cm−1, using the most recent ab initio potential energy surface. We show that fully quantum state-resolved differential alignment exhibits a noticeable parity-dependent behavior.
[21]On te role of dynamical barriers in barrierless reactions at low energies
Lara, M.; Jambrina, P. G.; Varandas, A. J. C.; Launay, J.-M.; Aoiz, F. J.
Journal of Chemical Physics
135; 134313-1 134313-14; 10/2011
2.920
Reaction probabilities as a function of total angular momentum (opacity functions) and the resulting reaction cross sections for the collision of open shell S(1D) atoms with para-hydrogen have been calculated in the kinetic energy range 0.09–10 meV (1–120 K). The quantum mechanical hyperspherical reactive scattering method and quasi-classical trajectory and statistical quasi-classical trajectory approaches were used. Two different ab initio potential energy surfaces (PESs) have been considered. The comparison of the results on both PESs is illustrative of the wealth of the dynamics at low collision energy. It is also illuminating about the difficulties encountered in modeling an all-purpose global potential energy surface.
LHM-UCM group
[22]Vibrational excitation of adsorbed molecules by photoelectrons of very low energy: acrylonitrile on Cu (100)
Tornero, J.; Telle, H. H.; García G.; González-Ureña, A.
Physical Chemistry Chemical Physics
13; 8475-8484; 03/2011
3.453
In this study, we report on a powerful method of primary photoelectron scattering by adsorbed species. Specifically, threshold-energy (Ekin,max < 0.5 eV) two-photon photoelectrons (2PPE) are used to probe acrylonitrile (ACN) molecules chemisorbed onto a Cu(100) substrate, held at room temperature. From the dynamics of the directional (perpendicular to the copper surface) electron energy loss we conclude that only a few fundamental vibrational motions of adsorbed ACN are excited. The interpretation of the excitation spectra suggests that the di-σ adsorption configuration of the terminal C- and N-atoms dominates, which agrees well with the orientation and bindings predicted in Density Functional Theory (DFT) calculations.
IONTRAP-UPO group
[23]Vibrational study of isolated 18-crown-6 ether complexes with alkaline-earth metal cations
Gámez, F.; Hurtado, P.; Martínez-Haya, B.; Berden, G.; Oomens, J.
International Journal of Mass Spectrometry
308; 217– 224; 07/2011
2.009
Laser infrared multiple photon dissociation (IRMPD) spectroscopy has been employed to probe the C–O and C–C stretching vibrational modes of 18-crown-6 ether (18c6) complexes with alkaline-earth metals (Mg2+, Ca2+, Sr2+ and Ba2+) stored in the cell of a Fourier Transform Ion Cyclotron Resonance mass spectrometer. A pronounced shift of the C–O stretching band, but not of the C–C band, is found in comparison to the similar IRMPD spectra reported previously for the 18c6 complexes with alkali metals. This is attributed to the tighter coordination and stronger binding of the divalent alkaline-earth cations to the oxygen sites.
[24]Crown Ether Complexes with H3O+ and NH4+: Proton Localization and Proton Bridge Formation
Hurtado, P.; Gamez, F.; Hamad, S.; Martinez-Haya, B.; Steill, J. D.; Oomens, J.
The Journal of Physical Chemistry A
115; 7275-7282; 06/2011
2.732
The complexes formed by crown ethers with hydronium and ammonium cations are of key relevance for the understanding of their supramolecular behavior in protic solvents. In this work, the complexes of the 15-crown-5 (15c5) and 18-crown-6 (18c6) ethers with H3O+ and NH4+ and their deuterated variants are investigated under isolated conditions. Remarkably, an appreciable broadening of the IRMPD vibrational bands is observed for the 15c5-H3O+/D3O+ complexes.
[25]Platinum Nanoparticles Prepared by Laser Ablation in Aqueous Solutions: Fabrication and Application to Laser Desorption Ionization
Cueto, M.; Sanz, M.; Oujja, M.; Gámez, F.; Martínez−Haya, B.; Castillejo, M.
The Journal of Physical Chemistry C
115 (45); 22217–22224; 10/2011
4.524
Aqueous suspensions of platinum colloidal nanoparticles of varying size and polydispersity have been produced by ablation of a platinum target with a nanosecond Q-switched Nd:YAG laser. Ultraviolet ablation of Pt at 266 nm, reported here for the first time, produces crystalline nanoparticles of small size (1–4 nm diameter), with a weak onset of larger particles (6–8 nm).
[26]Phase behavior of hard colloidal platelets using free energy calculations
Marechal, M.; Cuetos, A.; Martínez-Haya, B.; Dijkstra, M.
Journal of Chemical Physics
134; 094501-13; 03/2011
2.920
We investigate the phase behavior of a model for colloidal hard platelets and rigid discotic molecules: oblate hard spherocylinders (OHSC). We perform free energy calculations using Monte Carlo simulations to map out the phase diagram as a function of the aspect ratio L/D of the particles. Although we have found a cubatic phase, it was shown to be definitely unstable, whereas the stability of the cubatic phase of cut spheres is still disputed. Finally, we also show that the phase boundaries differ significantly from those for cut spheres. These are remarkable consequences of a subtle change in particle shape, which show that for a detailed comparison with the phase behavior of experimental particles, the OHSC should be used as a model particle.
in coll. with DINQUIM-UCM group
[27]Stereodynamics of the F + HD(v = 0, j = 1) reaction: direct vs. resonant mechanisms
Aldegunde, J.; Jambrina, P. G.; De Miranda, M. P.; Sáez-Rábanos, V.; Aoiz, F. J.
Physical Chemistry Chemical Physics
13; 8345-8358; 02/2011
3.453
The stereodynamics and mechanism of the F + HD(v = 0, j = 1) → HF (DF) + D (H) reactions have been thoroughly analysed at collision energies in the 0–160 meV range. Specifically, this study is focused on (i) the comparison between the stereodynamics of the collisions leading to HF and DF formation, and (ii) the stereodynamical fingerprints of the resonance that occurs at low collision energies in the HF channel and whose manifestation in the total cross section is greatly diminished for initial j > 0. The evolution of the PPs with the collision energy differs markedly between the two reaction channels. For the DF channel, the PP values are small and change very little in the energy range in which DF formation is appreciable. In contrast, rapid fluctuations in the magnitude and sign of the PPs are observed in the HF channel at low collision energies in and around the resonance. As the collision energy increases, direct (non-resonant) scattering prevails, and the various quantities are reasonably well accounted for by the QCT calculations, as in the case of the DF channel.
in coll. with DINQUIM-UCM group
[28]Energy dependent dynamics of the O(1D) + HCl reaction: A quantum, quasiclassical and statistical study
Bargueño, P.; Jambrina, P. G.; Alvariño, J. M.; Menéndez, M.; Verdasco, E.; Hankel, M.; Smith, S. C.; Aoiz, F. J.; González-Lezana, T.
Physical Chemistry Chemical Physics
13; 8502–8514; 04/2011
3.453
The dynamics of the reaction O(1D) + HCl → ClO + H, OH + Cl has been investigated in detail by means of a time-dependent wave packet (TDWP) method in comparison with quasiclassical trajectory (QCT) and statistical approaches on the ground potential energy surface. Fully coupled quantum mechanical (QM) reaction probabilities for high values of the total angular momentum (J ≤ 50) are reported for the first time. For the OH + Cl arrangement, only QCT probabilities are found to agree with the QM values. This suggests that the dynamics of the reaction are controlled by a direct mechanism. The comparison between the QCT and QM-TDWP results in the whole range of collision energies lends credence to the QCT description of the dynamics of this reaction.
in coll. with DINQUIM-UCM group
[29]Theoretical study of the dynamics of the Cl+O3 reaction I. Ab initio potential energy surface and quasiclassical trajectory results
Castillo, J. F.; Aoiz, F. J.; Martínez-Haya, B.
Physical Chemistry Chemical Physics
13; 8537-8548; 04/2011
3.453
We present a global full dimensional potential energy surface (PES) for the Cl + O3 → ClO + O2 reaction, which is an elementary step in a catalytic cycle that leads to the destruction of ozone in the stratosphere. The calculated product vibrational distributions (strongly inverted for ClO) and rate constants are compared with experimental determinations. Differential cross sections (DCS) summed over all final states are found to be in fairly good agreement with those derived from crossed molecular beam experiments.
LEMQC-UMU group
[30]Vibrational Dynamics of Polyatomic Molecules in Solution: Assigment, Time Evolution and Mixing of Normal Modes
Kalstein, A.; Fernandez-Alberti, S: Bastida, A.; Soler, M.A.; Faraq, M.H.; Zúñiga, J.; Requena, A.
Theoretical Chemistry Accounts
128; 769-782; 10/2010
2.903
we describe a novel method to assign the INMs using the ENMs as templates, which provides a unique relationship between the two sets of normal modes. The method is based specifically on the use of the so-called Min-Cost or Min-Sum algorithm, duly adapted to our problem, to maximize the overlaps between the two sets of modes. The usefulness of the method is illustrated by carrying out equilibrium molecular dynamics (MD) simulations of the deuterated N-methylacetamide (NMAD) molecule in D2O solution.
[31]Importance of Polarization and Charge Transfer Effects to Model the Infrared Spectra of Peptides in Solution
Ingoso, F.; Monard, G; Faraq, M.H.; Bastida, A.; Ruiz-López, M.F.
Journal of Chemical Theory and Computation
7 (6); 1840–1849; 05/2011
5.138
We present a study of the infrared spectrum of N-methyl acetamide (NMA) performed by using molecular dynamics (MD) with a quantum electronic Hamiltonian. A recently developed method, based on the Born–Oppenheimer approximation and on a semiempirical level of quantum chemistry (SEBOMD), is employed. We focus on the solvent effect on the infrared spectrum of the solute, on its geometry, and on its electrostatic properties. We find a satisfying agreement between our model and experimental measurements, not only for the solvent shift but also for the structural and electrostatic properties of the solute. It is stressed the importance of mutual polarization and charge transfer in an accurate modeling of the solute–solvent interactions.
[32]Combined effect of stacking and solvation on the spontaneous mutation in DNA
Cerón-Carrasco, J. P.; Zúñiga, J.; Requena, A.; Perpete, E.; Michaux, C.; Jacquemin, D.
Physical Chemistry Chemical Physics
13; 14584-14589; 06/2011
3.453
In DNA, base pairs are involved in two reciprocal interactions: interbase hydrogen bonds and stacking. Furthermore, base pairs also undergo the effects of the external entities present in the biological environment, such as water molecules and cations. In this contribution, the double spontaneous mutation has been studied with hybrid theoretical tools in a DNA-embedded guanine–cytosine model accounting for the impact of the first hydration shell. According to our findings, the combination of the neighboring base pairs and surrounding water molecules plays a crucial role in the double proton transfer.
[33]Atomistic Molecular Dynamics Simulations of the Interactions of Oleic and 2-Hydroxyoleic Acids with Phosphatidylcholine Bilayers
Cerezo, J.; Zúñiga, J.; Bastida, A.; Requena, A.; Cerón-Carrasco, J. P.
The Journal of Physical Chemistry B
115 (40); 11727–11738; 09/2011
3.603
Fatty oleic acid (OA) and, recently, its derivative 2-hydroxyoleic acid (2OHOA) have been reported to display an important therapeutic activity. To understand better these therapeutic effects at the molecular and cellular levels, in this work we have carried out molecular dynamics simulations. The results from these simulations show that accumulation of OA and 2OHOA up to high concentrations induces only small structural changes in the bilayers. An increase of the mobility of the lipid and fatty acid chains at rising fatty acid concentrations is also observed.
[34]Theoretical vibrational terms and rotational constants for the 15N substituted isotopologues of N2O calculated using normal hyperspherical coordinates
Zúñiga, J.; Bastida, A.; Requena, A.
Journal of Quantitative Spectroscopy and Radiative Transfer
113, Issue 1; 26-46; 01/2012
2.331
We calculate variationally vibrational terms and rotational constants of the 15N substituted isotoplogues of nitrous oxide. Variational calculations are preformed using normal hyperspherical coordinates. The spectroscopic constants calculated show an excellent agreement with those experimentally observed. Predicted calculated values of the spectroscopic constants for unobserved vibrational bands are reported.
GEM-UVA group
[35]Nuclear quadrupole coupling interactions in the rotational spectrum of tryptamine
Alonso, J.L.; Cortijo, V.; Mata, S.; Pérez, C.; Cabezas, C.; López, J.C.; Caminati, W.
Journal of Molecular Spectroscopy
269; 41–48; 05/2011
1.497
Four conformers of tryptamine have been detected in a supersonic expansion and characterized by laser ablation molecular beam Fourier transform microwave spectroscopy LA-MB-FTMW in the 5–10 GHz frequency range. The quadrupole hyperfine structure originated by two 14N nuclei has been completely resolved for all conformers and used for their unambiguous identification.
[36]The two conformers of acetanilide unraveled using LA-MB-FTMW spectroscopy
Cabezas, C.; Varela, M.; Caminati, W.; Mata, S.; López, J.C.; Alonso, J.L.
Journal of Molecular Spectroscopy
268; 42–46; 08/2011
1.497
Acetanilide has been investigated by laser ablation molecular beam Fourier transform microwave LA-MB-FTMW spectroscopy. The rotational spectrum of both trans and cis conformers have been analyzed to determine the rotational and 14N quadrupole coupling the constants. The spectrum of the less abundant cis conformer has been assigned for the first time.
[37]Spectroscopic investigation of fluoroiodomethane, CH2Fl: Fourier-transform microwave and millimeter-/submillimeter-wave spectroscopy and quantum-chemical calculations
Puzzarini, C.; Cazzoli, G.; López, J.C.; Alonso, J.L.; Baldacci, A.; Baldan, A.; Stopkowicz, S.; Cheng, L.; Gauss, J.
The Journal of Chemical Physics
134; 174312; 05/2011
2.920
The rotational spectrum of fluoroiodomethane, CH2Fl, has been recorded and assigned. Accurate values are reported for the ground-state rotational constants, all quartic, sextic, and two octic centrifugal-distortion constants. The relativistic corrections to the dipole moment, essential for the accurate theoretical prediction of the dipole moment and quadrupole-coupling constants, amount to up to 34% and to the iodine quadrupole-coupling tensor to about 15–16% of the total values.
[38]Jet-Cooled Rotational Spectrum of Laser-Ablated Phenylalanine
Pérez, C.; Mata, S.; Blanco, S.; López, J.C.; Alonso, J.L.
The Journal of Physical Chemistry A
05/2011; DOI: 10.1021/jp200800a
2.732
The rotational spectrum of neutral phenylalanine has been recorded for the first time using laser-ablation molecular-beam Fourier transform microwave spectroscopy (LA-MB-FTMW). Two conformers stabilized by conjugative O-H···N and N-H···π hydrogen bond interactions have been conclusively identified on the basis of experimental values of rotational and (14)N nuclear quadrupole coupling constants.
[39]Rapid probe of the nicotine spectra by high-resolution rotational spectroscopy
Grabow, J.-U.; Mata, S.; Alonso, J.L.; Peña, I.; Blanco, S.; López, J.C.; Cabezas, C.;
Physical Chemistry Chemical Physics
10/2011; DOI:10.1039/C1CP22197C
3.453
The rotational, centrifugal distortion and hyperfine quadrupole coupling constants of two conformers of nicotine have been determined and found to be in N-methyl trans configurations with the pyridine and pyrrolidine rings perpendicular to one another. The quadrupole hyperfine structure originated by two 14N nuclei has been completely resolved for both conformers and used for their unambiguous identification.
[40]Unveiling the Shape of Aspirin in the Gas Phase
Cabezas, C.; Alonso, J.L.; López, J.C.; Mata, S.;
Angewandte Chemie International Edition
12/2011; DOI: 10.1002/anie.201106621
12.73
The first high-resolution study of isolated gas-phase acetyl salicylic acid (aspirin) is reported. Solid aspirin was vaporized by laser ablation, expanded in a supersonic jet, and characterized by Fourier transform microwave spectroscopy. Two different neutral structures have been identified from the analysis of the rotational spectrum.
GAPT-IAA group
[41]Modelling the atmospheric CO2 10 microns non-thermal emission in Mars and Venus at high spectral resolution
Lopez-Valverde, M.A.; Sonnabend, G.; Sornig, M.; Kroetz, P.
Planetary and Space Science
59; 999–1009; 08/2011
2.344
A study of the CO(2) atmospheric emissions at 10 microns in the upper atmospheres of Mars and Venus is performed in order to explain a number of ground-based measurements of these emissions recently taken at very high spectral resolution in both planets. The larger solar flux available on Venus is found to produce larger vibrational populations and stronger emissions than equivalent atmospheric layers on Mars, in agreement with the observations. A number of perturbation studies were used to determine the exact emission altitudes, or weighting function peaks, for usual nadir sounding. The sensitivity of the emission to non-LTE model uncertainties and to atmospheric variations in temperature and CO(2) density is also presented. The dependence with the solar zenith angle and with the emission angle, as obtained with this model, could also be useful for guiding future observations.
[42]Analysis of Titan CH4 3.3 microns upper atmospheric emission as measured by Cassini/VIMS
García-Comas, M.; López-Puertas, M.; Funke, B.; Dinelli, B.; Moriconi, M.L.; Adriani, A.; Molina, A.; Coradini, A.
Icarus
214; 571–583; 03/2011
3.813
After molecular nitrogen, methane is the most abundant species in Titan’s atmosphere and plays a major role in its energy budget and its chemistry. Methane has strong bands at 3.3 microns emitting mainly at daytime after absorption of solar radiation. This emission is strongly affected by non-local thermodynamic equilibrium (non-LTE) in Titan’s upper atmosphere and, hence, an accurate modeling of the non-LTE populations of the emitting vibrational levels is necessary for its analysis. We present a sophisticated and extensive non-LTE model which considers 22 CH4 levels and takes into account all known excitation mechanisms in which they take part. Our retrievals show good agreement with previous measurements and model results, supporting a weak deviation from well mixed values from the lower atmosphere up to 1000 km.
[43]Distribution of HCN in Titan’s upper atmosphere from Cassini/VIMS observations at 3 μm
Adriani, A.; Dinelli, B.; López-Puertas, M.; García-Comas, M.; Moriconi, M.L.; D’Aversa, E.; Funke, B.; Coradini, A.
Icarus
214; 584–595; 08/2011
3.813
Cassini/VIMS limb observations have been used to retrieve vertical profiles of hydrogen cyanide (HCN) from its 3 μm emission in the region from 600 to 1100 km altitude at daytime. While the daytime emission is large up to about 1100 km, it vanishes at nighttime at very low altitudes, suggesting that the daytime emission originates under non-LTE conditions. We present the first concentration retrieval of HCN by Cassini-VIMS limb observations of the Titan upper atmosphere. HCN is thought to play an important role in the chemistry and in determining the thermal structure of Titan’s thermosphere. A model for non-LTE HCN emission in Titan atmospheric condition has been developed for the purpose.
RT-IAC group
[44]Determining the Magnetization of the Quiet Sun Photosphere from the Hanle Effect and Surface Dynamo Simulations
Shchukina, N.; Trujillo-Bueno, J.
The Astrophysical Journal
731; L21; 04/2011
5.158
It is shown that the scattering polarization amplitudes observed in the Sr I 4607 A line can be explained only after enhancing the magnetic strength of the photospheric model by a sizable scaling factor, F≈10, which implies an average B≈130 G in the upper photosphere.
[45]Scattering Polarization of Hydrogen Lines in Weakly Magnetized Stellar Atmospheres. I. Formulation and Application to Isothermal Models
Stepán, J.; Trujillo-Bueno, J.
The Astrophysical Journal
732; 80; 05/2011
6.063
Here we report on a basic theoretical investigation of the linear polarization produced by scattering processes and the Hanle effect in Lyα, Lyβ, and Hα taking into account multilevel radiative transfer effects in an isothermal stellar atmosphere model, the fine-structure of the hydrogen levels, as well as the impact of collisions with electrons and protons. We demonstrate that the linear polarization profile of the Hα line is sensitive to the presence of magnetic field gradients in the line core formation region, and that in solar-like chromospheres selective absorption of polarization components does not play any significant role in the emergent scattering polarization.
[46]The Hanle Effect of the Hydrogen Ly Line for Probing the Magnetism of the Solar Transition Region
Trujillo-Bueno, J.; Stepán, J.; Casini, R.
The Astrophysical Journal
738; L11; 08/2011
5.158
We present some theoretical predictions concerning the amplitude and magnetic sensitivity of the linear-polarization signals produced by scattering processes in the hydrogen Lyα line of the solar transition region. To this end, we have calculated the atomic-level polarization (population imbalances and quantum coherences) induced by anisotropic radiation pumping in semiempirical and hydrodynamical models of the solar atmosphere, taking into account radiative transfer and the Hanle effect caused by the presence of organized and random magnetic fields. The line-center amplitudes of the emergent linear-polarization signals are found to vary typically between 0.1% and 1%, depending on the scattering geometry and the strength and orientation of the magnetic field. The results shown here encourage the development of UV polarimeters for sounding rockets and space telescopes with the aim of opening up a diagnostic window for magnetic field measurements in the upper chromosphere and transition region of the Sun.
[47]Scattering Polarization and Hanle Effect in Stellar Atmospheres with Horizontal Inhomogeneities
Manso-Sainz, R.; Trujillo-Bueno, J.
The Astrophysical Journal
743;12; 12/2011
6.063
We develop a method to solve the transfer of polarized radiation in a scattering atmosphere with weak horizontal fluctuations of the opacity and source functions. It is shown (a) how the amplitudes of the fractional linear polarization signals change when considering increasingly smaller horizontal atmospheric inhomogeneities, (b) that in the presence of such inhomogeneities even a vertical magnetic field may modify the scattering line polarization, and (c) that forward scattering polarization may be produced without the need of an inclined magnetic field. These results are important to understand the physics of the problem and as benchmarks for multidimensional radiative transfer codes.
AM-CSIC and MIC-OAN groups
[48]The Widespread Occurrence of Water Vapor in the Circumstellar Envelopes of Carbon-rich Asymptotic Giant Branch Stars: First Results from a Survey with Herschel/HIFI
Neufeld, D.A.; González-Alfonso, E.; Melnick, G.; Szczerba, R.; Schmidt, M.; Decin, L.; Alcolea, J.; and 12 co-authors
The Astrophysical Journal
727(2); L29; 02/2011
5.158
We report the preliminary results of a survey for water vapor in a sample of eight C stars with large mid-IR continuum fluxes. This survey, performed using the HIFI instrument on board the Herschel Space Observatory, entailed observations of the lowest transitions of both ortho- and para-water: the 556.936 GHz 110-101 and 1113.343 GHz 111-000 transitions, respectively. Water vapor was unequivocally detected in all eight of the target stars. The water spectral line widths are typically similar to those of CO rotational lines, arguing against the vaporization of a Kuiper Belt analog being the general explanation for water vapor in carbon-rich AGB stars.
[49]A line confusion limited millimeter survey of Orion KL II. Silicon-bearing species
Tercero, B.; Vincent, L.; Cernicharo, J.; Viti, S.; Marcelino, N.
Astronomy and Astrophysics
528; A26; 04/2011
4.410
We present a study of the silicon-bearing species detected in a line-confusion limited survey towards Orion KL performed with the IRAM 30-m telescope. The analysis of the line survey is organized by families of molecules. The large number of transitions in different vibrationally excited states covered by our data, which range from 80 to 280 GHz, let us provide reliable source-average column densities (hence, isotopolog abundances and vibrational temperatures) for the detected molecules. For the v = 1 state of SiO, we detected the J = 2−1 line and, for the first time in this source, emission in the J = 4−3 transition, both of them showing a strong masering effect. For SiO v = 0, we detected 28SiO, 29SiO, and 30SiO; in addition, we have mapped the J = 5−4 SiO line. For SiS, we have detected the main species, 29SiS, and SiS v = 1. The results of our chemical models show that while it is possible to reproduce SiO in the gas phase (as well as on the grains), SiS is a product of surface reactions, most likely involving direct reactions of sulfur with silicon.
[50]Probing the dust formation region in IRC +10216 with the high vibrational states of hydrogen cyanide
Cernicharo, J.; Agúndez, M.; Kahane, C.; Guélin, M.; Goicoechea, J.R.; Marcelino, N.; De Beck, E.; Decin, L.
Astronomy and Astrophysics
529; L3; 05/2011
4.410
We report the detection in IRC +10216 of 63 rotational transitions of HCN, most of them with quantum numbers J = 3–2, pertaining to 28 different vibrational states with energies up to 10 700 K (ν1+3ν2+ν3). Some of the transitions were also observed for the rare isotopologue H13CN. The observations were carried out with the IRAM 30-m telescope. The HCN lines with level energies above 5000 K arise within 1.5 stellar radius from the photosphere. Their intensities imply a vibrational temperature of Tvib = 2400 K and a fractional HCN abundance relative to H2, x(HCN) = 5–7 × 10−5. These high-energy levels are mainly populated by photospheric radiation, and their vibrational temperature yields a direct measurement of the stellar photospheric temperature. This provides a unique insight into the physical conditions of the gas acceleration and dust formation region.
[51]OH emission from warm and dense gas in the Orion Bar PDR
Goicoechea, J.R.; Joblin, C.; Contursi, A.; Berné, O.; Cernicharo, J.; Gerin, M.; Le Bourlot, J.; Bergin, E.; Bell, T.A.; Röllig, M.
Astronomy and Astrophysics
530; L16; 06/2011
4.410
As part of a far-infrared (FIR) spectral scan with Herschel/PACS, we present the first detection of the hydroxyl radical (OH) towards the Orion Bar photodissociation region (PDR). The observed emission of rotationally excited OH lines is extended and correlates well with the high-J CO and CH+ J = 3−2 line emission (but apparently not with water vapour), pointing towards a common origin. We interpret the extended OH emission as coming from unresolved structures exposed to far-ultraviolet (FUV) radiation near the Bar edge(photoevaporating clumps or filaments) and not from the lower density “interclump” medium.
[52]Massive young disks around Herbig Ae stars
Boissier, J.; Alonso-Albi, T.; Fuente, A.; Berné, O.; Bachiller, R.; Neri, R.; Ginard, D.
Astronomy and Astrophysics
531; A50; 07/2011
4.410
Our aim is to determine the dust evolution and the lifetime of the disks associated with Herbig Ae stars. We imaged the continuum emission at ~3 mm and ~1.3 mm of the Herbig Ae/Be stars BD+61154, RR Tau, VY Mon, and LkHα 198 using the Plateau de Bure Interferometer (PdBI). Conclusions: these massive (M∗ > 3 M⊙) and young (~1 Myr) HAe stars are surrounded by massive (≳ 0.04 M⊙) disks with grains of micron-millimetre sizes. Although grain growth is proceeding in these disks, their evolutionary stage is prior to the formation of planetesimals. These disks are less evolved than those detected around T Tauri and Herbig Be stars.
[53]Collisional excitation of sulfur dioxide in cold molecular clouds
Cernicharo, J.; Spielfiedel, A.; Balança, C.; Dayou, F.; Senent, M.L.; and 5 co-authors
Astronomy and Astrophysics
531; A103; 07/2011
4.410
We present collisional rate coefficients for SO2 with ortho and para molecular hydrogen for the physical conditions prevailing in dark molecular clouds. Rate coefficients for the first 31 rotational levels of this species (energies up to 55 K) and for temperatures between 5 and 30 K are provided. We have found that these rate coefficients are about ten times more than those previously computed for SO2
with helium. The potential use of millimeter lines of SO2 as tracers of the physical conditions of dark clouds is discussed.
[54]HIFI detection of hydrogen fluoride in the carbon star envelope IRC +10216
Agúndez, M.; Cernicharo, J.; Waters, L.B.; Decin, L.; Encrenaz, P.; Neufeld, D.; Teyssier, D.; Daniel, F.
Astronomy and Astrophysics
533; L6; 09/2011
4.410
We report the detection of emission in the J = 1−0 rotational transition of hydrogen fluoride (HF), together with observations of the J = 1−0 to J = 3−2 rotational lines of H35Cl and H37Cl, towards the envelope of the carbon star IRC +10216. High-sensitivity, high-spectral resolution observations have been carried out with the HIFI instrument on board Herschel, allowing us to resolve the line profiles and providing insights into the spatial distribution of the emission. Our interpretation of the observations, with the use of radiative transfer calculations, indicates that both HF and HCl are formed in the inner regions of the envelope close to the AGB star. Thermochemical equilibrium calculations predict HF and HCl to be the major reservoirs of fluorine and chlorine in the atmospheres of AGB stars. The low abundance derived for HF in IRC +10216 makes it likely that the fluorine abundance is not enhanced over the solar value by nucleosynthesis in the AGB star, although this conclusion may not be robust because the HF abundance we derive is a lower limit to the elemental abundance of F. These observations suggest that both HF and HCl should be detectable through low J rotational transitions in other evolved stars.
[55]H2CO in the Horsehead PDR: Photo-desorption of dust grain ice mantles
Guzmán, V.; Pety, J.; Goicoechea, J.R.; Gerin, M.; Roueff, E.
Astronomy and Astrophysics
534; A49; 10/2011
4.410
We investigate the role of the grain surface chemistry in the Horsehead photo-dissociation region (PDR). We performed deep observations of several H2CO rotational lines toward the PDR and its associated dense-core in the Horsehead nebula, where the dust is cold (Tdust ≃ 20−30 K). The formation of H2CO on the surface of dust grains and subsequent photo-desorption into the gas-phase are needed in the PDR to explain the observed gas-phase H2CO abundance, because the gas-phase chemistry alone does not produce enough H2CO. Conclusions. Photo-desorption of H2CO ices is an efficient mechanism to release a significant amount of gas-phase H2CO into the Horsehead PDR.
[56]Intermediate-mass Hot Cores at ~500 AU: Disks or Outflows?
Palau, A.; Fuente, A.; Girart, J.M.; Fontani, F.; Boissier, J.; Piétu, V.; and 10 co-authors
The Astrophysical Journal
743(2); L32; 10/2011
5.158
Observations with the Plateau de Bure Interferometer in the most extended configuration toward two intermediate-mass star-forming regions, IRAS 22198+6336 and AFGL 5142, reveal the presence of several complex organic molecules at ~500 AU scales, confirming the presence of hot cores in both regions. The hot cores are not rich in CN-bearing molecules, as often seen in massive hot cores, and are mainly traced by CH3CH2OH, (CH2OH)2, CH3COCH3, and CH3OH, with, additionally, CH3CHO, CH3OD, and HCOOD for IRAS 22198+6336, and C6H and O13CS for AFGL 5142. A detailed comparison of the complex molecule peaks to the new CO (2-1) data and H2O maser data from the literature suggests also that for AFGL 5142 the complex molecules are mainly associated with disks.
[57]Rotational excitation of 45 levels of ortho/para-H2O by excited ortho/para-H2 from 5 K to 1500 K: state-to-state, effective, and thermalized rate coefficients
Daniel, F.; Dubernet, M.-L.; Grosjean, A.
Astronomy and Astrophysics
12/2011; DOI: http://dx.doi.org/10.1051/0004-6361/201118049
4.410
This work deals with the rotational excitation of ortho/para-H2O with para/ortho-H2 so that thermalized de-(excitation) rate coefficients up to 1500 K for the first 45th level of ortho/para-H2O are provided. Results are available in BASECOL with state-to-state rate coefficients, their fitting coefficients, and effective rate coefficients. In addition, we provide a routine that combines all data in order to create thermalized rate coefficients. These conclusions should simplify the future methodological choice for collisional excitation calculations applied to interstellar/circumstellar media.
[58]Sulfur depletion in dense clouds and circumstellar regions. I. H2S ice abundance and UV-photochemical reactions in the H2O-matrix
Jiménez-Escobar, A.; Muñoz-Caro, G. M.
Astronomy and Astrophysics
12/2011; DOI: 10.1051/0004-6361/201014821
4.410
This work aims to study the unexplained sulfur depletion observed toward dense clouds and protostars. We made simulation experiments of the UV-photoprocessing and sublimation of H2S and H2S:H2O ice in dense clouds and circumstellar regions, using the InterStellar Astrochemistry Chamber (ISAC), a state-of-the-art ultra-high-vacuum setup. UV-photoprocessing of H2S:H2O ice led to the formation of several species. Among them, H2S2 was found to photodissociate forming S2 and, by elongation, other species up to S8, which are refractory at room temperature. A large fraction of the missing sulfur in dense clouds and circumstellar regions could thus be polymeric sulfur residing in dust grains