Theoretical Study of Doubly Charged [X(H2O)] and [X(NH3)] (X = Si, Ge, Sn, Pb) Molecular Ions

Ab initio calculations have been used to study the structure and stability of several doubly charged molecular ions in the gas phase. In particular the complexes of water and ammonia with Si2+, Ge2+, Sn2+ and Pb2+ have been studied. Geometries have been obtained at B3LYP/6-31G(d) level and final energies at CCSD(T)/6-311+G(3df,2p) level. Different fragmentation channels have been considered. The loss of X+ (X = Si, Ge, Sn, Pb) is the most favorable one, except for [Si(H2O)]2+ where the loss of a H+ has a lower energy cost. Water complexes are thermodynamically stable, while loss of X+ in ammonia complexes are exothermic processes. In ammonia complexes a Coulomb barrier prevents the systems from spontaneous dissociation; to obtain these barriers the potential energy curves for the loss of Si+ or Pb+ in [Si(NH3)]2+ and [Pb(NH3)]2+ complexes have been obtained at CCSD(T)/6-311+G(3df,2p) level, the corresponding vibrational states have been located and their lifetimes evaluated using the exterior complex scaling. The barriers for dissociation of [X(NH3)]2+ complexes are similar to the ones obtained for [X(H2O)]2+ complexes

Isomers of hydrogenated polycyclic aromatic hydrocarbons explain the presence of infrared bands in the 3 μm region

A large number of hydrogenated coronene, circumcoronene, and circumcircumcoronene isomers have been investigated by means of density functional theory calculations. The computation of their IR spectra puts forward significant differences between the different isomers in the 3 μm region and shows that hydrogenated polycyclic aromatic hydrocarbons can account for the aromatic infrared bands resulting from the absorption of light by the interstellar medium. In particular, the intense 3.3 μm band, as well as the weak features observed at 3.40, 3.46, 3.51, and 3.56 μm are reasonably reproduced by the present calculations. The latter two are only observed when hydrogenation takes place in tertiary carbon atoms, showing that the frequencies at which these IR bands appear are a consequence of their position and chemical environment within the molecul

Structure, Ionization and Fragmentation of Neutral and Positively Charged Hydrogenated Carbon Clusters: CnHq+ m (n = 1 - 5, m = 1 - 4, Q = 0 - 3)

The CnHq+m family was studied at the DFT-B3LYP//CCSD(T) level of theory. Dissosiation energies, ionization potentials, geometries and frequencies were obtained. Different trends for these properteis have been observed and analyzed. The fragmentation behaviour has been studied within a combinatorial point of vie

Theoretical Study of Doubly Charged [X(H2O)] and [X(NH3)] (X = Si, Ge, Sn, Pb) Molecular Ions

Ab initio calculations have been used to study the structure and stability of several doubly charged molecular ions in the gas phase. In particular the complexes of water and ammonia with Si2+, Ge2+, Sn2+ and Pb2+ have been studied. Geometries have been obtained at B3LYP/6-31G(d) level and final energies at CCSD(T)/6-311+G(3df,2p) level. Different fragmentation channels have been considered. The loss of X+ (X = Si, Ge, Sn, Pb) is the most favorable one, except for [Si(H2O)]2+ where the loss of a H+ has a lower energy cost. Water complexes are thermodynamically stable, while loss of X+ in ammonia complexes are exothermic processes. In ammonia complexes a Coulomb barrier prevents the systems from spontaneous dissociation; to obtain these barriers the potential energy curves for the loss of Si+ or Pb+ in [Si(NH3)]2+ and [Pb(NH3)]2+ complexes have been obtained at CCSD(T)/6-311+G(3df,2p) level, the corresponding vibrational states have been located and their lifetimes evaluated using the exterior complex scaling. The barriers for dissociation of [X(NH3)]2+ complexes are similar to the ones obtained for [X(H2O)]2+ complexes

Theoretical Modeling of Mass Spectrometry

We present an implementation of the Microcanonical Metropolis Monte Carlo method based on statistical mechanics and electronic structure calculations. The method is designed to study any kind of fragmentation process. Here we show its capabilities to predict mass spectra of simple molecule

Mechanical Isolation of Highly Stable Antimonene under Ambient Conditions

Using mechanical exfoliation combined with a controlled double step transfer procedure we demonstrate that single layers of antimony can be readily produced. These flakes are not significantly contaminated upon exposure to ambient conditions and they do not react with water. DFT calculations confirm our experimental observations and predict a band gap of 1.2-1.3 eV (ambient conditions) for single layer antimonene, which is smaller than that calculated under vacuum conditions at 0 K. Our work confirms antimonene as a highly stable 2D material with promising relevant applications in optoelectronics.Comment: main paper: 5 pages, 4 figures supporting: 9 pages, 7 figures, Advanced Materials, 201

One-electron oxidation potentials and hole delocalization in heterogeneous single-stranded DNA

The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strandPID2019-110091GB-I00, PID2020-117806GA-I00, PID2022-138470NB-I00, CNS2022-135720, CEX2018-000805-

Reactivity of alloxydim herbicide: force and reaction electronic flux profiles

The reaction force profle and the electronic reaction fux concepts were explored for the herbicide alloxydim and some of its derivatives at B3LYP/6-311G(d,p) level of theory. The exploration was achieved by rotating the oxime bond which is the most reactive region of the molecule. The main objective is to understand how the rotation of this bond infuences the properties of the molecule and induces an electronic reorganization. The results show that the rotation of the dihedral angle triggers alloxydim to go through three transition states. The frst step of the transformation begins by the rupture of the hydrogen bond and is characterized by a pronounced structural reorganization. In the last step of the process the electronic reorganization is more importantThe work presented was funded by project PID2019-110091GB-I00 and PDC2021-121203-I00 of the Ministerio de Ciencia, Innovación of Spain and by the project Y2020/ EMT-6290 (PRIES-CM) of the Comunidad de Madrid, Spai

X-ray induced fragmentation dynamics of doubly charged L-alanine in gas phase

The molecular fragmentation of doubly charged L-alanine in gas phase was studied in radiation synchrotron experiments. In this presentation, we summarize our theoretical study on the dynamics of this fragmentation, using various computational methods. We show that in practice the ground state MD simulations are able to statistically reproduce the experimental results of the photo-fragmentation initiated at the excited stat