arXiv subjects

Andrea Lombardi

Publications and source records attributed to Andrea Lombardi.

14 recordsLinked to original sources

arXiv2026

Vectorial Imaging of the Photodissociation of 2-Bromobutane Oriented via Hexapolar State Selection

Molecular orientation techniques are becoming available in the study of elementary chemical processes, in order to highlight those structural and dynamical properties that would be concealed by random rotational motions. Recently successful orientation was achieved for asymmetric-top and chiral molecules of much larger complexity than hitherto. In this work, we report and discuss the correlation between the vectors photofragment recoil velocity v, transition dipole moment μ, and permanent dipole moment d in a dissociation experiment on hexapole oriented 2-bromobutane, photoinitiated by a linearly polarized laser. The sliced ion images of the Br* (2P1/2) and Br (2P3/2) photofragment were acquired at 234.0 and 254.1 nm, respectively, by (2+1) resonance-enhanced multiphoton ionization technique. A detailed analysis of the sliced ion images obtained at a tilting angle 45o of the laser polarization provides the information on correlation of the three vectors, which are confined by two polar angles α, \c{hi} and one azimuthal angle ϕμd in the recoil frame. The sliced ion images of Br fragments eliminated individually from the enantiomers at 254.1 nm yield the asymmetric factor close to zero; for this reason the photofragment angular distributions do not show significant differences. The elimination of Br* fragment at 234.0 nm is mainly correlated with a parallel transition, giving rise to a large anisotropy parameter of 1.85, and thus can be considered as a single state excitation. The resulting recoil frame angles are optimized to 163.8° and 164.1° for α and \c{hi}, respectively, whereas ϕμd approaches close to 0o for the best fit. Since in the present case, the three vectors have an only slight spatial arrangement, the photofragment angular distributions of the two enantiomers do not show appreciable differences...

physics.chem-ph↗

arXiv2021

Binary classification of proteins by a Machine Learning approach

In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each protein is fully described in its chemical-physical-geometric properties in a file in XML format. The aim of the work is to design a prototypical Deep Learning machinery for the collection and management of a huge amount of data and to validate it through its application to the classification of a sequences of amino acids. We envisage applying the described approach to more general classification problems in biomolecules, related to structural properties and similarities.

cs.LG↗

arXiv2021

A new method for binary classification of proteins with Machine Learning

In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank (PDB) database and reprocessed as images; for this purpose various tests have been conducted with pre-trained Convolutional Neural Networks, such as InceptionResNetV2 or InceptionV3, in order to extract significant features from these images and correctly classify the molecule. A comparative analysis of the performances of the various networks will therefore be produced.

cs.LG↗

arXiv2021

Gas Adsorption on Graphtriyne Membrane: Impact of the Induction Interaction Term on the Computational Cost

Graphynes are a family of porous carbon allotropes that are viewed as ideal 2D nanofilters. In this present work, the authors have modified the Improved Lennard-Jones (ILJ) semi-empirical potential used in the previous works by adding the induction term (iind) to define the full interaction. The evaluation of the computational cost was done comparing ILJ vs ILJ-iind and analyzing the adsorption of 1 gas (CO2) and a small mixture of gases containing CO2, N2 and H2O. The computational time of the different calculations is compared and possible improvements of the potential models are discussed.

physics.chem-ph↗

arXiv2021

Nucleophilic substitution vs elimination reaction of bisulfide ions with substituted methanes: exploration of chiral selectivity by stereodirectional first-principles dynamics and transition state theory

Control of molecular orientation is emerging as crucial for the characterization of the stereodynamics of kinetics processes beyond structural stereochemistry. The special role played in chiral discrimination phenomena has been particularly emphasized by the authors after their extensive probes of experimental control of molecular alignment and orientation. In this work, the role of the orientation has been demonstrated for the first time in first-principles molecular dynamics simulations: stationary points characterized on potential energy surfaces have been calculated for the study of chemical reactions occurring between the bisulfide anion HS- and oriented prototypical chiral molecules CHFXY (where X = CH3 or CN and Y = Cl or I). The important reaction channels are those corresponding to bimolecular nucleophilic substitution (SN2) and to bimolecular elimination (E2): their relative role has been assessed and alternative pathways due to the mirror forms of the oriented chiral molecule are revealed by the different reactivity of the two enantiomers of CHFCNI in SN2 reaction.

physics.chem-ph↗

arXiv2021

Quadrilaterals on the square screen of their diagonals: Regge symmetries of quantum-mechanical spin-networks and Grashof classical mechanisms of four-bar linkages

The four-bar linkage is a basic arrangement of mechanical engineering and represents the simplest movable system formed by a closed sequence of bar-shaped bodies. Although the mechanism can have in general a spatial arrangement, we focus here on the prototypical planar case, starting however from a spatial viewpoint. The classification of the mechanism relies on the angular range spanned by the rotational motion of the bars allowed by the ratios among their lengths and is established by conditions for the existence of either one or more bars allowed to move as cranks, namely to be permitted to rotate the full 360 degrees range (Grashof cases), or as rockers with limited angular ranges (non-Grashof cases). In this paper, we provide a view on the connections between the "classic" four-bar problem and the theory of 6j symbols of quantum mechanical angular momentum theory, occurring in a variety of contexts in pure and applied quantum mechanics. The general case and a series of symmetric configurations are illustrated, by representing the range of existence of the related quadrilaterals on a square "screen" (namely as a function of their diagonals) and by discussing their behavior according both to the Grashof conditions and to the Regge symmetries, concertedly considering the classification of the two mechanisms and that of the corresponding objects of the quantum mechanical theory of angular momentum. An interesting topological difference is demonstrated between mechanisms belonging to the two Regge symmetric configurations: the movements in the Grashof cases span chirality preserving configurations with a 2 pi-cycle of a rotating bar, while by contrast the non-Grashof cases span both enantiomeric configurations with a 4 pi-cycle.

quant-ph↗

arXiv2020

Carbon Capture and Separation from CO2/N2/H2O Gaseous Mixtures in Bilayer Graphtriyne: A Molecular Dynamics Study

Molecular dynamics simulations have been performed for CO2 capture and separation from CO2/N2/H2O gaseous mixtures in bilayer graphtriyne. The gas uptake capacity, permeability as well as selectivity of the layers were simulated based on an improved formulation of force fields tested on accurate ab initio calculations on specific systems for mixture separation in post-combustion process. The effect of pressure and temperature on the separation performances of graphtriyne layers was investigated. Compared with the single layer graphtriyne, bilayer graphtriyne can adsorb more molecules with relatively good selectivity, due to the action of the interlayer region as an adsorption site. The interlayer adsorption selectivity of CO2/N2 and CO2/H2O at a temperature of 333 K and a pressure of 4 atm have been found to be equal to about 20.23 and 1.85, respectively. We also observed that the bilayer graphtriyne membrane has high CO2 and H2O permeances compared to N2 with permeance selectivity ranging from 4.8 to 6.5. Moreover, we found that permeation and adsorption depend on the applied temperature; at high temperatures permeation and adsorption tend to decrease for all molecules.

physics.chem-ph↗

arXiv2020

Spherical and hyperspherical harmonics representation of van der Waals aggregates

The representation of the potential energy surfaces of atom molecule or molecular dimers interactions should account faithfully for the symmetry properties of the systems, preserving at the same time a compact analytical form. To this aim, the choice of a proper set of coordinates is a necessary precondition. Here we illustrate a description in terms of hyperspherical coordinates and the expansion of the intermolecular interaction energy in terms of hypersherical harmonics, as a general method for building potential energy surfaces suitable for molecular dynamics simulations of van der Waals aggregates. Examples for the prototypical case diatomic molecule diatomic molecule interactions are shown.

physics.chem-ph↗

arXiv2017

The spherical-harmonics representation for the interaction between diatomic molecules: the general case and applications to CO-CO and CO-HF

The spherical-harmonics expansion is a mathematically rigorous procedure and a powerful tool for the representation of potential energy surfaces of interacting molecular systems, determining their spectroscopic and dynamical properties, specifically in van der Waals clusters, with applications also to classical and quantum molecular dynamics simulations. The technique consists in the construction (by ab initio or semiempirical methods) of the expanded potential interaction up to terms that provide the generation of a number of leading configurations sufficient to account for faithful geometrical representations. This paper reports the full general description of the method of the spherical-harmonics expansion as applied to diatomic-molecule-diatomic-molecule systems of increasing complexity: the presentation of the mathematical background is given for providing both the application to the prototypical cases considered previously (O2-O2, N2-N2, and N2-O2 systems) and the generalization to: (i) the CO-CO system, where a characteristic feature is the lower symmetry order with respect to the cases studied before, requiring a larger number of expansion terms necessary to adequately represent the potential energy surface; and (ii) the CO-HF system, which exhibits the lowest order of symmetry among this class of aggregates and therefore the highest number of leading configurations.

physics.chem-ph↗

arXiv2017

Interactions of Hydrogen Molecules with Halogen-Containing Diatomics from Ab Initio Calculations: Spherical-Harmonics Representation and Characterization of the Intermolecular Potentials

For the prototypical diatomic-molecule - diatomic molecule interactions H2-HX and H2-X2, where X = F, Cl, Br, quantum-chemical ab initio calculations are carried out on grids of the configuration space, which permit a spherical-harmonics representation of the potential energy surfaces (PESs). Dimer geometries are considered for sets of representative leading configurations, and the PESs are analyzed in terms of isotropic and anisotropic contributions. The leading configurations are individuated by selecting a minimal set of mutual orientations of molecules needed to build the spherical-harmonic expansion on geometrical and symmetry grounds. The terms of the PESs corresponding to repulsive and bonding dimer geometries and the averaged isotropic term, for each pair of interacting molecules, are compared with representations in terms of a potential function proposed by Pirani et al. (see Chem. Phys. Lett. 2004, 394, 37-44 and references therein). Connections of the involved parameters with molecular properties provide insight into the nature of the interactions.

physics.chem-ph↗

arXiv2017

Hexapole-Oriented Asymmetric-Top Molecules and Their Stereodirectional Photodissociation Dynamics

Molecular orientation is a fundamental requisite in the study of stereodirected dynamics of collisional and photoinitiated processes. In this last decade, variable hexapolar electric filters have been developed and employed for the rotational-state selection and the alignment of molecules of increasing complexity, for which main difficulties are their mass, their low symmetry and the very dense rotational manifold. In this work, for the first time, a complex molecule such as 2-bromobutane, an asymmetric-top containing a heavy atom (the bromine), has been successfully oriented by a weak homogeneous field placed downstream the hexapolar filter. Efficiency of the orientation has been characterized experimentally, by combining time-of-flight measurements and a slice-ion-imaging detection technique. The application is described to the photodissociation dynamics of the oriented 2-bromobutane, which was carried out at a laser wavelength of 234 nm, corresponding to the breaking of the C Br bond. The Br photofragment is produced in both the ground Br (2P3/2) and the excited Br (2P1/2) electronic states and both channels are studied by the slice imaging technique, revealing new features in the velocity and angular distributions with respect to previous investigations on non-oriented molecules.

physics.chem-ph↗

arXiv2017

Stereodirectional Photodynamics: Experimental and Theoretical Perspectives

Hexapole oriented 2-bromobutane is photodissociated and detected by a slice ion imaging technique at 234 nm. The laser wavelength corresponds to the C Br bond breaking with emission of a Br atom fragment in two accessible fine structure states: the ground state Br and the excited state Br*, both observable separately by resonance enhanced multiphoton ionization (REMPI). Orientation is evaluated by time of flight measurements combined with slice ion imaging.

physics.chem-ph↗

arXiv2017

Rotational state-selection and alignment of chiral molecules by electrostatic hexapoles

Electrostatic hexapoles are revealed as a powerful tool in the rotational state-selection and alignment of molecules to be utilized in beam experiments on collisional and photoinitiated processes. In the paper, we report results on the application of the hexapolar technique on the recently studied chiral molecules propylene oxide, 2-butanol and 2bromobutane, to be investigated in selective photodissociation and enantiomeric discrimination.

physics.chem-ph↗

arXiv2013

Statistics of energy partitions for many-particle systems in arbitrary dimension

In some previous articles, we defined several partitions of the total kinetic energy T of a system of N classical particles in the d-dimensional Euclidean space into components corresponding to various modes of motion. In the present paper, we propose formulas for the mean values of these components in the normalization T=1 (for any d and N) under the assumption that the masses of all the particles are equal. These formulas are proven at the "physical level" of rigor and numerically confirmed for planar systems (d=2) at N from 3 through 100. The case where the masses of the particles are chosen at random is also considered. The paper complements our article of 2008 [Russian J Phys Chem B, 2(6), 947-963] where similar numerical experiments were carried out for spatial systems (d=3) at N from 3 through 100.

math-ph↗