Andrea Lombardi

Quantum Chemistry of C3H6O Molecules: Structure and Stability, Isomerization Pathways, and Chirality Changing Mechanisms

Electronic structure calculations were carried out to study the various isomers of formula C(3)H(6)O, as a part of our current quantum chemical and dynamical approaches to intra- and intermolecular kinetics for the C(n)H(2n)O (n = 1, 2, 3) molecules. The usefulness of the GRRM (global reaction route mapping) program developed by Ohno and Maeda in predicting the structure of all isomers and of the transition states connecting them is fully exploited. All the isomers are identified as local minima on the MP2/CC-PVDZ potential energy surface. Acetone is the most stable isomer. In increasing order of stability the others are propanal, 2-propenol, 1-propenol, allyl alcohol, methyl vinyl ether, cyclopropanol, propylene oxide, and oxetane. Various isomerization paths connecting them are identified. All the transition states are fully characterized using intrinsic reaction coordinate calculations. The isomerization reactions may proceed through a single step or involve an intermediate species which is either a carbene or a diradical. Special attention is devoted to propylene oxide, a favorite molecule in current photochemical and stereodynamical studies because of its chiral nature. It is a rigid molecule, and chirality switching is found to be supported by its isomers. Two different chirality switching mechanisms which are assisted by propanal and allyl alcohol are presented.

A quantum chemical study of H2S2: Intramolecular torsional mode and intermolecular interactions with rare gases

The structural and energetic properties of the H(2)S(2) molecule have been studied using density functional theory, second-order Moller-Plesset method, and coupled cluster theory with several basis sets. In order to extend previous work on intra- and intermolecular dynamics of the chirality changing modes for H(2)O(2) and its derivatives, our focus has been on the torsion around the S-S bond, along with an extensive characterization of the intermolecular potentials of H(2)S(2) with the rare gases (He, Ne, Ar, and Kr). Use is made of previously defined coordinates and expansion formulas for the potentials which allow for a faithful representation of geometrical and symmetry properties of these systems that involve the interaction of an atom with a floppy molecule. The potential energy surfaces obtained in this work are useful for classical and quantum mechanical simulations of molecular collisions responsible for chirality changing processes of possible interest in the modeling of prebiotic phenomena.

A full dimensional grid empowered simulation of the CO2 + CO2 processes

A recently introduced bond–bond formulation of the intermolecular interaction has been extended to six‐atom systems to the end of assembling a new potential energy surface (PES) and has been incorporated into a grid empowered simulator able to handle the modeling of the CO2 + CO2 processes. The proposed PES is full dimensional and accounts for the dependence of the intermolecular interaction on some basic physical properties of the colliding partners, including modulations induced by the monomer deformation. The used analytical formulation of the interaction involves a limited number of parameters, each having a clear physical meaning. Guess values for these parameters can also be obtained from analytical correlation formulae. Such estimates can then be fine tuned by exploiting experimental and theoretical information. The resulting PES well describes stretched and bent asymptotic CO2 monomers as well as the CO2–CO2 interaction in the most and less stable configurations. On this potential massive quasiclassical elastic and inelastic detailed scattering trajectories have been integrated, by exploiting the innovative computational technologies of the grid. The efficiency of the approach used and the reliability of the estimates of the dynamical properties obtained in this way is such that we can now plan a systematic evaluation of the state specific rate coefficient matrix elements needed for space craft reentry modeling. Here, we present probabilities and cross sections useful to rationalize some typical mechanisms characterizing the vibrational transitions of the CO2 + CO2 system on the flexible monomer proposed PES. On such PES, the key dynamical outcomes are: (a) there is a strong energy interchange between symmetric stretching of the reactants and bending of the products (and viceversa) while asymmetric stretching is strongly adiabatic (b) reactant energy is more efficiently allocated (with respect to the rigid monomers PES) as product vibration when reactant stretching modes are excited while the contrary is true when the reactant bending mode is excited.

The origin of chiral discrimination: supersonic molecular beam experiments and molecular dynamics simulations of collisional mechanisms

The target of the present paper is the study of chirality effects in molecular dynamics from both a theoretical and an experimental point of view under the hypothesis of a molecular dynamics mechanism as the origin of chiral discrimination. This is a fundamental problem per se, and of possible relevance for the problem of the intriguing homochirality in Nature, so far lacking satisfactory explanations. We outline the steps that have been taken so far toward this direction, motivated by various experimental studies of supersonic molecular beams carried out in this laboratory, such as the detection of aligned oxygen in gaseous streams and further evidence on nitrogen, benzene and various hydrocarbons, showing the insurgence of molecular orientation in the dynamics of molecules in flows and in molecular collisions. Chiral effects are theoretically demonstrated to show up in the differential scattering of oriented molecules, also when impinging on surfaces. Focus on possible mechanisms for chiral bio-stereochemistry of oriented reactants may be of pre-biotical interest, for example when flowing in atmospheres of rotating bodies, specifically the planet Earth, as well as in vortex motions of celestial objects. Molecular dynamics simulations and experimental verifications of the hypothesis are reviewed and objectives of future research activity proposed.

Phase-space invariants for aggregates of particles: Hyperangular momenta and partitions of the classical kinetic energy

Rigorous definitions are presented for the kinematic angular momentum K of a system of classical particles (a concept dual to the conventional angular momentum J), the angular momentum L(xi) associated with the moments of inertia, and the contributions to the total kinetic energy of the system from various modes of the motion of the particles. Some key properties of these quantities are described-in particular, their invariance under any orthogonal coordinate transformation and the inequalities they are subject to. The main mathematical tool exploited is the singular value decomposition of rectangular matrices and its differentiation with respect to a parameter. The quantities introduced employ as ingredients particle coordinates and momenta, commonly available in classical trajectory studies of chemical reactions and in molecular dynamics simulations, and thus are of prospective use as sensitive and immediately calculated indicators of phase transitions, isomerizations, onsets of chaotic behavior, and other dynamical critical phenomena in classical microaggregates, such as nanoscale clusters.

Isomerization dynamics and thermodynamics of ionic argon clusters

The dynamics and thermodynamics of small Ar(n) (+) clusters, n=3, 6, and 9, are investigated using molecular dynamics (MD) and exchange Monte Carlo (MC) simulations. A diatomic-in-molecule Hamiltonian provides an accurate model for the electronic ground state potential energy surface. The microcanonical caloric curves calculated from MD and MC methods are shown to agree with each other, provided that the rigorous conservation of angular momentum is accounted for in the phase space density of the MC simulations. The previously proposed projective partition of the kinetic energy is used to assist MD simulations in interpreting the cluster dynamics in terms of inertial, internal, and external modes. The thermal behavior is correlated with the nature of the charged core in the cluster by computing a dedicated charge localization order parameter. We also perform systematic quenches to establish a connection with the various isomers. We find that the Ar(3) (+) cluster is very stable in its linear ground state geometry up to about 300 K, and then isomerizes to a T-shaped isomer in which a quasineutral atom lies around a charged dimer. In Ar(6) (+) and Ar(9) (+), the covalent trimer core is solvated by neutral atoms, and the weakly bound solvent shell melts at much lower energies, occasionally leading to a tetramer or pentamer core with weakly charged extremities. At high energies the core itself becomes metastable and the cluster transforms into Ar(2) (+) solvated by a fluid of neutral argon atoms.

Collective hyperspherical coordinates for polyatomic molecules and clusters

For n-body dynamics an analysis is made of the properties of configuration space within a symmetric hyperspherical framework. Coordinates are conveniently broken up into spatial (or external) rotations, kinematic invariants (related to the inertia moments) and kinematic (or internal) rotations. Their usefulness is demonstrated for the study of constrained intramolecular motions and of concerted reactions and for collective modes of polyatomic molecules and clusters. For a fixed hyperradius, which is a measure of total inertia, the space of kinematic invariants is the surface of a right spherical triangle that leads to the tetrahedral (for n = 4) or octahedral (for n ≥ 5) tessellation of the sphere. Alternative parametrizations are discussed, including the proper one to deal with the umbrella inversion motion of ammonia.

Modeling of energy transfer from vibrationally excited CO2 molecules: cross sections and probabilities for kinetic modeling of atmospheres, flows, and plasmas.

We present extended applications of an established theoretical and computational machinery suitable for the study of the dynamics of CO2+CO2 collisions, focusing on vibrational energy exchange, considered over a wide range of energies and rotational temperatures. Calculations are based on quasi-classical trajectories on a potential energy function (a critical component of dynamics simulations), tailored to accurately describe the intermolecular interactions, modeled by the recently proposed bond-bond semiempirical formulation that allows the colliding molecules to be stretchable, rather than frozen at their equilibrium geometry. In a previous work, the same potential energy surface has been used to show that modifications in the geometry (and in physical properties such as polarizability and charge distribution) of the colliding partners affect the intermolecular interaction and determine the features of the energy exchange, to a large extent driven by long-range forces. As initial partitioning of the energy among the molecular degrees of freedom, we consider the excitation of the vibrational bending mode, assuming an initial rotational distribution and a rotational temperature. The role of the vibrational angular momentum is also carefully assessed. Results are obtained by portable implementations of this approach in a Grid-computing framework and on high performance platforms. Cross sections are basic ingredients to obtain rate constants of use in advanced state-to-state kinetic models, under equilibrium or nonequilibrium conditions, and this approach is suitable for gas dynamics applications to plasmas and modeling of hypersonic flows.

Modeling the intermolecular interactions and characterization of the dynamics of collisional autoionization processes

The autoionization dynamics of triatomic molecules induced by He*(23,1S1,0) and Ne*(3P2,0) collisions has been discussed. The systems are analyzed by using an optical potential model within a semiclassical approach. The real part of the potential is formulated applying a semiempirical method, while the imaginary part has been used in the fitting procedure of the data adjusting its pre-exponential factor. The good agreement between calculations and experiment confirms the attractive nature of the potential energy surface driving the He* and Ne*-H2O dynamics.

Aligned molecules: chirality discrimination in photodissociation and in molecular dynamics

Emergence of biochemical homochirality is an intriguing topic, and none of the proposed scenarios has encountered a unanimous consensus. Candidates for naturally occurring processes, which may originate chiral selection, involve interaction of matter with light and molecular collisions. We performed and report here: (1) simulations of photodissociation of an oriented chiral molecule by linearly polarized (achiral) light observing that the angular distribution of the photofragments is characteristic of each enantiomer and both differ from the racemic mixture; and (2) molecular dynamics simulations (elastic collisions of oriented hydrogen peroxide, one of the most simple chiral molecules, with Ne atom) demonstrating that the scattering and the recoil angles are specific of the enantiomeric form. The efficacy of non-chiral light (in the case of photodissociation) and of non-chiral projectile (in the case of collisions) is due to the molecular orientation, as an essential requirement to observe chiral effects. The results of the simulations, that we report in this article, provide the background for the perspective realization of experiments which go beyond the well-documented ones involving interaction of circularly polarized laser (chiral light) with the matter, specifically by making use of non-chiral, i.e. linearly polarized or unpolarized light sources, and also by obtaining chiral effects with no use at all of light, but simply inducing them by molecular collisions. The case of vortices is discussed in a companion paper.