CO2 packing polymorphism under confinement in cylindrical nanopores

We investigate the effect of cylindrical nano-confinement on the phase behaviour of a rigid model of carbon dioxide using both molecular dynamics and well tempered metadynamics. To this aim we study a simplified pore model across a parameter space comprising pore diameter, CO2-pore wall potential and CO2 density. In order to systematically identify ordering events within the pore model we devise a generally applicable approach based on the analysis of the distribution of intermolecular orientations. Our simulations suggest that, while confinement in nano-pores inhibits the formation of known crystal structures, it induces a remarkable variety of ordered packings unrelated to their bulk counterparts, and favours the establishment of short range order in the fluid phase. We summarise our findings by proposing a qualitative phase diagram for this model

CO2 packing polymorphism under pressure: mechanism and thermodynamics of the I-III polymorphic transition

In this work we describe the thermodynamics and mechanism of CO$_2$ polymorphic transitions under pressure from form I to form III combining standard molecular dynamics, well-tempered metadynamics and committor analysis. We find that the phase transformation takes place through a concerted rearrangement of CO$_2$ molecules, which unfolds via an anisotropic expansion of the CO$_2$ supercell. Furthermore, at high pressures we find that defected form I configurations are thermodynamically more stable with respect to form I without structural defects. Our computational approach shows the capability of simultaneously providing an extensive sampling of the configurational space, estimates of the thermodynamic stability and a suitable description of a complex, collective polymorphic transition mechanism

A molecular modelling journey from packing to conformational polymorphism

The efficient and reproducible crystallisation of a polymorph showing the desired properties and functionalities is crucial in a variety of fields, such as the pharmaceutical sector. Characterising thermodynamics and mechanisms of polymorphic transitions at the molecular level is thus a key step towards developing a rational design of crystallisation processes and products. Despite its relevance, a systematic computational analysis of polymorphism and polymorphic transitions still represents a major challenge. In this thesis, metadynamics is employed in combination with state-of-the-art techniques, such as committor analysis and Markov State Models, to provide insight into polymorphism in molecular systems. The first part of the work focuses on packing polymorphism. The investigation of the transition between phases I and III in bulk carbon dioxide aims at testing a set of computational tools able to characterise in detail thermodynamics and mechanism of polymorphic transitions. This set-up is then applied and further developed for the study of CO2 confined in cylindrical nanopores, unveiling a complex landscape of ordered structures, unaccessible in unconfined conditions. Next, the serendipitous and irreproducible discovery of a new polymorph of succinic acid, γ, provides a challenging context to tackle the study of conformational polymorphism. Form γ presents folded conformers in its unit cell, while the other known polymorphs show planar molecules. From molecular dynamics and metadynamics, γ appears labile and metastable, a characteristic that might hinder its crystallisation. The study of the conformational behaviour of succinic acid in water reveals fast interconversions within a network of nine conformers, both folded and planar, among which the folded conformation observed in γ is the most thermodynamically stable. The high flexibility of this molecule is relevant in determining the nucleation mechanism. Simulations of supersaturated solutions and of crystal seeds dissolution suggest that nucleation cannot be classical, but it is rather likely to be a multi-step process

Building Maps in Collective Variable Space

Enhanced sampling techniques such as umbrella sampling and metadynamics are now routinely used to provide information on how the thermodynamic potential, or free energy, depends on a small number of collective variables. The free energy surfaces that one extracts by using these techniques provide a simplified or coarse-grained representation of the configurational ensemble. In this work we discuss how auxiliary variables can be mapped in collective variable (CV) space and how the dependence of the average value of a function of the atomic coordinates on the value of a small number of CVs can thus be visualised. We show that these maps allow one to analyse both the physics of the molecular system under investigation and the quality of the reduced representation of the system that is encoded in a set of CVs. We apply this approach to analyse the degeneracy of CVs and to compute entropy and enthalpy surfaces in CV space both for conformational transitions in alanine dipeptide and for phase transitions in carbon dioxide molecular crystals under pressure.Comment: 13 pages, 8 figure

Reaction Dynamics of O(3P) + Propyne: II. Primary Products, Branching Ratios, and Role of Intersystem Crossing from Ab Initio Coupled Triplet/Singlet Potential Energy Surfaces and Statistical Calculations

The mechanism of the O(3P) + CH3CCH reaction was investigated using a combined experimental/theoretical approach. Experimentally the reaction dynamics was studied using crossed molecular beams (CMB) with mass-spectrometric detection and time-of-flight analysis at 9.2 kcal/mol collision energy. Theoretically master equation (ME) simulations were performed on a potential energy surface (PES) determined using high-level ab initio electronic structure calculations. In this paper (II) the theoretical results are described and compared with experiments, while in paper (I) are reported and discussed the results of the experimental study. The PES was investigated by determining structures and vibrational frequencies of wells and transition states at the CASPT2/aug-cc-pVTZ level using a minimal active space. Energies were then determined at the CASPT2 level increasing systematically the active space and at the CCSD(T) level extrapolating to the complete basis set limit. Two separate portions of the triplet PES were investigated, as O(3P) can add either on the terminal or the central carbon of the unsaturated propyne bond. Minimum energy crossing points (MECPs) between the triplet and singlet PESs were searched at the CASPT2 level. The calculated spin-orbit coupling constants between the T1 and S0 electronic surfaces were ∼25 cm-1 for both PESs. The portions of the singlet PES that can be accessed from the MECPs were investigated at the same level of theory. The system reactivity was predicted integrating stochastically the one-dimensional ME using Rice-Ramsperger-Kassel-Marcus theory to determine rate constants on the full T1/S0 PESs, accounting explicitly for intersystem crossing (ISC) using the Landau-Zener model. The computational results are compared both with the branching ratios (BRs) determined experimentally in the companion paper (I) and with those estimated in a recent kinetic study at 298 K. The ME results allow to interpret the main system reactivity: CH3CCO + H and CH3 + HCCO are the major channels active on the triplet PES and are formed from the wells accessed after O addition to the terminal and central C, respectively; 1CH3CH + CO and C2H3 + HCO are the major channels active on the singlet PES and are formed from the methylketene and acrolein wells after ISC. However, also a large number of minor channels (∼15) are active, so that the system reactivity is quite complicated. The comparison between computational and experimental BRs is quite good for the kinetic study, while some discrepancy with the CMB estimations suggests that dynamic non-ergodic effects may influence the system reactivity. Channel specific rate constants are calculated in the 300-2250 K and 1-30 bar temperature and pressure ranges. It is found that as the temperature increases the H abstraction reaction, whose contribution is negligible in the experimental conditions, increases in relevance, and the extent of ISC decreases from ∼80% at 300 K to less than 2% at 2250 K

Reaction Dynamics of O(³P) + Propyne: II. Primary Products, Branching Ratios, and Role of Intersystem Crossing from Ab Initio Coupled Triplet/Singlet Potential Energy Surfaces and Statistical Calculations

The mechanism of the O­(³P) + CH₃CCH reaction was investigated using a combined experimental/theoretical approach. Experimentally the reaction dynamics was studied using crossed molecular beams (CMB) with mass-spectrometric detection and time-of-flight analysis at 9.2 kcal/mol collision energy. Theoretically master equation (ME) simulations were performed on a potential energy surface (PES) determined using high-level ab initio electronic structure calculations. In this paper (II) the theoretical results are described and compared with experiments, while in paper (I) are reported and discussed the results of the experimental study. The PES was investigated by determining structures and vibrational frequencies of wells and transition states at the CASPT2/aug-cc-pVTZ level using a minimal active space. Energies were then determined at the CASPT2 level increasing systematically the active space and at the CCSD­(T) level extrapolating to the complete basis set limit. Two separate portions of the triplet PES were investigated, as O­(³P) can add either on the terminal or the central carbon of the unsaturated propyne bond. Minimum energy crossing points (MECPs) between the triplet and singlet PESs were searched at the CASPT2 level. The calculated spin–orbit coupling constants between the T1 and S0 electronic surfaces were ∼25 cm^–1 for both PESs. The portions of the singlet PES that can be accessed from the MECPs were investigated at the same level of theory. The system reactivity was predicted integrating stochastically the one-dimensional ME using Rice–Ramsperger–Kassel–Marcus theory to determine rate constants on the full T1/S0 PESs, accounting explicitly for intersystem crossing (ISC) using the Landau–Zener model. The computational results are compared both with the branching ratios (BRs) determined experimentally in the companion paper (I) and with those estimated in a recent kinetic study at 298 K. The ME results allow to interpret the main system reactivity: CH₃CCO + H and CH₃ + HCCO are the major channels active on the triplet PES and are formed from the wells accessed after O addition to the terminal and central C, respectively; ¹CH₃CH + CO and C₂H₃ + HCO are the major channels active on the singlet PES and are formed from the methylketene and acrolein wells after ISC. However, also a large number of minor channels (∼15) are active, so that the system reactivity is quite complicated. The comparison between computational and experimental BRs is quite good for the kinetic study, while some discrepancy with the CMB estimations suggests that dynamic non-ergodic effects may influence the system reactivity. Channel specific rate constants are calculated in the 300–2250 K and 1–30 bar temperature and pressure ranges. It is found that as the temperature increases the H abstraction reaction, whose contribution is negligible in the experimental conditions, increases in relevance, and the extent of ISC decreases from ∼80% at 300 K to less than 2% at 2250 K

Isomer-Specific Chemistry in the Propyne and Allene Reactions with Oxygen Atoms: CH3CH + CO versus CH2CH2 + CO Products

reserved9We report direct experimental and theoretical evidence that, under single-collision conditions, the dominant product channels of the O(3P) + propyne and O(3P) + allene isomeric reactions lead in both cases to CO formation, but the coproducts are singlet ethylidene (1CH3CH) and singlet ethylene (CH2CH2), respectively. These data, which settle a long-standing issue on whether ethylidene is actually formed in the O(3P) + propyne reaction, suggest that formation of CO + alkylidene biradicals may be a common mechanism in O(3P) + alkyne reactions, in contrast to formation of CO + alkene molecular products in the corresponding isomeric O(3P) + diene reactions, either in combustion or other gaseous environments. These findings are of fundamental relevance and may have implications for improved combustion models. Moreover, we predict that the so far neglected 1CH3CH + CO channel is among the main reaction routes also when the C3H4O singlet potential energy surface is accessed from the OH + C3H3 (propargyl) entrance channel, which are radical species playing a key role in many combustion systems.Vanuzzo, Gianmarco; Balucani, Nadia; Leonori, Francesca; Stranges, Domenico; Falcinelli, Stefano; Bergeat, Astrid; Casavecchia, Piergiorgio; Gimondi, Ilaria; Cavallotti, CarloVanuzzo, Gianmarco; Balucani, Nadia; Leonori, Francesca; Stranges, Domenico; Falcinelli, Stefano; Bergeat, Astrid; Casavecchia, Piergiorgio; Gimondi, Ilaria; Cavallotti, CARLO ALESSANDR