Dynamic simulation of liquid molecular nanoclusters: structure, stability and quantification of internal (pseudo)symmetries

The atom\u2013atom intermolecular force field AA-CLP is applied to the molecular dynamics simulation of liquid nanoclusters of benzene, chloroform, methanol and pyridine. Bulk liquids are also simulated for validation and comparison with experimental data. The applied software has been produced de novo to deal with the unusual analytical form of the intermolecular potential, and it includes some novel features for the control of net rotational momenta in isolated systems. The nanoclusters have been studied as a function of size (150\u20131000 molecules) in relation to cohesion energies, rotational correlation, self-diffusion coefficients, and evaporation rates. Internal structure has been studied with traditional radial distribution functions, plus diagrams of the distribution of intermolecular vectors for flat compounds. In addition, a new algorithm for the quantification of pseudo- or near-symmetries between molecules in aggregates of any structure has been developed and tested, with reference to the inversion, mirror plane and rotation axis symmetries of organic crystals, with possible importance in the investigation of crystallization processes. The results confirm the reliability of the AA-CLP formulation for molecular dynamics simulation and throw some light on relationships between cluster and bulk properties. The computer codes are available for open-source download to ensure full reproducibility of all results

CLPdyn: a cheap and reliable tool for molecular dynamics studies of organic molecules in condensed phase

We present CLPdyn, a freely available code intended to perform Molecular Dynamics simulations of organic molecules in condensed phase.[1\u20133] CLPdyn can handle both continuous phases (liquids, crystals) and finite-size clusters (liquid droplets, nanoparticles), and exploits the thoroughly tested Coulomb-London-Pauli atom-atom intermolecular potential[4,5]. The implementation relies on standard MD algebra, but also includes new algorithms, specifically designed to deal with isolated clusters, to (i) suppress net overall translational and rotational momenta, (ii) handle the evaporation of molecules from the cluster surface, and (iii) measure the amount of residual symmetry from the number and kind of isometries present in the cluster. Application to organic solvents (benzene, chloroform, methanol and pyridine) [2] and crystals spanning very different intermolecular recognition patterns (maleic/succinic anhydrides, alanine/glutamic acid, methylurea, 1,4-cyclohexadiene and methyl-2-amino-5-hydroxybenzoate) [3], shows that CLPdyn reliably reproduces macroscopic thermodynamic quantities, and highlights the effect of the relative strengths of intermolecular forces on rotational correlation times, self-diffusion coefficients and pair distribution functions. Possible applications of CLPdyn to the molecular\u2013level study of non\u2013equilibrium solution chemistry, including the early stages of crystal nuclei formation, are also discussed. [1] A. Gavezzotti, CLPdyn, Monte Carlo and Molecular Dynamics modules, Description and user manual, www.angelogavezzotti.it (2018). [2] A. Gavezzotti, L. Lo Presti, New J. Chem., 2019,43, 2077-2084. [3] A. Gavezzotti, L. Lo Presti, in preparation [4] A. Gavezzotti, New J. Chem. 2011, 35, 1360\u20131368. [5] A. Gavezzotti and L. Lo Presti, Crystal Growth Des. 2016, 16, 2952\u20132962

The "sceptical chymist" : intermolecular doubts and paradoxes

Physico-chem. doubts and paradoxes abound in the description of forces and in the mol. simulation of the cryst. state, as they did in Boyle's times about the inner structure of matter. Solid-state structuring and bonding are still characterized in sometimes doubtful, sometimes paradoxical, and sometimes distorted terminologies. Phase transitions are mostly considered as just relationships between the two termini, without an operational understanding of the in-between transition mechanisms. Drawing from personal experience and recent computational results, this highlight provides a few answers, many caveats, and some suggestions for a better handling of these tortuous matters

The TACO Puzzle: A Phase-Transition Mystery Revisited

The organic salt (5-methyl-1-thia-5-azacyclo-octane-1-oxide) perchlorate (TACO) is known to undergo a single-crystal-to-single-crystal phase transition in the 276-298 K T range without a change in the external shape of the sample. Despite extensive computational and experimental investigations, no safe conclusions about the transition mechanism could be drawn till now. The two packing patterns are very similar, and symmetry is conserved, apart from an interchange of cell axes from P21/c (\u3b1-TACO, low-T) to P21/a (\u3b2-TACO, high-T). Yet, the phase transition implies a significant conformational rearrangement, coupled with 3c180\ub0-wide rotations, of 1/2 of the cations, in conjunction with reorientation of the anions. Here, we analyze the crystal packing of the two phases in terms of pairwise molecule-molecule interaction energies, as derived from the PIXEL approach. Rigid-body molecular reorientations are simulated by solid-state Monte Carlo calculations, while the likelihood of conformational rearrangements is estimated through gas-phase density functional theory M06/6-311G(p,d) simulations. We demonstrate that rotational motion of the cations is not hampered by substantial energetic barriers, while the ring flip can be described as a two-step process with a main kinetic barrier of 3c45 kJ\ub7mol-1, which might explain the metastable behavior of the \u3b2 phase at low T. A possible mechanism of the phase transition is proposed, accounting for the present computational evidences in the context of the former experimental findings

Two-component organic crystals without hydrogen bonding: structure and intermolecular interactions in bimolecular stacking

A survey of crystal structures including two organic compounds unable to form hydrogen bonding has been carried out using the Cambridge Structural Database. Such systems are common and numerous. Association modes mostly include stacking of flat systems, one of them usually being an aromatic hydrocarbon. \u201cAlternate-ladder\u201d (AL) and \u201cslanted column\u201d (SC) motifs occur most frequently; AL is somewhat prevalent in fluoroarene and pyromellitic dianhydride cocrystals, whereas SC occurs preferentially, but not exclusively, with quinones, nitrobenzene, TCNB and TCNQ coformers. Segregation of A and B chemical units in separate columns is very seldom observed, while A efB is the energetically dominating pair in a vast majority of the cases. A stable network of stacked A efB units seems to be a strict requirement for observing cocrystallization, even more than an overall higher stability of the cocrystal with respect to its coformers. This highlights the central role of kinetic factors in determining the drive to stacking heterorecognition. Energy dissection using the PIXEL scheme shows that dispersion energies play a dominant but not exclusive role. The interaction between flat organic systems is found to be a viable synthetic approach for cocrystallization, on the same footing as the more popular O\u2013H efO, O\u2013H efN and N\u2013H efO hydrogen bonding. Some practical suggestions for the choice of the best coformers are provided

A quantitative measure of halogen bond activation in cocrystallization

A theoretical investigation of bond lengths and bond energies for several kinds of halogen bonding interactions is carried out using the PIXEL method. The effect of different kinds of activating agents, fluoro-, nitro-, ethynyl substitution and combinations thereof, is assessed quantitatively, and is found to be fully consistent with the results of literature screenings of the corresponding strengths, as judged by the ease of formation of cocrystals. In the best combination of activators the halogen bond is comparable or superior to a strong O-HO hydrogen bond in what concerns stabilization energies and stretching force constants. At least with iodine acceptors, in our picture the halogen-bonding effect is a localized interaction arising from the detail of the electron distribution at the halogen atom, mainly of a Coulombic-polarization nature but with dispersion energies contributing significantly. Binding energies correlate with the electrostatic potential at the tip of the halogen and even with Mulliken population analysis atomic charges, providing easily accessible guidelines for crystal engineers. For one typical cocrystal structure the analysis of separate molecule-molecule energies reveals the nature of the packing forces and rank halogen bonding as the main influence, closely followed by coplanar stacking of coformers

Building Blocks of Crystal Engineering: A Large-Database Study of the Intermolecular Approach between C–H Donor Groups and O, N, Cl, or F Acceptors in Organic Crystals

The nature of CH\ub7\ub7\ub7X interactions in organic crystals, with X being an electronegative atom, has been the subject of extensive consideration with sometimes contradictory results and ensuing opinions. We perform statistical analysis on large databases of crystal structures retrieved from the Cambridge Structural Database. Crystals containing C\u2013H donors only are considered in conjunction with each of O, N, Cl, or F acceptors in turn. The analysis of Coulombic polarization and dispersion components reveals that the lattice energies of these crystals are largely dominated by dispersive interactions. The frequency of short H\ub7\ub7\ub7X contacts decreases through the series CHO > CHN > CHCl > CHF, being just sporadic in the latter. The presence of such contacts is positively correlated with the Coulombic contribution to molecule\u2013molecule interaction energies but do not generally determine the pair energy. Short CH\ub7\ub7\ub7O or CH\ub7\ub7\ub7N contacts are often relegated to weakly bound pairs; their minor energy contributions might be relevant for driving crystal packing of small molecules, where the contact energy is a substantial part of the lattice energy. In reproducible crystal engineering, and even more in crystal structure prediction, weak CH\ub7\ub7\ub7X contacts are seldom responsible for the whole picture, and the wider context of competing energies should be considered

Use of the PIXEL method to investigate gas adsorption in metal–organic frameworks

PIXEL has been used to perform calculations of adsorbate-adsorbent interaction energies between a range of metal–organic frameworks (MOFs) and simple guest molecules. Interactions have been calculated for adsorption between MOF-5 and Ar, H(2), and N(2); Zn(2)(BDC)(2)(TED) (BDC = 1,4-benzenedicarboxylic acid, TED = triethylenediamine) and H(2); and HKUST-1 and CO(2). The locations of the adsorption sites and the calculated energies, which show differences in the Coulombic or dispersion characteristic of the interaction, compare favourably to experimental data and literature energy values calculated using density functional theory