Ab initio periodic modelling of the vibrational spectra of molecular crystals: the case of uracil

Ab initio simulation of molecular crystal regrowth of paracetamol from solution

The morphology of molecular crystals depends strongly on both thermodynamic stability and the growth kinetics which are themselves dependent on the fine details of intermolecular interactions and challenging to model with ab initio methods. Here, the combination of density functional theory with the effective screen medium-reference interaction site model (DFT/ESM-RISM) is used to study the fast regrowth of a form I paracetamol crystal post-breakage, recently reported by [Bade et al., Mater. Horiz., 2023, 10, 1425-1430]. It is demonstrated that both the thermodynamic and the kinetic factors affecting regrowth are successfully captured by DFT/ESM-RISM with relatively low computational costs. With inclusion of all the externally observed facets, the morphology predicted from thermodynamic considerations alone is found to agree well with observation. Deviation from this morphology is predicated upon inclusion into the model of the fast-growing internal (010) plane, indicating the strong influence of kinetic effects on morphology. The paracetamol molecules at the surface are characterised by unsaturated hydrogen bonds; the resultant strong interaction with the solutes and the solvent significantly altering surface thermodynamics and the structure of the near-surface solvent. For example, the competition between ethanol and solvated paracetamol molecules for the formation of hydrogen bonds is found to reduce the growth rate due to steric hindrance. This effect becomes less prominent for the (010) surface, which presents no broken hydrogen bonds, resulting in a more uniform near-surface solvent structure that facilitates surface growth. As the first attempt to investigate the complicated solid-liquid interface of molecular crystals, this study broadens the applicability of DFT/ESM-RISM. The kinetic mechanisms underpinning the fast regrowth of form I paracetamol post-breakage are qualitatively elucidated, suggesting new strategies for efficient morphology control in molecular crystals.

Vapor phase detection of explosives by surface enhanced Raman scattering under ambient conditions with metal nanogap structures

Non-invasive and passive detection of explosives in the vapor phase is advantageous for military, counter-terrorism, and homeland security applications. Detection of explosives using SERS has been an active research topic. However, the vapor pressures of most explosives are low at room temperature, and consequently, the vapor phase detection by SERS is highly challenging without intentionally heating explosive powder to increase the vapor pressure. In this work, we report the rapid and sensitive detection of 2,4,6-trinitrotoluene (TNT) and 2,4-dinitrotoluene (2,4-DNT) in the vapor phase, using a gold nanogap (AuNG) SERS substrate. The AuNG SERS substrate was fabricated with electron beam evaporation, rapid thermal annealing, and wet etching. SERS measurements were carried out with an incident power as low as 0.56 mW at 785 nm. To prevent the condensation effect, the TNT and 2,4-DNT powders inside the cuvette were taken out before inserting the nanogap substrate. Our SERS results demonstrate the feasibility of the non-invasive detection of vapor phase explosives under ambient conditions.

Anisotropic Phonon Bands in H-Bonded Molecular Crystals: The Instructive Case of α-Quinacridone

Phonons play a crucial role in the thermodynamic and transport properties of solid materials. Nevertheless, rather little is known about phonons in organic semiconductors. Thus, we employ highly reliable quantum mechanical calculations for studying the phonons in the α-polymorph of quinacridone. This material is particularly interesting, as it has highly anisotropic properties with distinctly different bonding types (H-bonding, π-stacking, and dispersion interactions) in different spatial directions. By calculating the overlaps of modes in molecular quinacridone and the α-polymorph, we associate Γ-point phonons with molecular vibrations to get a first impression of the impact of the crystalline environment. The situation becomes considerably more complex when analyzing phonons in the entire 1st Brillouin zone, where, due to the low symmetry of α-quinacridone, a multitude of avoided band crossings occur. At these, the character of the phonon modes typically switches, as can be inferred from mode participation ratios and mode longitudinalities. Notably, avoided crossings are observed not only as a function of the length but also as a function of the direction of the phonon wave vector. Analyzing these avoided crossings reveals how it is possible that the highest frequency acoustic band is always the one with the largest longitudinality, although longitudinal phonons in different crystalline directions are characterized by fundamentally different molecular displacements. The multiple avoided crossings also give rise to a particularly complex angular dependence of the group velocities, but combining the insights from the various studied quantities still allows drawing general conclusions, e.g., on the relative energetics of longitudinal vs transverse deformations (i.e., compressions and expansions vs slips of neighboring molecules). They also reveal how phonon transport in α-quinacridone is impacted by the reinforcing H-bonds and by π-stacking interactions (resulting from a complex superposition of van der Waals, charge penetration, and exchange repulsion).

Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study

We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.

Cluster-model DFT simulations of the infrared spectra of triazine-based molecular crystals

A cluster-model approach is developed to simulate the IR spectra of triazine-based molecular crystals, and the distinct hydrogen-bonding environments of the crystallographically independent molecules can be clearly revealed.