Syntheses, pi-stacking interactions and base-pairings of uracil pyridinium salts and uracilyl betaines with nucleobases

The rise and fall of adenine clusters in the gas phase: a glimpse into crystal growth and nucleation

The emergence of a crystal nucleus from disordered states is a critical and challenging aspect of the crystallization process, primarily due to the extremely short length and timescales involved. Methods such as liquid-cell or low-dose focal-series transmission electron microscopy (TEM) are often employed to probe these events. In this study, we demonstrate that ion mobility spectrometry-mass spectrometry (IMS-MS) offers a complementary and insightful perspective on the nucleation process by examining the sizes and shapes of small clusters, specifically those ranging from n = 2 to 40. Our findings reveal the significant role of sulfate ions in the growth of adeninediium sulfate clusters, which are the precursors to the formation of single crystals. Specifically, sulfate ions stabilize adenine clusters at the 1:1 ratio. In contrast, guanine sulfate forms smaller clusters with varied ratios, which become stable as they approach the 1:2 ratio. The nucleation size is predicted to be between n = 8 and 14, correlating well with the unit cell dimensions of adenine crystals. This correlation suggests that IMS-MS can identify critical nucleation sizes and provide valuable structural information consistent with established crystallographic data. We also discuss the strengths and limitations of IMS-MS in this context. IMS-MS offers rapid and robust experimental protocols, making it a valuable tool for studying the effects of various additives on the assembly of small molecules. Additionally, it aids in elucidating nucleation processes and the growth of different crystal polymorphs.

Orbital-based insights into parallel-displaced and twisted conformations in π-π interactions

Dispersion and electrostatics are known to stabilize π-π interactions, but the preference for parallel-displaced (PD) and/or twisted (TW) over sandwiched (S) conformations is not well understood. Orbital interactions are generally believed to play little to no role in π-stacking. However, orbital analysis of the dimers of benzene, pyridine, cytosine and several polyaromatic hydrocarbons demonstrates that PD and/or TW structures convert one or more π-type dimer MOs with out-of-phase or antibonding inter-ring character at the S stack to in-phase or bonding in the PD/TW stack. This change in dimer MO character can be described in terms of a qualitative stack bond order (SBO) defined as the difference between the number of occupied in-phase/bonding and out-of-phase/antibonding inter-ring π-type MOs. The concept of an SBO is introduced here in analogy to the bond order in molecular orbital theory. Thus, whereas the SBO of the S structure is zero, parallel displacement or twisting the stack results in a non-zero SBO and overall bonding character. The shift in bonding/antibonding character found at optimal PD/TW structures maximizes the inter-ring density, as measured by intermolecular Wiberg bond indices (WBIs). Values of WBIs calculated as a function of the parallel-displacement are found to correlate with the dispersion and other contributions to the π-π interaction energy determined by the highly accurate density-fitting DFT symmetry adapted perturbation theory (DF-DFT-SAPT) method. These DF-DFT-SAPT calculations also suggest that the dispersion and other contributions are maximized at the PD conformation rather than the S when conducted on a potential energy curve where the inter-ring distance is optimized at fixed slip distances. From these results of this study, we conclude that descriptions of the qualitative manner in which orbitals interact within π-stacking interactions can supplement high-level calculations of the interaction energy and provide an intuitive tool for applications to crystal design, molecular recognition and other fields where non-covalent interactions are important.