Complexes of the `proton sponge' 1,8-bis(dimethylamino)naphthalene (DMAN). III. Structure of [DMANH]+.[pentachlorophenolate]−.[pentachlorophenol]2 at 100 K

Unraveling the Nature of Hydrogen Bonds of "Proton Sponges" Based on Car-Parrinello and Metadynamics Approaches

The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as "proton sponges". Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted "proton sponge" served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car-Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in "proton sponges" are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.

Continuous symmetry numbers and entropy

Traditionally, entropy changes are corrected for rotational permutability only if the molecule is perfectly rotationally symmetric. By this approach, only a small fraction of all known molecules must be evaluated in terms of symmetry numbers, while all other molecules are totally exempt of these considerations. A general approach which encompasses all molecules, symmetric or not, is proposed here. It is based on introducing the notion of continuity to symmetry numbers and on allowing noninteger values. In the first part of the account, we provide arguments as to why continuity is needed and what difficulties one may encounter by adopting the "black-or-white" approach to symmetry. In the second part, we provide a working methodology of how to evaluate the symmetry number content of any molecule, symmetric or not. Finally, in the third part, we demonstrate the implications of this approach on entropy issues involving melting points, Jahn-Teller distortions (of fullerene) upon ionization, molecular distortion due to overcrowdedness, permutability of isotopes, and the structure of proton sponges. It is shown that continuous symmetry numbers provide entropy values, which better agree with experimental observations, and that they are capable of identifying correlations between symmetry and physical/chemical measurables.

Crystal chemistry of tetraradial species. Part 8. Mix and match: cation geometry, ion packing, hydrogen bonding, and π–π interactions in cis-2,2′-bipyridinium(1+) and 1,10-phenanthrolinium(1+) tetraphenylborates — and what about proton sponges?

The crystal structures at −20 °C of cis-2,2′-bipyridinium(1+) (BPTB, P21/n, a = 9.249(3), b = 14.093(7), c = 20.285(3) Å, β = 92.86(2)°, Z = 4) and 1,10-phenanthrolinium(1+) (PTB, P21/c, a = 11.194(2), b = 13.837(3), c = 18.303(3) Å, β = 107.82(1)°, Z = 4) tetraphenylborates have been determined. Inasmuch as 1,10-phenanthroline is an aromatically bridged cis-2,2′-bipyridine, monoprotonation results, in both systems, in the formation of an intra-cation N—H … N′ hydrogen bond, the geometric and spectroscopic properties of which we have investigated. The cation skeleton in PTB is planar to 0.03(2) Å; in BPTB the dihedral angle between the two cation ring planes is 5.2°. In the pale yellow PTB there are significant π–π stacking interactions that persist into solution. The effect of protonation on the geometry of the 2,2′-bipyridine and 1,10-phenanthroline systems is examined in considerable detail and compared with the corresponding effects in the paraquat(2+) and similar cations. On both geometric and spectroscopic (infrared spectra between 10 and 295 K) evidence, the N—H … N′ hydrogen-bonding interaction is stronger in BPTB; in PTB this interaction is among the weakest reported in crystals, the ν(NH) stretching frequency at 10 K being as high as 3279 cm−1. A detailed comparison of the geometries of the intra-cation N—H … N′ bonds in BPTB and PTB with those in classical and modified proton-sponge cations has led to the formulation of criteria useful in predicting the occurrence of proton-sponge-like properties. Key words: bipyridinium ions, hydrogen bonding, phenanthrolinium ions, proton sponges, tetraphenylborates.