Assembling Phenomena of Calix[4]hydroquinone Nanotube Bundles by One-Dimensional Short Hydrogen Bonding and Displaced π−π Stacking

Abstract

Using the computer-aided molecular design approach, we recently reported the synthesis of calix[4]hydroquinone (CHQ) nanotube arrays self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (H-bonds) and aromatic-aromatic interactions. Here, we assess various calculation methods employed for both the design of the CHQ nanotubes and the study of their assembly process. Our calculations include ab initio and density functional theories and first principles calculations using ultrasoft pseudopotential plane wave methods. The assembly phenomena predicted prior to the synthesis of the nanotubes and details of the refined structure and electronic properties obtained after the experimental characterization of the nanotube crystal are reported. For better characterization of intriguing 1-D short H-bonds and exemplary displaced pi-pi stacks, the X-ray structures have been further refined with samples grown in different solvent conditions. Since X-ray structures do not contain the positions of H atoms, it is necessary to analyze the system using quantum theoretical calculations. The competition between H-bonding and displaced pi-pi stacking in the assembling process has been clarified. The IR spectroscopic features and NMR chemical shifts of 1-D short H-bonds have been investigated both experimentally and theoretically. The dissection of the two most important interaction components leading to self-assembly processes would help design new functional materials and nanomaterials.

Theoretical Determination of Interaction and Cohesive Energies of Weakly Bound Cycloparaphenylene Molecules

“…In the case of [6]CPP, the tubular dimer contributes to 27.5 %, the parallel-like with 45.7 %, and the diagonal with 26.7 %, indicating a slightly biased preference for a layered growth concomitantly with an epitaxial mechanism. On the other hand, the corresponding values for [12]CPP are 32.1 % for the tubular-like and 28.0 % for the herringbone, largely separated from the rest of dimer interactions.…”

“…we switch now to the [12]CPP supramolecular structure, m i = 2 in all cases, it leads to a cohesive energy U = 57.55 kcal/mol, and thus slightly higher than that obtained for [6]CPP.…”

“…We processed the corresponding files with the Mercury program. 26 Solvent molecules were conveniently removed in [7]CPP and [12]CPP cases to exclusively investigate the non-covalent interactions between chemically relevant pairs of [n]CPP molecules. These solvent molecules were always found occluded within the cavity of the compounds, and are thus not expected to greatly affect the conclusions reached here for the studied intermolecular interactions between neighbouring dimers in the crystal.…”

Understanding Drug-Protein Interactions in Escherichia coli FabI and Various FabI Inhibitor Complexes

“…For π-stacking interaction is maximal when two π-rings are displaced by forming a half overlapped sandwich. 29,30 The π-π stacking interaction is known to be compatible to the H-π interaction according to their substituents. 31,32 From the MD simulations the total interaction energies of ligands decreased by 5.8% for TCL, 9.7% for S54 and 14.9% for IDN case.…”

Structure, Modified Scaled Quantum Mechanical Force Field and A Priori Prediction of Vibrational Spectra and Their Assignment and Exponential Scaling of Frequencies of Triphenylene

“…The specific/complete vibrational analysis was done on various systems e.g. water clusters, 8 sundry weak complexes of benzene and ethene, 9 calix [4]hydroquinone nanotube bundles 10 and many other systems. The nature of inter-ring couplings is also the focus of attention in some of the papers.…”