Molecular Dynamics Study on the Structure-Property Relationship of Self-Assembled Gear-Shaped Amphiphile Molecules with/without Methyl Groups

Gaining insight into the encapsulation mechanism is important for controlling the encapsulation rate toward the self-assembly of gear-shaped amphiphile molecules (GSAs). To this aim, we conducted molecular dynamics (MD) simulations for three different hexameric nanocubes (1₆¹²⁺, 2₆¹²⁺, and 3₆¹²⁺) of GSAs (1²⁺, 2²⁺, and 3²⁺, respectively) to elucidate the quantitative structure-property relationship between the stability of the nanocubes and the rate of encapsulation of a guest molecule. The 1²⁺, 2²⁺, and 3²⁺ monomers differ from each other in the number of methyl groups, having three, zero, and two methyl groups, respectively. The 3₆¹²⁺ hexamer has methyl groups only on the equatorial region. In the cases of the simulations of 1₆¹²⁺ and 3₆¹²⁺, the cubic structures are maintained due to a tight triple-π stacking around the equator region. Meanwhile, 2₆¹²⁺ deforms easily due to the occurrence of a large fluctuation. These results indicate that the methyl groups on the equator are crucial to stabilize the nanocubes. The encapsulation of an iodide ion as a guest molecule is revealed to occur through the pole region via a gap that is easily formed in the nanocubes without methyl groups on the poles. Our study clearly suggests that self-assembled nanocubes can be designed to attain a specific stability and encapsulation efficiency simultaneously.

Hexabenzocoronene functionalized with antiaromatic S- and Se-core-modified porphyrins (isophlorins): comparison with the dyad with regular porphyrin

The important and perspective molecular building blocks composed of hexaphenylbenzenes (HPBs) or their oxidized derivatives, hexa-peri-hexabenzocoronenes (HBCs), and metalloporphyrins have recently received significant attention of the researchers. In this study, motivated by recent findings, we have addressed the modifications of structures and properties of HBC-porphyrin compounds by using instead of aromatic porphyrins antiaromatic 20π isophlorin derivatives of thiophene or selenophene. We have reported the first comparative computational investigation of the following systems: (i) HBC with one non-metallated aromatic porphyrin, P(N4H2), unit, HBC-P(N4H2), (ii) HBC with one S-core-modified antiaromatic porphyrin (S-isophlorin), PS4, unit, HBC-PS4, and (iii) HBC with one Se-core-modified antiaromatic porphyrin (Se-isophlorin), PSe4, unit, HBC-PSe4. The study has been done employing the B3LYP/6-31G* approach (in the gas phase and in the implicit solvents, benzene and dichloromethane), and comparison with the B3LYP/6-31G** and B3LYP/6-311G* approaches was performed, where relevant. The effects of the core-modified antiaromatic isophlorins on the structures, electronic, and other properties, potentially including reactivity, of the whole building block HBC-isophlorin have been shown to be quite pronounced and to be noticeably stronger than the effects of the original aromatic non-metallated porphyrin. Thus, we have demonstrated theoretically that the complete porphyrin core-modification with other elements, this time with S and Se leading to the formation of the antiaromatic isophlorins, should be considered as a promising way for modifying and tuning structures, electronic properties and reactivity of the hexabenzocoronene-porphyrin(s) building blocks.

Molecular Dynamics Study on Dynamical Features of Reorganization Process for Nanocapsule Formed with Gear-Shaped Amphiphile Molecules

We have analyzed the dynamical feature of a hexameric structure of nanocube (1₆) from a gear-shaped amphiphile molecule (1) upon addition of solvophobic spherical adamantane molecule (G), by means of molecular dynamics (MD) simulation, to elucidate the conversion mechanism from the hexameric nanocube G@1₆ to a tetrameric G@1₄ tetrahedron. The adamantane molecule (G) in the nanocube G@1₆ is located around the triple π stacking, although G in the G@1₄ tetrahedron is at the central position of the capsule. Our MD simulation shows that the nanocube G@1₆ is more fluctuated than the G@1₄ tetrahedron. We have also found that a demethylated nanocube G@2₆ is converted to a tetrameric G@2₃ tetrahedron due to the solvophobic effect for the adamantane molecule.

Induced-fit expansion and contraction of a self-assembled nanocube finely responding to neutral and anionic guests

Induced-fit or conformational selection is of profound significance in biological regulation. Biological receptors alter their conformation to respond to the shape and electrostatic surfaces of guest molecules. Here we report a water-soluble artificial molecular host that can sensitively respond to the size, shape, and charged state of guest molecules. The molecular host, i.e. nanocube, is an assembled structure consisting of six gear-shaped amphiphiles (GSAs). This nanocube can expand or contract its size upon the encapsulation of neutral and anionic guest molecules with a volume ranging from 74 to 535 Å3 by induced-fit. The responding property of this nanocube, reminiscent of a feature of biological molecules, arises from the fact that the GSAs in the nanocubes are connected to each other only through the hydrophobic effect and very weak intermolecular interactions such as van der Waals and cation-π interactions.

Self-Assembly of Nanocubic Molecular Capsules via Solvent-Guided Formation of Rectangular Blocks

We investigate the mechanism underlying the self-assembly of gear-shaped amphiphilic molecules into a highly ordered nanocubic capsule ("nanocube") in aqueous methanol. Simulation results show that the solvent molecules play a significant role in the assembly process by directing the primitive intermediates to orthogonal/rectangular shapes, thus creating appropriate building blocks for cubic assembly while avoiding off-pathway stacked aggregates. Free-energy analyses reveal that the interplay of the direct intermonomer interaction and the solvent-mediated repulsion between large aromatic cores (via preferential solvation of methanol on hydrophobic surfaces) leads to the strong trend for perpendicular binding of monomers and hence the solvent-guided formation of rectangular blocks. Furthermore, we report the self-assembly simulation of the nanocube using replica exchange with solute tempering and demonstrate that the simulation can predict a highly ordered nanocapsule structure, assembly intermediates, and encapsulated molecules, which helps promote computer-aided design of functional molecular self-assemblies in explicit solvent.

Importance of Molecular Meshing for the Stabilization of Solvophobic Assemblies

The effect of the methyl groups in neutral gear-shaped amphiphiles (GSAs) on the stability of nanocubes was investigated using a novel C_{2 v}-symmetric GSA, which was synthesized using selective alternate trilithiation of a pentabrominated hexaphenylbenzene derivative. The lack of only one methyl group in the GSA decreased the association constant for the assembly of the nanocube by 3 orders of magnitude. A surface analysis recently developed by the authors (SAVPR: surface analysis with varying probe radii) was carried out for characteristic isomers of the nanocube consisting of C_{2 v}-symmetric GSAs. It was found that the methyl groups near the equator of the nanocube play a significant role in the stabilization of the nanocubes.

Programed dynamical ordering in self-organization processes of a nanocube: a molecular dynamics study

Self-organization processes of a gear-shaped amphiphile molecule (1) to form a hexameric structure (nanocube,1₆) were inferred from sequential dissociation processes by using molecular dynamics (MD) simulations.