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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.

The interactions of cyclic peptides containing glycines with cations (Li + , Na + , Be 2+ , Mg 2+ ) and anions (Fand Cl -) have been investigated using ab initio calculations. The cyclic peptides are found to be exciting noVel amphi-ionophores which show strong affinities for both cations and anions. In the presence of a cation, the CdO groups orient toward the center, whereas in the presence of an anion, the N-H groups do so. To our knowledge, we believe that these cyclic peptides are the first amphi-ionophores reported in the literature.Since there are few ionophores for anions, the cyclic peptides would be important anionophores in that they have large anion affinities. Although the individual amide group is rigid, the entire cyclic structures are very flexible, resulting in amphi-ionophores. If glycines are substituted by other residues, it could be utilized to design cyclic peptide ionophores to show different selectivities for cations and anions with varying flexibilities.Host-guest complexation plays a central role in biological processes, such as ion-transfer, enzyme catalysis, and inhibition. 1 In order to elucidate the crucial nature of complex host-(protein)-guest(ions or organic molecules) interactions in biological processes, various experimental 2 and theoretical 3 studies have been done. To design useful ionophores, various important concepts such as host-guest size complementarity, rigidity of host molecule, and ion dipolar moiety orientations in host-guest complexes have been proposed. 4 Considering that real biological hosts are mainly proteins which are polypeptides, it is more desirable to mimic proteins with compounds comprised mainly of peptide bonds. In recent years cyclic polypeptides have been synthesized and used as inhibitors and antagonists. 5 Considering that more than a quarter of all known enzymes require the presence of metal atoms for full catalytic activity, we have performed an ab initio study of the interactions between cyclic peptides and ions, which may have much theoretical and practical importance. To our knowledge, this is the first ab initio study concerning cyclic peptides. In the present study, we investigate a cyclic tetrapeptide (1) and a cyclic hexapeptide (2) which contain only glycines. Although a number of cyclic polypeptides were reported, 5 no cyclic peptide containing only glycines has been reported in the literature. Since this structure exhibits good flexibility, it may show amphi-ionophore characteristics, which will be discussed below.All the structures of compounds 1 and 2 and their ion complexes were fully optimized by Hartree-Fock (HF) calculations. The 6-31+G* (5d) basis set was employed. Calculations based on density functional theory (DFT) employing Becke's three parameter hybrid method using the Lee-Yang-Parr correlation functional (B3LYP) were also performed at the HF/ 6-31+G* optimized geometries for both 1 and 2, and secondorder Möller-Plesset perturbation (MP2) calculations were performed for 1. 6 Basis set superposition error corrections (BSSEC)...

Protonation plays an important catalytic role in amide bond hydrolysis. Although the protonation site of an amide is still debatable, O-protonation is generally preferred to N-protonation in ordinary amides. However, N-protonation can be favored in strained molecular systems. To investigate this strain effect systematically, we studied formamide, strained N-formylazetidine, and highly strained N-formylaziridine using ab initio calculations. The electron correlation effect is found to be important in determining the protonation sites of strained amides, since it contributes to stabilize N-protonation somewhat more than O-protonation. Although O-protonation is highly favored in N-formylazetidine as well as in formamide, N-protonation is favored in N-formylaziridine in both aqueous and gas phases. In case of O-protonation, the geometries become planar even for highly strained amides. The presence of polar solvents contributes to stabilize N-protonation more than O-protonation. The planarity found in O-protonated strained amides and the nonplanarity in N-protonated strained amides would have an important bearing in enzymatic reactions as well as in asymmetric syntheses.

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Incorporation of duplex DNA with higher molecular weights has attracted attention for a new opportunity towards a better organic light-emitting diode (OLED) capability. However, biological recognition by OLED materials is yet to be addressed. In this study, specific oligomeric DNA–DNA recognition is successfully achieved by tri (8-hydroxyquinoline) aluminium (Alq3), an organic semiconductor. Alq3 rods crystallized with guidance from single-strand DNA molecules show, strikingly, a unique distribution of the DNA molecules with a shape of an ‘inverted' hourglass. The crystal's luminescent intensity is enhanced by 1.6-fold upon recognition of the perfect-matched target DNA sequence, but not in the case of a single-base mismatched one. The DNA–DNA recognition forming double-helix structure is identified to occur only in the rod's outer periphery. This study opens up new opportunities of Alq3, one of the most widely used OLED materials, enabling biological recognition.