Ryuma Sato

Ion-Pairing Crystal Polymorphs of Interlocked [2 + 1]-Type Receptor–Anion Complexes

The formation of a solid-state totally charge-segregated assembly (polymorph A) of negatively charged layers comprising [2 + 1]-type Cl(-) complexes of an arylethynyl-substituted dipyrrolyldiketone boron complex and positively charged layers of tetrabutylammonium (TBA) cations has already been reported. The formation of two new crystalline polymorphs (polymorphs B and C), in addition to polymorph A, is reported in this study. Both polymorphs B and C formed charge-by-charge assemblies, and the dihedral angles between two receptor units in the interlocked complexes depended on the geometries of TBA cations and the resulting packing structures. Two nonorthogonally arranged planes induced P- and M-form chiral geometries, providing diverse arrangements of chiral species according to crystal polymorphs. Furthermore, the stabilities of the three polymorphs were examined by interfragment interaction energies, which were calculated by ab initio electronic structure calculations using the fragment molecular orbital (FMO) method.

Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase

Aromaticity of photoexcited molecules is an important concept in organic chemistry. Its theory, Bairds rule for triplet aromaticity since 1972 gives the rationale of photoinduced conformational changes and photochemical reactivities of cyclic π-conjugated systems. However, it is still challenging to monitor the dynamic structural change induced by the excited-state aromaticity, particularly in condensed materials. Here we report direct structural observation of a molecular motion and a subsequent packing deformation accompanied by the excited-state aromaticity. Photoactive liquid crystal (LC) molecules featuring a π-expanded cyclooctatetraene core unit are orientationally ordered but loosely packed in a columnar LC phase, and therefore a photoinduced conformational planarization by the excited-state aromaticity has been successfully observed by time-resolved electron diffractometry and vibrational spectroscopy. The structural change took place in the vicinity of excited molecules, producing a twisted stacking structure. A nanoscale torque driven by the excited-state aromaticity can be used as the working mechanism of new photoresponsive materials.

Theoretical analyses on a flipping mechanism of UV-induced DNA damage

As for UV-induced DNA damage, which may induce skin cancer in animals and growth inhibition in plants, there are two types of photoproducts, namely cis-sin cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts. When they are to be repaired, base-flipping occurs, and they bind to enzymes. However, this process remains relatively unknown at a molecular level. We analyze conformation and interaction energy changes upon base-flipping using classical molecular dynamics (CMD) simulations and ab initio electronic structure calculations. CMD simulations starting with a CPD in the flipped-in and flipped-out states showed that both states were unchanged for 500 ns, indicating the flipped-in and flipped-out processes do not occur spontaneously (without any help of the enzyme) after photo-damage. To deeply understand the reasons, we investigated interaction energy changes among bases upon structure changes during the flipped-in and flipped-out processes using Parallel Cascade Selection-MD (PaCS-MD) simulations at 400 K, followed by a fragment molecular orbital (FMO) method. The total inter-fragment interaction energy (IFIE) between CPD and other bases at the flipped-in state is estimated to be −60.08 kcal/mol. In particular, four bases strongly interact with CPD with interaction energies being −10.96, −13.70, −21.52, and −14.46 kcal/mol each. On the other hand, the total IFIE at the obtained flipped-out state increased to −10.40 kcal/mol by partly losing hydrogen bonds and π-π stacking interactions, respectively. These results clearly indicate that the base-flipping process of DNA lesions occurs with the help of external forces like interactions with appropriate enzymes such as photolyases.

Coulomb and CH–π interactions in (6–4) photolyase–DNA complex dominate DNA binding and repair abilities

Abstract (6–4) Photolyases ((6–4)PLs) are flavoenzymes that repair the carcinogenic UV-induced DNA damage, pyrimidine(6–4)pyrimidone photoproducts ((6–4)PPs), in a light-dependent manner. Although the reaction mechanism of DNA photorepair by (6–4)PLs has been intensively investigated, the molecular mechanism of the lesion recognition remains obscure. We show that a well-conserved arginine residue in Xenopus laevis (6–4)PL (Xl64) participates in DNA binding, through Coulomb and CH–π interactions. Fragment molecular orbital calculations estimated attractive interaction energies of –80–100 kcal mol–1 for the Coulomb interaction and –6 kcal mol–1 for the CH–π interaction, and the loss of either of them significantly reduced the affinity for (6–4)PP-containing oligonucleotides, as well as the quantum yield of DNA photorepair. From experimental and theoretical observations, we formulated a DNA binding model of (6–4)PLs. Based on the binding model, we mutated this Arg in Xl64 to His, which is well conserved among the animal cryptochromes (CRYs), and found that the CRY-type mutant exhibited reduced affinity for the (6–4)PP-containing oligonucleotides, implying the possible molecular origin of the functional diversity of the photolyase/cryptochrome superfamily.

The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study

Photolyases (PHRs) and cryptochromes (CRYs) belong to the same family known as blue-light photoreceptors. Although their amino acid sequences and corresponding structures are similar to each other, they exert different functions. PHRs function as an enzyme to repair UV-induced deoxyribonucleic acid (DNA) lesions such as a cyclobutane pyrimidine dimer (CPD) and a (6-4) photoproduct ((6-4)pp), whereas CRYs are a circadian photoreceptor in plants and animals and at the same time they control the photoperiodic induction of flowering in plants. When a new type cryptochrome was identified, it was assumed that another type of CRYs, cryptochrome-DASH (CRY-DASH), which is categorized as a subfamily of photolyase/cryptochrome family, would possess the DNA photolyase activity. However, CRY-DASH had a weak DNA photolyase activity, but the reason for this is still unclear. To clarify the reason, we performed molecular dynamics (MD) simulations for a complex of CPD-PHR or CRY-DASH with damaged double-stranded DNA (dsDNA) and estimated the binding free energy, ΔGbind, between the protein and the damaged dsDNA by using a molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) method. ΔGbind for both proteins were −35 and 57 kcal mol−1, respectively, indicating that the structural stability of CRY-DASH was lower than that of CPD-PHR upon the damaged dsDNA binding. In particular, the number of amino acid residues relevant to the damaged dsDNA binding on the CRY-DASH surface was smaller than that on CPD-PHR. Therefore, the present result suggests that CRY-DASH has a weak DNA photolyase activity because it has a lower binding affinity than CPD-PHR.

H-Aggregated π-Systems Based on Disulfide-Linked Dimers of Dipyrrolyldiketone Boron Complexes

Dipyrrolyldiketone boron complexes linked by a disulfide bond were synthesized, forming H-aggregated dimers assisted by intramolecular π-π and hydrogen-bonding interactions. The conformations of the dimers, with small C-S-S-C dihedral angles, were examined by UV-vis absorption and 1H NMR spectra as well as single-crystal X-ray analysis and theoretical studies.

Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior

Amphiphilic diarylethenes bearing octyloxycarbonyl and N-octylcarbamoyl groups have been designed and synthesized. These ester- and amide-linked compounds form micrometer-sized supramolecular assemblies in water, and these assemblies exhibit photoinduced macroscopic morphological transformations upon alternate irradiation with UV and visible light. The ester-linked diarylethene showed a transformation between colorless spheres and a red-purple hazy fringe, whereas the microspheres of the amide-linked diarylethene showed changes in color, size, and shape, but the spheres did not show division. TEM images revealed that the spheres of the open-ring isomers have coacervate structures, with bicontinuous aqueous and organic phases. The closed-ring isomers of the ester- and amide-linked compounds were found to form nanofibers and thin layers, respectively. These compounds showed absorption spectral shifts at temperatures corresponding to the lower critical solution temperature (LCST) transition. This morphological transformation can be rationalized as the photoinduced phase transition between the high- and low-temperature phases of the LCST transition. These results open up a new avenue for the design of phototransformative supramolecular assemblies based on a combination of photochromism and LCST behavior.

Novel Techniques for Observing Structural Dynamics of Photoresponsive Liquid Crystals

We discuss in this article the experimental measurements of the molecules in liquid crystal (LC) phase using the time-resolved infrared (IR) vibrational spectroscopy and time-resolved electron diffraction. Liquid crystal phase is an important state of matter that exists between the solid and liquid phases and it is common in natural systems as well as in organic electronics. Liquid crystals are orientationally ordered but loosely packed, and therefore, the internal conformations and alignments of the molecular components of LCs can be modified by external stimuli. Although advanced time-resolved diffraction techniques have revealed picosecond-scale molecular dynamics of single crystals and polycrystals, direct observations of packing structures and ultrafast dynamics of soft materials have been hampered by blurry diffraction patterns. Here, we report time-resolved IR vibrational spectroscopy and electron diffractometry to acquire ultrafast snapshots of a columnar LC material bearing a photoactive core moiety. Differential-detection analyses of the combination of time-resolved IR vibrational spectroscopy and electron diffraction are powerful tools for characterizing structures and photoinduced dynamics of soft materials.

Classical cumulant dynamics for statistical chemical physics

Abstract We developed classical cumulant dynamics for statistical mechanics in order to evaluate thermal equilibrium properties of a given system. The equations of motion (EOMs) for momentum and position were formulated together with those for second-order cumulant variables, which are functions of second-order moments. From the Kramers equation, and simplified EOMs were obtained by assuming a stationary state limit. The present method combined with the umbrella integration method was applied to evaluate free energy surface of a seven-particle Morse cluster. With low computational costs, the present approach gave almost equivalent free energy barrier those by conventional classical molecular dynamics.