novel-techniques-for-observing-structural-dynamics-photoresponsive

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 ...

university of tsukuba

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.

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

As fascinating examples of closely connected multiple π-electronic systems involving noncovalent interactions, the cooperatively interlocked [2+1]-type anion complexes of well-designed π-electronic molecules are reported. The anion-responsive π-electronic molecules investigated in this study are the boron complexes of dipyrrolyldiketones bearing arylethynyl moieties at the pyrrole α-positions. Diverse substituents were introduced at the terminal aryl moieties, thus controlling the cooperativity to form [2+1]-type complexes. Theoretical studies showed that this cooperativity was induced by effective interactions between the introduced arylethynyl moieties. The investigations of the anion-binding processes showed that the first and second bindings to the guest anion were energetically almost equivalent, indicating the fundamental and important features of the electronic states of the halide anions. Furthermore, the interlocked anion complexes, whose geometries were distorted from the orthogonal arrangements, had the racemic states of the chiral conformations, either of which was induced by ion pairing with an appropriate chiral π-electronic cation, resulting in the chiroptical property as shown by circular dichroism.

Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes.

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  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  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.

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

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.

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

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 H NMR spectra as well as single-crystal X-ray analysis and theoretical studies.

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

Aromaticity of photoexcited molecules is an important concept in organic chemistry. Its theory, Baird's 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.

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

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, Δ, between the protein and the damaged dsDNA by using a molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Δ for both proteins were -35 and 57 kcal mol, 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.

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

(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.

Article	Year
Ion-Pairing Crystal Polymorphs of Interlocked [2 + 1]-Type Receptor-Anion Complexes. The Journal of organic chemistry\| PubMed ID: 27526079	2016
Cooperatively Interlocked [2+1]-Type π-System-Anion Complexes. Chemistry (Weinheim an der Bergstrasse, Germany)\| PubMed ID: 28087882	2017
Theoretical analyses on a flipping mechanism of UV-induced DNA damage. Biophysics and physicobiology\| PubMed ID: 28409083	2016
Phototransformative Supramolecular Assembly of Amphiphilic Diarylethenes Realized by a Combination of Photochromism and Lower Critical Solution Temperature Behavior. Chemistry (Weinheim an der Bergstrasse, Germany)\| PubMed ID: 28696577	2017
H-Aggregated π-Systems Based on Disulfide-Linked Dimers of Dipyrrolyldiketone Boron Complexes. The Journal of organic chemistry\| PubMed ID: 28960078	2017
Structural Monitoring of the Onset of Excited-State Aromaticity in a Liquid Crystal Phase. Journal of the American Chemical Society\| PubMed ID: 29037042	2017
The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study. Biophysics and physicobiology\| PubMed ID: 29450111	2018
Coulomb and CH-π interactions in (6-4) photolyase-DNA complex dominate DNA binding and repair abilities. Nucleic acids research\| PubMed ID: 29762762	2018

Ryuma Sato

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