Development of Photoredox Cross-Electrophile Coupling of Strained Heterocycles with Aryl Bromides Using High-Throughput Experimentation for Library Construction.

Microscale high-throughput experimentation was used to develop a photoredox-assisted reductive cross-coupling reaction of aryl halides with strained aliphatic heterocycles facilitated via a ring-opening reaction. This methodology was found to be applicable to medicinally relevant substrates including Boc-protected strained aliphatic heterocycles and (hetero)aryl bromides and was used for compound library construction via parallel medicinal chemistry. Furthermore, the coupling reactions were shown to be scalable to the gram scale by continuous flow reaction. A possible reaction mechanism is also discussed.

RNAapt3D: RNA aptamer 3D-structural modeling database.

RNA aptamers are oligonucleotides with high binding affinity and specificity for target molecules and are expected to be a new generation of therapeutic molecules and targeted delivery materials. The tertiary structure of RNA molecules and RNA-protein interaction sites are increasingly important as potential targets for new drugs. The pathological mechanisms of diseases must be understood in detail to guide drug design. In developing RNA aptamers as drugs, information about the interaction mechanisms and structures of RNA aptamer-target protein complexes are useful. We constructed a database, RNA aptamer 3D-structural modeling (RNAapt3D), consisting of RNA aptamer data that are potential drug candidates. The database includes RNA sequences and computationally predicted RNA tertiary structures based on secondary structures and implements methods that can be used to predict unknown structures of RNA aptamer-target molecule complexes. RNAapt3D should enable the design of RNA aptamers for target molecules and improve the efficiency and productivity of candidate drug selection. RNAapt3D can be accessed at https://rnaapt3d.medals.jp.

Ion-pairing π-electronic systems: ordered arrangement and noncovalent interactions of negatively charged porphyrins.

In this study, charged π-electronic species are observed to develop stacking structures based on electrostatic and dispersion forces. i π- i π Interaction, defined herein, functions for the stacking structures consisting of charged π-electronic species and is in contrast to conventional π-π interaction, which mainly exhibits dispersion force, for electronically neutral π-electronic species. Establishing the concept of i π- i π interaction requires the evaluation of interionic interactions for π-electronic ion pairs. Free base (metal-free) and diamagnetic metal complexes of 5-hydroxy-10,15,20-tris(pentafluorophenyl)porphyrin were synthesized, producing π-electronic anions upon the deprotonation of the hydroxy unit. Coexisting cations in the ion pairs with porphyrin anions were introduced as the counter species of the hydroxy anion as a base for commercially available cations and as ion-exchanged species, via Na+ in the intermediate ion pairs, for synthesized π-electronic cations. Solid-state ion-pairing assemblies were constructed for the porphyrin anions in combination with aliphatic tetrabutylammonium (TBA+) and π-electronic 4,8,12-tripropyl-4,8,12-triazatriangulenium (TATA+) cations. The ordered arrangements of charged species, with the contributions of the charge-by-charge and charge-segregated modes, were observed according to the constituent charged building units. The energy decomposition analysis (EDA) of single-crystal packing structures revealed that electrostatic and dispersion forces are important factors in stabilizing the stacking of π-electronic ions. Furthermore, crystal-state absorption spectra of the ion pairs were correlated with the assembling modes. Transient absorption spectroscopy of the single crystals revealed the occurrence of photoinduced electron transfer from the π-electronic anion in the charge-segregated mode.

Dynamic Polymer Free Volume Monitored by Single-Molecule Spectroscopy of a Dual Fluorescent Flapping Dopant.

Single-molecule spectroscopy (SMS) of a dual fluorescent flapping molecular probe (N-FLAP) enabled real-time nanoscale monitoring of local free volume dynamics in polystyrenes. The SMS study was realized by structural improvement of a previously reported flapping molecule by nitrogen substitution, leading to increased brightness (22 times) of the probe. In a polystyrene thin film at the temperature of 5 K above the glass transition, the spectra of a single N-FLAP molecule undergo frequent jumps between short- and long-wavelength forms, the latter one indicating planarization of the molecule in the excited state. The observed spectral jumps were statistically analyzed to reveal the dynamics of the molecular environment. The analysis together with MD and QM/MM calculations show that the excited-state planarization of the flapping probe occurs only when sufficiently large polymer free volume of more than, at least, 280 Å3 is available close to the molecule, and that such free volume lasts for an average of 1.2 s.

Key interactions with deazariboflavin cofactor for light-driven energy transfer in Xenopus (6-4) photolyase.

Photolyases are flavoenzymes responsible for light-driven repair of carcinogenic crosslinks formed in DNA by UV exposure. They possess two non-covalently bound chromophores: flavin adenine dinucleotide (FAD) as a catalytic center and an auxiliary antenna chromophore that harvests photons and transfers solar energy to the catalytic center. Although the energy transfer reaction has been characterized by time-resolved spectroscopy, it is strikingly important to understand how well natural biological systems organize the chromophores for the efficient energy transfer. Here, we comprehensively characterized the binding of 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF) to Xenopus (6-4) photolyase. In silico simulations indicated that a hydrophobic amino acid residue located at the entrance of the binding site dominates translocation of a loop upon binding of 8-HDF, and a mutation of this residue caused dysfunction of the efficient energy transfer in the DNA repair reaction. Mutational analyses of the protein combined with modification of the chromophore suggested that Coulombic interactions between positively charged residues in the protein and the phenoxide moiety in 8-HDF play a key role in accommodation of 8-HDF in the proper direction. This study provides a clear evidence that Xenopus (6-4) photolyase can utilize 8-HDF as the light-harvesting chromophore. The obtained new insights into binding of the natural antenna molecule will be helpful for the development of artificial light-harvesting chromophores and future characterization of the energy transfer in (6-4) photolyase by spectroscopic studies.

Conformation-Changeable π-Electronic Systems with Metastable Bent-Core Conformations and Liquid-Crystalline-State Electric-Field-Responsive Properties.

This study focused on the use of nonconventional bent-core π-electronic systems, 2,2'-bipyrroles substituted with modified benzoyl units, as building units of stimuli-responsive assemblies. Electric-field-responsive mesophase behaviors were observed in homochiral synclinic ferroelectric smectic C structures comprising the syn conformations. Electric-field application induced changes in the polarized optical microscopy textures with dynamic behaviors derived from the conversion from twisted to untwisted states.

Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH.

Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.

Enhanced DNA repair by DNA photolyase bearing an artificial light-harvesting chromophore.

Photolyases are flavoenzymes responsible for the repair of carcinogenic DNA damage caused by ultraviolet radiation. They harbor the catalytic cofactor flavin adenine dinucleotide (FAD). The light-driven electron transfer from the excited state of the fully-reduced form of FAD to the DNA lesions causes rearrangement of the covalent bonds, leading to the restoration of intact nucleobases. In addition to the catalytic chromophore, some photolyases bear a secondary chromophore with better light absorption capability than FAD, acting as a light-harvesting chromophore that harvests photons in sunlight efficiently and transfers light energy to the catalytic center, as observed in natural photoreceptor proteins. Inspired by nature, we covalently and site-specifically attached a synthetic chromophore to the surface of photolyase using oligonucleotides containing a modified nucleoside and a cyclobutane-type DNA lesion, and successfully enhanced its enzymatic activity in the light-driven DNA repair. Peptide mapping in combination with theoretical calculations identified the amino acid residue that binds to the chromophore, working as an artificial light-harvesting chromophore. Our results broaden the strategies for protein engineering and provide a guideline for tuning of the light perception abilities and enzymatic activity of the photoreceptor proteins.

Self-Associating Curved π-Electronic Systems with Electron-Donating and Hydrogen-Bonding Properties.

Curved π-electronic molecules, dipyrrolylbenzodiazepines (dpbs), were synthesized via condensation of 1,3-dipyrrolyldiketones and phenylenediamines. Dpbs exhibited 1D hydrogen-bonding chains between pyrrole NH and diazepine N and the resulting packing structures in the solid state. The pyrrole and diazepine N sites coordinate RhI, providing curved π-electronic systems of increasing rigidity. Dpb underwent coassembly with C60, which was surrounded by a hydrogen-bonding ring structure of six dpbs. On photoexcitation, the coassembly exhibited ultrafast electron transfer from the dpb moiety to C60, depending on their proximal arrangement as well as electron-donating and -accepting properties.

Implications of a Water Molecule for Photoactivation of Plant (6-4) Photolyase.

Photolyases (PLs) are flavoproteins able to repair cross-links formed between adjacent pyrimidine bases in DNA in a light-dependent manner via an electron transfer. The catalytically active redox state of the flavin chromophore for the DNA repair is a fully reduced form of flavin adenine dinucleotide (FADH-). PLs and their relative, cryptochromes (CRYs), share a physicochemical process attributable to the light-dependent reduction of the chromophore via an ultrafast successive electron transfer through exclusively conserved three tryptophan side chains. In some (6-4) PLs and animal CRYs, an additional tryptophan participates in this photoactivation process. In a search for the intrinsic difference between the Trp triad and tetrad, a water molecule proximal to the second and third Trp was found in the reported crystal structure of Arabidopsis thaliana (6-4) PL. Here, we investigated the involvement of the water molecule in photoactivation. Molecular dynamics simulations indicated that the water molecule is stably captured in the binding site, while mutation of S412 increased water displacement from the binding site. Photochemical analysis of recombinant proteins revealed that the S412A mutation significantly decelerated the FAD photoreduction as compared to the wild type. The hydrogen-bonding network including the water molecule would play a key role in the stabilization of the FAD-Trp radical pair.

Pyrrole-Based π-System-PtII Complexes: Chiroptical Properties and Excited-State Dynamics with Microsecond Triplet Lifetimes.

Heteroleptic PtII complexes comprising π-extended dipyrrins and 2-phenylquinoline were prepared. Single-crystal X-ray analysis disclosed the stepped conformations of two ligand moieties in these PtII complexes. The enantiomers could be separated by HPLC and their configurations were determined from CD spectroscopy results and TD-DFT calculations. Transient absorption measurements revealed excited-state dynamics characterized by fast intersystem crossing and microsecond-order triplet-state lifetimes.

Quadruply N-methylated octaphyrin: a helical macrocycle exhibiting chiroptical properties and dynamic conformation changes correlated with helical and inner N-methyl orientations.

[38]Octaphyrin(1.1.1.1.1.1.1.1) bearing four methyl moieties at the inner nitrogen sites has been synthesized. This expanded porphyrin has helical chirality as correlated with the orientations of the inner N-methyl groups, exhibiting chiroptical properties as observed in CD Cotton effects from the enantiomers through optical resolution. The chirality of the octaphyrin was retained at r.t. but the racemization occurred at higher temperature as examined by CD spectral changes. The dynamic conversion processes between the enantiomers were investigated by theoretical studies, suggesting the plausible pathways via the intermediates with appropriate conformations.

Synergetic Effects of Triplet-Triplet Annihilation and Directional Triplet Exciton Migration in Organic Crystals for Photon Upconversion.

In condensed solids, triplet exciton migration and succeeding triplet-triplet annihilation (TTA) are major bottleneck processes for efficient photon upconversion (UC) using sunlight excitation. We theoretically investigated the reaction times of TTA and the triplet-triplet energy transfer (TTET) as the elementary processes of triplet exciton migration in organic crystals of two molecular species: 9,10-diphenylanthracene (DPA) and its double-strapped alkyl  derivative (C7-sDPA) as the models of a recently reported crystalline system of TTA-UC by Kamada et al. The reaction times calculated based on Marcus theory clarified that the dimensionality of TTET and synergetic effects of TTA and TTET are responsible for the high UC quantum yield as well as their triplet lifetimes.

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.

Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited.

The photoinduced electron transfer (ET) reaction of cyclobutane pyrimidine dimer (CPD) photolyase plays an essential role in its DNA repair reaction, and the molecular mechanism of the ET reaction has attracted a large number of experimental and theoretical studies. We investigated the quantum mechanical nature of their ET reactions, characterized by multiple ET pathways of the CPD photolyase derived from Anacystis nidulans. Using the generalized Mulliken-Hush (GMH) method and the bridge green function (GF) methods, we estimated the electronic coupling matrix element, TDA, to be 36 ± 30 cm-1 from the donor (FADH-) to the acceptor (CPD). The estimated ET time was 386 ps, in good agreement with the experimental value (250 ps) in the literature. Furthermore, we performed the molecular dynamics (MD) simulations and ab initio molecular orbital (MO) calculations, and explored the electron tunneling pathway. We examined 20 different structures during the MD trajectory and quantitatively evaluated the electron tunneling currents for each of them. As a result, we demonstrated that the ET route via Asn349 was the dominant pathway among the five major routes via (Adenine/Asn349), (Adenine/Glu283), (Adenine/Glu283/Asn349/Met353), (Met353/Asn349), and (Asn349), indicating that Asn349 is an essential amino acid residue in the ET reaction.

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

(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.

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, 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.

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.