Phylogenetic tree reconstruction via graph cut presented using a quantum-inspired computer.

Phylogenetic trees are essential tools in evolutionary biology that present information on evolutionary events among organisms and molecules. From a dataset of n sequences, a phylogenetic tree of (2n-5)!! possible topologies exists, and determining the optimum topology using brute force is infeasible. Recently, a recursive graph cut on a graph-represented-similarity matrix has proven accurate in reconstructing a phylogenetic tree containing distantly related sequences. However, identifying the optimum graph cut is challenging, and approximate solutions are currently utilized. Here, a phylogenetic tree was reconstructed with an improved graph cut using a quantum-inspired computer, the Fujitsu Digital Annealer (DA), and the algorithm was named the "Normalized-Minimum cut by Digital Annealer (NMcutDA) method". First, a criterion for the graph cut, the normalized cut value, was compared with existing clustering methods. Based on the cut, we verified that the simulated phylogenetic tree could be reconstructed with the highest accuracy when sequences were diverged. Moreover, for some actual data from the structure-based protein classification database, only NMcutDA could cluster sequences into correct superfamilies. Conclusively, NMcutDA reconstructed better phylogenetic trees than those using other methods by optimizing the graph cut. We anticipate that when the diversity of sequences is sufficiently high, NMcutDA can be utilized with high efficiency.

Chiroptical Response Control of Planar and Axially Chiral Polymethylene-Vaulted Platinum(II) Complexes Bearing 1,1'-Binaphthyl Frameworks.

In this study, the synthesis, structure, and chiroptical response control of planar chiral polymethylene-vaulted trans-bis[(ß-iminomethyl)aryloxy]platinum(II) complexes bearing axially chiral 1,1'-binaphthyl ligands are described. A series of enantiopure polymethylene (n = 4-10)-vaulted complexes were prepared in 6 steps using commercially available (R)- or (S)-BINOL as the starting material without an optical resolution process. The trans-coordination and three-dimensional vaulted structures of the platinum complexes were elucidated from X-ray diffraction (XRD) studies. The complexes were found to show structural dependence of chiroptical responses in the dilute solution state such that the absolute values of [α]D, dissymmetry factors gabs in circular dichroism (CD), and glum in circularly polarized luminescence (CPL) increased upon shortening the length of the polymethylene bridges. The enhanced chiroptical responses were theoretically investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations, and the results are discussed in terms of the molecular structures and transition dipole moments of the ground states. The structural dependence of the chiroptical responses was ascribed to the distortion of the coordination platforms caused by restriction of the vaulting methylene linkers.

Small Figure-Eight Luminophores: Double-Twisted Tethered Cyclic Binaphthyls Boost Circularly Polarized Luminescence.

Invited for the cover of this issue are Masashi Hasegawa, Yoshitane Imai and co-workers at Kitasato University and Kindai University. The image depicts the reported figure-eight molecule as an M. C. Escher-inspired 'impossible object'. Read the full text of the article at 10.1002/chem.202005320.

Small Figure-Eight Luminophores: Double-Twisted Tethered Cyclic Binaphthyls Boost Circularly Polarized Luminescence.

Double-twisted cyclic binaphthyls, in which two naphthalenes are tethered by -O(CH2 )n O- linkage (n=1-3), have been synthesized. X-ray analyses and DFT calculations revealed a tightly constrained stereogenic figure-eight geometry. Tethering of two naphthalenes by short linkage forces a small dihedral angle, and the cyclic binaphthyls with short tether (n=1, 2) exhibit remarkable boosting of the glum value (1.0-1.6×10-2 ) in circularly polarized luminescence (CPL) and unusual glum /gabs ratios (0.93-1.3). These experimental high |glum | values are in accord with the results of excited state TD-DFT calculations, which show transannular interactions and that consequent extensive delocalization occurs throughout the figure-eight π-core. As a result, the present figure-eight luminophore promote the elongation of the magnetic transition dipole moment that results in significant increases in glum values.

Circularly Polarized Luminescence of a Stereogenic Curved Paraphenylene Anchoring a Chiral Binaphthyl in Solution and Solid State.

A curved stereogenic [6]paraphenylene ([6]PP), anchoring a chiral binaphthyl scaffold at 7,7'-positions, was prepared and investigated for its properties as a solid-state circularly polarized luminescence (CPL) dye. X-ray analysis revealed a helically twisted structure of PP units induced by axial chirality of binaphthyl framework. The curved [6]PP exhibits fluorescence in powder and polymethyl methacrylate (PMMA) film as well as solution. A significant increase in quantum yield was observed for a non-fluid PMMA film owing the suppression of the molecular motion. The gCPL values of the dye in solution and as PMMA film were almost the same (4.3-4.4×10-3 ) and lager than that in powder. TD-DFT calculations in the excited state suggest that the exciton can be delocalized into a twisted PP unit to produce a larger magnetic transition dipole moment.

Circularly Polarized Luminescence of a Stereogenic Curved Paraphenylene Anchoring a Chiral Binaphthyl in Solution and Solid State.

Invited for the cover of this issue are Masashi Hasegawa, Yoshitane Imai, Yasuhiro Mazaki and co-workers at Kitasato University, Kindai University and Osaka University. The image depicts a stereogenic twisted cycloparaphenylene that exhibits circularly polarized luminescence in a polymethyl methacrylate thin film. Read the full text of the article at 10.1002/chem.202004283.

Helical Oligophenylene Linked with [2.2]Paracyclophane: Stereogenic π-Conjugated Dye for Highly Emissive Chiroptical Properties.

A stereogenic π-system based on dimer (2) and trimer (3) of [2.2]paracyclophane (PC) and biphenyl was prepared and its structural, photophysical, and chiroptical properties were investigated. X-ray analysis revealed that the quaterphenyl moieties in 2 adopt a double helical structure anchoring [2.2]PC from both sides. Furthermore, 3 forms a isosceles triangle structure with a large chiral cavity. A homodesmotic reaction using DFT calculations revealed that 2 has a larger strain energy than 3 owing to its highly twisted phenylene linkers. Electronic and circular dichroic (CD) spectra were recorded in CH2 Cl2 solution. The spectra of both 2 and 3 are similar, and their longest absorption band accompanying a remarkable Cotton effect is attributed to the transition from HOMO to LUMO, which is delocalized to the quaterphenyl moiety. These compounds exhibit fairly high fluorescence quantum yields (ϕ=0.70-0.83) and moderate dissymmetry factor (|gCPL |=1.6×10-3 ) in circularly polarized luminescence (CPL).

Sign dependence of MCPL spectra on type and position of substituent groups of pyrene and phenanthrene derivatives.

Diamagnetic achiral pyrene and phenanthrene derivatives substituted with electron-donating hydroxyl/methoxy groups and electron-withdrawing carboxylic acid groups exhibited clear magnetic circularly polarised luminescence (MCPL) spectra at 360-460 nm in dilute solvents upon the application of N-up and S-up Faraday geometries under an external magnetic field of 1.6 T. Their MCPL signs were also susceptible upon application of the same Faraday geometry.

Excimer-origin CPL vs. monomer-origin magnetic CPL in photo-excited chiral binaphthyl-ester-pyrenes: critical role of ester direction.

Two chiral binaphthyl (BNp) derivatives bearing oppositely oriented ester linkers to two pyrene (Py) moieties [(R)/(S)-1 and (R)/(S)-2] enabled Py-origin circularly polarized luminescence (CPL), magnetic CPL (MCPL), and circular dichroism (CD). (R)-1 that exhibited (-)-sign CD showed (+)-sign Py-excimer CPL but did not exhibit MCPL. Conversely, (R)-2, with (-)-sign CD, did not show excimer-origin CPL, but exhibited clear Py-monomer MCPL.

Circularly polarised luminescence from planar-chiral Phanephos/Tb(iii)(hfa)3 hybrid luminophores.

Planar-chiral Phanephos, containing the coordinatable P(iii), formed P(iii)/Tb(iii)(hfa)3 hybrid luminophores that successfully emitted characteristic circularly polarised luminescence (CPL) due to 5D4→7F5 transitions in solution. On the other hand, BINAP, containing P(iii)[double bond, length as m-dash]O as axially chiral ligand, exhibited no detectable CPL with Tb(iii)(hfa)3.

Synthesis and Photochemical Properties of Axially Chiral Bis(dinaphthofuran).

Both enantiomers of axially chiral bis(dinaphthofuran) were prepared in only two steps from 1'-hydroxy-4'-methoxy-2,2'-binaphthalenyl-1,4-dione, followed by optical resolution via high-performance liquid chromatography (HPLC) using a chiral stationary phase (CSP). The absolute configurations were determined by comparison of experimental and calculated vibrational circular dichroism (VCD) spectra. Synthetic bis(dinaphthofuran) exhibited a broad and unstructured emission derived from an intramolecular excimer in both solution and solid state. The methylene bridge brings both chromophores close to each other and induces significant changes in the photophysical behavior. Chiral bis(dinaphthofuran) displayed a bathochromic shift in emission, as compared to the racemic mixture in the solid state. Furthermore, the compounds showed high circularly polarized luminescence (CPL) with a dissymmetry factor ( glum) of 10-3 at 405 nm upon excitation at 265 nm in a methanol solution. This compound serves as a model for the design and synthesis of organic materials having CPL activity.

Solvent-sensitive signs and magnitudes of circularly polarised luminescence and circular dichroism spectra: probing two phenanthrenes as emitters endowed with BINOL derivatives.

A C2-symmeric binaphthyl framework bearing phenanthrene as the emitter exhibited circularly polarised luminescence (CPL) in dilute solutions. The CPL and circular dichroism signs of the luminophores were altered by solvents (chloroform, methanol, acetonitrile, and dimethylformamide). DFT and TD-DFT calculations indicated that the dihedral angle between the phenanthrene and naphthyl rings was responsible for the apparent sign inversion. The role of solvent molecules in the ground and photoexcited states was discussed based on Hansen solubility parameters (δ, δd, δp and δh).

Extra-Annulated Chlorophyll Derivatives by Scholl Reaction.

The ferric chloride assisted Scholl reaction of methyl (3,5-dimethoxyphenyl)carbonyl-pyropheophorbide-a produced an extra-annulated, didehydrogenated chlorophyll derivative with a six-membered ring fused at the pyrrole A-ring. The steric interaction of the substituents on the additional tetralone and B-rings induced molecular helicity. The helically cyclized stereoisomers were separated by recrystallization, and their (P/M)-stereochemistry was confirmed by circular dichroism spectra. The distortion of their chlorin π-systems broadened electronic absorption bands to cover all visible regions and reach the near-infrared region.

Data on the solution and processing time reached when constructing a phylogenetic tree using a quantum-inspired computer.

Phylogenetic trees provide insight into the evolutionary trajectories of species and molecules. However, because (2n-5)! Phylogenetic trees can be constructed from a dataset containing n sequences, but this method of phylogenetic tree construction is not ideal from the viewpoint of a combinatorial explosion to determine the optimal tree using brute force. Therefore, we developed a method for constructing a phylogenetic tree using a Fujitsu Digital Annealer, a quantum-inspired computer that solves combinatorial optimization problems at a high speed. Specifically, phylogenetic trees are generated by repeating the process of partitioning a set of sequences into two parts (i.e., the graph-cut problem). Here, the optimality of the solution (normalized cut value) obtained by the proposed method was compared with the existing methods using simulated and real data. The simulation dataset contained 32-3200 sequences, and the average branch length according to a normal distribution or the Yule model ranged from 0.125 to 0.750, covering a wide range of sequence diversity. In addition, the statistical information of the dataset is described in terms of two indices: transitivity and average p-distance. As phylogenetic tree construction methods are expected to continue to improve, we believe that this dataset can be used as a reference for comparison and confirmation of the validity of the results. Further interpretation of these analyses is explained in W. Onodera, N. Hara, S. Aoki, T. Asahi, N. Sawamura, Phylogenetic tree reconstruction via graph cut presented using a quantum-inspired computer, Mol. Phylogenet. Evol. 178 (2023) 107636.

Chiral B-N AIEgens: Intense Blue Circularly Polarized Luminescence and Piezochromism.

We present a new class of blue circularly polarized luminescent emitters based on tetraarylaminoborane (TAAB) with considerable dissymmetry factor in the solid state. The chiral pendant 1-phenylethylamine in BN-RR and BN-SS imparts chirality to the core chromophore, resulting in circularly polarized luminescence signals (glum = 0.8 × 10-3) with a quantum yield of 33% in the crystalline state. This novel set of compounds also showcases intriguing thermally reversible piezochromism.

Sign inversion in magnetic circularly polarised luminescence of fused aromatics with 1.6 T N-up/S-up Faraday geometry.

Although 12 diamagnetic fused aromatics with or without substituents exhibit mirror-symmetric magnetic circularly polarised luminescence (MCPL) through N-up and S-up Faraday geometries under a magnetic field intensity of 1.6 T, their signs (single and multiple) and magnitudes depend strongly on either the aromatic structures or the peripheral positions of the substituents.

Inter- and intramolecular excimer circularly polarised luminescence of planar chiral paracyclophane-pyrene luminophores.

Two types of planar chiral [2,2]paracyclophane-pyrene luminophores (1 and 2) with different binding positions of the fluorescent pyrene units were synthesised. (R)/(S)-1 with 1-pyrene units exhibited green intermolecular excimer circularly polarised luminescence (CPL) at 530 nm in the KBr-pellet, but exhibited no CPL signal in dilute CHCl3 solution. In contrast, (R)/(S)-2 with 2-pyrene units exhibited a blue intramolecular excimer CPL at 450 nm in CHCl3 solution. This is the first example of using the binding position of pyrene and the external environment to tune the type (inter- or intramolecular) and chiroptical sign of excimer CPL.

Multiple Fused Anthracenes as Helical Polycyclic Aromatic Hydrocarbon Motif for Chiroptical Performance Enhancement.

Polycyclic aromatic hydrocarbons consisting of three fused anthracene units were designed as new π-conjugated compounds having helical structures. These expanded helicenes were synthesized by Pt-catalyzed cycloisomerization of the corresponding ethynyl-substituted precursors. The nonplanar and helical structure was confirmed by X-ray analysis and DFT calculations, and the barrier to helical inversion was estimated to be 34 kJ mol-1 . The enantiomers of the diphenyl derivative were successfully resolved by chiral HPLC. Enantiopure samples showed good chiroptical performance in the CD (|Δϵ| 1380 L mol-1 cm-1 ) and CPL (|glum | 0.013) spectra, and these values were considerably large for simple organic molecules. The unique chiroptical properties are discussed on the basis of the molecular structure and the electronic state with the aid of time-dependent DFT calculations.

Stereogenic cyclic oligonaphthalenes displaying ring size-dependent handedness of circularly polarized luminescence (CPL).

A series of cyclic oligomers with Dn symmetry (n = 2-5) based on chiral (R)/(S)-binaphthyl exhibiting intensive chiroptical properties were synthesized by using a Ni(0)-catalyzed coupling reaction. The intensity and the handedness of circularly polarized luminescence (CPL) were dependent on the ring size of the cyclic oligomers, in which the 1,1'-binaphthyl moieties form s-cis (n = 2, 3) or s-trans (n = 4, 5) conformers in the excited state. The relationship between the structure and chiroptical properties is discussed with the aid of X-ray analysis and DFT calculations.