With the aim of realizing an in situ nucleic acid analysis, we have developed functional nucleic acid probes that can autonomously detect and analyze nucleic acid sequences of interest. Fluorophore-labeled artificial oligonucleotide probes with target-dependent self-ligation or self-digestion functionalities can be used to sense nucleic acids in solution, on solid supports, or even in cells. In addition, we have successfully established a new sensing system using nonmodified nucleic acids as a probe. These probes and sensors are all composed of nonmodified natural-type nucleic acids, and thus can be transcribed directly from dsDNA, giving a high potency for in situ or in-cell application.
With the aim of realizing an in situ nucleic acid analysis, we have developed functional nucleic acid probes that can autonomously detect and analyze nucleic acid sequences of interest. This paper provides an overview of our effort towards this goal.
Two kinds of diarylperfluorocyclopentenes having 5-phenyl-2-propyl-3-thienyl and 2-isobutyl-5-phenyl-3-thienyl group as the aryl groups were newly synthesized, and the thermal stability of their closed-ring isomers was investigated. The bulkiness of the substituent (R) at the reacting positions in photochromic diarylethenes plays an important role in the thermal cycloreversion reactivity of the photogenerated closed-ring isomers. The steric substituent constant was introduced to investigate the relationship between the steric hindrance of the substituent R and the thermal cycloreversion reactivity. We employed three steric substituent constants, Es(R), Esc(R), and v(R) values. We found that there is a good correlation between the Esc(R) value and the thermal cycloreversion reactivity. Furthermore, the Es(CH2R) value has also a good correlation with the thermal cycloreversion reactivity, while Es(R) has no correlation. These results indicate that the steric hindrance has an effect on the thermal cycloreversion and there is no hyperconjugation of the α-hydrogen on the 2-substituent on the thiophene ring. Moreover, the activation energy was also found to be related to the steric substituent constant. These findings would give a new useful strategy to design novel diarylethenes having desired thermal stability.
The bulkiness of the substituent at the reacting positions in photochromic diarylethenes plays an important role in thermal cycloreversion. We found that there is a good correlation between specific steric substituent constants and the thermal cycloreversion reactivity.
Near-infrared (NIR) luminescent Yb(III) complexes composed of low-vibrational frequency (LVF) fluorinated acetylacetonate and phosphine oxide ligands are reported. Their structures are determined using X-ray single-crystal analyses and categorized as eight-coordinated square antiprism. The radiative rate constants (kr), the nonradiative rate constants (knr), and the 4f–4f emission quantum efficiency (ΦEm) are estimated using their absorption spectra of magnetic dipole transition in Yb(III) complexes (2F5/2 → 2F7/2) and the observed emission lifetimes. Characteristic NIR luminescence properties of Yb(III) complexes with LVF phosphine oxide and fluorinated acetylacetonate ligands are elucidated in terms of the radiative and nonradiative rate constants.
Tetrakis(triphenylphosphine)palladium(0) catalyzes the highly regioselective addition of phenyl thiocyanate to terminal alkynes, which attains the simultaneous introduction of thio and cyano groups into the internal and terminal positions of alkynes, respectively. In addition, dicobalt octacarbonyl indicates moderate catalytic activity toward the same cyanothiolation of alkynes with excellent regioselectivity. By using [Co2(CO)8] as the catalyst, novel cyanoselenation of alkynes with phenyl selenocyanate has also been attained in moderate yield with excellent regioselectivity.
Direct observation of the molecular structural change during chemical reactions including transition states is desirable to fully clarify the mechanism of chemical reactions. Time-dependent frequency variations in molecular vibration modes reflect structural change in transition states. Ultrafast changes in molecular structure during bond breaking and bond reformation can be clearly visualized using ultrafast spectroscopy. This study elucidated molecular structural information in states along the chemical reaction including transition state in the proton transfer of indigodisulfonate salt. The photoexcited proton transfer was found to follow a stepwise pathway. The monoalcohol intermediate generated by the proton transfer was found to return immediately to the original indigo without proton-transfer configuration. This back reaction of this is the reason for the ultra-photostability of indigo over extremely long exposure to light. This shows that real-time vibrational spectroscopy by a few femtosecond pulse laser enables the observation of dynamic behavior of molecular vibrations during chemical reactions, leading to the clarification of reaction mechanisms or the development of new chemical reactions.
The equilibrium and transition geometric structures from bithiophene to hexachlorobithiophene derivatives and relative energies of bithiophene derivatives in electrophilic chlorination were fully optimized using the ab initio Hartree–Fock and second-order Møller–Plesset perturbation method with a 6-311+G** basis set. The regioselectivity of the electrophilic chlorination of bithiophene derivatives was determined primarily by the gaps (ΔE1, ΔE2, ΔE3, … ) of the relative transition energy levels in the transition π-complexes. The gaps of the relative transition energy level were correlated with both the chlorinated positions and atomic charges of the carbon atoms on the bithiophene ring, the HOMO–LUMO gaps of the transition π-complexes due to the (Cl+···Cδ−) interaction, the geometric structures of the neutral and transition derivatives, and the π-conjugation effect (delocalization energy) originating from the π-orbitals. The order of relative stability in the transition π-complexes was found to be 5,5′-dichlorinated > 3,3′-dichlorinated > 4,4′-dichlorinated derivatives. Particularly, with increasing the relative transition energy gaps (ΔE2, ΔE3, ΔE8, ΔE9, … ) in the transition π-complexes, the regioselective chlorinations from BT to 6Cl-BT occurred at specific position of bithiophenes.
The proton transfers in base pairs of guanine (G)/8-oxoguanine (8G), 8G+•–C, PhOH–G(-H)•, PhOH–8G(-H)•, and 8G–G(-H)•, have been theoretically examined in the gas phase at the B3LYP level of theory. For the 8G+•–C base pair, the single proton transfer proceeds from N1(8G+•) to N3(C) with the activation energy of 2.2 kcal mol−1. The repairs of G(-H)• and 8G(-H)• bases to G and 8G have been studied by reaction with phenol, and the repair of G(-H)• base has been also studied for the pair with the 8G base. These three reactions proceed under the PCET mechanism, in which the proton transfers through the σ-path, while the electron transfers through the π-path. For reactions with PhO• and G(-H)•, 8G easily delivers a proton and electron to yield PhOH and G. It is expected that 8G functions to protect other bases and amino acids from oxidation.
The excited-state hydrogen and dihydrogen bonding of a dihydrogen-bonded phenol–borane–dimethylamine (BDMA) complex was investigated theoretically by use of time-dependent density functional theory (TDDFT). The coexistence of an intermolecular dihydrogen bond (B–H···H–O) and hydrogen bond (N–H···O) was confirmed by the optimized geometric structure of the dihydrogen-bonded phenol–BDMA complex. The infrared spectra for both the ground and excited states of the dihydrogen-bonded phenol–BDMA complex were also calculated by use of density functional theory (DFT)/TDDFT. As a result, we demonstrated theoretically that the intermolecular dihydrogen bonds B–H···H–O can be significantly strengthened in the excited state. However, the intermolecular hydrogen bond N–H···O in the dihydrogen-bonded phenol–BDMA complex is weakened upon photoexcitation to the S1 state. The dynamic changes of the intermolecular dihydrogen and hydrogen bonding are consistent with the calculated bond lengths in different electronic states. The coexistent dihydrogen and hydrogen bonding in the electronic excited states of this dihydrogen-bonded complex was studied theoretically in this work. Furthermore, it was found that the N–H···O hydrogen bond in the cyclic structure of phenol–BDMA complex hindered the dehydrogenation reaction between dihydrogen bonded O–H and B–H1 groups, which has been reported for the phenol–borane–trimethylamine complex.
The chiral oxazaborolidinium ion catalyzed Diels–Alder reaction between 2-methyl-1,3-butadiene and 2,3-dimethyl-1,4-benzoquinone was studied by means of density functional theory (DFT) at the B3LYP/6-31G(d) level of theory. Different DFT-based theoretical approaches including the reaction force, the natural population analysis of the charge transfer, the topological analysis of the electron localization function (ELF), and the global and local reactivity indices were applied to investigate and rationalize the mechanism and the endo/exo selectivity of this reaction. The changes in the physical and chemical properties of the reacting molecules along the intrinsic reaction coordinate (IRC) were also monitored to shed light on the mechanistic details. The analysis of the studied Diels–Alder reaction within the framework of DFT revealed and explained the preference of the endo path to the exo channel, and pointed out a concerted but highly asynchronous reaction mechanism.
Synthesis and characterization of complexes with formulations [M(nopi)2Cl2] (M = Co, 1; Ni, 3; Cu, 6; Zn, 9), [M(nopi)6](X)2 (X− = NO3−, M = Co, 2; Ni, 4; Zn, 10; X− = ClO4−, M = Ni, 5; Cu, 8; Zn, 11) and [Cu(nopi)4(NO3)2] (7) imparting 1-(4-nitrophenyl)imidazole (nopi) have been described. The complexes have been characterized by elemental analyses and spectral (IR, 1H NMR, electronic absorption and emission) studies. Molecular structures of 7 and 9 have been determined crystallographically. Weak interaction studies on 7 and 9 revealed the presence of various interesting motifs resulting from C–H···N, C–H···Cl, and π–π stacking interactions. Temperature-dependent (313–373 K) pressed pellet conductivity and activation energy calculations from the plot of ln σ vs. 1/T suggested semiconducting behavior of 2, 6, and 7.
A dicyanoamide-bridged 2D polynuclear zinc(II) complex having formula [Zn2(L)(μ-dca-κN1κN5)2]n, 1 has been synthesized using the Schiff base ligand N,N′-bis(salicylidene)-1,3-diaminopentane, (H2L) and sodium dicyanoamide [Na(dca)]. The complex presents a 2D hexagonal structure formed by 1,5-dca singly bridged helical chains connected through double 1,5-dca bridges. The ligand and the complex are well characterized by elemental analyses, IR and UV–vis spectroscopy. Thermogravimetric analysis is performed to investigate the thermal stability of the metal–organic framework. Photoluminescence studies of the Schiff base ligand in methanol and of the zinc(II) complex 1 in solid state show the presence of blue emission. The emission of the ligand occurs from an excited state involving an intramolecular proton-transfer process as a result of keto–enol tautomerisation and the zinc(II) complex emits from a ligand-centered excited state.
A series of cyclometalated dinuclear platinum(II) complexes bridged by pyridine-2-thiolate (pyt) ions, [Pt2(L)2(pyt)2] (HL = 2-(p-tolyl)pyridine (Hptpy), 2-(2-thienyl)pyridine (Hthpy), or benzo[h]quinoline (Hbzqn)), as well as their two-electron-oxidized dinuclear platinum(III) complexes, [Pt2Cl2(L)2(pyt)2], have been synthesized and characterized. The structures and luminescence properties have been investigated by comparing them with those of the corresponding 2-phenylpyridinato (ppy) complex. All divalent complexes have similar dinuclear frameworks, with short Pt···Pt distances (ca. 2.85 Å), and exhibit similar intense luminescence from the triplet metal–metal-to-ligand charge-transfer (3MMLCT) state in glassy solutions. However, they provide different luminescence features reflecting their dynamic behaviors in fluid solutions and their intermolecular interactions in the solid state. [Pt2(bzqn)2(pyt)2] containing fused aromatic rings exhibits the most sensitive features to the environment, i.e., it shows the most red-shifted luminescence spectrum in the solid state due to the intermolecular π–π interaction. However, in fluid solution, it provides very weak luminescence based on a rapid nonradiative deactivation mainly caused by the fluctuation of the intramolecular π–π repulsion between the ligands. [Pt2(ptpy)2(pyt)2], on the other hand, is the most stable luminophore, which always exhibits intense luminescence with an almost constant emission maximum independent of its temperature and state.
Simple aromatic acids showed successive 2:1 (acid:anion) and 1:1 heteroassociation with anions in polar CH3CN. The formation of 2:1 heteroassociate was rationalized from their sigmoidal titration profiles of acids by anions and ESI-MS measurement. Boronic acid and sulfonamide derivatives having different acidic functionalities also exhibited similar titration profiles.
The synthesis of an eight-membered lactone, cephalosporolide D is described using an iterative acetylene–epoxide coupling strategy. The terminal triple bond compound prepared in situ from the known epoxy chloride was coupled with (R)-methyloxirane to afford the propargyl alcohol. The selective protection of the propargylic hydroxy group as TBS ether followed by reduction of the triple bond gave the saturated alcohol. Removal of THP group followed by selective oxidation of the primary hydroxy group was achieved using BAIB–TEMPO to furnish the aldehyde, which was converted to the corresponding acid by Pinnick oxidation, followed by Yamaguchi lactonization and finally removal of the TBS group afforded the target molecule. A concise synthesis of (−)-cephalosporolide D is described. The salient features are the utilization of acetylene–epoxide coupling strategy and Yamaguchi lactonization.