Plane Of Aromatic Ring Research Articles

Structuring polarity-inverted TBA to G-quadruplex for selective recognition of planarity of natural isoquinoline alkaloids.

Efficient structuring of DNA by small molecules is very crucial in developing DNA-based novel switches with an ideal performance. In this work, we found that inverting only the polarity of the 3' terminal guanine of the thrombin-binding aptamer (3iTBA) totally eradicates the original TBA G-quadruplex (G4) structure in K+. The unstructured 3iTBA can be further refolded upon specifically interacting with small molecules of natural isoquinoline alkaloids (IAs) due to their fruitful binding patterns with variant nucleic acid structures. We identified that 3iTBA can serve as a topology selector for planar IAs. Nitidine (NIT), owing to the planar aromatic ring and coplanar substituents, is the most efficient to restructure the 3iTBA random coil toward the anti-parallel G4 conformation. However, common metal ions can't realize this structuring. The topology selector competency of 3iTBA toward IAs' planarity can be visualized using gold nanoparticles (AuNPs) as the chromogenic readout. Our work expands the G4 repertoire by exploring the polarity inversion regulation and provides a new approach to switch nucleic acid structures toward a small molecule structure-sensitive sensor.

Characterization of Pegylated Liposomal Mitomycin C Lipid-Based Prodrug (Promitil) by High Sensitivity Differential Scanning Calorimetry and Cryogenic Transmission Electron Microscopy.

The effect of a lipidated prodrug of mitomycin C (MLP) on the membrane of a pegylated liposome formulation (PL-MLP), also known as Promitil, was characterized through high-sensitivity differential scanning calorimetry (DSC) and cryo-TEM. The thermodynamic analysis demonstrated that MLP led to the formation of heterogeneous domains in the membrane plane of PL-MLP. MLP concentrated in prodrug-rich domains, arranged in high-ordered crystal-like structures, as suggested by the sharp and high enthalpy endotherm in the first heating scanning. After thiolytic cleavage of mitomycin C from MLP by dithiothreitol (DTT) treatment, the crystal-like prodrug domain disappears and a homogeneous membrane with stronger lipid interactions and higher phase transition temperature compared with the blank (MLP-free) liposomes is observed by DSC. In parallel, the rod-like discoid liposomes and the "kissing liposomes" seen by cryo-TEM in the PL-MLP formulation disappear, and liposome mean size and polydispersity increase after DTT treatment. Both MLP and the residual postcleavage lipophilic moiety of the prodrug increased the rigidity of the liposome membrane as indicated by DSC. These results confirm that MLP is inserted in the PL-MLP liposome membrane via its lipophilic anchor, and its mitomycin C moiety located mainly at the region of the phospholipid glycerol backbone and polar headgroup. We hypothesize that π-π stacking between the planar aromatic rings of the mitomycin C moieties leads to the formation of prodrug-rich domains with highly ordered structure on the PL-MLP liposome membrane. This thermodynamically stable conformation may explain the high stability of the PL-MLP formulation. These results also provide us with an interesting example of the application of high sensitivity DSC in understanding the composition-structure-behavior dynamics of liposomal nanocarriers having a lipid-based drug as pharmaceutical ingredient.

Dithiopheneindenofluorene (TIF) Semiconducting Polymers with Very High Mobility in Field-Effect Transistors.

The charge-carrier mobility of organic semiconducting polymers is known to be enhanced when the energetic disorder of the polymer is minimized. Fused, planar aromatic ring structures contribute to reducing the polymer conformational disorder, as demonstrated by polymers containing the indacenodithiophene (IDT) repeat unit, which have both a low Urbach energy and a high mobility in thin-film-transistor (TFT) devices. Expanding on this design motif, copolymers containing the dithiopheneindenofluorene repeat unit are synthesized, which extends the fused aromatic structure with two additional phenyl rings, further rigidifying the polymer backbone. A range of copolymers are prepared and their electrical properties and thin-film morphology evaluated, with the co-benzothiadiazole polymer having a twofold increase in hole mobility when compared to the IDT analog, reaching values of almost 3 cm2 V-1 s-1 in bottom-gate top-contact organic field-effect transistors.

Precise through-space control of an abiotic electrophilic aromatic substitution reaction

Nature has evolved selective enzymes for the efficient biosynthesis of complex products. This exceptional ability stems from adapted enzymatic pockets, which geometrically constrain reactants and stabilize specific reactive intermediates by placing electron-donating/accepting residues nearby. Here we perform an abiotic electrophilic aromatic substitution reaction, which is directed precisely through space. Ester arms—positioned above the planes of aromatic rings—enable it to distinguish between nearly identical, neighbouring reactive positions. Quantum mechanical calculations show that, in two competing reaction pathways, both [C–H···O]–hydrogen bonding and electrophile preorganization by coordination to a carbonyl group likely play a role in controlling the reaction. These through-space-directed mechanisms are inspired by dimethylallyl tryptophan synthases, which direct biological electrophilic aromatic substitutions by preorganizing dimethylallyl cations and by stabilizing reactive intermediates with [C–H···N]–hydrogen bonding. Our results demonstrate how the third dimension above and underneath aromatic rings can be exploited to precisely control electrophilic aromatic substitutions.

Optical biosensing using newly synthesized metal salphen complexes: A potential DNA diagnostic tool

A solid-state DNA optode sensor has been developed based on the employment of glutaraldehyde (GD)-activated aminated silica nanoparticles (SiO2NPs-NH2) DNA carrier matrix, and the newly synthesized yellowish N,N’-bis-5-(hydroxysalicylidene)phenylene-diamine-zinc(II) (i.e. the Zn salphen complex) oligonucleotide label. Some three Schiff base complexes with three different transition metal ions (Zn2+, Ni2+, Cu2+) were synthesized through a simple one-pot reaction (5h), and characterized by their physical and chemical properties based on FTIR, NMR and ESI–MS analyses. Due to the square planar geometry and aromatic ring structured characteristics of the metal complex intercalators, they could intercalate between DNA bases via π-π stacking interaction, and rendered a yellowish pink hue on the DNA biosensor surface. Reflectometric optimization revealed high selectivity of the nanosilica-based DNA biosensor in the detection of dengue serotype 2 DNA, which capable of discriminating even a single nucleotide mismatch. The optical DNA biosensor demonstrated a linear reflectance response between 1.0×10−15M and 1.0×10−11M cDNA (R2=0.9975) with a fast DNA hybridization time of 30min and a limit of detectable (LOD) DNA concentration as low as 1zM. In addition, this biosensor showed high shelf life stability with a 20-day operational duration and reusable for five consecutive DNA testings. The proposed optical DNA biosensor offers biosensing performance far superior to that of previously reported electrochemical DNA biosensor for early diagnosis of dengue infection with respect to dynamic linear range, LOD and response time.

Determination of genotoxic potential by comparison of structurally related azo dyes using DNA repair-deficient DT40 mutant panels

Azo dyes, including Sudan I, Orange II and Orange G, are industrial dyes that are assumed to have genotoxic potential. However, neither the type of DNA damage induced nor the structural features responsible for toxicity have been determined. We used a panel of DNA-repair-pathway-deficient mutants generated from chicken DT40 cells to evaluate the ability of these azo dyes to induce DNA damage and to identify the type of DNA damage induced. We compared the structurally related azo dyes Sudan I, Orange II and Orange G to identify the structural features responsible for genotoxicity. Compared with wild type cells, the double-strand break repair defective RAD54−/−/KU70−/− cells were significantly more sensitive to Sudan I, but not to Orange II or Orange G. The quantum-chemical calculations revealed that Sudan I, but not Orange II or Orange G, has a complete planar aromatic ring structure. These suggest that the planar feature of Sudan I is critical to the inducing of double-strand breaks. In summary, we used a DNA-repair mutant panel in combination with quantum-chemical calculations to provide a clue to the chemical structure responsible for genotoxicity.

Colorimetric Naphthalene‐Based Thiosemicarbazide Anion Chemosensors with an Internal Charge Transfer Mechanism

A series of thiosemicarbazide anion chemosensors substituted with naphthalene and 4‐nitrophenyl or phenyl units were synthesized. The molecules were characterized by using 1H,13C DEPT and 15N NMR spectroscopy. The anion binding properties of compounds 1–4 were investigated by UV/Vis absorption and fluorescence spectroscopy in DMSO, DMSO/H2O (9:1 v/v), and acetonitrile with hydroxide, fluoride, acetate, hypophosphate, and chloride anions. Striking color changes were observed with nitro‐containing chemosensors 2–4 with all anions, with the exception of chloride, which was attributed to an internal charge‐transfer mechanism. 1H/13C/15N NMR titration studies and DFT and charge distribution calculations support a mechanism involving deprotonation of the central N–H bond. Compound 4 with a methylene spacer between the naphthalene and thiosemicarbazide moieties was deliberately designed as a fluorescent photoinduced electron‐transfer anion (PET) sensor. However, the methylene spacer did not prevent delocalization of the HOMO orbital between the planar aromatic ring and the thiosemicarbazide unit as expected on the basis of the “fluorophore–spacer–receptor” PET model.

Crystal structure of (1S*,2R*)-7-benz-yloxy-2-methyl-3-tosyl-2,3,4,5-tetra-hydro-1H-3-benz-azepin-1-ol: elucidation of the relative configuration of potent allosteric GluN2B selective NMDA receptor antagonists.

In the title compound, C25H27NO4S, which crystallized as a racemate, the relative configuration of the adjacent OH and CH3 groups on the azepine ring is trans. The seven-membered azepin ring has a chair-like conformation. The planar aromatic rings of the benzyl and tosyl-ate moiety are inclined to the planar 3-benzazepine ring by 78.39 (15) and 77.03 (14)°, respectively, and to each another by 13.82 (15)°. In the crystal, mol-ecules are linked via O-H⋯O and C-H⋯O hydrogen bonds, forming double-stranded chains along the a-axis direction. The chains are linked via C-H⋯π inter-actions, forming a three-dimensional architecture.

Characterization of Conformation and Locations of C-F Bonds in Graphene Derivative by Polarized ATR-FTIR.

It is still a challenge to explore the orientation and location of chemical groups in the two-dimensional derivative of graphene. In this study, polarized attenuated total reflectance Fourier transform infrared spectroscopy (polarized ATR-FTIR) was employed to investigate the orientation and location of C-F groups in the corresponding graphene derivative sheets, which facilitates building a relationship between the bonding nature and fine structure. There were two types of C-F bonding, (C-F)I and (C-F)II, in fluorinated graphene sheets. It was found that (C-F)II bonds were linked at the coplanar carbon atoms in the weakly fluorinated region (CxF, x ≥ 2), whereas the (C-F)I bonds cluster at the strongly deformed carbon framework with a F/C ratio of about 1. The thermostability of (C-F)II is lower than that of (C-F)I bonds. This is because the coplanar structure of the weakly fluorinated region tends to transform to the planar aromatic ring with the breaking of the C-F bond as compared with the strong fluorinated nonplanar region.

Crystal structure of 1-[(2,4,6-triiso-propyl-phen-yl)sulfon-yl]aziridine.

The title compound, C17H27NO2S, exhibits a distorted geometry of the aromatic ring with elongated bonds at the ipso-C atom. The S atom deviates from the aromatic ring plane by 0.393 (4) Å. Similar to this, the adjacent isopropyl groups are bent out of the aromatic ring plane by −0.125 (4) and −0.154 (4) Å. Even the distant isopropyl group in para-position to the sulfonyl moiety shows a slight deviation from the ring plane of 0.111 (5) Å. These distortions, which are caused by the bulky substituents, can also be observed in related sulfonyl­aziridine structures.

Crystal structure of 4-(tri-methyl-germ-yl)benzoic acid.

The title compound, [Ge(CH3)3(C7H5O2)], was obtained as a by-product in the synthesis of the corresponding aldehyde. Two slightly different mol-ecules are present in the asymmetric unit. In both mol-ecules, the geometry of the aromatic ring plane is distorted by varying intensities. Additionally, the Ge atoms deviate from the mean aromatic ring planes. Whereas the distance of the Ge atom to the ring plane is only 0.101 (4) Å in the first mol-ecule, this distance is increased to 0.210 (4) Å in the second. In the crystal structure, centrosymmetric O-H⋯O hydrogen-bonded dimers are formed. The title compound is isostructural with the Si analogue [Haberecht et al. (2004 ▶). Acta Cryst. E60, o329-0330].

Infrared Signature of the Cation-π Interaction between Calcite and Aromatic Hydrocarbons.

The cation-π interaction is proposed as an important mechanism for the adsorption of aromatic hydrocarbons having non-zero quadrupole moments by mineral surfaces. Direct evidence supporting such a mechanism is, however, limited. Using the model mineral calcite, we probe the cation-π interaction with adsorbed benzene, toluene, and ethylbenzene (BTE) molecules using attenuated total reflectance Fourier transform infrared spectroscopy. We show that the presence of calcite increases the energy required to excite the synchronized bending of aromatic C-H bonds of BTE molecules. The unique conformation of this vibrational mode indicates that the planar aromatic rings of BTE molecules are constrained in a tilted face-down position by the cation-π interaction, as further confirmed by density functional theory calculations. Our results suggest that the shift of the excitation energy of the aromatic C-H bending may be used as an infrared signature for the cation-π interaction occurring on mineral surfaces.

Enhanced electroactive and mechanical properties of poly(vinylidene fluoride) by controlling crystallization and interfacial interactions with low loading polydopamine coated BaTiO3

Poly(vinylidene fluoride) (PVDF) is a semi-crystalline polymer and the polar β-phase of PVDF shows superb electroactive properties. In order to enhance the β-phase of PVDF, extreme low content of BaTiO3 nanoparticles (BT-NPs) coated with polydopamine (Pdop) were incorporated into PVDF matrix by solution casting. The β-phase of the resulting PVDF nanocomposites film was dramatically increased and the d33 value reached 34.3±0.4pCN−1. It is found that the Pdop layer could improve the dispersibility and stability of the BT NPs in solution and endow the BT NPs good dispersity in the PVDF matrix. Moreover, the interfacial interaction between PVDF chains and the surface of BT-Pdop nanoparticles (BT-Pdop NPs) were revealed, in which the CF2 groups on PVDF could interact with the electron-rich plane of aromatic ring of Pdop moiety. This interaction, led to the increase of the crystallization activation energy as derived from the DSC nonisothermal crystallization measurement. The α–β crystal transformation, organization of interfacial interactions as well as the prevention of agglomeration of BT-NPs confer the improvement of mechanical and thermal properties of PVDF, such as toughness, tensile strength, elongation at break, and thermal conductivity.

Conformational preferences of 3,4-dihydroxyphenylacetic acid (DOPAC)

The conformational space of 3,4-dihydroxyphenylacetic acid (DOPAC), an important dopamine metabolite, has been investigated by quantum chemical methods (B3LYP and MP2, with the 6-311++G(d,p) basis set) and matrix-isolation infrared spectroscopy. Detailed analysis of the calculated potential energy surfaces of the molecule led to identification of thirteen unique conformers, all of them showing the acetic acid side chain out of the aromatic ring plane by 60–95°. According to the calculated Gibbs energies, the five lowest energy conformers make up 99.7% of the conformational mixture at 298.15K, exhibiting individual populations falling between 16% and 24%. The main conformational trends of this molecule were interpreted on the grounds of a thorough analysis of the structural parameters and by the application of the Natural Bond Orbital theory. The role of the intramolecular interactions on the relative stability and structure of the conformers was also investigated. The infrared spectrum of DOPAC was registered after isolation of its monomers in argon and xenon matrices. Only one of DOPAC forms populated in the gas phase could be trapped in both matrix gases. This result is in agreement with the predicted low energy barriers for conformational isomerization and is also supported by annealing experiments. The spectra of matrix-isolated model compounds, phenylacetic acid and catechol, were studied under the same experimental conditions. These data were used as references and assisted in the interpretation of the results obtained for DOPAC.

Nature of the water/aromatic parallel alignment interactions

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE(CCSD)(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O-H) between the monomers also exists.

Crystal structure of [propane-1,3-diylbis(piperidine-4,1-di-yl)]bis-[(pyridin-4-yl)methanone]-4,4'-oxydi-benzoic acid (1/1).

In the title co-crystal, C25H32N4O2·C14H10O5, mol­ecules are connected into supra­molecular chains aligned along [102] by O—H⋯N hydrogen bonding. These aggregate into supra­molecular layers oriented parallel to (20-1) by C—H⋯O inter­actions. These layers then stack in an ABAB pattern along the c crystal direction to give the full three-dimensional crystal structure. The central chain in the dipyridylamide has an anti–anti conformation. The dihedral angle between the aromatic ring planes is 29.96 (3)°. Disorder is noted in some of the residues in the structure and this is manifested in two coplanar dispositions of one statistically disordered carb­oxy­lic acid group.

Bis{2-[(Tri-phenyl-meth-yl)amino]-phen-yl} diselenide aceto-nitrile monosolvate.

The mol­ecular structure of the title compound, C50H40N2Se2·C2H3N, shows a syn conformation of the benzene rings bound to the Se atoms, with an Se—Se bond length of 2.3529 (6) Å and a C—Se—Se—C torsion angle of 93.53 (14)°. The two Se-bonded aromatic ring planes make a dihedral angle of 18.42 (16)°. Intra­molecular N—H⋯Se hydrogen bonds are noted. Inter­molecular C—H⋯Se inter­actions give rise to supra­molecular chains extended along [100]. One severely disordered aceto­nitrile solvent mol­ecule per asymmetric unit was treated with SQUEEZE in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]; the crystal data take the presence of this mol­ecule into account.

Synthesis of three-dimensional graphene from petroleum asphalt by chemical vapor deposition

The synthesis of three-dimensional (3D) graphene with petroleum asphalt as a carbon source by chemical vapor deposition on a Ni foam substrate has been studied. The morphology and properties of three-dimensional graphene synthesized from asphalt were characterized by scanning electron microscopy, transmission electron microscopy, Raman spectroscopy and X-ray diffraction. The results demonstrate that most of as-prepared 3D graphene foams have 2–5 layers, and small amounts of them have sheets more than 5 layers. The hydrocarbon fragments in asphalt consist of planar aromatic ring structures are considered to play a key role during the formation of 3D graphene. The results demonstrate that asphalt is one of the suitable starting carbon sources for making 3D graphene networks.

1-Piperonylpiperazinium picrate.

In the cation of the title salt [systematic name: 4-(2H-1,3-benzodioxol-5-ylmeth­yl)piperazin-1-ium 2,4,6-tri­nitro­phen­o­late], C12H17N2O2 +·C6H2N3O7 −, the piperazine ring adopts a slightly disordered chair conformation. The piperonyl ring system and the piperazine ring are twisted with respect to each other with an N—C—C—C torsion angle of 40.7 (2)°. In the anion, the dihedral angles between the mean planes of the nitro substituents ortho to the phenolate O atom and the mean plane of the phenyl ring are 28.8 (9) and 32.2 (8)°. In contrast, the nitro group in the para position lies much closer to the aromatic ring plane, subtending a dihedral angle of 3.0 (1)°. In the crystal, the cations and anions inter­act through N—H⋯O hydrogen bonds and a weak C—H⋯O inter­action. Weak C—H⋯O inter­actions are also observed between the anions, forming R 2 2(10) graph-set ring motifs. In addition, a weak centroid–centroid π–π stacking inter­action between the aromatic rings of the cation and the anion, with an inter­centroid distance of 3.7471 (9) Å, contributes to the crystal packing, resulting in a two-dimensional network along (10-1).

3-(1H-Imidazol-1-yl)propanaminium picrate

In the title salt [systematic name: 3-(1H-imidazol-1-yl)propanaminium 2,4,6-tri­nitro­phenolate], C6H12N3 +·C6H2N3O7 −, there are five independent cation–anion pairs (A, B, C, D, E) in the asymmetric unit. In the cation, the ammonium group is protonated with the amino­propyl group nearly at right angles to the mean plane of the imidazole ring showing C—N—C—C torsion angles ranging from 79.6 (2) to 99.79 (19)° in the five cations. The nitro groups in the anion are twisted from the benzene mean plane with maximum dihedral angles subtended by nitro substituents ortho to the phenolate O atom of 26.0 (2) and 37.3 (7) (A), 28.9 (5) and 35.3 (1) (B), 34.7 (7) and 36.9 (7) (C), 14.7 (4) and 36.9 (2) (D) and 33.1 (1) and 35.4 (3)° (E). In contrast, the nitro groups in the para positions lie much closer to the aromatic ring plane, subtending dihedral angles of 1.8 (3) (A), 3.5 (3) (B), 6.03 (C), 2.1 (3) (D) and 7.7 (1)° (E). Disorder is observed for one O atom of an ortho nitro group in anion D with an occupancy ratio of 0.53 (5):0.47 (5). In the crystal, N—H⋯O cation–anion and N—H⋯N cation–cation hydrogen bonds are observed, linking the ions into chains along [010]. In addition, weak C—H⋯O cation–anion inter­actions occur.