Electrochemical DNA biosensor for polycyclic aromatic hydrocarbon detection

Four DNA electrochemical biosensors using four types of DNA (calf thymus ssDNA, calf thymus dsDNA, salmon testis ssDNA and salmon testis dsDNA) were constructed using graphite screen printed electrodes. These biosensors were exploited as analytical tool to detect polycyclic aromatic hydrocarbons-DNA interactions using benzo(a)anthracene and phenantrene as model analytes, the guanine oxidation peak variation being the signal revealing the interaction between PAHs and immobilized DNA. The salmon testis ssDNA biosensor resulted as the most promising device and was further evaluated for benzo(a)anthracene, fluorene, indeno(1,2,3-cd)pyrene, anthracene, and phenanthrene in 5–40 ng mL^?1 solutions, and for benzo(a)pyrene (5–50 ng mL^?1). A concentration dependent variation of the DNA guanine oxidation peak was observed for all compounds. The effect of benzo(a)pyrene ultraviolet (UV) activation on the benzo(a)pyrene (BaP)-DNA interaction was evaluated at concentration levels of 20 and 50 ng mL^?1, and a 3.5- and 2.7-fold increases of the guanine oxidation peak was measured respectively. The salmon testis ssDNA biosensor was examined with PAHs contaminated samples of Mytilus galloprovincialis. Upon UV irradiation of three sample extracts exceeding the BaP maximum level, a positive variation of the DNA guanine oxidation was obtained. An average 2.4-fold increase of the guanine oxidation peak was detected demonstrating that the sensor can be used to detect toxic degradation products of PAHs.     

Electronic spectra and ionization potentials of a stable class of closed shell polycyclic aromatic hydrocarbon cations

Due to their stability, closed shell polycyclic aromatic hydrocarbon (PAH) cations are possible candidates as carriers for some of the diffuse interstellar bands (DIBs). The electronic absorption spectra and ionization potentials of several closed shell PAH cations are determined in this study. We use density functional theory (DFT) at the BLYP/6-31G* level to determine the ionization potentials and thus confirm the stability of the PAH cations of interest. We use time-dependent density functional theory (TDDFT), again at the BLYP/6-31G* level, to calculate the vertical excitation energies and oscillator strengths of the PAH cations. We observe dominant single absorptions within the DIB spectral region of interest in all of the PAH cation spectra except for the smallest member of the series.     

Model calculations for reactivities of polycyclic aromatic hydrocarbon metabolites

Structure-resonance theory calculations correlate reactivities and mutagenicities of polycylic aromatic hydrocarbon metabolites.     

Closed-shell polycyclic aromatic hydrocarbon cations: a new category of interstellar polycyclic aromatic hydrocarbons

Density functional theory has been employed to calculate the harmonic frequencies and intensities of a range of polycyclic aromatic hydrocarbon (PAH) cations that explore both size and electronic structure effects on the infrared spectroscopic properties of these species. The sample extends the size range of PAH species considered to more than 50 carbon atoms and includes several representatives from each of two heretofore unexplored categories of PAH cations: (1) fully benzenoid PAH cations whose carbon skeleton is composed of an odd number of carbon atoms (C(odd) PAHs); and (2) protonated PAH cations (HPAH+). Unlike the radical electronic structures of the PAH cations that have been the subject of previous theoretical and experimental work, the species in these two classes have a 'closed'-shell electronic configuration. The calculated spectra of circumcoronene, C54H18, in both neutral and (radical) cationic form are also reported and compared with those of the other species. Overall, the C(odd) PAHs spectra are dominated by strong CC stretching modes near 1600 cm(-1) and display spectra that are remarkably insensitive to molecular size. The HPAH+ species evince a more complex spectrum consistent with the added contributions of aliphatic modes and their generally lower symmetry. Finally, for both classes of closed-shell cations, the intensity of the aromatic CH stretching modes is found to increase with molecular size far out of proportion with the number of CH groups, approaching a value more typical of neutral PAHs for the largest species studied.     

Nonplanar distortions and strain energies of polycyclic aromatic hydrocarbons

On the basis of HF/6-31G(d) optimized structures, the nonplanar distortions of 135 polycyclic aromatic hydrocarbons (PAHs) have been classified as splitting (S-) and arching (A-) distortions. Three bay structures are proposed as the structural origin of S-distortion. Due to the limitation of sample molecules, a set of universal motifs for molecules containing A-distortions is not available; however, a set of motifs and parameters are developed for the semiquantitative estimation of the nonplanar strain energies of PAHs containing the corannulene structure, and the differences between the E(np) values from quantum calculations and those from these estimations vary from -5.60 to 5.51 kcal/mol. The above results are fundamentally important for the understanding of nonplanar distortion of PAHs and fullerenes, and this method can also be employed to semiquantitatively estimate strain energies of such molecules containing hundreds of carbon atoms.     

Single and double core-hole ionization energies in molecules

The recently demonstrated ability to measure double-hole core-ionization energies in first-row elements has led to a renewed interest in the use of such energies to investigate the effects of initial-state charge distribution and final-state charge rearrangement on the energies of chemical processes that involve addition of charge to a molecule. With theoretical calculations for the molecules CH(4-n)X(n), X = F, Cl, and for C(CH(3))(4) as a basis, the relationships between one-hole and two-hole ionization energies, on one hand, and initial-state and final-state effects, on the other, are reviewed. It is shown that higher-order corrections to the traditionally used relationships are quantitatively significant but do not lead to qualitatively different conclusions. The role of the Wagner plot as a way to display the relationships among the various quantities of interest is discussed, and a generalized Wagner plot for displaying two-site double-hole ionization energies is presented. Some possible applications of measurements of double-hole ionization energies to the investigation of molecular conformation and molecular fragmentation are discussed.     

Vibrations and thermodynamics of clusters of polycyclic aromatic hydrocarbon molecules: the role of internal modes

The vibrational spectra of clusters of coronene molecules are theoretically calculated using a mixed quantum/classical scheme, each molecule being described by a tight-binding Hamiltonian, the intermolecular forces being provided by explicit Lennard-Jones and point charge sites. The normal modes of vibrations are shown to exhibit significant variations upon clustering. In particular, for large clusters intra- and intermolecular modes tend to mix and fill the mid-infrared range. We also calculate the heat capacity of the (C24H12)8 cluster as a function of temperature, emphasizing the isomerizations that take place during melting. Quantum delocalization effects, as obtained from the Pitzer-Gwinn semiclassical approximation, are important enough to wash out all signatures of the structural transitions on the caloric curve. On the basis of a simple two-state model we estimate that clusters containing about 300 molecules are required for melting to be detected on the caloric curve.     

Analysis of intermediates from polycyclic aromatic hydrocarbon biodegradation

A major difficulty in assessing bioremediation in hydrocarbon impacted field sites is the determination of the extent and products of contaminant biodegradation. Previously, various analytical techniques, including mass spectrometry and chromatography, have been used to characterize components in mixtures resulting from biodegradation. In this work, the applicability of capillary electrophoresis (CE) to this area of research is demonstrated. CE methods were optimized for analysis of compounds that are known metabolites of polycyclic aromatic hydrocarbon (PAH) biodegradation.     

Suppressing aggregation in a large polycyclic aromatic hydrocarbon

With the approach presented herein, a large aromatic pi-system is synthesized, which shows extraordinarily high solubility and an effective suppression of aggregation. This was due to a distortion of the aromatic core by bulky tert-butyl groups and the solubilizing effects of alkyl chains in the corona of the aromatic core. Therefore not only the processing and cleaning of the materials with standard laboratory techniques became possible, but moreover the first structure-rich UV/vis and a resolved (1)H NMR spectra for an aromatic system two times larger than hexa-peri-hexabenzocoronene were recorded. The bulk properties in an extruded fiber as well as on the surface showed a columnar self-assembly including a phase in which a homeotropic alignment on a substrate was observed, which turns the material into an interesting candidate for future applications in electronic devices.     

Synthesis of a three-dimensional spiro-annulated polycyclic aromatic hydrocarbon

We describe the results of our investigation on the preparation, structural characterization, and optical properties of a spiro-annulated polycyclic aromatic hydrocarbon prepared by the cyclodehydrogenation of a hexa{2-(9,9′-spirobifluorenyl)}benzene precursor molecule. Single-crystal X-ray diffraction analysis reveals that the anthracene backbone adopts one of the largest end-to-end twists thus far reported.     

Triplet state dynamics in polycyclic aromatic molecules

Utilizing the technique of triplet absorption detection of magnetic resonance (TADMR), we have determined the rates of intersystem crossing for the individual spin levels of the anthracene-h₁₀ and -d₁₀ and 3,4-benzpyrene triplet states in Shpolskii solvents. The anthracene results are in agreement with other experimental and theoretical work on intersystem crossing in aromatic hydrocarbons. The benzpyrene results, however, are unique, showing a large contribution from the out-of-plane spin level. Possible explanations of this result are discussed.     

Ab initio-based intermolecular carbon-carbon pair potentials for polycyclic aromatic hydrocarbon clusters

We derived the carbon-carbon pair potentials for polycyclic aromatic hydrocarbon (PAH) clusters, which exhibited a strikingly similar geometry to that of the two-layer graphite. The binding energy of PAH clusters ranging in size from the benzene dimer to the pyrene dimer obtained by ab initio calculations at the MP2 level was used to extract the pair potentials in the form of the Lennard-Jones and Exponential-6 functions. Identical binding energy and equilibrium interlayer distance were reproduced by these functions to those calculated by the ab initio method. The pair potentials for PAHs yield the same equilibrium C-C distance as the known pair potentials for graphite and fullerenes, but nearly twice the well depth because of the polarization of the C-H bond.     

Novel boron- and sulfur-doped polycyclic aromatic hydrocarbon as multiple resonance emitter for ultrapure blue thermally activated delayed fluorescence polymers

Boron(B)-and sulfur(S)-doped polycyclic aromatic hydrocarbons(PAHs)are developed as a novel kind of multiple resonance emitters for ultrapure blue thermally activated delayed fluorescence(TADF)polymers with narrowband electroluminescence.The combination of electron-deficient B atom and electron-rich S atom in PAH can form an intramolecular push-pull electronic system in a rigid aromatic framework,leading to reduced singlet-triplet energy splitting and limited structure relaxation of excited states.The critical roles of S atom in determining emission properties with respect to the oxygen analogues are in two aspects:(i)reducing energy bandgap to shift emission from human-eye-insensitive ultraviolet zone to blue region,and(ii)promoting reverse intersystem crossing process by heavy-atom effect to activate TADF effect.The resulting polymer containing B,S-doped PAH as emitter and acridan as host exhibits efficient blue electroluminescence at 458 nm with small full-width at halfmaximum of 31 nm,representing the first example for ultrapure TADF polymer with narrowband electroluminescence.     

A Fourier-transform ion-cyclotron-resonance study of the reactions of polycyclic aromatic hydrocarbon cations with molecules of interstellar interest

The reactivity of naphthalene and pyrene radical cations and their derivatives (C₁₀H_n⁺, n=6,7,8,9), C₁₆H_n (n=9,10,11) has been studied with molecules of interstellar interest in an ion cyclotron resonance apparatus. The radical cations C₁₀H₈⁺ and C₁₆H₁₀⁺ are unreactive with H₂,CO,H₂O and NH₃. Adduct formation is the only channel for almost all reactions of C₁₀H₇⁺ with these molecules. The implications of these results for the stability of polycyclic aromatic hydrocarbon (PAH) cations in the interstellar medium are briefly discussed. Exploratory studies of the ion chemistry of a larger PAH, coronene, have also been done.     

van der Waals interactions of polycyclic aromatic hydrocarbon dimers

Density functional theory is in principle exact and includes also long-range interactions, such as the van der Waals interactions. These are, however, part of the exchange-correlation energy functional that needs to be approximated, and are absent in the local and semilocal standard implementations. Recently a density functional which includes van der Waals interactions for planar systems has been developed, which we show can be extended to provide a treatment of planar molecules. We use this functional to calculate binding distances and energies for dimers of three of the smallest polycyclic aromatic hydrocarbons (PAHs)--naphthalene, anthracene, and pyrene.     

Indium-catalyzed construction of polycyclic aromatic hydrocarbon skeletons via dehydration

Polycyclic aromatic compounds can be synthesized from 2-benzylic- or 2-allylbenzaldehydes using a catalytic amount of In(III) or Re(I) complexes. By using this method, polycyclic aza-aromatic compounds can also be prepared efficiently. In these reactions, only water is formed as a side product.     

Chromium aromatic hydrocarbon sandwich molecules and the eighteen-electron rule

Ab initio density functional theory (DFT) calculations are reported for the chromium sandwich structure CrnR2, where n = 7 and R is the aromatic hydrocarbon hexabenzocoronene (C42H18). This system is remarkable in that the structure of the chromium sites strongly resemble those in chromium bis-benzene Cr1(C6H6)2, as judged by geometry and charge density properties. The electron localization function of the sandwich shows a hexagonally arrayed set of V(C, Cr, C) valence basins about each chromium atom with modification due to local site symmetry. This system satisfies an extension of the 18-electron rule to components of a conjugated molecular system. This idea is explored further by examining the electronic and geometric properties of the series CrnR2, where n and R are given by n = 1, benzene C6H6 as reference; n = 2, biphenyl (C6H5)2; n = 3, triphenylene C18H12; n = 3, coronene C24H18; and n = 4, dibenzopyrene C24H14. On the basis of electron counting and ring isolation, all the sandwich structures in this series could satisfy the extension of the 18-electron rule, with the exception of coronene, which was deliberately included. The DFT calculations predict spin-paired ground states for some but not all of the sandwich structures, implying that the Cr-ring interactions at work require understanding at a deeper level. Thus, while sandwiches with n = 1, n = 2, n = 4 and n = 7 have spin paired singlet ground states and appear to satisfy the rule, those with n = 3 (triphenylene, coronene) have antiferromagnetic singlet ground states and do not. This is attributed to nonuniformity in the electronic charge density of the rings of the isolated hydrocarbons and to a reduction of symmetry from D3h to C2v with a concomitant spin-charge density change in the sandwiches.     

Correlation of free-electron molecular orbital energies with π ionization energies of aromatic hydrocarbons

With the introduction of an effective mass m^* into the simple free-electron model, the π-orbital energies of aromatic hydrocarbons containing up to 10 condensed benzene rings correlate closely with the π-band positions of the corresponding photoelectron spectra. For a sample of 70 π-orbitals the linear regression yields a standard error SE = 0.129 eV. Compared to HMO results, the number of accidental degeneracies is drastically reduced and the correlation is significantly improved. The free-electron results also compare favorably to those obtained by the PPP, EH and MINDO/2 methods which were scaled by two additional parameters.     

K-shell ionization energies in molecules by SCF GF calculations

Energies of CH₄, NH₃, H₂O and C₂H₄ K-ionized molecules are calculated by means of a Group Function method using minimal or near minimal basis sets of STO's. Further results from very large basis sets are reported for CH₄, NH₃, and H₂O. Results seemingly do not suffer the shortcomings of a previous SCF MO treatment.