Enhanced diradical nature in oxyallyl derivatives leads to near infra red absorption: a comparative study of the squaraine and croconate dyes using computational techniques

We apply many criteria to estimate the diradical character of the ground state singlets of several oxyallyl derivatives. This is carried out as the oxyallyl derivatives like squaraine and croconate dyes can be represented by both mesoionic and diradical formulas, the domination of which would characterize its lowest energy transition. One criterion applied is the singlet-triplet gap, which is known to be inversely proportional to the diradical character. Another criterion is the occupation number; this is determined for the symmetry broken state of the molecules in the unrestricted formalism, and the difference of occupation in the HOMO and LUMO is related to the diradical character. The diradical character of all of the croconates and few squaraines is estimated to be large. All of these have absorption above 750 nm and can be classified as near infrared (NIR) dyes, leading to the inference that NIR absorptions in these molecules are largely due to the dominance of the diradical character. To understand the reliability of the DFT methods for the absorption property predictions of these molecules, TD-DFT studies to calculate the vertical excitation energies have been carried out, using the B3LYP/ BLYP exchange correlation functionals and the LB94 asymptotic functional with and without the inclusion of solvent. The deviations, in both the squaraine series (average lower diradical character), are found to be systematic, and with the inclusion of the solvent in the calculation, the deviations decrease. The best least-squares fit with the experimentally observed values using B3LYP /6-311G(d, p) for the symmetric squaraines yields an R value of 0.92 and, for the unsymmetric squaraines, an R value of 0.936. With inclusion of the solvent, the R value is 0.96 for the symmetric squaraines and 0.961 for the unsymmetric squaraines, indicating that these DFT functionals with linear scaling may be used to study these systems. The croconate dyes, however, have larger deviation from the experimentally observed values in all of the functionals studied even after inclusion of the solvent effects. The deviations are also not systematic. The deviation with respect to the experiment in this case is attributed to the average larger diradical character in this series.     

Nonequilibrium solvation for vertical photoemission and photoabsorption processes using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model

In this paper, we present the theory and implementation of a nonequilibrium solvation model for the symmetry-adapted cluster (SAC) and symmetry-adapted cluster-configuration interaction (SAC-CI) method in the polarizable continuum model. For nonequilibrium solvation, we adopted the Pekar partition scheme in which solvent charges are divided into dynamical and inertial components. With this nonequilibrium solvation scheme, a vertical transition from an initial state to a final state may be described as follows: the initial state is described by equilibrium solvation, while in the final state, the inertial component remains in the solvation for the initial state; the dynamical component will be calculated self-consistently for the final state. The present method was applied to the vertical photoemission and absorption of s-trans acrolein and methylenecyclopropene. The effect of nonequilibrium solvation was significant for a polar solvent.     

Theoretical study of valence photoelectron spectra of Re(CO)5X (X=Cl, Br, and I): a spin-orbit DK3 symmetry-adapted cluster/symmetry-adapted cluster-configuration interaction study

The valence photoelectron spectra of Re(CO)(5)X (X=Cl, Br, and I) are studied theoretically using symmetry-adapted cluster (SAC)/SAC-configuration interaction (SAC-CI) theory. The relativistic effects are included by the third-order Douglas-Kroll (DK3) method, and the spin-orbit coupling is also considered. Both electron correlation and relativistic effects are significant in assigning the valence photoelectron spectra of Re(CO)(5)X (X=Cl, Br, and I). DK3-SAC/SAC-CI provides values for the relative peak positions in a reasonable agreement with the observed photoelectron spectra. The sequence of ionization energies for Re(CO)(5)Cl, Re(CO)(5)Br, and Re(CO)(5)I are calculated as e(')[a(1)(Cl)]>e(')[e(Re+Cl)] approximately e(")[e(Re+Cl)]>e(")[b(2)(Re)]>e(')[e(Re-Cl)]>e(")[e(Re-Cl)], e(')[a(1)(Br)]>e(')[e(Re+Br)]>e(")[e(Re+Br)+b(2)(Re)]>e(")[b(2)(Re)+e(Re+Br)]>e(')[e(Re-Br)]>e(")[e(Re-Br)], and e(')[e(Re+I)+a(1)(I)]>e(")[b(2)(Re)+e(Re+I)] approximately e(')[a(1)(I)+e(Re+I)]>e(")[e(Re+I)+b(2)(Re)]>e(')[e(Re-I)]>e(")[e(Re-I)], respectively. These assignments are quite new and different from previous assignments.     

Excited-state geometries and vibrational frequencies studied using the analytical energy gradients of the direct symmetry-adapted cluster-configuration interaction method. I. HAX-type molecules

In this series of studies, we systematically apply the analytical energy gradients of the direct symmetry-adapted cluster-configuration interaction singles and doubles nonvariational method to calculate the equilibrium geometries and vibrational frequencies of excited and ionized states of molecules. The harmonic vibrational frequencies were calculated using the second derivatives numerically computed from the analytical first derivatives and the anharmonicity was evaluated from the three-dimensional potential energy surfaces around the local minima. In this paper, the method is applied to the low-lying valence singlet and triplet excited states of HAX-type molecules, HCF, HCCl, HSiF, HSiCl, HNO, HPO, and their deuterium isotopomers. The vibrational level emission spectra of HSiF and DSiF and absorption spectra of HSiCl and DSiCl were also simulated within the Franck-Condon approximation and agree well with the experimental spectra. The results show that the present method is useful and reliable for calculating these quantities and spectra. The change in geometry in the excited states was qualitatively interpreted in the light of the electrostatic force theory. The effect of perturbation selection with the localized molecular orbitals on the geometrical parameters and harmonic vibrational frequencies is also discussed.     

Binding interaction of cationic phenazinium dyes with calf thymus DNA: a comparative study

Absorption, steady-state fluorescence, steady-state fluorescence anisotropy, and intrinsic and induced circular dichroism (CD) have been exploited to explore the binding of calf thymus DNA (ctDNA) with three cationic phenazinium dyes, viz., phenosafranin (PSF), safranin-T (ST), and safranin-O (SO). The absorption and fluorescence spectra of all the three dyes reflect significant modifications upon interaction with the DNA. A comparative study of the dyes with respect to modification of fluorescence and fluorescence anisotropy upon binding, effect of urea, iodide-induced fluorescence quenching, and CD measurements reveal that the dyes bind to the ctDNA principally in an intercalative fashion. The effect of ionic strength indicates that electrostatic attraction between the cationic dyes and ctDNA is also an important component of the dye-DNA interaction. Intrinsic and induced CD studies help to assess the structural effects of dyes binding to DNA and confirm the intercalative mode of binding as suggested by fluorescence and other studies. Finally it is proposed that dyes with bulkier substitutions are intercalated into the DNA to a lesser extent.     

Electronic spectra and photodissociation of vinyl chloride: a symmetry-adapted cluster configuration interaction study

The vertical absorption spectrum and photodissociation mechanism of vinyl chloride (VC) were studied by using symmetry-adapted cluster configuration interaction theory. The important vertical pi --> pi* excitation was intensively examined with various basis sets up to aug-cc-pVTZ augmented with appropriate Rydberg functions. The excitation energy for pi --> pi* transition obtained in the present study, 6.96 eV, agrees well with the experimental value, 6.7-6.9 eV. Calculated excitation energies along with the oscillator strengths clarify that the main excitation in VC is the pi --> pi* excitation. Contrary to the earlier theoretical reports, the results obtained here support that the C-Cl bond dissociation takes place through the n(Cl-)sigma(C-Cl)* state.     

Red light in chemiluminescence and yellow-green light in bioluminescence: color-tuning mechanism of firefly, Photinus pyralis, studied by the symmetry-adapted cluster-configuration interaction method

The yellow-green luminescence from firefly luciferase has long been understood to be the emission from enol-oxyluciferin. However, a recent experiment showed that an oxyluciferin constrained to the keto form produced a yellow-green emission in luciferase (Branchini, B. R.; Murtiashaw, M. H.; Magyar, R. A.; Portier, N. C.; Ruggiero, M. C.; Stroh, J. G. J. Am. Chem. Soc. 2002, 124, 2112-2113). The present quantum mechanical/molecular mechanical and symmetry-adapted cluster-configuration interaction (SAC-CI) theoretical study supports the keto-form to be the yellow-green bioluminescence state in luciferase. We give the theoretically optimized structure of the excited state of oxyluciferin within luciferase, which gives luminescence calculated by the SAC-CI method that is close to the experimental value. Coulombic interactions with neighboring residues, in particular Arg218 and the phosphate group of AMP, play important roles in the color-tuning mechanism. Transformation to the enol form is energetically unfavorable in the luciferase environment. The twisted intramolecular charge-transfer (TICT) state is meta stable and would be easily relaxed to the co-planer structure. Further analyses were performed to verify the spectral-tuning mechanism based on the protonation state and the resonance structure of oxyluciferin.     

Electronic excitation spectra of radical anions of cyanoethylenes and cyanobenzenes: symmetry adapted cluster-configuration interaction study

Electronic excitation spectra of the radical anions of cyanoethylenes (trans-dicyanoethylene and tetracyanoethylene) and cyanobenzenes (1,2-dicyanobenzene: o-DCNB, 1,3-dicyanobenzene: m-DCNB, and 1,4-dicyanobenzene: p-DCNB) were studied by the symmetry adapted cluster-configuration interaction (SAC-CI) method. Theoretical calculations predicted positive electron affinities for all the molecules in good agreement with the experimental observations. Electronic excitation spectra of open-shell radicals is a topic that has not been studied as much as such spectra of closed-shell molecules, but this can be easily addressed using SAC-CI theory. The present paper systematically describes the calculation procedures for radical anions by investigating several basis sets, including anion diffuse and Rydberg functions. The calculated excitation energies were in good agreement with the experimental UV∕NIR (near infrared region) spectra, which had been observed by one of the present authors in 2-methyltetrahydrofuran matrix frozen to transparent glassy solids at 77 K. For p-DCNB, the SAC-CI theoretical spectrum agreed particularly well with the experimental spectrum. An extremely weak π*(SOMO) - π* excitation at 1.41 eV predicted in the present work, but had been overlooked in the previous experimental spectrum published in 1988, was confirmed to be real by a careful re-examination of the old spectrum.     

Spectroscopy of sodium atom in liquid helium cluster: a symmetry adapted cluster-configuration interaction (SAC-CI) study

Excitation line shift of the principal resonance line of sodium atom embedded in liquid helium is estimated using symmetry adapted cluster-configuration interaction (SAC-CI) method with a reasonably good choice of basis set. The effect of the liquid surroundings is considered by taking only the nearest neighbor interaction using several model clusters of helium atoms with a centrally located isolated sodium atom. The transition wavelength of the ²P ← ²S line of Na is estimated both for the free Na and for the Na atom centrally located inside a model helium cluster. The shift depends obviously on the model cluster and the distance of the central Na atom from the surrounding He atom. With a physically realizable structure, SAC-CI calculation correctly predicts the theoretical results obtained previously on such estimates.     

Investigation of aggregation behavior using computational methods and absorption spectra for trisazo direct dyes

Direct dyes are likely to self-associate in aqueous solutions. Here, we present the aggregation characteristics of three trisazo direct dyes investigated using a procedure, which combines computational and experimental approaches. The geometric features of the molecules and their aggregates were elucidated by molecular modeling and optimization. The relative energies specific for the aggregation process yielded the optimum number of molecules forming an aggregate: two for AHDS dye and three for SDH and AIDS dyes. The results were further confirmed by using spectrometric determination and mathematical analysis. Accordingly, molecular aggregation was studied in aqueous solutions as a function of dye concentration (10^?6–10^?3 mol/l) and solution pH (4–10). As the dye concentration increased, shifts in absorption spectra were observed, suggesting the formation of aggregates. The pH variation produced a change in the spectral maximum, confirming the aggregation. The mathematical processing of the absorption spectrum data confirmed the number of chemical species of each aggregate as resulted from computational calculations.     

Green synthesis of banana flavor using different catalysts: a comparative study of different methods

ABSTRACT

Esterification of isoamyl alcohol with acetic acid was studied using different ion-exchange resins, namely Amberlyst 15 dry, Amberlyst 16 wet, Amberlite 120-IR. Esterification was carried out using different esterification methods that are quite new (ohmic, ultrasonic probe, and ultrasonic bath) and the results were compared with microwave-assisted esterification (MAE). The highest isoamyl acetate yield (99%) was obtained by MAE, using a mixture of acetic acid and isoamyl alcohol (mole ratio of 1:2) after 2?h of reaction time. In this process, 2% Amberlyst 15 dry was used. MAE had the least specific energy consumption (0.42?kWh/g isoamyl acetate) and specific CO₂ emission (34?g/g isoamyl acetate). According to the images obtained by scanning electron microscopy, lower amounts of Amberlyst 15 dry beads were destroyed by MAE method compared to other esterification methods. In conclusion, MAE proved to be an economic and environmentally-friendly method for esterification of different flavoring compounds.     

Near-infrared fluorescent probes: synthesis and spectroscopic investigations of a few amphiphilic squaraine dyes

With the objective of developing near-infrared fluorescence probes for biological applications, a few squaraine dyes 3a-d, containing amphiphilic substituents, were synthesized and their photophysical properties have been investigated in the presence and absence of the organized media. These dyes exhibited absorption in the range 630-650 nm, with significant absorption coefficients (epsilon = 1-3 x 10(5) M(-1) cm(-1)) in the aqueous medium. The fluorescence spectra of these dyes showed emission maximum from 660 to 675 nm, depending on the nature of substituents. The fluorescence quantum yields were in the range from 0.15 to 0.21 in ethanol, but 10 times lower values were observed (phi(f) = 0.01-0.02) in the aqueous medium. In the presence of micelles such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, and Triton X-100, these dyes showed negligible changes in their absorption properties, whereas a significant enhancement (5-10-folds) in their fluorescence yields was observed. Picosecond time-resolved studies indicated that these dyes show single-exponential decay in ethanol and ethanol-water mixtures; however, they exhibit biexponential decay with longer lifetimes in the presence of the micellar media. The results indicate that these novel amphiphilic squaraine dyes 3a-d, which exhibit favorable photophysical properties, good solubility in the aqueous medium, and interact efficiently with micelles, can have potential biological applications as near-infrared fluorescence sensors.     

Charge reduction in a vermiculite by acid and hydrothermal methods: a comparative study

A comparative study on acid and hydrothermal methods as ways to reduce interlamellar charge has been carried out on a vermiculite. This study showed that the application of the hydrothermal treatment as a previous step to pillaring the vermiculites, reported here for the first time, is a new route to obtain the porous material with a particular interest as heterogeneous catalysts, starting from mineral clays with a high density of charge. Modified clays have been characterized by atomic absorption, emission spectrograph, X-ray diffraction, cation-exchange capacity, total acidity, infrared spectroscopy (DRIFT), and nitrogen adsorption. The results have shown that all solids have been structurally modified. However, acid and hydrothermal methods showed different behavior. For the vermiculite, the hydrothermal treatment did not produce major differences in terms of the crystalline structure, whereas the acid method caused severe structural damage. The catalytic properties have been tested over Pt-impregnated samples (1%) using the hydroisomerization of heptane. Important catalytic activity was established for all solids with high selectivity regarding the isomer products.     

Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry-adapted cluster/configuration interaction methodology

UV photoelectron spectra of hypoxanthine, xanthine, and caffeine, up to 20 eV, were calculated and compared with the experimental spectra reported in literature. The calculations were performed using a novel version of the quantum mechanical symmetry-adapted cluster/configuration interaction (SAC-CI) method termed, direct SAC-CI. The Duning/Huzinaga valance double-zeta D95+(d,p) Gaussian basis set was also employed with this method. The ionization energies and intensities were calculated, and the corresponding spectral bands were assigned. Natural bonding orbital (NBO) calculations were employed for better spectral band assignment. The calculated ionization energies and intensities reasonably produced the experimental photoelectron spectra.     

Adsorption study of cationic dyes having a trimethylammonium anchor group on hectorite using electrooptic and spectroscopic methods

Clay minerals are natural or synthetic material of colloidal dimensions. Due to the sheetlike structure clay minerals offer a huge specific surface area and hence optimal properties for modification through adsorption. The current work studies the adsorption of five cationic dyes on the synthetic clay mineral hectorite. All dyes have a trimethylammonium anchoring group in common. The adsorbed dye molecules are characterized by means of pulsed electric linear dichroism and UV-VIS spectroscopy. With increasing dye loading a continuous shift in the absorption spectra is observed. But there is no occurrence of a new absorption band. Therefore we conclude that the dyes preferentially adsorb as amorphous aggregates on the clay surface. At low dye loadings the dye molecules lie flat on the clay mineral surface. Increasing dye concentration leads to a continuous increase in average tilt angle. However the orientation of the dye molecules is very sensitive to functional groups. The introduction of a nitro group to a particular dye increases significantly the tendency to lie flat on the surface whereas the introduction of a methoxy group at the same position has the opposite effect.     

Hard sphere fluids at a soft repulsive wall: a comparative study using Monte Carlo and density functional methods

Hard-sphere fluids confined between parallel plates at a distance D apart are studied for a wide range of packing fractions including also the onset of crystallization, applying Monte Carlo simulation techniques and density functional theory. The walls repel the hard spheres (of diameter σ) with a Weeks-Chandler-Andersen (WCA) potential V(WCA)(z) = 4ε[(σ(w)/z)(12) - (σ(w)/z)(6) + 1/4], with range σ(w) = σ/2. We vary the strength ε over a wide range and the case of simple hard walls is also treated for comparison. By the variation of ε one can change both the surface excess packing fraction and the wall-fluid (γ(wf)) and wall-crystal (γ(wc)) surface free energies. Several different methods to extract γ(wf) and γ(wc) from Monte Carlo (MC) simulations are implemented, and their accuracy and efficiency is comparatively discussed. The density functional theory (DFT) using fundamental measure functionals is found to be quantitatively accurate over a wide range of packing fractions; small deviations between DFT and MC near the fluid to crystal transition need to be studied further. Our results on density profiles near soft walls could be useful to interpret corresponding experiments with suitable colloidal dispersions.     

Analysis of chloramphenicol residues in swine tissues and milk: comparative study using different screening and quantitative methods

Both screening and quantitative methods for chloramphenicol residues in swine tissues and milk were compared, using samples from animals treated with chloramphenicol. For screening purposes a previously developed streptavidin-biotin enzyme-linked immunosorbent assay and a commercially available immunochemical card test were used. For quantitative purposes two previously developed high-performance liquid chromatographic procedures were applied using antibody-mediated clean-up and solid-phase extraction. Some improvements in both methods were also described. The results obtained with the screening tests and those obtained with the quantitative methods correspond well with each other. Using a combination of these methods, an effective control of residues of chloramphenicol can be performed in milk from the 1 microgram/kg level and in swine tissues from the 10 micrograms/kg level.     

Role of donor-acceptor strengths and separation on the two-photon absorption response of cytotoxic dyes: a TD-DFT study

Time-dependent density functional theory (TD-DFT) is applied to model one-photon (OPA) and two-photon (TPA) absorption spectra in a series of conjugated cytotoxic dyes. Good agreement with available experimental data is found for calculated excitation energies and cross sections. Calculations show that both OPA and TPA spectra in the molecules studied are typically dominated by two strong peaks corresponding to different electronic states. We find that donor-acceptor strengths and conjugated bridge length have a strong impact on the cross-section magnitudes of low- and high-frequency TPA maxima, respectively. These trends are analyzed in terms of the natural transition orbitals of the corresponding electronic states. Observed structure-property relationships may have useful implications on design of organic conjugated chromophores with tunable two-photon absorption properties for photodynamic therapy applications.     

Conformational preferences in alkylbenzenes and aryl-alkylamines: A comparative study using CAMSEQ,MM2 and molecular dynamics methods

Conformational preferences in a series of alkylbenzenes and protonated and neutral aryl-alkylamines of biological interest have been examined. First, a general picture was obtained for the 25 compounds in the series by means of the CAMSEQ empirical potential software system. This provided solution as well as vacuum data. A low-energy “folded” conformation (alkyl chain coiled toward aromatic ring) was observed in every case. The presence of an amino nitrogen atom in the alkyl chain did not significantly influence conformational preference. Secondly, a group of 14 compounds, representative of the subgroupings within the main series, was selected and the previously established (CAMSEQ) folded and extended minimum positions were further examined by means of a modified MM2 program. Energy differences between conformers were also calculated, and the presence of a stable folded form was confirmed. A feature common to many of the folded conformations is the positioning over the ring of a hydrogen atom from the terminal group of the chain. The MM2 folded/extended energy differences were in some cases smaller than those determined by CAMSEQ, with the “extended” form in many cases being about 1 or 2 kcal/mol more stable. Thirdly, three representative compounds from the series were examined by means of a molecular dynamics program which permitted the sampling of conformational space throughout the transition from extended to folded forms. This method gave energy differences between folded and extended conformations which agreed with the corresponding MM2 differences.     

Substitutional and orientational disorder in organic crystals: a symmetry-adapted ensemble model

Modelling of disorder in organic crystals is highly desirable since it would allow thermodynamic stabilities and other disorder-sensitive properties to be estimated for such systems. Two disordered organic molecular systems are modeled using a symmetry-adapted ensemble approach, in which the disordered system is treated as an ensemble of the configurations of a supercell with respect to substitution of one disorder component for another. Computation time is kept manageable by performing calculations only on the symmetrically inequivalent configurations. Calculations are presented on a substitutionally disordered system, the dichloro/dibromobenzene solid solution, and on an orientationally disordered system, eniluracil, and the resultant free energies, disorder patterns, and system properties are discussed. The results are found to be in agreement with experiment, when some physically implausible configurations are removed from the ensemble average for eniluracil, highlighting the dangers of a completely automated approach to organic crystal thermodynamics which ignores the barriers to equilibration once the crystal has been formed.