Chemistry and Chemical Biology Works

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Assessing the accuracy of the isotropic periodic sum method through Madelung energy computation
(2014-04) Ojeda-May, Pedro; Pu, Jingzhi
We tested the isotropic periodic sum (IPS) method for computing Madelung energies of ionic crystals. The performance of the method, both in its nonpolar (IPSn) and polar (IPSp) forms, was compared with that of the zero-charge and Wolf potentials [D. Wolf, P. Keblinski, S. R. Phillpot, and J. Eggebrecht, J. Chem. Phys.110, 8254 (1999)]. The results show that the IPSn and IPSp methods converge the Madelung energy to its reference value with an average deviation of ∼10−4 and ∼10−7 energy units, respectively, for a cutoff range of 18–24a (a/2 being the nearest-neighbor ion separation). However, minor oscillations were detected for the IPS methods when deviations of the computed Madelung energies were plotted on a logarithmic scale as a function of the cutoff distance. To remove such oscillations, we introduced a modified IPSn potential in which both the local-region and long-range electrostatic terms are damped, in analogy to the Wolf potential. With the damped-IPSn potential, a smoother convergence was achieved. In addition, we observed a better agreement between the damped-IPSn and IPSp methods, which suggests that damping the IPSn potential is in effect similar to adding a screening potential in IPSp.
Rapid and Accurate Determination of Stern-Volmer Quenching Constants
(1999) Goodpaster, John V.; McGuffin, Victoria L
In this work, a novel system has been designed, characterized, and validated for the determination of fluorescence quenching constants. Capillary flow injection methods are used to automate the preparation and mixing of the fluorophore and quencher solutions. Because of the small diameter of the capillary (75-200 mu m), fluorescence measurements can be made without corrections for primary and secondary absorbance effects. The fluorescence spectrometer is equipped with a charge-coupled device (CCD) that has a detection limit of 3.0 X 10-9 M (2.3 ppb) and a linear dynamic range of 10 5 for integration times of 0.01-10 s. This spectrometer has a 300 nm spectral range with 1 nm resolution, allowing the fluorescence quenching constants to be calculated at single wavelengths or over integrated wavelength ranges. This system was validated by comparison to traditional methods for the determination of Stern-Volmer constants for alternant and nonalternant polycyclic aromatic hydrocarbons with nitromethane and triethylamine.
Characterization of Automotive Paint Clear Coats by Ultraviolet Absorption Microspectrophotometry with Subsequent Chemometric Analysis
(2010-10) Liszewski, Elisa A; Lewis, Simon W; Siegel, Jay A; Goodpaster, John V.
Clear coats have been a staple in automobile paints for almost thirty years and are of forensic interest when comparing transferred and native paints. However, the ultraviolet (UV) absorbers in these paint layers are not typically characterized using UV microspectrophotometry, nor are the results studied using multivariate statistical methods. In this study, measurements were carried out by UV microspectrophotometry on 71 samples from American and Australian automobiles, with subsequent chemometric analysis of the absorbance spectra. Sample preparation proved to be vital in obtaining accurate absorbance spectra and a method involving peeling the clear coat layer and not using a mounting medium was preferred. Agglomerative hierarchical clustering indicated three main groups of spectra, corresponding to spectra with one, two, and three maxima. Principal components analysis confirmed this clustering and the factor loadings indicated that a substantial proportion of the variance in the data set originated from specific spectral regions (230–265 nm, 275–285 nm, and 300–370 nm). The three classes were well differentiated using discriminant analysis, where the cross-validation accuracy was 91.6% and the external validation accuracy was 81.1%. However, results showed no correlation between the make, model, and year of the automobiles.
Quantitative Analysis of Humectants in Tobacco Products Using Gas Chromatography (GC) with Simultaneous Mass Spectrometry (MSD) and Flame Ionization Detection (FID)
(2013-06) Rainey, Christina L; Shifflett, John R; Goodpaster, John V.; Bezabeh, Dawit Z
This paper describes the modification of an existing gas chromatographic (GC) method to incorporate simultaneous mass spectrometric (MSD) and flame ionization detection (FID) into the analysis of tobacco humectants. Glycerol, propylene glycol, and triethylene glycol were analyzed in tobacco labeled as roll-your-own (RYO), cigar, cigarette, moist snuff, and hookah tobacco. Tobacco was extracted in methanol containing 1,3-butanediol (internal standard), filtered, and separated on a 15 m megabore DB-Wax column. Post-column flow was distributed using a microfluidic splitter between the MSD and FID for simultaneous detection. The limits of detection for the FID detector were 0.5 μg/mL (propylene glycol and triethylene glycol) and 0.25 μg/mL (glycerol) with a linear range of 2–2000 μg/mL (propylene glycol and triethylene glycol) and 1–4000 μg/mL (glycerol). The limits of detection for the MSD detector were 2 μg/mL (propylene glycol and triethylene glycol) and 4 μg/mL (glycerol) with a linear range of 20–2000 μg/mL (propylene glycol and triethylene glycol) and 40–4000 μg/mL (glycerol). Significant improvement in the sensitivity of the MSD can be achieved by employing selective ion monitoring (SIM) detection mode. Although a high degree of correlation was observed between the results from FID and MSD analyses, marginal chromatographic resolution between glycerol and triethylene glycol limits the applicability of FID to samples containing low levels of both of these humectants. Utilizing MSD greatly improves the reliability of quantitative results because compensation for inadequate chromatographic resolution can be accomplished with mass selectivity in detection.
Spore photoproduct lyase: the known, the controversial, and the unknown
(2015) Yang, Linlin; Li, Lei; Department of Chemistry & Chemical Biology, IU School of Science
Spore photoproduct lyase (SPL) repairs 5-thyminyl-5,6-dihydrothymine, a thymine dimer that is also called the spore photoproduct (SP), in germinating endospores. SPL is a radical S-adenosylmethionine (SAM) enzyme, utilizing the 5′-deoxyadenosyl radical generated by SAM reductive cleavage reaction to revert SP to two thymine residues. Here we review the current progress in SPL mechanistic studies. Protein radicals are known to be involved in SPL catalysis; however, how these radicals are quenched to close the catalytic cycle is under debate.
Separation of Opiate Isomers using Electrospray Ionization and Paper Spray Coupled to High-Field Asymmetric Waveform Ion Mobility Spectrometry
(Springer, 2015-05) Manicke, Nicholas E.; Belford, Michael; Department of Chemistry & Chemical Biology, IU School of Science
One limitation in the growing field of ambient or direct analysis methods is reduced selectivity caused by the elimination of chromatographic separations prior to mass spectrometric analysis. We explored the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS), an ambient pressure ion mobility technique, to separate the closely related opiate isomers of morphine, hydromorphone, and norcodeine. These isomers cannot be distinguished by tandem mass spectrometry. Separation prior to MS analysis is, therefore, required to distinguish these compounds, which are important in clinical chemistry and toxicology. FAIMS was coupled to a triple quadrupole mass spectrometer, and ionization was performed using either a pneumatically assisted heated electrospray ionization source (H-ESI) or paper spray, a direct analysis method that has been applied to the direct analysis of dried blood spots and other complex samples. We found that FAIMS was capable of separating the three opiate structural isomers using both H-ESI and paper spray as the ionization source.
Rapid measurement of tacrolimus in whole blood by paper spray-tandem mass spectrometry (PS-MS/MS)
(Elsevier, 2015-02) Shi, Run-Zhang; El Gierari, El Taher M.; Manicke, Nicholas E.; Faix, James D.; Department of Chemistry & Chemical Biology, IU School of Science
Background Liquid chromatography-tandem mass spectrometry (LC-MS/MS) provides sensitivity and specificity for monitoring tacrolimus drug level in blood, but it requires an LC system and sample preparation, which is not amenable to random access testing typical of immunoassays. Paper spray (PS) ionization generates gas phase analyte ions directly from dried blood spots without sample preparation and LC. We evaluated a PS-MS/MS method for tacrolimus drug monitoring in a clinical diagnostic laboratory. Methods Whole blood sample was mixed with stable isotope labeled internal standard ([13C, 2H2]-FK506) and spotted onto a cartridge containing triangular shaped card paper. After drying, samples were analyzed by PS MS/MS in the selected reaction monitoring (SRM) mode, with a run time of 3 min/sample. Results Analytical measurement range was 1.5–30 ng/ml. Assay inter-day imprecision was 13%, 8%, and 5% at tacrolimus concentrations of 4.5, 10.5, and 24.5 ng/ml, respectively. Accuracy was determined by pure tacrolimus solution and was confirmed by result correlation to an immunoassay (slope = 1.0, intercept = − 0.02; r2 = 0.99), and to a conventional LC-MS/MS method (slope = 0.90, intercept = 0.4; r2 = 0.94). Conclusions PS-MS/MS provides accurate results for tacrolimus with rapid turnaround time amenable to random access testing protocols.
Direct Aerobic Carbonylation of C(sp2)-H and C(sp3)-H Bonds through Ni/Cu Synergistic Catalysis with DMF as the CO Source
(ACS, 2015-03) Wu, Xuesong; Zhao, Yan; Ge, Haibo; Department of Chemistry & Chemical Biology, IU School of Science
The direct carbonylation of aromatic sp2 and unactivated sp3 C–H bonds of amides was achieved via nickel/copper catalysis under atmospheric O2 with the assistance of a bidentate directing group. The sp2 C–H functionalization showed high regioselectivity and good functional group compatibility. The sp3 C–H functionalization showed high site-selectivity by favoring the C–H bonds of α-methyl groups over those of the α-methylene, β- or γ-methyl groups. Moreover, this reaction showed a predominant preference for functionalizing the α-methyl over α-phenyl group. Mechanistic studies revealed that nickel/copper synergistic catalysis is involved in this process.
Mechanistic Study of the Formation of Bright White Light-Emitting Ultrasmall CdSe Nanocrystals: Role of Phosphine Free Selenium Precursors
(ACS, 2015-01) Dolai, Sukanta; Dutta, Poulami; Muhoberac, Barry B.; Irving, Charles D.; Sardar, Rajesh; Department of Chemistry & Chemical Biology, IU School of Science
We have designed a new nonphosphinated reaction pathway, which includes synthesis of a new, highly reactive Se-bridged organic species (chalcogenide precursor), to produce bright white light-emitting ultrasmall CdSe nanocrystals of high quality under mild reaction conditions. The detailed characterization of structural properties of the selenium precursor through combined 77Se NMR and laser desorption ionization–mass spectrometry (LDI-MS) provided valuable insights into Se release and delineated the nanocrystal formation mechanism at the molecular level. The 1H NMR study showed that the rate of disappearance of Se precursor maintained a single-exponential decay with a rate constant of 2.3 × 10–4 s–1 at room temperature. Furthermore, the combination of LDI-MS and optical spectroscopy was used for the first time to deconvolute the formation mechanism of our bright white light-emitting nanocrystals, which demonstrated initial formation of a smaller key nanocrystal intermediate (CdSe)19. Application of thermal driving force for destabilization resulted in (CdSe)n nanocrystal generation with n = 29–36 through continuous dissolution and addition of monomer onto existing nanocrystals while maintaining a living-polymerization type growth mode. Importantly, our ultrasmall CdSe nanocrystals displayed an unprecedentedly large fluorescence quantum yield of ∼27% for this size regime (<2.0 nm diameter). These mixed oleylamine and cadmium benzoate ligand-coated CdSe nanocrystals showed a fluorescence lifetime of ∼90 ns, a significantly large value for such small nanocrystals, which was due to delocalization of the exciton wave function into the ligand monolayer. We believe our findings will be relevant to formation of other metal chalcogenide nanocrystals through expansion of the understanding and manipulation of surface ligand chemistry, which together will allow the preparation of “artificial solids” with high charge conductivity and mobility for advanced solid-state device applications.
Examining the base stacking interaction in a dinucleotide context via reversible cyclobutane dimer analogue formation under UV irradiation
(Royal Society of Chemistry, 2013-11-14) Liu, Degang; Li, Lei; Chemistry & Chemical Biology, School of Science
Substituted tolyl groups are considered as close isosteres of the thymine (T) residue. They can be recognized by DNA polymerases as if they were thymine. Although these toluene derivatives are relatively inert toward radical additions, our recent finding suggests that the dinucleotide analogue TpTo (To = 2'-deoxy-1-(3-tolyl)-β-D-ribofuranose) supports an ortho photocycloaddition reaction upon UV irradiation, producing two cyclobutane pyrimidine dimer (CPD) analogues 2 and 3. Our report here further shows that formation of these CPD species is reversible under UVC irradiation, resembling the photochemical property of the CPD species formed between two Ts. Analyzing the stability of these CPD analogues suggests that one (2) is more stable than the other (3). The TpTo conformer responsible for 2 formation is also more stable than that responsible for 3 formation, as indicated by the Gibbs free energy change calculated from the constructed Bordwell thermodynamic cycle. These different stabilities are not due to the varying photochemical properties, as proved by quantum yields determined from the corresponding photoreactions. Instead, they are ascribed to the different stacking interaction between the T and the To rings both in the TpTo dinucleotide as well as in the formed CPD analogues. Factors contributing to the ring stacking interactions are also discussed. Our proof-of-concept approach suggests that a carefully designed Bordwell cycle coupled with reversible CPD formations under UV irradiation can be very useful in studying DNA base interactions.

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