Browsing by Author "Department of Chemistry & Chemical Biology, IU School of Science"
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Item 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 ScienceThe 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.Item Kinetic and pH Studies on Human Phenylethanolamine N-Methyltransferase(Elsevier, 2013-11) Wu, Qian; McLeish, Michael J.; Department of Chemistry & Chemical Biology, IU School of SciencePhenylethanolamine N-methyltransferase (PNMT) catalyzes the conversion of norepinephrine (noradrenaline) to epinephrine (adrenaline) while, concomitantly, S-adenosyl-l-methionine (AdoMet) is converted to S-adenosyl-l-homocysteine. This reaction represents the terminal step in catecholamine biosynthesis and inhibitors of PNMT have been investigated, inter alia, as potential antihypertensive agents. At various times the kinetic mechanism of PNMT has been reported to operate by a random mechanism, an ordered mechanism in which norepinephrine binds first, and an ordered mechanism in which AdoMet binds first. Here we report the results of initial velocity studies on human PNMT in the absence and presence of product and dead end inhibitors. These, coupled with isothermal titration calorimetry and fluorescence binding experiments, clearly shown that hPNMT operates by an ordered sequential mechanism in which AdoMet binds first. Although the log V pH-profile was not well defined, plots of log V/K versus pH for AdoMet and phenylethanolamine, as well as the pKi versus pH for the inhibitor, SK&F 29661, were all bell-shaped indicating that a protonated and an unprotonated group are required for catalysis.Item 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 ScienceWe 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.Item Microbial Degradation of Gasoline in Soil: Effect of Season of Sampling(Elsevier, 2015-06) Turner, Dee A.; Pichtel, J.; Rodenas, Y.; McKillip, John L.; Goodpaster, John V.; Department of Chemistry & Chemical Biology, IU School of ScienceIn cases where fire debris contains soil, microorganisms can rapidly and irreversibly alter the chemical composition of any ignitable liquid residue that may be present. In this study, differences in microbial degradation due to the season in which the sample is collected was examined. Soil samples were collected from the same site during Fall, Winter, Spring and Summer and the degradation of gasoline was monitored over 30 days. Predominant viable bacterial populations enumerated using real-time PCR and reverse transcriptase polymerase chain reaction (RT-PCR) enumeration revealed the predominant viable bacterial genera to be Alcaligenes, Bacillus, and Flavobacterium. Overall, the compounds most vulnerable to microbial degradation are the n-alkanes, followed by the mono-substituted alkylbenzenes (e.g., toluene, ethylbenzene, propylbenzene and isopropylbenzene). Benzaldehyde (a degradation product of toluene) was also identified as a marker for the extent of biodegradation. Ultimately, it was determined that soil collected during an unusually hot and dry summer exhibited the least degradation with little to no change in gasoline for up to 4 days, readily detectable n-alkanes for up to 7 days and relatively high levels of resilient compounds such as o-xylene, p-xylene and 1,3,5-trimethylbenzene. These results demonstrate, however, that prompt preservation and/or analysis of soil evidence is required in order to properly classify an ignitable liquid residue.Item Optimized CGenFF force-field parameters for acylphosphate and N-phosphonosulfonimidoyl functional groups(Springer, 2013-11) Hegazy, Lamees; Richards, Nigel G.; Department of Chemistry & Chemical Biology, IU School of ScienceWe report an optimized set of CGenFF parameters that can be used to model small molecules containing acylphosphate and N-phosphonosulfonimidoyl functional groups in combination with the CHARMM force field. Standard CGenFF procedures were followed to obtain bonded interaction parameters, which were validated by geometry optimizations, comparison to the results of calculations at the MP2/6-31+G(d) level of theory, and molecular dynamics simulations. In addition, partial atomic charges were assigned so that the energy of hydrogen bonding of the model compounds with water was correctly reproduced. The availability of these parameters will facilitate computational studies of enzymes that generate acyladenylate intermediates during catalytic turnover. In addition, given that the N-phosphonosulfonimidoyl moiety is a stable transition state analog for the reaction of ammonia with an acyladenylate, the parameters developed in this study should find use in efforts to develop novel and potent inhibitors of various glutamine-dependent amidotransferases that have been validated as drug targets. Topology and parameter files for the model compounds used in this study, which can be combined with other CGenFF parameters in computational studies of more complicated acylphosphates and N-phosphonosulfonimidates are made available.Item 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 ScienceBackground 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.Item 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 ScienceOne 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.Item Spore photoproduct lyase: the known, the controversial, and the unknown(2015) Yang, Linlin; Li, Lei; Department of Chemistry & Chemical Biology, IU School of ScienceSpore 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.Item Structural basis for a six nucleotide genetic alphabet(ACS, 2015-05) Georgiadis, Millie M.; Singh, Isha; Kellet, Whitney F.; Hoshika, Shuichi; Benner, Steven A.; Richards, Nigel G. J.; Department of Chemistry & Chemical Biology, IU School of ScienceExpanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard “edge on” Watson–Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.Item Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations(AIP, 2015-11) Ojeda-May, Pedro; Pu, Jingzhi; Department of Chemistry & Chemical Biology, IU School of ScienceThe Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r −1 term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.