Processing MALDI Mass Spectra to Improve Mass Spectral Direct Tissue Analysis

Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.     

Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment

The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.     

Efficient discrimination of transplutonium actinides by in vivo models

Transplutonium actinides are among the heaviest elements whose macroscale chemical properties can be experimentally tested. Being scarce and hazardous, their chemistry is rather unexplored, and they have traditionally been considered a rather homogeneous group, with most of their characteristics extrapolated from lanthanide surrogates. Newly emerged applications for these elements, combined with their persistent presence in nuclear waste, however, call for a better understanding of their behavior in complex living systems. In this work, we explored the biodistribution and excretion profiles of four transplutonium actinides (²⁴⁸Cm, ²⁴⁹Bk, ²⁴⁹Cf and ²⁵³Es) in a small animal model, and evaluated their in vivo sequestration and decorporation by two therapeutic chelators, diethylenetriamine pentaacetic acid and 3,4,3-LI(1,2-HOPO). Notably, the organ deposition patterns of those transplutonium actinides were element-dependent, particularly in the liver and skeleton, where lower atomic number radionuclides showed up to 7-fold larger liver/skeleton accumulation ratios. Nevertheless, the metal content in multiple organs was significantly decreased for all tested actinides, particularly in the liver, after administering the therapeutic agent 3,4,3-LI(1,2-HOPO) post-contamination. Lastly, the systematic comparison of the radionuclide biodistributions showed discernibly element-dependent organ depositions, which may provide insights into design rules for new bio-inspired chelating systems with high sequestration and separation performance.

Transplutonium actinides are among the heaviest elements whose macroscale chemical properties can be experimentally tested.     

Structural characterization of G-quadruplexes in deoxyguanosine clusters using ion mobility mass spectrometry

The aggregation and conformation of deoxyguanosine (dG) in an ammonium acetate buffer solution were examined using mass spectrometry, ion mobility, and molecular mechanics/dynamics calculations. The nano-ESI mass spectrum indicated that 4 and 6 dGs cluster with 1 NH4+; 11 dGs with 2 NH4+; 14, 16, and 17 dGs with 3 NH4+; and 23 dGs with 4 NH4+. The collision cross sections with helium were measured and compared with calculated cross sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct arrival time distribution (ATD) peaks were observed for (4dG + NH4)+. One peak was assigned to the quadruplex structure of (4dG + NH4)+, while the other two peaks corresponded to the quadruplex structures of (8dG + 2NH4)2+ and (12dG + 3NH4)3+, all with the same m/z. Four ATD peaks were observed for (6dG + NH4)+ and assigned to the globular structure of (6dG + NH4)+, and the quadruplex structures of (12dG + 2NH4)2+, (18dG + 3NH4)3+, and (24dG + 4NH4)4+. Two ATD peaks were observed for (11dG + 2NH4)2+ and assigned to the quadruplex structures of (11dG + 2NH4)2+ and (22dG + 4NH4)4+. All of the other clusters in the mass spectrum (14, 16, and 17 dGs with 3 NH4+ and 23 dGs with 4 NH4+) only had one peak in their ATDs and in all cases the theoretical structures in a quadruplex arrangement agreed with the experimental cross sections. These results provide compelling evidence that quadruplexes are present in solution and retain their structure during the spray process, dehydration, and detection.     

Catalysis of the Michael addition reaction by late transition metal complexes of BINOL-derived salens

Salen metal complexes incorporating two chiral BINOL moieties have been synthesized and characterized by X-ray crystallography. The X-ray structures show that this new class of Ni-BINOL-salen catalysts contains an unoccupied apical site for potential coordination of an electrophile and naphthoxides that are independent from the Lewis acid center. These characteristics allow independent alteration of the Lewis acidic and Br?nsted basic sites. These unique complexes have been shown to catalyze the Michael reaction of dibenzyl malonate and cyclohexenone with good selectivity (up to 90% ee) and moderate yield (up to 79% yield). These catalysts are also effective in the Michael reaction between other enones and malonates. Kinetic data show that the reaction is first order in the Ni*Cs-BINOL-salen catalyst. Further experiments probed the reactivity of the individual Lewis acid and Br?nsted base components of the catalyst and established that both moieties are essential for asymmetric catalysis. All told, the data support a bifunctional activation pathway in which the apical Ni site of the Ni*Cs-BINOL-salen activates the enone and the naphthoxide base activates the malonate.     

Structural,spectroscopic, and reactivity comparison of xanthene- and dibenzofuran-bridged cofacial bisporphyrins

A comparison of the structure, spectroscopy, and oxygen atom-transfer reactivity of cofacial bisporphyrins anchored by xanthene (DPX) and dibenzofuran (DPD) pillars is presented. The synthesis and characterization of dicopper(II) and dinickel(II) complexes of DPD completes a homologous series of homobimetallic zinc(II), copper(II), and nickel(II) complexes for both cofacial platforms. X-ray crystallographic analysis of the parent free-base porphyrins H(4)DPX (1) and H(4)DPD (5) confirms the face-to-face arrangement of the two porphyrin macrocycles with a large available range of vertical pocket sizes: 1 (C(80)H(92)Cl(2)N(8)O), triclinic, space group P1 macro, a = 13.5167(12) A, b = 21.7008(18) A, c = 23.808(2) A, alpha = 80.116(2) degrees, beta = 76.832(2) degrees, gamma = 80.4070(10) degrees, Z = 4; 5 (C(80)H(83)N(8)O(2)), monoclinic, space group C2/c, a = 22.666(2) A, b = 13.6749(14) A, c = 42.084(4) A, beta = 94.554(2) degrees, Z = 8. EPR spectroscopy of dicopper(II) derivatives Cu(2)DPX (3) and Cu(2)DPD (7) complements the crystallographic studies by probing intramolecular metal-metal arrangements in frozen solution. Exciton interactions between the porphyrin subunits in fluid solution are revealed by steady-state and time-resolved electronic absorption and emission spectroscopy. The resulting compilation of structural and spectroscopic data provides a benchmark for the use of these and related platforms for the activation of small-molecule substrates. A structure-function relation is developed for the photoinduced oxygen atom-transfer reactions of bisiron(III) mu-oxo derivatives of DPX and DPD. The efficiency of the photochemical process is markedly dependent (approximately 10(4)-fold) on the vertical flexibility of cofacial architecture provided by the spacer.     

Quantum chemical and master equation simulations of the oxidation and isomerization of vinoxy radicals

The vinoxy radical, a common intermediate in gas-phase alkene ozonolysis, reacts with O2 to form a chemically activated alpha-oxoperoxy species. We report CBS-QB3 energetics for O2 addition to the parent (*CH2CHO, 1a), 1-methylvinoxy (*CH2COCH3, 1b), and 2-methylvinoxy (CH3*CHCHO, 1c) radicals. CBS-QB3 predictions for peroxy radical formation agree with experimental data, while the G2 method systematically overestimates peroxy radical stability. RRKM/master equation simulations based on CBS-QB3 data are used to estimate the competition between prompt isomerization and thermalization for the peroxy radicals derived from 1a, 1b, and 1c. The lowest energy isomerization pathway for radicals 4a and 4c (derived from 1a and 1c, respectively) is a 1,4-shift of the acyl hydrogen requiring 19-20 kcal/mol. The resulting hydroperoxyacyl radical decomposes quantitatively to form *OH. The lowest energy isomerization pathway for radical 4b (derived from 1b) is a 1,5-shift of a methyl hydrogen requiring 26 kcal/mol. About 25% of 4a, but only approximately 5% of 4c, isomerizes promptly at 1 atm pressure. Isomerization of 4b is negligible at all pressures studied.     

Structure of the nitrogen-centered radical formed during inactivation of E. coli ribonucleotide reductase by 2'-azido-2'-deoxyuridine-5'-diphosphate: trapping of the 3'-ketonucleotide

Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides providing the monomeric precursors required for DNA replication and repair. The class I RNRs are composed of two homodimeric subunits: R1 and R2. R1 has the active site where nucleotide reduction occurs, and R2 contains the diiron tyrosyl radical (Y*) cofactor essential for radical initiation on R1. Mechanism-based inhibitors, such as 2'-azido-2'-deoxyuridine-5'-diphosphate (N(3)UDP), have provided much insight into the reduction mechanism. N(3)UDP is a stoichiometric inactivator that, upon interaction with RNR, results in loss of the Y* in R2 and formation of a nitrogen-centered radical (N*) covalently attached to C225 (R-S-N*-X) in the active site of R1. N(2) is lost prior to N* formation, and after its formation, stoichiometric amounts of 2-methylene-3-furanone, pyrophosphate, and uracil are also generated. On the basis of the hyperfine interactions associated with N*, it was proposed that N* is also covalently attached to the nucleotide through either the oxygen of the 3'-OH (R-S-N*-O-R') or the 3'-C (R-S-N*-C-OH). To distinguish between the proposed structures, the inactivation was carried out with 3'-[(17)O]-N(3)UDP and N* was examined by 9 and 140 GHz EPR spectroscopy. Broadening of the N* signal was detected and the spectrum simulated to obtain the [(17)O] hyperfine tensor. DFT calculations were employed to determine which structures are in best agreement with the simulated hyperfine tensor and our previous ESEEM data. The results are most consistent with the R-S-N*-C-OH structure and provide evidence for the trapping of a 3'-ketonucleotide in the reduction process.     

1H-1H dipolar couplings provide a unique probe of RNA backbone structure

A NMR method is described that permits simultaneous measurement of the geminal 2JH1H2 + 2DH1H2 splitting and the sum of the 1JCH1 + 1DCH1 + 1JCH2 + 1DCH2 couplings for methylene groups, where 2DH1H2 and 1DCH are residual dipolar couplings, occurring when molecules are weakly oriented relative to the magnetic field. By suppressing either the upfield or downfield half of the 1H-1H geminal doublet, the experiment yields improved resolution relative to regular two-dimensional 1H-13C correlation spectra, making it applicable to systems of considerable complexity. The method is demonstrated for measurement of all 2DH5'H5' couplings in a 24-nucleotide 13C-enriched RNA stem loop structure, weakly aligned in liquid crystalline Pf1. The method is equally applicable to methylene groups in 13C-labeled proteins and to natural abundance samples of smaller molecules.     

Reactive scattering dynamics in atom+polyatomic systems: F+C2H6-->HF(v,J)+C2H5

State-to-state scattering dynamics of F+C2H6-->HF(v,J)+C2H5 have been investigated at Ecom=3.2(6) kcalmol under single-collision conditions, via detection of nascent rovibrationally resolved HF(v,J) product states with high-resolution infrared laser absorption methods. State-resolved Doppler absorption profiles are recorded for multiple HF(v,J) transitions originating in the v=0,1,2,3 manifold, analyzed to yield absolute column-integrated densities via known HF transition moments, and converted into nascent probabilities via density-to-flux analysis. The spectral resolution of the probe laser also permits Doppler study of translational energy release into quantum-state-resolved HF fragments, which reveals a remarkable linear correlation between (i) HF(v,J) translational recoil and (ii) the remaining energy available, Eavail=Etot-E(HF(v,J)). The dynamics are interpreted in the context of a simple impulsive model based on conservation of linearangular momentum that yields predictions in good agreement with experiment. Deviations from the model indicate only minor excitation of ethyl vibrations, in contrast with a picture of extensive intramolecular vibrational energy flow but consistent with Franck-Condon excitation of the methylene CH2 bending mode. The results suggest a relatively simple dynamical picture for exothermic atom+polyatomic scattering, i.e., that of early barrier dynamics in atom+diatom systems but modified by impulsive recoil coupling at the transition state between translationalrotational degrees of freedom.