Use of a quadrupole linear ion trap mass spectrometer in metabolite identification and bioanalysis

A new type of quadrupole linear ion trap mass spectrometer, Q TRAP trade mark LC/MS/MS system (Q TRAP trade mark ), was evaluated for its performance in two studies: firstly, the in vitro metabolism of gemfibrozil in human liver microsomes, and, secondly, the quantification of propranolol in rat plasma. With the built-in information-dependent-acquisition (IDA) software, the instrument utilizes full scan MS in the ion trap mode and/or constant neutral loss scans as survey scans to trigger product ion scan (MS(2)) and MS(3) experiments to obtain structural information of drug metabolites 'on-the-fly'. Using this approach, five metabolites of gemfibrozil were detected in a single injection. This instrument combines some of the unique features of a triple quadrupole mass spectrometer, such as constant neutral loss scan, precursor ion scan and multiple reaction monitoring (MRM), together with the capability of a three-dimensional ion trap. Therefore, it becomes a powerful instrument for metabolite identification. The fast duty cycle in the ion trap mode allows the use of full product ion scan for quantification. For the quantification of propranolol, both MRM mode and full product ion scan in the ion trap mode were employed. Similar sensitivity, reproducibility and linearity values were established using these two approaches. The use of the product ion scan mode for quantification provided a convenient tool in selecting transitions for improving selectivity during the method development stage.     

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.     

Synthesis of (R)-5-(2′-pentyl)barbituric acid derivatives of high optical purity

Natural (R)-(+)-pulegone ( 1 ) was converted to 3-methylhexanoic acid ( 4 ) by a sequence which precluded racemization. Conversion of this to malonic esters 8 , 5 , and 11 permitted the synthesis of pentobarbital ( 6 ) secobarbital ( 12 ), thiopental ( 9 ), thiamylal(10 ), and 5-(2′-pentyl)barbituric acid ( 7 ), all having the ( R )-configuration in the side chain.     

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.     

Synthesis and structure of mercurous ion and dinuclear lead(II) complexes of the 28-membered selenaaza macrocycle: dominance of the chelate ring size effect and conformational requirement over soft-soft interactions

The flexible and larger ring size macrocycle 4 (C(36)H(46)N(6)Se(2)) afforded stable complex 5 [Hg(2)(PF(6))(2)[C(36)H(46)N(6)Se(2)]] on treatment with 1 equiv of mercuric acetate followed by addition of NH(4)PF(6). The reaction of Pb(OCOCH(3))(2).4H(2)O with 4 followed by treatment with NH(4)PF(6) resulted in a dinuclear lead complex (6) [Pb(2)(PF(6))(2)(OCOCH(3))(2)[C(36)H(46)N(6)Se(2)]]. The crystal structures of complexes 5 and 6 are described: C(36)H(46)F(12)Hg(2)N(6)P(2)Se(2) a = 9.5106(5) A, b = 11.5222(6) A, c = 11.8161(6) A, alpha = 115.6110(10) degrees , beta = 96.5190(10) degrees , gamma = 106.2910(10) degrees , monoclinic, P, Z =1; C(44)H(57)F(12)N(8)O(4)P(2)Pb(2)Se(2) a = 9.4668(5) A, b = 11.9937(6) A, c = 25.2319(14) A, alpha = 102.4130(10) degrees , beta = 97.6130(10) degrees , gamma = 94.8540(10) degrees , monoclinic, P, Z = 2. The crystal structure of 5 revealed that Hg(2)(2+) is trapped inside the cavity of the macrocycle. The geometry around the mercurous ion is antiprismatic with Hg(2)(2+) coordinating to six nitrogen atoms forming four five-membered rings, and there is no interaction between the mercurous ion and the selenium donor atoms. The single crystal X-ray crystal structure of 6 indicates a distorted octahedral geometry around each lead atom in the cavity of the macrocycle due to presence of the sterochemically active lone pair on Pb(II). The octahedral geometry around each Pb(II) is satisfied by coordination to 3 nitrogen atoms, two oxygen atoms of the chelating acetate group, and bridging of one of the oxygen atoms of the nearby acetate.     

Structure of the copper(II) complex of 2-acetylpyridine hexamethyleneiminylthiosemicarbazone, [Cu(Lhexim)Br]

Summary An anion (loss of ³N hydrogen) of a 2-acetylpyridine azacyclothiosemicarbazone coordinates in a planar conformation to the central Cu atom through the pyridyl N, azomethine N and thiolato S atoms. The interatomic distances are Cu{ie449-01}N = 2.016(6), Cu{ie449-02}N = 1.963(5) and Cu{ie449-03}S = 2.236(3) Å, respectively, with the fourth co-ordination site occupied by a bromine atom, Cu{ie449-04}Br = 2.359(2) Å.     

Ab initio study of molecular oxygen adsorption on Pu (111) surface

Using the generalized gradient approximation to density functional theory (DFT), molecular and dissociative oxygen adsorptions on a Pu (111) surface has been studied in detail. Dissociative adsorption with a layer‐by‐layer alternate spin arrangement of the plutonium layer is found to be energetically more favorable, and adsorption of oxygen does not change this feature. Hor1 (O₂ is parallel to the surface and lattice vectors) approach on the center2 (center of the unit cell, where there is a Pu atom directly below on the third layer) site, both without and with spin polarization, was found to be the preferred chemisorbed site among all cases studied with chemisorption energies of 8.365 and 7.897 eV, respectively. The second‐highest chemisorption energy occurs at the Ver (O₂ is vertical to the surface) approach of the bridge site with chemisorption energies of 8.294 eV (non‐spin‐polarized) and 7.859 eV (spin‐polarized), respectively. We find that 5f electrons are more localized in the spin‐polarized case than the non‐spin‐polarized counterparts. Localization of the 5f electrons is higher in the oxygen‐adsorbed plutonium layers compared with the bare layers. The ionic part of O? Pu bonding plays a significant role in the chemisorption process, along with Pu 5f? O 2p hybridization. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Constant-isomer benzenoid series and their topological characteristics

Summary New constant-isomer series are presented. Two classes of constant-isomer series based on the topological correspondence of their member benzenoids are identified. The isomer numbers for the constant-isomer series alternate between singlet and doublet occurrence. Constant-isomer series with the same isomer number possess a pairwise one-to-one topological correspondence between their benzenoid membership. A correspondence also exists between threefold monoradical and diradical benzenoids belonging to these constant-isomer series. These topological relationships represent a new paradigm that we ascribe as an edge effect of our periodic table for benzenoids.     

The structure of nitrocubane: the last in the series of nitrocubanes

The structure of nitrocubane, C₈H₇NO₂, 1, reported herein, is the last to be reported in a series of nitrocubanes, ranging from mono- to octanitrocubane. Compound 1 crystallizes in the orthorhombic space group Pnma with cell dimensions a = 17.507(5), b = 6.584(2), and c = 5.832(2) Å and Z = 4. Thus the nitrocubane molecule possesses a crystallographically imposed mirror plane. Since the nitro group is in the mirror plane, it is coplanar with the C1–C6 bond in the cubane skeleton. As has been found previously, the C1–C6 bond in the cubane skeleton that is coplanar to its attached nitro groups is shortened (1.533(4) compared to an average value of 1.543(2) Å for all other cubane C–C bonds). In addition the single substitution of the nitro group into the cubane skeleton causes a tetrahedral distortion which is exhibited by alternating C–C–C angles which are greater than and less than 90°.     

A new class of flexible energetic salts. Part 7: The structures of the guanidinium and hydroxyguanidinium salts of dinitramide

The crystal structures of two amine base salts of dinitramide, the guanidinium 1, and the hydroxyguanidinium 2, have been determined. 1 crystallizes in the triclinic space group with cell dimensions a = 8.325(2) Å, b = 9.301 (2) Å, c = 9.868(2) Å, = 84.73(3)°, = 69.25(3)°, = 67.55(3)°, while 2 crystallizes in the noncentric monoclinic space group Pc with cell dimensions a = 7.098 (2) Å, b = 3.5160 (10) Å, c = 14.358(3) Å, = 98.940(10)°. The structures of 1 and 2 contain protonated amine cations and dinitramide anions linked by hydrogen bonding. In both structures the conformations adopted by the dinitramine anions can be related to the types of hydrogen bonds it forms with the surrounding amine cations.