Matching unknown empirical formulas to chemical structure using LC/MS TOF accurate mass and database searching: example of unknown pesticides on tomato skins

Traditionally, the screening of unknown pesticides in food has been accomplished by GC/MS methods using conventional library searching routines. However, many of the new polar and thermally labile pesticides and their degradates are more readily and easily analyzed by LC/MS methods and no searchable libraries currently exist (with the exception of some user libraries, which are limited). Therefore, there is a need for LC/MS approaches to detect unknown non-target pesticides in food. This report develops an identification scheme using a combination of LC/MS time-of-flight (accurate mass) and LC/MS ion trap MS (MS/MS) with searching of empirical formulas generated through accurate mass and a ChemIndex database or Merck Index database. The approach is different than conventional library searching of fragment ions. The concept here consists of four parts. First is the initial detection of a possible unknown pesticide in actual market-place vegetable extracts (tomato skins) using accurate mass and generating empirical formulas. Second is searching either the Merck Index database on CD (10,000 compounds) or the ChemIndex (77,000 compounds) for possible structures. Third is MS/MS of the unknown pesticide in the tomato-skin extract followed by fragment ion identification using chemical drawing software and comparison with accurate-mass ion fragments. Fourth is the verification with authentic standards, if available. Three examples of unknown, non-target pesticides are shown using a tomato-skin extract from an actual market place sample. Limitations of the approach are discussed including the use of A + 2 isotope signatures, extended databases, lack of authentic standards, and natural product unknowns in food extracts.     

Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions

Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.     

Synthesis and Structure of 2‐Substituted Thieno[3′,2′:5,6]pyrido[4,3‐d]pyrimidin‐4(3H)‐one Derivatives

A series of new 2‐substituted 3‐(4‐chlorophenyl)‐5,8,9‐trimethylthieno[3′,2′: 5,6]pyrido[4,3‐d]pyrimidin‐4(3H)‐ones 8 were synthesized via an aza‐Wittig reaction. Phosphoranylideneamino derivatives 6a or 6b reacted with 4‐chlorophenyl isocyanate to give carbodiimide derivatives 7a or 7b , respectively, which were further treated with amines or phenols to give compounds 8 in the presence of a catalytic amount of EtONa or K₂CO₃. The structure of 2‐(4‐chlorophenoxy)‐3‐(4‐chlorophenyl)‐5,8,9‐trimethylthieno[3′,2′: 5,6]pyrido[4,3‐d]pyrimidin‐4(3H)‐one ( 8j ) was comfirmed by X‐ray analysis.     

Synthesis and Crystal Structure of a Novel Polymeric Lead(II) Compound: [Pb2(phen)2(N3)3(ClO4)]n

A 2D lead(II) coordination polymer [Pb₂(phen)₂(N₃)₃(ClO₄)]_n,( 1 ) containing 1,10‐phenanthroline (phen) and two different anions, has been synthesized and characterized by elemental analysis, IR and ¹H NMR spectroscopy and X‐ray crystallography. The single‐crystal X‐ray data show two different kinds of Pb²⁺ ions with coordination numbers of eight, Pb1 = PbN₆O₂ and Pb2 = PbN₈, with hemidirected and holodirected structures, respectively. The supramolecular features in 1 is negiotated through the weak but directional C‐H···O and C‐H···N interactions and aromatic π–π stacking interactions.     

4‐(2‐Hydroxyphenyl)‐2‐phenyl‐2,3‐dihydro‐1H‐1,5‐benzodiazepine and the 2‐(2,3‐dimethoxyphenyl)‐, 2‐(3,4‐dimethoxyphenyl)‐ and 2‐(2,5‐dimethoxyphenyl)‐substituted derivatives

The 1,5‐benzodiazepine ring system exhibits a puckered boat‐like conformation for all four title compounds [4‐(2‐hydroxyphenyl)‐2‐phenyl‐2,3‐dihydro‐1H‐1,5‐benzodiazepine, C₂₁H₁₈N₂O, (I), 2‐(2,3‐dimethoxyphenyl)‐4‐(2‐hydroxyphenyl)‐2,3‐dihydro‐1H‐1,5‐benzodiazepine, C₂₃H₂₂N₂O₃, (II), 2‐(3,4‐dimethoxyphenyl)‐4‐(2‐hydroxyphenyl)‐2,3‐dihydro‐1H‐1,5‐benzodiazepine, C₂₃H₂₂N₂O₃, (III), and 2‐(2,5‐dimethoxyphenyl)‐4‐(2‐hydroxyphenyl)‐2,3‐dihydro‐1H‐1,5‐benzodiazepine, C₂₃H₂₂N₂O₃, (IV)]. The stereochemical correlation of the two C₆ aromatic groups with respect to the benzodiazepine ring system is pseudo‐equatorial–equatorial for compounds (I) (the phenyl group), (II) (the 2,3‐dimethoxyphenyl group) and (III) (the 3,4‐dimethoxyphenyl group), while for (IV) (the 2,5‐dimethoxyphenyl group) the system is pseudo‐axial–equatorial. An intramolecular hydrogen bond between the hydroxyl OH group and a benzodiazepine N atom is present for all four compounds and defines a six‐membered ring, whose geometry is constant across the series. Although the molecular structures are similar, the supramolecular packing is different; compounds (I) and (IV) form chains, while (II) forms dimeric units and (III) displays a layered structure. The packing seems to depend on at least two factors: (i) the nature of the atoms defining the hydrogen bond and (ii) the number of intermolecular interactions of the types O—H...O, N—H...O, N—H...π(arene) or C—H...π(arene).     

Essential of Proline and Valine Residues in the Peptide Derived from Lactoferrin for Angiotensin Converting Enzyme Inhibition

We synthesized Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu, the peptide contained in lactoferrin (Lf), to identify the angiotensin converting enzyme (ACE) inhibition. In an attempt to know the structure‐activity relationship of this peptide, we replaced Pro (the third amino acid residues from N‐terminal) or Val (the fourth amino acid residues from N‐terminal) with Ala (neutral amino acid), Glu (acidic amino acid) or Lys (basic amino acid) to produce six peptides. From the in vitro ACE inhibition (IC₅₀) of these synthesized peptides, the original peptide (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu) showed higher ACE inhibition than the replaced six peptides. Thus, replacement of Pro at the third amino acid residues or Val at the fourth position with Ala, Glu or Lys revealed the ACE inhibition to be lower than the original form of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu. Otherwise, we added one peptide at the C‐terminal of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu and found both products with an addition of Val (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Val) or Ile (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Ile) showing a lower ACE inhibition than the original one. The ACE inhibitions produced by both replaced peptides were without significance. Also, deletion of the last peptide at the C‐terminal (Leu‐Arg‐Pro‐Val‐Ala‐Ala) failed to produce a marked change of ACE inhibition as compared to the original one. These results suggest that Pro and Val are essential in the peptide for inhibition of ACE activity.     

Syntheses and Characterizations of Two Palladium(II) Complexes of 5‐Mercapto‐1‐methyltetrazole

Reaction of PdCl₂(CH₃CN)₂ with the sodium salt of 5‐mercapto‐1‐methyltetrazole (MetzSNa) in methanol solution affords an interesting dinuclear palladium complex [Pd₂(MetzS)₄ ] ( 1 ). However, treatment of PdCl₂(CH₃CN)₂ with neutral MetzSH ligand in methanol solution produces a mononuclear palladium complex [Pd(MetzSH)₄]Cl₂ ( 2 ). Both complexes were characterized by IR, ¹HNMR, UV‐Vis spectroscopy as well as X‐ray crystallography. Single‐crystal X‐ray diffraction analyses of two complexes lead to the elucidation of the structures and show that 1 possesses an asymmetric structure: one Pd atom is tetracoordinated by three sulfur atoms and one nitrogen atom to form PdS₃N coordination sphere, the other Pd atom is tetracoordinated by three nitrogen atoms and one sulfur atom to form PdSN₃ coordination sphere. The molecules of 1 are associated to 1‐D infinite linear chain by weak intermolecular Pd···S contacts in the crystal lattice. In 2 , the Pd atom lies on an inversion center and has a square‐planar coordination involving the S atoms from four MetzSH ligands. The two chloride ions are not involved in coordination, but are engaged in hydrogen bonding.     

catena‐Poly[[diiodo­zinc(II)]‐μ‐4,4′‐bipyridine‐κ2N:N′]

The title compound, [ZnI₂(bipy)]_n (bipy is 4,4′‐bipyridine, C₁₀H₈N₂), has been prepared by the hydro­thermal reaction of ZnI₂ and bipy at 433 K. Each Zn atom is coordinated by two N atoms from two different bipy ligands and by two I atoms in a distorted tetra­hedral geometry, with Zn—N distances ranging from 2.068 (7) to 2.101 (8) Å and Zn—I distances ranging from 2.5471 (13) to 2.5673 (13) Å. The mol­ecular structure features a zigzag polymeric chain. Face‐to‐face π–π stacking inter­actions between adjacent bipy ligands stabilize the structure.     

ESR Studies on a Friedel‐Crafts Alkylation Reaction in [bmim]Cl‐AlCl3 Ionic Liquid

The paramagnetic complexes formed in Friedel‐Crafts alkylation reaction systems are invistigated by electron spin resonance (ESR) spectroscopy, in room temperature ionic liquids system 1‐butyl‐3‐methyl‐limidazolium chloride‐aluminium chloride ([bmim]Cl‐AlCl₃). The results indicate that ESR spectra observed are due to polycyclic aromatic radical cations formed from their parent hydrocarbons. ESR spectrum of spin adduct is obtained in an ionic liquid system composed of [bmim]Cl‐AlCl₃. In acidic solution the ¹⁴N hyperfine coupling constant of 4‐oxo‐TEMPO, 2.15 mT, is appreciably larger due to an adduct formed with AlCl₃.