Gas-phase chemistry of the negative ions of fully-protected peptides by high-resolution electrospray ionization tandem mass spectrometry

Fully-protected C-terminal free peptides can be conveniently analyzed by high-resolution electrospray tandem mass spectrometry (ESI-MS/MS) in a quadrupole quadrupole time-of-flight tandem hybrid mass spectrometer, operated in the negative (-) ionizaionization mode. The unusual choice of negative ions in mass spectrometry applications to peptide analysis was needed to obtain exhaustive sequence and structural data. The low-energy collision-induced dissociation (CID) experiments provided, in fact, tandem mass spectra displaying highly diagnostic fragments with a good signal-to-noise ratio. The method is applied to segments of porcine calcitonin (Cal), Cal (1016, 1), Cal (1724, 2) and Cal (2528, 3) whose [M H]- deprotonated molecular ions provided low-energy CID mass spectra which allow the evaluation either of the primary structure of the peptide and of the location of the side-chain protective groups. ESI (+) MS can be conveniently used, in the high resolution mode, to achieve precise information on the elemental composition of the examined peptides.     

Crystal and molecular structure of a 1:1 complex of a chiral α-d-glucosido-benzo-18-crown-6 and potassium thiocyanate

C₂₈H₃₆O₁₀. KSCN is monoclinic, space groupP2₁ withZ=2,a=10.390(3),b=8.959(7),c=16.377(7) Å, =92.49(5)°. FinalR=0.053 for 1437 reflections measured at room temperature. The K^– ion lies on the least-squares plane formed by the six oxygen atoms in the macrocyclic ring. The SCN^– ion was found on the same face of the macrocycle as the chiral glucopyranoside moiety.Methyl-4,6-O-benzylidene-2,3-O-(1,2-bis(ethoxyethoxy)benzenediyl)--d-glucopyranoside.     

The osmylation of flexible 3-substituted cyclopentenes

The osmylation of several 3-substituted cyclopentenes has been studied. A preference for OsO₄ addition syn to an allylic CHR₂ substituent is observed. By contrast, bulkier substituents of type CMeR₂ give rise to a striking reversal of selectivity. These results are interpreted in terms of the stereodivergent nature of the two differently reactive envelope conformations.     

The fragmentation of 5- and 3-substituted thiophene-2-carboxamides under electron impact

The 70 eV electron impact mass spectra of twelve 5- and 3-substituted thiophene-2-carboxamides are discussed with the aid of exact mass measurements and labelling experiments. All mass spectra exhibit pronounced molecular ions. Some isomeric 5- and 3-substituted title compounds can be differentiated by mass spectrometry. The fragmentation is influenced by a strong ‘ortho-effect’ which activates the NH₃ elimination. In the other cases the most important fragmentation is NH₂˙ loss, followed by CO elimination.     

Synthesis of new pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidines and related heterocycles

The reaction between 5-amino-4-imino-1(2)-substituted-1(2)H-4,5-dihydropyrazolo[3,4-d]pyrimidines and several commercially available reactants afforded new heterocycles with a conserved pyrazolo[3,4-d]pyrimidine nucleus. The key intermediates employed proved to be suitable compounds by virtue of their two vicinal amino and imino groups that were used to obtain five, six and seven-membered rings.     

New insight into solvent effects on the formal HOO. + HOO. reaction

The 2,2'-azobis(isobutyronitrile)(AIBN)-induced autoxidation of gamma-terpinene (TH) at 50 degrees C produces p-cymene and hydrogen peroxide in a radical-chain reaction having HOO* as one of the chain-carrying radicals. The kinetics of this reaction in cyclohexane and tert-butyl alcohol show that chain termination involves the formal HOO. + HOO. self-reaction over a wide range of gamma-terpinene, AIBN, and O2 concentrations. However, in acetonitrile this termination process is accompanied by termination via the cross-reaction of the terpinenyl radical, T., with the HOO. radical under conditions of relatively high [TH] (140-1000 mM) and low [O2] (2.0-5.5 mM). This is because the formal HOO. + HOO. reaction is comparatively slow in acetonitrile (2k approximately 8 x 10(7) M(-1) s(-1)), whereas, this reaction is almost diffusion-controlled in tert-butyl alcohol and cyclohexane, 2k approximately 6.5 x 10(8) and 1.3 x 10(9) M(-1) s(-1), respectively. Three mechanisms for the bimolecular self-reaction of HOO. radicals are considered: 1) a head-to-tail hydrogen-atom transfer from one radical to the other, 2) a head-to-head reaction to form an intermediate tetroxide, and 3) an electron-transfer between HOO. and its conjugate base, the superoxide radical anion, O2-.. The rate constant for reaction by mechanism (1) is shown to be dependent on the hydrogen bond (HB) accepting ability of the solvent; that by mechanism (2) is shown to be too slow for this process to be of any importance; and that by mechanism (3) is dependent on the pH of the solvent and its ability to support ionization. Mechanism (3) was found to be the main termination process in tert-butyl alcohol and acetonitrile. In the gas phase, the rate constant for the HOO. + HOO. reaction (mechanism (1)) is about 1.8 x 10(9) M(-1) s(-1) but in water at pH< or =2 where the ionization of HOO. is completely suppressed, this rate constant is only 8.6 x 10(5) M(-1) s(-1). The very large retarding effect of water on this reaction has not previously been explained. We find that it can be quantitatively accounted for by using Abraham's HB acceptor parameter, beta(2)(H), for water of 0.38 and an estimated HB donor parameter, alpha(2)(H), for HOO. of about 0.87. These Abraham parameters allow us to predict a rate constant for the HOO. + HOO. reaction in water at 25 degrees C of 1.2 x 10(6) M(-1) s(-1) in excellent agreement with experiment.     

On the reaction of Ph2PNHPPh2 with RNCS (R=Et, Ph, p-NO2C6H4): preparation of the zwitterionic ligand EtNHC(S)Ph2P==NPPh2C(S)NEt (HSNS) and the zwitterionic metalate [(SNS)Rh(CO)

The reaction of Ph(2)PNHPPh(2) (PNP) with RNCS (Et, Ph, p-NO(2)(C(6)H(4))) gives addition products resulting from the attack of the P atoms of PNP on the electrophilic carbon atom of the isothiocyanate. When PNP is reacted with EtNCS in a 1:2 molar ratio, the zwitterionic molecule EtNHC(S)PPh(2)==NP(+)Ph(2)C(S)N(-)Et (HSNS) is obtained in high yield. HSNS can be protonated (H(2)SNS(+)) or deprotonated (SNS(-)), behaving in the latter form as an S,N,S-donor pincer ligand. The reaction of HSNS with [(acac)Rh(CO)(2)] (acac=acetylacetonate) affords the zwitterionic metalate [(SNS)Rh(CO)]. Other products can be obtained depending on the R group, the PNP/RNCS ratio (1:1 or 1:2), and the reaction temperature. The proposed product of the primary attack of PNP on RNCS, Ph(2)PN==PPh(2)C(S)NHR (A), cannot be isolated. Reaction of A with another RNCS molecule leads to 1:2 addition compounds of the general formula RNHC(S)PPh(2)==NP(+)Ph(2)C(S)N(-)R (1), which can rearrange into the non-zwitterionic product RNHC(S)PPh(2)==NP(S)Ph(2) (2) by eliminating a molecule of RNC. Two molecules of A can react together, yielding 1:1 PNP/RNCS zwitterionic products of the formula RNHCH[PPh(2)==NP(S)Ph(2)]PPh(2)==NP(+)Ph(2)C(S)N(-)R (3). Compound 3 can then rearrange into RNHCH[PPh(2)==NP(S)Ph(2)](2) (4) by losing a RNC molecule. When R=Et (a), compounds 1 a, 2 a (HSNS), and 4 a have been isolated and characterized. When R=Ph (b), compounds 2 b and 4 b can be prepared in high yield. When R=p-NO(2)C(6)H(4) (c), only compound 3 c is observed and isolated in high yield. The crystal structures of HSNS, [(SNS)Rh(CO)], and of the most representative products have been determined by X-ray diffraction methods.     

Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR

Summary An example of a CoMFA study is described with the aim to discuss one of the major problems of this 3D QSAR method: lack of variable selection. It is shown that the use of nonrelevant energy parameters might produce CoMFA contour maps which poorly reflect the actual nature of the binding site and are in part statistical artefacts. The data set employed in our analysis comparises triazine inhibitors of dihydrofolate reductase (DHFR), isolated from chicken liver, which have already been the object of a QSAR study by other authors. Since three-dimensional structures of triazine-DHFR complexes are known, it was possible not only to reduce ambiguities in the superimposition of the ligands, but also to compare the resulting CoMFA contour maps with the enzyme active site.Supplementary material available: The Cartesian coordinates and the atomic charges of the PM3-optimized structures used in the CoMFA study are available as MOL2 files upon request.To whose memory this paper is dedicated.     

Factors influencing conformer equilibria in retro models of cisplatin-DNA adducts as revealed by moderately dynamic (N,N'-dimethyl-2,3-diaminobutane)PtG(2) retro models (G = a guanine derivative)

Typical cis-PtA(2)G(2) models of key DNA lesions formed by cis-type Pt anticancer drugs are very dynamic and difficult to characterize (A(2) = diamine or two amines; G = guanine derivative). Retro models have A(2) carrier ligands designed to decrease dynamic motion without eliminating any of three possible conformers with bases oriented head-to-tail (two: DeltaHT and LambdaHT) or head-to-head (one: HH). All three were found in NMR studies of eight Me(2)DABPtG(2) retro models (Me(2)DAB = N,N'-dimethyl-2,3-diaminobutane with S,R,R,S and R,S,S,R configurations at the chelate ring N, C, C, and N atoms, respectively; G = 5'-GMP, 3'-GMP, 5'-IMP, and 3'-IMP). The bases cant to the left (L) in (S,R,R,S)-Me(2)DABPtG(2) adducts and to the right (R) in (R,S,S,R)-Me(2)DABPtG(2) adducts. Relative to the case in which the bases are both not canted, canting will move the six-membered rings closer in to each other ("6-in" form) or farther out from each other ("6-out" form). Interligand interactions between ligand components near to Pt (first-first sphere communication = FFC) or far from Pt (second-sphere communication = SSC) influence stability. In typical cases at pH < 8, the "6-in" form is favored, although the larger six-membered rings of the bases are close. In minor "6-out" HT forms, the proximity of the smaller five-membered rings could be sterically favorable. Also, G O6 is closer to the sterically less demanding NH part of the Me(2)DAB ligand, possibly allowing G O6-NH hydrogen bonding. These favorable FFC effects do not fully compensate for possibly stronger FFC dipole effects in the "6-in" form. SSC, phosphate-N1H cis G interactions favor LambdaHT forms in 5'-GMP and 5'-IMP complexes and DeltaHT forms in 3'-GMP and 3'-IMP complexes. When SSC and FFC favor the same HT conformer, it is present at >90% abundance. In six adducts [four (S,R,R,S)-Me(2)DABPtG(2) and (R,S,S,R)-Me(2)DABPtG(2) (G = 3'-GMP and 3'-IMP)], the minor "6-out" HT form at pH approximately 7 becomes the major form at pH approximately 10, where G N1H is deprotonated, because the large distance between the negatively charged N1 atoms minimizes electrostatic repulsion and probably because the G O6-(NH)Me(2)DAB H-bond (FFC) is strengthened by N1H deprotonation. At pH approximately 10, phosphate-negative N1 repulsion is an unfavorable SSC term. This factor disfavors the LambdaHT R form of two (R,S,S,R)-Me(2)DABPtG(2) (G = 5'-GMP and 5'-IMP) adducts to such an extent that the "6-in" DeltaHT R form remains the dominant form even at pH approximately 10.     

Separation and characterisation of sphingoceramides by high-performance liquid chromatography-electrospray ionisation mass spectrometry

We developed a simple and reliable analytical method for the quantification and the characterization of ceramides extracted from biological samples by high-performance liquid chromatography (HPLC) coupled to electrospray ionisation tandem mass spectrometry (ESI/MS/MS). The chromatographic separation of analytes was carried out in a RP8 column, eluting with a methanol-water mixture in gradient elution mode. The separated lipids were detected by total ion monitoring and characterised by MS/MS spectra; quantitative analysis was performed by integrating the extracted ion peaks obtained in the negative ion mode. Good repeatability was obtained for retention time (0.3-2%), peak area ratio (A(S)/A(IS), 2-8%), as well as limit of detection (LOD, 5-26 pg) and quantification (LOQ, 13-53 pg). The method was validated for the analysis of N-palmitoyl-D-erythro-sphingosine (Cer16), N-stearoyl-D-erythro-sphingosine (Cer18), N-tetracosanoyl-D-erythro-sphingosine (N24:0, lignoceric ceramide, Cer24:0), and N-tetracos-15'-enoyl-D-erythro-sphingosine (N24:1, nervonic ceramide, Cer24:1), giving good results. Lipid mixtures, extracted from skin and epidermal cells, were analysed for their content of the studied ceramides.