Mass and charge assignment for electrospray ions by cation adduction

The assignment of the mass (m) value from the m/z value for ions with a multiple number of charges (z) in electrospray mass spectra usually utilizes multiple peaks of the same m but different z values, or unit-mass—separated isotopic peaks of the same z value from high resolution spectra. The latter approach is also feasible with much less resolving power using adduct ions of much higher mass separation. The application of this to mixture spectra containing many masses, such as spectra from tandem mass spectrometry (MS/MS) ion dissociation, does not appear to have been pointed out previously. Thus, replacing two protons by one Cu²⁺ ion increases the mass by 61.5 Da, with this shift providing a mass scale for assignment of m and z from this pair of m/z values. The more common Na⁺ adduct peaks provide a 22.0 Da separation, of utility for 1000 resolving power only below approximately 10 kDa. Further, collisional dissociation lowers the degree of Cu²⁺ adduction in the resulting sequence-specific fragment ions much less than that of the corresponding Na⁺ adducts, making the Cu²⁺ adducts far more useful for m and z determination in MS/MS studies.     

Conformational analysis,barriers to internal rotation and vibrational assignment for dimethylethylamine

The IR (50–3500 cm^?1) and Raman (20–3500 cm^?1) spectra have been recorded for gaseous and solid dimethylethylamine. Additionally, the Raman spectrum of the liquid has been recorded and qualitative depolarization values have been obtained. Due to the fact that three distinct Raman lines disappear on going from the fluid phases to the solid state, it is concluded that the molecule exists as a mixture of the gauche and trans conformers in the fluid phases with the gauche conformer being more stable and the only one present in the spectra of the unannealed solid. From the temperature study of the Raman spectrum of the liquid a rough estimate of 3.9 kcal mol^?1 has been obtained for ΔH. Relying mainly on group frequencies and relative intensities of the IR and Raman lines, a complete vibrational assignment is proposed for the gauche conformer. The potential functions for the three methyl rotors have been obtained, and the barriers to internal rotation for the two CH₃ rotors attached to the nitrogen atom have been calculated to be 3.51 and 3.43 kcal mol^?1, whereas the barrier for the CH₃ rotor of the ethyl group has been calculated to be 3.71 kcal mol^?1. The asymmetric torsional mode for the gauche conformer has been observed in both the IR and Raman spectra of the gas at 105 cm^?1 with at least one hot band at a lower frequency. Since the corresponding mode has not been observed for the trans conformer, it is not possible to obtain the potential function for the asymmetric rotation although estimates on the magnitudes of some of the terms have been made. Significant changes occur in the low-frequency IR and Raman spectra of the solid with repeated annealing; several possible reasons for these changes are discussed and one possible explanation is that a conformational change is taking place in the solid where the trans form is stabilized by crystal packing forces. These results are compared to the corresponding quantities for some similar amines.     

Automated assignment of charge states from resolved isotopic peaks for multiply charged ions

The recent proliferation of electrospray as an ionization method has greatly increased the ability to perform analyses of large biomolecules by using mass spectrometry. The major advantage of electrospray is the ability to produce multiply charged ions, which brings large molecules down to a mass-to-charge ratio range amenable to most instruments. Multiple charging is also a disadvantage because mass (m) becomes ambiguous unless charge (z) can be assigned. This is typically performed with simple algorithms that use multiple peaks of the same m and different z, but these methods are difficult to apply to complex mixtures and not applicable when only one z appears for each m. The use of mass analyzers with higher resolving powers, like the Fourier transform mass spectrometer, allows resolution of isotopic peaks, providing an internal 1-Da mass scale that can be used for unambiguous charge assignment. Manual assignment of charge state from the isotopic peaks is time consuming and becomes inaccurate when either the signal level or resolving power are low. For these cases, computer algorithms based on pattern recognition techniques have been developed to assist in assignment of charge states to isotopic clusters. These routines provide for more rapid analysis with higher accuracy than available manually.     

A convenient method for the assignment of the absolute configuration to cyclic amines

We have assigned the absolute configuration to trans-2,5-dimethylpyrrolidine and trans-2,6-dimethyl-piperidine through radical chlorination in ω-1 position of optically active amines, 2 and 5, of known absolute configuration, followed by cyclization. CD curves of 1f and 4g derivatives indicate that the reaction is stereospecific. The absolute configuration of trans-2,5-dimethyl-Δ³-pyrròline has also been determined.     

Synthesis and stereochemical assignment of (+)-Cladospolide D

Cladospolides A-D are 12-membered, α,β-unsaturated lactones isolated from various species of Cladosporium. Cladospolide D is unique in its γ-keto functionality and possesses antifungal activity; however, the stereochemistry of Cladoapolide D was unknown. We report the asymmetric syntheses to generate both possible diastereomers of Cladospolide D. Two regioselective cross-metatheses were applied to form the carbon skeleton, and the two olefins were differentiated by Michael addition, hydrogenation, and elimination. Later, the macrocycle was achieved through the Yamaguchi protocol. After comparing the spectroscopic data of the synthetic Cladospolide D with the reported values, the stereochemistry of Cladospolide D is confirmed as (2E,5R,11S).     

2D F/F NOESY for the assignment of NMR spectra of fluorochemicals

Two-dimensional (2D) NMR is an invaluable technique for the complete analysis and assignment of chemical structures. Although ¹⁹F/¹⁹F COSY experiments are routinely used for assignments in perfluorochemicals, interpretation can be difficult because four-bond (⁴J_FF) coupling constants are typically 5-10-fold larger than vicinal (³J_FF) coupling constants. Furthermore, the dependence of long range coupling constants on stereochemistry is not always known. Fluorine-fluorine NOESY correlations represent an enhancement in the arsenal of 2D ¹⁹F NMR experiments. The NOESY and COSY spectra of 2,2,3,3,4,4,4-heptafluorobutanol and a telomeric perfluorochemical iodide show that COSY identifies the 1,4-fluorine interactions whereas NOESY identifies the vicinal fluorine atoms. The combined experiments have been used to unambiguously assign all of the fluorines in a mixture of cis- and trans-perfluoro-1,3-dimethylcyclohexane and in a substituted perfluorotetrahydrofuran.     

Vibrational assignment and analysis for 2,3-dihydrofuran and 2,5-dihydrofuran

The vibrational spectra of 2,3-dihydrofuran and 2,5-dihydrofuran have been recorded using IR and Raman spectroscopy for the gas, liquid and solid states. A vibrational assignment consisting of a nearly complete set of vapor phase wavenumbers is proposed for both molecules based on the observed spectra and normal coordinate analyses. The normal coordinate analyses have been made by scaling the AM1 force field for each molecule with scale factors transferred from an analysis of the cyclopentene fundamental vibrations. The predicted a priori vibrational frequencies justify one reassignment of the fundamentals for 2,5-dihydrofuran from that previously reported. The vibrational assignment for 2,3-dihydrofuran is reported for the first time. Thermodynamic functions are computed for each molecule using the experimentally determined vibrational frequencies.     

Prediction and assignment of site occupation and energy levels for Pb ions in crystal hosts

The environmental factor h_e of the host was calculated quantitatively in Pb²⁺-doped 23 compounds based on the dielectric theory of chemical bond for complex crystals. The relationship between the A band energy E_A of Pb²⁺ and the environmental factor h_e was intensively studied. The results indicate that E_A of Pb²⁺ decreases linearly with increasing of h_e. A linear model was proposed which allows us to correctly predict and assign the site occupations and the position of A band for Pb²⁺-doped compounds if the crystal structure and the refraction index were known. Applied to SrGa₂O₄:Pb²⁺, CaAl₂B₂O₇:Pb²⁺ and SrAl₂B₂O₇:Pb²⁺, the theoretical predictions are in very good agreement with the experimental data. In SrGa₂O₄:Pb²⁺, the excitation spectrum of Pb²⁺ from two different cation sites was identified: the higher energy band of A (265 nm) from the site of Sr2, and the lower ones (280 nm) from the site of Sr1.     

Large-scale assignment of N-glycosylation sites using complementary enzymatic deglycosylation

Endoglycosidase is a class of glycosidases that specifically cleaves the glycosidic bond between two proximal residues of GlcNAc in the pentasaccharide core of N-glycan, leaving the innermost GlcNAc still attached to its parent protein, which provides a different diagnostic maker for N-glycosylation site assignment. This study aims to validate the use of endoglycosidase for high throughput N-glycosylation analysis. An endoglycosidase of Endo H and the conventional PNGase F were employed, with a similar accessible procedure, for large-scale assignment of N-glycosylation sites and then N-glycoproteome for rat liver tissue. ConA affinity chromatography was used to enrich selectively high-mannose and hybrid glycopeptides before enzymatic deglycosylation. As a result, a total of 1063 unique N-glycosites were identified by nano liquid chromatography tandem mass spectrometry, of which 53.0% were unknown in the Swiss-Prot database and 47.1% could be assigned only by either of the methods, confirmed the possibility of large-scale glycoproteomics by use of endoglycosidase. In addition, 11 glycosites were assigned with core-fucosylation by Endo H. A comparison between the two enzymatic deglycosylation methods was also investigated. Briefly, Endo H provides a more confident assignment but a smaller dataset compared with PNGase F, showing the complementary nature of the two N-glycosite assignment methods.     

Complete vapor phase assignment for the fundamental vibrations of furan,pyrrole and thiophene

Vibrational spectroscopic studies, including IR vapor, Raman vapor and Raman liquid spectra, have been made to obtain the complete set of fundamental vibrational frequencies in the vapor and liquid states for furan, pyrrole and thiophene. For furan, vapor values have been determined for the two previously ambiguous fundamentals, ν₁₁ and ν₁₈. Also determined is the vapor frequncy of two fundamentals of furan for which only the liquid value had been known. The fundamental vibrational frequencies of pyrrole have been completely determined in the gas and liquid states. The thiophene results confirm the assignment of Rico et al. [Spectrochim. Acta 21, 689 (1965)], although for several of the fundamental modes the vapor frequency is now measured. The Raman vapor spectra are conclusive concerning the refinements in vibrational assignment for furan and pyrrole, where virtually every binary combination band involving the out-of-plane fundamentals that yield an A₁ transition is observed. The Raman vapor results establish two significant Fermi resonances affecting fundamental vibration levels in pyrrole. Also, ¹³C and ³⁴S isotopomers are identified in the Q-branches of the Raman vapor spectra at natural abundance. A comparison of the spectroscopic and calorimetric ideal-gas thermodynamic properties is made. The differences are negligible in the region where the calorimetric data are most reliable.     

Synthesis and stereochemical assignment of geraniol- and nerol-derived Cygerol enantiomers

The enantiomers (up to 99% ee) of both geraniol- and nerol-derived 2-cyclohexyl-5,9-dimethyldeca-4,8-dienoic acid, the active ingredient of the wound healing medication Cygerol, were prepared via a low-temperature alkylation, basic hydrolysis, derivatization with (S)-4-benzyloxazolidin-2-one and chromatographic separation steps. The absolute configuration of stereocenters in the antipodes having an (E)- or (Z)-geometry of the internal double bond was determined based on characteristic ¹H NMR signals of the corresponding (S)-4-benzyloxazolidin-2-one-derived imides and on conversion to the known diethyl (S)-2-cyclohexylsuccinate and (S)-2-cyclohexylbutane-1,4-diol with reported specific rotations.     

Iridodials: enantiospecific synthesis and stereochemical assignment of the pheromone for the golden-eyed lacewing, Chrysopa oculata

1R,2S,5R,8R; 1R,2S,5R,8S; 1S,2S,5R,8R; and 1S,2S,5R,8S-Iridodials have been prepared in five steps from 4aS,7S,7aR and 4aS,7S,7aS-nepetalactones, major components of catnip oil. 1R,2S,5R,8R-Iridodial has been identified as a male-produced male-aggregation pheromone for Chrysopa oculata, the first pheromone of any kind identified for lacewings.     

Application of chiral bidentate NMR solvents for assignment of the absolute configuration of alcohols: scope and limitation

The ¹³C NMR behaviors of several cyclic and biaryl secondary alcohols as well as acyclic tertiary alcohols have been studied in the chiral bidentate NMR solvent BMBA-p-Me (1). An empirical rule has been advanced to correlate the absolute configuration of each type of alcohols with the ¹³C chemical shift behaviors in (R,R)- and (S,S)-BMBA-p-Me.     

Infrared and raman spectra,vibrational assignment and barriers to internal rotation for methyldisilylamine

The Raman spectra of gaseous and liquid (SiH₃)₂NCH₃ and (SiH₃)₂NCD₃ have been recorded to within 10 cm^?1 of the exciting line. The IR spectra of (SiH₃)₂NCH₃ and (SiH₃)₂NCD₃ have been recorded from 80 cm^?1 to 3800 cm^?1 in the gaseous state, and from 80 cm^?1 to 450 cm^?1 in the solid state. A vibrational assignment has been made, and from the low-frequency vibrational data, an upper limit of 3.3 kcal mol^?1 was calculated for the barrier to internal rotation of the silyi groups, whereas a barrier of ~450 cal was calculated for internal rotation of the methyl group. It is concluded that there exists a significantly strong d_π—p_π interaction in methyldisilylamine.     

The unambiguous synthesis and NMR assignment of 4-alkoxy and 3-alkylquinazolines

Contrary to a number of reports, alkylations of the privileged 3,4-dihydroquinazoline scaffold provide N3-alkylated products, and not 4-alkoxyquinazolines. To correctly assign the structure, ¹³C NMR shifts of the –Z–CH_n– (Z=O, N) fragment are necessary; resonances in the 45–55 ppm range are indicative of N3-alkylation. Treatment of 3,4-dihydroquinazoline-4-one with p-TsCl afforded the N3-tosylated compound, whose reaction with an amine yielded the corresponding N3-alkyl derivative. A mechanism corroborated by ¹⁵N-labeling involving pyrimidine ring opening and recyclisation is proposed. Finally, the unambiguous preparation of 4-alkoxyquinazolines is described via treatment of 3,4-dihydroquinazoline-4-ones with PCl₅ followed by an alkoxide.     

Stereochemical assignment of the fungal metabolite xestodecalactone A by total synthesis

The first synthesis of the macrocyclic natural product xestodecalactone A, a metabolite of a sponge-derived fungus, is described. By the use of methyl 5-hydroxyhexanoate in its R- or S-configured form, or as its racemate as the precursors, both enantiomers of xestodecalactone A as well as the racemic compound were obtained. Comparison of these synthetic products with the natural product by circular dichroism (CD) spectroscopy and by HPLC on a chiral phase revealed the natural product to have the (R)-configuration.     

13C NMR chemical shifts of benzophenone azine as a benchmark for configurational assignment of azines with aromatic substituents

An analysis of the ¹³C NMR spectral data and quantum chemical calculations for benzophenone azine shows that the shielding constant of the C _ipso atom of its molecule is stereo-specific. The characteristic difference in chemical shifts of the C _ipso atoms of the phenyl rings in the cis- and trans-positions with respect to the lone pair of the neighboring nitrogen atom is 2–3 ppm. The stereospecificity observed for chemical shifts was proposed to be used for the configurational assignment of azines containing aromatic substituents.     

Resolution of racemic carbonucleosides and assignment of the absolute configuration by NMR

Resolution of racemic cis-6-chloro-9-[2-(hydroxymethyl)cyclopentyl]-9H-purine 1 was performed using HPLC with a semipreparative column of β-cyclodextrin using 85:15 water/acetonitrile as eluent. The absolute configurations of the enantiomers were determined by NMR studies of their (R)- and (S)-methoxyphenylacetates.     

Microwave-assisted tandem Wittig-intramolecular Diels-Alder cycloaddition. Product distribution and stereochemical assignment

The IMDA cycloadditions of 10 different ester-tethered 1,3,8-nonatrienes have been examined under controlled microwave heating (MeCN, 180 °C, 30 min), giving 90-99% yields, and the stereochemical outcome of the exo and endo adducts established together with X-ray crystal structural analysis. A microwave-assisted tandem Wittig-IMDA cycloaddition protocol has been established for a modular synthesis of the bicyclic lactones starting from α-bromoacetates of 2,4-pentadien-1-ols and α-oxo carbonyl compounds in the presence of PPh₃ and 2,6-lutidine (MeCN, 180 °C, 30 min). The overall yields of the tandem reactions are 68-80% and the stereoselectivity of the major adducts formed from E-substituted 1,3,8-nonatriene is the same as that observed for the purified 1,3,8-nonatrienes.     

Raman spectra,conformational stability,structural parameters,vibrational assignment,and ab initio calculations for epifluorohydrin

The Raman spectra (3200–100 cm⁻¹) of epifluorohydrin, OCH₂CH(CH₂F), in variable solvents, as well as that of the gas have been recorded and several of the bands due to the two less stable conformers have been identified. The variable solvent studies were inconclusive on the relative conformer stabilities. The conformational energy differences and optimized geometries for all three conformers have been obtained from ab initio calculations with the 3–21G, 4–31G and 6–31G* basis sets. A normal coordinate analysis has also been performed for each conformer with a force field determined from the 3–21G basis set. Assignment of the vibrational fundamentals observed in the Raman spectra of the fluid phases is proposed based on the normal coordinate calculations. In the liquid phase, one of the conformers with a large dipole moment predominates and it appears to be the gauche-I form which is the only one found in the solid. Utilizing the three rotational constants previously reported for each conformer, along with restricted relative distances for several of the structural parameters among the conformers from ab initio calculations, r₀ structural parameters for the heavy atoms have been determined.