Comparison of electron ionization mass spectra of some organic compounds (MW < 200 Da) recorded on mass spectrometers of various types

Low-resolution electron ionization mass spectra recorded on various types of mass spectrometers (time-of-flight, quadrupole, and three-dimensional ion trap) were compared. A model mixture of 10 organic compounds (MW < 200 Da) was analyzed by gas chromatography-mass spectrometry. Pure mass spectra of analytes were extracted using the AMDIS software. The best repeatability was achieved for the time-of-flight mass spectrometer. The mass spectra recorded by a quadrupole and a time-of-flight mass spectrometer were quite similar. In the case of these instruments, library search using a commercial mass spectral data base (NIST’05) gave satisfactory result for each analyte (rank 1 or 2 in the “hit list”; Match > 900). In some cases, the mass spectra of model compounds recorded by the ion trap mass spectrometer differed in intensity of certain mass spectral peaks (but not in the set of peaks) from the mass spectra presented in the library and from the experimental mass spectra recorded by the time-of-flight and quadrupole instruments.     

Numerical Simulation of Chemical Equilibria and Photostationary States Using Spectrophotometric and Spectrofluorometric Data

A mathematical model describing series of experimental absorption and fluorescence spectra of multicomponent systems via equilibrium and photostationary concentrations of components of the systems was constructed. With photostationary concentrations, it is possible to take into account changes in the fluorescence spectra resulting from photochemical reactions. Ther unknown equilibrium and kinetic parameters of the model and also the spectra of pure components are found from experimental data by the nonlinear least-squares method. A software for the model was developed, and its applicability to the determination of the composition of multicomponent systems, resolution of the spectra of pure components, and determination of equilibrium and kinetic constants was demonstrated.__________Translated from Zhurnal Obshchei Khimii, Vol. 75, No. 3, 2005, pp. 386–394.Original Russian Text Copyright © 2005 by Rusalov.     

Measuring molecular force fields: Terahertz,inelastic neutron scattering,Raman, FTIR,DFT, and BOMD molecular dynamics of solid l-serine

A vibrational analysis of polycrystalline l-serine is provided using experimental terahertz, FTIR, Raman and inelastic neutron scattering (INS) spectra, calculated INS spectra – and Born–Oppenheimer molecular dynamics (BOMD) simulations from which the power spectra for the electronegative elements are compared to the THz spectra. Corrections are made to density functional theory (DFT) calculations for van der Waals interactions. Assignments and potential energy distributions are included for all 3N = 336 normal modes of an eight molecule supercell, including those for 48 non-bonded whole molecule translating and rotating vibrations, of which three are acoustic modes, usually not considered. Calculated and observed frequencies differ by an average 3 cm⁻¹ (s = 4). The INS spectrum of these modes below 100 cm⁻¹, calculated from energy second derivatives, show a remarkable similarity to the experimental 10 K spectra. The calculated low frequency modes are insensitive to small changes in cell parameters and geometry. THz intensities are represented by power spectra and not calculated explicitly. Nevertheless, power spectra of 13 ps BOMD trajectories at classical temperatures of 20 K, 400 K, and 500 K are markedly similar to the experimental terahertz spectra at 77 K and 298 K. Calculations on a serine crystal supercell 2 × 2 × 2 molecules deep appear to include, in a crude but fortuitously accurate way, enough of the principle out of phase dispersion to yield a match with experimental frequencies and intensities.     

Field desorption mass spectra of flavonoid acylglycosides. I. Natural acetyl derivatives

The field desorption mass spectra (FD spectra) of 17 natural flavonoid acetylglycosides have been studied. In the spectra of each of the 0-monoglycosides the molecular ion (M or M + H) appears as the main peak and it is accompanied by the ions of the aglycone (A or A + H) and of the acylated anhydrosugar (S). The intensity of the latter peak is largely connected with the structure of the substance. In the FD spectra of flavone 0-biosides, fragment S is absent but its mass can be calculated from the difference (M – A). Useful information for establishing the position of the acetyl group is given by the fragments S₁ and (M – S₁) corresponding to the detachment of the terminal sugar residue. The FD spectra of flavone C-glycosides differ greatly from the spectra of the 0-glycosides: In them the main peak is that of the ion (M), but peaks (A) and (S) are absent and the ions present resemble the fragmentation of the C-glycosides under the action of electron impact.All-Union Scientific-Institute of Medicinal Plants, Moscow. L. Ya. Karpov Scientific-Research Institute of Physical Chemistry, Moscow. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 573–582, September–October, 1984.     

Synthesis and structure of diphospholenebutadienes

Conclusions A method was developed for the synthesis and purification of 2,3-bis(1-oxophospholen-1-yl)-1,3-butadienes, which were identified via the IR and PMR spectra.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1144–1146, May, 1981.The authors thank N. V. Teptin, T. A. Zyablikov, and É. I. Gol'dfarb for recording the indicated spectra.     

Synthesis of indoles from pyridinium salts. 1. Recyclization of 4-alkyl-2,6-dimethyl-3-nitropyridine methiodides in the presence of ketones

A method for the synthesis of 4-alkylpolymethylindoles by recyclization of 4-alkyl-2,6-dimethyl-3-nitropyridine methiodides in the presence of ketones was developed. A method for establishing the structures of the polyalkylindoles on the basis of data from the PMR spectra and the proton-coupled ¹³C NMR spectra is proposed.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 509–518, April, 1985.     

Common components and specific weights analysis: a tool for monitoring the molecular structure of semi-hard cheese throughout ripening

Twelve semi-hard (Raclette) cheeses, belonging to four brand products, namely A (n = 3), B (n = 3), C (n = 3) and D (n = 3), were produced during summer period and ripened at an industrial scale. Tryptophan, riboflavin and vitamin A fluorescence spectra were scanned on the 12 cheeses at 2, 30 and 60 days of ripening. The physico-chemical analyses were performed only at the end of the ripening stage (60 days). Common components and specific weights analysis (CCSWA) were applied on the four data tables. CCSWA showed that the common component 1 (q₁), discriminating cheeses labelled A, B and C from those labelled D, expressed 94.4 and 59% of the inertia of vitamin A and tryptophan fluorescence spectra and a less amount for riboflavin fluorescence spectra and physico-chemical data (24.2 and 13.2%, respectively). Common component 3 (q₃), differentiating between cheeses labelled B and those labelled A and C, explained 34.6 and 23.9% of the inertia of the physico-chemical data and tryptophan fluorescence spectra, respectively, and a tiny part of the inertia of riboflavin and vitamin A fluorescence spectra (3.2 and 0.7%, respectively). The CCSWA showed its ability to describe the overall information collected from fluorescence and physico-chemical data tables and to extract relevant information at the molecular level throughout ripening of the investigated semi-hard cheeses.     

Bootstrap classification and point-based feature selection from age-staged mouse cerebellum tissues of matrix assisted laser desorption/ionization mass spectra using a fuzzy rule-building expert system

A bootstrap method for point-based detection of candidate biomarker peaks has been developed from pattern classifiers. Point-based detection methods are advantageous in comparison to peak-based methods. Peak determination and selection are problematic when spectral peaks are not baseline resolved or on a varying baseline. The benefit of point-based detection is that peaks can be globally determined from the characteristic features of the entire data set (i.e., subsets of candidate points) as opposed to the traditional method of selecting peaks from individual spectra and then combining the peak list into a data set. The point-based method is demonstrated to be more effective and efficient using a synthetic data set when compared to using Mahalanobis distance for feature selection. In addition, probabilities that characterize the uniqueness of the peaks are determined.This method was applied for detecting peaks that characterize age-specific patterns of protein expression of developing and adult mouse cerebella from matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) data. The mice comprised three age groups: 42 adults, 19 14-day-old pups, and 16 7-day-old pups. Three sequential spectra were obtained from each tissue section to yield 126, 57 and 48 spectra for adult, 14-day-old pup, and 7-day-old pup spectra, respectively. Each spectrum comprised 71,879 mass measurements in a range of 3.5-50 kDa. A previous study revealed that 846 unique peaks were detected that were consistent for 50% of the mice in each age group (C. Laurent, D.F. Levinson, S.A. Schwartz, P.B. Harrington, S.P. Markey, R.M. Caprioli, P. Levitt, Direct profiling of the cerebellum by MALDI MS: a methodological study in postnatal and adult mouse, J. Neurosci. Res. 81 (2005) 613-621.).A fuzzy rule-building expert system (FuRES) was applied to investigate the correlation of age with features in the MS data. FuRES detected two outlier pup-14 spectra. Prediction was evaluated using 100 bootstrap samples of 2 Latin-partitions (i.e., 50:50 split between training and prediction set) of the mice. The spectra without the outliers yielded classification rates of 99.1 ± 0.1%, 90.1 ± 0.8%, and 97.0 ± 0.6% for adults, 14-day-old pups, and 7-day-old pups, respectively. At a 95% level of significance, 100 bootstrap samples disclosed 35 adult and 21 pup distinguishing peaks for separating adults from pups; and 8 14-day-old and 15 7-day-old predictive peaks for separating 14-day-old pup from 7-day-old pup spectra. A compressed matrix comprising 40,393 points that were outside the 95% confidence intervals of one of the two FuRES discriminants was evaluated and the classification improved significantly for all classes. When peaks that satisfied a quality criterion were integrated, the 55 integrated peak areas furnished significantly improved classification for all classes: the selected peak areas furnished classification rates of 100%, 97.3 ± 0.6%, and 97.4 ± 0.3% for adult, 14-day-old pups, and 7-day-old pups using 100 bootstrap Latin partitions evaluations with the predictions averaged. When the bootstrap size was increased to 1000 samples, the results were not significantly affected. The FuRES predictions were consistent with those obtained by discriminant partial least squares (DPLS) classifications.     

Chemical-ionization mass spectra of diterpene alkaloids

The chemical-ionization spectra of diterpene alkaloids have been investigated for the first time with the recording of positive and negative ions [Cl(+) and (–)). A comparison has been made of the CI(+) spectra with the EI and SIMS spectra. It has been shown that the nature of the CI(+) and (–) spectra depends greatly on the type and position of substituents in the lycoctonine skeleton.Deceased.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, fax (3712) 89 14 75. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 114–122, January-February, 1995. Original article submitted October 31, 1994.     

The fluorescence spectrum of HCN (A≈1 A′' → X≈1 Σ+) using ArF laser excitation

The fluorescence spectrum of HCN A≈(¹A′') → X≈(¹Σ⁺) is reported using a tuned ArF laser as the excitation source. Assignments for the fluorescence spectra from two upper state vibrational levels are given. Franck—Condon factors for the absorption and fluorescence spectra are calculated. A laser-induced fluorescence spectrum is given which agrees with published absorption spectra of HCN.     

Sequence Dependent Repair of 1,N6-Ethenoadenine by DNA Repair Enzymes ALKBH2, ALKBH3, and AlkB

Mutation patterns of DNA adducts, such as mutational spectra and signatures, are useful tools for diagnostic and prognostic purposes. Mutational spectra of carcinogens derive from three sources: adduct formation, replication bypass, and repair. Here, we consider the repair aspect of 1,N⁶-ethenoadenine (εA) by the 2-oxoglutarate/Fe(II)-dependent AlkB family enzymes. Specifically, we investigated εA repair across 16 possible sequence contexts (5′/3′ flanking base to εA varied as G/A/T/C). The results revealed that repair efficiency is altered according to sequence, enzyme, and strand context (ss- versus ds-DNA). The methods can be used to study other aspects of mutational spectra or other pathways of repair.     

Sum frequency generation spectroscopic study of the condensation effect of cholesterol on a lipid monolayer

Sum frequency generation (SFG) spectra and surface pressure–molecular area (π–A) isotherms have been obtained for mixed cholesterol–DPPC monolayers with cholesterol mole fractions, x(chol.), from 0 to 1.0, at the air–water interface, under same conditions, at 22 °C. Analysis of the spectra indicated that incorporation of cholesterol into the monolayers at 3 mN m⁻¹ greatly increases the conformational and orientational order of the alkyl chains of DPPC, maximizing these properties at x(chol.)=0.4. Analysis also indicated that order in the mixed monolayers at 15 and 35 mN m⁻¹ is not affected by incorporation of cholesterol. The π–A isotherms measured at 3 mN m⁻¹ for the mixed monolayer with x(chol.)=0.4 have the largest negative deviation of the molecular area relative to those of ideal mixtures (the so-called “condensation effect” of cholesterol), indicating the most thermodynamically stable state. Comparison of results from SFG spectra and π–A isotherms explicitly proved that the condensation effect can be interpreted in terms of conformational and orientational ordering of the alkyl chains of DPPC.     

Analysis of the hyperfine structures and

From the theories of the nuclear hyperfine structure (HFS) and Λ doubling of diatomic molecules, several brief algebraic equations for interpretation of HFS and Λ doubling of transitions of diatomic molecule have been developed. A few important parameters of HFS and Λ doubling of¹⁵N¹⁶O have been efficiently and accurately obtained from the analysis of the high resolution spectra of¹⁵N¹⁶O (X²∏) observed in our experiments with these equations. This method can provide an effective approach to obtain important hyperfine parameters of novel radicals from their high resolution laser magnetic resonance spectra. Liu Yu-yan, Guo Yuan-qing, Assignments of FIR-LMR spectra of CF X²∏(υ= 1) and MIR-LMR spectra of NO X²∏ (υ =1←0), Spectroscopy and Spectral Analysis (in press).     

Procedure for preparing infrared spectra on gas chromatographic fractions

A convenient technique is described for the preparation of microinfrared spectra on materials which elute from a gas chromatograph. The technique involves trapping the sample on KBr and then pressing this material in a die between two portions of pure KBr. Samples as small as 10 μg grams and as low boiling as 150 °C produce acceptable spectra. Since no solvents are employed, solvent band compensation is unnecessary.     

13C NMR spectra of the aminoglycoside antibiotic neomycin B,monomycin A,and kanamycin A. Complete assignment of the signals

On the basis of the results of a study of the dependence of the chemical shifts of the signals in the¹³C NMR spectra of neomycin B, monomycin A, and kanamycin A, over a wide pH range (from 1.0 to 10.0) a complete assignment of the spectra signals of these antibiotics has been made. Optimum pH values of solutions are proposed for which the more complete resolution of the resonance signals in the spectra of neomycin B, monomycin A, and kanamycin A is observed. All-Union Scientific-Research Institute of Antibiotics, Moscow. I. M. Sechenov 1st Moscow Medical Institute. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 686–695, September–October, 1980.     

Mass spectra of alliosterol and its dehydration product and of allosides A and B

The EI and LSIMS mass spectra of alliosterol and its dehydration product and of allosides A and B have been studied. The spectra of alliosterol show features characteristic for sterols of the cholestane series. A comparison of the B/E spectra of some fragments of the ions from alliosterol and its dehydro product has shown the unimportance of the conversion of the former into the latter under mass-spectrometric conditions.Institute of Chemistry of Plant Substances, Uzbekistan Academy of Sciences, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, Nos. 3,4, pp. 344–349, May–August, 1992.     

Quantitative analysis of unlabelled and polydeuterated compounds by gas chromatography-mass spectrometry

Summary A system for computer evaluation of gas chromatographic-mass spectrometric analyses of unlabelled and polydeuterated compounds is described. The system has been in routine use for two years and has been found to fulfil most of the needs of the laboratory in connection with studies of steroid and bile acid metabolism. Complete or partial spectra are taken by repetitive magnetic scanning and are recorded on magnetic tape. Methods for qualitative evaluation have been described previously [6, 9]. Quantitative determinations of unlabelled compounds are based on areas of gas chromatographic peaks in selected specific fragment ion current chromatograms generated by the computer. Percentage distribution of molecular or fragment ion species containing 0–19 deuterium atoms is calculated from averaged spectra by comparison with spectra of the unlabelled reference compound analyzed on the same day. When small amounts of material are available and when ions occur in low abundance, repetitive accelerating voltage scanning over a short mass range is used. A slow scan rate, 1–5 s, and a high data sampling rate, 10 kHz, permit a 100–300 fold increase of amplification. After bunching of intensity readings, partial mass spectra are constructed which are treated in the same way as complete spectra.     

Quinoline derivatives

A number of difficult-to-obtain heterocyclic compounds — tetrahydroquinolino- and quinolinopyrazines — were synthesized from o-dinitrotetrahydroquinolines. The UV spectra of the synthesized compounds were studied.See [1] for communication III.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 525–527, April, 1973.     

Spectra of primary nitramines,vibrational spectra of ethylenedinitramine and its isotopically substituted analogs

Conclusions The vibrational spectra of crystalline ethylenedinitramine, ethylenedinitramine labeled with N¹⁵, as well as their deutero-derivatives were studied. Assignment of the vibration frequencies of the nitramine fragment is proposed.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 10, pp. 2194–2197, October, 1969.The authors would like to thank B. Lokshin for recording the IR spectra in this region, as well as A. Bobrov for recording the Raman spectra.     

An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data

A method is presented for extracting individual component spectra from gas chromatography/mass spectrometry (GC/MS) data files and then using these spectra to identify target compounds by matching spectra in a reference library. It extends a published “model peak” approach which uses selected ion chromatograms as models for component shape. On the basis of this shape, individual mass spectral peak abundance profiles are extracted to produce a “purified” spectrum. In the present work, ion-counting noise is explicitly treated and a number of characteristic features of GC/MS data are taken into account. This allows spectrum extraction to be reliably performed down to very low signal levels and for overlapping components. A spectrum match factor for compound identification is developed that incorporates a number of new corrections, some of which employ information derived from chromatographic behavior. Test results suggest that the ability of this system to identify compounds is comparable to that of conventional analysis.