Dissimilarity analysis and automatic identification of monomethylalkanes from gas chromatography mass spectrometry data 1. Principle and protocols

Monomethylalkanes are common but important components in many naturally occurring and synthetic organic materials. Generally, this kind of compounds is routinely analyzed by gas chromatography mass spectrometry (GC–MS) and identified by the retention pattern or similarity matching to the reference mass spectral library. However, these identification approaches rely on the limited standard database or costly standard compounds. When unknown monomethylalkane is absent from the reference library, these approaches might be less useful. In this study, based on the fragmentation rules and empirical observation, many interesting mass spectral characteristics of monomethylalkanes were discovered and employed to infer the number of carbon atoms and methylated position. Combined with the retention pattern, a protocol was described for the identification of monomethylalkane analyzed by GC–MS. After tested by simulated data and GC–MS data of the gasoline sample, it was demonstrated that the developing approach could automatically and correctly identify monomethylalkanes in complicated GC–MS data.     

Equivalent chain lengths of all C4-C23 saturated monomethyl branched fatty acid methyl esters on methylsilicone OV-1 stationary phase

Isomer mixtures of monomethyl branched saturated C7-C23 fatty acid methyl esters (FAME) were prepared by performing a methylene insertion reaction to the straight chain FAME and this study model was completed by using commercially available standards of C4-C7 FAME. The equivalent chain lengths (ECL) of all 220 C4-C23 monomethyl branched FAME on OV-1 stationary phase were measured, achieving an average repeatability of ±0.0004 ECL units. The monomethyl branched FAME was identified by GC on the basis of regularity of the fractional chain lengths (FCL) dependence on the number of carbon atoms (C(z)) of individual homologous series of methyl 2-, 3-, …, 21-FAME. The prediction of retention of the first homologues, having the new position of methyl group beginning at higher carbon atoms number, and analogously for the second, third, fourth, and other members of the homologous series, allowed the dependence FCL=f(C(z)) for the first and subsequent members of beginning homologous of monomethyl derivatives of FAME. The identification was confirmed by mass spectrometry. All of the methyl isomers of FAME, which could not be completely separated by gas chromatography due to having a methyl group in surroundings of the middle of the carbon chain, were resolved by mass spectrometry using deconvolution in a SIM-mode. Measured gas chromatographic and mass spectrometric data were applied for identification of the monomethyl branched saturated FAME in tongue coating.     

直链单烯烃保留指数与分子结构关系的研究

根据同系直链单烯烃保留指数与同碳数正构烷烃保留指数差值与分子碳数间关系曲线拟合,提出预测同系直链单烯烃保留指数的准确公式。在ＳＱ,ＰＦＥ,ＰＥＧ－４０００上,利用所提出的公式对检验集中化合物保留指数预测值与实测值差的标准偏差在±０．９ｉ．ｕ．～±１．５ｉ．ｕ．之间。并且研究发现,同碳数、同几何构型直链单烯烃各位置异构体分子中双键位置与化合物保留指数具有指数关系。首次提出依据分子中双键位置预测其保留指数的准确公式。公式适合各种不同极性固定相。     

GC behaviour of symmetrical n-dialkyl sulphides under isothermal and temperature programming conditions

Retention indices were determined for a homologous series of n-dialkyl sulphides on three stationary phases (SE-30, OV-17 and XE-60) under isothermal and linear temperature programming conditions. Under these two different GC conditions, equations were derived for each of the three stationary phases which showed the dependence of retention index on the number of carbon atoms and the boiling points for a homologous series of n-dialkyl sulphides. The equation for the correlation isothermal retention index was shown to be applicable to the identification of n-dialkyl sulphides using linear temperature programming. It was found that the GC behaviour of n-dialkyl sulphides makes these compounds suitable for use as a standard series instead of n-alkanes for the calculation of retention indices in GC analysis in which detectors insensitive to n-alkanes are employed. The use of the homologous series of n-dialkyl sulphides for the calculation of sulphide retention indices can be great practical importance in the microanalysis of natural compounds. We have used this method successfully in the analysis of pesticides containing S-atoms.     

The kinetics of the reactions of C2 (a 3pi(u)) with alcohols

The reactions of C2 (a 3pi(u)) radicals with a series of alcohols have been studied at about 6.5 Torr total pressure and room temperature using the pulsed laser photolysis/laser-induced fluorescence technique. The relative concentration of C2 (a 3pi(u)) radicals, which are generated via the photolysis of C2Cl4 with the focused output from the fourth harmonic of a Nd:YAG laser (266 nm), was monitored by laser-induced fluorescence (LIF) in the (0, 0) band of the C2 (d 3pi(g)<--a 3pi(u)) transition at 516.5 nm. Under pseudo-first-order conditions, we measured the time evolution of C2 (a 3pi(u)) and determined the rate constants for reactions of C2 (a 3pi(u)) with alcohols. The rate constants increase linearly with the number of C atoms in the alcohols. All of them are larger than those for reactions of C2 (a 3pi(u)) with alkanes (C1-C5). Based on the bond dissociation energy and linear free energy correlations, we believe the reactions of C2 (a 3pi(u)) with alcohols proceed via the mechanism of hydrogen abstraction. The experimental results show that the H-atom on the C-H bonds is activated at the presence of the OH substituent group in the alcohol molecule. The theoretical calculations for the reaction of C2 (a 3pi(u)) with methanol also support these hypotheses.     

A method of calculating the second dimension retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry

A method was developed to calculate the second dimension retention index of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) data using n-alkanes as reference compounds. The retention times of the C(7)-C(31) alkanes acquired during 24 isothermal experiments cover the 0-6s retention time area in the second dimension retention time space, which makes it possible to calculate the retention indices of target compounds from the corresponding retention time values without the extension of the retention space of the reference compounds. An empirical function was proposed to show the relationship among the second dimension retention time, the temperature of the second dimension column, and the carbon number of the n-alkanes. The proposed function is able to extend the second dimension retention time beyond the reference n-alkanes by increasing the carbon number. The extension of carbon numbers in reference n-alkanes up to two more carbon atoms introduces <10 retention index units (iu) of deviation. The effectiveness of using the proposed method was demonstrated by analyzing a mixture of compound standards in temperature programmed experiments using 6 different initial column temperatures. The standard deviation of the calculated retention index values of the compound standards fluctuated from 1 to 12 iu with a mean standard deviation of 5 iu.     

Semi-empirical topological method for the prediction of the chromatographic retention of cis- and trans-alkene isomers and alkanes.

A new index is proposed for the prediction of the chromatographic retention of the cis- and trans-n-alkene isomers and alkanes. This index is based on the hypothesis that the chromatographic retention of the molecule is due to the interaction of each carbon atom with the stationary phase, and consequently the index is reduced by its neighbours' steric effects. The topological values are obtained by a numerical approximation considering the general behaviour of the chromatographic retention of the compounds. The simple linear regressions between the chromatographic retention and the index proposed for all branched alkanes and also isomers of the studied straight-chain C5 and C14 alkenes (1-ene, cis- and trans-2-, 3-, 4-, 5-, 6- and 7-enes) is very good (the correlation coefficient is r = 0.9999), and the elution sequence is correct for most of them. The models have a high predictive ability, as established by cross-validation values (r2cv). Thus, this new method, different from those already existent, can be used as complementary tool for the elucidation of the molecular structure, or prediction of the chromatographic retention of the cis- and trans-alkene isomers and branched alkanes. It could be extended with success, in the future, to the other types of compounds.     

Theoretical study of endohedral C36 and its dimers

It is found that atoms of lithium and carbon can be encapsulated in C(36) on the basis of the calculation of their encapsulation energies using density functional theory. Specifically, they can be encapsulated in C(36) better than in C(60) despite the smaller (70%) cavity size of the former. In C@C(36), the encapsulated carbon atom forms covalent bonds with the carbon atoms of the cage, which is in contrast with the case of N@C(60.) Two isomers are expected to be in an equilibrium which involves spin quenching and generation. Li@C(36) and C@C(36) are expected to exist in the form of dimers with nonendohedral fullerenes, i.e., as Li@C(36)-C(36) and C@C(36)-C(36). Three stable isomers were found for the former (A, B, and C). Equilibrium between A and C as well as that between B and C is accompanied by spin transfer between two fullerene units, while that between A and B is not. The two stable isomers in C@C(36)-C(36) form an equilibrium accompanied by spin quenching and generation, allowing the dimer to be potentially useful for molecular devices.     

Preparation of 6-O-(4-alkoxytrityl)celluloses and their properties

Cellulose was reacted with a series of 4-alkoxytrityl chlorides (C(n)TCl, n: number of carbon atoms in a saturated alkyl chain) under homogeneous reaction conditions in LiCl-N,N-dimethyl acetoamide to give a series of 6-O-(4-alkoxytrityl)celluloses (C(n)TC) with a high degree of substitution (DS), from 0.94 to 0.99, and with high regioselectivity at the 6-O position. Solubility of the C(n)TC in nonpolar solvents depended on the alkyl chain length: as the alkyl chain lengthens, cellulose derivatives become more hydrophobic and are readily soluble in nonpolar solvents, but not in polar solvents. Acetates of the C(4)-C(18)TC (C(4)-C(18)TCAc) showed anisotropic structures over melting temperatures (T(m)) examined under a polarized optical microscope (POM). Over isotropization temperatures (T(i)), flow birefringence were detected for C(12)-C(18)TCAc. The T(m) and T(i) decreased linearly with an increasing number of carbon atoms in the alkyl substituent. Wide-angle X-ray scattering (WAXS) studies of C(n)TC indicated that the fully extended side chains were perpendicular to the polymer backbone and interdigitated. These C(n)TC with the improved solubility may be used as starting materials for further derivatization focused on the secondary hydroxyl groups at the C-2 and C-3 positions.     

From pure C(60) to silicon carbon fullerene-based nanotube: an ab initio study

The energetics, geometrical, and electronic properties of the silicon carbon fullerene-based materials, obtained from C(60) by replacing 12 carbon atoms of the C(60) cage with silicon atoms, are studied based on ab initio calculations. We have found that, of the two C(48)Si(12) isomers obtained, the one with the carbon atoms and the silicon atoms located in separated region, i.e., with a phase-separated structure is more stable. Fullerene-based C(36)Si(24) cluster, C(36)Si(24)-C(36)Si(24) dimer, and the nanotube constructed from the clusters are then studied. The calculations on the electronic properties of these silicon carbon fullerene-based nanomaterials demonstrate that the energy gaps are greatly modified and show a decreasing trend with increasing the size of the clusters. The silicon carbon fullerene-based nanotube has a narrow and direct energy band gap, implying that it is a narrow gap semiconductor and may be a promising candidate for optoelectronic devices.     

Preparation and structural characterization of the Ih and the D5h isomers of the endohedral fullerenes Tm3N@C80: icosahedral C80 cage encapsulation of a trimetallic nitride magnetic cluster with three uncoupled Tm3+ ions

We report an efficient method for the preparation and purification of the Ih and the D5h isomers of Tm3N@C80. Following preparation in a Kratschmer-Huffman electric-arc generator, the Tm3N@C80 isomers were obtained by a chemical separation process followed by a one-stage isomer selective chromatographic high-performance liquid chromatography (HPLC) separation (pyrenyl, 5PYE column). The HPLC chromatographic retention behavior on a pentabromobenzyl (5PBB) column suggests a charge transfer of approximately 6 electrons; [M3N] 6+@C80(6-) and the chromatographic retention mechanisms of the Ih and the D5h isomers of Tm3N@C80 on both 5PBB and 5PYE columns are discussed. Single-crystal X-ray diffraction data demonstrate that the Tm3N cluster has a planar structure but represents a tight fit for trapping the Tm3N cluster inside the I h - and the D 5h -C 80 cages. Specifically, the Tm atoms punch out the cage carbon atoms adjacent to them. The "punched out" effect can be demonstrated by cage radii and pyramidal angles at cage carbon atoms near the Tm atoms. The magnetic susceptibility (chiT) for Tm3N@ Ih -C80 was found to exhibit Curie-Weiss behavior with C = 23.4 emu.K/mol, which is consistent with the calculated value for three uncoupled Tm3+ ions by considering the spin and orbital contributions with no quenching of the orbital angular momentum ( L = 5, S = 1, and J = 6; Ccalcd = 23.3 emu.K/mol). The electrochemical measurements demonstrate that both the Ih and the D5h isomers of Tm3N@C80 have a large electrochemical gap.     

直链单炔烃保留指数与分子结构关系研究

根据同系直链单炔烃保留指数与同碳数正构烷烃保留指数差值与分子碳数间关系曲线拟合，提出预测同系直链单炔烃保留指数的较准确公式。研究并发现同碳数直链单炔烃各异构体分子中三键位置与化合物保留指数具有指数关系，首次提出了据分子中三键位置预测其保留指数的较准确公式。解决了从低碳数直链单炔烃保留指数预测高碳数直链单炔烃保留指数问题。     

A DFT study on the dimerization of C62, H2-C62, and F2-C62

On the basis of calculations using the density functional theory, we show that C(62), a recently synthesized nonclassical fullerene, will presumably undergo dimerization with various isomers at elevated temperatures. This is shown by calculating the dimerization energy and the activation barrier of the dimerization. Eight possible isomers of the dimer were identified, all of which are more stable than the two isolated monomers. The relative stability of various isomers depends upon the kind of C=C bonds within the four-membered carbon ring involved in the dimerization. In addition, similar calculations were performed for the monomers and dimers of H(2)-C(62) and F(2)-C(62). Six isomers were identified for each of the dimers. Although less pronounced than the case of the C(62) dimer, all isomers of the H(2)-C(62) dimer are appreciably more stable than the individual monomers. Although a large steric repulsion due to F atoms significantly reduces the stability of F(2)-C(62) dimer, its two isomers are still more stable than separate monomers.     

HPLC Retention Index Scale for Nitrogen-Bridged Compounds

Abstract

Retention indices of some nitrogen-bridged compounds having pharmacological activity have been determined. A retention index scale based on the relative retention of a homologous series of C₃-C₂₃ 2-keto alkanes has been worked out. Linear relationships were found between RI and logP, allowing a prediction of retention indices.

The relationships between the structures and the retention indices of these compounds have been interpreted.     

Retention index calculation without n-alkanes--the virtual carbon number

For the fast gas chromatographic identification of separated components the retention index is still one of the most often used tools, although mass spectrometry is available in almost all analytical laboratories. For the calculation of the retention indices it is not necessary to use n-alkanes or any other homologous series. If the analyte contains some compounds, not necessarily belonging to a homologous series, with well-known retention indices those compounds can be used as index references and the index of the other compounds can be calculated as is done using n-alkanes. The only difference is that instead of the carbon number of the n-alkanes, virtual carbon numbers of the reference compounds should be used. The method of calculation, and the effect of this method of calculation on the reproducibility are discussed in this paper, and analyses of some halogenated compounds and marjoram oil are used as experimental examples.     

Application of target factor analysis of gas chromatography. Reproduction,prediction and classification

Summary Using the method of target factor analysis (TFA) described by Malinowski and Howery a computer program has been developed to study different sets of gas chromatographic retention data. Physico-chemical, topological and uniqueness parameters have been found to be basic factors to describe solute behaviour problems. Factor analytical solutions have been used to reproduce the data matrices and to make predictions based on best sets of basic factors. The mean absolute error in the reproduction step is between 1.72 retention index units (i.u.) for a relatively simple matrix consisting of retention indices of alcohols and 7.36 i.u. for a combined data matrix of alcohol, aldehyde and ketone retention indices. TFA has also been used to classify solutes based on their retention behaviour. Alkanes have been classified from cycloalkanes, alkanes from alkenes, and alcohols from aldehydes and ketones using only their retention data and a special kind of uniqueness vector.     

Systematic characterisation of long-chain aliphatic esters of wool wax by gas chromatography-electron impact ionisation mass spectrometry

A detailed structural characterisation of the aliphatic high-molecular-mass esters extracted from raw wool based on high-temperature gas chromatography-electron impact ionisation mass spectrometry is described. The raw wool esters extracted are in the range of C37 to C54 (i.e., molecular mass 550-788). The selected ion chromatogram exhibited four isomers for the esters with an odd number of carbon atoms (i:a, i:n, a:n and n:n) and five for those with an even number of carbon atoms (i:i, a:a, i:n, a:n and n:n). Isomeric structural elucidation is discussed with respect to the long-chain fatty acid and long-chain fatty alcohol structures, on the basis of chromatographic retention behaviour and mass spectral information.     

Diffusion of Noble Metals,Zn and Ge in GaSb Single Crystals

Diffusion of Cu, Ag, Au, Ge and Zn in single crystal gallium antimonide has been carried out by measuring Hall effect according to van der Pauw, conductivity, energy dispersive X-ray (EDX) and surface electron microscopy. The best results have been obtained in excess of antimony. The resulting diffusion data in GaSb are diffusivity D_o, activation enthalpy Q, carrier density p and mobility μ at 300 K: Ag: D_o=1.8·10⁻⁴ cm² s⁻¹, Q=1.2 eV, p=6·10¹⁸ cm⁻³, μ=550 cm² (Vs)⁻¹ Au: D_o=6.6·10⁺³ cm² s⁻¹, Q=2.7 eV, p=5·10¹⁸ cm⁻³, μ=500 cm² (Vs)⁻¹ Cu: D_o=3.2·10⁺⁸ cm² s⁻¹, Q=2.7 eV, p=2·10¹⁸ cm⁻³, μ=150 cm² (Vs)⁻¹ Zn: D_o=9.2·10⁻² cm² s⁻¹, Q=1.8 eV, p=2·10²⁰ cm⁻³, μ=80 cm² (Vs)⁻¹ Ge: D_o=1.0·10⁻¹ cm² s⁻¹, Q=1.7 eV, p=1·10¹⁹ cm⁻³, μ=320 cm² (Vs)⁻¹. This revised version was published online in August 2006 with corrections to the Cover Date.     

Rediscovering the problem of interpretation of chromatographically determined enthalpy and entropy of adsorption of different adsorbates on carbon materials. Critical appraisal of literature data

Adsorbate-adsorbent and adsorbate-adsorbate interactions having decisive influence on the distribution of adsorbate between gas-solid phases in inverse gas chromatography (IGC) have been thermodynamically explained. Specific retention volumes, second adsorption virial coefficients and Kováts retention indices, likewise their dependencies on column temperature, T, number of carbon atoms, n(C) (or methylene groups CH(2)) and mutual ones have been briefly presented. The results of the molar differential enthalpy and entropy of adsorption obtained for different carbon materials employing inverse gas chromatography have been collected and interpreted. An attempt has been made to elucidate abnormal behaviour of the specific and net retention volumes, the second adsorption virial coefficients and the Kováts retention indices, e.g., the magnitudes on which the values of the afore-mentioned thermodynamic values have been determined and compared. The detailed analysis of the errors associated with the experimental parameters necessary for calculating retention volumes, second adsorption virial coefficients and Kováts retention indices has been presented.     

Large endohedral fullerenes containing two metal ions, Sm2@D2(35)-C88, Sm2@C1(21)-C90, and Sm2@D3(85)-C92, and their relationship to endohedral fullerenes containing two gadolinium ions

The carbon soot obtained by electric arc vaporization of carbon rods doped with Sm(2)O(3) contains a series of monometallic endohedral fullerenes, Sm@C(2n), along with smaller quantities of the dimetallic endohedrals Sm(2)@C(2n) with n = 44, 45, 46, and the previously described Sm(2)@D(3d)(822)-C(104). The compounds Sm(2)@C(2n) with n = 44, 45, 46 were purified by high pressure liquid chromatography on several different columns. For endohedral fullerenes that contain two metal atoms, there are two structural possibilities: a normal dimetallofullerene, M(2)@C(2n), or a metal carbide, M(2)(μ-C(2))@C(2n-2). For structural analysis, the individual Sm(2)@C(2n) endohedral fullerenes were cocrystallized with Ni(octaethylporphyrin), and the products were examined by single-crystal X-ray diffraction. These data identified the three new endohedrals as normal dimetallofullerenes and not as carbides: Sm(2)@D(2)(35)-C(88), Sm(2)@C(1)(21)-C(90), and Sm(2)@D(3)(85)-C(92). All four of the known Sm(2)@C(2n) endohedral fullerenes have cages that obey the isolated pentagon rule (IPR). As the cage size expands in this series, so do the distances between the variously disordered samarium atoms. Since the UV/vis/NIR spectra of Sm(2)@D(2)(35)-C(88) and Sm(2)@C(1)(21)-C(90) are very similar to those of Gd(2)C(90) and Gd(2)C(92), we conclude that Gd(2)C(90) and Gd(2)C(92) are the carbides Gd(2)(μ-C(2))@D(2)(35)-C(88) and Gd(2)(μ-C(2))@C(1)(21)-C(90), respectively.