Comparison of quartz and Teflon filters for simultaneous collection of size-separated ultrafine aerosol particles and gas-phase zero samples

In this research, the two most common filter media, quartz and Teflon, were tested to obtain information about the possible adsorption of gas-phase compounds onto filters during long sample collection of atmospheric aerosols. Particles of nanometer-size for off-line chemical characterization were collected using a recently introduced differential mobility analyzer for size separation. Samples were collected at an urban site (Helsinki, SMEARIII station) during spring 2010. Sampling time was 4 to 10 days for particles 50, 40, or 30 nm in diameter. Sample air flow was 4 L/min. The sampling setup was arranged so that two samples were obtained for each sampling period almost simultaneously: one containing particles and adsorbed gas-phase compounds and one containing adsorbed gas-phase compounds only. Filters were extracted and analyzed for the presence of selected carboxylic acids, polyols, nitrogen-containing compounds, and aldehydes. The results showed that, in quartz filter samples, gas-phase adsorption may be responsible for as much as 100% of some compound masses. Whether quartz or Teflon, simultaneous collection of gas-phase zero samples is essential during the whole sampling period. The dependence of the adsorption of gas-phase compounds on vapor pressure and the effect of adsorption on the deposited aerosol layer are discussed.     

Data,knowledge and method bases in chemical sciences. Part IV. Current status in databases

Computer readable databases have become an integral part of chemical research right from planning data acquisition to interpretation of the information generated. The databases available today are numerical, spectral and bibliographic. Data representation by different schemes--relational, hierarchical and objects--is demonstrated. Quality index (QI) throws light on the quality of data. The objective, prospects and impact of database activity on expert systems are discussed. The number and size of corporate databases available on international networks crossed manageable number leading to databases about their contents. Subsets of corporate or small databases have been developed by groups of chemists. The features and role of knowledge-based or intelligent databases are described.     

The PHARMSEARCH database

PHARMSEARCH, a database produced by the French Patent and Trademark Office (INPI), covers pharmaceutical patents issued by the Europeans, French, and United States patent offices from November 1986 onward. PHARMSEARCH is composed of MPHARM, a structure file searchable using Markush DARC software, and PHARM, the companion bibliographic file. Markush structures claimed in the patent documents are entered into the database as variable generic structures. Specific structures are also included in the database, when they are not part of a Markush structure in the patent document. Chemical index terms describe all moieties of the structure. Indexing also describes the therapeutic activities and preparation processes for the compounds. The indexing policies used in the production of this database are described.     

胺丶醇丶醚类化合物气相碱性的CNDO/2计算

The gas-phase basicities of compounds can be measured by their proton affinities. In this paper we he calculated the gas-phase basicities of about seventy compounds containing N or O by means of the method CNDO/2. For the alkylamines, alcohols, ethers and carbonyl compounds, computational results agree qualitatively with the experimental values. The sequences of gas-phase basicities for the series of these compounds are as follows: Et2NH>Me3N>t-BuNH2>Me2NH>i-PrNH2>n-BuNH2>n-PrNH2>EtNH2>MeNH2>NH3; Et2O>EtOMe>t-BuOH>Me2O>i-PrOH>n-BuOH>n-PrOH>EtOH>MeOH>H2O; n-PrCHO>EtCHO>MeCHO>HCHO; n-BuCO2H>n-PrCO2H>EtCO2H>MeCO2H>HCO2H; HCO2Bu-n>HCO2Pr-N>HCO2Et>HCO2Me>HCO2H Obviously, alkyl substitution plays a role to increase the gas-phase basicities. The squence of increasing effectiveness is t-Bu>i-Pr>n-Bu>n-Pr>Et>Me For the amines containing heteroatoms investigated here, the gas-phase basicities have the following order repectively: CH3NH2>NH2NH2>NH2OH>NH2F>NHF2>NF3 The gas-phase basicities of these compounds change regularly with various substitutents. For the aliphatic compounds, the gas-phase basicity increases with thosizo and the degree of branching of the alkyl groups. For the amines containing heteroatoms, the gas-phase basicity decreases with increasing of the electro-negativity of the substitutent. For the relationship between the gas-phase basksity and the charge distribution and the ionization potentials, the conclusions are as follows: (1) The gas-phase basicities of the homologous compounds are proportional to the electron density of the atom N or O, but those of Rn NH3-n and Rn OH2-n are inversely proportional to the electron denisty of atom N or O. This shows that the base strength of the molecule cannot be determined solely by the electron density of the individual atom. (2) In the protonation reaction the alkyl groups spread the charges from the charged center. This effect enables protonated cations to become more stable because of the charge distribution av     

Correlation between retention behaviour and GC-FTIR data in the study of flavonoids

Trimethylsilyl derivatives of 10 different hydroxy- and methoxyhydroxyflavonoid compounds were studied by the GC-FTIR technique. Optimal deviation parameters were determined for the flavonoids studied. The correlation found between retention and gas-phase IR data can successfully be used in structural identification of compounds having very similar chromatographic behaviour. The shift of the carbonyl frequency gives information on the presence of substituting agents.     

Mass Spectrometric Study of the Gas-Phase Difluorocarbene Expulsion of Polyfluorophenyl Cations via F-Atom Migration

An increasing number of fluorinated drugs, pesticides, and fine chemicals are now produced and applied, especially those containing polyfluorinated aromatic moieties. However, at present, the extent of literature covering the special mass spectrometric behaviors of these compounds remains limited. Herein, we report an unexpected but also general gas-phase dissociation mode of polyfluorinated aromatics in mass spectrometry: expulsion of difluorocarbene (50-Da neutral loss). Results from accurate mass measurements, tandem mass spectrometric experiments, and density functional theory (DFT) calculations support an intramolecular F-atom “ring-walk” migration mechanism for gas-phase CF₂ loss. Based on an assessment of the electron ionization-mass spectrometry (EI-MS) data of more than 40 polyfluorinated aromatic compounds from the National Institute of Standards and Technology data bank, we generalized on the substitution group effects on the difluorocarbene dissociation process of polyfluorinated aromatic compounds in EI-MS. These studies have enriched our knowledge of the special gas-phase reactivity of polyfluorinated aromatics and will provide valuable information in further analytical research of these compounds by mass spectrometry.

Carbohydrate Structure Database (CSDB): new features

Russian Chemical Bulletin - Carbohydrate Structure Database (CSDB) is a regularly updated database containing structural, taxonomic, bibliographic, NMR spectroscopic, and other information on...     

CNDO/2 calculation on gas-phase basicity of amines,alcohols and ethers

The gas-phase basicity of about seventy compounds containing N or O have been calculated by means of the CNDO/2 method. For alkylamines, alcohols, ethers and carbonyl compounds, computational results agree qualitatively with the experimental values. We have also discussed the relationships between gas-phase basicities and charge distributions and ionization potentials of these molecules.     

Real-time 2D separation by LC × differential ion mobility hyphenated to mass spectrometry

The liquid chromatography–mass spectrometry (LC-MS) analysis of complex samples such as biological fluid extracts is widespread when searching for new biomarkers as in metabolomics. The success of this hyphenation resides in the orthogonality of both separation techniques. However, there are frequent cases where compounds are co-eluting and the resolving power of mass spectrometry (MS) is not sufficient (e.g., isobaric compounds and interfering isotopic clusters). Different strategies are discussed to solve these cases and a mixture of eight compounds (i.e., bromazepam, chlorprothixene, clonapzepam, fendiline, flusilazol, oxfendazole, oxycodone, and pamaquine) with identical nominal mass (i.e., m/z 316) is taken to illustrate them. Among the different approaches, high-resolution mass spectrometry or liquid chromatography (i.e., UHPLC) can easily separate these compounds. Another technique, mostly used with low resolving power MS analyzers, is differential ion mobility spectrometry (DMS), where analytes are gas-phase separated according to their size-to-charge ratio. Detailed investigations of the addition of different polar modifiers (i.e., methanol, ethanol, and isopropanol) into the transport gas (nitrogen) to enhance the peak capacity of the technique were carried out. Finally, a complex urine sample fortified with 36 compounds of various chemical properties was analyzed by real-time 2D separation LC×DMS-MS(/MS). The addition of this orthogonal gas-phase separation technique in the LC-MS(/MS) hyphenation greatly improved data quality by resolving composite MS/MS spectra, which is mandatory in metabolomics when performing database generation and search.     

Quantum-chemical calculations of the enthalpies and entropies of gas-phase reactions possible in chemical vapor deposition of Group III-Group V element binary compounds

The results of quantum-chemical modeling of possible gas-phase reactions in chemical vapor deposition of Group III-Group V element binary compounds are generalized. Modern computational methods are shown to be capable of obtaining the thermodynamic characteristics of gas-phase reactions in agreement with experimental data. Quantum-chemical methods can be used to estimate the possibility and determine the temperature conditions of formation of oligomeric intermediates during deposition, predict the feasibility of synthesizing new rod-like inorganic polymers, and develop the concept of precursors for the controlled synthesis of III–V composites.     

A fluorine NMR database

We have established a fluorine chemical shift database for compounds with the empirical formula C_xF_y. Each record contains the compound's name, literature reference, empirical formula, functional group information, and a nine digit location code and chemical shift for each resonance. The database has over 500 compounds and 3000 chemical shifts. We can ask questions both about compounds as a whole or individual flourines. Some structures in the literature are inconsistent with the reported nmr parameters. Chemical shift assignments which were not possible earlier can now be made because of the correlations developed in this work.     

Phytochemical databases of Chinese herbal constituents and bioactive plant compounds with known target specificities

Two databases have been constructed to facilitate applications of cheminformatics and molecular modeling to medicinal plants. The first contains data on known chemical constituents of 240 commonly used Chinese herbs, the other contains information on target specificities of bioactive plant compounds. Structures are available for all compounds. In the case of the Chinese herbal constituents database, further details include trivial and systematic names, compound class and skeletal type, botanical and Chinese (pinyin) names of associated herb(s), CAS registry number, chirality, pharmacological and toxicological information, and chemical references. For the bioactive plant compounds database, details of molecular target(s), IC50 and related measures, and associated botanical species are given. For Chinese herbs, approximately 7000 unique compounds are listed, though some are found in more than one herb, the total number for all herbs being 8264. For bioactive plant compounds, 2597 compounds active against 78 molecular targets are covered. Statistical relationships within and between the two databases are explored.     

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions     

A personal reminiscence about theories used and misused in structural chemistry

In the last half-century, chemists acquired enough information about the structures and force fields of molecules to formulate what appeared to be successful theories (better called models) of molecular properties. For various reasons, chemists relied particularly heavily on studies of small hydrogen-containing compounds to shape their thinking. As discussed in the following text, this led to some inappropriate generalizations. In my first studies of molecular structure by gas-phase electron diffraction (GED), I was fortunate to find contradictions to the theories proposed at the time. What follows are reminiscences of how that came about and what happened subsequently. The main lesson to be earned, at least for molecules with central atoms that are not extremely large, is that the principal forces governing molecular structure are neither hybridization nor even the popular valence shell electron pair repulsions, explanations still taught routinely in chemistry courses but, instead, are the forces between geminal atoms resulting in the close-packing of ligands.     

Interpretation of high-throughput liquid chromatography mass spectrometry data for quality control analysis and analytical method development

An approach to rapidly process and interpret high-throughput liquid chromatography mass spectrometry data is presented. This approach applies an in-house developed computer application to process LC-MS report files containing spectral and chromatographic data from four different detectors (i.e. electrospray positive ionization, electrospray negative ionization mass spectrometry, UV absorption, and evaporative light scattering detection). Properties characteristic of detection and chromatographic retention are extracted and populated into a database. Approaches to applying this analytical information database for quality control analysis of ca. 400,000 samples are presented. Compound quality assessment methods employing average purity and detection data fields are compared to methods employing multiple quality control criteria (e.g. detection, purity, retention, and signal to noise). Structural similarity searches were applied with the analytical information database to identify compounds that may be undetectable by electrospray mass spectrometry. In addition, an approach to applying the database to aid in the selection of analytical detection and chromatography conditions for rapid analytical method development is also discussed.     

Development of a database of amino acid sequences for proteins identified and isolated on two-dimensional polyacrylamide gels

As part of our continuing studies into the biochemical basis of long-term changes in neuronal function in Aplysia, we have developed a simple method for obtaining amino acid sequence information from proteins isolated on two-dimensional gels. Proteins isolated on preparative two-dimensional gels are digested in situ with Staphylococcus aureus V8 protease, and the resulting peptides electrophoresed, transferred to a polyvinylidene difluoride membrane, and sequenced in a gas-phase sequencer. The method is simple and should be applicable to a variety of other systems where the development of a two-dimensional gel database is underway.     

Pi* orbital system of alternating phenyl and ethynyl groups: measurements and calculations

The temporary anion states of a series of alternating phenyl-ethynyl compounds are studied by means of electron transmission spectroscopy. Calculations of the virtual orbital energies of these compounds are computed with ab initio HF methods as well as DFT, and excellent correlations with the experimental vertical attachment energies are obtained. Scaled orbital energies for long-chain molecules are used to predict the vertical attachment energies of these compounds. In the absence of scaling, HOMO-LUMO gaps computed by DFT are found to be in substantial disagreement with gas-phase data. Such discrepancies may cause significant errors in theoretical studies of molecular conductance.     

Toxicology information systems: a historical perspective

Toxicology information systems have evolved swiftly from early, library-based bibliographic tools to advanced packages utilizing sophisticated computer and telecommunication technologies. These systems have evolved concurrently with the rapid expansion of the science of toxicology itself. Bibliographic files such as TOXLINE represent first attempts to handle the toxicology literature through on-line retrieval. Subsequent approaches applied the use of computers to provide literature-derived data, as in TDB or RTECS, or to capture data directly in the laboratory. Societal concerns about hazardous substances, manifested in legislation and regulations, have been responsible for the creation of many computerized systems. Advanced, integrated information management systems are being explored as a method of accessing a large number of independently maintained toxicology databases. Changes in information technologies such as the trend toward microcomputers and novel high-density storage devices will affect the future of toxicology information systems as will impending developments in toxicology itself related to biotechnology, analytical methodology, and alternatives to whole animal testing.