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BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. RESULTS: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. CONCLUSIONS: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

Introduction 3 Purpose and scope of report 4 Acknowledgments 5 Properties of water 5 Composition of the earth's crust 6 Water as a geochemical agent The role of water in erosion Chemistry of weathering processes Collection of quality-of-water data Collection of water samples Surface-water sampling Ground-water sampling Completeness of sample coverage Analyses of water samples Field testing of water Electric logs as indicators of ground-water quality Laboratory procedures Expression of water analyses Analyses reported in terms of hypothetical combinations Analyses expressed in terms of ions Determinations included in analyses Units used in reporting analyses Weight-per-weight units Weight-per-volume units Equivalent-weight units Composition of anhydrous residue Parts per million as calcium carbonate Comparison of units of expression Significance of properties and constituents reported in water analyses_ _ Specific electrical conductance Units for reporting conductance Physical basis of conductance Range of conductance values Accuracy and reproducibility of conductance values Hydrogen-ion concentration (pH) Hydrolysis Buffered solutions Interpretation of pH data Range of pH values Accuracy and reproducibility of pH values Color Sources and significance of color in water 49 Residue on evaporition 49 Theoretical basis of determination 50 Range of concentration 51 Accuracy and reproducibility of results 51 III Significance of properties and constituents reported in water analyses-Continued Acidity Sources of acidity of natural water Chemistry of acidity determination Range of concentration Reproducibility of acidity data Sulfate Sources of sulfate in natural water Chemistry of sulfate in natural water Range of concentration Accuracy and reproducibility of results Chloride Sources of chloride in water Chemistry of chloride in natural water Oceanic chloride Juvenile chloride Cyclic chloride Range of concentration Accuracy and reproducibility of results Fluoride Source of fluoride in water Chemistry of fluoride in natural water Range of concentration Accuracy and reproducibility of results Nitrate Source of nitrate in water Chemistry of nitrate in natural water 116 Range of concentration Accuracy and reproducibility of results Phosphate Sources of phosphate Chemistry of phosphate in natural water 119 Range of concentration 120 Accuracy and reproducibility of results 120 Boron 120 Sources of boron 120 Chemistry of boron in natural water Range of concentration 122 Accuracy and reproducibility of results 122 Trace or minor constituents-Cations 124 Heavy metals 124 Titanium 124 Chromium 124 Zinc 125 Nickel and cobalt 126 Copper 126 Tin 127 Lead 127 Cadmium 128 Mercury 128 Arsenic 129 Selenium 130 Significance of properties and constituents reported in water analyses-Continued Trace or minor constituents-Cations-Continued Alkaline-earth metals Beryllium Strontium Barium Alkali metals and ammonium Lithium Rubidium Cesium Ammonium Radioactive components Uranium Radium Radon Thorium Trace or minor constituents-Anions Bromide Iodide Sulfite and thiosulf ate Total dissolved solids-Computed Chemistry of dissolved solids determination Accuracy and reproducibility of results Dissolved gases Biochemical oxygen demand Hardness Utilization Range of concentration Accuracy and reproducibility of results Percent sodium Sodium-adsorption ratio Density Organization and study of water-analysis data Evaluation of water analyses Tabulation Study techniques Inspection and comparison Use of ratios Use of averages 156 Palmer's geochemical classification 162 Graphical representation 164 Scatter diagrams 165 Ionic-concentration diagrams 168 Percentage-composition diagrams Frequency diagrams Chemical analyses plotted against nonchemical variables 186 Hydrographs 186 Dissolved-solids rating curves 188 Water-quality profiles 192 Quality-of-water maps 192 Selection of study techniques 10. Effect of temperature on solubility of calcium carbonate (calcite) in water in the presence of CO2 VIII CONTENTS Page FIGURE 11. Solubility of magnesium carbonate in water at 25C in the presence of CO2 81 12. Relation of conductance to chloride, hardness, and sulfate concentrations, Gila River at Bylas, Ariz., Oct. 1, 1943 to Sept. 30, 1944 13. Sodium-chloride relationship, Gila River at Bylas, Ariz., Oct. 1, 1943, to Sept. 30, 1944 14. Analyses represented by vertical bar graphs of equivalents per million 15. Analyses represented by bar graphs of parts per million 16. Bar graph of equivalents per million which also shows hardness values in parts per million 17. Analyses in equivalents per million represented by vectors__ _ 18. Analyses represented by patterns based on equivalents per million 19. Analyses represented by linear plotting of cumulative percentage composition based on parts per million 20. Analyses represented by logarithmic plotting of concentrations in parts per million 21. Analyses represented by circular diagrams subdivided on the basis of percent of total equivalents per million 22. Analyses represented by bar-patterns based on percent of total equivalents per million 23. Analyses represented by patterns drawn on radial coordinates.. 24. Analyses represented by three points plotted in trilinear diagram (after A. M. Piper) 25. Number of samples having percent sodium within ranges indicated, San Simon artesian basin, Ariz 26. Cumulative frequency curve of specific conductance, Allegheny, Monongahela and Ohio River waters, Pittsburgh area, Pennsylvania, 1944-50 27. Specific conductance of daily samples and daily mean discharge, San Francisco River at Clifton, Ariz., Oct. 1, 1943 to Sept. 30, 1944 28. Bicarbonate, sulfate, hardness, and pH of samples collected in cross section of Susquehanna River at Harrisburg, Pa., July 8, 1947 29. Temperature and dissolved solids of water in Lake Mead in Virgin and Boulder Canyons, 1948 194 30. Total concentration and hardness of water from deeper wells in Prairie Creek Unit, Nebr 31. Ratio of alkalinity to sulfate in water from unconsolidated deposits in the Torrington area, Nebr 32. Map of portions of Apache and Navajo counties, Ariz., showing mineral content of ground water in the Coconino sandstone_ 198 33. Analyses of waters associated with igneous rocks 206 34. Analyses of waters associated with resistate sediments 209 35. Analyses of waters associated with hydrolyzate sediments_ _ _ 36. Weighted-average analyses for Rio Grande at San Acacia, N. Mex., for two periods in the 1945-46 water year 212 37. Analyses of waters associated with precipitate-type sediments.. 38. Analyses of waters associated with evaporate sediments 215 39. Analyses of waters associated with metamorphic rocks 217 40. Diagram for use in interpreting the analysis of irrigation water_ 251 2 CHEMICAL CHARACTERISTICS OF NATURAL WATER

The Merck Index is a one-volume encyclopedia of chemicals, drugs and biologicals that contains more than 10,000 monographs. Each monograph in this authoritative reference source is a concise description of a single substance or a small group of closely related compounds. Compounds included: * human and veterinary drugs * biotech drugs and monoclonal antibodies * substances used for medical imaging * biologicals and natural products * plants and traditional medicines * nutraceuticals and cosmeceuticals * agriculturals, pesticides and herbicides * Organic chemicals used in research * Food additives and supplements * dyes, colors and indicators * environmentally significant substances Information provided: * chemical, common and generic names * Over 15,000 trademarks and associated companies * CAS Registry Numbers for over 12,000 compounds * Over 8,500 chemical structures * molecular formulae, weights and percentage composition * capsule statements identifying compound classes and scientific significance * scientific and patent literature references * physical and toxicity data * therapeutic and commercial uses * caution and hazard information In addition, there are more than 700 new and completely revised monographs, thousands of new references, trademarks and uses added to existing monographs. Now includes a companion CD-ROM which features 989 monographs no longer available in print, organic name reactions, supplemental tables and a new user interface for user-friendly searching. Features of the CD: * Searchable by keywords, references, and numerical properties * Search the complete contents of the 14th edition, plus nearly a thousand monographs archived from previous editions * Comes with a free one-year subscription to the Merck Index Internet Edition * Windows-compatible CD powered by CambridgeSoft's ChemFinder * Extensively revised supplemental tables now including acronyms, vaccines, and physical constants * More than 70 pages of hard to find information in one easy-to-use place

This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutine Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.

BACKGROUND: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. RESULTS: The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. CONCLUSIONS: Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

Chemical Thermodynamics and Kinetics Acid-Base Dissolved Carbon Dioxide Atmosphere-Water Interactions Metal Ions in Aqueous Solution Aspects of Coordination Chemistry Precipitation and Dissolution Oxidation and Reduction Equilibria the Solid-Solution Interface Trace Metals: Cycling, Regulation and Biological Role Kinetics and Redox Processes Photochemical Processes Kinetics at the Solid-Water Interface Adsorption Dissolution of Minerals Nucleation and Crystal Growth Particle-Particle Interaction Colloids Coagulation and Filtration Regulation of the Chemical Composition of Natural Waters (Examples) Thermodynamic Data.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical Routes for the Transformation of Biomass into ChemicalsAvelino Corma, Sara Iborra, and Alexandra VeltyView Author Information Instituto de Tecnología Química, UPV-CSIC, Universidad Politécnica de Valencia, Avenida de los Naranjos, s/n, Valencia, Spain Cite this: Chem. Rev. 2007, 107, 6, 2411–2502Publication Date (Web):May 30, 2007Publication History Received31 January 2007Published online30 May 2007Published inissue 1 June 2007https://pubs.acs.org/doi/10.1021/cr050989dhttps://doi.org/10.1021/cr050989dresearch-articleACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views55308Altmetric-Citations5138LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Alcohols,Carbohydrates,Catalysts,Lipids,Selectivity Get e-Alerts

One of the active areas in reaction kinetics during the post-war years has
\nbeen that of electron-transfer reactions. These reactions constitute one type
\nof oxidation-reduction process and include both chemical and electrochemical
\nsystems. Many rate constants have now been measured (1-8) and
\nthey have stimulated a variety of theoretical studies (9-37). The field has
\nbeen characterized by a strong interplay of theory and experiment, which
\nnow includes the testing of theoretically predicted quantitative correlations
\n(34). Because of a certain unique feature of the purely electron-transfer
\nreactions--the absence of bond rupture in the reaction step--these correlations
\nare unusual. They do not have the arbitrary parameters that occur
\nin theoretical studies of most other reactions in chemical kinetics. This review
\nwill be limited to purely electron transfer reactions.

Soil chemical analysis , Soil chemical analysis , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

The definitive reference for more than half a century,—updated for the first time in more than a decade. Since 1934, Perry9s Chemical Engineer9s Handbook has delivered unrivaled, state-of-the-art coverage of all aspects of chemical engineering—from the fundamentals to details on computer applications and control. Featuring 2,700 pages and 1900 illustrations, the eighth edition is a comprehensive source for the newest developments, advances, achievements, and methods in the field.

The solar chemical composition is an important ingredient in our understanding of the formation, structure, and evolution of both the Sun and our Solar System. Furthermore, it is an essential reference standard against which the elemental contents of other astronomical objects are compared. In this review, we evaluate the current understanding of the solar photospheric composition. In particular, we present a redetermination of the abundances of nearly all available elements, using a realistic new three-dimensional (3D), time-dependent hydrodynamical model of the solar atmosphere. We have carefully considered the atomic input data and selection of spectral lines, and accounted for departures from local thermodynamic equilibrium (LTE) whenever possible. The end result is a comprehensive and homogeneous compilation of the solar elemental abundances. Particularly noteworthy findings are significantly lower abundances of C, N, O, and Ne compared to the widely used values of a decade ago. The new solar chemical composition is supported by a high degree of internal consistency between available abundance indicators, and by agreement with values obtained in the Solar Neighborhood and from the most pristine meteorites. There is, however, a stark conflict with standard models of the solar interior according to helioseismology, a discrepancy that has yet to find a satisfactory resolution.

Indirect evidence is presented that free-standing Si quantum wires can be fabricated without the use of epitaxial deposition or lithography. The novel approach uses electrochemical and chemical dissolution steps to define networks of isolated wires out of bulk wafers. Mesoporous Si layers of high porosity exhibit visible (red) photoluminescence at room temperature, observable with the naked eye under <1 mW unfocused (<0.1 W cm−2) green or blue laser line excitation. This is attributed to dramatic two-dimensional quantum size effects which can produce emission far above the band gap of bulk crystalline Si.

Twelve zeolitic imidazolate frameworks (ZIFs; termed ZIF-1 to -12) have been synthesized as crystals by copolymerization of either Zn(II) (ZIF-1 to -4, -6 to -8, and -10 to -11) or Co(II) (ZIF-9 and -12) with imidazolate-type links. The ZIF crystal structures are based on the nets of seven distinct aluminosilicate zeolites: tetrahedral Si(Al) and the bridging O are replaced with transition metal ion and imidazolate link, respectively. In addition, one example of mixed-coordination imidazolate of Zn(II) and In(III) (ZIF-5) based on the garnet net is reported. Study of the gas adsorption and thermal and chemical stability of two prototypical members, ZIF-8 and -11, demonstrated their permanent porosity (Langmuir surface area = 1,810 m(2)/g), high thermal stability (up to 550 degrees C), and remarkable chemical resistance to boiling alkaline water and organic solvents.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMetal–Organic Framework Materials as Chemical SensorsLauren E. Kreno†, Kirsty Leong‡, Omar K. Farha†, Mark Allendorf*‡, Richard P. Van Duyne†, and Joseph T. Hupp*†View Author Information† Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States‡ Sandia National Laboratories, Mail Stop 9291, Livermore, California 94551-0969, United States*Phone: (925) 294-2895 (M.A.); (847) 491-3504 (J.T.H.). E-mail: [email protected] (M.A.); [email protected] (J.T.H.).Cite this: Chem. Rev. 2012, 112, 2, 1105–1125Publication Date (Web):November 9, 2011Publication History Received18 August 2011Published online9 November 2011Published inissue 8 February 2012https://pubs.acs.org/doi/10.1021/cr200324thttps://doi.org/10.1021/cr200324treview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views71971Altmetric-Citations6186LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Luminescence,Metal organic frameworks,Molecules,Sensors,Thin films Get e-Alerts