August 15, 2000Peter Murray-RustHenry. S. RzepaMichael WrightDepartment of Chemistry, Imperial College of Science, Technology and Medicine, UKSchool of Pharmaceutical Sciences, University of Nottingham, UKChiMeraL, XML, CML, chemical markup language, chemistry, applet, SVG, FOP
1Comparing different ways of displaying chemical structures
Taxol intermediate as a .gif image (bitmap) - a 'dead' format, human comprehensible but chemical information can't be automatically extracted
Riboflavin using a plugin - Uses the EMBED tag and an external data file (Chime or an equivalent is required)
Cochineal using Chemaxion's Marvin applet - the structure is being stored as CML within this document, hence no data file is needed
2Dynamic selection of stylesheets - this is a much simpler version of the ChiMeraL demonstration
3Ethanol using the .mol format
rows 1-3:
Comment lines; sometimes these contain a title, a filename and the source of the file but there is no common convention. These lines are normally discarded on converting to CML (note line 3 is blank).
row 4:
The first digit is the total number of atoms in the molecule, the second is the total number of bonds (hydrogen atoms and bonds to them, are sometimes neglected).
rows 5-13:
Each row refers to an atom and gives (in order) Cartesian coordinates x, y and z (in Angstrom) and the element type (as its periodic table letter). The remaining columns are used for electrons, charges etc. and are not yet included in CML, since mol files rarely use them.
rows 14-21:
Each row refers to a bond. The first two digits refer to the atoms the bond is between (hence 2 3 means a bond between the second and third atoms in the list above) and the third digit refers to the empirical bond order (2 = double bond etc.) Again, the remaining columns are rarely used.
row 22:
M END indicates the end of the molecule. Files that contain multiple .mol molecules (e.g. reaction .rxn or .sd files) also include a delimiter between molecules ($MOL or $$$$).
4JME editor with Java Script integration - toolbars used for editing, left click/drag to translate, right click/drag to rotate
5Jmol 3D viewer and .xyz format - click/drag to rotate, shift-c/d to zoom, ctrl-c/d to translate, TAB changes drawing style, L adds atom labels
6Marvin (left) and SDA applets - Marvin: left click/drag to rotate, shift-lc/d to zoom, ctrl-lc/d to translate, right click for menu - SDA: tool bars contain editing tools, applet can be 'floated' to a separate window by clicking the top left button
7Tetrahydrofuran mass spectrum using the JCAMP-DX format
8JSpec spectra viewer showing caffeine mass and UV/Vis spectra - click drag to select an area then click buttons
9SVG molecule and infra red spectrum - right click for menu
10Cross Metathesis (example of a catalytic cycle)
Warning: you need to be online and the server-returned page will overwrite this one
11Server side conversion of .mol, .rxn and .dx files to CML - http://www.ch.ic.ac.uk/chimeral/resources/file2cml.html
Markup and display of molecules, spectra and reactions
Multiple stylesheet selection and the use of data islands
Testing XML/XSL functionality with various browsers
Scaling test - ECTOC database (9 Mb XML file)
Writing a complex XML document and display through IE and .pdf (via FOP)
Schema
CML schema 0.2 - based on published DTD
CML schema 0.2 (IE version) - includes unique @id and data links
ChiMeraL schema 0.1 - extends CML to include spectrum
Document schema 0.1 - developed to write this report
XSL Stylesheets
generic.xsl - displays all CML
datasheet.xsl - property information as an HTML table
jme.xsl - Java Molecular Editor applet - editor
jme_format.xsl - JME data string
marvinview.xsl - Marvin applet, 3D viewer mode
marvinedit.xsl - Marvin applet, editor mode
sda.xsl - Structure Drawing Applet - editor
mol.xsl - MDL .mol file format
jmol.xsl - Open Source applet - 3D viewer
xyz.xsl - .xyz file format
jspec.xsl - Java Spectrum Viewer - viewer
jcamp.xsl - JCAMP .dx format
reaction.xsl - stepwise, linear and cycle.4 reactions using Marvin
document.xsl - displaying complex XML document in IE5
document.css - CSS stylesheet for above
doc2fo.xsl - convert complex XML document to formatting object (for use with FOP)
perl converters
MDL .mol to CML
MDL .mol to JME format
.sd to CML (multiple mol archive)
.xyz to CML
JCAMP .dx and .cs to CML
REACSS .rxn to CML
.rd to CML
.mol, .rxn and .dx 2 CML are all available as an online cgi script
A large number of example CML files are also available, these contain properties, structures, spectra and reactions. Further archives of CML files will be made available as they are converted.
The published CML 1.0 DTD declares valid elements and attributes but puts few restrictions on how these elements and attributes are used. As a consequence of this, it is possible to markup a CML object (e.g. a molecule) using a variety of different syntaxes. Whilst this gives great flexibility, it also makes it significantly more difficult to build CML applications. In particularl some of these syntaxes can not be easily parsed using stylesheets. I have selected what I feel is the syntax best suited to XSL and small molecule markup. This, along with the syntax for chimeral:spectrum and reaction (still experimental) is as follows: (comments on syntax are in green)
This version of the schema is based directly on the CML 1.0 DTD but includes datatype declarations for use in IE 5.x. These datatypes allow the use of @id and @href for intra-document linking. A platform independent version (plus schemas for chimeral: and docml:) are available from the ChiMeraL site. (comments on syntax are in green)
This is a copy of the DTD for CML 1.0 published in JCICS by Peter Murray-Rust and Henry S. Rzepa
Applet (Java)
A small program designed to run embedded within a web page (either HTML or XML). The applet is downloaded from the same site as the web page and does not require installation (unlike a plugin). For security reasons, applets has restricted access to the local hard drive.
ASCII
Refers to the standard set of text characters used for all computers. An ASCII file can be opened in a normal text editor (in contrast to a binary file which can not). XML/HTML and most of the legacy formats use ASCII.
Attribute
Used to give more specific information within an HTML/XML tag (hence FONT SIZE="+1" has attribute 'SIZE'), @href is shorthand for 'attribute called href'
CML (Chemical Markup Language)
XML language optimised for marking up chemistry.
CSS (Cascading stylesheet)
Stylesheet primarily designed for HTML, allows tag properties to be changed (over-riding the parser defaults).
DTD
Older standard for describing XML languages, uses a unique syntax.
DOM (Document Object Model)
'Tree' model of a document, allows the parser scripting access to all 'objects' within the tree. Under development by the W3C
Element
XML equivalent to HTML tags. Refers to the tag pair, any attributes and their contents
HTML(hypertext markup language)
Text formatting and display language - standard electronic format on the web
JavaScript
A scripting language (which has little to do with Java, although they can communicate) used to add interactivity to web pages. Javascript functions need to be triggered in some way (normally using a FORM button).
Markup
Procedure of labelling and organising information using tag/tag pairs and attributes. Basis for most formatting languages.
Namespaces
System for assigning elements to different XML languages. Very important if a document is to be validated.
Parser
Program able to read XML, comprehend its structure and build a DOM and/or use a stylesheet to display it. This project uses Internet Explorer 5.x
Plugin
Small, platform dependent program that 'plugs into' a web browser and allows it to display additional file formats (e.g. .mol, .svg, .vrml). Needs to be installed by the user.
Perl
Powerful text search and replace language (amongst other things) and used to build all the legacy2CML converters in this project. Also used for server-side cgi scripts.
Schema
Newer standard for describing XML languages, uses XML rules and syntax.
SVG (Scalable Vector Graphics)
XML language optimised for describing vector ('line' as compared to bitmap/gif/jpg) images.
Tag
Basic unit of markup, delimited by square brackets: tag
Well formed
A well formed document is one that complies to XML rules and syntax.
Valid
A valid document is well formed and conforms to a language description given in a DTD or schema.
XHTML(extensible hypertext markup language)
HTML tags corrected to follow XML rules
XML(extensible markup language)
A series of rules for writing other 'XML compliant' languages
XSL(extensible stylesheet language)
Stylesheet language, includes powerful scripting and querying features.
1 Demonstrations, examples and further information can be found in the ChiMeraL websiteFor a formal description of CML version 1.0, see 2P. Murray-Rust and H. S. RzepaJ. Chem. Inf. Comp. Sci.19993992810H. S. Rzepa, B. J. Whitaker and M. J. WinterJ. Chem. Soc., Chem. Commun.1994190711O. Casher, G. Chandramohan, M. Hargreaves, C. Leach, P. Murray-Rust, R. Sayle, H. S. Rzepa and B. J. WhitakerJ. Chem. Soc., Perkin Trans 2199573H. S. Rzepa, P. Murray-Rust and B. J. WhitakerChem. Soc. Revs.1997112P. Murray-Rust, C. Leach and H. S. RzepaAbs. Papers. Am . Chem. Soc.199521040-COMP39J. Gasteiger, B. M. P. Hendriks, P. Hoever, C. Jochum and H. SombergApp. Spec.1991454-1137A. N. Davies and P. LampenApp. Spec.1993471093-109938P. Lampen, H. Hillig, A. N. Davis and M. LinscheidApp. Spec.1994481545-155250R. S. McDonald and P. A. Wilks Jr.App. Spec.198842151-16229WWW-based Chemical Information System9Microsoft - XML Schema Developer's Guide8W3C - XML Schema development24W3C - Extensible Stylesheet Language (XSL) development4W3C - XHTML and HTML development5W3C - Scalable Vector Graphics (SVG) overview19W3C - Mathematical Markup Language development6Adobe SVG browser plugin21W3C - XML Namespaces recommendation17W3C - XML recommendation18W3C - Annotated XML specification51Netscape XML31Jmol - Open source Java 3D viewer49Laelia: a system for storage, retrieval and querying of XML and CML Documents40jspec: A Java Spectral Visualiser for JCAMP-DX and SPC Format Files48Open source Java 2D editor20XML-CML homesite26IBM alphaworks - XML/Java development site33Marvin display and editing applet - Chemaxon13MDL information systems35NIST Webbook25Microsoft - XML/XSL development32The Open Science Project 44W3C - XLink specifications45W3C - XPointer specifications41Corel Draw 9 SVG plugin42Mayura Draw - editor able to export SVG43Csiro SVG Toolkit7Apache.com - FOP project (XML convertion to Adobe Acrobat)14Rasmol and Chime - Molecular Visualization Freeware15Brookhaven Protein Data Bank22Adobe Acrobat16Universal approach to Web-based Chemistry using XML and CML by Peter Murray-Rust, Henry S. Rzepa, Michael Wright and Stephen Zara (awaiting pulication) 23W3C - Cascading Stylesheets27Sun - Java Technology Homepage28W3C - Document Object Model (DOM) Level 1 Specification30ChemFinder.com34ACD Labs - Structure Drawing Applet36SPC - Spectroscopy Software Solutions52Adobe Illustrator46Perl.com Homesite4753XML IE5 - Programmer's ReferenceA.HomerXML IE5 - Programmer's Reference, Wrox Press199954XML How to ProgramHarvey Deitel, Paul Deitel, Ted Lin and Tem Nieto H.DietelP.DeitelT.LinT.NeitoXML How to Program, Prentice Hall200055The Complete XML Training Course, Student EditionHarvey Deitel, Paul Deitel, Ted Lin and Tem Nieto H.DietelP.DeitelT.LinT.NeitoThe Complete XML Training Course, Student Edition, Prentice Hall2000?xml version="1.0"??xml-stylesheet type="text/xsl" href="document.xsl" ?!-- Declares this document as XML and indicate the URL of its stylesheet --document title="Lipids" id="cmldoc_karne_lipids" xmlns="http://www.w3.org/1999/xhtml" xmlns:chimeral="x-schema:http://www.ch.ic.ac.uk/chimeral/spectrum_schema_ie_01.xml"!-- document isn't part of CML but represents the top element of any XML compliant document, this might contain CML, XHTML, MaML etc. - note the XHTML and chimeral namespaces --cml title="Cholesterol" id="cml_karne_cholesterol" xmlns="x-schema:http://www.ch.ic.ac.uk/chimeral/cml_schema_ie_02.xml"!-- The CML namespace points to a copy of the schema, cml this may contain any number of CML 'objects' e.g. molecule, reaction or chimeral:spectrum --molecule title="cholesterol" id="mol_cholesterol"formulaC27 H46 O/formula!-- Information specific to this molecule is included here as string, float or integer - additional elements can be added as required but note the use of @title to label them. Alternate names are marked up as a list of strings --string title="CAS"57-88-5/stringstring title="ACX"I1001660/stringstring title="RTECS"FZ8400000/stringfloat title="molecule weight"386.6598/floatfloat title="melting point" units="degC"148.5/floatfloat title="boiling point" units="degC"360/floatfloat title="specific gravity"1.067/floatlist title="alternate names"string title="name"Cholesterin/stringstring title="name"(3beta)-Cholest-5-en-3-ol/stringstring title="name"Cholest-5-en-3-ol (3beta)-/stringstring title="name"cholest-5-ene-3beta-ol/stringstring title="name"3beta-hydroxycholest-5-ene/string/list!-- The following is used for small molecular structures - this format is much preferred but rather verbose. integer builtin="atomId" would normally be that used in the MDL .mol format but in contrast, 'id' must be unique over (at least) this document. Additional strings are 'formalCharge' and 'hydrogenCount'. 2D structures will use builtin="x2 | y2" but are otherwise the same --list title="atoms"!-- repeat --atom id="cholesterol_a_1"integer builtin="atomId"1/integerfloat builtin="x3" units="A"-1.9901/floatfloat builtin="y3" units="A"2.1889/floatfloat builtin="z3" units="A"-1.8776/floatstring builtin="elementType"H/string/atom!-- /repeat (74 atoms) --/list!-- Large molecular structures - this format is terse but much harder to format/refer to in XSL. I have chosen not to use it --atomArray id="methanol"stringArray title="label"a1 a2 a3 a4 a5 a6/stringArraystringArray builtin="elementType"C O H H H H/stringArrayfloatArray builtin="x3"-0.748 ../floatArrayfloatArray builtin="y3"-0.015 ../floatArrayfloatArray builtin="z3"0.024 ../floatArrayintegerArray builtin="formalCharge"/integerArray/atomArray!-- A list of bonds is used for small molecules - large ones will probably ignore bonds and calculate then directly --list title="bonds"!-- repeat --bond id="cholesterol_b_1"integer title="bondId"1/integerinteger builtin="atomRef"2/integerinteger builtin="atomRef"1/integerinteger builtin="order" convention="MDL"1/integer/bond!-- /repeat (77 bonds) --/list/molecule!-- Elements in spectra tend to match the LDHs in the JCAMP format. The namespace chimeral: is very important as spectrum isn't found in CML 1.0 --chimeral:spectrum title="Cholesterol" id="spect_cholesterol_ms_1" convention="JCAMP-DX=4.24"string title="datatype"MASS SPECTRUM/stringstring title="EPA"67286/stringstring title="origin"T.IIDA NIHON UNIVERSITY, KORIYAMA, FUKUSHIMA-KEN, JAPAN/stringstring title="owner"NIST Mass Spectrometry Data Center/stringstring title="spectrometer"LKB 9000/string!-- The following information is required for the rendering of spectra in Jspec --float title="xunits"M/Z/floatfloat title="yunits"RELATIVE ABUNDANCE/floatfloat title="firstx" convention="M/Z"18/floatfloat title="lastx" convention="M/Z"387/floatfloat title="deltax" convention="M/Z"/floatfloat title="xfactor"1/floatfloat title="firsty" convention="RELATIVE ABUNDANCE"700/floatfloat title="miny" convention="RELATIVE ABUNDANCE"100/floatfloat title="maxy" convention="RELATIVE ABUNDANCE"9999/floatfloat title="yfactor"1/floatfloat title="npoints"169/float!-- One of the following syntaxes is then used, depending on the type of spectrum --!-- A: simplest and prefered spectra format. Try and avoid (X++(Y..Y)) --list title="xypairs" convention="(XY..XY)"!-- repeat --coordinate2 id="cholesterol_ms_c_1"18, 700/coordinate2!-- /repeat (169 data pairs) --/list!-- B: alternate format for peak tables rather then data --list title="peak table" convention="(XY..XY)"!-- repeat --coordinate2 id="mol_s_1"X, Y/coordinate2!-- /repeat --/list!-- C: convention often used for NMR peak tables is (XYM) --list title="peak table" convention="(XYM)"!-- repeat --coordinate3 id="mol_s_1"X, Y, M/coordinate3!-- /repeat --/list/chimeral:spectrum!-- Reactions are made up of a series of lists, each list containing a number of links @href to molecule @id --reaction title="Reactions" id="simple_rxn_1" convention="stepwise | linear | cycle.4 | .."!-- Linear markup is much preferred since it's the simplest, others provided for formatting purposes. The following three elements can be used either at the reaction level or at each reaction step --string title="description"Diels-Alder cycloaddition/stringfloat title="yield" units="%"88/floatstring title="notes"example/string!-- Stepwise (x1 y1, x2 y2); use as many reactants, reagents and products as needed for each step, reactions steps will be displayed separately. Additional links to catalysts, intermediates, transition states etc. can be used as required --!-- repeat --list title="reactionStep" id="simple_s_1"link title="reactant" href="mol_x"/link title= "reagent" href= "mol_r"integer title="index"1/integerstring title="solvent"Acetonitrile/stringstring title="temperature" units="degC"100/stringstring title="duration" units="hours"3/stringstring title= "notes"reflux/string/linklink title="reagent"integer title="index"2/integerstring title="notes"workup/string/linklink title="product" href="mol_y"//list!-- /repeat --!-- Linear (x y z); reactant refers to the first reactants, product refers to the final product; intermediates use linearReactant and linearProduct --list title= "linearstep" id="step_1"link title="reactant" href="mol_1"/link title="reagent" href="mol_r1"!-- .. --/linklink title="linearProduct" href="mol_2"//listlist title= "linearstep" id="step_2"link title="linearReactant" href="mol_2"/link title="reagent" href="mol_r2"!-- .. --/linklink title="linearProduct" href="mol_3"//listlist title= "linearstep" id="step_3"link title="linearReactant" href="mol_3"/link title="reagent" href="mol_r3"!-- .. --/linklink title="Product" href="mol_4"//list!-- Catalytic cycle - much more complex (.. x y z ..) reactant and product refer to substances 'in' and 'out' of the cycle in each step, use cycleReactant and cycleProduct for 'within' the cycle. Markup should be cyclic (final cycleProduct == first cycleReactant) --list title="reactionStep" id="step_1"link title="cycleReactant" href="mol_1" id="cycle_lk_1"/link title="reactant" href="mol_3" id="cycle_lk_2"/link title="cycleProduct" href="mol_7" id="cycle_lk_3"//listlist title="reactionStep" id="step_2"link title="cycleReactant" href="mol_7" id="cycle_lk_4"/link title="cycleProduct" href="mol_6" id="cycle_lk_5"/link title="product" href="mol_8" id="cycle_lk_6"//listlist title="reactionStep" id="step_3"link title="cycleReactant" href="mol_6" id="cycle_lk_7"/link title="reactant" href="mol_5" id="cycle_lk_8"/link title="cycleProduct" href="mol_4" id="cycle_lk_9"//listlist title="reactionStep" id="step_4"link title="cycleReactant" href="mol_4" id="cycle_lk_10"/link title="cycleProduct" href="mol_1" id="cycle_lk_11"/link title="product" href="mol_2" id="cycle_lk_12"//list!-- list title="atomMap" could be placed within each step --/reaction/document?xml version="1.0"?Schema name="cml_dev_karne" xmlns="urn:schemas-microsoft-com:xml-data" xmlns:dt="urn:schemas-microsoft-com:datatypes"descriptionCML development - Version 0.2 - 7/4/00This document is the first draft of an XML Schema compatible with CMLV1.0 published in JCICS... In converting the schema we have suggestedsome closed and some open content models. As CML develops it seems likelythat there will be advantage in opening some of the models (e.g. angle),perhaps for annotations and ancillary information. Readers should notethat the XML Schema activity is still at draft stage and that this schemamay be revised in the future for compatibility. This schema is intended for use with IE5 - a platform independent versionis available. XML documents can be validated against this schema by addingxmlns="x-schema:URL" within the cml element. Please see cml_schema_ie_02.html for further comments and explanations.Peter Murray Rust, Henry Rzepa, Michael WrightComments to Michael Wright - karne@innocent.com/description!-- ********** Attribute Types ********** --!-- *** common *** --!-- It is expected that these attributes will be found on almost all elements. @title is used for display and general labelling and @id indicates a document unique identity string for that element. This identity can then be used to reference that element (and hence the object it represents) by the use of @href. Care must be taken that @id is unique. The use (for example) of atom id="1" will cause trouble in a document with more than one molecule and should be avoided. Note that @title on data elements (string/integer/float) can be used to markup data for which there is no explicit CML element (e.g. string title="CAS"58-08-2/string) and @convention should be declared if this is not obvious. @builtin implies an element with a meaning predefined in the DTD --AttributeType name="title" required="no"/AttributeType name="id" required="no" dt:type="id"/AttributeType name="convention" required="no"/AttributeType name="builtin" required="no" dt:type="enumeration" dt:values="x2 y2 xy2 x3 y3 z3 xyz3 xFract yFract zFract xyzFract elementType atomId isotope occupancy hydrogenCount atomParity residueType residueId formalCharge atomRef atomRefs length order stereo acell bcell ccell alpha beta gamma z spacegroup" /!-- *** linkers *** --!-- Designed to allow the linking of an element to another via @id. For example link href="mol_543" indicates a link to any element with @id="mol_543".@unitsRef and @dictRef are intended for future use --AttributeType name="href" required="no" dt:type="idrefs"/AttributeType name="dictRef" required="no" dt:type="idrefs"/AttributeType name="unitsRef" required="no" dt:type="idrefs"/AttributeType name="atomRef" required="no" dt:type="idref"/AttributeType name="atomRefs" required="no" dt:type="idrefs"/!-- *** quantifiers/constraints *** --!-- Various constraints on the values of data elements, only 'units' is in common use --AttributeType name="count" required="no"/AttributeType name="size" required="no"/AttributeType name="rows" required="no"/AttributeType name="columns" required="no"/AttributeType name="min" required="no"/AttributeType name="max" required="no"/AttributeType name="units" required="no"/!-- ********** Element Types ************ --!-- *** data *** --!-- These elements are intended to contain only text string and attributes - they may not contain other elements - and are hence 'closed' (no additional markup can be added beyond the schema). If additional data holders are required, they should be of the form string title="CAS"58-08-2/string where the title value is used to identify the elements contents. For full list of attributes, please see the schema --ElementType name="string" content="textOnly" model="closed"attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="dictRef"//ElementTypeElementType name="float" content="textOnly" model="closed"attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="min"/attribute type="max"/attribute type="units"/attribute type="unitsRef"/attribute type="dictRef"//ElementTypeElementType name="integer" content="textOnly" model="closed"attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="min"/attribute type="max"/attribute type="units"/attribute type="unitsRef"/attribute type="dictRef"//ElementType!-- The arrays should be used only when large amounts of data need to be stored. In all cases explicit markup of each unit of data is preferred since this is much easier to manipulate with a stylesheet. In some cases this may not be possible (e.g. large molecules with 200+ atoms) and arrays can be used. These would probably need to be parsed by dedicated chemical tools. floatMatrix is intended for computational chemistry --ElementType name="stringArray" content="textOnly" model="closed"attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="size"/attribute type="min"/attribute type="max"/attribute type="dictRef"//ElementTypeElementType name="floatArray" content="textOnly" model="closed"attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="size"/attribute type="min"/attribute type="max"/attribute type="units"/attribute type="unitsRef"/attribute type="dictRef"//ElementTypeElementType name="integerArray" content="textOnly" model="closed"attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="size"/attribute type="min"/attribute type="max"/attribute type="units"/attribute type="unitsRef"/attribute type="dictRef"//ElementTypeElementType name="floatMatrix" content="textOnly" model="closed"attribute type="id"/attribute type="title"/attribute type="convention"/attribute type="rows"/attribute type="columns"/attribute type="min"/attribute type="max"/attribute type="units"/attribute type="unitsRef"/attribute type="dictRef"//ElementType!-- Coordinates consist of 2 or 3 comma separated numbers. They should be used for logically linked number groups - e.g. a data point in a spectrum --ElementType name="coordinate2" content="textOnly" model="closed"!-- use for data pairs (e.g spectra xy) --attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="units"/attribute type="unitsRef"/attribute type="dictRef"//ElementTypeElementType name="coordinate3" content="textOnly" model="closed"!-- use for data triplets (e.g spectra x, y, m) --attribute type="id"/attribute type="builtin"/attribute type="title"/attribute type="convention"/attribute type="units"/attribute type="unitsRef"/attribute type="dictRef"//ElementType!-- Angle and torsion haven't yet been developed, hence they have been left open --ElementType name="angle" content="textOnly" model="open"attribute type="id"/attribute type="title"/attribute type="convention"/attribute type="atomRefs"/attribute type="min"/attribute type="max"/attribute type="units" default="deg"/attribute type="unitsRef"/attribute type="dictRef"//ElementTypeElementType name="torsion" content="textOnly" model="open"attribute type="id"/attribute type="title"/attribute type="convention"/attribute type="atomRefs"/attribute type="min"/attribute type="max"/attribute type="units" default="deg"/attribute type="unitsRef"/attribute type="dictRef"//ElementType!-- *** mixed *** --!-- Link is used as a 'holder' element - e.g. for 'href' or 'unitsRef' and indicates a logical link to another CML object --ElementType name="link" content="mixed" model="open"attribute type="id"/attribute type="title"/attribute type="href"//ElementTypeElementType name="formula" content="mixed" model="open"attribute type="id"/attribute type="title"/attribute type="convention"/attribute type="count"/attribute type="dictRef"//ElementType!-- *** structural *** --!-- These elements define the tree structure of the CML document and are not expected to contain text strings - only other elements. Since they are 'open', additional sub elements - whether CML or not - can be added with correct namespacing. Attributes and elements for these elements have been declared in the schema but these are only suggestions - the DTD allows anything. Many, like electron and the crystalagraphic markup have yet to be developed --ElementType name="atom" content="eltOnly" model="open" order="many"attribute type="id"/attribute type="title"/attribute type="convention" default="mol"/attribute type="count"/attribute type="dictRef"/element type="float" minOccurs="0" maxOccurs="*"/element type="string" minOccurs="0" maxOccurs="*"/element type="integer" minOccurs="0" maxOccurs="*"/element type="link" minOccurs="0" maxOccurs="*"//ElementTypeElementType name="bond" content="eltOnly" model="open" order="many"attribute type="id"/attribute type="convention" default="mol"/attribute type="atomRef"/attribute type="atomRefs"/!-- avoid using these and use a subelement with builtin="atomRef" --element type="integer" minOccurs="0" maxOccurs="*"/element type="float" minOccurs="0" maxOccurs="*"/element type="string" minOccurs="0" maxOccurs="*"/element type="link" minOccurs="0" maxOccurs="*"/element type="angle" minOccurs="0" maxOccurs="*"/element type="torsion" minOccurs="0" maxOccurs="*"//ElementTypeElementType name="list" content="eltOnly" model="open" order="many"attribute type="id"/attribute type="title"/!-- required: atoms/bonds/xypairs/peak table/atom map--attribute type="convention"/!-- should be included for spectra: (XY..XY), (XYM) --element type="string" minOccurs="0" maxOccurs="*"/element type="integer" minOccurs="0" maxOccurs="*"/element type="float" minOccurs="0" maxOccurs="*"/element type="floatArray" minOccurs="0" maxOccurs="*"/element type="stringArray" minOccurs="0" maxOccurs="*"/element type="integerArray" minOccurs="0" maxOccurs="*"/element type="floatMatrix" minOccurs="0" maxOccurs="*"/element type="angle" minOccurs="0" maxOccurs="*"/element type="torsion" minOccurs="0" maxOccurs="*"/element type="coordinate2" minOccurs="0" maxOccurs="*"/element type="coordinate3" minOccurs="0" maxOccurs="*"/element type="link" minOccurs="0" maxOccurs="*"/element type="formula" minOccurs="0" maxOccurs="*"/element type="atom" minOccurs="0" maxOccurs="*"/element type="bond" minOccurs="0" maxOccurs="*"//ElementTypeElementType name="atomArray" content="eltOnly" model="open" order="many"!-- only use for large molecules --attribute type="id"/attribute type="title"/attribute type="convention"/attribute type="dictRef"/element type="stringArray" minOccurs="0" maxOccurs="*"/element type="floatArray" minOccurs="0" maxOccurs="*"/element type="integerArray" minOccurs="0" maxOccurs="*"/element type="link" minOccurs="0" maxOccurs="*"//ElementTypeElementType name="bondArray" content="eltOnly" model="open" order="many"!-- only use for large molecules --attribute type="id"/attribute type="convention"/attribute type="dictRef"/element type="stringArray" minOccurs="0" maxOccurs="*"/element type="floatArray" minOccurs="0" maxOccurs="*"/element type="integerArray" minOccurs="0" maxOccurs="*"/element type="link" minOccurs="0" maxOccurs="*"//ElementTypeElementType name="electron" content="eltOnly" model="open"attribute type="id"/attribute type="count"/attribute type="convention"/attribute type="dictRef"//ElementTypeElementType name="crystal" content="eltOnly" model="open"attribute type="id"/attribute type="title" default="crystal"/attribute type="convention"/attribute type="dictRef"//ElementTypeElementType name="sequence" content="eltOnly" model="open"attribute type="id"/attribute type="title"/attribute type="convention"/attribute type="dictRef"//ElementTypeElementType name="feature" content="eltOnly" model="open"attribute type="id"/attribute type="title"/attribute type="convention"/attribute type="dictRef"//ElementTypeElementType name="molecule" content="eltOnly" model="open" order="many"attribute type="id"/attribute type="title" default="molecule"/attribute type="convention" default="mol"/attribute type="dictRef"/element type="formula" minOccurs="0" maxOccurs="*"/element type="list" minOccurs="0" maxOccurs="*"/element type="atomArray" minOccurs="0" maxOccurs="*"/element type="bondArray" minOccurs="0" maxOccurs="*"/element type="string" minOccurs="0" maxOccurs="*"/element type="float" minOccurs="0" maxOccurs="*"/element type="integer" minOccurs="0" maxOccurs="*"/element type="link" minOccurs="0" maxOccurs="*"//ElementTypeElementType name="reaction" content="eltOnly" model="open" order="many"attribute type="id"/attribute type="title" default="reaction"/attribute type="convention"/attribute type="dictRef"/element type="string" minOccurs="0" maxOccurs="*"/element type="float" minOccurs="0" maxOccurs="*"/element type="integer" minOccurs="0" maxOccurs="*"/element type="list" minOccurs="0" maxOccurs="*"//ElementType!-- ********** root ********** --!--This is the general 'holder' for all CML documents. Normally this would then be embedded within an XML document Namespaces/schema should be declared within this element or the document root--ElementType name="cml" content="mixed" model="open" order="many"attribute type="id"/attribute type="title" default="cml document"/attribute type="convention"/attribute type="dictRef"/element type="molecule" minOccurs="0" maxOccurs="*"/element type="crystal" minOccurs="0" maxOccurs="*"/element type="reaction" minOccurs="0" maxOccurs="*"//ElementType/Schema!-- Appendix A - CML DTD-1999-05-15 --!-- Authors: P.Murray-Rust H.RzepaThis DTD is fully described in Journal of Chemical Information and Computer Science, Vol xxx, 1999, pp. xxx--!-- =======================================================--!-- PARAMETER ENTITIES --!-- =======================================================--!-- ======attributes found on almost all elements ==========--!ENTITY % title 'title CDATA #IMPLIED'!ENTITY % id 'id CDATA #IMPLIED'!ENTITY % convention 'convention CDATA "CML"'!ENTITY % dictRef 'dictRef CDATA #IMPLIED'!-- ======linking information ==============================--!ENTITY % simpleLink 'href CDATA #REQUIRED'!-- ======quantifiers and constraints on some primitives ===--!ENTITY % count 'count CDATA "1"'!ENTITY % size 'size CDATA #IMPLIED'!ENTITY % rows 'rows CDATA #REQUIRED'!ENTITY % columns 'columns CDATA #REQUIRED'!-- ======constraints on some numeric data primitives ===--!ENTITY % min 'min CDATA #IMPLIED'!ENTITY % max 'max CDATA #IMPLIED'!ENTITY % units 'units CDATA #IMPLIED'!ENTITY % angleUnits 'units (degrees | radians) "degrees"'!ENTITY % unitsRef 'unitsRef CDATA #IMPLIED'!-- values which may be useful in min and max attributes --!ENTITY % integer.zero '0'!ENTITY % integer.max '2147483647'!ENTITY % integer.min '-2147483648'!ENTITY % float.zero '0.0'!ENTITY % float.max '8.98846567431158E307'!ENTITY % float.min '4.9E-324'!-- ======= builtin values for any element ================--!ENTITY % builtinId 'id'!-- ======= builtin values for atoms ======================--!ENTITY % elementType 'elementType'!ENTITY % atomId 'atomId'!ENTITY % x2 'x2'!ENTITY % y2 'y2'!ENTITY % x3 'x3'!ENTITY % y3 'y3'!ENTITY % z3 'z3'!ENTITY % xy2 'xy2'!ENTITY % xyz3 'xyz3'!ENTITY % xFract 'xFract'!ENTITY % yFract 'yFract'!ENTITY % zFract 'zFract'!ENTITY % xyzFract 'xyzFract'!ENTITY % occupancy 'occupancy'!ENTITY % isotope 'isotope'!ENTITY % formalCharge 'formalCharge'!ENTITY % nonHydrogenCount 'nonHydrogenCount'!ENTITY % hydrogenCount 'hydrogenCount'!ENTITY % atomParity 'atomParity'!ENTITY % residueType 'residueType'!ENTITY % residueId 'residueId'!ENTITY % atomStringBuiltin ' %elementType; | %atomId; | %residueType; | %residueId; ' !ENTITY % atomFloatBuiltin ' %x2; | %y2; | %x3; | %y3; | %z3; | %xFract; | %yFract; | %zFract; | %occupancy; | %isotope; | %formalCharge; | %hydrogenCount; | %nonHydrogenCount; | %atomParity; ' !ENTITY % atomIntegerBuiltin ' %isotope; | %formalCharge; | %hydrogenCount; | %nonHydrogenCount; | %atomParity; ' !ENTITY % atomCoordinate2Builtin ' %xy2; ' !ENTITY % atomCoordinate3Builtin ' %xyz3; | %xyzFract; ' !-- ======= builtin values for bonds ======================--!ENTITY % atomRef 'atomRef'!ENTITY % builtinAtomRefs 'atomRefs'!ENTITY % length 'length'!ENTITY % order 'order'!ENTITY % stereo 'stereo'!ENTITY % atomRefs 'atomRefs CDATA #IMPLIED'!ENTITY % bondStringBuiltin ' %atomRef; | %builtinAtomRefs; | %order; | %stereo; ' !ENTITY % bondFloatBuiltin ' %length; ' !ENTITY % bondIntegerBuiltin '' !-- ======= builtin values for crystal ====================--!ENTITY % acell 'acell'!ENTITY % bcell 'bcell'!ENTITY % ccell 'ccell'!ENTITY % alpha 'alpha'!ENTITY % beta 'beta'!ENTITY % gamma 'gamma'!ENTITY % z 'z'!ENTITY % spacegroup 'spacegroup'!ENTITY % crystalStringBuiltin ' %spacegroup; '!ENTITY % crystalFloatBuiltin ' %acell; | %bcell; | %ccell; | %alpha; | %beta; | %gamma; | %z; ' !ENTITY % crystalIntegerBuiltin ' %z; ' !-- =======================================================--!ENTITY % stringBuiltin ' builtin ( %builtinId; | %atomStringBuiltin; | %bondStringBuiltin; | %crystalStringBuiltin; ) #IMPLIED '!ENTITY % floatBuiltin ' builtin ( %atomFloatBuiltin; | %bondFloatBuiltin; | %crystalFloatBuiltin; ) #IMPLIED '!ENTITY % integerBuiltin ' builtin ( %atomIntegerBuiltin; | %crystalIntegerBuiltin; ) #IMPLIED '!ENTITY % coordinate2Builtin ' builtin ( %atomCoordinate2Builtin; ) #IMPLIED '!ENTITY % coordinate3Builtin ' builtin ( %atomCoordinate3Builtin; ) #IMPLIED '!-- =======================================================--!-- ELEMENTS for widely used data primitives --!-- =======================================================--!ELEMENT string (#PCDATA)!ATTLIST string %title; %id; %stringBuiltin; %dictRef; %convention; !ELEMENT link (#PCDATA)!ATTLIST link %title; %id; %simpleLink; %convention; !ELEMENT float (#PCDATA)!ATTLIST float %title; %id; %floatBuiltin; %min; %max; %units; %unitsRef; %dictRef; %convention; !ELEMENT integer (#PCDATA)!ATTLIST integer %title; %id; %integerBuiltin; %min; %max; %units; %unitsRef; %dictRef; %convention; !ELEMENT stringArray (#PCDATA)!ATTLIST stringArray %title; %id; %stringBuiltin; %size; %min; %max; delimiter CDATA #IMPLIED %dictRef; %convention; !ELEMENT floatArray (#PCDATA)!ATTLIST floatArray %title; %id; %floatBuiltin; %size; %min; %max; %units; %unitsRef; %dictRef; %convention; !ELEMENT integerArray (#PCDATA)!ATTLIST integerArray %title; %id; %integerBuiltin; %size; %min; %max; %units; %unitsRef; %dictRef; %convention; !ELEMENT floatMatrix (#PCDATA)!ATTLIST floatMatrix %title; %id; %rows; %columns; %min; %max; %units; %unitsRef; %dictRef; %convention; !ELEMENT coordinate2 (#PCDATA)!ATTLIST coordinate2 %title; %id; %coordinate2Builtin; %unitsRef; %dictRef; %convention; !ELEMENT coordinate3 (#PCDATA)!ATTLIST coordinate3 %title; %id; %coordinate3Builtin; %unitsRef; %dictRef; %convention; !ELEMENT angle (#PCDATA)!ATTLIST angle %title; %id; %atomRefs; %angleUnits; %min; %max; %dictRef; %convention; !ELEMENT torsion (#PCDATA)!ATTLIST torsion %title; %id; %atomRefs; %angleUnits; %min; %max; %dictRef; %convention; !ELEMENT list ANY!ATTLIST list %title; %id;!-- =======================================================--!-- ELEMENTS for chemical and crystallographic concepts --!-- =======================================================--!-- NOTE for elements which have element-specific values for the builtin attribute, those values are already listed as entities--!-- =======================================================--!ELEMENT molecule ANY!ATTLIST molecule %title; %id; %count; %dictRef; %dictRef; %convention; !-- ========================================================--!ELEMENT formula ANY!ATTLIST formula %title; %id; %count; %dictRef; %convention; !-- ========================================================--!ELEMENT atom ANY!ATTLIST atom %title; %id; %count; %dictRef; %convention; !-- .......................................................--!ELEMENT atomArray ANY!ATTLIST atomArray %title; %id; %dictRef; %convention; !-- ========================================================--!ELEMENT bond ANY!ATTLIST bond %id; %atomRefs; %dictRef; %convention; !-- ========================================================--!ELEMENT bondArray ANY!ATTLIST bondArray %id; %dictRef; %convention; !-- ========================================================--!ELEMENT electron ANY!ATTLIST electron %id; %count; %dictRef; %convention; !-- ========================================================--!ELEMENT reaction ANY!ATTLIST reaction %id; %dictRef; %convention; !-- ======================================================= --!ELEMENT crystal ANY!ATTLIST crystal %title; %id; %dictRef; %convention; !-- ======================================================= --!ELEMENT sequence ANY!ATTLIST sequence %title; %id; %dictRef; %convention; !-- ======================================================= --!ELEMENT feature ANY!ATTLIST feature %title; %id; %dictRef; %convention; C4 H8 O109-99-972.1066I1001473UN 2056LU5950000-108.3650.88630 Colorless liquid with an ether-like odor detectable at 2 to 50 ppm. HYGROSCOPICTHF1,4-EpoxybutaneButylene oxideCyclotetramethylenetetramethylene oxideC8 H10 N4 O258-08-2I1001269UN 1544EV6475000194.192381.231-5White powder or white glistening needles usually melted together. LIGHT SENSITIVE1,3,7-Trimethylxanthine3,7-dihydro-1,3,7-trimethyl-1H-Purine-2,6-dione1,3,7-Trimethyl-2,6-dioxopurine7-MethyltheophyllineAlert-PepCafeinaCafipelGuaranineKoffeinMateinaMethyltheobromineNo-DozRefresh'nStimTheine1-methyltheobrominemethyltheobromideeldiatric corganex1,3,7-trimethyl-2,6-dioxo-1,2,3,6-tetrahydropurinecaffenium1-2.8709-1.04990.1718C2-2.90990.27470.1062N3-1.80260.9662-0.1184C4-0.64110.2954-0.2316C5-0.6549-1.0889-0.1279C6-1.7352-1.71870.0624N70.60520.7432-0.4434N81.2863-0.4175-0.4514C90.5994-1.5633-0.2698N101.08752.0867-0.6139C11-1.83492.1699-0.2205O12-4.21780.98100.2003C13-3.8944-1.67460.3323O14-1.6764-3.19970.1458C152.3776-0.4481-0.6036H162.19022.0944-0.7699H170.60742.5547-1.5032H180.86062.69150.2934H19-4.09422.00970.6091H20-4.66991.0338-0.8167H21-4.91010.45180.8943H22-2.3049-3.6334-0.6659H23-0.6444-3.60300.0359H24-2.0682-3.52181.1381H11212161311324231521216341731128452947110561115911261411378114710115892168151171016118101711910181201219121122012212211231422124142312514241MASS SPECTRUM250547Virginia Division of Forensic ScienceNIST Mass Spectrometry Data CenterM/ZRELATIVE ABUNDANCE14197170109999110414, 7015, 84016, 5017, 4018, 6020, 1025, 1026, 5027, 15028, 90029, 15030, 4031, 1032, 15034, 1038, 12039, 19040, 68041, 58042, 124143, 6044, 1045, 1050, 1051, 13052, 35053, 47054, 57055, 338356, 73057, 11058, 14059, 1062, 1063, 1064, 3065, 12066, 64067, 415368, 45069, 17070, 43071, 1072, 1076, 1077, 7078, 7079, 12080, 23081, 74082, 274283, 33085, 1091, 1092, 2093, 6094, 39095, 13096, 6097, 210104, 10105, 10106, 20107, 70109, 5935110, 750111, 120112, 10120, 10121, 20122, 90123, 50124, 60125, 10126, 10132, 10133, 10134, 10135, 70136, 500137, 460138, 200139, 10140, 10147, 10148, 10149, 50150, 120151, 40152, 40153, 10161, 10163, 20164, 60165, 570166, 90167, 10179, 10190, 10193, 1461194, 9999195, 1050196, 90197, 10MASS SPECTRUM61352D.HENNEBERG, MAX-PLANCK INSTITUTE, MULHEIM, WEST GERMANYNIST Mass Spectrometry Data CenterM/ZRELATIVE ABUNDANCE2473143999913224, 425, 3026, 17127, 154529, 79230, 2131, 25833, 534, 2635, 1037, 10538, 16539, 118240, 90641, 406042, 999943, 158644, 32545, 10046, 349, 750, 1151, 1953, 2754, 1055, 668, 769, 2070, 10771, 255772, 286873, 147C2 H6 O64-17-546.0711.03030.88470.9763C21.88471.98891.5717C33.18831.48071.7425O40.00001.23300.8324H50.99490.00001.6255H61.40970.55580.0000H71.90502.87420.9059H81.47532.32252.5456H93.70562.18202.1139H11212141315141615231627172818391C27 H46 O57-88-5I1001660FZ8400000386.6598148.53601.067Cholesterin(3beta)-Cholest-5-en-3-olCholest-5-en-3-ol (3beta)-cholest-5-ene-3beta-ol3beta-hydroxycholest-5-ene1-1.99012.1889-1.8776H2-2.10591.6157-0.9459C3-3.57871.7234-0.4719C4-3.77971.06070.8120C5-2.84821.60031.9235C6-1.37201.54121.5004C7-0.47021.00602.3207C81.00431.02831.9762C91.36141.87010.8105C100.32151.7261-0.3221C11-1.09632.17830.1259C120.75032.4279-1.6345C132.16772.0593-2.0888C143.19722.3720-0.9408C152.78951.55630.2449C163.96631.64531.2237C175.13541.50870.2960C184.64871.7527-1.1872C193.24503.8521-0.6813C20-1.30663.64190.2349C215.63292.5278-2.0553C225.11802.8440-3.4537C237.01851.8022-2.1116C248.13142.6591-2.5153C259.47481.9697-2.5572C2610.68372.8620-2.8793C2710.56563.6361-4.1508C2811.94282.0228-2.7290C29-1.87020.5579-1.1345H30-4.23061.2525-1.2225H31-3.84432.7860-0.3705H32-3.5980-0.01660.6840H33-2.98450.99262.8302H34-3.11662.64522.1386H35-0.79740.54603.2519H36-5.18261.28611.2631O371.3205-0.00331.7620H381.55361.40602.8511H391.35682.91711.1476H400.25500.6517-0.5486H410.70643.5158-1.4783H420.04472.1427-2.4288H432.42842.6460-2.9820H442.20580.9869-2.3304H452.73540.5091-0.0874H463.93960.82851.9599H473.98042.61191.7486H485.55880.49720.3832H495.90312.25150.5587H504.52250.7794-1.6839H513.55164.3755-1.5989H523.96984.06070.1194H532.24864.2030-0.3745H54-2.33933.84080.5573H55-1.13134.1114-0.7442H56-0.60544.05920.9725H575.79453.4951-1.5571H585.88603.4016-4.0098H594.20483.4527-3.3792H604.89141.9061-3.9818H616.94410.9731-2.8306H627.23811.4013-1.1111H638.19693.4944-1.8026H647.91553.0506-3.5203H659.42471.1825-3.3239H669.64841.5118-1.5723H6710.72713.6239-2.0872H6811.47214.2419-4.2967H699.68774.2967-4.0977H7010.45022.9399-4.9946H7111.92171.5002-1.7613H7212.82652.6762-2.7736H7311.99101.2847-3.5432H74-5.78360.96490.6011H1211232132111443154516364175618672961111078111891121091139151141110115101211611201171213118131411914181201419121151412215161231617124181712518211262122127212312823241292425130252613126271322628133229134330135331136432137533138534139735140837141838142939143104014412411451242146134314713441481545149164615016471511748152174915318501541951155195215619531572054158205515920561602157161225816222591632260164236116523621662463167246416825651692566170266717127681722769173277017428711752872176287317736741C5 H9 N351-45-6111.15I1009215MS105000088Histamine Dihydrochloride1H-Imidazole-4-ethanamineb-Imidazolyl-4-ethylamineEraminErgamineErgotidineImidazole-4-ethylamine2-(4-Imidazolyl)ethylamine5-ImidazoleethylamineEthylamine2-imidazol-4-yl-Free histamineImidazole4-(2-aminoethyl)-Theramine4-Imidazoleethylamine4-(2-Aminoethyl)-1H-imidazoleb-Aminoethylglyoxalineb-Aminoethylimidazole1-1.75600.00000.3080C2-0.36000.07600.2880C30.1400-1.15200.5080N4-0.9160-1.96800.6520C5-2.0640-1.28000.5320N60.45201.36000.0640C71.95601.07200.1080C82.73602.3040-0.1040N9-2.45200.81200.1640H10-0.8520-3.03200.8400H110.18802.08800.8320H120.18401.7800-0.9040H132.22400.3480-0.6600H142.22400.65601.0840H152.49603.03200.6680H162.49202.7240-1.0840H17-3.0120-1.78400.6240H1175121681315814147151371612617116181041991110871117611262113541145111543216321172121-0.5960-2.1520-0.1440C2-0.5520-1.14400.8320C30.4760-1.04401.7280C41.4880-1.97201.6760C51.4120-2.96800.6920C60.4000-3.0760-0.2160C72.6040-1.95202.5800C83.6040-2.98002.5120C93.4960-3.96801.5000C102.4160-3.93600.6040C11-1.6800-2.2080-1.0480C12-2.7200-1.2640-0.9800C13-2.7080-0.26400.0080C14-1.6120-0.20800.8960C150.4040-3.9560-1.0480O160.4840-0.14802.5440O172.6640-0.81603.5880C184.3400-5.01201.2560O19-1.7240-3.1840-1.9960O20-3.7520-1.3480-1.8680O21-1.64000.77201.8400O22-3.82000.75200.1520C23-4.91200.32001.1560C24-4.44401.0280-1.0920O25-6.22401.07600.8680C26-5.88002.45200.2720C27-5.20002.2400-1.1000C28-5.98802.1280-1.8800H29-7.09603.15200.0440O302.73200.16403.0600H313.5240-0.79604.2800H321.7720-0.81204.2560H334.8800-5.46001.8920H34-2.5240-3.2320-2.5040H35-3.5080-0.8600-2.6720H36-1.14401.54401.5200H37-5.22003.02400.9640H38-7.43603.42000.8880H39-3.35601.69200.5120H40-6.88401.27602.1080O414.6760-3.07203.3760C425.6240-4.04003.2840O434.8040-2.26004.2680O446.2200-3.96804.0520H452.3760-4.7120-0.1760H46-4.55600.56002.1920H47-5.1840-1.06401.0520O48-4.6200-1.53601.6560H49-6.88000.52400.1600H50-7.42400.51602.2760H51-4.26803.3960-1.5120C52-3.83603.1920-2.5160H53-5.00804.6040-1.5400O54-3.42003.5000-0.8000H55-4.49205.2760-1.9720H1535512515413515314515215474816424417414328414219405011029381112751112272811326371142629115262711625491172540118252611924271202347121234612223251232239124222412522231262136127203512819341291833130173213117311321730133142113413221351314236122013712131381119139111224010451419181429102438411448914571714678247615248510149561504715145252316253341542141552315611115716158122Example of a simple A + B -> C + D reaction.75taken from Warrenreflux18.4076-1.08780.0000C27.6930-0.67520.0000C36.9806-1.08760.0000C46.9814-1.91250.0000C57.7007-2.32320.0000C68.4102-1.90840.0000C79.1208-0.67080.0000C89.8333-1.08330.0000C99.8333-0.25420.0000O145122313562461151226171734287819791109811-0.7348-0.97500.0000C2-0.7359-1.80230.0000C3-0.0211-2.21520.0000C40.6953-1.80190.0000C50.6925-0.97130.0000C6-0.0229-0.56220.0000C71.4042-0.55420.0000C82.1167-0.96670.0000O92.8292-0.55000.0000O103.5417-0.96250.0000H111.40000.27080.0000O12-0.0292-3.03750.0000Cl161121223571434257816891745189101923110711211562123121112.3069-1.07500.0000C212.3016-1.89820.0000C313.0107-2.31250.0000C413.7256-1.90490.0000C513.7270-1.07850.0000C613.0172-0.66780.0000C713.0042-3.13750.0000Cl814.4375-0.65830.0000C915.0208-1.24170.0000O1014.43330.16670.0000O1115.8458-1.24170.0000H1562261131224371534265817891845198102102311191111-4.1716-0.87110.0000C2-4.8861-0.45850.0000C3-5.5986-0.87100.0000C4-5.5978-1.69580.0000C5-4.8785-2.10650.0000C6-4.1690-1.69180.0000C7-3.4583-0.45420.0000C8-2.7458-0.86670.0000C14512231356246115122617173428782Catalytic cyclefrom Dr. Braddock's lecture notes14.1042-3.36670.0000Ru24.9292-3.36670.0000C35.5125-2.77920.0000C46.3133-2.99360.0000C56.8963-2.40690.0000C66.6794-1.60700.0000C75.8741-1.39700.0000C85.2946-1.98520.0000C1451223135624122567163427782883112.8375-1.65420.0000C23.6625-1.65420.0000C112214.0833-8.66250.0000C24.9083-8.66250.0000C33.4958-9.24580.0000C1122213115.8328-7.16820.0000C25.0348-6.95090.0000C34.4497-7.53270.0000C44.6613-8.33190.0000C55.4634-8.54620.0000C66.0450-7.96290.0000C77.2496-5.75870.0000C86.4246-5.75870.0000C96.4246-6.58370.0000C107.2496-6.58370.0000Ru1231256236114781512263427451889199101101071119111-1.1764-3.90000.0000C2-1.1776-4.72730.0000C3-0.4628-5.14020.0000C40.2537-4.72690.0000C50.2508-3.89630.0000C6-0.4646-3.48720.0000C70.9625-3.47920.0000C80.9583-2.65420.0000C1451223135624611512265717342878211.0625-7.65830.0000C21.8875-7.65830.0000Ru112219.2661-7.06820.0000C28.4682-6.85090.0000C37.8830-7.43270.0000C48.0946-8.23190.0000C58.8967-8.44620.0000C69.4784-7.86290.0000C710.6830-5.65870.0000C89.8580-5.65870.0000C99.8580-6.48370.0000C1010.6830-6.48370.0000Ru119.2667-5.07080.0000C15622611378141225342645178918910191071109111123112811117.3132-7.24140.0000C28.0236-7.65400.0000C38.7340-7.24510.0000C48.7352-6.42390.0000C58.0202-6.01310.0000C67.3127-6.42430.0000C75.8875-7.24580.0000C86.6000-7.65830.0000C95.1708-7.65420.0000C145122313562461151226342778287919811UV/VIS SPECTRUMINSTITUTE OF ENERGY PROBLEMS OF CHEMICAL PHYSICS, RASINEP CP RAS, NIST OSRDWavelength (nm)Logarithm epsilon219.7779295.54181.0000001.000000428219.7779, 3.895839220.0433, 3.922294220.2532, 3.942352220.4787, 3.962316220.7910, 3.988491221.2615, 4.027182221.2615, 4.027182221.3642, 4.033363221.4759, 4.039639221.5920, 4.046098221.5920, 4.046098221.6090, 4.051541221.6303, 4.057168221.6606, 4.062889221.6606, 4.062889221.7664, 4.065087221.8810, 4.067470222.0000, 4.069946222.0000, 4.069946222.0182, 4.073754222.0408, 4.077745222.0723, 4.081830222.0723, 4.081830222.1512, 4.084717222.2301, 4.087604222.3091, 4.090491222.5638, 4.102431222.5638, 4.102431222.5739, 4.092874222.5978, 4.088958222.6561, 4.087324222.6739, 4.109827222.7750, 4.117220222.8716, 4.124612222.8716, 4.124612223.0108, 4.128215223.1502, 4.131635223.2896, 4.134965223.2896, 4.134965223.3220, 4.137838223.3454, 4.140708223.3643, 4.143577223.3643, 4.143577223.5762, 4.149504223.8521, 4.160087224.4287, 4.184395224.4287, 4.184395224.5474, 4.187294224.6616, 4.190192224.7668, 4.193087224.7668, 4.193087224.8239, 4.197180224.8765, 4.201180224.9202, 4.204996224.9202, 4.204996225.2986, 4.218078225.6428, 4.228787226.2477, 4.246302226.2477, 4.246302226.3707, 4.251475226.4995, 4.255013226.7444, 4.259951226.7444, 4.259951226.8846, 4.261205227.0204, 4.262367227.1473, 4.263345227.1473, 4.263345227.2687, 4.262685227.3854, 4.262205227.4930, 4.261813227.4930, 4.261813227.6160, 4.259002227.7344, 4.256281227.8437, 4.253739227.8437, 4.253739228.0687, 4.234739228.2591, 4.219126228.4668, 4.202950228.7438, 4.182262229.1419, 4.153111229.7131, 4.111548229.7131, 4.111548229.7951, 4.110346229.8770, 4.109144229.9590, 4.107941229.9590, 4.107941230.0794, 4.108675230.1953, 4.109225230.3024, 4.109681230.3024, 4.109681230.7632, 4.127046230.9517, 4.135057231.0295, 4.140580231.0295, 4.140580231.1485, 4.143055231.2631, 4.145438231.3688, 4.147636231.3688, 4.147636231.5533, 4.157009231.8306, 4.168865232.0149, 4.178510232.0149, 4.178510232.4942, 4.192244232.7921, 4.201561233.1640, 4.214445233.1640, 4.214445233.3585, 4.219367233.6712, 4.228960234.2356, 4.245447234.2356, 4.245447234.3556, 4.246696234.4711, 4.247852234.5777, 4.248823234.5777, 4.248823234.9403, 4.248872235.1140, 4.248501235.2478, 4.247390235.2478, 4.247390235.4771, 4.238884235.7063, 4.230470235.9355, 4.222237235.9355, 4.222237235.9774, 4.219387236.0148, 4.216535236.0432, 4.213680236.0432, 4.213680236.1873, 4.209648236.3269, 4.205706236.4574, 4.201943236.4574, 4.201943236.8212, 4.186176237.2582, 4.168977237.8585, 4.144283237.8585, 4.144283237.9441, 4.138173238.0297, 4.132064238.1154, 4.125954238.1154, 4.125954238.3747, 4.119488238.5524, 4.113815238.8006, 4.104073238.8006, 4.104073238.9233, 4.101671239.0414, 4.099358239.1503, 4.097225239.1503, 4.097225239.5502, 4.096649239.9409, 4.096252240.3271, 4.095945240.3271, 4.095945240.8061, 4.105089241.2805, 4.114232241.7460, 4.123371241.7460, 4.123371241.9210, 4.125348242.0871, 4.127141242.2488, 4.128841242.2488, 4.128841242.4898, 4.128793242.6638, 4.127997242.9200, 4.125772242.9200, 4.125772243.3300, 4.111595243.7309, 4.097505244.1272, 4.083597244.1272, 4.083597244.1635, 4.081169244.1908, 4.078829244.2134, 4.076669244.2134, 4.076669244.3361, 4.074267244.4542, 4.071955244.5631, 4.069821244.5631, 4.069821244.9876, 4.071510245.2230, 4.072960245.4712, 4.075414245.4712, 4.075414245.8743, 4.081596246.2778, 4.087323246.7341, 4.094612246.7341, 4.094612246.9365, 4.093976247.1344, 4.093521247.3231, 4.093154247.3231, 4.093154247.3911, 4.090463247.4766, 4.088686247.6525, 4.086300247.6525, 4.086300247.7931, 4.082040247.9074, 4.076772248.0934, 4.065981248.0934, 4.065981248.2707, 4.064823248.4389, 4.063753248.6025, 4.062863248.6025, 4.062863248.8294, 4.057629249.0562, 4.052486249.2829, 4.047525249.2829, 4.047525249.5201, 4.047597249.7483, 4.047666249.9720, 4.047734249.9720, 4.047734250.1453, 4.051877250.3097, 4.056017250.4695, 4.060156250.4695, 4.060156250.6299, 4.062538250.7905, 4.064737250.9511, 4.066846250.9511, 4.066846251.1392, 4.075448251.2672, 4.079941251.4450, 4.084176251.4450, 4.084176251.5860, 4.085430251.7270, 4.086594251.8682, 4.087576251.8682, 4.087576252.5979, 4.087797253.3275, 4.088018254.0571, 4.088239254.0571, 4.088239254.1999, 4.087070254.3426, 4.085992254.4852, 4.085096254.4852, 4.085096254.6646, 4.081060254.8351, 4.077021255.0010, 4.072981255.0010, 4.072981255.0027, 4.070648255.0043, 4.068497255.0059, 4.066437255.0059, 4.066437255.2327, 4.061310255.4593, 4.056364255.6859, 4.051509255.6859, 4.051509256.1822, 4.034373256.4512, 4.026077256.7233, 4.019508256.7233, 4.019508256.9458, 4.020273257.1683, 4.020855257.3910, 4.021347257.3910, 4.021347257.5302, 4.024949257.6696, 4.028370257.8090, 4.031699257.8090, 4.031699257.9445, 4.040315258.0801, 4.048840258.2158, 4.057183258.2158, 4.057183258.3296, 4.059657258.4344, 4.062037258.5349, 4.064233258.5349, 4.064233258.6000, 4.070525258.7061, 4.076284258.9441, 4.086446258.9441, 4.086446259.2756, 4.088970259.6211, 4.090771260.2769, 4.093394260.2769, 4.093394260.5194, 4.096421261.0002, 4.100066262.1315, 4.107453262.1315, 4.107453262.3285, 4.112058262.6732, 4.118071263.0308, 4.124905263.0308, 4.124905263.9874, 4.138981264.9351, 4.152873265.8784, 4.166672265.8784, 4.166672266.0996, 4.169072266.3209, 4.171290266.5423, 4.173417266.5423, 4.173417266.7449, 4.177660267.0464, 4.182205267.7051, 4.190949267.7051, 4.190949267.8254, 4.191683267.9414, 4.192233268.0484, 4.192689268.0484, 4.192689268.3029, 4.196842268.5484, 4.200900268.7895, 4.204776268.7895, 4.204776269.3448, 4.210277269.7563, 4.215279270.3767, 4.224072270.3767, 4.224072270.5180, 4.224812270.6595, 4.225370270.8011, 4.225837270.8011, 4.225837271.1626, 4.230446271.5240, 4.235055271.8855, 4.239663271.8855, 4.239663272.1877, 4.242194272.4900, 4.244634272.7924, 4.246892272.7924, 4.246892273.2180, 4.247021273.6436, 4.247149274.0692, 4.247278274.0692, 4.247278274.5954, 4.234303275.4822, 4.215164277.4893, 4.173458277.4893, 4.173458277.6960, 4.167097277.8981, 4.160917278.0911, 4.154825278.0911, 4.154825278.2692, 4.152545278.4382, 4.150445278.6026, 4.148435278.6026, 4.148435278.6648, 4.145590278.7225, 4.142744278.7712, 4.139896278.7712, 4.139896279.3175, 4.131183279.7906, 4.123994280.2278, 4.116612280.2278, 4.116612280.2897, 4.114192280.3470, 4.111861280.3951, 4.109709280.3951, 4.109709280.5379, 4.108540280.6806, 4.107462280.8232, 4.106566280.8232, 4.106566281.1479, 4.098923281.8783, 4.085040283.6403, 4.053016283.6403, 4.053016283.8929, 4.045457284.1126, 4.039797284.4877, 4.031185284.4877, 4.031185284.6355, 4.023169284.7833, 4.015336284.9309, 4.007594284.9309, 4.007594285.1721, 3.983140285.4132, 3.958776285.6542, 3.934594285.6542, 3.934594286.1811, 3.896055286.6682, 3.862450287.0710, 3.834878287.3450, 3.814438287.3450, 3.814438287.4676, 3.812142287.5856, 3.810027287.6944, 3.807999287.6944, 3.807999287.7320, 3.803936287.7605, 3.799960287.7843, 3.796164287.7843, 3.796164288.5323, 3.757607288.8501, 3.740100289.0103, 3.728634289.0103, 3.728634289.4102, 3.705879290.0106, 3.667823290.4112, 3.643977290.4112, 3.643977290.6104, 3.616741290.8039, 3.589540290.9936, 3.562415291.1812, 3.535405291.1812, 3.535405291.4084, 3.482074291.5271, 3.451911291.5761, 3.433768291.5940, 3.416498291.5940, 3.416498291.6322, 3.409815291.6845, 3.399095291.7495, 3.384737291.8258, 3.367143291.9119, 3.346712292.0066, 3.323845292.1084, 3.298942292.2158, 3.272402292.3277, 3.244627292.4424, 3.216017292.5587, 3.186972292.6751, 3.157891292.7903, 3.129176292.9029, 3.101227293.0114, 3.074443293.1145, 3.049225293.2108, 3.025974293.2989, 3.005089293.3773, 2.986971293.4448, 2.972020293.4448, 2.972020293.5917, 2.948288293.7383, 2.924557293.8844, 2.900826294.0298, 2.877094294.1743, 2.853362294.3176, 2.829630294.4594, 2.805897294.5996, 2.782164294.5996, 2.782164294.7903, 2.757272294.9805, 2.732391295.1695, 2.707533295.3568, 2.682708295.5418, 2.657928
